format-version: 1.2 date: 13:12:2013 21:12 saved-by: He Zhang auto-generated-by: OBO-Edit 2.3-beta5 subsetdef: biosapiens "biosapiens protein feature ontology" subsetdef: Cross_product_review "Involved_in" subsetdef: DBVAR "database of genomic structural variation" subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation" subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation" subsetdef: GOLD "GOLD" subsetdef: goslim_aspergillus "Aspergillus GO slim" subsetdef: goslim_candida "Candida GO slim" subsetdef: goslim_generic "Generic GO slim" subsetdef: goslim_metagenomics "Metagenomics GO slim" subsetdef: goslim_pir "PIR GO slim" subsetdef: goslim_plant "Plant GO slim" subsetdef: goslim_pombe "Fission yeast GO slim" subsetdef: goslim_yeast "Yeast GO slim" subsetdef: gosubset_prok "Prokaryotic GO subset" subsetdef: gram-negative_bacterial_infectious_disease "gram-negative bacterial infectious disease" subsetdef: gram-positive_bacterial_infectious_disease "gram-positive bacterial infectious disease" subsetdef: mf_needs_review "Catalytic activity terms in need of attention" subsetdef: sexually_transmitted_infectious_disease "sexually transmitted infectious disease" subsetdef: SOFA "SO feature annotation" subsetdef: termgenie_unvetted "Terms created by TermGenie that do not follow a template and require additional vetting by editors" subsetdef: tick-borne_infectious_disease "tick-borne infectious disease" subsetdef: virus_checked "Viral overhaul terms" subsetdef: zoonotic_infectious_disease "zoonotic infectious disease" synonymtypedef: aa1 "amino acid 1 letter code" synonymtypedef: aa3 "amino acid 3 letter code" synonymtypedef: AAMOD "amino acid modification" synonymtypedef: BS "biosapiens" synonymtypedef: dbsnp "dbsnp variant terms" synonymtypedef: dbvar "DBVAR" synonymtypedef: ebi_variants "ensembl variant terms" synonymtypedef: PRO-common-name "Label appended to organism-specific terms in place of scientific name" EXACT synonymtypedef: PRO-short-label "Unique short label for PRO terms for display purposes" EXACT synonymtypedef: PSI-MOD-label "Unique short label curated by PSI-MOD" EXACT synonymtypedef: RNAMOD "RNA modification" EXACT synonymtypedef: systematic_synonym "Systematic synonym" EXACT default-namespace: OMIT remark: Filtered by Name equals "Entity" OR Ancestor Name equals "Entity" OR Is Property [Term] id: BFO:0000024 name: fiat object namespace: BFO is_a: snap:MaterialEntity ! material_entity [Term] id: bfo:Entity name: entity namespace: def: "Something that exists as a particular and discrete unit" [] creation_date: 2013-09-27T11:52:15Z [Term] id: CHEBI:23367 name: molecular entity namespace: CHEBI def: "Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity." [fake:2] is_a: snap:Object ! object [Term] id: CHEBI:33708 name: amino-acid residue namespace: protein def: "When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue." [Dummy:dummy] synonym: "amino acid residue" EXACT [] synonym: "protein residue" NARROW [PRO:DAN] is_a: BFO:0000024 ! fiat object [Term] id: DOID:0001816 name: angiosarcoma namespace: disease_ontology alt_id: DOID:267 alt_id: DOID:4508 def: "A malignant vascular tumor that results_in rapidly proliferating, extensively infiltrating anaplastic cells derived_from blood vessels and derived_from the lining of irregular blood-filled spaces." [url:http\://emedicine.medscape.com/article/276512-overview] synonym: "Hemangioendothelioma, malignant (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:33176006] synonym: "hemangiosarcoma" EXACT [] synonym: "primary hemangiosarcoma" EXACT [NCI2004_11_17:C9275] xref: MSH:D006394 xref: NCI:C3088 xref: SNOMEDCT_2010_1_31:33176006 xref: SNOMEDCT_2010_1_31:39000009 xref: SNOMEDCT_2010_1_31:403977003 xref: UMLS_CUI:C0018923 xref: UMLS_CUI:C0854893 is_a: DOID:1115 ! sarcoma [Term] id: DOID:0014667 name: disease of metabolism namespace: disease_ontology def: "A disease that involving errors in metabolic processes of building or degredation of molecules." [url:http\://www.ncbi.nlm.nih.gov/books/NBK22259/] synonym: "metabolic disease " EXACT [SNOMEDCT_2005_07_31:75934005] xref: ICD9CM:277.9 xref: MSH:D008659 xref: NCI:C3235 xref: SNOMEDCT_2010_1_31:154733004 xref: SNOMEDCT_2010_1_31:190961002 xref: SNOMEDCT_2010_1_31:267456000 xref: SNOMEDCT_2010_1_31:30390004 xref: SNOMEDCT_2010_1_31:75934005 xref: UMLS_CUI:C0025517 is_a: DOID:4 ! disease [Term] id: DOID:0050117 name: disease by infectious agent namespace: disease_ontology alt_id: DOID:10115 alt_id: DOID:11078 alt_id: DOID:1304 alt_id: DOID:1321 alt_id: DOID:2040 alt_id: DOID:2288 alt_id: DOID:3099 alt_id: DOID:4120 alt_id: DOID:4620 alt_id: DOID:5256 alt_id: DOID:945 alt_id: DOID:95 alt_id: DOID:9532 alt_id: DOID:9696 def: "A disease that is the consequence of the presence of pathogenic microbial agents, including pathogenic viruses, pathogenic bacteria, fungi, protozoa, multicellular parasites, and aberrant proteins known as prions." [DO:wk] synonym: "infectious disease" EXACT [] xref: ICD9CM:079.0 xref: UMLS_CUI:C0001485 is_a: DOID:4 ! disease [Term] id: DOID:0050155 name: sensory system disease namespace: disease_ontology def: "A body system disease which is located in a part of the nervous system responsible for processing sensory information that consists of sensory receptors, neural pathways, and parts of the brain involved in sensory perception. Commonly recognized sensory systems are those for vision, hearing, somatic sensation (touch), taste and olfaction (smell)." [url:http\://en.wikipedia.org/wiki/Sensory_system] is_a: DOID:863 ! nervous system disease [Term] id: DOID:0050615 name: respiratory system cancer namespace: disease_ontology def: "An organ system cancer located_in the respiratory system that is characterized by uncontrolled cellular proliferation in the respiratory tract." [url:http\://en.wikipedia.org/wiki/Respiratory_tract_neoplasm] is_a: DOID:0050686 ! organ system cancer [Term] id: DOID:0050686 name: organ system cancer namespace: disease_ontology def: "A cancer that is classified based on the organ it starts in." [url:http\://cancerguide.org/basic.html] is_a: DOID:162 ! cancer created_by: snadendla creation_date: 2011-06-13T03:28:33Z [Term] id: DOID:0050687 name: cell type cancer namespace: disease_ontology def: "A cancer that is classified by the type of cell from which it is derived." [url:http\://cancerguide.org/basic.html, url:http\://en.wikipedia.org/wiki/Cancer] is_a: DOID:162 ! cancer created_by: snadendla creation_date: 2011-06-13T03:28:50Z [Term] id: DOID:0050695 name: malignant pleural solitary fibrous tumor namespace: disease_ontology is_a: DOID:9917 ! pleural cancer created_by: snadendla creation_date: 2011-06-27T09:57:44Z [Term] id: DOID:0050743 name: mature T-cell and NK-cell neoplasm namespace: disease_ontology is_a: DOID:0060058 ! lymphoma created_by: lschriml creation_date: 2012-09-18T01:56:52Z [Term] id: DOID:0050744 name: anaplastic large cell lymphoma namespace: disease_ontology def: "A mature T-cell and NK-cell neoplasm involving aberrant T-cells." [url:http\://en.wikipedia.org/wiki/Anaplastic_large-cell_lymphoma#Epidemiology] is_a: DOID:0050743 ! mature T-cell and NK-cell neoplasm created_by: lschriml creation_date: 2012-09-18T01:57:40Z [Term] id: DOID:0050745 name: diffuse large B-cell lymphoma namespace: disease_ontology def: "A B-cell lymphocytic neoplasm that is a cancer of B cells presenting as an aggressive tumour which can arise in virtually any part of the body." [url:http\://en.wikipedia.org/wiki/Diffuse_large_B-cell_lymphoma] is_a: DOID:707 ! B-cell lymphocytic neoplasm created_by: lschriml creation_date: 2012-09-18T01:58:25Z [Term] id: DOID:0050746 name: mantle cell lymphoma namespace: disease_ontology def: "A B-cell lymphocytic neoplasm due to CD5 positive antigen-naive pregerminal center B-cell within the mantle zone that surrounds normal germinal center follicles." [url:http\://en.wikipedia.org/wiki/Mantle_cell_lymphoma] is_a: DOID:707 ! B-cell lymphocytic neoplasm created_by: lschriml creation_date: 2012-09-18T02:00:45Z [Term] id: DOID:0050749 name: peripheral T-cell lymphoma namespace: disease_ontology def: "A mature T-cell and NK-cell neoplasm includes a group of T-cell lymphomas that develop away from the thymus." [url:http\://en.wikipedia.org/wiki/Peripheral_T-cell_lymphoma] is_a: DOID:0050743 ! mature T-cell and NK-cell neoplasm created_by: lschriml creation_date: 2012-09-18T02:01:49Z [Term] id: DOID:0050751 name: T-cell large granular lymphocyte leukemia namespace: disease_ontology def: "A chronic lymphocytic leukemia that exhibits an unexplained, chronic (> 6 months) elevation in large granular lymphocytes (LGLs) in the peripheral blood." [url:http\://en.wikipedia.org/wiki/T-cell_large_granular_lymphocyte_leukemia] synonym: "Large granular lymphocytic leukemia" EXACT [] is_a: DOID:1040 ! chronic lymphocytic leukemia created_by: lschriml creation_date: 2012-09-18T02:05:41Z [Term] id: DOID:0060058 name: lymphoma namespace: disease_ontology alt_id: DOID:1033 alt_id: DOID:353 def: "A hematologic cancer that affects lymphocytes that reside in the lymphatic system and in blood-forming organs." [url:http\://en.wikipedia.org/wiki/Lymphoma, url:http\://www.nlm.nih.gov/medlineplus/lymphoma.html] synonym: "lymphoid cancer" EXACT [] xref: MSH:D008223 xref: NCI:C3208 xref: SNOMEDCT_2010_1_31:118600007 xref: SNOMEDCT_2010_1_31:188676008 xref: SNOMEDCT_2010_1_31:188694002 xref: SNOMEDCT_2010_1_31:188695001 xref: SNOMEDCT_2010_1_31:188704004 xref: SNOMEDCT_2010_1_31:189959002 xref: SNOMEDCT_2010_1_31:189965002 xref: SNOMEDCT_2010_1_31:21964009 xref: SNOMEDCT_2010_1_31:269627002 xref: SNOMEDCT_2010_1_31:414628006 xref: UMLS_CUI:C0024299 xref: UMLS_CUI:C0598798 is_a: DOID:2531 ! hematologic cancer [Term] id: DOID:0060061 name: cutaneous T cell lymphoma namespace: disease_ontology def: "A non-Hodgkin's lymphoma that is caused by a mutation of T cells." [url:http\://en.wikipedia.org/wiki/Cutaneous_T-cell_lymphoma] is_a: DOID:0050749 ! peripheral T-cell lymphoma [Term] id: DOID:0060071 name: pre-malignant neoplasm namespace: disease_ontology def: "A disease of cellular proliferation that results in abnormal growths in the body, which do not invade or destroy the surrounding tissue but, given enough time, will transform into a cancer." [url:http\://en.wikipedia.org/wiki/Neoplasm] is_a: DOID:14566 ! disease of cellular proliferation created_by: lschriml creation_date: 2011-05-11T12:18:41Z [Term] id: DOID:0060072 name: benign neoplasm namespace: disease_ontology def: "A disease of cellular proliferation that results in abnormal growths in the body which lack the ability to metastasize." [url:http\://en.wikipedia.org/wiki/Benign_neoplasm, url:http\://www.nlm.nih.gov/medlineplus/benigntumors.html] is_a: DOID:14566 ! disease of cellular proliferation created_by: lschriml creation_date: 2011-05-11T12:18:41Z [Term] id: DOID:0060083 name: immune system cancer namespace: disease_ontology def: "An organ system cancer located_in the immune system that is characterized by uncontrolled cellular proliferation in organs of the immune system." [url:http\://en.wikipedia.org/wiki/Immune_system] is_a: DOID:0050686 ! organ system cancer created_by: lschriml creation_date: 2011-06-08T01:11:18Z [Term] id: DOID:0060084 name: cell type benign neoplasm namespace: disease_ontology def: "A benign neoplasm that is classified by the type of cell or tissue from which it is derived." [url:http\://en.wikipedia.org/wiki/Benign_tumor] is_a: DOID:0060072 ! benign neoplasm created_by: lschriml creation_date: 2011-07-14T11:59:48Z [Term] id: DOID:0060100 name: musculoskeletal system cancer namespace: disease_ontology def: "An organ system cancer located_in the muscular and skeltal organs and characterized by uncontrolled cellular proliferation of the musculoskeletal organs." [url:http\://en.wikipedia.org/wiki/Musculoskeletal_system#Diseases_and_disorders] is_a: DOID:0050686 ! organ system cancer created_by: lschriml creation_date: 2011-07-15T02:30:51Z [Term] id: DOID:0060158 name: acquired metabolic disease namespace: disease_ontology def: "A disease of metabolism that has _material_basis_in enzyme deficiency or accumulation of enzymes or toxins which interfere with normal function due to an endocrine organ disease, organ malfunction, inadequate intake, dietary deficiency, or malabsorption." [url:http\://en.wikipedia.org/wiki/Inborn_error_of_metabolism, url:http\://www.ncbi.nlm.nih.gov/mesh/68008659] is_a: DOID:0014667 ! disease of metabolism created_by: lschriml creation_date: 2011-08-24T02:53:03Z [Term] id: DOID:0070004 name: myeloma namespace: disease_ontology def: "A bone marrow cancer that affects plasma cells in which abnormal plasma cells multiply uncontrollably in the bone marrow and occasionally in other parts of the body." [url:http\://www.merck.com/mmhe/sec14/ch175/ch175c.html#sec14-ch175-ch175c-328] is_a: DOID:4960 ! bone marrow cancer [Term] id: DOID:1036 name: chronic leukemia namespace: disease_ontology def: "A leukemia that develops slowly." [url:http\://www.nlm.nih.gov/medlineplus/leukemiaadultchronic.html] synonym: "adult chronic leukemia" RELATED [] synonym: "CLL" RELATED [] synonym: "CML" RELATED [] xref: UMLS_CUI:C0085670 is_a: DOID:1240 ! leukemia [Term] id: DOID:1037 name: lymphoblastic leukemia namespace: disease_ontology xref: ICD9CM:204 xref: ICD9CM:204.9 xref: MSH:D007945 xref: NCI:C7539 xref: SNOMEDCT_2010_1_31:154587007 xref: SNOMEDCT_2010_1_31:188725004 xref: SNOMEDCT_2010_1_31:188731001 xref: SNOMEDCT_2010_1_31:190033006 xref: SNOMEDCT_2010_1_31:269631008 xref: SNOMEDCT_2010_1_31:32280000 xref: SNOMEDCT_2010_1_31:93170002 xref: UMLS_CUI:C0023448 is_a: DOID:1240 ! leukemia [Term] id: DOID:1038 name: mature T-cell neoplasm namespace: disease_ontology xref: NCI:C27909 xref: UMLS_CUI:C1334640 is_obsolete: true [Term] id: DOID:104 name: bacterial infectious disease namespace: disease_ontology def: "A disease by infectious agent that results_in infection, has_material_basis_in Bacteria." [url:http\://en.wikipedia.org/wiki/Pathogenic_bacteria] xref: MSH:D001424 xref: NCI:C2890 xref: SNOMEDCT_2010_1_31:154311004 xref: SNOMEDCT_2010_1_31:154317000 xref: SNOMEDCT_2010_1_31:154318005 xref: SNOMEDCT_2010_1_31:186335000 xref: SNOMEDCT_2010_1_31:186406007 xref: SNOMEDCT_2010_1_31:186470002 xref: SNOMEDCT_2010_1_31:186472005 xref: SNOMEDCT_2010_1_31:187314009 xref: SNOMEDCT_2010_1_31:187346009 xref: SNOMEDCT_2010_1_31:187347000 xref: SNOMEDCT_2010_1_31:266182006 xref: SNOMEDCT_2010_1_31:266187000 xref: SNOMEDCT_2010_1_31:301811001 xref: SNOMEDCT_2010_1_31:87628006 xref: UMLS_CUI:C0004623 is_a: DOID:0050117 ! disease by infectious agent [Term] id: DOID:1040 name: chronic lymphocytic leukemia namespace: disease_ontology xref: EFO:0000095 xref: MSH:D015451 xref: UMLS_CUI:C0023458 is_a: DOID:1036 ! chronic leukemia is_a: DOID:1037 ! lymphoblastic leukemia [Term] id: DOID:1115 name: sarcoma namespace: disease_ontology alt_id: DOID:3936 def: "A cell type cancer that has_material_basis_in abnormally proliferating cells derived_from embryonic mesoderm." [url:http\://en.wikipedia.org/wiki/Sarcoma] synonym: "connective and soft tissue neoplasm" EXACT [] synonym: "tumor of soft tissue and skeleton" EXACT [NCI2004_11_17:C3810] xref: ICD9CM:171 xref: ICD9CM:171.9 xref: SNOMEDCT_2010_1_31:187985009 xref: SNOMEDCT_2010_1_31:93765001 xref: UMLS_CUI:C0153519 is_a: DOID:0050687 ! cell type cancer [Term] id: DOID:120 name: female reproductive organ cancer namespace: disease_ontology alt_id: DOID:1244 alt_id: DOID:1281 def: "A reproductive organ cancer that is manifested in the female genitals. This includes organs such as the ovaries, fallopian tubes, uterus, cervix, vagina and vulva." [url:http\://en.wikipedia.org/wiki/Template\:Female_genital_neoplasia, url:http\://www.wrongdiagnosis.com/g/genital_system_cancer/intro.htm] synonym: "female reproductive cancer" EXACT [] synonym: "malignant Gynecologic tumor" EXACT [NCI2004_11_17:C4913] synonym: "malignant neoplasm of female genital organ" EXACT [] xref: MSH:D005833 xref: NCI:C3053 xref: SNOMEDCT_2010_1_31:126907002 xref: SNOMEDCT_2010_1_31:188207007 xref: UMLS_CUI:C0017416 xref: UMLS_CUI:C0153585 xref: UMLS_CUI:C0699889 is_a: DOID:193 ! reproductive organ cancer [Term] id: DOID:1240 name: leukemia namespace: disease_ontology alt_id: DOID:9145 def: "A cancer that affects the blood or bone marrow characterized by an abnormal proliferation of blood cells." [url:http\://en.wikipedia.org/wiki/Leukemia] xref: ICD9CM:208 xref: ICD9CM:208.9 xref: MSH:D007938 xref: NCI:C3161 xref: SNOMEDCT_2010_1_31:154598008 xref: SNOMEDCT_2010_1_31:188762002 xref: SNOMEDCT_2010_1_31:188767008 xref: SNOMEDCT_2010_1_31:190024009 xref: SNOMEDCT_2010_1_31:190025005 xref: SNOMEDCT_2010_1_31:190029004 xref: SNOMEDCT_2010_1_31:190071003 xref: SNOMEDCT_2010_1_31:255049003 xref: SNOMEDCT_2010_1_31:87163000 xref: SNOMEDCT_2010_1_31:93143009 xref: UMLS_CUI:C0023418 is_a: DOID:2531 ! hematologic cancer [Term] id: DOID:1271 name: capillary disease namespace: disease_ontology synonym: "disease of capillaries" EXACT [] xref: ICD9CM:448 xref: SNOMEDCT_2010_1_31:155446001 xref: SNOMEDCT_2010_1_31:155449008 xref: SNOMEDCT_2010_1_31:195250004 xref: SNOMEDCT_2010_1_31:195380006 xref: SNOMEDCT_2010_1_31:195390003 xref: SNOMEDCT_2010_1_31:266324004 xref: SNOMEDCT_2010_1_31:57223003 xref: SNOMEDCT_2010_1_31:58729003 xref: UMLS_CUI:C0155765 is_a: DOID:178 ! vascular disease [Term] id: DOID:1287 name: cardiovascular system disease namespace: disease_ontology alt_id: DOID:73 def: "A disease of anatomical entity which occurs in the blood, heart, blood vessels or the lymphatic system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells or lymph to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis." [url:http\://en.wikipedia.org/wiki/Circulatory_system] synonym: "cardiovascular system disease" EXACT [] synonym: "disease of subdivision of hemolymphoid system" EXACT [] xref: ICD9CM:429.2 xref: MSH:D002318 xref: NCI:C2931 xref: SNOMEDCT_2010_1_31:105980002 xref: SNOMEDCT_2010_1_31:155263000 xref: SNOMEDCT_2010_1_31:194707003 xref: SNOMEDCT_2010_1_31:195139006 xref: SNOMEDCT_2010_1_31:195594006 xref: SNOMEDCT_2010_1_31:266275004 xref: SNOMEDCT_2010_1_31:266336005 xref: SNOMEDCT_2010_1_31:49601007 xref: UMLS_CUI:C0007222 is_a: DOID:7 ! disease of anatomical entity [Term] id: DOID:1324 name: lung cancer namespace: disease_ontology alt_id: DOID:13075 alt_id: DOID:1322 alt_id: DOID:9881 def: "A respiratory system cancer that is located_in the lung." [url:http\://en.wikipedia.org/wiki/Lung_cancer] xref: ICD9CM:162.3 xref: OMIM:211980 xref: OMIM:608935 xref: OMIM:612593 xref: OMIM:614210 xref: SNOMEDCT_2010_1_31:187860004 xref: SNOMEDCT_2010_1_31:187863002 xref: SNOMEDCT_2010_1_31:187864008 xref: SNOMEDCT_2010_1_31:187867001 xref: SNOMEDCT_2010_1_31:187868006 xref: SNOMEDCT_2010_1_31:187871003 xref: SNOMEDCT_2010_1_31:187874006 xref: SNOMEDCT_2010_1_31:269464000 xref: UMLS_CUI:C0024624 xref: UMLS_CUI:C0153491 xref: UMLS_CUI:C0153492 xref: UMLS_CUI:C0153493 is_a: DOID:0050615 ! respiratory system cancer [Term] id: DOID:1398 name: parasitic infectious disease namespace: disease_ontology alt_id: DOID:11681 alt_id: DOID:13509 alt_id: DOID:1396 alt_id: DOID:1494 alt_id: DOID:2114 alt_id: DOID:2293 alt_id: DOID:2922 alt_id: DOID:3564 alt_id: DOID:4191 alt_id: DOID:886 alt_id: DOID:948 alt_id: DOID:9639 alt_id: DOID:9644 def: "A disease by infectious agent that is carried out by a parasite which by definition is a pathogen that simultaneously injures and derives sustenance from its host." [url:http\://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=mmed&part=A4071] synonym: "Ectoparasitic disease" EXACT [SNOMEDCT_2005_07_31:240876009] synonym: "parasitemia" EXACT [] xref: ICD9CM:360.13 xref: NCI:C34587 xref: SNOMEDCT_2010_1_31:193273005 xref: SNOMEDCT_2010_1_31:57100005 xref: UMLS_CUI:C0014238 is_a: DOID:0050117 ! disease by infectious agent [Term] id: DOID:14566 name: disease of cellular proliferation namespace: disease_ontology alt_id: DOID:0000818 def: "A disease that is characterized by abnormally rapid cell division." [url:http\://en.wikipedia.org/w/index.php?title=Cell_proliferation] synonym: "cell process disease" EXACT [] is_a: DOID:4 ! disease [Term] id: DOID:1475 name: lymphangioma namespace: disease_ontology synonym: "benign lymphangioma (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:253057002] synonym: "Congenital lymphangioma" EXACT [SNOMEDCT_2005_07_31:189200000] synonym: "Congenital lymphangioma" EXACT [MTHICD9_2006:228.1] synonym: "Congenital lymphangioma (disorder)" EXACT [SNOMEDCT_2005_07_31:254836000] synonym: "lymphangioma" EXACT [CSP2005:2004-0139] synonym: "Lymphangioma (disorder)" EXACT [SNOMEDCT_2005_07_31:400178008] synonym: "Lymphangioma NOS (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:189875000] synonym: "Lymphangioma of unspecified site (disorder)" EXACT [SNOMEDCT_2005_07_31:93168006] synonym: "Lymphangioma, any site" EXACT [ICD9CM_2006:228.1] synonym: "Lymphangioma, no ICD-O subtype (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:69044001] xref: ICD9CM:228.1 xref: MSH:D008202 xref: NCI:C8965 xref: SNOMEDCT_2010_1_31:154625006 xref: SNOMEDCT_2010_1_31:189200000 xref: SNOMEDCT_2010_1_31:189875000 xref: SNOMEDCT_2010_1_31:253057002 xref: SNOMEDCT_2010_1_31:254836000 xref: SNOMEDCT_2010_1_31:269646001 xref: SNOMEDCT_2010_1_31:400178008 xref: SNOMEDCT_2010_1_31:69044001 xref: SNOMEDCT_2010_1_31:93168006 xref: UMLS_CUI:C0024221 is_a: DOID:0060084 ! cell type benign neoplasm [Term] id: DOID:1564 name: fungal infectious disease namespace: disease_ontology def: "A disease by infectious agent that results_in infection, has_material_basis_in Fungi, which pass the resistance barriers of the human or animal body." [url:http\://en.wikipedia.org/wiki/Mycoses] synonym: "mycoses" RELATED [] synonym: "mycosis" EXACT [] xref: ICD9CM:110-118.99 xref: MSH:D009181 xref: NCI:C3245 xref: SNOMEDCT_2010_1_31:154393000 xref: SNOMEDCT_2010_1_31:154394006 xref: SNOMEDCT_2010_1_31:187110007 xref: SNOMEDCT_2010_1_31:187472001 xref: SNOMEDCT_2010_1_31:187498007 xref: SNOMEDCT_2010_1_31:266214005 xref: SNOMEDCT_2010_1_31:3218000 xref: UMLS_CUI:C0026946 is_a: DOID:0050117 ! disease by infectious agent [Term] id: DOID:1612 name: breast cancer namespace: disease_ontology alt_id: DOID:1648 alt_id: DOID:4241 def: "A thoracic cancer that originates in the mammary gland." [url:http\://en.wikipedia.org/wiki/Mammary_tumor] comment: OMIM mapping confirmed by DO. [SN]. synonym: "breast cancer" EXACT [] synonym: "breast tumor" EXACT [NCI2004_11_17:C2910] synonym: "Ca breast - NOS" EXACT [SNOMEDCT_2005_07_31:154521006] synonym: "malignant neoplasm of breast" EXACT [] synonym: "malignant tumor of the breast" EXACT [NCI2004_11_17:C9335] synonym: "mammary cancer" EXACT [] synonym: "mammary neoplasm" RELATED [] synonym: "mammary tumor" EXACT [CSP2005:2016-0671] synonym: "primary breast cancer" EXACT [] xref: MSH:D001943 xref: NCI:C9335 xref: OMIM:114480 xref: SNOMEDCT_2010_1_31:126926005 xref: SNOMEDCT_2010_1_31:154521006 xref: SNOMEDCT_2010_1_31:190121004 xref: SNOMEDCT_2010_1_31:254837009 xref: SNOMEDCT_2010_1_31:269595005 xref: UMLS_CUI:C0006142 xref: UMLS_CUI:C0153555 xref: UMLS_CUI:C1458155 is_a: DOID:5093 ! thoracic cancer [Term] id: DOID:162 name: cancer namespace: disease_ontology def: "A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis." [stedman:rlc, url:http\://en.wikipedia.org/wiki/cancer, url:http\://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=cancer] synonym: "malignant neoplasm" EXACT [] synonym: "malignant tumor " EXACT [] synonym: "primary cancer" EXACT [] xref: ICD9CM:239.4 xref: SNOMEDCT_2010_1_31:189535002 xref: UMLS_CUI:C0027639 is_a: DOID:14566 ! disease of cellular proliferation [Term] id: DOID:175 name: vascular cancer namespace: disease_ontology alt_id: DOID:3339 alt_id: DOID:5454 alt_id: DOID:5548 alt_id: DOID:7019 alt_id: DOID:7020 alt_id: DOID:7392 def: "A cardiovascular cancer that is located_in blood vessels." [url:http\://en.wikipedia.org/wiki/Vascular] synonym: "Blood Vessel neoplasm" EXACT [NCI2004_11_17:C7387] synonym: "blood vessel neoplasm" EXACT [CSP2005:2007-0683] synonym: "Blood vessel tumor (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:115235003] synonym: "Blood vessel tumors (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:189862000] synonym: "Blood vessel tumour disorder" EXACT [SNOMEDCT_2005_07_31:126736007] synonym: "Haemangiomatous tumour" EXACT [SNOMEDCT_2005_07_31:189874001] synonym: "leiomyosarcoma of the renal Vein" EXACT [NCI2004_11_17:C5388] synonym: "malignant great vessel tumor" EXACT [] synonym: "malignant tumor of pulmonary artery" EXACT [NCI2004_11_17:C5380] synonym: "malignant tumor of pulmonary Vein" EXACT [NCI2004_11_17:C5383] synonym: "malignant vascular neoplasm" EXACT [] synonym: "malignant vascular tumor" EXACT [NCI2004_11_17:C7390] synonym: "neoplasm of great vessel" EXACT [] synonym: "pulmonary artery malignant neoplasm" EXACT [] synonym: "pulmonary vein malignant neoplasm" EXACT [] synonym: "renal vein leiomyosarcoma" EXACT [] synonym: "vascular tissue neoplasm" EXACT [] synonym: "vascular tumors" EXACT [NCI2004_11_17:C7388] xref: MSH:D019043 xref: NCI:C7387 xref: NCI:C7388 xref: SNOMEDCT_2010_1_31:115235003 xref: SNOMEDCT_2010_1_31:126736007 xref: SNOMEDCT_2010_1_31:126737003 xref: SNOMEDCT_2010_1_31:188012003 xref: SNOMEDCT_2010_1_31:189862000 xref: SNOMEDCT_2010_1_31:189874001 xref: SNOMEDCT_2010_1_31:93817006 xref: UMLS_CUI:C0282607 xref: UMLS_CUI:C0346845 xref: UMLS_CUI:C1290407 xref: UMLS_CUI:C1334616 xref: UMLS_CUI:C1334617 xref: UMLS_CUI:C1334630 xref: UMLS_CUI:C1335753 is_a: DOID:176 ! cardiovascular cancer [Term] id: DOID:176 name: cardiovascular cancer namespace: disease_ontology def: "An organ system cancer that located_in the heart and blood vessels." [url:http\://www.cancer.gov/dictionary?CdrID=44005, url:http\://www.healthcentral.com/heart-disease/h/cardiovascular-cancer.html] synonym: "cardiovascular neoplasm" EXACT [CSP2005:2007-0683] synonym: "Cardiovascular tumors" EXACT [NCI2004_11_17:C4784] xref: NCI:C4784 xref: UMLS_CUI:C0497243 is_a: DOID:0050686 ! organ system cancer [Term] id: DOID:178 name: vascular disease namespace: disease_ontology alt_id: DOID:2869 alt_id: DOID:45 def: "A cardiovascular system disease that primarily affects the blood vessels." [url:http\://en.wikipedia.org/wiki/Vascular_disease] synonym: "Arterial disease" RELATED [SNOMEDCT_2005_07_31:155413007] synonym: "arteriopathy" EXACT [] synonym: "internal elastic lamina" EXACT [] xref: MSH:D014652 xref: NCI:C35117 xref: SNOMEDCT_2010_1_31:27550009 xref: UMLS_CUI:C0042373 xref: UMLS_CUI:C0264951 is_a: DOID:1287 ! cardiovascular system disease [Term] id: DOID:1790 name: malignant mesothelioma namespace: disease_ontology alt_id: DOID:4487 alt_id: DOID:6965 alt_id: DOID:7434 def: "A cell type cancer that has_material_basis_in meothelial tissue." [url:http\://en.wikipedia.org/wiki/Mesothelioma, url:http\://www.merriam-webster.com/medlineplus/mesothelioma] comment: OMIM mapping confirmed by DO. [SN]. synonym: "advanced malignant mesothelioma" EXACT [] synonym: "asbestos-related malignant mesothelioma" EXACT [] synonym: "Diffuse malignant Mesothelioma" EXACT [NCI2004_11_17:C8420] synonym: "diffuse malignant mesothelioma" EXACT [] synonym: "malignant tumor of Mesothelium" EXACT [NCI2004_11_17:C4456] synonym: "Mesothelioma, malignant (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:62064005] xref: NCI:C7865 xref: OMIM:156240 xref: SNOMEDCT_2010_1_31:62064005 xref: UMLS_CUI:C0278752 xref: UMLS_CUI:C0345967 xref: UMLS_CUI:C0392400 xref: UMLS_CUI:C1332338 is_a: DOID:0050687 ! cell type cancer [Term] id: DOID:193 name: reproductive organ cancer namespace: disease_ontology alt_id: DOID:1900 def: "An organ system cancer that is manifested in the reproductive organs." [url:http\://en.wikipedia.org/wiki/Reproductive_system#Examples_of_cancers] synonym: "cancer of reproductive system" RELATED [] synonym: "malignant reproductive system neoplasm" EXACT [] synonym: "Reproductive tumor" EXACT [NCI2004_11_17:C3674] xref: NCI:C3674 xref: UMLS_CUI:C0178830 is_a: DOID:0050686 ! organ system cancer [Term] id: DOID:201 name: connective tissue cancer namespace: disease_ontology def: "A musculoskeletal system cancer that is located_in connective tissue." [url:http\://en.wikipedia.org/wiki/Connective_tissue] synonym: "connective tissue neoplasm" EXACT [CSP2005:2008-3809] synonym: "neoplasm of connective tissues (disorder)" EXACT [SNOMEDCT_2005_07_31:126598008] synonym: "Tumour of connective tissue" EXACT [SNOMEDCT_2005_07_31:254821003] xref: MSH:D009372 xref: SNOMEDCT_2010_1_31:126598008 xref: SNOMEDCT_2010_1_31:254821003 xref: UMLS_CUI:C0027656 is_a: DOID:0060100 ! musculoskeletal system cancer [Term] id: DOID:2014 name: perinatal digestive system disorder namespace: disease_ontology xref: ICD9CM:777 xref: ICD9CM:777.9 xref: SNOMEDCT_2010_1_31:157156008 xref: SNOMEDCT_2010_1_31:206536001 xref: SNOMEDCT_2010_1_31:268885004 xref: SNOMEDCT_2010_1_31:42357009 xref: UMLS_CUI:C0159000 is_obsolete: true [Term] id: DOID:2151 name: malignant ovarian surface epithelial-stromal neoplasm namespace: disease_ontology xref: NCI:C40026 xref: UMLS_CUI:C1518236 is_a: DOID:2152 ! ovary epithelial cancer [Term] id: DOID:2152 name: ovary epithelial cancer namespace: disease_ontology synonym: "epithelial tumor of ovary" RELATED [] synonym: "epithelial tumor of ovary (disorder)" EXACT [SNOMEDCT_2005_07_31:237057005] synonym: "Ovarian Surface epithelial-Stromal tumor" EXACT [NCI2004_11_17:C4381] xref: NCI:C4381 xref: SNOMEDCT_2010_1_31:237057005 xref: UMLS_CUI:C0341823 is_a: DOID:2394 ! ovarian cancer [Term] id: DOID:2226 name: chronic myeloproliferative disease namespace: disease_ontology alt_id: DOID:6002 def: "A myeloma that is characterized by a group of slow growing blood cancers in which large numbers of abnormal red blood cells, white blood cells, or platelets grow and spread in the bone marrow and the peripheral blood." [url:http\://www.cancer.gov/cancertopics/types/myeloproliferative] synonym: "CMPD" EXACT [NCI2004_11_17:C4345] synonym: "CMPD, U" EXACT [NCI2004_11_17:C27350] xref: NCI:C4345 xref: SNOMEDCT_2010_1_31:115248004 xref: SNOMEDCT_2010_1_31:128842008 xref: SNOMEDCT_2010_1_31:20921005 xref: UMLS_CUI:C1292778 is_a: DOID:0070004 ! myeloma [Term] id: DOID:2394 name: ovarian cancer namespace: disease_ontology alt_id: DOID:0060070 alt_id: DOID:2144 alt_id: DOID:9595 comment: OMIM mapping confirmed by DO. [SN]. synonym: "malignant Ovarian tumor" EXACT [NCI2004_11_17:C7431] synonym: "malignant tumor of ovary (disorder)" EXACT [SNOMEDCT_2005_07_31:363443007] synonym: "malignant tumour of ovary" EXACT [SNOMEDCT_2005_07_31:154528000] synonym: "neoplasm of ovary (disorder)" EXACT [SNOMEDCT_2005_07_31:123843001] synonym: "ovarian cancer" EXACT [CSP2005:2016-1387] synonym: "ovarian neoplasm" EXACT [MTH:NOCODE] synonym: "ovary cancer" EXACT [] synonym: "ovary neoplasm" EXACT [CSP2005:2016-1387] synonym: "primary malignant neoplasm of ovary and other uterine adnexa (disorder)" EXACT [SNOMEDCT_2005_07_31:372117006] synonym: "primary ovarian cancer" EXACT [] synonym: "tumor of the Ovary" EXACT [NCI2004_11_17:C4984] xref: MSH:D010051 xref: NCI:C4984 xref: OMIM:167000 xref: SNOMEDCT_2010_1_31:123843001 xref: SNOMEDCT_2010_1_31:154528000 xref: SNOMEDCT_2010_1_31:363443007 xref: SNOMEDCT_2010_1_31:372117006 xref: SNOMEDCT_2010_1_31:93934004 xref: UMLS_CUI:C0919267 xref: UMLS_CUI:C1140680 xref: UMLS_CUI:C1299247 is_a: DOID:120 ! female reproductive organ cancer [Term] id: DOID:2431 name: glomus tumor namespace: disease_ontology def: "A hemangiopericytic tumor that is a mesenchymal neoplasm composed of cells that closely resemble the modified smooth muscle cells of the normal glomus body." [url:www.iarc.fr/en/publications/pdfs-online/pat-gen/bb5/bb5-chap5.pdf] synonym: "Glomus neoplasm" EXACT [NCI2004_11_17:C3060] synonym: "Glomus tumor (disorder)" EXACT [SNOMEDCT_2005_07_31:403969002] synonym: "Glomus tumor (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:10438002] synonym: "Glomus tumour" EXACT [SNOMEDCT_2005_07_31:393567008] synonym: "Glomus tumour" EXACT [SNOMEDCT_2005_07_31:189193002] xref: MSH:D005918 xref: NCI:C3060 xref: SNOMEDCT_2010_1_31:10438002 xref: SNOMEDCT_2010_1_31:189193002 xref: SNOMEDCT_2010_1_31:393567008 xref: SNOMEDCT_2010_1_31:403969002 xref: UMLS_CUI:C0017653 is_a: DOID:3850 ! hemangiopericytic tumor [Term] id: DOID:2479 name: central nervous system origin vertigo namespace: disease_ontology synonym: "central vestibular vertigo" EXACT [SNOMEDCT_2005_07_31:20425006] synonym: "Vertigo of central origin" EXACT [ICD9CM_2006:386.2] synonym: "Vertigo of central origin (disorder)" EXACT [SNOMEDCT_2005_07_31:38403006] synonym: "Vertigo of central origin NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:194362009] xref: ICD9CM:386.2 xref: MSH:D014717 xref: SNOMEDCT_2010_1_31:194362009 xref: SNOMEDCT_2010_1_31:20425006 xref: SNOMEDCT_2010_1_31:38403006 xref: UMLS_CUI:C0155503 is_a: DOID:3426 ! vestibular disease is_a: DOID:936 ! brain disease [Term] id: DOID:2493 name: gastric antral vascular ectasia namespace: disease_ontology synonym: "gastric antral vascular ectasia (disorder)" EXACT [SNOMEDCT_2005_07_31:412795008] synonym: "Watermelon stomach (disorder)" EXACT [SNOMEDCT_2005_07_31:43935004] xref: MSH:D020252 xref: NCI:C84724 xref: SNOMEDCT_2010_1_31:412795008 xref: SNOMEDCT_2010_1_31:43935004 xref: UMLS_CUI:C0267211 is_a: DOID:1271 ! capillary disease [Term] id: DOID:2531 name: hematologic cancer namespace: disease_ontology alt_id: DOID:1034 alt_id: DOID:2532 def: "An immune system cancer located_in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." [url:http\://en.wikipedia.org/wiki/Blood_cancer, url:http\://www.cancer.gov/dictionary/?CdrID=45708] synonym: "blood cancer" EXACT [CSP2005:2004-0139] synonym: "Hematologic malignancy" EXACT [SNOMEDCT_2005_07_31:269475001] synonym: "Hematologic malignancy (disorder)" EXACT [SNOMEDCT_2005_07_31:127221002] synonym: "Hematologic neoplasm (disorder)" EXACT [SNOMEDCT_2005_07_31:129154003] synonym: "Hematological tumors" EXACT [NCI2004_11_17:C27134] synonym: "hematopoietic and lymphoid system tumor" EXACT [] synonym: "hematopoietic cancer" EXACT [] synonym: "hematopoietic neoplasm (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:414388001] synonym: "hematopoietic tumors" EXACT [NCI2004_11_17:C27134] synonym: "malignant hematopoietic neoplasm (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:414644002] xref: MSH:D019337 xref: NCI:C27134 xref: SNOMEDCT_2010_1_31:414388001 xref: SNOMEDCT_2010_1_31:414644002 xref: UMLS_CUI:C0376544 is_a: DOID:0060083 ! immune system cancer [Term] id: DOID:255 name: hemangioma namespace: disease_ontology def: "A cell type benign neoplasm that has_physical_basis_in endothelial cells that line blood vessels and is characterised by increased number of normal or abnormal vessels filled with blood." [url:http\://en.wikipedia.org/wiki/Hemangioma] xref: ICD9CM:228.0 xref: ICD9CM:228.00 xref: MSH:D006391 xref: NCI:C3085 xref: SNOMEDCT_2010_1_31:154625006 xref: SNOMEDCT_2010_1_31:189192007 xref: SNOMEDCT_2010_1_31:189193002 xref: SNOMEDCT_2010_1_31:189194008 xref: SNOMEDCT_2010_1_31:189199003 xref: SNOMEDCT_2010_1_31:189863005 xref: SNOMEDCT_2010_1_31:2099007 xref: SNOMEDCT_2010_1_31:253053003 xref: SNOMEDCT_2010_1_31:254822005 xref: SNOMEDCT_2010_1_31:269646001 xref: SNOMEDCT_2010_1_31:367337005 xref: SNOMEDCT_2010_1_31:400210000 xref: SNOMEDCT_2010_1_31:93474003 xref: UMLS_CUI:C0018916 is_a: DOID:0060084 ! cell type benign neoplasm [Term] id: DOID:2571 name: Langerhans-cell histiocytosis namespace: disease_ontology def: "A disease of metabolism and histiocytic and dendritic cell cancer and histiocytosis and interstitial lung disease that results_in the proliferation of Langerhans cells." [url:http\://en.wikipedia.org/wiki/Langerhans_cell_histiocytosis] comment: OMIM mapping confirmed by DO. [SN]. synonym: "Histiocytosis X" EXACT [SNOMEDCT_2005_07_31:269628007] synonym: "Langerhan's cell histiocytosis (disorder)" EXACT [SNOMEDCT_2005_07_31:234439008] synonym: "Langerhans cell granulomatosis" EXACT [CSP2005:0427-5330] xref: MSH:D006646 xref: NCI:C3107 xref: NCI:C6920 xref: OMIM:604856 xref: SNOMEDCT_2010_1_31:110450007 xref: SNOMEDCT_2010_1_31:128809007 xref: SNOMEDCT_2010_1_31:154583006 xref: SNOMEDCT_2010_1_31:190955000 xref: SNOMEDCT_2010_1_31:190956004 xref: SNOMEDCT_2010_1_31:234439008 xref: SNOMEDCT_2010_1_31:269628007 xref: SNOMEDCT_2010_1_31:65399007 xref: UMLS_CUI:C0019621 is_a: DOID:3405 ! histiocytosis [Term] id: DOID:264 name: hemangiopericytoma namespace: disease_ontology alt_id: DOID:5372 def: "A soft tissue cancer that is a soft tissue sarcoma and originates in the pericytes in the walls of capillaries." [url:http\://en.wikipedia.org/wiki/Hemangiopericytoma] synonym: "Haemangiopericytic meningioma [obs]" EXACT [SNOMEDCT_2005_07_31:36060005] synonym: "hemangiopericytoma" EXACT [CSP2005:2007-1041] synonym: "hemangiopericytoma" EXACT [MTH:NOCODE] synonym: "hemangiopericytoma (disorder)" EXACT [SNOMEDCT_2005_07_31:134335004] synonym: "hemangiopericytoma, malignant (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:84664004] synonym: "malignant hemangiopericytoma" EXACT [] xref: MSH:D006393 xref: NCI:C3087 xref: SNOMEDCT_2010_1_31:134335004 xref: SNOMEDCT_2010_1_31:36060005 xref: UMLS_CUI:C0018922 is_a: DOID:201 ! connective tissue cancer [Term] id: DOID:2742 name: auditory system disease namespace: disease_ontology alt_id: DOID:1490 alt_id: DOID:2011 synonym: "Destruction - ear drum" EXACT [SNOMEDCT_2005_07_31:155253008] synonym: "Destruction - ear drum" EXACT [SNOMEDCT_2005_07_31:267768008] synonym: "disorder of ear (disorder)" EXACT [SNOMEDCT_2005_07_31:25906001] synonym: "ear and mastoid disease" EXACT [] synonym: "ear disease" EXACT [SNOMEDCT_2005_07_31:194193002] synonym: "ear disorder" EXACT [NCI2004_11_17:C26757] synonym: "ear disorder" EXACT [CSP2005:0977-5187] synonym: "ear disorder NOS" EXACT [SNOMEDCT_2005_07_31:155261003] synonym: "ear disorder NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:194410006] synonym: "Mastoiditis and related conditions" EXACT [] synonym: "Unspecified disorder of ear" EXACT [ICD9CM_2006:388.9] xref: ICD9CM:388.9 xref: MSH:D004427 xref: NCI:C26757 xref: SNOMEDCT_2010_1_31:155253008 xref: SNOMEDCT_2010_1_31:155261003 xref: SNOMEDCT_2010_1_31:194193002 xref: SNOMEDCT_2010_1_31:194410006 xref: SNOMEDCT_2010_1_31:25906001 xref: SNOMEDCT_2010_1_31:267768008 xref: UMLS_CUI:C0013447 is_a: DOID:0050155 ! sensory system disease [Term] id: DOID:285 name: hairy cell leukemia namespace: disease_ontology xref: ICD9CM:202.4 xref: MSH:D007943 xref: NCI:C7402 xref: SNOMEDCT_2010_1_31:118613001 xref: SNOMEDCT_2010_1_31:188644003 xref: SNOMEDCT_2010_1_31:188653005 xref: SNOMEDCT_2010_1_31:190066005 xref: SNOMEDCT_2010_1_31:54087003 xref: SNOMEDCT_2010_1_31:85228003 xref: UMLS_CUI:C0023443 is_a: DOID:1040 ! chronic lymphocytic leukemia [Term] id: DOID:2914 name: immune system disease namespace: disease_ontology def: "A disease of anatomical entity that is located_in the immune system." [url:http\://en.wikipedia.org/wiki/Immune_system] xref: EFO:0000540 xref: ICD9CM:279 xref: ICD9CM:279.9 xref: SNOMEDCT_2010_1_31:154782004 xref: SNOMEDCT_2010_1_31:191015009 xref: SNOMEDCT_2010_1_31:191019003 xref: SNOMEDCT_2010_1_31:191035005 xref: UMLS_CUI:C0041806 is_a: DOID:7 ! disease of anatomical entity [Term] id: DOID:2952 name: inner ear disease namespace: disease_ontology synonym: "disease of inner ear (disorder)" EXACT [SNOMEDCT_2005_07_31:194690003] synonym: "disorder of inner ear (disorder)" EXACT [SNOMEDCT_2005_07_31:232297009] synonym: "Inner ear disorder" EXACT [NCI2004_11_17:C27166] xref: NCI:C27166 xref: SNOMEDCT_2010_1_31:194690003 xref: SNOMEDCT_2010_1_31:232297009 xref: UMLS_CUI:C0494559 is_a: DOID:2742 ! auditory system disease [Term] id: DOID:3007 name: ductal carcinoma namespace: disease_ontology synonym: "duct carcinoma, NOS" EXACT [SNOMEDCT_2005_07_31:82711006] xref: MSH:D044584 xref: SNOMEDCT_2010_1_31:82711006 xref: UMLS_CUI:C1176475 is_obsolete: true [Term] id: DOID:305 name: carcinoma namespace: disease_ontology alt_id: DOID:2428 alt_id: DOID:6570 def: "A cell type cancer that has_material_basis_in abnormally proliferating cells derived_from epithelial cells." [url:http\://en.wikipedia.org/wiki/Carcinoma] synonym: "carcinoma" EXACT [CSP2005:2000-1867] synonym: "epithelioma" EXACT [CSP2005:2000-5801] synonym: "Epithelioma, malignant (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:71298006] synonym: "malignant Epithelioma" EXACT [NCI2004_11_17:C6927] synonym: "malignant epithelioma" EXACT [] xref: MSH:D002277 xref: NCI:C2916 xref: SNOMEDCT_2010_1_31:118285006 xref: SNOMEDCT_2010_1_31:134207000 xref: SNOMEDCT_2010_1_31:154433003 xref: SNOMEDCT_2010_1_31:188083002 xref: SNOMEDCT_2010_1_31:189546004 xref: SNOMEDCT_2010_1_31:189549006 xref: SNOMEDCT_2010_1_31:189559007 xref: SNOMEDCT_2010_1_31:269513004 xref: SNOMEDCT_2010_1_31:68453008 xref: SNOMEDCT_2010_1_31:71298006 xref: UMLS_CUI:C0007097 xref: UMLS_CUI:C0553707 xref: UMLS_CUI:C1368683 is_a: DOID:0050687 ! cell type cancer [Term] id: DOID:3275 name: thymoma namespace: disease_ontology synonym: "thymoma" EXACT [NCI2004_11_17:C3411] synonym: "Thymoma (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:128856005] synonym: "Thymoma NOS (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:189721001] xref: MSH:D013945 xref: NCI:C3411 xref: SNOMEDCT_2010_1_31:128856005 xref: SNOMEDCT_2010_1_31:189721001 xref: SNOMEDCT_2010_1_31:444231005 xref: UMLS_CUI:C0040100 is_a: DOID:3277 ! thymus cancer [Term] id: DOID:3277 name: thymus cancer namespace: disease_ontology alt_id: DOID:10143 def: "An immune system cancer located_in the thymus." [url:http\://en.wikipedia.org/wiki/Thymus] synonym: "neoplasm of thymus (disorder)" EXACT [SNOMEDCT_2005_07_31:127231009] synonym: "thymic neoplasm" EXACT [CSP2005:2004-8826] synonym: "Thymic tumor" EXACT [NCI2004_11_17:C3412] synonym: "Thymus cancer" EXACT [NCI2004_11_17:C4962] synonym: "thymus cancer" EXACT [] xref: MSH:D013953 xref: NCI:C3412 xref: SNOMEDCT_2010_1_31:127231009 xref: SNOMEDCT_2010_1_31:363434003 xref: SNOMEDCT_2010_1_31:94096009 xref: UMLS_CUI:C0040116 xref: UMLS_CUI:C0751552 is_a: DOID:0060083 ! immune system cancer [Term] id: DOID:331 name: central nervous system disease namespace: disease_ontology def: "A nervous system disease that affects either the spinal cord (myelopathy) or brain (encephalopathy) of the central nervous system." [url:http\://en.wikipedia.org/wiki/Central_nervous_system_disease] xref: MSH:D002493 xref: NCI:C2934 xref: SNOMEDCT_2010_1_31:138748005 xref: SNOMEDCT_2010_1_31:154981003 xref: SNOMEDCT_2010_1_31:155049004 xref: SNOMEDCT_2010_1_31:155059003 xref: SNOMEDCT_2010_1_31:192641002 xref: SNOMEDCT_2010_1_31:193076009 xref: SNOMEDCT_2010_1_31:194566008 xref: SNOMEDCT_2010_1_31:23853001 xref: SNOMEDCT_2010_1_31:267144009 xref: SNOMEDCT_2010_1_31:267679005 xref: SNOMEDCT_2010_1_31:267700003 xref: SNOMEDCT_2010_1_31:267702006 xref: SNOMEDCT_2010_1_31:275539005 xref: UMLS_CUI:C0007682 is_a: DOID:863 ! nervous system disease [Term] id: DOID:3316 name: perivascular tumor namespace: disease_ontology alt_id: DOID:5234 synonym: "malignant perivascular cancer" EXACT [] xref: NCI:C6530 xref: UMLS_CUI:C1334611 xref: UMLS_CUI:C1335392 is_a: DOID:175 ! vascular cancer [Term] id: DOID:3405 name: histiocytosis namespace: disease_ontology alt_id: DOID:3344 def: "A reticuloendotheliosis that is characterized by an excessive number of histiocytes." [url:http\://en.wikipedia.org/wiki/Histiocytosis, url:http\://www.nlm.nih.gov/medlineplus/ency/article/000068.htm, XX:http\://en.wikipedia.org/wiki/Histiocytosis] synonym: "chronic Histiocytosis X" EXACT [MTHICD9_2006:277.89] synonym: "Hand Schuller Christian disease" EXACT [CSP2005:0427-5330] xref: MSH:D015614 xref: NCI:C3106 xref: SNOMEDCT_2010_1_31:190957008 xref: SNOMEDCT_2010_1_31:60657004 xref: SNOMEDCT_2010_1_31:65396000 xref: UMLS_CUI:C0019618 is_a: DOID:75 ! lymphatic system disease [Term] id: DOID:3426 name: vestibular disease namespace: disease_ontology synonym: "disorder of vestibular function, unspecified" EXACT [SNOMEDCT_2005_07_31:194379003] synonym: "disorder of vestibular function, unspecified (disorder)" EXACT [SNOMEDCT_2005_07_31:194695008] synonym: "Vertigo, vestibular disorder" EXACT [SNOMEDCT_2005_07_31:267761002] synonym: "Vestibular disorder, NOS" EXACT [SNOMEDCT_2005_07_31:20425006] xref: MSH:D015837 xref: NCI:C27166 xref: SNOMEDCT_2010_1_31:194379003 xref: SNOMEDCT_2010_1_31:194695008 xref: SNOMEDCT_2010_1_31:20425006 xref: SNOMEDCT_2010_1_31:267761002 xref: UMLS_CUI:C0042594 is_a: DOID:4539 ! labyrinthine disease [Term] id: DOID:3457 name: invasive lobular carcinoma namespace: disease_ontology synonym: "Lobular carcinoma (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:89740008] synonym: "Lobular carcinoma NOS (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:189713007] synonym: "Lobular carcinoma of breast (disorder)" EXACT [SNOMEDCT_2005_07_31:278054005] synonym: "Lobular carcinoma of the breast" EXACT [NCI2004_11_17:C3771] xref: MSH:D018275 xref: NCI:C3771 xref: SNOMEDCT_2010_1_31:189713007 xref: SNOMEDCT_2010_1_31:278054005 xref: SNOMEDCT_2010_1_31:89740008 xref: UMLS_CUI:C0206692 is_a: DOID:3459 ! breast carcinoma [Term] id: DOID:3459 name: breast carcinoma namespace: disease_ontology def: "A breast cancer that derives_from breast tissue." [url:http\://en.wikipedia.org/wiki/Breast_cancer] synonym: "carcinoma OF breast" EXACT [MTH:118] synonym: "carcinoma of breast" EXACT [SNOMEDCT_2005_07_31:154513000] synonym: "carcinoma of breast (disorder)" EXACT [SNOMEDCT_2005_07_31:254838004] synonym: "carcinoma of breast NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:286898006] synonym: "Mammary carcinoma" EXACT [NCI2004_11_17:C4872] xref: EFO:0000305 xref: NCI:C4872 xref: SNOMEDCT_2010_1_31:154513000 xref: SNOMEDCT_2010_1_31:254838004 xref: SNOMEDCT_2010_1_31:286898006 xref: UMLS_CUI:C0678222 is_a: DOID:1612 ! breast cancer [Term] id: DOID:374 name: nutrition disease namespace: disease_ontology synonym: "Nutritional disorder" EXACT [NCI2004_11_17:C26836] xref: MSH:D009748 xref: NCI:C26836 xref: SNOMEDCT_2010_1_31:191077005 xref: SNOMEDCT_2010_1_31:2492009 xref: UMLS_CUI:C0028709 is_a: DOID:0060158 ! acquired metabolic disease [Term] id: DOID:3850 name: hemangiopericytic tumor namespace: disease_ontology synonym: "Hemangiopericytic neoplasm" EXACT [SNOMEDCT_2005_07_31:189866002] synonym: "Hemangiopericytic neoplasm NOS (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:189867006] xref: NCI:C7076 xref: SNOMEDCT_2010_1_31:189866002 xref: SNOMEDCT_2010_1_31:189867006 xref: UMLS_CUI:C0476144 is_a: DOID:3316 ! perivascular tumor [Term] id: DOID:3905 name: lung carcinoma namespace: disease_ontology def: "A lung cancer that is located_in the lungs and has_symptom cough and has_symptom chest discomfort or pain and has_symptom weight loss and has_symptom hemoptysis." [url:https\://merck.com/mmpe/sec05/ch062/ch062b.html] comment: OMIM mapping confirmed by DO. [SN]. synonym: "cancer of lung" EXACT [NCI2004_11_17:C4878] synonym: "carcinoma OF LUNG" EXACT [MTH:460] synonym: "carcinoma of lung" RELATED [] synonym: "lung carcinoma" EXACT [SNOMEDCT_2005_07_31:269561006] synonym: "lung carcinoma" EXACT [SNOMEDCT_2005_07_31:154485001] xref: EFO:0001071 xref: NCI:C4878 xref: OMIM:612571 xref: SNOMEDCT_2010_1_31:154485001 xref: SNOMEDCT_2010_1_31:187875007 xref: SNOMEDCT_2010_1_31:269561006 xref: UMLS_CUI:C0684249 is_a: DOID:1324 ! lung cancer [Term] id: DOID:3908 name: non-small cell lung carcinoma namespace: disease_ontology synonym: "Non-small cell lung cancer (disorder)" EXACT [SNOMEDCT_2005_07_31:254637007] synonym: "NSCLC" EXACT [CSP2005:4005-0042] synonym: "NSCLC" EXACT [NCI2004_11_17:C2926] xref: EFO:0003060 xref: KEGG:05223 xref: MSH:D002289 xref: NCI:C2926 xref: SNOMEDCT_2010_1_31:254637007 xref: UMLS_CUI:C0007131 is_a: DOID:3905 ! lung carcinoma [Term] id: DOID:4 name: disease namespace: disease_ontology def: "A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." [url:http\://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf] xref: MSH:D004194 xref: NCI:C2991 xref: SNOMEDCT_2010_1_31:64572001 xref: UMLS_CUI:C0012634 is_a: OMIT:0000122 ! DOIDTerms [Term] id: DOID:4001 name: ovarian carcinoma namespace: disease_ontology comment: OMIM mapping confirmed by DO. [SN]. synonym: "Ovarian carcinoma" EXACT [NCI2004_11_17:C4908] xref: EFO:0001075 xref: MSH:C538090 xref: NCI:C4908 xref: UMLS_CUI:C0677886 is_a: DOID:2151 ! malignant ovarian surface epithelial-stromal neoplasm [Term] id: DOID:4539 name: labyrinthine disease namespace: disease_ontology xref: MSH:D007759 xref: SNOMEDCT_2010_1_31:20425006 xref: SNOMEDCT_2010_1_31:267761002 xref: SNOMEDCT_2010_1_31:267763004 xref: SNOMEDCT_2010_1_31:286945007 xref: UMLS_CUI:C0022890 is_a: DOID:2952 ! inner ear disease [Term] id: DOID:4556 name: lung large cell carcinoma namespace: disease_ontology synonym: "large cell carcinoma of lung (disorder)" EXACT [SNOMEDCT_2005_07_31:254629004] synonym: "large cell lung carcinoma" EXACT [NCI2004_11_17:C4450] xref: NCI:C4450 xref: SNOMEDCT_2010_1_31:254629004 xref: UMLS_CUI:C0345958 is_a: DOID:3908 ! non-small cell lung carcinoma [Term] id: DOID:4960 name: bone marrow cancer namespace: disease_ontology alt_id: DOID:2356 alt_id: DOID:2761 def: "A hematopoietic cancer that derives_from the blood-forming stem cells of the bone marrow." [url:http\://nci.nih.gov/dictionary/?CdrID=430857] synonym: "bone marrow neoplasm" EXACT [CSP2005:2004-0492] synonym: "bone Marrow tumor" EXACT [NCI2004_11_17:C35370] synonym: "malignant bone Marrow tumor" EXACT [NCI2004_11_17:C35501] synonym: "malignant neoplasm of bone marrow" EXACT [] synonym: "Myeloid neoplasm (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:414792005] synonym: "myeloproliferative disease" EXACT [] synonym: "Myeloproliferative disease NOS" EXACT [MTHICD9_2006:238.7] synonym: "Myeloproliferative disease, no ICD-O subtype (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:128925001] synonym: "Myeloproliferative disease, NOS" EXACT [SNOMEDCT_2005_07_31:20921005] synonym: "myeloproliferative disorder" EXACT [] synonym: "Myeloproliferative disorder (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:414794006] synonym: "myeloproliferative neoplasm" EXACT [CSP2005:2004-0893] synonym: "Myeloproliferative tumors" EXACT [NCI2004_11_17:C9290] synonym: "neoplasm of bone marrow (disorder)" EXACT [SNOMEDCT_2005_07_31:414824005] synonym: "primary malignant neoplasm of bone marrow (disorder)" EXACT [SNOMEDCT_2005_07_31:93720005] xref: EFO:0004251 xref: MSH:D009196 xref: SNOMEDCT_2010_1_31:128925001 xref: SNOMEDCT_2010_1_31:188772004 xref: SNOMEDCT_2010_1_31:20921005 xref: SNOMEDCT_2010_1_31:414792005 xref: SNOMEDCT_2010_1_31:414794006 xref: SNOMEDCT_2010_1_31:425333006 xref: UMLS_CUI:C002702 is_a: DOID:2531 ! hematologic cancer [Term] id: DOID:4961 name: bone marrow disease namespace: disease_ontology synonym: "bone marrow disorder" EXACT [CSP2005:0427-3773] xref: MSH:D001855 xref: NCI:C34433 xref: SNOMEDCT_2010_1_31:127035006 xref: UMLS_CUI:C0005956 is_a: DOID:74 ! hematopoietic system disease [Term] id: DOID:5093 name: thoracic cancer namespace: disease_ontology alt_id: DOID:3937 def: "An organ system cancer located_in the thoracic cavity that develops in the different types of cells within the lungs, as well as less common cancers of the esophagus, the trachea, or the chest wall." [url:http\://www.advocatehealth.com/cmc/body.cfm?id=203] synonym: "Thoracic tumor" EXACT [NCI2004_11_17:C3406] synonym: "thorax cancer" EXACT [] synonym: "thorax neoplasm" EXACT [CSP2005:2005-5041] synonym: "tumor of thorax (disorder)" EXACT [SNOMEDCT_2005_07_31:255058005] xref: MSH:D013899 xref: NCI:C3406 xref: SNOMEDCT_2010_1_31:188361007 xref: SNOMEDCT_2010_1_31:188365003 xref: SNOMEDCT_2010_1_31:255058005 xref: UMLS_CUI:C0039981 xref: UMLS_CUI:C0153661 is_a: DOID:0050686 ! organ system cancer [Term] id: DOID:5113 name: nutritional deficiency disease namespace: disease_ontology xref: MSH:D003677 xref: UMLS_CUI:C0011156 is_a: DOID:374 ! nutrition disease [Term] id: DOID:5158 name: pleural neoplasm namespace: disease_ontology synonym: "neoplasm of pleura" EXACT [SNOMEDCT_2005_07_31:126719004] synonym: "pleural neoplasm" EXACT [CSP2005:2005-3967] synonym: "Pleural tumor" EXACT [NCI2004_11_17:C3332] xref: MSH:D010997 xref: NCI:C3332 xref: SNOMEDCT_2010_1_31:126719004 xref: UMLS_CUI:C0032229 is_a: DOID:201 ! connective tissue cancer [Term] id: DOID:5399 name: ovine pulmonary adenomatosis namespace: disease_ontology alt_id: DOID:3802 def: "A viral infectious disease that results_in bronchioloalveolar carcinoma in ovine, located_in lung, has_material_basis_in Jaagsiekte sheep retrovirus, characterized by proliferation of the pulmonary alveolar epithelium and occlusion of the alveoli and terminal bronchioles, presenting as a collection of benign growths of grandular origin." [url:http\://www.cfsph.iastate.edu/Factsheets/pdfs/ovine_pulmonary_adenomatosis.pdf] synonym: "Jaagziekte (disorder)" EXACT [SNOMEDCT_2005_07_31:7238003] synonym: "ovine pulmonary adenomatosis" EXACT [] synonym: "pulmonary adenomatosis" EXACT [NCI2004_11_17:C3763] synonym: "pulmonary adenomatosis (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:32434004] synonym: "Tumor Virus Infections" RELATED [] xref: MSH:D011648 xref: SNOMEDCT_2010_1_31:32434004 xref: SNOMEDCT_2010_1_31:7238003 xref: UMLS_CUI:C0034049 xref: UMLS_CUI:C0206676 is_obsolete: true [Term] id: DOID:5599 name: precursor T-lymphoblastic lymphoma/leukemia namespace: disease_ontology synonym: "Precursor T-Lymphoblastic Lymphoma/Leukemia" EXACT [NCI2004_11_17:C8694] xref: UMLS_CUI:C0854857 is_a: DOID:5600 ! precursor lymphoblastic lymphoma/leukemia [Term] id: DOID:5600 name: precursor lymphoblastic lymphoma/leukemia namespace: disease_ontology xref: NCI:C7055 xref: UMLS_CUI:C1335469 is_a: DOID:0060058 ! lymphoma [Term] id: DOID:5601 name: T-cell neoplasm namespace: disease_ontology xref: NCI:C27908 xref: UMLS_CUI:C1336554 is_obsolete: true [Term] id: DOID:5602 name: T-cell adult acute lymphocytic leukemia namespace: disease_ontology synonym: "adult Precursor T Lymphoblastic Leukemia" EXACT [NCI2004_11_17:C9142] xref: NCI:C9142 xref: UMLS_CUI:C0279592 is_a: DOID:5604 ! adult acute lymphocytic leukemia [Term] id: DOID:5604 name: adult acute lymphocytic leukemia namespace: disease_ontology synonym: "adult acute lymphoid Leukemia" EXACT [NCI2004_11_17:C4967] xref: NCI:C4967 xref: UMLS_CUI:C0751606 is_a: DOID:9952 ! acute lymphocytic leukemia [Term] id: DOID:6179 name: ovarian small cell carcinoma namespace: disease_ontology xref: NCI2009_04D:C27390 xref: UMLS_CUI:C1335179 is_a: DOID:4001 ! ovarian carcinoma [Term] id: DOID:630 name: genetic disease namespace: disease_ontology def: "A disease that has_material_basis_in genetic variations in the human genome." [url:http\://ghr.nlm.nih.gov/] xref: MSH:D030342 xref: NCI:C3101 xref: SNOMEDCT_2010_1_31:264530000 xref: SNOMEDCT_2010_1_31:32895009 xref: UMLS_CUI:C0019247 is_a: DOID:4 ! disease [Term] id: DOID:649 name: prion disease namespace: disease_ontology synonym: "Prion disease (disorder)" EXACT [SNOMEDCT_2005_07_31:20484008] synonym: "Prion disease pathway" EXACT [NCI2004_11_17:C38853] synonym: "prion induced disorder" EXACT [CSP2005:2042-5006] synonym: "prion induced disorder" EXACT [CSP2005:2042-5040] synonym: "Prion protein disease" EXACT [SNOMEDCT_2005_07_31:193172009] synonym: "Spongiform Encephalopathy" EXACT [NCI2004_11_17:C27585] synonym: "Spongiform encephalopathy (disorder)" EXACT [SNOMEDCT_2005_07_31:230284004] xref: KEGG:05020 xref: MSH:D017096 xref: NCI:C27585 xref: NCI:C38853 xref: SNOMEDCT_2010_1_31:193172009 xref: SNOMEDCT_2010_1_31:20484008 xref: SNOMEDCT_2010_1_31:230284004 xref: UMLS_CUI:C0162534 is_a: DOID:936 ! brain disease [Term] id: DOID:6658 name: pulmonary large cell neuroendocrine carcinoma namespace: disease_ontology alt_id: DOID:5721 synonym: "large cell neuroendocrine carcinoma" EXACT [] synonym: "large cell neuroendocrine carcinoma (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:128628002] synonym: "pulmonary large cell neuroendocrine carcinoma" EXACT [NCI2004_11_17:C5672] xref: NCI:C6875 xref: SNOMEDCT_2010_1_31:128628002 xref: UMLS_CUI:C1265996 xref: UMLS_CUI:C1334363 is_a: DOID:4556 ! lung large cell carcinoma [Term] id: DOID:67 name: neural tissue disease namespace: disease_ontology synonym: "nervous tissue disease" EXACT [] is_obsolete: true [Term] id: DOID:7 name: disease of anatomical entity namespace: disease_ontology alt_id: DOID:1 alt_id: DOID:2 alt_id: DOID:5 alt_id: DOID:71 alt_id: DOID:72 alt_id: DOID:8 def: "A disease that manifests in a defined anatomical structure." [DO:wk\,ls, URL:http\://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=anatomic] is_a: DOID:4 ! disease [Term] id: DOID:706 name: mature B-cell neoplasm namespace: disease_ontology synonym: "mature B-cell lymphocytic neoplasm" EXACT [] synonym: "mature B-cell neoplasm" EXACT [] xref: EFO:0000096 xref: NCI:C27910 xref: UMLS_CUI:C1334633 is_a: DOID:707 ! B-cell lymphocytic neoplasm [Term] id: DOID:7061 name: precursor B lymphoblastic lymphoma/leukemia namespace: disease_ontology xref: NCI:C8936 xref: UMLS_CUI:C0862030 is_a: DOID:5600 ! precursor lymphoblastic lymphoma/leukemia is_a: DOID:707 ! B-cell lymphocytic neoplasm [Term] id: DOID:707 name: B-cell lymphocytic neoplasm namespace: disease_ontology synonym: "B-cell neoplasm (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:413616009] xref: NCI:C27907 xref: SNOMEDCT_2010_1_31:413616009 xref: UMLS_CUI:C1332362 is_a: DOID:0060058 ! lymphoma [Term] id: DOID:74 name: hematopoietic system disease namespace: disease_ontology synonym: "Blood disease" EXACT [SNOMEDCT_2005_07_31:154785002] synonym: "blood disorder" EXACT [CSP2005:0427-3600] synonym: "Blood dyscrasia NOS" EXACT [MTHICD9_2006:289.9] synonym: "disease of hematopoietic system" EXACT [] synonym: "DISEASE OF THE BLOOD AND BLOOD-FORMING ORGANS" EXACT [ICD9CM_2006:280-289.99] synonym: "Hematological disease" EXACT [MTH:NOCODE] xref: ICD9CM:280-289.99 xref: ICD9CM:289.9 xref: MSH:D006402 xref: SNOMEDCT_2010_1_31:154785002 xref: SNOMEDCT_2010_1_31:154842002 xref: SNOMEDCT_2010_1_31:191124002 xref: SNOMEDCT_2010_1_31:191402006 xref: SNOMEDCT_2010_1_31:191446003 xref: SNOMEDCT_2010_1_31:267552000 xref: SNOMEDCT_2010_1_31:267573000 xref: SNOMEDCT_2010_1_31:34093004 xref: UMLS_CUI:C0018939 is_a: DOID:2914 ! immune system disease [Term] id: DOID:75 name: lymphatic system disease namespace: disease_ontology synonym: "Adenopathy" EXACT [SNOMEDCT_2005_07_31:269044004] synonym: "Adenopathy" EXACT [SNOMEDCT_2005_07_31:141342003] synonym: "disease of lympoid system" EXACT [] synonym: "disorder of lymph node and lymphatics (disorder)" EXACT [SNOMEDCT_2005_07_31:234087005] synonym: "disorder of lymphatic system" EXACT [SNOMEDCT_2005_07_31:362971004] synonym: "disorder of lymphoid system" EXACT [SNOMEDCT_2005_07_31:111590001] synonym: "Lymphangiopathy, NOS" EXACT [SNOMEDCT_2005_07_31:3305006] synonym: "Lymphatic disease" EXACT [MTH:NOCODE] synonym: "Lymphatic disease" EXACT [SNOMEDCT_2005_07_31:266326002] synonym: "Lymphatic disease" EXACT [SNOMEDCT_2005_07_31:155452000] synonym: "Lymphatic disease" EXACT [MTH:461] synonym: "Lymphatic disorder" EXACT [NCI2004_11_17:C3206] synonym: "lymphatic disorder" EXACT [CSP2005:0427-7757] synonym: "lympoid system disease" EXACT [] xref: MSH:D008206 xref: NCI:C3206 xref: SNOMEDCT_2010_1_31:111590001 xref: SNOMEDCT_2010_1_31:141342003 xref: SNOMEDCT_2010_1_31:155452000 xref: SNOMEDCT_2010_1_31:234087005 xref: SNOMEDCT_2010_1_31:266326002 xref: SNOMEDCT_2010_1_31:269044004 xref: SNOMEDCT_2010_1_31:3305006 xref: SNOMEDCT_2010_1_31:362971004 xref: UMLS_CUI:C0024228 is_a: DOID:2914 ! immune system disease [Term] id: DOID:7650 name: pulmonary type ovarian small cell carcinoma namespace: disease_ontology xref: NCI:C40440 xref: UMLS_CUI:C1518737 is_a: DOID:6179 ! ovarian small cell carcinoma [Term] id: DOID:8432 name: polycythemia namespace: disease_ontology synonym: "Erythrocythemia" EXACT [SNOMEDCT_2005_07_31:165401000] synonym: "Erythrocythemia" EXACT [SNOMEDCT_2005_07_31:109992005] synonym: "Polycythaemia" EXACT [SNOMEDCT_2005_07_31:127062003] synonym: "POLYCYTHEMIA" EXACT [MTH:NOCODE] synonym: "polycythemia" EXACT [CSP2005:0427-4465] synonym: "Polycythemia, NOS" EXACT [SNOMEDCT_2005_07_31:44865000] xref: MSH:D011086 xref: NCI:C26863 xref: SNOMEDCT_2010_1_31:109992005 xref: SNOMEDCT_2010_1_31:127062003 xref: SNOMEDCT_2010_1_31:165401000 xref: SNOMEDCT_2010_1_31:44865000 xref: UMLS_CUI:C0032461 is_a: DOID:4961 ! bone marrow disease [Term] id: DOID:8567 name: Hodgkin's lymphoma namespace: disease_ontology alt_id: DOID:0060059 alt_id: DOID:8652 alt_id: DOID:8671 alt_id: DOID:8685 alt_id: DOID:8710 alt_id: DOID:8715 alt_id: DOID:8841 alt_id: DOID:8953 alt_id: DOID:9096 alt_id: DOID:9107 def: "A lymphoma that is marked by the presence of a type of cell called the Reed-Sternberg cell." [url:v] comment: OMIM mapping confirmed by DO. [SN]. synonym: "HL" EXACT [NCI2004_11_17:C9357] synonym: "Hodgkin disease" EXACT [MTH:NOCODE] synonym: "Hodgkin's sarcoma" EXACT [ICD9CM_2006:201.2] synonym: "Hodgkins lymphoma" EXACT [] synonym: "stage I Subdiaphragmatic Hodgkin Lymphoma" EXACT [NCI2004_11_17:C5012] synonym: "stage II Subdiaphragmatic Hodgkin Lymphoma" EXACT [NCI2004_11_17:C5010] xref: EFO:0000183 xref: ICD9CM:201 xref: ICD9CM:201.0 xref: ICD9CM:201.2 xref: ICD9CM:201.9 xref: MSH:D006689 xref: NCI:C26956 xref: NCI:C9357 xref: OMIM:236000 xref: SNOMEDCT_2010_1_31:118599009 xref: SNOMEDCT_2010_1_31:118605002 xref: SNOMEDCT_2010_1_31:118606001 xref: SNOMEDCT_2010_1_31:14537002 xref: SNOMEDCT_2010_1_31:154582001 xref: SNOMEDCT_2010_1_31:188521005 xref: SNOMEDCT_2010_1_31:188522003 xref: SNOMEDCT_2010_1_31:188532005 xref: SNOMEDCT_2010_1_31:188543002 xref: SNOMEDCT_2010_1_31:188552006 xref: SNOMEDCT_2010_1_31:188595005 xref: SNOMEDCT_2010_1_31:188596006 xref: SNOMEDCT_2010_1_31:188605006 xref: SNOMEDCT_2010_1_31:189987006 xref: SNOMEDCT_2010_1_31:189991001 xref: SNOMEDCT_2010_1_31:189992008 xref: SNOMEDCT_2010_1_31:269509006 xref: SNOMEDCT_2010_1_31:309831004 xref: SNOMEDCT_2010_1_31:46923007 xref: SNOMEDCT_2010_1_31:52337003 xref: SNOMEDCT_2010_1_31:70600005 xref: UMLS_CUI:C0019829 is_a: DOID:0060058 ! lymphoma [Term] id: DOID:8584 name: Burkitt's lymphoma namespace: disease_ontology comment: OMIM mapping confirmed by DO. [SN]. synonym: "Burkitt Lymphoma" EXACT [MTH:NOCODE] synonym: "Burkitt lymphoma/leukaemia" EXACT [SNOMEDCT_2005_07_31:397400006] synonym: "Burkitt's lymphoma" EXACT [SNOMEDCT_2005_07_31:154581008] synonym: "Burkitt's lymphoma - disorder" EXACT [SNOMEDCT_2005_07_31:118617000] synonym: "Burkitt's lymphoma NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:188518008] synonym: "Burkitt's lymphoma of unspecified site (disorder)" EXACT [SNOMEDCT_2005_07_31:188509006] synonym: "Burkitt's tumor" EXACT [CSP2005:2004-6947] synonym: "Burkitt's tumor NOS (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:190023003] synonym: "Burkitt's tumor or lymphoma" EXACT [] synonym: "Burkitt's tumors (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:190022008] synonym: "Burkitt's tumour [obs]" EXACT [SNOMEDCT_2005_07_31:77381001] synonym: "malignant lymphoma, Burkitt's type" EXACT [MTHICD9_2006:200.2] synonym: "small Non-Cleaved cell Lymphoma, Burkitt's type" EXACT [NCI2004_11_17:C2912] xref: ICD9CM:200.2 xref: MSH:D002051 xref: NCI:C2912 xref: NCI:C7400 xref: OMIM:113970 xref: SNOMEDCT_2010_1_31:118617000 xref: SNOMEDCT_2010_1_31:154581008 xref: SNOMEDCT_2010_1_31:188509006 xref: SNOMEDCT_2010_1_31:188518008 xref: SNOMEDCT_2010_1_31:190022008 xref: SNOMEDCT_2010_1_31:190023003 xref: SNOMEDCT_2010_1_31:22197008 xref: SNOMEDCT_2010_1_31:277571004 xref: SNOMEDCT_2010_1_31:397400006 xref: SNOMEDCT_2010_1_31:77381001 xref: UMLS_CUI:C0006413 is_a: DOID:706 ! mature B-cell neoplasm [Term] id: DOID:863 name: nervous system disease namespace: disease_ontology def: "A disease of anatomical entity that is located_in the central nervous system or located_in the peripheral nervous system." [url:http\://en.wikipedia.org/wiki/Nervous_system] xref: ICD9CM:349.9 xref: MSH:D009422 xref: NCI:C26835 xref: SNOMEDCT_2010_1_31:118940003 xref: SNOMEDCT_2010_1_31:154981003 xref: SNOMEDCT_2010_1_31:155262005 xref: SNOMEDCT_2010_1_31:192641002 xref: SNOMEDCT_2010_1_31:267679005 xref: SNOMEDCT_2010_1_31:286946008 xref: UMLS_CUI:C0027765 is_a: DOID:7 ! disease of anatomical entity [Term] id: DOID:8632 name: Kaposi's sarcoma namespace: disease_ontology alt_id: DOID:12761 alt_id: DOID:12762 alt_id: DOID:12764 alt_id: DOID:12766 alt_id: DOID:12767 alt_id: DOID:12768 alt_id: DOID:12770 alt_id: DOID:12771 alt_id: DOID:12772 alt_id: DOID:12774 alt_id: DOID:12775 alt_id: DOID:12776 alt_id: DOID:12777 alt_id: DOID:12778 alt_id: DOID:6480 alt_id: DOID:7239 alt_id: DOID:8631 def: "A connective tissue cancer that derives_from lymphatic endothelium, and derives_from spindle cells, results_in_formation_of vascular channels that fill with blood cells, has_material_basis_in Human herpesvirus 8 (HHV8)." [url:http\://cancerres.aacrjournals.org/content/58/8/1599.full.pdf, url:http\://en.wikipedia.org/wiki/Kaposi%27s_sarcoma] comment: OMIM mapping confirmed by DO. [SN]. synonym: "African lymphadenopathic Kaposi's sarcoma" RELATED [] synonym: "anal Kaposi's sarcoma" EXACT [] synonym: "cardiac Kaposi's sarcoma" EXACT [] synonym: "central nervous system Kaposi's sarcoma" EXACT [] synonym: "Conjunctival Kaposi's sarcoma" EXACT [NCI2004_11_17:C4578] synonym: "conjunctival Kaposi's sarcoma" EXACT [] synonym: "Corneal Kaposi's sarcoma" EXACT [NCI2004_11_17:C4579] synonym: "corneal Kaposi's sarcoma" EXACT [] synonym: "Cutaneous Kaposi's sarcoma" EXACT [NCI2004_11_17:C3550] synonym: "cutaneous Kaposi's sarcoma" EXACT [] synonym: "esophageal Kaposi's sarcoma" EXACT [] synonym: "gallbladder Kaposi's sarcoma" EXACT [] synonym: "gastric Kaposi's sarcoma" EXACT [] synonym: "intestinal Kaposi's sarcoma" EXACT [] synonym: "Kaposi's sarcoma of anus" EXACT [NCI2004_11_17:C5602] synonym: "Kaposi's sarcoma of central nervous system" EXACT [] synonym: "Kaposi's sarcoma of conjunctiva (disorder)" EXACT [SNOMEDCT_2005_07_31:255114007] synonym: "Kaposi's sarcoma of cornea (disorder)" EXACT [SNOMEDCT_2005_07_31:255115008] synonym: "Kaposi's sarcoma of esophagus" EXACT [NCI2004_11_17:C5706] synonym: "Kaposi's sarcoma of gastrointestinal sites" EXACT [] synonym: "Kaposi's sarcoma of Heart" EXACT [NCI2004_11_17:C5363] synonym: "Kaposi's sarcoma of lung (disorder)" EXACT [SNOMEDCT_2005_07_31:109390005] synonym: "Kaposi's sarcoma of lymph nodes" EXACT [SNOMEDCT_2005_07_31:188775002] synonym: "Kaposi's sarcoma of lymph nodes (disorder)" EXACT [SNOMEDCT_2005_07_31:109391009] synonym: "Kaposi's sarcoma of palate (disorder)" EXACT [SNOMEDCT_2005_07_31:109388009] synonym: "Kaposi's sarcoma of penis" EXACT [NCI2004_11_17:C6377] synonym: "Kaposi's sarcoma of skin" EXACT [SNOMEDCT_2005_07_31:188144002] synonym: "Kaposi's sarcoma of skin (disorder)" EXACT [SNOMEDCT_2005_07_31:109386008] synonym: "Kaposi's sarcoma of soft tissue (disorder)" EXACT [SNOMEDCT_2005_07_31:188029000] synonym: "Kaposi's sarcoma of soft tissues (disorder)" EXACT [SNOMEDCT_2005_07_31:109387004] synonym: "Kaposi's sarcoma of the CNS" EXACT [NCI2004_11_17:C7006] synonym: "Kaposi's sarcoma of the gallbladder" EXACT [NCI2004_11_17:C5842] synonym: "Kaposi's sarcoma of the prostate" EXACT [NCI2004_11_17:C5523] synonym: "Kaposi's sarcoma, lung" EXACT [ICD9CM_2006:176.4] synonym: "Kaposi's sarcoma, skin" EXACT [ICD9CM_2006:176.0] synonym: "Kaposi's sarcoma-associated herpesvirus (KSHV)" RELATED [] synonym: "lymph node Kaposi's sarcoma" EXACT [] synonym: "lymphadenopathic Kaposi's sarcoma" EXACT [] synonym: "Palate Kaposi's sarcoma" EXACT [NCI2004_11_17:C6749] synonym: "palate Kaposi's sarcoma" EXACT [] synonym: "penis Kaposi's sarcoma" EXACT [] synonym: "prostate Kaposi's sarcoma" EXACT [] synonym: "pulmonary Kaposi's sarcoma" EXACT [NCI2004_11_17:C3551] synonym: "soft tissue Kaposi's sarcoma" EXACT [] xref: ICD9CM:176 xref: ICD9CM:176.9 xref: MSH:C538559 xref: MSH:D012514 xref: NCI:C9087 xref: OMIM:148000 xref: SNOMEDCT_2010_1_31:109385007 xref: SNOMEDCT_2010_1_31:109386008 xref: SNOMEDCT_2010_1_31:109387004 xref: SNOMEDCT_2010_1_31:109388009 xref: SNOMEDCT_2010_1_31:109390005 xref: SNOMEDCT_2010_1_31:109391009 xref: SNOMEDCT_2010_1_31:154604006 xref: SNOMEDCT_2010_1_31:188029000 xref: SNOMEDCT_2010_1_31:188144002 xref: SNOMEDCT_2010_1_31:188483007 xref: SNOMEDCT_2010_1_31:188775002 xref: SNOMEDCT_2010_1_31:190112000 xref: SNOMEDCT_2010_1_31:255114007 xref: SNOMEDCT_2010_1_31:255115008 xref: SNOMEDCT_2010_1_31:49937004 xref: UMLS_CUI:C0036220 xref: UMLS_CUI:C0153560 xref: UMLS_CUI:C0153561 xref: UMLS_CUI:C0153562 xref: UMLS_CUI:C0153563 xref: UMLS_CUI:C0153564 xref: UMLS_CUI:C0153565 xref: UMLS_CUI:C0346935 xref: UMLS_CUI:C0346936 xref: UMLS_CUI:C1332265 xref: UMLS_CUI:C1332847 xref: UMLS_CUI:C1333453 xref: UMLS_CUI:C1333744 xref: UMLS_CUI:C1333776 xref: UMLS_CUI:C1334318 xref: UMLS_CUI:C1334457 xref: UMLS_CUI:C1335372 xref: UMLS_CUI:C1335509 is_a: DOID:201 ! connective tissue cancer [Term] id: DOID:8654 name: Hodgkin's lymphoma, mixed cellularity namespace: disease_ontology synonym: "Hodgkin lymphoma, mixed cellularity" EXACT [SNOMEDCT_2005_07_31:41529000] synonym: "Hodgkin's disease, mixed cellularity" RELATED [] synonym: "Hodgkin's disease, mixed cellularity (disorder)" EXACT [SNOMEDCT_2005_07_31:118609008] synonym: "Hodgkin's disease, mixed cellularity NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:188583005] synonym: "Hodgkin's disease, mixed cellularity of unspecified site (disorder)" EXACT [SNOMEDCT_2005_07_31:188574000] synonym: "MCHL" EXACT [NCI2004_11_17:C3517] xref: ICD9CM:201.6 xref: MSH:D006689 xref: NCI:C3517 xref: SNOMEDCT_2010_1_31:118609008 xref: SNOMEDCT_2010_1_31:188574000 xref: SNOMEDCT_2010_1_31:188583005 xref: SNOMEDCT_2010_1_31:41529000 xref: UMLS_CUI:C0152266 is_a: DOID:8567 ! Hodgkin's lymphoma [Term] id: DOID:8691 name: mycosis fungoides namespace: disease_ontology alt_id: DOID:8737 comment: OMIM mapping confirmed by DO. [SN]. synonym: "MF" EXACT [NCI2004_11_17:C3246] synonym: "Mycosis Fungoides" EXACT [MTH:U002093] synonym: "Mycosis fungoides" EXACT [SNOMEDCT_2005_07_31:190003004] synonym: "Mycosis fungoides (disorder)" EXACT [SNOMEDCT_2005_07_31:118618005] synonym: "Mycosis fungoides (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:90120004] synonym: "mycosis fungoides lymphoma" EXACT [CSP2005:2004-7126] synonym: "Mycosis fungoides NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:188628007] synonym: "Mycosis fungoides NOS (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:190004005] synonym: "Mycosis fungoides of unspecified site (disorder)" EXACT [SNOMEDCT_2005_07_31:188618003] synonym: "Mycosis fungoides, unspecified site, extranodal and solid organ sites" EXACT [] xref: ICD9CM:202.1 xref: MSH:D009182 xref: NCI:C3246 xref: OMIM:254400 xref: SNOMEDCT_2010_1_31:118618005 xref: SNOMEDCT_2010_1_31:188618003 xref: SNOMEDCT_2010_1_31:188628007 xref: SNOMEDCT_2010_1_31:190003004 xref: SNOMEDCT_2010_1_31:190004005 xref: SNOMEDCT_2010_1_31:90120004 xref: UMLS_CUI:C0026948 is_a: DOID:0060061 ! cutaneous T cell lymphoma [Term] id: DOID:8692 name: myeloid leukemia namespace: disease_ontology alt_id: DOID:8878 alt_id: DOID:8879 alt_id: DOID:8910 alt_id: DOID:9066 alt_id: DOID:9126 synonym: "LEUKEMIA MYELOGENOUS" EXACT [MTH:NOCODE] synonym: "Myelogenous Leukemia in Remission" EXACT [NCI2004_11_17:C4899] synonym: "myeloid granulocytic leukemia" EXACT [CSP2005:2004-4431] synonym: "Myeloid leukaemia" EXACT [SNOMEDCT_2005_07_31:269631008] synonym: "Myeloid leukaemia" EXACT [SNOMEDCT_2005_07_31:154587007] synonym: "Myeloid leukaemia (category)" EXACT [SNOMEDCT_2005_07_31:128934006] synonym: "Myeloid leukemia" EXACT [ICD9CM_2006:205] synonym: "Myeloid leukemia (disorder)" EXACT [SNOMEDCT_2005_07_31:188732008] synonym: "Myeloid leukemia in remission (disorder)" EXACT [SNOMEDCT_2005_07_31:94716000] synonym: "Myeloid leukemia NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:188743000] synonym: "Myeloid leukemia, disease (disorder)" EXACT [SNOMEDCT_2005_07_31:324170002] synonym: "Myeloid leukemia, disease [Ambiguous]" EXACT [SNOMEDCT_2005_07_31:94717009] synonym: "Myeloid leukemia, no ICD-O subtype (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:37810007] synonym: "Myeloid leukemia, NOS, without mention of remission" EXACT [SNOMEDCT_2005_07_31:94717009] synonym: "Myeloid leukemias (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:190047005] synonym: "Non-Lymphocytic Leukemia" EXACT [NCI2004_11_17:C3172] synonym: "Other myeloid leukemia" EXACT [] synonym: "Other myeloid leukemia (disorder)" EXACT [SNOMEDCT_2005_07_31:188740002] synonym: "Other myeloid leukemia (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:190159007] synonym: "Other myeloid leukemia in remission" EXACT [] synonym: "Other myeloid leukemia NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:188742005] synonym: "Other myeloid leukemia NOS (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:190051007] synonym: "Other myeloid leukemia without mention of remission" EXACT [] synonym: "Unspecified myeloid leukemia in remission" EXACT [] synonym: "Unspecified myeloid leukemia without mention of remission" EXACT [] xref: ICD9CM:205 xref: ICD9CM:205.9 xref: MSH:D007951 xref: MSH:D015473 xref: NCI:C3172 xref: SNOMEDCT_2010_1_31:128934006 xref: SNOMEDCT_2010_1_31:154587007 xref: SNOMEDCT_2010_1_31:188732008 xref: SNOMEDCT_2010_1_31:188743000 xref: SNOMEDCT_2010_1_31:190047005 xref: SNOMEDCT_2010_1_31:269631008 xref: SNOMEDCT_2010_1_31:324170002 xref: SNOMEDCT_2010_1_31:37810007 xref: SNOMEDCT_2010_1_31:94717009 xref: UMLS_CUI:C0023470 is_a: DOID:1240 ! leukemia [Term] id: DOID:8838 name: Hodgkin's lymphoma, nodular sclerosis namespace: disease_ontology synonym: "Classical Hodgkin lymphoma, nodular sclerosis" EXACT [SNOMEDCT_2005_07_31:52248008] synonym: "Hodgkin's disease nodular sclerosis NOS" EXACT [MTHICD9_2006:201.5] synonym: "Hodgkin's disease, nodular sclerosis" RELATED [] synonym: "Hodgkin's disease, nodular sclerosis (disorder)" EXACT [SNOMEDCT_2005_07_31:118608000] synonym: "Hodgkin's disease, nodular sclerosis NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:188573006] synonym: "Hodgkin's disease, nodular sclerosis NOS (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:134178004] synonym: "Hodgkin's disease, nodular sclerosis of unspecified site (disorder)" EXACT [SNOMEDCT_2005_07_31:188564003] synonym: "NSHL" EXACT [NCI2004_11_17:C3518] xref: ICD9CM:201.5 xref: NCI:C3518 xref: SNOMEDCT_2010_1_31:118608000 xref: SNOMEDCT_2010_1_31:134178004 xref: SNOMEDCT_2010_1_31:188564003 xref: SNOMEDCT_2010_1_31:188573006 xref: SNOMEDCT_2010_1_31:52248008 xref: UMLS_CUI:C0152268 is_a: DOID:8567 ! Hodgkin's lymphoma [Term] id: DOID:8997 name: polycythemia vera namespace: disease_ontology comment: OMIM mapping confirmed by DO. [SN]. synonym: "Erythremia (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:278190000] synonym: "Osler-Vaquez syndrome" EXACT [SNOMEDCT_2005_07_31:109992005] synonym: "Polycythaemia rubra vera" EXACT [SNOMEDCT_2005_07_31:154644004] synonym: "polycythemia vera" EXACT [CSP2005:2004-0979] synonym: "Proliferative polycythaemia" EXACT [SNOMEDCT_2005_07_31:128841001] xref: ICD9CM:238.4 xref: MSH:D011087 xref: NCI:C3336 xref: OMIM:263300 xref: SNOMEDCT_2010_1_31:109992005 xref: SNOMEDCT_2010_1_31:128841001 xref: SNOMEDCT_2010_1_31:134182002 xref: SNOMEDCT_2010_1_31:154644004 xref: SNOMEDCT_2010_1_31:269652000 xref: SNOMEDCT_2010_1_31:278190000 xref: SNOMEDCT_2010_1_31:31569001 xref: UMLS_CUI:C0032463 is_a: DOID:8432 ! polycythemia [Term] id: DOID:9119 name: acute myeloid leukemia namespace: disease_ontology alt_id: DOID:9118 alt_id: DOID:9171 comment: OMIM mapping confirmed by DO. [SN]. synonym: "acute myeloblastic leukemia (disorder)" EXACT [SNOMEDCT_2005_07_31:277600006] synonym: "acute myeloid leukaemia" EXACT [SNOMEDCT_2005_07_31:154591002] synonym: "acute myeloid leukaemia, disease" EXACT [SNOMEDCT_2005_07_31:91861009] synonym: "acute myeloid leukemia without mention of remission" EXACT [] synonym: "AML" EXACT [CSP2005:4000-0108] synonym: "AML - acute Myeloid Leukemia" EXACT [NCI2004_11_17:C3171] synonym: "ANLL in Remission" EXACT [NCI2004_11_17:C3588] synonym: "Leukemia, Myelocytic, acute" EXACT [MTH:NOCODE] xref: ICD9CM:205.0 xref: KEGG:05221 xref: MSH:D015470 xref: NCI:C27753 xref: NCI:C3171 xref: OMIM:601626 xref: OMIM:602439 xref: SNOMEDCT_2010_1_31:154591002 xref: SNOMEDCT_2010_1_31:17788007 xref: SNOMEDCT_2010_1_31:277600006 xref: SNOMEDCT_2010_1_31:413443009 xref: SNOMEDCT_2010_1_31:91861009 xref: UMLS_CUI:C0023467 is_a: DOID:8692 ! myeloid leukemia [Term] id: DOID:934 name: viral infectious disease namespace: disease_ontology alt_id: DOID:1329 def: "A disease by infectious agent that results_in infection, has_material_basis_in Viruses." [url:http\://www.merck.com/mmhe/sec17/ch198/ch198a.html] synonym: "arbovirus infectious disease" EXACT [] synonym: "arthropod-borne viruses" RELATED [] synonym: "Viral disease" EXACT [SNOMEDCT_2005_07_31:154319002] synonym: "Viral disease" EXACT [SNOMEDCT_2005_07_31:266188005] synonym: "Viral disease (disorder)" EXACT [SNOMEDCT_2005_07_31:34014006] synonym: "Viral Infection" EXACT [NCI2004_11_17:C3439] synonym: "Viral infection NOS" EXACT [MTHICD9_2006:079.99] synonym: "Viral infection NOS" EXACT [SNOMEDCT_2005_07_31:154372003] synonym: "Viral infection NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:266116004] synonym: "Viral infection, unspecified (disorder)" EXACT [SNOMEDCT_2005_07_31:187471008] synonym: "Viral: [infection NOS] or [illness]" EXACT [SNOMEDCT_2005_07_31:186754003] synonym: "virus infection" EXACT [CSP2005:3099-8150] synonym: "virus infection" EXACT [CSP2005:3099-7852] xref: ICD9CM:060-066.99 xref: ICD9CM:066.9 xref: MSH:D001102 xref: NCI:C34396 xref: SNOMEDCT_2010_1_31:154319002 xref: SNOMEDCT_2010_1_31:154345006 xref: SNOMEDCT_2010_1_31:154372003 xref: SNOMEDCT_2010_1_31:186619002 xref: SNOMEDCT_2010_1_31:186754003 xref: SNOMEDCT_2010_1_31:187471008 xref: SNOMEDCT_2010_1_31:266116004 xref: SNOMEDCT_2010_1_31:266188005 xref: SNOMEDCT_2010_1_31:266194002 xref: SNOMEDCT_2010_1_31:34014006 xref: SNOMEDCT_2010_1_31:40610006 xref: UMLS_CUI:C0003723 xref: UMLS_CUI:C0042769 is_a: DOID:0050117 ! disease by infectious agent [Term] id: DOID:936 name: brain disease namespace: disease_ontology alt_id: DOID:8510 synonym: "encephalopathy" EXACT [] xref: MSH:D001927 xref: SNOMEDCT_2010_1_31:155053002 xref: SNOMEDCT_2010_1_31:193051008 xref: SNOMEDCT_2010_1_31:76011009 xref: SNOMEDCT_2010_1_31:81308009 xref: UMLS_CUI:C0006111 xref: UMLS_CUI:C0085584 is_a: DOID:331 ! central nervous system disease [Term] id: DOID:9917 name: pleural cancer namespace: disease_ontology xref: ICD9CM:163 xref: ICD9CM:163.9 xref: NCI:C3547 xref: SNOMEDCT_2010_1_31:187880003 xref: SNOMEDCT_2010_1_31:363433009 xref: SNOMEDCT_2010_1_31:93966009 xref: UMLS_CUI:C0153494 is_a: DOID:5158 ! pleural neoplasm [Term] id: DOID:9952 name: acute lymphocytic leukemia namespace: disease_ontology synonym: "acute lymphoblastic leukemia" EXACT [] xref: EFO:0000220 xref: ICD9CM:204.0 xref: NCI:C3167 xref: OMIM:613065 xref: OMIM:613067 xref: SNOMEDCT_2010_1_31:128822004 xref: SNOMEDCT_2010_1_31:154588002 xref: SNOMEDCT_2010_1_31:190034000 xref: SNOMEDCT_2010_1_31:90151006 xref: SNOMEDCT_2010_1_31:91857003 xref: UMLS_CUI:C0023449 is_a: DOID:1037 ! lymphoblastic leukemia [Term] id: GO:0000083 name: regulation of transcription involved in G1/S transition of mitotic cell cycle namespace: biological_process def: "Any process that regulates transcription such that the target genes are involved in the transition between G1 and S phase of the mitotic cell cycle." [GOC:mtg_cell_cycle] xref: Reactome:REACT_683 "G1/S-Specific Transcription, Homo sapiens" is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter [Term] id: GO:0000117 name: regulation of transcription involved in G2/M transition of mitotic cell cycle namespace: biological_process def: "Any process that regulates transcription such that the target genes are transcribed as part of the G2/M transition of the mitotic cell cycle." [GOC:mtg_cell_cycle] synonym: "G2/M-specific transcription in mitotic cell cycle" RELATED [] synonym: "regulation of transcription from RNA polymerase II promoter during G2/M transition of mitotic cell cycle" RELATED [] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006355 ! regulation of transcription, DNA-dependent [Term] id: GO:0000122 name: negative regulation of transcription from RNA polymerase II promoter namespace: biological_process alt_id: GO:0010553 alt_id: GO:0045816 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:go_curators, GOC:txnOH] synonym: "down regulation of global transcription from RNA polymerase II promoter" RELATED [] synonym: "down regulation of transcription from RNA polymerase II promoter" EXACT [] synonym: "down-regulation of global transcription from RNA polymerase II promoter" RELATED [] synonym: "down-regulation of transcription from RNA polymerase II promoter" EXACT [] synonym: "downregulation of global transcription from RNA polymerase II promoter" RELATED [] synonym: "downregulation of transcription from RNA polymerase II promoter" EXACT [] synonym: "inhibition of global transcription from RNA polymerase II promoter" RELATED [] synonym: "inhibition of transcription from RNA polymerase II promoter" EXACT [] synonym: "negative regulation of gene-specific transcription from RNA polymerase II promoter" RELATED [] synonym: "negative regulation of global transcription from Pol II promoter" RELATED [] synonym: "negative regulation of transcription from Pol II promoter" EXACT [] synonym: "negative regulation of transcription from RNA polymerase II promoter, global" RELATED [] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent intersection_of: negatively_regulates GO:0006366 ! transcription from RNA polymerase II promoter relationship: negatively_regulates GO:0006366 ! transcription from RNA polymerase II promoter [Term] id: GO:0000154 name: rRNA modification namespace: biological_process alt_id: GO:0016548 def: "The covalent alteration of one or more nucleotides within an rRNA molecule to produce an rRNA molecule with a sequence that differs from that coded genetically." [GOC:curators] comment: The term 'RNA editing' (GO:0016547) was merged into 'RNA modification' (GO:0009451) on the basis of statements in the preface of Modification and Editing of RNA (ISBN:1555811337) that there is no clear distinction between modification and editing. Parallel changes were made for substrate (e.g. tRNA, rRNA, etc.) specific child terms of 'RNA editing'. subset: gosubset_prok synonym: "rRNA editing" NARROW [GOC:hjd] is_a: GO:0006364 ! rRNA processing [Term] id: GO:0000179 name: rRNA (adenine-N6,N6-)-dimethyltransferase activity namespace: molecular_function alt_id: GO:0043790 def: "Catalysis of the dimethylation two adjacent A residues in the loop closing the 3'-terminal stem of the 18S rRNA, using S-adenosyl-L-methionine as a methyl donor." [ISBN:1555811337, PMID:10690410] subset: gosubset_prok synonym: "18S rRNA dimethylase activity" EXACT [] synonym: "dimethyladenosine transferase activity" EXACT [IMG:02532] synonym: "S-adenosylmethionine-6-N', N'-adenosyl(rRNA) dimethyltransferase activity" EXACT [IMG:02532] xref: EC:2.1.1.- is_a: GO:0016433 ! rRNA (adenine) methyltransferase activity [Term] id: GO:0000183 name: chromatin silencing at rDNA namespace: biological_process def: "Repression of transcription of ribosomal DNA by altering the structure of chromatin." [PMID:10219245] synonym: "chromatin silencing at ribosomal DNA" EXACT [] synonym: "heterochromatic silencing at rDNA" EXACT [] synonym: "rDNA chromatin silencing" EXACT [GOC:mah] is_a: GO:0006342 ! chromatin silencing [Term] id: GO:0000244 name: assembly of spliceosomal tri-snRNP namespace: biological_process alt_id: GO:0000351 alt_id: GO:0000355 def: "The formation of a tri-snRNP complex containing U4 and U6 (or U4atac and U6atac) snRNAs and U5 snRNAs and associated proteins. This includes reannealing of U4 and U6 (or U4atac and U6atac) snRNAs released from previous rounds of splicing to reform the U4/U6 snRNP (or U4atac/U6atac snRNP) as well as the subsequent association of the U5 snRNP with the U4/U6 snRNP (or U4atac/U6atac snRNP) to form a tri-snRNP that is ready to reassemble into another spliceosome complex." [ISBN:0879695897, PMID:9452384] synonym: "assembly of spliceosomal tri-snRNP U4/U6.U5" NARROW [] synonym: "assembly of spliceosomal tri-snRNP U4atac/U6atac.U5" NARROW [] synonym: "snRNP recycling" BROAD [] synonym: "spliceosomal tri-snRNP assembly" EXACT [] synonym: "spliceosomal tri-snRNP U4/U6.U5 assembly" NARROW [] synonym: "spliceosomal tri-snRNP U4atac/U6atac.U5 assembly" NARROW [] relationship: part_of GO:0000387 ! spliceosomal snRNP assembly [Term] id: GO:0000245 name: spliceosomal complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of a spliceosomal complex, a ribonucleoprotein apparatus that catalyzes nuclear mRNA splicing via transesterification reactions." [PMID:9476892] synonym: "spliceosome assembly" BROAD [] relationship: part_of GO:0000398 ! mRNA splicing, via spliceosome [Term] id: GO:0000289 name: nuclear-transcribed mRNA poly(A) tail shortening namespace: biological_process def: "Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length." [GOC:krc] synonym: "3' to 5' mRNA deadenylation" RELATED [] synonym: "mRNA deadenylation" RELATED [] synonym: "nuclear mRNA poly(A) tail shortening" RELATED [] xref: Reactome:REACT_102415 "Deadenylation of mRNA, Rattus norvegicus" xref: Reactome:REACT_104397 "Deadenylation of mRNA, Danio rerio" xref: Reactome:REACT_109691 "Deadenylation of mRNA, Bos taurus" xref: Reactome:REACT_111968 "Deadenylation of mRNA, Drosophila melanogaster" xref: Reactome:REACT_20514 "Deadenylation of mRNA, Homo sapiens" xref: Reactome:REACT_30693 "Deadenylation of mRNA, Xenopus tropicalis" xref: Reactome:REACT_31579 "Deadenylation of mRNA, Canis familiaris" xref: Reactome:REACT_78492 "Deadenylation of mRNA, Mus musculus" xref: Reactome:REACT_83021 "Deadenylation of mRNA, Taeniopygia guttata" is_a: GO:0031124 ! mRNA 3'-end processing [Term] id: GO:0000348 name: mRNA branch site recognition namespace: biological_process alt_id: GO:0000370 alt_id: GO:0000371 def: "Recognition of the pre-mRNA branch site sequence by components of the assembling spliceosome." [GOC:krc, ISBN:0879695897] comment: Note that this step represents the formation of the B complex (yeast) or the A complex (mammalian). synonym: "nuclear mRNA branch site recognition" EXACT [GOC:vw] synonym: "spliceosomal A complex biosynthesis" NARROW [] synonym: "spliceosomal A complex formation" NARROW [] synonym: "spliceosomal B complex biosynthesis" NARROW [] synonym: "spliceosomal B complex formation" NARROW [] synonym: "U12-type nuclear mRNA branch site recognition" NARROW [] synonym: "U2-type nuclear mRNA branch site recognition" NARROW [] relationship: part_of GO:0000245 ! spliceosomal complex assembly [Term] id: GO:0000349 name: generation of catalytic spliceosome for first transesterification step namespace: biological_process alt_id: GO:0000356 alt_id: GO:0000357 def: "Formation of a catalytic spliceosome complex ready to perform the first splicing reaction. This occurs by an ATP-dependent conformational change of the pre-catalytic spliceosome." [GOC:krc, ISBN:0879695897] comment: Note that this step represents the formation of the A2-2 complex (yeast) or the C1 complex (mammalian). synonym: "catalytic spliceosome assembly for first transesterification step" RELATED [] synonym: "formation of catalytic spliceosome for first transesterification step" EXACT [] synonym: "spliceosomal A2-2 complex biosynthesis" NARROW [] synonym: "spliceosomal A2-2 complex formation" NARROW [] synonym: "spliceosomal C1 complex biosynthesis" NARROW [] synonym: "spliceosomal C1 complex formation" NARROW [] synonym: "U12-type catalytic spliceosome formation for first transesterification step" NARROW [] synonym: "U2-type catalytic spliceosome formation for first transesterification step" NARROW [] relationship: part_of GO:0000393 ! spliceosomal conformational changes to generate catalytic conformation [Term] id: GO:0000350 name: generation of catalytic spliceosome for second transesterification step namespace: biological_process alt_id: GO:0000358 alt_id: GO:0000359 def: "Conformational rearrangement of the spliceosomal complex containing the RNA products from the 1st step of splicing to form the catalytic site for the second step of splicing." [GOC:krc, ISBN:0879695897] comment: Note that this step represents formation of the A2-3 complex (yeast) or the C2 complex (mammalian). synonym: "catalytic spliceosome assembly for second transesterification step" RELATED [] synonym: "formation of catalytic spliceosome for second transesterification step" EXACT [] synonym: "formation of catalytic U12-type spliceosome for second transesterification step" NARROW [] synonym: "formation of catalytic U2-type spliceosome for second transesterification step" NARROW [] synonym: "formation of spliceosomal A2-2 complex" NARROW [] synonym: "formation of spliceosomal C1 complex" NARROW [] synonym: "lariat formation, 5'-splice site cleavage" RELATED [] synonym: "spliceosomal A2-3 complex biosynthesis" NARROW [] synonym: "spliceosomal A2-3 complex formation" NARROW [] synonym: "spliceosomal C2 complex biosynthesis" NARROW [] synonym: "spliceosomal C2 complex formation" NARROW [] relationship: part_of GO:0000393 ! spliceosomal conformational changes to generate catalytic conformation [Term] id: GO:0000352 name: trans assembly of SL-containing precatalytic spliceosome namespace: biological_process def: "Assembly of a spliceosomal complex containing the SL RNA and the pre-mRNA to be joined, as well as all the spliceosomal snRNPs involved in trans leader splicing. Formation of the trans leader spliceosome brings together the quadruple SL/U4/U5/U6 snRNP and the complex of the U2 snRNP with the splice site of the pre-mRNA." [GOC:krc, GOC:mtg_mpo, ISBN:0879695897] synonym: "trans assembly of spliced leader-containing precatalytic spliceosome" EXACT [] relationship: part_of GO:0000245 ! spliceosomal complex assembly relationship: part_of GO:0045291 ! mRNA trans splicing, SL addition [Term] id: GO:0000353 name: formation of quadruple SL/U4/U5/U6 snRNP namespace: biological_process def: "Formation of a quadruple snRNP complex composed of the spliced leader (SL) RNA along with the U4/U6-U5 tri-snRNP complex. Interactions that may facilitate this include a duplex between the SL and U6 RNAs and interactions between the U5 RNA and the exon sequence at the 5' splice site within the SL RNA." [GOC:krc, ISBN:0879695897] comment: Note that this step is analogous to 5' splice site selection in cis-splicing. relationship: part_of GO:0045291 ! mRNA trans splicing, SL addition [Term] id: GO:0000354 name: cis assembly of pre-catalytic spliceosome namespace: biological_process alt_id: GO:0000360 alt_id: GO:0000361 def: "Assembly of a spliceosomal complex containing the intact pre-mRNA and all of the spliceosomal snRNPs. This occurs when the tri-snRNP associates with the pre-mRNA and associated snRNPs in an ATP-dependent manner." [GOC:krc, GOC:mtg_mpo, ISBN:0879695897] comment: Note that this step represents formation of the A2-1 complex (yeast) or the B1 complex (mammals). synonym: "cis assembly of U12-type pre-catalytic spliceosome" NARROW [] synonym: "cis assembly of U2-type pre-catalytic spliceosome" NARROW [] synonym: "formation of spliceosomal A2-1 complex" NARROW [] synonym: "formation of spliceosomal B1 complex" NARROW [] synonym: "spliceosomal A2-1 complex biosynthesis" NARROW [] synonym: "spliceosomal A2-1 complex formation" NARROW [] synonym: "spliceosomal B1 complex biosynthesis" NARROW [] synonym: "spliceosomal B1 complex formation" NARROW [] relationship: part_of GO:0000245 ! spliceosomal complex assembly relationship: part_of GO:0045292 ! mRNA cis splicing, via spliceosome [Term] id: GO:0000365 name: mRNA trans splicing, via spliceosome namespace: biological_process def: "The joining together of exons from two different primary transcripts of messenger RNA (mRNA) via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced." [GOC:krc, ISBN:0879695897] synonym: "nuclear mRNA trans splicing, via spliceosome" EXACT [GOC:vw] synonym: "nuclear mRNA trans splicing, via U2-type spliceosome" NARROW [] is_a: GO:0000398 ! mRNA splicing, via spliceosome [Term] id: GO:0000366 name: intergenic mRNA trans splicing namespace: biological_process def: "The joining together of two independently transcribed RNAs from two different genes, each of which also produces mRNA(s) via cis-splicing." [GOC:krc, PMID:11726664, PMID:12110900] synonym: "intergenic nuclear mRNA trans splicing" EXACT [GOC:vw] is_a: GO:0000365 ! mRNA trans splicing, via spliceosome is_a: GO:0000380 ! alternative mRNA splicing, via spliceosome [Term] id: GO:0000372 name: Group I intron splicing namespace: biological_process def: "The splicing of Group I introns. This occurs by a ribozymic mechanism where the intron sequence forms a distinct 3D structure, characteristic of Group I introns and involved in determining the locations of the splice sites (there do not appear to be consensus splice site sequences) as well as having a role in catalyzing the splicing reactions, though protein factors are also required in vivo. Splicing occurs by a series of two transesterification reactions, generally with exogenous guanosine as the initiating nucleophile. The intron is excised as a linear piece (though it may subsequently circularize)." [GOC:krc, PMID:11377794] comment: Note that Group I introns are known to be found in a number of places: rRNA, mRNA, and tRNA in organelles of fungi, plants, and protists; tRNA and mRNA of bacteria and bacteriophage; rRNA of protists and fungi; and occasionally in mRNA of animal mitochondria (e.g. sea anemone). subset: gosubset_prok synonym: "mRNA splicing" RELATED [] is_a: GO:0000376 ! RNA splicing, via transesterification reactions with guanosine as nucleophile [Term] id: GO:0000373 name: Group II intron splicing namespace: biological_process def: "The splicing of Group II introns. This occurs by a ribozymic mechanism where the intron sequence forms a distinct 3D structure, characteristic of Group II introns and containing splice site consensus sequences, that is involved in catalyzing the splicing reactions, though protein factors are also required in vivo. Splicing occurs by a series of two transesterification reactions (mechanistically similar to those for splicing of nuclear mRNAs) initiated by a bulged adenosine residue within the intron sequence as the initiating nucleophile. The intron is excised as a lariat." [GOC:krc, PMID:11377794] comment: Note that Group II introns are known to be found in a number of places: rRNA, mRNA, and tRNA in organelles of fungi, plants, and protists; and mRNA of bacteria. subset: gosubset_prok synonym: "mRNA splicing" RELATED [] is_a: GO:0000377 ! RNA splicing, via transesterification reactions with bulged adenosine as nucleophile [Term] id: GO:0000374 name: Group III intron splicing namespace: biological_process def: "The splicing of Group III introns. This occurs by a ribozymic mechanism where the intron sequence forms a distinct 3D structure, characteristic of Group III introns, that is involved in catalyzing the splicing reactions, though protein factors are also required in vivo. Splicing occurs by a series of two transesterification reactions begun by a bulged adenosine residue within the intron sequence as the initiating nucleophile. The intron is excised as a lariat. Though very similar in structure and mechanism to Group II introns, Group III introns are smaller and more streamlined and the splice site consensus sequences are not as well conserved." [GOC:krc, PMID:11377794] comment: Note that Group III introns are known to be found in mRNA of plastids of euglenoid protists. subset: gosubset_prok synonym: "mRNA splicing" RELATED [] is_a: GO:0000377 ! RNA splicing, via transesterification reactions with bulged adenosine as nucleophile [Term] id: GO:0000375 name: RNA splicing, via transesterification reactions namespace: biological_process alt_id: GO:0000385 alt_id: GO:0031202 def: "Splicing of RNA via a series of two transesterification reactions." [GOC:krc] comment: Note that nuclear mRNA, Group I, Group II, and Group III introns are all spliced by a series of two transesterification reactions that occur within the RNA itself, or between two RNAs in trans splicing. Some of these require one or more proteins to stabilize the catalytic conformation, while others are autocatalytic. Note that tRNA introns are spliced by a different catalytic mechanism. subset: gosubset_prok synonym: "pre-mRNA splicing factor activity" RELATED [GOC:krc, GOC:mah] synonym: "RNA splicing factor activity, transesterification mechanism" RELATED [GOC:krc, GOC:mah] synonym: "spliceosomal catalysis" RELATED [] is_a: GO:0008380 ! RNA splicing [Term] id: GO:0000376 name: RNA splicing, via transesterification reactions with guanosine as nucleophile namespace: biological_process def: "Splicing of RNA via a series of two transesterification reactions with exogenous guanosine as the initiating nucleophile." [GOC:krc, PMID:11377794] subset: gosubset_prok is_a: GO:0000375 ! RNA splicing, via transesterification reactions [Term] id: GO:0000377 name: RNA splicing, via transesterification reactions with bulged adenosine as nucleophile namespace: biological_process def: "Splicing of RNA via a series of two transesterification reactions with a bulged adenosine residue from the intron branch point as the initiating nucleophile. When the initial RNA for the splicing reaction is a single molecule (cis splicing), the excised intron is released in a lariat structure." [GOC:krc, PMID:11377794] subset: gosubset_prok synonym: "lariat RNA biosynthesis" RELATED [] synonym: "lariat RNA formation" RELATED [] is_a: GO:0000375 ! RNA splicing, via transesterification reactions [Term] id: GO:0000378 name: RNA exon ligation namespace: biological_process def: "The RNA metabolic process that joins two exons, each of which has free ends that were generated by endonucleolytic cleavages, by a ligation reaction." [GOC:krc, ISBN:0879695897] comment: Note that this is not a part of spliceosomal RNA splicing. subset: gosubset_prok relationship: part_of GO:0000394 ! RNA splicing, via endonucleolytic cleavage and ligation [Term] id: GO:0000379 name: tRNA-type intron splice site recognition and cleavage namespace: biological_process def: "RNA processing that begins when the tertiary structure of a tRNA type intron is recognized, and ends when the endonucleolytic cleavage of the RNA at both the 5' and 3' splice sites occurs." [GOC:krc, GOC:mah, ISBN:0879695897] subset: gosubset_prok is_a: GO:0006396 ! RNA processing relationship: part_of GO:0006388 ! tRNA splicing, via endonucleolytic cleavage and ligation [Term] id: GO:0000380 name: alternative mRNA splicing, via spliceosome namespace: biological_process def: "The process of generating multiple mRNA molecules from a given set of exons by differential use of exons from the primary transcript(s) to form multiple mature mRNAs that vary in their exon composition." [GOC:krc, PMID:12110900] comment: Note that this process most commonly occurs in cis, selecting or skipping exons from the same primary transcript, but it has also been observed to occur in trans at low frequency, at least in some mammals. synonym: "alternative nuclear mRNA splicing, via spliceosome" EXACT [GOC:vw] synonym: "splice site selection" BROAD [] is_a: GO:0000398 ! mRNA splicing, via spliceosome [Term] id: GO:0000381 name: regulation of alternative mRNA splicing, via spliceosome namespace: biological_process def: "Any process that modulates the frequency, rate or extent of alternative splicing of nuclear mRNAs." [GOC:krc] synonym: "regulation of alternative nuclear mRNA splicing, via spliceosome" EXACT [GOC:vw] synonym: "splice site selection" BROAD [] is_a: GO:0048024 ! regulation of mRNA splicing, via spliceosome intersection_of: regulates GO:0000380 ! alternative mRNA splicing, via spliceosome relationship: regulates GO:0000380 ! alternative mRNA splicing, via spliceosome [Term] id: GO:0000384 name: first spliceosomal transesterification activity namespace: molecular_function def: "Catalysis of the first transesterification reaction of spliceosomal mRNA splicing. The intron branch site adenosine is the nucleophile attacking the 5' splice site, resulting in cleavage at this position. In cis splicing, this is the step that forms a lariat structure of the intron RNA, while it is still joined to the 3' exon." [GOC:krc, ISBN:0879695897] synonym: "lariat formation, 5'-splice site cleavage" RELATED [] relationship: part_of GO:0000375 ! RNA splicing, via transesterification reactions [Term] id: GO:0000386 name: second spliceosomal transesterification activity namespace: molecular_function def: "Catalysis of the second transesterification reaction of spliceosomal mRNA splicing. Ligation of the two exons occurs via a transesterification reaction where the free 3'-hydroxyl group of the 5' exon is the nucleophile attacking the 3' splice site. Non-expressed sequences are now detached from the exons. In cis splicing, the intron is in a lariat structure." [GOC:krc, ISBN:0879695897] synonym: "3'-splice site cleavage, exon ligation" BROAD [] synonym: "lariat formation, 5'-splice site cleavage" RELATED [] relationship: part_of GO:0000375 ! RNA splicing, via transesterification reactions [Term] id: GO:0000387 name: spliceosomal snRNP assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of one or more snRNA and multiple protein components to form a ribonucleoprotein complex that is involved in formation of the spliceosome." [GOC:krc, GOC:mah, ISBN:0879695897] synonym: "spliceosomal snRNP biogenesis" RELATED [GOC:mah] xref: Reactome:REACT_10002 "snRNA Cap hypermethylation, Homo sapiens" xref: Reactome:REACT_10041 "Loading and methylation of Sm proteins onto SMN Complexes, Homo sapiens" xref: Reactome:REACT_100869 "snRNP:Snurportin complex formation, Canis familiaris" xref: Reactome:REACT_100915 "snRNP:Snurportin complex formation, Rattus norvegicus" xref: Reactome:REACT_101141 "snRNP Assembly, Mus musculus" xref: Reactome:REACT_102135 "snRNA Cap hypermethylation, Danio rerio" xref: Reactome:REACT_102362 "snRNP complex assembly, Danio rerio" xref: Reactome:REACT_107811 "snRNP Assembly, Gallus gallus" xref: Reactome:REACT_108169 "snRNA Cap hypermethylation, Rattus norvegicus" xref: Reactome:REACT_108689 "snRNP Assembly, Rattus norvegicus" xref: Reactome:REACT_109502 "Loading and methylation of Sm proteins onto SMN Complexes, Danio rerio" xref: Reactome:REACT_11066 "snRNP Assembly, Homo sapiens" xref: Reactome:REACT_112455 "Loading and methylation of Sm proteins onto SMN Complexes, Xenopus tropicalis" xref: Reactome:REACT_29060 "snRNP:Snurportin complex formation, Drosophila melanogaster" xref: Reactome:REACT_29381 "snRNA Cap hypermethylation, Gallus gallus" xref: Reactome:REACT_29703 "snRNP Assembly, Taeniopygia guttata" xref: Reactome:REACT_29866 "snRNP:Snurportin complex formation, Mus musculus" xref: Reactome:REACT_30125 "snRNP complex assembly, Bos taurus" xref: Reactome:REACT_30397 "snRNP Assembly, Sus scrofa" xref: Reactome:REACT_30799 "snRNP:Snurportin complex formation, Danio rerio" xref: Reactome:REACT_30895 "snRNP complex assembly, Canis familiaris" xref: Reactome:REACT_31007 "snRNP complex assembly, Mus musculus" xref: Reactome:REACT_31363 "snRNP complex assembly, Gallus gallus" xref: Reactome:REACT_31615 "snRNP Assembly, Drosophila melanogaster" xref: Reactome:REACT_32359 "snRNP complex assembly, Rattus norvegicus" xref: Reactome:REACT_54083 "snRNA Cap hypermethylation, Bos taurus" xref: Reactome:REACT_77054 "snRNP Assembly, Canis familiaris" xref: Reactome:REACT_79845 "snRNA Cap hypermethylation, Xenopus tropicalis" xref: Reactome:REACT_81235 "Loading and methylation of Sm proteins onto SMN Complexes, Mus musculus" xref: Reactome:REACT_81911 "snRNP complex assembly, Xenopus tropicalis" xref: Reactome:REACT_82745 "snRNA Cap hypermethylation, Drosophila melanogaster" xref: Reactome:REACT_85882 "snRNP Assembly, Danio rerio" xref: Reactome:REACT_86133 "snRNP complex assembly, Drosophila melanogaster" xref: Reactome:REACT_88437 "snRNP Assembly, Xenopus tropicalis" xref: Reactome:REACT_88858 "snRNA Cap hypermethylation, Canis familiaris" xref: Reactome:REACT_93259 "snRNP:Snurportin complex formation, Xenopus tropicalis" xref: Reactome:REACT_93444 "snRNP Assembly, Bos taurus" xref: Reactome:REACT_93869 "snRNP:Snurportin complex formation, Gallus gallus" xref: Reactome:REACT_95210 "snRNA Cap hypermethylation, Mus musculus" xref: Reactome:REACT_99021 "snRNP:Snurportin complex formation, Bos taurus" xref: Reactome:REACT_9946 "snRNP:Snurportin complex formation, Homo sapiens" xref: Reactome:REACT_9957 "snRNP complex assembly, Homo sapiens" relationship: part_of GO:0000398 ! mRNA splicing, via spliceosome [Term] id: GO:0000388 name: spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) namespace: biological_process alt_id: GO:0000396 alt_id: GO:0000397 def: "Rearrangement of the pre-catalytic spliceosome containing U4 (or U4atac) and U1 (or U11) snRNPs to unpair U4 (or U4atac) from U6 (or U6atac) and release it from the spliceosomal complex along with U1 (or U11)." [GOC:krc, ISBN:0879695897] comment: Note that this step represents formation of the A1 complex (yeast) or the B2 complex (mammalian). synonym: "3'-splice site cleavage, exon ligation" BROAD [] synonym: "spliceosomal A1 complex biosynthesis" NARROW [] synonym: "spliceosomal A1 complex formation" NARROW [] synonym: "spliceosomal B2 complex biosynthesis" NARROW [] synonym: "spliceosomal B2 complex formation" NARROW [] synonym: "U12-type spliceosome conformational change to release U4atac and U11" NARROW [] synonym: "U2-type spliceosome conformational change to release U4 and U1" NARROW [] relationship: part_of GO:0000393 ! spliceosomal conformational changes to generate catalytic conformation [Term] id: GO:0000389 name: mRNA 3'-splice site recognition namespace: biological_process alt_id: GO:0000382 alt_id: GO:0000383 def: "Recognition of the intron 3'-splice site by components of the assembling U2- or U12-type spliceosome." [GOC:krc, ISBN:0879695897] synonym: "nuclear mRNA 3'-splice site recognition" EXACT [GOC:vw] synonym: "U12-type nuclear mRNA 3'-splice site recognition" NARROW [] synonym: "U2-type nuclear mRNA 3'-splice site recognition" NARROW [] is_a: GO:0006376 ! mRNA splice site selection [Term] id: GO:0000390 name: spliceosomal complex disassembly namespace: biological_process alt_id: GO:0000391 alt_id: GO:0000392 def: "Disassembly of a spliceosomal complex with the ATP-dependent release of the product RNAs, one of which is composed of the joined exons. In cis splicing, the other product is the excised sequence, often a single intron, in a lariat structure." [GOC:krc, ISBN:0879695897] synonym: "spliceosome complex disassembly" EXACT [] synonym: "spliceosome disassembly" BROAD [] synonym: "U12-type spliceosome disassembly" NARROW [] synonym: "U2-type spliceosome disassembly" NARROW [] relationship: part_of GO:0000398 ! mRNA splicing, via spliceosome [Term] id: GO:0000393 name: spliceosomal conformational changes to generate catalytic conformation namespace: biological_process def: "Structural rearrangements of the spliceosome complex, containing RNA to be spliced, to generate a catalytic conformation." [GOC:krc] synonym: "3'-splice site cleavage, exon ligation" BROAD [] relationship: part_of GO:0000398 ! mRNA splicing, via spliceosome [Term] id: GO:0000394 name: RNA splicing, via endonucleolytic cleavage and ligation namespace: biological_process def: "Splicing of RNA via recognition of the folded RNA structure that brings the 5' and 3' splice sites into proximity and cleavage of the RNA at both the 3' and 5' splice sites by an endonucleolytic mechanism, followed by ligation of the exons." [GOC:krc, ISBN:0879695897] comment: Note that while typically associated with tRNA splicing, this mechanism of splicing is known to be used for some non-tRNA substrates, e.g. HAC1 (YFL031W) in S. cerevisiae and an intron in the 23S rRNA of the Archaeal species Desulfurococcus mobilis. subset: gosubset_prok synonym: "mRNA splicing" BROAD [] is_a: GO:0008380 ! RNA splicing [Term] id: GO:0000395 name: mRNA 5'-splice site recognition namespace: biological_process alt_id: GO:0000368 alt_id: GO:0000369 def: "Recognition of the intron 5'-splice site by components of the assembling spliceosome." [GOC:krc, ISBN:0879695897] comment: Note that this step represents formation of the Commitment Complex (CC, in yeast) or the E complex (mammalian). synonym: "nuclear mRNA 5' splice site recognition" EXACT [] synonym: "nuclear mRNA 5'-splice site recognition" EXACT [GOC:vw] synonym: "spliceosomal CC complex biosynthesis" NARROW [] synonym: "spliceosomal CC complex formation" NARROW [] synonym: "spliceosomal commitment complex biosynthesis" NARROW [] synonym: "spliceosomal commitment complex formation" NARROW [] synonym: "spliceosomal E complex biosynthesis" NARROW [] synonym: "spliceosomal E complex formation" NARROW [] synonym: "U12-type nuclear mRNA 5' splice site recognition" NARROW [] synonym: "U12-type nuclear mRNA 5'-splice site recognition" NARROW [] synonym: "U2-type nuclear mRNA 5' splice site recognition" NARROW [] synonym: "U2-type nuclear mRNA 5'-splice site recognition" NARROW [] is_a: GO:0006376 ! mRNA splice site selection relationship: part_of GO:0045292 ! mRNA cis splicing, via spliceosome [Term] id: GO:0000398 name: mRNA splicing, via spliceosome namespace: biological_process alt_id: GO:0006374 alt_id: GO:0006375 def: "The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced." [GOC:krc, ISBN:0198506732, ISBN:0879695897] comment: Note that although the many U12-type introns have the sequence AT-AC at the intron termini, some introns with these terminal sequences are spliced by the U2-type spliceosome. The distinguishing characteristics are sequences near the 5' splice site and the branch point sequences of the intron. Note that although the majority of U2-type introns have the sequence GU-AG at the intron termini, some introns with these terminal sequences are spliced by the U12-type spliceosome. The distinguishing characteristics are sequences near the 5' splice site and the branch point sequences of the intron. synonym: "mRNA splicing" BROAD [] synonym: "nuclear mRNA splicing via U12-type spliceosome" NARROW [] synonym: "nuclear mRNA splicing via U2-type spliceosome" NARROW [] synonym: "nuclear mRNA splicing, via spliceosome" EXACT [GOC:krc, GOC:vw] synonym: "pre-mRNA splicing" BROAD [] synonym: "splicing AT-AC intron" RELATED [] synonym: "splicing GT-AG intron" RELATED [] xref: Reactome:REACT_101135 "mRNA Splicing - Minor Pathway, Drosophila melanogaster" xref: Reactome:REACT_101749 "mRNA Splicing - Minor Pathway, Caenorhabditis elegans" xref: Reactome:REACT_106268 "mRNA Splicing - Major Pathway, Gallus gallus" xref: Reactome:REACT_107907 "mRNA Splicing - Minor Pathway, Schizosaccharomyces pombe" xref: Reactome:REACT_109091 "mRNA Splicing - Minor Pathway, Rattus norvegicus" xref: Reactome:REACT_112200 "mRNA Splicing - Major Pathway, Arabidopsis thaliana" xref: Reactome:REACT_114266 "mRNA Splicing - Major Pathway, Oryza sativa" xref: Reactome:REACT_114738 "mRNA Splicing - Major Pathway, Taeniopygia guttata" xref: Reactome:REACT_1753 "mRNA Splicing - Minor Pathway, Homo sapiens" xref: Reactome:REACT_30984 "mRNA Splicing - Minor Pathway, Plasmodium falciparum" xref: Reactome:REACT_32449 "mRNA Splicing - Minor Pathway, Canis familiaris" xref: Reactome:REACT_34020 "mRNA Splicing - Minor Pathway, Dictyostelium discoideum" xref: Reactome:REACT_467 "mRNA Splicing - Major Pathway, Homo sapiens" xref: Reactome:REACT_81417 "mRNA Splicing - Major Pathway, Canis familiaris" xref: Reactome:REACT_82149 "mRNA Splicing - Minor Pathway, Danio rerio" xref: Reactome:REACT_85452 "mRNA Splicing - Major Pathway, Bos taurus" xref: Reactome:REACT_86489 "mRNA Splicing - Minor Pathway, Mus musculus" xref: Reactome:REACT_88186 "mRNA Splicing - Minor Pathway, Oryza sativa" xref: Reactome:REACT_89168 "mRNA Splicing - Minor Pathway, Gallus gallus" xref: Reactome:REACT_90296 "mRNA Splicing - Major Pathway, Danio rerio" xref: Reactome:REACT_91088 "mRNA Splicing - Minor Pathway, Arabidopsis thaliana" xref: Reactome:REACT_91611 "mRNA Splicing - Major Pathway, Drosophila melanogaster" xref: Reactome:REACT_91773 "mRNA Splicing - Minor Pathway, Bos taurus" xref: Reactome:REACT_93740 "mRNA Splicing - Major Pathway, Caenorhabditis elegans" xref: Reactome:REACT_93843 "mRNA Splicing - Major Pathway, Rattus norvegicus" xref: Reactome:REACT_95764 "mRNA Splicing - Major Pathway, Mus musculus" xref: Reactome:REACT_99123 "mRNA Splicing - Major Pathway, Xenopus tropicalis" xref: Reactome:REACT_99763 "mRNA Splicing - Minor Pathway, Xenopus tropicalis" is_a: GO:0000377 ! RNA splicing, via transesterification reactions with bulged adenosine as nucleophile is_a: GO:0006397 ! mRNA processing [Term] id: GO:0000409 name: regulation of transcription by galactose namespace: biological_process def: "Any process involving galactose that modulates the frequency, rate or extent or transcription." [GOC:go_curators] subset: gosubset_prok is_a: GO:0045990 ! carbon catabolite regulation of transcription [Term] id: GO:0000410 name: negative regulation of transcription by galactose namespace: biological_process def: "Any process involving galactose that stops, prevents or reduces the rate of transcription." [GOC:mah] synonym: "down regulation of transcription by galactose" EXACT [] synonym: "down-regulation of transcription by galactose" EXACT [] synonym: "downregulation of transcription by galactose" EXACT [] synonym: "inhibition of transcription by galactose" NARROW [] is_a: GO:0000409 ! regulation of transcription by galactose is_a: GO:0045013 ! carbon catabolite repression of transcription [Term] id: GO:0000411 name: positive regulation of transcription by galactose namespace: biological_process def: "Any process involving galactose that activates or increases the rate of transcription." [GOC:go_curators] synonym: "activation of transcription by galactose" NARROW [] synonym: "stimulation of transcription by galactose" NARROW [] synonym: "up regulation of transcription by galactose" EXACT [] synonym: "up-regulation of transcription by galactose" EXACT [] synonym: "upregulation of transcription by galactose" EXACT [] is_a: GO:0000409 ! regulation of transcription by galactose is_a: GO:0045991 ! carbon catabolite activation of transcription [Term] id: GO:0000429 name: carbon catabolite regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A transcription regulation process in which the presence of one carbon source leads to the modulation of the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other carbon sources." [GOC:krc, GOC:mah] synonym: "regulation of transcription from RNA polymerase II promoter by carbon catabolites" EXACT [GOC:mah] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter is_a: GO:0045990 ! carbon catabolite regulation of transcription [Term] id: GO:0000430 name: regulation of transcription from RNA polymerase II promoter by glucose namespace: biological_process def: "Any process involving glucose that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:krc] is_a: GO:0000429 ! carbon catabolite regulation of transcription from RNA polymerase II promoter is_a: GO:0046015 ! regulation of transcription by glucose [Term] id: GO:0000431 name: regulation of transcription from RNA polymerase II promoter by galactose namespace: biological_process def: "Any process involving galactose that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:krc] is_a: GO:0000409 ! regulation of transcription by galactose is_a: GO:0000429 ! carbon catabolite regulation of transcription from RNA polymerase II promoter [Term] id: GO:0000432 name: positive regulation of transcription from RNA polymerase II promoter by glucose namespace: biological_process def: "Any process involving glucose that activates or increases the rate of transcription from an RNA polymerase II promoter." [GOC:krc] synonym: "activation of transcription from RNA polymerase II promoter by glucose" NARROW [] synonym: "stimulation of transcription from RNA polymerase II promoter by glucose" NARROW [] synonym: "up regulation of transcription from RNA polymerase II promoter by glucose" EXACT [] synonym: "up-regulation of transcription from RNA polymerase II promoter by glucose" EXACT [] synonym: "upregulation of transcription from RNA polymerase II promoter by glucose" EXACT [] is_a: GO:0000430 ! regulation of transcription from RNA polymerase II promoter by glucose is_a: GO:0000436 ! carbon catabolite activation of transcription from RNA polymerase II promoter is_a: GO:0046016 ! positive regulation of transcription by glucose [Term] id: GO:0000433 name: negative regulation of transcription from RNA polymerase II promoter by glucose namespace: biological_process def: "Any process involving glucose that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter." [GOC:krc] synonym: "down regulation of transcription from RNA polymerase II promoter by glucose" EXACT [] synonym: "down-regulation of transcription from RNA polymerase II promoter by glucose" EXACT [] synonym: "downregulation of transcription from RNA polymerase II promoter by glucose" EXACT [] synonym: "inhibition of transcription from RNA polymerase II promoter by glucose" NARROW [] is_a: GO:0000430 ! regulation of transcription from RNA polymerase II promoter by glucose is_a: GO:0000437 ! carbon catabolite repression of transcription from RNA polymerase II promoter is_a: GO:0045014 ! negative regulation of transcription by glucose [Term] id: GO:0000434 name: negative regulation of transcription from RNA polymerase II promoter by galactose namespace: biological_process def: "Any process involving galactose that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter." [GOC:krc] synonym: "down regulation of transcription from RNA polymerase II promoter by galactose" EXACT [] synonym: "down-regulation of transcription from RNA polymerase II promoter by galactose" EXACT [] synonym: "downregulation of transcription from RNA polymerase II promoter by galactose" EXACT [] synonym: "inhibition of transcription from RNA polymerase II promoter by galactose" NARROW [] is_a: GO:0000410 ! negative regulation of transcription by galactose is_a: GO:0000431 ! regulation of transcription from RNA polymerase II promoter by galactose is_a: GO:0000437 ! carbon catabolite repression of transcription from RNA polymerase II promoter [Term] id: GO:0000435 name: positive regulation of transcription from RNA polymerase II promoter by galactose namespace: biological_process def: "Any process involving galactose that activates or increases the rate of transcription from an RNA polymerase II promoter." [GOC:krc] synonym: "activation of transcription from RNA polymerase II promoter by galactose" NARROW [] synonym: "stimulation of transcription from RNA polymerase II promoter by galactose" NARROW [] synonym: "up regulation of transcription from RNA polymerase II promoter by galactose" EXACT [] synonym: "up-regulation of transcription from RNA polymerase II promoter by galactose" EXACT [] synonym: "upregulation of transcription from RNA polymerase II promoter by galactose" EXACT [] is_a: GO:0000411 ! positive regulation of transcription by galactose is_a: GO:0000431 ! regulation of transcription from RNA polymerase II promoter by galactose is_a: GO:0000436 ! carbon catabolite activation of transcription from RNA polymerase II promoter [Term] id: GO:0000436 name: carbon catabolite activation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process involving carbon catabolites that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:krc] synonym: "positive regulation of transcription from RNA polymerase II promoter by carbon catabolites" EXACT [GOC:mah] is_a: GO:0000429 ! carbon catabolite regulation of transcription from RNA polymerase II promoter is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter is_a: GO:0045991 ! carbon catabolite activation of transcription [Term] id: GO:0000437 name: carbon catabolite repression of transcription from RNA polymerase II promoter namespace: biological_process def: "A transcription regulation process in which the presence of one carbon source leads to a decrease in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other carbon sources." [GOC:krc] synonym: "negative regulation of transcription from RNA polymerase II promoter by carbon catabolites" EXACT [GOC:mah] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter is_a: GO:0000429 ! carbon catabolite regulation of transcription from RNA polymerase II promoter is_a: GO:0045013 ! carbon catabolite repression of transcription [Term] id: GO:0000447 name: endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage between the SSU-rRNA and the 5.8S rRNA of an rRNA molecule originally produced as a tricistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript." [GOC:curators, PMID:10690410] synonym: "endonucleolytic cleavage at A2" NARROW [] is_a: GO:0000479 ! endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) relationship: part_of GO:0000462 ! maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) relationship: part_of GO:0000466 ! maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [Term] id: GO:0000448 name: cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process alt_id: GO:0000490 def: "Endonucleolytic cleavage within ITS2 between the 5.8S rRNA and the LSU-rRNA of an rRNA molecule originally produced as a tricistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript." [GOC:curators, PMID:10690410] synonym: "cleavage at C2" RELATED [] synonym: "cleavage in ITS2 of tricistronic rRNA transcript to separate 5.8S and LSU rRNAs (SSU-rRNA, 5.8S rRNA, LSU-rRNA)" EXACT [] is_a: GO:0000479 ! endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) relationship: part_of GO:0000463 ! maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) relationship: part_of GO:0000466 ! maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [Term] id: GO:0000449 name: endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 5S) namespace: biological_process def: "Endonucleolytic cleavage of a pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the Large Subunit (LSU) rRNA, and the 5S rRNA, in that order, from 5' to 3' along the primary transcript. For example, primary ribosomal RNA transcripts containing three genes, in this order, are produced in E. coli and other prokaryotic species. Note that the use of the word tricistronic refers only to the number of mature rRNA molecules which will be produced from the primary transcript and ignores tRNAs that may also be present within the primary transcript." [GOC:curators] is_a: GO:0000478 ! endonucleolytic cleavage involved in rRNA processing [Term] id: GO:0000450 name: cleavage of bicistronic rRNA transcript (SSU-rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage of pre-rRNAs originally produced as a bicistronic rRNA transcript that contains the SSU-rRNA and the LSU-rRNA in that order from 5' to 3' along the primary transcript. Primary ribosomal RNA transcripts with two genes in this order are produced in Archaeal species." [GOC:curators] is_a: GO:0000478 ! endonucleolytic cleavage involved in rRNA processing [Term] id: GO:0000451 name: rRNA 2'-O-methylation namespace: biological_process def: "The addition of a methyl group to the 2'-oxygen atom of a nucleotide residue in an rRNA molecule during ribosome biogenesis." [GOC:curators, ISBN:1555811337] is_a: GO:0031167 ! rRNA methylation [Term] id: GO:0000452 name: snoRNA guided rRNA 2'-O-methylation namespace: biological_process def: "The posttranscriptional addition of methyl groups to the 2'-oxygen atom of nucleotide residues in an rRNA molecule during ribosome biogenesis using a snoRNA guide that targets the position of methylation." [GOC:curators, ISBN:1555811337] synonym: "snoRNA guided rRNA 2'-O-ribose methylation" RELATED [GOC:ascb_2009, GOC:dph, GOC:tb] is_a: GO:0000451 ! rRNA 2'-O-methylation [Term] id: GO:0000453 name: enzyme-directed rRNA 2'-O-methylation namespace: biological_process def: "The addition of methyl groups to the 2'-oxygen atom of nucleotide residues in an rRNA molecule during ribosome biogenesis where the methylase specifies the site that becomes methylated without using a guide RNA." [GOC:curators, ISBN:1555811337] is_a: GO:0000451 ! rRNA 2'-O-methylation [Term] id: GO:0000454 name: snoRNA guided rRNA pseudouridine synthesis namespace: biological_process def: "The intramolecular conversion of uridine to pseudouridine in an rRNA molecule during ribosome biogenesis using a snoRNA guide that targets the position of pseudouridylation." [GOC:curators, ISBN:1555811337] is_a: GO:0031118 ! rRNA pseudouridine synthesis [Term] id: GO:0000455 name: enzyme-directed rRNA pseudouridine synthesis namespace: biological_process def: "The intramolecular conversion of uridine to pseudouridine during ribosome biogenesis where the enzyme specifies the site that becomes pseudouridylated without using a guide RNA." [GOC:curators, ISBN:1555811337] is_a: GO:0031118 ! rRNA pseudouridine synthesis [Term] id: GO:0000456 name: dimethylation involved in SSU-rRNA maturation namespace: biological_process def: "Dimethylation of the N6 amino groups of two consecutive adenosine residues near the 3'-end of the SSU rRNA. This process has been conserved from bacteria to eukaryotes." [GOC:curators, GOC:dph, GOC:tb, ISBN:1555811337] is_a: GO:0031167 ! rRNA methylation relationship: part_of GO:0030490 ! maturation of SSU-rRNA [Term] id: GO:0000457 name: endonucleolytic cleavage between SSU-rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 5S) namespace: biological_process def: "Endonucleolytic cleavage to separate a pre-SSU-rRNA from a pre-LSU-rRNA originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the Large Subunit (LSU) rRNA, and the 5S rRNA, in that order, from 5' to 3' along the primary transcript. Note that the use of the word tricistronic refers only to the number of mature rRNA molecules which will be produced from the primary transcript and ignores tRNAs that may also be present within the primary transcript." [GOC:curators] is_a: GO:0000449 ! endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 5S) relationship: part_of GO:0002108 ! maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) relationship: part_of GO:0002109 ! maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) [Term] id: GO:0000458 name: endonucleolytic cleavage between LSU-rRNA and 5S rRNA of tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 5S) namespace: biological_process def: "Endonucleolytic cleavage to separate a pre-LSU-rRNA from a pre-5S rRNA originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the Large Subunit (LSU) rRNA, and the 5S rRNA, in that order, from 5' to 3' along the primary transcript. Note that the use of the word tricistronic refers only to the number of mature rRNA molecules which will be produced from the primary transcript and ignores tRNAs that may also be present within the primary transcript." [GOC:curators] is_a: GO:0000449 ! endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 5S) relationship: part_of GO:0002108 ! maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) [Term] id: GO:0000459 name: exonucleolytic trimming involved in rRNA processing namespace: biological_process def: "Exonucleolytic digestion of a pre-rRNA molecule in the process to generate a mature rRNA molecule." [GOC:curators] synonym: "exonucleolytic trimming during rRNA processing" RELATED [GOC:dph, GOC:tb] is_a: GO:0000469 ! cleavage involved in rRNA processing intersection_of: part_of GO:0006364 ! rRNA processing [Term] id: GO:0000460 name: maturation of 5.8S rRNA namespace: biological_process def: "Any process involved in the maturation of a precursor 5.8S ribosomal RNA (rRNA) molecule into a mature 5.8S rRNA molecule." [GOC:curators] is_a: GO:0006364 ! rRNA processing [Term] id: GO:0000461 name: endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage at the 3'-end of the SSU-rRNA from an originally tricistronic rRNA transcript that contained the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript, to produce the mature end of the SSU-rRNA." [GOC:krc, PMID:10690410] synonym: "endonucleolytic cleavage at site D" NARROW [] is_a: GO:0000479 ! endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) is_a: GO:0031125 ! rRNA 3'-end processing relationship: part_of GO:0000462 ! maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [Term] id: GO:0000462 name: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process alt_id: GO:1990041 def: "Any process involved in the maturation of a precursor Small SubUnit (SSU) ribosomal RNA (rRNA) molecule into a mature SSU-rRNA molecule from the pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, 5.8S rRNA, and the Large Subunit (LSU) in that order from 5' to 3' along the primary transcript." [GOC:curators] synonym: "maturation of 18S rRNA" NARROW [] is_a: GO:0030490 ! maturation of SSU-rRNA [Term] id: GO:0000463 name: maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule from the pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, 5.8S rRNA, and Large Subunit (LSU) in that order from 5' to 3' along the primary transcript." [GOC:curators] is_a: GO:0000470 ! maturation of LSU-rRNA [Term] id: GO:0000464 name: endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage within Internal Transcribed Spacer 1 (ITS1) upstream of the 5.8S rRNA derived from an originally tricistronic rRNA transcript that contained the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript. In S. cerevisiae, this endonucleolytic cleavage within ITS1 initiates the maturation of the LSU and the 5.8S rRNAs." [GOC:krc, PMID:10690410] synonym: "endonucleolytic cleavage at A3" NARROW [] is_a: GO:0000479 ! endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) relationship: part_of GO:0000463 ! maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) relationship: part_of GO:0000466 ! maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [Term] id: GO:0000465 name: exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Exonucleolytic digestion of a pre-rRNA molecule to generate the mature 5'-end of a 5.8S rRNA molecule derived from an originally tricistronic pre-rRNA transcript that contained the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript." [GOC:krc, PMID:10690410] is_a: GO:0000459 ! exonucleolytic trimming involved in rRNA processing is_a: GO:0000967 ! rRNA 5'-end processing relationship: part_of GO:0000466 ! maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [Term] id: GO:0000466 name: maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Any process involved in the maturation of an rRNA molecule originally produced as part of a tricistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript." [GOC:curators, PMID:10690410] is_a: GO:0000460 ! maturation of 5.8S rRNA [Term] id: GO:0000467 name: exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Exonucleolytic digestion of a pre-rRNA molecule to generate the mature 3'-end of a 5.8S rRNA molecule derived from an originally tricistronic pre-rRNA transcript that contained the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript." [GOC:krc, PMID:10690410] is_a: GO:0000459 ! exonucleolytic trimming involved in rRNA processing is_a: GO:0031125 ! rRNA 3'-end processing relationship: part_of GO:0000466 ! maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [Term] id: GO:0000468 name: generation of mature 3'-end of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Any process involved in generating the mature 3'-end of an LSU-rRNA derived from a tricistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript." [GOC:krc, PMID:10690410] synonym: "processing at B2" NARROW [] is_a: GO:0031125 ! rRNA 3'-end processing relationship: part_of GO:0000463 ! maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [Term] id: GO:0000469 name: cleavage involved in rRNA processing namespace: biological_process def: "Any phosphodiester bond hydrolysis involved in the conversion of a primary ribosomal RNA (rRNA) transcript into a mature rRNA molecule." [GOC:curators] synonym: "cleavage during rRNA processing" RELATED [GOC:dph, GOC:tb] intersection_of: part_of GO:0006364 ! rRNA processing relationship: part_of GO:0006364 ! rRNA processing [Term] id: GO:0000470 name: maturation of LSU-rRNA namespace: biological_process def: "Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule." [GOC:curators] is_a: GO:0006364 ! rRNA processing [Term] id: GO:0000471 name: endonucleolytic cleavage in 3'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage within the 3'-External Transcribed Spacer (ETS) of a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript. In S. cerevisiae, endonucleolytic cleavage within the 3'-ETS of the pre-RNA, which may occur cotranscriptionally, is the first step in rRNA processing, and initiates a cascade of subsequent processing and modification events." [GOC:krc, PMID:10690410] is_a: GO:0000479 ! endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [Term] id: GO:0000472 name: endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage between the 5'-External Transcribed Spacer (5'-ETS) and the 5' end of the SSU-rRNA of a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript, to produce the mature end of the SSU-rRNA." [GOC:curators, PMID:10690410] synonym: "endonucleolytic cleavage at A1" NARROW [] is_a: GO:0000479 ! endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) is_a: GO:0000967 ! rRNA 5'-end processing relationship: part_of GO:0000462 ! maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [Term] id: GO:0000473 name: maturation of LSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) namespace: biological_process def: "Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule from the pre-rRNA molecule originally produced as a tetracistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, 5.8 S rRNA, 2S rRNA, and Large Subunit (LSU) in that order from 5' to 3' along the primary transcript." [GOC:curators] is_a: GO:0000470 ! maturation of LSU-rRNA [Term] id: GO:0000474 name: maturation of SSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) namespace: biological_process def: "Any process involved in the maturation of a precursor Small SubUnit (SSU) ribosomal RNA (rRNA) molecule into a mature SSU-rRNA molecule from the pre-rRNA molecule originally produced as a tetracistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, 5.8 S rRNA, 2S rRNA, and Large Subunit (LSU) in that order from 5' to 3' along the primary transcript." [GOC:curators] is_a: GO:0030490 ! maturation of SSU-rRNA [Term] id: GO:0000475 name: maturation of 2S rRNA namespace: biological_process def: "Any process involved in the maturation of a precursor 2S ribosomal RNA (rRNA) molecule into a mature 2S rRNA molecule." [GOC:curators] is_a: GO:0006364 ! rRNA processing [Term] id: GO:0000476 name: maturation of 4.5S rRNA namespace: biological_process def: "Any process involved in the maturation of a precursor 4.5S ribosomal RNA (rRNA) molecule into a mature 4.5S rRNA molecule." [GOC:curators] is_a: GO:0006364 ! rRNA processing [Term] id: GO:0000477 name: generation of mature 5'-end of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Cleavage within ITS2 to generate the mature 5'-end of an LSU-rRNA derived from a tricistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript." [GOC:curators, PMID:10690410] synonym: "processing at C1" NARROW [] is_a: GO:0000469 ! cleavage involved in rRNA processing is_a: GO:0000967 ! rRNA 5'-end processing relationship: part_of GO:0000463 ! maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [Term] id: GO:0000478 name: endonucleolytic cleavage involved in rRNA processing namespace: biological_process def: "Any endonucleolytic cleavage involved in the conversion of a primary ribosomal RNA (rRNA) transcript into a mature rRNA molecule. Some endonucleolytic cleavages produce the mature end, while others are a step in the process of generating the mature end from the pre-rRNA." [GOC:krc, PMID:10690410] synonym: "endonucleolytic cleavage during rRNA processing" RELATED [GOC:dph, GOC:tb] is_a: GO:0000469 ! cleavage involved in rRNA processing intersection_of: part_of GO:0006364 ! rRNA processing [Term] id: GO:0000479 name: endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage of a pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript. Primary ribosomal RNA transcripts with three genes, in this order, are produced in the nuclei of many eukaryotic species, including S. cerevisiae." [GOC:curators, PMID:10690410] is_a: GO:0000478 ! endonucleolytic cleavage involved in rRNA processing [Term] id: GO:0000480 name: endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage within the 5'-External Transcribed Spacer (ETS) of a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript. Endonucleolytic cleavage within the 5'-ETS of the pre-RNA is conserved as one of the early steps of rRNA processing in all eukaryotes, but the specific position of cleavage is variable." [GOC:curators, PMID:10690410, PMID:15282326] synonym: "endonucleolytic cleavage at A-prime" NARROW [PMID:15282326] synonym: "endonucleolytic cleavage at A0" NARROW [] is_a: GO:0000479 ! endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) relationship: part_of GO:0000462 ! maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [Term] id: GO:0000481 name: maturation of 5S rRNA namespace: biological_process def: "Any process involved in the maturation of a precursor 5S ribosomal RNA (rRNA) molecule into a mature 5S rRNA molecule." [GOC:curators] is_a: GO:0006364 ! rRNA processing [Term] id: GO:0000482 name: maturation of 5S rRNA from tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Any process involved in the maturation of a precursor 5S ribosomal RNA (rRNA) molecule into a mature 5S rRNA molecule from the pre-rRNA molecule originally produced as a tetracistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, Large Subunit (LSU) the 4.5S rRNA, and the 5S rRNA in that order from 5' to 3' along the primary transcript." [GOC:curators] is_a: GO:0000481 ! maturation of 5S rRNA [Term] id: GO:0000483 name: endonucleolytic cleavage of tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage of a pre-rRNA molecule originally produced as a tetracistronic rRNA transcript that contains the Small SubUnit (SSU) rRNA, the 5.8S rRNA, 2S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript. Primary ribosomal RNA transcripts with four genes, in this order, are produced in the nuclei of D. melanogaster as well as in those of other dipteran species." [GOC:curators] is_a: GO:0000478 ! endonucleolytic cleavage involved in rRNA processing [Term] id: GO:0000484 name: cleavage between SSU-rRNA and 5.8S rRNA of tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage between the SSU-rRNA and the 5.8S rRNA of an rRNA molecule originally produced as a tetracistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, 2S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript." [GOC:curators] is_a: GO:0000483 ! endonucleolytic cleavage of tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) relationship: part_of GO:0000474 ! maturation of SSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) relationship: part_of GO:0000487 ! maturation of 5.8S rRNA from tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) [Term] id: GO:0000485 name: cleavage between 2S rRNA and LSU-rRNA of tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage between the LSU-rRNA and the 2S rRNA of an rRNA molecule originally produced as a tetracistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, 2S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript." [GOC:curators, PMID:768488] is_a: GO:0000483 ! endonucleolytic cleavage of tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) relationship: part_of GO:0000473 ! maturation of LSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) relationship: part_of GO:0000475 ! maturation of 2S rRNA [Term] id: GO:0000486 name: cleavage between 5.8S rRNA and 2S rRNA of tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage between the 5.8S rRNA and the 2S rRNA of an rRNA molecule originally produced as a tetracistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, 2S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript." [GOC:curators, PMID:768488] is_a: GO:0000483 ! endonucleolytic cleavage of tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) relationship: part_of GO:0000475 ! maturation of 2S rRNA relationship: part_of GO:0000487 ! maturation of 5.8S rRNA from tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) [Term] id: GO:0000487 name: maturation of 5.8S rRNA from tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) namespace: biological_process def: "Any process involved in the maturation of a precursor 5.8S ribosomal RNA (rRNA) molecule into a mature 5.8S rRNA molecule from the pre-rRNA molecule originally produced as a tetracistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 8.8S rRNA, the 2S rRNA, and the Large Subunit (LSU) in that order from 5' to 3' along the primary transcript." [GOC:curators] is_a: GO:0000460 ! maturation of 5.8S rRNA [Term] id: GO:0000488 name: maturation of LSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA) namespace: biological_process def: "Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule from the pre-rRNA molecule originally produced as a tetracistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, Large Subunit (LSU) the 4.5S rRNA, and the 5S rRNA in that order from 5' to 3' along the primary transcript." [GOC:curators] is_a: GO:0000470 ! maturation of LSU-rRNA [Term] id: GO:0000489 name: maturation of SSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA) namespace: biological_process def: "Any process involved in the maturation of a precursor Small SubUnit (SSU) ribosomal RNA (rRNA) molecule into a mature SSU-rRNA molecule from the pre-rRNA molecule originally produced as a tetracistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, Large Subunit (LSU) the 4.5S rRNA, and the 5S rRNA in that order from 5' to 3' along the primary transcript." [GOC:curators] is_a: GO:0030490 ! maturation of SSU-rRNA [Term] id: GO:0000494 name: box C/D snoRNA 3'-end processing namespace: biological_process def: "Any process involved in forming the mature 3' end of a box C/D snoRNA molecule." [GOC:krc] synonym: "box C/D snoRNA 3' end processing" EXACT [] is_a: GO:0031126 ! snoRNA 3'-end processing is_a: GO:0034963 ! box C/D snoRNA processing [Term] id: GO:0000495 name: box H/ACA snoRNA 3'-end processing namespace: biological_process def: "Any process involved in forming the mature 3' end of a box H/ACA snoRNA molecule." [GOC:krc] synonym: "box H/ACA snoRNA 3' end processing" EXACT [] is_a: GO:0031126 ! snoRNA 3'-end processing is_a: GO:0034964 ! box H/ACA snoRNA processing [Term] id: GO:0000900 name: translation repressor activity, nucleic acid binding namespace: molecular_function def: "Antagonizes the ribosome-mediated translation of mRNA into a polypeptide via direct binding (through a selective and non-covalent interaction) to nucleic acid." [GOC:clt, GOC:vw] is_a: GO:0030371 ! translation repressor activity is_a: GO:0090079 ! translation regulator activity, nucleic acid binding [Term] id: GO:0000901 name: translation repressor activity, non-nucleic acid binding namespace: molecular_function def: "Antagonizes the ribosome-mediated translation of mRNA into a polypeptide but does not bind directly to nucleic acid." [GOC:clt] is_a: GO:0030371 ! translation repressor activity is_a: GO:0045183 ! translation factor activity, non-nucleic acid binding [Term] id: GO:0000963 name: mitochondrial RNA processing namespace: biological_process def: "The conversion of a primary RNA molecule transcribed from a mitochondrial genome into one or more mature RNA molecules; occurs in the mitochondrion." [GOC:krc, GOC:mah] is_a: GO:0006396 ! RNA processing intersection_of: GO:0006396 ! RNA processing [Term] id: GO:0000964 name: mitochondrial RNA 5'-end processing namespace: biological_process def: "Any process involved in forming the mature 5' end of an RNA molecule transcribed from a mitochondrial genome; occurs in the mitochondrion." [GOC:krc, GOC:mah] synonym: "mitochondrial RNA 5' end processing" RELATED [] is_a: GO:0000963 ! mitochondrial RNA processing is_a: GO:0000966 ! RNA 5'-end processing intersection_of: GO:0000966 ! RNA 5'-end processing [Term] id: GO:0000965 name: mitochondrial RNA 3'-end processing namespace: biological_process def: "Any process involved in forming the mature 3' end of an RNA molecule transcribed from a mitochondrial genome; occurs in the mitochondrion." [GOC:krc, GOC:mah] synonym: "mitochondrial RNA 3' end processing" RELATED [] is_a: GO:0000963 ! mitochondrial RNA processing is_a: GO:0031123 ! RNA 3'-end processing intersection_of: GO:0031123 ! RNA 3'-end processing [Term] id: GO:0000966 name: RNA 5'-end processing namespace: biological_process def: "Any process involved in forming the mature 5' end of an RNA molecule." [GOC:krc] synonym: "RNA 5' end processing" EXACT [] is_a: GO:0006396 ! RNA processing [Term] id: GO:0000967 name: rRNA 5'-end processing namespace: biological_process def: "Any process involved in forming the mature 5' end of an rRNA molecule." [GOC:krc] synonym: "rRNA 5' end processing" EXACT [] is_a: GO:0034471 ! ncRNA 5'-end processing [Term] id: GO:0000968 name: tRNA exon ligation namespace: biological_process def: "An RNA exon ligation process that rejoins two exons of a pre-tRNA which has had the intron removed." [GOC:krc] is_a: GO:0000378 ! RNA exon ligation relationship: part_of GO:0006388 ! tRNA splicing, via endonucleolytic cleavage and ligation created_by: kchris creation_date: 2009-04-28T10:22:40Z [Term] id: GO:0000969 name: tRNA exon ligation utilizing ATP as source of linkage phosphate namespace: biological_process def: "A tRNA exon ligation process in which the splice junction phosphate is derived from exogenous ATP. This type of ligation to rejoin the 5' and 3' exons of a tRNA is observed in vertebrate species." [GOC:krc, PMID:17786051] is_a: GO:0000968 ! tRNA exon ligation created_by: kchris creation_date: 2009-04-28T10:29:37Z [Term] id: GO:0000970 name: tRNA exon ligation utilizing GTP as source of linkage phosphate namespace: biological_process def: "A tRNA exon ligation process in which the splice junction phosphate is derived from exogenous GTP. This type of ligation to rejoin the 5' and 3' exons of a tRNA is observed in the yeast Saccharomyces cerevisiae where the ligation reaction also produces a 2'-phosphate at the splice junction which is subsequently removed as part of the ligation process." [GOC:krc, PMID:18217203, PMID:9299409] is_a: GO:0000968 ! tRNA exon ligation created_by: kchris creation_date: 2009-04-28T10:33:25Z [Term] id: GO:0000971 name: tRNA exon ligation utilizing 2',3' cyclic phosphate of 5'-exon as source of linkage phosphate namespace: biological_process def: "A tRNA exon ligation process in which the splice junction phosphate is derived from the 2',3' cyclic phosphate at the 3'-end of the 5'-exon. This type of ligation to rejoin the 5' and 3' exons of a tRNA is observed in wheat, Chlamydomonas, and vertebrate species including humans." [GOC:krc, PMID:17786051, PMID:18217203, PMID:9299409] is_a: GO:0000968 ! tRNA exon ligation created_by: kchris creation_date: 2009-04-28T10:36:17Z [Term] id: GO:0000981 name: sequence-specific DNA binding RNA polymerase II transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH] is_a: GO:0003700 ! sequence-specific DNA binding transcription factor activity relationship: part_of GO:0006357 ! regulation of transcription from RNA polymerase II promoter relationship: part_of GO:0006366 ! transcription from RNA polymerase II promoter created_by: kchris creation_date: 2010-08-10T02:37:21Z [Term] id: GO:0000982 name: RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II." [GOC:txnOH] is_a: GO:0000981 ! sequence-specific DNA binding RNA polymerase II transcription factor activity created_by: kchris creation_date: 2010-08-10T02:39:46Z [Term] id: GO:0000983 name: RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence in an RNA polymerase II (Pol II) core promoter, the region composed of the transcription start site and binding sites for transcription factors of the Pol II basal transcription machinery, in order to modulate transcription by Pol II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH] is_a: GO:0000981 ! sequence-specific DNA binding RNA polymerase II transcription factor activity created_by: kchris creation_date: 2010-08-10T02:47:56Z [Term] id: GO:0000991 name: core RNA polymerase II binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] relationship: part_of GO:0006366 ! transcription from RNA polymerase II promoter created_by: kchris creation_date: 2010-08-10T05:03:45Z [Term] id: GO:0000995 name: core RNA polymerase III binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH, PMID:12381659] relationship: part_of GO:0006383 ! transcription from RNA polymerase III promoter created_by: kchris creation_date: 2010-08-11T03:59:13Z [Term] id: GO:0000999 name: RNA polymerase III type 1 promoter transcriptional preinitiation complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins on a type 1 RNA polymerase III (Pol III) promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is the first step of transcription. Type 1 promoters require TFIIIA for promoter recognition, which then recruits TFIIIC. TFIIIC in turn recruits TFIIIB, which recruits Pol III to the promoter." [GOC:txnOH, PMID:12381659] is_a: GO:0070898 ! RNA polymerase III transcriptional preinitiation complex assembly relationship: part_of GO:0001022 ! transcription initiation from RNA polymerase III type 1 promoter created_by: kchris creation_date: 2010-08-19T04:16:04Z [Term] id: GO:0001004 name: RNA polymerase III promoter sequence-specific DNA binding TFIIIB recruiting transcription factor activity namespace: molecular_function def: "The function of binding to a specific DNA sequence motif in an RNA polymerase III (Pol III) promoter in order to recruit the Pol III recruiting factor TFIIIB to the promoter." [GOC:txnOH, PMID:12381659] is_a: GO:0001010 ! sequence-specific DNA binding transcription factor recruiting transcription factor activity is_a: GO:0001034 ! sequence-specific DNA binding RNA polymerase III transcription factor activity is_a: GO:0001153 ! RNA polymerase III transcription factor recruiting transcription factor activity created_by: kchris creation_date: 2010-08-18T05:53:32Z [Term] id: GO:0001005 name: RNA polymerase III type 1 promoter sequence-specific DNA binding TFIIIB recruiting transcription factor activity namespace: molecular_function def: "The function of binding to a specific DNA sequence motif in a type 1 RNA polymerase III (Pol III) promoter in order to recruit the Pol III recruiting factor TFIIIB to the promoter. For type 1 Pol III promoters, this requires both TFIIIA and TFIIIC." [GOC:txnOH, PMID:12381659] comment: This represents TFIIIA. synonym: "TFIIIA activity" RELATED [] synonym: "TFIIIC-type activity" RELATED [] is_a: GO:0001004 ! RNA polymerase III promoter sequence-specific DNA binding TFIIIB recruiting transcription factor activity relationship: part_of GO:0000999 ! RNA polymerase III type 1 promoter transcriptional preinitiation complex assembly created_by: kchris creation_date: 2010-08-18T05:57:29Z [Term] id: GO:0001007 name: RNA polymerase III transcription factor binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase III transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] relationship: part_of GO:0006359 ! regulation of transcription from RNA polymerase III promoter relationship: part_of GO:0006383 ! transcription from RNA polymerase III promoter created_by: kchris creation_date: 2010-08-18T06:24:07Z [Term] id: GO:0001008 name: RNA polymerase III type 2 promoter sequence-specific DNA binding TFIIIB recruiting transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence motif in a type 2 RNA polymerase III (Pol III) promoter in order to recruit TFIIIB to the promoter. For type 2 Pol III promoters, this requires TFIIIC activity." [GOC:txnOH, PMID:12381659] synonym: "TFIIIC-type activity" RELATED [] synonym: "type 2 RNA polymerase III promoter recognition" EXACT [] is_a: GO:0001004 ! RNA polymerase III promoter sequence-specific DNA binding TFIIIB recruiting transcription factor activity relationship: part_of GO:0001021 ! RNA polymerase III type 2 promoter transcriptional preinitiation complex assembly created_by: kchris creation_date: 2010-08-18T06:30:45Z [Term] id: GO:0001009 name: transcription from RNA polymerase III type 2 promoter namespace: biological_process def: "The synthesis of RNA from a DNA template by RNA polymerase III (RNAP III), originating at a type 2 RNAP III promoter. Type 2 RNAP III promoters consist of an A box and a B box downstream of the transcription start site within the sequence within the sequence of the mature RNA. Type 2 promoters are found in many tRNA genes as well as in other small RNAs." [GOC:txnOH, PMID:12381659] is_a: GO:0006383 ! transcription from RNA polymerase III promoter created_by: kchris creation_date: 2010-08-18T06:37:56Z [Term] id: GO:0001010 name: sequence-specific DNA binding transcription factor recruiting transcription factor activity namespace: molecular_function def: "The function of binding to a specific DNA sequence and recruiting another transcription factor to the DNA in order to modulate transcription. The recruited factor may bind DNA directly, or may be colocalized via protein-protein interactions." [GOC:txnOH] is_a: GO:0003700 ! sequence-specific DNA binding transcription factor activity created_by: kchris creation_date: 2010-08-18T06:46:33Z [Term] id: GO:0001011 name: sequence-specific DNA binding RNA polymerase recruiting transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence and recruiting RNA polymerase to the DNA in order to form the preinitiation complex (PIC)." [GOC:txnOH] is_a: GO:0003700 ! sequence-specific DNA binding transcription factor activity created_by: kchris creation_date: 2010-08-18T06:49:16Z [Term] id: GO:0001014 name: snoRNA transcription from a type 2 RNA polymerase III promoter namespace: biological_process def: "The synthesis of small nucleolar RNA (snoRNA) from a DNA template by RNA polymerase III, originating at a type 2 RNA polymerase III promoter." [GOC:txnOH] is_a: GO:0001009 ! transcription from RNA polymerase III type 2 promoter is_a: GO:0009302 ! snoRNA transcription created_by: kchris creation_date: 2010-08-18T07:13:45Z [Term] id: GO:0001015 name: snoRNA transcription from an RNA polymerase II promoter namespace: biological_process def: "The synthesis of small nucleolar RNA (snoRNA) from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter." [GOC:txnOH] is_a: GO:0006366 ! transcription from RNA polymerase II promoter is_a: GO:0009302 ! snoRNA transcription created_by: kchris creation_date: 2010-08-18T07:21:18Z [Term] id: GO:0001020 name: RNA polymerase III type 3 promoter transcriptional preinitiation complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins on a type 1 RNA polymerase III (Pol III) promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is the first step of transcription." [GOC:txnOH, PMID:12381659] is_a: GO:0070898 ! RNA polymerase III transcriptional preinitiation complex assembly relationship: part_of GO:0001024 ! transcription initiation from RNA polymerase III type 3 promoter created_by: kchris creation_date: 2010-08-19T04:18:46Z [Term] id: GO:0001021 name: RNA polymerase III type 2 promoter transcriptional preinitiation complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins on a type 2 RNA polymerase III (Pol III) promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is the first step of transcription. Type 2 promoters require TFIIIC for promoter recognition, which then recruits TFIIIB, which in turn which recruits Pol III to the promoter." [GOC:txnOH, PMID:12381659] is_a: GO:0070898 ! RNA polymerase III transcriptional preinitiation complex assembly relationship: part_of GO:0001023 ! transcription initiation from RNA polymerase III type 2 promoter created_by: kchris creation_date: 2010-08-19T04:18:53Z [Term] id: GO:0001022 name: transcription initiation from RNA polymerase III type 1 promoter namespace: biological_process def: "A transcription initiation process on a type 1 RNA polymerase III (Pol III) that results in RNA synthesis by Pol III. Type 1 promoters are found in 5S rRNA genes, downstream of the transcription start site within the sequence of the mature RNA, and require TFIIIA for recognition." [GOC:txnOH, PMID:12381659] is_a: GO:0006384 ! transcription initiation from RNA polymerase III promoter relationship: part_of GO:0042791 ! 5S class rRNA transcription from RNA polymerase III type 1 promoter created_by: kchris creation_date: 2010-08-19T04:33:52Z [Term] id: GO:0001023 name: transcription initiation from RNA polymerase III type 2 promoter namespace: biological_process def: "A transcription initiation process on a type 2 RNA polymerase III (Pol III) that results in RNA synthesis by Pol III. Type 2 promoters consist of an A box and a B box downstream of the transcription start site within the sequence within the sequence of the mature RNA. Type 2 promoters are found in many tRNA genes as well as in other small RNAs." [GOC:txnOH, PMID:12381659] is_a: GO:0006384 ! transcription initiation from RNA polymerase III promoter relationship: part_of GO:0001009 ! transcription from RNA polymerase III type 2 promoter created_by: kchris creation_date: 2010-08-19T04:35:09Z [Term] id: GO:0001024 name: transcription initiation from RNA polymerase III type 3 promoter namespace: biological_process def: "A transcription initiation process on a type 3 RNA polymerase III (Pol III) that results in RNA synthesis by Pol III. A type 3 Pol III promoter is composed of elements upstream of the transcription start site, including a TATA box. The human U6 snRNA gene has a type 3 promoter. Type 3 Pol III promoters have not been observed in S. cerevisiae." [GOC:txnOH, PMID:12381659] is_a: GO:0006384 ! transcription initiation from RNA polymerase III promoter relationship: part_of GO:0001035 ! transcription from RNA polymerase III type 3 promoter created_by: kchris creation_date: 2010-08-19T04:35:14Z [Term] id: GO:0001026 name: TFIIIB-type transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way, Once recruited to an RNA polymerase III promoter by one or more other transcription factors, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex." [GOC:txnOH] synonym: "RNA polymerase III recruiting transcription factor activity" EXACT [] is_a: GO:0000995 ! core RNA polymerase III binding transcription factor activity is_a: GO:0001007 ! RNA polymerase III transcription factor binding transcription factor activity created_by: kchris creation_date: 2010-08-23T12:24:31Z [Term] id: GO:0001027 name: RNA polymerase III type 1 promoter TFIIIB-type transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way. Once recruited to an RNA polymerase III type 1 promoter by TFIIIA-type and TFIIIC-type factors, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex." [GOC:txnOH, PMID:12381659] synonym: "RNA polymerase III type 1 promoter polymerase recruiting transcription factor activity" RELATED [] is_a: GO:0001026 ! TFIIIB-type transcription factor activity relationship: part_of GO:0000999 ! RNA polymerase III type 1 promoter transcriptional preinitiation complex assembly created_by: kchris creation_date: 2010-08-23T12:50:20Z [Term] id: GO:0001028 name: RNA polymerase III type 2 promoter TFIIIB-type transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way. Once recruited to an RNA polymerase III type 2 promoter by a TFIIIC-type factor, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex." [GOC:txnOH, PMID:12381659] synonym: "RNA polymerase III type 2 promoter polymerase recruiting transcription factor activity" RELATED [] is_a: GO:0001026 ! TFIIIB-type transcription factor activity relationship: part_of GO:0001021 ! RNA polymerase III type 2 promoter transcriptional preinitiation complex assembly created_by: kchris creation_date: 2010-08-23T12:52:01Z [Term] id: GO:0001029 name: RNA polymerase III type 3 promoter TFIIIB-type transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way. Once recruited to an RNA polymerase III type 3 promoter by SNAP-type and TFIIIC-type factors, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex." [GOC:txnOH, PMID:12381659] synonym: "RNA polymerase III type 3 promoter polymerase recruiting transcription factor activity" RELATED [] is_a: GO:0001026 ! TFIIIB-type transcription factor activity relationship: part_of GO:0001020 ! RNA polymerase III type 3 promoter transcriptional preinitiation complex assembly created_by: kchris creation_date: 2010-08-23T12:52:40Z [Term] id: GO:0001033 name: RNA polymerase III type 3 promoter TFIIIB recruiting transcription factor activity namespace: molecular_function def: "The function of binding to a specific DNA sequence motif in a type 3 RNA polymerase III (Pol III) promoter in order to recruit TFIIIB to the promoter. For type 3 Pol III promoters, this requires SNAPc activity." [GOC:txnOH, PMID:12381659] comment: This represents TFIIIC. synonym: "SNAPc-type activity" RELATED [] synonym: "type 3 RNA polymerase III promoter recognition" EXACT [] is_a: GO:0001004 ! RNA polymerase III promoter sequence-specific DNA binding TFIIIB recruiting transcription factor activity relationship: part_of GO:0001020 ! RNA polymerase III type 3 promoter transcriptional preinitiation complex assembly created_by: kchris creation_date: 2010-08-23T03:04:17Z [Term] id: GO:0001034 name: sequence-specific DNA binding RNA polymerase III transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase III. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH, PMID:12381659] is_a: GO:0003700 ! sequence-specific DNA binding transcription factor activity relationship: part_of GO:0006359 ! regulation of transcription from RNA polymerase III promoter relationship: part_of GO:0006383 ! transcription from RNA polymerase III promoter created_by: kchris creation_date: 2010-08-23T03:41:48Z [Term] id: GO:0001035 name: transcription from RNA polymerase III type 3 promoter namespace: biological_process def: "The synthesis of RNA from a DNA template by RNA polymerase III (RNAP III), originating at a type 3 RNAP III promoter. A type 3 RNAP III promoter is composed of elements upstream of the transcription start site, including a TATA box. The human U6 snRNA gene has a type 3 promoter. Type 3 Pol III promoters have not been observed in S. cerevisiae." [GOC:txnOH, PMID:12381659] synonym: "U6 snRNA transcription (mammalian)" NARROW [] is_a: GO:0006383 ! transcription from RNA polymerase III promoter created_by: kchris creation_date: 2010-08-23T04:17:41Z [Term] id: GO:0001036 name: transcription initiation from RNA polymerase III hybrid type promoter namespace: biological_process def: "A transcription initiation process on a hybrid type RNA polymerase III (Pol III) that results in RNA synthesis by Pol III (Pol III). A hybrid Pol III promoter contains both regulatory elements both upstream and downstream of the transcription initiation site. An example gene with such a promoter is the S. cerevisiae U6 gene." [GOC:txnOH, PMID:12381659] is_a: GO:0006384 ! transcription initiation from RNA polymerase III promoter relationship: part_of GO:0001041 ! transcription from a RNA polymerase III hybrid type promoter created_by: kchris creation_date: 2010-08-23T06:08:55Z [Term] id: GO:0001038 name: RNA polymerase III hybrid type promoter TFIIIB recruiting transcription factor activity namespace: molecular_function def: "Once recruited to an RNA polymerase III hybrid type promoter by sequence-specific DNA binding transcription factors, direct DNA binding, or a combination of both, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex." [GOC:txnOH, PMID:12381659] is_a: GO:0001004 ! RNA polymerase III promoter sequence-specific DNA binding TFIIIB recruiting transcription factor activity relationship: part_of GO:0001043 ! RNA polymerase III hybrid type promoter transcriptional preinitiation complex assembly created_by: kchris creation_date: 2010-08-23T06:17:33Z [Term] id: GO:0001040 name: RNA polymerase III hybrid type promoter TFIIIB-type transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way. Once recruited to an RNA polymerase III hybrid type promoter, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex." [GOC:txnOH, PMID:12381659] is_a: GO:0001026 ! TFIIIB-type transcription factor activity relationship: part_of GO:0001043 ! RNA polymerase III hybrid type promoter transcriptional preinitiation complex assembly created_by: kchris creation_date: 2010-08-23T06:28:23Z [Term] id: GO:0001041 name: transcription from a RNA polymerase III hybrid type promoter namespace: biological_process def: "The synthesis of RNA from a DNA template by RNA polymerase III, originating at a hybrid type RNA polymerase III (RNAP III) promoter. A hybrid RNAP III promoter contains both regulatory elements both upstream and downstream of the transcription initiation site. An example gene with such a promoter is the S. cerevisiae U6 gene." [GOC:txnOH, PMID:12381659] synonym: "U2 snRNA transcription (S. cerevisiae)" NARROW [] is_a: GO:0006383 ! transcription from RNA polymerase III promoter created_by: kchris creation_date: 2010-08-24T02:11:52Z [Term] id: GO:0001043 name: RNA polymerase III hybrid type promoter transcriptional preinitiation complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins on a hybrid type RNA polymerase III (Pol III) promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is the first step of transcription. Hybrid type promoters contain both gene-internal and upstream elements. An example of a hybrid promoter is the U6 snRNA gene." [GOC:txnOH, PMID:12381659] is_a: GO:0070898 ! RNA polymerase III transcriptional preinitiation complex assembly created_by: kchris creation_date: 2010-08-24T02:19:52Z [Term] id: GO:0001054 name: RNA polymerase I activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase I specific promoter to direct initiation and catalyzes DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] synonym: "DNA-directed RNA polymerase activity involved in transcription from RNA polymerase I promoter" EXACT [] intersection_of: part_of GO:0006360 ! transcription from RNA polymerase I promoter relationship: part_of GO:0006360 ! transcription from RNA polymerase I promoter created_by: kchris creation_date: 2010-09-23T03:36:11Z [Term] id: GO:0001055 name: RNA polymerase II activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase II specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] synonym: "DNA-directed RNA polymerase activity involved in transcription from RNA polymerase II promoter" EXACT [] intersection_of: part_of GO:0006366 ! transcription from RNA polymerase II promoter relationship: part_of GO:0006366 ! transcription from RNA polymerase II promoter created_by: kchris creation_date: 2010-09-23T03:44:23Z [Term] id: GO:0001056 name: RNA polymerase III activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase III specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] synonym: "DNA-directed RNA polymerase activity involved in transcription from RNA polymerase III promoter" EXACT [] intersection_of: part_of GO:0006383 ! transcription from RNA polymerase III promoter relationship: part_of GO:0006383 ! transcription from RNA polymerase III promoter created_by: kchris creation_date: 2010-09-23T03:44:47Z [Term] id: GO:0001057 name: RNA polymerase IV activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase IV specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] synonym: "DNA-directed RNA polymerase activity involved in transcription from RNA polymerase IV promoter" EXACT [] intersection_of: part_of GO:0001059 ! transcription from RNA polymerase IV promoter relationship: part_of GO:0001059 ! transcription from RNA polymerase IV promoter created_by: kchris creation_date: 2010-09-23T03:44:55Z [Term] id: GO:0001058 name: RNA polymerase V activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase V specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] synonym: "DNA-directed RNA polymerase activity involved in transcription from RNA polymerase V promoter" EXACT [] intersection_of: part_of GO:0001060 ! transcription from RNA polymerase V promoter relationship: part_of GO:0001060 ! transcription from RNA polymerase V promoter created_by: kchris creation_date: 2010-09-23T03:45:01Z [Term] id: GO:0001059 name: transcription from RNA polymerase IV promoter namespace: biological_process def: "The synthesis of RNA from a DNA template by RNA polymerase IV (Pol III), originating at a Pol IV-specific promoter." [GOC:txnOH, PMID:19110459] synonym: "transcription from RNA pol IV promoter" EXACT [] is_a: GO:0006351 ! transcription, DNA-dependent created_by: kchris creation_date: 2010-09-23T03:51:35Z [Term] id: GO:0001060 name: transcription from RNA polymerase V promoter namespace: biological_process def: "The synthesis of RNA from a DNA template by RNA polymerase V (Pol III), originating at a Pol V-specific promoter." [GOC:txnOH, PMID:19110459] synonym: "transcription from RNA pol V promoter" EXACT [] is_a: GO:0006351 ! transcription, DNA-dependent created_by: kchris creation_date: 2010-09-23T03:54:04Z [Term] id: GO:0001061 name: bacterial-type RNA polymerase activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains a bacterial-type specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] relationship: part_of GO:0001121 ! transcription from bacterial-type RNA polymerase promoter created_by: kchris creation_date: 2010-10-19T03:36:01Z [Term] id: GO:0001062 name: plastid PEP-A RNA polymerase activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains a plastid PEP-A RNA polymerase II specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH, PMID:20701995] is_a: GO:0001061 ! bacterial-type RNA polymerase activity relationship: part_of GO:0042793 ! transcription from plastid promoter created_by: kchris creation_date: 2010-10-19T03:38:49Z [Term] id: GO:0001063 name: plastid PEP-B RNA polymerase activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains a plastid PEP-B RNA polymerase II specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH, PMID:20701995] is_a: GO:0001061 ! bacterial-type RNA polymerase activity relationship: part_of GO:0042793 ! transcription from plastid promoter created_by: kchris creation_date: 2010-10-19T03:46:46Z [Term] id: GO:0001065 name: mitochondrial single subunit type RNA polymerase activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains a single subunit type mitochondrial RNA polymerase specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] relationship: part_of GO:0006390 ! transcription from mitochondrial promoter created_by: kchris creation_date: 2010-10-19T03:50:51Z [Term] id: GO:0001066 name: plastid single subunit type RNA polymerase activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains a single subunit type plastid RNA polymerase specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH, PMID:20701995] relationship: part_of GO:0042793 ! transcription from plastid promoter created_by: kchris creation_date: 2010-10-19T03:54:57Z [Term] id: GO:0001072 name: RNA binding transcription antitermination factor activity namespace: molecular_function def: "Binds to RNA, typically within the nascent RNA transcript, to promote readthrough of a transcription termination site and thus extending the length of the RNA transcript produced. Examples of antitermination factors which bind the nascent RNA include the lambda N protein and the HIV-1 tat protein." [GOC:txnOH, PMID:8332211] subset: gosubset_prok relationship: part_of GO:0031564 ! transcription antitermination created_by: kchris creation_date: 2010-10-21T04:48:17Z [Term] id: GO:0001073 name: DNA binding transcription antitermination factor activity namespace: molecular_function def: "Binds to DNA, typically within region of the promoter and transcribed region, to promote readthrough of a transcription termination site and thus extending the length of the RNA transcript produced. Examples of antitermination factors which bind DNA include the lambda Q protein." [GOC:txnOH, PMID:8332211] subset: gosubset_prok is_a: GO:0003700 ! sequence-specific DNA binding transcription factor activity relationship: part_of GO:0031564 ! transcription antitermination created_by: kchris creation_date: 2010-10-21T05:18:52Z [Term] id: GO:0001074 name: RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to promote assembly of the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from an RNA polymerase II promoter." [GOC:txnOH] is_a: GO:0000982 ! RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity relationship: part_of GO:0051123 ! RNA polymerase II transcriptional preinitiation complex assembly created_by: kchris creation_date: 2010-10-22T02:30:43Z [Term] id: GO:0001075 name: RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence in an RNA polymerase II (Pol II) core promoter, the region composed of the transcription start site and binding sites for transcription factors of the Pol II basal transcription machinery, in order to promote assembly of the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from an RNA polymerase II promoter." [GOC:txnOH] synonym: "sequence-specific core promoter binding RNA polymerase II transcription factor activity involved in preinitiation complex assembly" EXACT [] is_a: GO:0000983 ! RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity relationship: part_of GO:0051123 ! RNA polymerase II transcriptional preinitiation complex assembly created_by: kchris creation_date: 2010-10-22T02:35:51Z [Term] id: GO:0001076 name: RNA polymerase II transcription factor binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] relationship: part_of GO:0006357 ! regulation of transcription from RNA polymerase II promoter relationship: part_of GO:0006366 ! transcription from RNA polymerase II promoter created_by: kchris creation_date: 2010-10-22T02:49:32Z [Term] id: GO:0001077 name: RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter." [GOC:txnOH] is_a: GO:0000982 ! RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity is_a: GO:0001228 ! RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription created_by: kchris creation_date: 2010-10-26T03:40:43Z [Term] id: GO:0001078 name: RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:txnOH] is_a: GO:0000982 ! RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity is_a: GO:0001227 ! RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription created_by: kchris creation_date: 2010-10-26T03:56:48Z [Term] id: GO:0001079 name: nitrogen catabolite regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A transcription regulation process in which the presence of one nitrogen source leads to the modulation of the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources." [GOC:mah, GOC:txnOH, PMID:19104072] synonym: "regulation of transcription from RNA polymerase II promoter by nitrogen catabolites" EXACT [GOC:mah] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter is_a: GO:0090293 ! nitrogen catabolite regulation of transcription created_by: kchris creation_date: 2010-10-27T03:29:01Z [Term] id: GO:0001080 name: nitrogen catabolite activation of transcription from RNA polymerase II promoter namespace: biological_process def: "A transcription regulation process in which the presence of one nitrogen source leads to an increase in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources." [GOC:mah, GOC:txnOH, PMID:19104072] synonym: "positive regulation of transcription from RNA polymerase II promoter by nitrogen catabolites" EXACT [GOC:mah] is_a: GO:0001079 ! nitrogen catabolite regulation of transcription from RNA polymerase II promoter is_a: GO:0090294 ! nitrogen catabolite activation of transcription created_by: kchris creation_date: 2010-10-27T03:32:34Z [Term] id: GO:0001081 name: nitrogen catabolite repression of transcription from RNA polymerase II promoter namespace: biological_process def: "A transcription regulation process in which the presence of one nitrogen source leads to a decrease in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources." [GOC:mah, GOC:txnOH, PMID:19104072] synonym: "negative regulation of transcription from RNA polymerase II promoter by nitrogen catabolites" EXACT [GOC:mah] is_a: GO:0001079 ! nitrogen catabolite regulation of transcription from RNA polymerase II promoter is_a: GO:0090295 ! nitrogen catabolite repression of transcription created_by: kchris creation_date: 2010-10-27T03:38:05Z [Term] id: GO:0001082 name: RNA polymerase I transcription factor binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase I transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] relationship: part_of GO:0006356 ! regulation of transcription from RNA polymerase I promoter relationship: part_of GO:0006360 ! transcription from RNA polymerase I promoter created_by: kchris creation_date: 2010-10-27T04:03:47Z [Term] id: GO:0001083 name: RNA polymerase II basal transcription factor binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] is_a: GO:0001076 ! RNA polymerase II transcription factor binding transcription factor activity created_by: kchris creation_date: 2010-10-27T04:12:55Z [Term] id: GO:0001084 name: TFIID-class binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH] is_a: GO:0001083 ! RNA polymerase II basal transcription factor binding transcription factor activity created_by: kchris creation_date: 2010-10-27T04:15:22Z [Term] id: GO:0001086 name: TFIIA-class binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIA class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH] is_a: GO:0001083 ! RNA polymerase II basal transcription factor binding transcription factor activity created_by: kchris creation_date: 2010-10-28T02:14:59Z [Term] id: GO:0001087 name: TFIIB-class binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIB class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH] is_a: GO:0001083 ! RNA polymerase II basal transcription factor binding transcription factor activity created_by: kchris creation_date: 2010-10-28T02:18:00Z [Term] id: GO:0001088 name: TFIIE-class binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIE class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH] is_a: GO:0001083 ! RNA polymerase II basal transcription factor binding transcription factor activity created_by: kchris creation_date: 2010-10-28T02:25:22Z [Term] id: GO:0001089 name: TFIIF-class binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIF class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH] is_a: GO:0001083 ! RNA polymerase II basal transcription factor binding transcription factor activity created_by: kchris creation_date: 2010-10-28T02:27:12Z [Term] id: GO:0001090 name: TFIIH-class binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIH class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH] is_a: GO:0001083 ! RNA polymerase II basal transcription factor binding transcription factor activity created_by: kchris creation_date: 2010-10-28T02:28:01Z [Term] id: GO:0001104 name: RNA polymerase II transcription cofactor activity namespace: molecular_function alt_id: GO:0016455 def: "Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to modulate transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between regulatory transcription factors and the basal RNAP II transcription machinery." [GOC:txnOH, PMID:10213677, PMID:16858867] subset: gosubset_prok synonym: "RNA polymerase II transcription mediator activity" RELATED [] synonym: "RNA polymerase II transcriptional co-regulator" EXACT [] synonym: "RNA polymerase II transcriptional cofactor activity" EXACT [] synonym: "thyroid receptor-associated protein" RELATED [] synonym: "TRAP protein" RELATED [] is_a: GO:0001076 ! RNA polymerase II transcription factor binding transcription factor activity created_by: kchris creation_date: 2010-11-24T03:02:15Z [Term] id: GO:0001105 name: RNA polymerase II transcription coactivator activity namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal RNAP II transcription machinery." [GOC:txnOH, PMID:10213677, PMID:16858867] comment: Note that some basal transcription factors are themselves considered to have coactivator activity, in that they mediate interactions between an activator and either RNA polymerase II itself or another basal transcription factor. subset: gosubset_prok synonym: "RNA polymerase II transcription co-activator activity" EXACT [] is_a: GO:0001104 ! RNA polymerase II transcription cofactor activity is_a: GO:0001190 ! RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription relationship: part_of GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: kchris creation_date: 2010-11-24T03:08:19Z [Term] id: GO:0001106 name: RNA polymerase II transcription corepressor activity namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase II repressing transcription factor and also with the RNA polymerase II basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery." [GOC:txnOH, PMID:10213677, PMID:16858867] synonym: "RNA polymerase II transcription co-repressor activity" EXACT [] is_a: GO:0001104 ! RNA polymerase II transcription cofactor activity is_a: GO:0001191 ! RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription relationship: part_of GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: kchris creation_date: 2010-11-24T03:14:44Z [Term] id: GO:0001109 name: promoter clearance during DNA-dependent transcription namespace: biological_process def: "Any process involved in the transition from the initiation to the elongation phases of transcription by a DNA-dependent RNA polymerase, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors." [GOC:txnOH, PMID:15020047, PMID:18280161] synonym: "promoter escape" BROAD [] relationship: part_of GO:0006351 ! transcription, DNA-dependent created_by: kchris creation_date: 2010-12-01T02:13:09Z [Term] id: GO:0001110 name: promoter clearance from RNA polymerase III promoter namespace: biological_process def: "Any process involved in the transition from the initiation to the elongation phases of transcription by RNA polymerase III, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase." [GOC:txnOH] is_a: GO:0001109 ! promoter clearance during DNA-dependent transcription relationship: part_of GO:0006383 ! transcription from RNA polymerase III promoter created_by: kchris creation_date: 2010-12-01T03:08:29Z [Term] id: GO:0001111 name: promoter clearance from RNA polymerase II promoter namespace: biological_process def: "Any process involved in the transition from the initiation to the elongation phases of transcription by RNA polymerase II, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors." [GOC:txnOH, PMID:15020047] synonym: "promoter escape from RNA polymerase II promoter" EXACT [] is_a: GO:0001109 ! promoter clearance during DNA-dependent transcription relationship: part_of GO:0006366 ! transcription from RNA polymerase II promoter created_by: kchris creation_date: 2010-12-01T03:09:31Z [Term] id: GO:0001112 name: DNA-dependent transcriptional open complex formation namespace: biological_process def: "Any process involved in the melting of the DNA hybrid of the core promoter region within the transcriptional closed complex of an RNA polymerase preinitiation complex (PIC) to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble." [GOC:txnOH, PMID:15020047, PMID:18280161] synonym: "promoter melting" BROAD [] relationship: part_of GO:0006352 ! DNA-dependent transcription, initiation created_by: kchris creation_date: 2010-12-02T02:15:04Z [Term] id: GO:0001113 name: transcriptional open complex formation at RNA polymerase II promoter namespace: biological_process def: "Any process involved in the melting of the DNA hybrid of the core promoter region within the transcriptional closed complex of an RNA polymerase II preinitiation complex (PIC) to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble." [GOC:txnOH, PMID:15020047, PMID:18280161] synonym: "RNA polymerase II promoter melting" EXACT [] is_a: GO:0001112 ! DNA-dependent transcriptional open complex formation relationship: part_of GO:0006367 ! transcription initiation from RNA polymerase II promoter created_by: kchris creation_date: 2010-12-02T02:27:19Z [Term] id: GO:0001118 name: transcription ternary complex disassembly namespace: biological_process def: "The disaggregation of a transcription ternary complex, composed of RNA polymerase, template DNA, and an RNA transcript, into its constituent components." [GOC:txnOH] synonym: "transcription protein-DNA-RNA complex disassembly" EXACT [] relationship: part_of GO:0006353 ! DNA-dependent transcription, termination created_by: kchris creation_date: 2010-12-03T04:11:34Z [Term] id: GO:0001121 name: transcription from bacterial-type RNA polymerase promoter namespace: biological_process def: "The synthesis of RNA from a DNA template by a bacterial-type RNA polymerase, originating at a bacterial-type promoter." [GOC:txnOH] is_a: GO:0006351 ! transcription, DNA-dependent created_by: kchris creation_date: 2010-12-06T03:32:13Z [Term] id: GO:0001122 name: promoter clearance from bacterial-type RNA polymerase promoter namespace: biological_process def: "Any process involved in the transition from the initiation to the elongation phase of transcription by a bacterial-type RNA polymerase, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance generally involves dissociation of the sigma initiation factor." [GOC:txnOH, PMID:18280161] is_a: GO:0001109 ! promoter clearance during DNA-dependent transcription relationship: part_of GO:0001121 ! transcription from bacterial-type RNA polymerase promoter created_by: kchris creation_date: 2010-12-06T03:38:10Z [Term] id: GO:0001123 name: transcription initiation from bacterial-type RNA polymerase promoter namespace: biological_process def: "Any process involved in the assembly of bacterial-type RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription." [GOC:txnOH, PMID:18280161] is_a: GO:0006352 ! DNA-dependent transcription, initiation relationship: part_of GO:0001121 ! transcription from bacterial-type RNA polymerase promoter created_by: kchris creation_date: 2010-12-06T03:40:12Z [Term] id: GO:0001124 name: transcription elongation from bacterial-type RNA polymerase promoter namespace: biological_process def: "The extension of an RNA molecule after transcription initiation and promoter clearance at a bacterial-type RNA polymerase promoter by the addition of ribonucleotides catalyzed by a bacterial-type RNA polymerase." [GOC:txnOH, PMID:18280161] synonym: "RNA elongation from bacterial-type RNA polymerase promoter" EXACT [] is_a: GO:0006354 ! DNA-dependent transcription, elongation relationship: part_of GO:0001121 ! transcription from bacterial-type RNA polymerase promoter created_by: kchris creation_date: 2010-12-06T03:46:27Z [Term] id: GO:0001125 name: transcription termination from bacterial-type RNA polymerase promoter namespace: biological_process def: "The process in which the synthesis of an RNA molecule by a bacterial-type RNA polymerase using a DNA template is completed." [GOC:txnOH, PMID:18280161] is_a: GO:0006353 ! DNA-dependent transcription, termination relationship: part_of GO:0001121 ! transcription from bacterial-type RNA polymerase promoter created_by: kchris creation_date: 2010-12-06T03:47:43Z [Term] id: GO:0001126 name: bacterial-type RNA polymerase preinitiation complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins on a bacterial-type RNA polymerase promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase." [GOC:txnOH, PMID:18280161] synonym: "bacterial-type RNA polymerase transcription PIC biosynthesis" EXACT [] synonym: "bacterial-type RNA polymerase transcription PIC formation" EXACT [] synonym: "bacterial-type RNA polymerase transcriptional preinitiation complex formation" EXACT [] is_a: GO:0070897 ! DNA-dependent transcriptional preinitiation complex assembly relationship: part_of GO:0001123 ! transcription initiation from bacterial-type RNA polymerase promoter created_by: kchris creation_date: 2010-12-06T03:54:45Z [Term] id: GO:0001127 name: transcriptional open complex formation at bacterial-type RNA polymerase promoter namespace: biological_process def: "Any process involved in the melting of the DNA hybrid of the core promoter region within the transcriptional closed complex of an RNA polymerase II preinitiation complex (PIC) to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble." [GOC:txnOH, PMID:18280161] is_a: GO:0001112 ! DNA-dependent transcriptional open complex formation relationship: part_of GO:0001123 ! transcription initiation from bacterial-type RNA polymerase promoter created_by: kchris creation_date: 2010-12-06T04:04:16Z [Term] id: GO:0001128 name: RNA polymerase II transcription coactivator activity involved in preinitiation complex assembly namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to increase the frequency, rate or stability of the aggregation, arrangement and bonding together of proteins on RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC). Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal RNAP II transcription machinery." [GOC:txnOH, PMID:16858867] comment: Note that some basal transcription factors are themselves considered to have coactivator activity, in that they mediate interactions between an activator and either RNA polymerase II itself or another basal transcription factor. is_a: GO:0001105 ! RNA polymerase II transcription coactivator activity relationship: part_of GO:0051123 ! RNA polymerase II transcriptional preinitiation complex assembly created_by: kchris creation_date: 2011-01-20T02:13:36Z [Term] id: GO:0001129 name: TBP-class protein binding RNA polymerase II transcription factor activity involved in preinitiation complex assembly namespace: molecular_function def: "Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs), to facilitate the aggregation, arrangement and bonding together of proteins on RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase." [GOC:txnOH, PMID:16858867] comment: For example, both TFIIA as well as TFIIB interact with TBP bound to DNA to stabilize formation of the preinitiation complex. synonym: "TATA-binding protein binding RNA polymerase II transcription factor activity involved in preinitiation complex assembly" NARROW [] is_a: GO:0001132 ! TBP-class protein binding RNA polymerase II transcription factor activity relationship: part_of GO:0051123 ! RNA polymerase II transcriptional preinitiation complex assembly created_by: kchris creation_date: 2011-01-20T02:53:35Z [Term] id: GO:0001130 name: sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH] is_a: GO:0003700 ! sequence-specific DNA binding transcription factor activity relationship: part_of GO:0001121 ! transcription from bacterial-type RNA polymerase promoter created_by: kchris creation_date: 2011-01-26T10:36:02Z [Term] id: GO:0001131 name: bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase in order to modulate transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH] is_a: GO:0001130 ! sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity created_by: kchris creation_date: 2011-01-26T10:50:37Z [Term] id: GO:0001132 name: TBP-class protein binding RNA polymerase II transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs), in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH, PMID:16858867] synonym: "TATA-binding protein binding RNA polymerase II transcription factor activity" NARROW [] synonym: "TRF protein binding RNA polymerase II transcription factor activity" NARROW [] is_a: GO:0001083 ! RNA polymerase II basal transcription factor binding transcription factor activity created_by: kchris creation_date: 2011-01-20T04:15:44Z [Term] id: GO:0001133 name: sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA by RNA polymerase II and recruiting another transcription factor to the DNA in order to modulate transcription by RNAP II." [GOC:txnOH, PMID:16858867] is_a: GO:0001010 ! sequence-specific DNA binding transcription factor recruiting transcription factor activity created_by: kchris creation_date: 2011-01-20T04:40:20Z [Term] id: GO:0001135 name: RNA polymerase II transcription factor recruiting transcription factor activity namespace: molecular_function def: "The function of binding to an RNA polymerase II (RNAP II) transcription factor and recruiting it to the transcription machinery complex in order to modulate transcription by RNAP II." [GOC:txnOH, PMID:16858867] is_a: GO:0001076 ! RNA polymerase II transcription factor binding transcription factor activity created_by: kchris creation_date: 2011-01-20T05:13:12Z [Term] id: GO:0001136 name: TFIIE-class transcription factor recruiting transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II (RNAP II) transcription factor of the TFIIE-class in order to recruit it to the RNAP II preinitiation complex (PIC) in order to modulate transcription by RNAP II." [GOC:txnOH, PMID:16858867] is_a: GO:0001088 ! TFIIE-class binding transcription factor activity is_a: GO:0001135 ! RNA polymerase II transcription factor recruiting transcription factor activity relationship: part_of GO:0051123 ! RNA polymerase II transcriptional preinitiation complex assembly created_by: kchris creation_date: 2011-01-20T05:24:07Z [Term] id: GO:0001137 name: TFIIF-class transcription factor recruiting transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II (RNAP II) transcription factor of the TFIIF-class in order to recruit it to the RNAP II preinitiation complex (PIC) in order to modulate transcription by RNAP II." [GOC:txnOH, PMID:16858867] is_a: GO:0001089 ! TFIIF-class binding transcription factor activity is_a: GO:0001135 ! RNA polymerase II transcription factor recruiting transcription factor activity relationship: part_of GO:0051123 ! RNA polymerase II transcriptional preinitiation complex assembly created_by: kchris creation_date: 2011-01-20T05:35:02Z [Term] id: GO:0001138 name: TFIIH-class transcription factor recruiting transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II (RNAP II) transcription factor of the TFIIH-class in order to recruit it to the RNAP II preinitiation complex (PIC) in order to modulate transcription by RNAP II." [GOC:txnOH, PMID:16858867] is_a: GO:0001090 ! TFIIH-class binding transcription factor activity is_a: GO:0001135 ! RNA polymerase II transcription factor recruiting transcription factor activity relationship: part_of GO:0051123 ! RNA polymerase II transcriptional preinitiation complex assembly created_by: kchris creation_date: 2011-01-20T05:39:10Z [Term] id: GO:0001139 name: core RNA polymerase II recruiting transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way in order to facilitate the aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase." [GOC:txnOH, PMID:16858867] is_a: GO:0000991 ! core RNA polymerase II binding transcription factor activity relationship: part_of GO:0051123 ! RNA polymerase II transcriptional preinitiation complex assembly created_by: kchris creation_date: 2011-01-20T05:55:01Z [Term] id: GO:0001140 name: bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase in order to modulate transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH, PMID:20491932, PMID:20629756] is_a: GO:0001131 ! bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity is_a: GO:0001216 ! sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in positive regulation of transcription created_by: kchris creation_date: 2011-01-26T03:09:27Z [Term] id: GO:0001141 name: bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase in order to stop, prevent, or reduce the frequency, rate or extent of transcription from a bacterial-type RNA polymerase promoter." [GOC:txnOH, PMID:20491932, PMID:20629756] is_a: GO:0001131 ! bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity is_a: GO:0001217 ! sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in negative regulation of transcription created_by: kchris creation_date: 2011-01-26T03:15:45Z [Term] id: GO:0001142 name: sequence-specific DNA binding mitochondrial RNA polymerase transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by mitochondrial RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH, PMID:18391175] is_a: GO:0003700 ! sequence-specific DNA binding transcription factor activity relationship: part_of GO:0006390 ! transcription from mitochondrial promoter created_by: kchris creation_date: 2011-01-27T01:55:21Z [Term] id: GO:0001143 name: mitochondrial RNA polymerase core promoter sequence-specific DNA binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence that is part of the core promoter for mitochondrial RNA polymerase in order to modulate transcription by mitochondrial RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH, PMID:18391175] is_a: GO:0001142 ! sequence-specific DNA binding mitochondrial RNA polymerase transcription factor activity created_by: kchris creation_date: 2011-01-27T02:08:44Z [Term] id: GO:0001144 name: mitochondrial RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a mitochondrial RNA polymerase in order to modulate transcription by mitochondrial RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH, PMID:18391175] is_a: GO:0001142 ! sequence-specific DNA binding mitochondrial RNA polymerase transcription factor activity created_by: kchris creation_date: 2011-01-27T02:11:59Z [Term] id: GO:0001146 name: mitochondrial RNA polymerase terminator site sequence-specific DNA binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is a terminator for mitochondrial RNA polymerase in order to promote transcription termination by mitochondrial RNA polymerase." [GOC:txnOH, PMID:18391175] is_a: GO:0001142 ! sequence-specific DNA binding mitochondrial RNA polymerase transcription factor activity relationship: part_of GO:0006393 ! termination of mitochondrial transcription created_by: kchris creation_date: 2011-01-27T02:42:23Z [Term] id: GO:0001149 name: bacterial-type RNA polymerase termination site sequence-specific DNA binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is a termination site for bacterial-type RNA polymerase in order to promote transcription termination by bacterial-type RNA polymerase." [GOC:txnOH, PMID:18280161] is_a: GO:0001130 ! sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity created_by: kchris creation_date: 2011-01-27T03:08:41Z [Term] id: GO:0001151 name: bacterial-type RNA polymerase transcription enhancer sequence-specific DNA binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is a bacterial-type enhancer region in order to activate transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. Enhancers for sigma-54 holoenzymes are typically located 80 to 150 base pairs upstream from the transcription start site. Some transcription units dependent on sigma-70 holoenzymes may also include enhancer sequences." [GOC:txnOH, PMID:20629756] is_a: GO:0001130 ! sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity created_by: kchris creation_date: 2011-01-27T03:47:54Z [Term] id: GO:0001152 name: RNA polymerase III type 1 promoter sequence-specific DNA binding TFIIIC recruiting transcription factor activity namespace: molecular_function def: "The function of binding to a specific DNA sequence motif in a type 1 RNA polymerase III (Pol III) promoter in order to recruit the transcription factor TFIIIC to the promoter." [GOC:txnOH, PMID:12381659] comment: This represents TFIIIA. synonym: "TFIIIA activity" RELATED [] synonym: "type 1 RNA polymerase III promoter recognition" EXACT [] is_a: GO:0001010 ! sequence-specific DNA binding transcription factor recruiting transcription factor activity is_a: GO:0001153 ! RNA polymerase III transcription factor recruiting transcription factor activity relationship: part_of GO:0000999 ! RNA polymerase III type 1 promoter transcriptional preinitiation complex assembly created_by: kchris creation_date: 2011-01-27T04:18:21Z [Term] id: GO:0001153 name: RNA polymerase III transcription factor recruiting transcription factor activity namespace: molecular_function def: "The function of binding to an RNA polymerase III (RNAP III) transcription factor and recruiting it to the transcription machinery complex in order to modulate transcription by RNAP III." [GOC:txnOH] is_a: GO:0001007 ! RNA polymerase III transcription factor binding transcription factor activity created_by: kchris creation_date: 2011-01-27T04:45:37Z [Term] id: GO:0001157 name: RNA polymerase III type 1 promoter TFIIIB recruiting transcription factor activity namespace: molecular_function def: "The function of binding to a specific DNA sequence motif in a type 1 RNA polymerase III (Pol III) promoter in order to recruit the Pol III recruiting factor TFIIIB to the promoter. For type 1 Pol III promoters, this requires both TFIIIA and TFIIIC." [GOC:txnOH, PMID:12381659] comment: This represents TFIIIA. synonym: "TFIIIC-type activity" RELATED [] is_a: GO:0001153 ! RNA polymerase III transcription factor recruiting transcription factor activity relationship: part_of GO:0000999 ! RNA polymerase III type 1 promoter transcriptional preinitiation complex assembly created_by: kchris creation_date: 2011-01-27T05:27:28Z [Term] id: GO:0001167 name: sequence-specific DNA binding RNA polymerase I transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase I. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH] is_a: GO:0003700 ! sequence-specific DNA binding transcription factor activity relationship: part_of GO:0006356 ! regulation of transcription from RNA polymerase I promoter relationship: part_of GO:0006360 ! transcription from RNA polymerase I promoter created_by: kchris creation_date: 2011-02-03T04:07:46Z [Term] id: GO:0001168 name: RNA polymerase I upstream control element sequence-specific DNA binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with the upstream control element (UCE, or alternately referred to as the upstream element, UE), a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase I in order to modulate transcription by RNA polymerase I." [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832] is_a: GO:0001167 ! sequence-specific DNA binding RNA polymerase I transcription factor activity created_by: kchris creation_date: 2011-02-03T04:10:23Z [Term] id: GO:0001169 name: RNA polymerase I CORE element sequence-specific DNA binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with CORE element, a regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase I transcription machinery in order to modulate transcription by RNA polymerase I." [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832] synonym: "RNA polymerase I core promoter sequence-specific DNA binding transcription factor" EXACT [] is_a: GO:0001167 ! sequence-specific DNA binding RNA polymerase I transcription factor activity created_by: kchris creation_date: 2011-02-03T04:10:42Z [Term] id: GO:0001170 name: RNA polymerase I enhancer sequence-specific DNA binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a RNA polymerase I (Pol I) enhancer in order to modulate transcription by RNA polymerase I." [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832] is_a: GO:0001167 ! sequence-specific DNA binding RNA polymerase I transcription factor activity created_by: kchris creation_date: 2011-02-03T04:10:59Z [Term] id: GO:0001173 name: DNA-dependent transcriptional start site selection namespace: biological_process def: "Any process involved in the selection of the specific location within the template strand of a DNA-dependent RNA polymerase promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript." [GOC:txnOH, PMID:16826228, PMID:18846104] relationship: part_of GO:0006352 ! DNA-dependent transcription, initiation created_by: kchris creation_date: 2011-06-20T12:44:11Z [Term] id: GO:0001174 name: transcriptional start site selection at RNA polymerase II promoter namespace: biological_process def: "Any process involved in the selection of the specific location within the template strand of an RNA polymerase II promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript." [GOC:txnOH, PMID:16826228, PMID:18846104] is_a: GO:0001173 ! DNA-dependent transcriptional start site selection relationship: part_of GO:0006367 ! transcription initiation from RNA polymerase II promoter created_by: kchris creation_date: 2011-06-20T01:35:28Z [Term] id: GO:0001175 name: transcriptional start site selection at RNA polymerase III promoter namespace: biological_process def: "Any process involved in the selection of the specific location within the template strand of an RNA polymerase III promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript." [GOC:txnOH] is_a: GO:0001173 ! DNA-dependent transcriptional start site selection relationship: part_of GO:0006384 ! transcription initiation from RNA polymerase III promoter created_by: kchris creation_date: 2011-06-20T01:47:38Z [Term] id: GO:0001176 name: transcriptional start site selection at bacterial-type RNA polymerase promoter namespace: biological_process def: "Any process involved in the selection of the specific location within the template strand of a bacterial-type RNA polymerase promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript." [GOC:txnOH] is_a: GO:0001173 ! DNA-dependent transcriptional start site selection relationship: part_of GO:0001123 ! transcription initiation from bacterial-type RNA polymerase promoter created_by: kchris creation_date: 2011-06-20T01:48:56Z [Term] id: GO:0001177 name: regulation of transcriptional open complex formation at RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the rate, frequency or extent of a process involved the melting of the DNA hybrid of the core promoter region within the transcriptional closed complex of an RNA polymerase II preinitiation complex (PIC) to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble." [GOC:txnOH] is_a: GO:0060260 ! regulation of transcription initiation from RNA polymerase II promoter intersection_of: regulates GO:0001113 ! transcriptional open complex formation at RNA polymerase II promoter relationship: regulates GO:0001113 ! transcriptional open complex formation at RNA polymerase II promoter created_by: kchris creation_date: 2011-06-20T02:01:18Z [Term] id: GO:0001178 name: regulation of transcriptional start site selection at RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the rate, frequency or extent of a process involved in the selection of the specific location within the template strand of an RNA polymerase II promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript." [GOC:txnOH] is_a: GO:0060260 ! regulation of transcription initiation from RNA polymerase II promoter intersection_of: regulates GO:0001174 ! transcriptional start site selection at RNA polymerase II promoter relationship: regulates GO:0001174 ! transcriptional start site selection at RNA polymerase II promoter created_by: kchris creation_date: 2011-06-20T02:06:00Z [Term] id: GO:0001180 name: transcription initiation from RNA polymerase I promoter for nuclear large rRNA transcript namespace: biological_process def: "Any process involved in the assembly of the RNA polymerase I preinitiation complex (PIC) at an polymerase I promoter for the nuclear large ribosomal RNA (rRNA) transcript, resulting in the subsequent synthesis of rRNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription." [GOC:txnOH] is_a: GO:0006361 ! transcription initiation from RNA polymerase I promoter relationship: part_of GO:0042790 ! transcription of nuclear large rRNA transcript from RNA polymerase I promoter created_by: kchris creation_date: 2011-08-15T03:45:49Z [Term] id: GO:0001181 name: core RNA polymerase I binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase I (RNAP I) complex, typically composed of fourteen subunits, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] relationship: part_of GO:0006360 ! transcription from RNA polymerase I promoter created_by: kchris creation_date: 2011-08-12T04:13:30Z [Term] id: GO:0001182 name: promoter clearance from RNA polymerase I promoter namespace: biological_process def: "Any process involved in the transition from the initiation to the elongation phases of transcription by RNA polymerase I, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors." [GOC:txnOH] is_a: GO:0001109 ! promoter clearance during DNA-dependent transcription relationship: part_of GO:0006360 ! transcription from RNA polymerase I promoter created_by: kchris creation_date: 2011-08-15T03:49:28Z [Term] id: GO:0001183 name: transcription elongation from RNA polymerase I promoter for nuclear large rRNA transcript namespace: biological_process def: "The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase I promoter for the nuclear large ribosomal RNA (rRNA) transcript by the addition of ribonucleotides catalyzed by RNA polymerase I." [GOC:txnOH] is_a: GO:0006362 ! transcription elongation from RNA polymerase I promoter relationship: part_of GO:0042790 ! transcription of nuclear large rRNA transcript from RNA polymerase I promoter created_by: kchris creation_date: 2011-08-15T03:57:25Z [Term] id: GO:0001184 name: promoter clearance from RNA polymerase I promoter for nuclear large rRNA transcript namespace: biological_process def: "Any process involved in the transition from the initiation to the elongation phases of transcription by RNA polymerase I at a promoter for the nuclear large ribosomal RNA (rRNA) transcript, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors." [GOC:txnOH] is_a: GO:0001182 ! promoter clearance from RNA polymerase I promoter relationship: part_of GO:0042790 ! transcription of nuclear large rRNA transcript from RNA polymerase I promoter created_by: kchris creation_date: 2011-08-15T04:03:52Z [Term] id: GO:0001185 name: termination of RNA polymerase I transcription from promoter for nuclear large rRNA transcript namespace: biological_process def: "The process in which the synthesis of an rRNA molecule from a promoter for the nuclear large ribosomal RNA (rRNA) transcript by RNA polymerase I using a DNA template is completed. RNAP I termination requires binding of a terminator protein so specific sequences downstream of the transcription unit." [GOC:txnOH] is_a: GO:0006363 ! termination of RNA polymerase I transcription relationship: part_of GO:0042790 ! transcription of nuclear large rRNA transcript from RNA polymerase I promoter created_by: kchris creation_date: 2011-08-15T04:07:43Z [Term] id: GO:0001186 name: RNA polymerase I transcription factor recruiting transcription factor activity namespace: molecular_function def: "The function of binding to an RNA polymerase I (RNAP I) transcription factor and recruiting it to the transcription machinery complex in order to modulate transcription by RNAP I." [GOC:txnOH, PMID:12381659, PMID:14969726, PMID:8057832] is_a: GO:0001082 ! RNA polymerase I transcription factor binding transcription factor activity created_by: kchris creation_date: 2011-08-24T04:00:18Z [Term] id: GO:0001187 name: RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with the CORE element, a regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase I transcription machinery and also binding to an RNA polymerase I (RNAP I) transcription factor to recruit it to the transcription machinery complex in order to modulate transcription by RNA polymerase I." [GOC:txnOH, PMID:12381659, PMID:14969726, PMID:8057832] is_a: GO:0001169 ! RNA polymerase I CORE element sequence-specific DNA binding transcription factor activity is_a: GO:0001186 ! RNA polymerase I transcription factor recruiting transcription factor activity relationship: part_of GO:0001189 ! RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript created_by: kchris creation_date: 2011-08-24T04:07:50Z [Term] id: GO:0001188 name: RNA polymerase I transcriptional preinitiation complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins on promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from an RNA polymerase I promoter." [GOC:txnOH, PMID:12381659, PMID:14969726, PMID:8057832] is_a: GO:0070897 ! DNA-dependent transcriptional preinitiation complex assembly relationship: part_of GO:0006361 ! transcription initiation from RNA polymerase I promoter created_by: kchris creation_date: 2011-08-24T04:16:28Z [Term] id: GO:0001189 name: RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins on CORE promoter element DNA of the nuclear large ribosomal RNA (rRNA) transcript to form a transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from the large rRNA promoter, resulting in the subsequent synthesis of the large rRNA transcript." [GOC:txnOH, PMID:12381659, PMID:14969726, PMID:8057832] is_a: GO:0001188 ! RNA polymerase I transcriptional preinitiation complex assembly relationship: part_of GO:0001180 ! transcription initiation from RNA polymerase I promoter for nuclear large rRNA transcript created_by: kchris creation_date: 2011-08-24T04:20:43Z [Term] id: GO:0001190 name: RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to increase the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] is_a: GO:0001076 ! RNA polymerase II transcription factor binding transcription factor activity relationship: part_of GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: kchris creation_date: 2011-08-25T02:07:14Z [Term] id: GO:0001191 name: RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH, PMID:9811836] is_a: GO:0001076 ! RNA polymerase II transcription factor binding transcription factor activity relationship: part_of GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: kchris creation_date: 2011-08-25T02:12:30Z [Term] id: GO:0001192 name: maintenance of transcriptional fidelity during DNA-dependent transcription elongation namespace: biological_process def: "Suppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation on a DNA template." [GOC:txnOH] relationship: part_of GO:0006354 ! DNA-dependent transcription, elongation created_by: kchris creation_date: 2011-09-02T02:25:30Z [Term] id: GO:0001193 name: maintenance of transcriptional fidelity during DNA-dependent transcription elongation from RNA polymerase II promoter namespace: biological_process def: "Suppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation from an RNA polymerase II promoter." [GOC:txnOH, PMID:14531857, PMID:16492753, PMID:17535246] is_a: GO:0001192 ! maintenance of transcriptional fidelity during DNA-dependent transcription elongation relationship: part_of GO:0006368 ! transcription elongation from RNA polymerase II promoter created_by: kchris creation_date: 2011-09-02T02:31:00Z [Term] id: GO:0001194 name: maintenance of transcriptional fidelity during DNA-dependent transcription elongation from bacterial-type RNA polymerase promoter namespace: biological_process def: "Suppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation from a bacterial-type RNA polymerase promoter." [GOC:txnOH] is_a: GO:0001192 ! maintenance of transcriptional fidelity during DNA-dependent transcription elongation relationship: part_of GO:0001124 ! transcription elongation from bacterial-type RNA polymerase promoter created_by: kchris creation_date: 2011-09-02T02:37:59Z [Term] id: GO:0001195 name: maintenance of transcriptional fidelity during DNA-dependent transcription elongation from RNA polymerase III promoter namespace: biological_process def: "Suppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation from a RNA polymerase III promoter." [GOC:txnOH] is_a: GO:0001192 ! maintenance of transcriptional fidelity during DNA-dependent transcription elongation relationship: part_of GO:0006385 ! transcription elongation from RNA polymerase III promoter created_by: kchris creation_date: 2011-09-02T02:41:29Z [Term] id: GO:0001196 name: regulation of mating-type specific transcription from RNA polymerase II promoter namespace: biological_process def: "Any mating-type specific process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:txnOH] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter is_a: GO:0007532 ! regulation of mating-type specific transcription, DNA-dependent created_by: kchris creation_date: 2011-11-23T09:25:32Z [Term] id: GO:0001197 name: positive regulation of mating-type specific transcription from RNA polymerase II promoter namespace: biological_process def: "Any mating-type specific process that activates or increases the rate of transcription from an RNA polymerase II promoter." [GOC:txnOH] synonym: "activation of transcription from an RNA polymerase II promoter, mating-type specific" NARROW [] synonym: "stimulation of transcription from an RNA polymerase II promoter, mating-type specific" NARROW [] synonym: "up regulation of transcription from an RNA polymerase II promoter, mating-type specific" EXACT [] synonym: "up-regulation of transcription from an RNA polymerase II promoter, mating-type specific" EXACT [] synonym: "upregulation of transcription from an RNA polymerase II promoter, mating-type specific" EXACT [] is_a: GO:0001196 ! regulation of mating-type specific transcription from RNA polymerase II promoter is_a: GO:0045895 ! positive regulation of mating-type specific transcription, DNA-dependent created_by: kchris creation_date: 2011-11-23T09:31:33Z [Term] id: GO:0001198 name: negative regulation of mating-type specific transcription from RNA polymerase II promoter namespace: biological_process def: "Any mating-type specific process that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter." [GOC:txnOH] synonym: "down regulation of RNA polymerase II transcription, mating-type specific" EXACT [] synonym: "down-regulation of RNA polymerase II transcription, mating-type specific" EXACT [] synonym: "downregulation of RNA polymerase II transcription, mating-type specific" EXACT [] synonym: "inhibition of RNA polymerase II transcription, mating-type specific" NARROW [] is_a: GO:0001196 ! regulation of mating-type specific transcription from RNA polymerase II promoter is_a: GO:0045894 ! negative regulation of mating-type specific transcription, DNA-dependent created_by: kchris creation_date: 2011-11-23T09:36:06Z [Term] id: GO:0001199 name: metal ion regulated sequence-specific DNA binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor in order to modulate transcription by an RNA polymerase. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist." [GOC:txnOH, PMID:12829264, PMID:12829265, PMID:22084422, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. is_a: GO:0003700 ! sequence-specific DNA binding transcription factor activity created_by: kchris creation_date: 2011-11-23T10:52:49Z [Term] id: GO:0001200 name: metal ion regulated sequence-specific DNA binding RNA polymerase II transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor in order to modulate transcription by RNA polymerase II. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist." [GOC:txnOH, PMID:12829264, PMID:12829265, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. is_a: GO:0000981 ! sequence-specific DNA binding RNA polymerase II transcription factor activity is_a: GO:0001199 ! metal ion regulated sequence-specific DNA binding transcription factor activity created_by: kchris creation_date: 2011-11-23T11:18:49Z [Term] id: GO:0001201 name: metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor that binds the core promoter proximal region in order to modulate transcription by RNA polymerase II. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist." [GOC:txnOH, PMID:12829264, PMID:12829265, PMID:22084422, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. is_a: GO:0000982 ! RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity is_a: GO:0001200 ! metal ion regulated sequence-specific DNA binding RNA polymerase II transcription factor activity created_by: kchris creation_date: 2011-11-23T11:22:42Z [Term] id: GO:0001202 name: copper ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) and interacting selectively and non-covalently with copper(I) (Cu+) ion(s) and responding, e.g. by conformational change, to changes in the cellular level of copper(I) (Cu+), such a way that copper ion binding regulates the activity of the transcription factor, perhaps by regulating the ability to interact selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II), or by regulating some other function of the transcription factor, in order to modulate transcription by RNAP II." [GOC:txnOH, PMID:22084422, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. is_a: GO:0001201 ! metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity created_by: kchris creation_date: 2011-11-23T11:27:57Z [Term] id: GO:0001203 name: zinc ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) and interacting selectively and non-covalently with zinc (Zn) ion(s) and responding, e.g. by conformational change, to changes in the cellular level of zinc (Zn), in such a way that zinc ion binding regulates the activity of the transcription factor, perhaps by regulating the ability to interact selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II), or by regulating some other function of the transcription factor, in order to modulate transcription by RNAP II." [GOC:txnOH, PMID:22084422] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. is_a: GO:0001201 ! metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity created_by: kchris creation_date: 2011-11-23T11:36:25Z [Term] id: GO:0001204 name: metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a specific bacterial-type transcription regulatory DNA sequence and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor in order to modulate transcription by a bacterial-type RNA polymerase. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist." [GOC:txnOH, PMID:12829264, PMID:12829265, PMID:22084422, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. is_a: GO:0001130 ! sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity is_a: GO:0001199 ! metal ion regulated sequence-specific DNA binding transcription factor activity created_by: kchris creation_date: 2011-11-23T12:07:06Z [Term] id: GO:0001205 name: RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter." [GOC:txnOH] synonym: "sequence-specific distal enhancer binding RNA polymerase II transcription factor activity involved in positive regulation of transcription" EXACT [] is_a: GO:0001228 ! RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription is_a: GO:0003705 ! RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity created_by: kchris creation_date: 2012-01-26T03:10:20Z [Term] id: GO:0001206 name: RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:txnOH] synonym: "sequence-specific distal enhancer binding RNA polymerase II transcription factor activity involved in negative regulation of transcription" EXACT [] is_a: GO:0001227 ! RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription is_a: GO:0003705 ! RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity created_by: kchris creation_date: 2012-01-26T03:10:40Z [Term] id: GO:0001209 name: metal ion regulated sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor in order to activate or increase the frequency, rate or extent of cellular DNA-dependent transcription by an RNA polymerase. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist." [GOC:txnOH, PMID:12829264, PMID:12829265, PMID:22084422, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. is_a: GO:0001199 ! metal ion regulated sequence-specific DNA binding transcription factor activity relationship: part_of GO:0045893 ! positive regulation of transcription, DNA-dependent created_by: kchris creation_date: 2012-04-04T02:26:42Z [Term] id: GO:0001210 name: metal ion regulated sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor in order to stop, prevent, or reduce the frequency, rate or extent of cellular DNA-dependent transcription by an RNA polymerase. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist." [GOC:txnOH, PMID:12829264, PMID:12829265, PMID:22084422, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. is_a: GO:0001199 ! metal ion regulated sequence-specific DNA binding transcription factor activity relationship: part_of GO:0045892 ! negative regulation of transcription, DNA-dependent created_by: kchris creation_date: 2012-04-04T02:53:25Z [Term] id: GO:0001211 name: copper ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity involved in positive regulation of transcription namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) and interacting selectively and non-covalently with copper(I) (Cu+) ion(s) and responding, e.g. by conformational change, to changes in the cellular level of copper(I) (Cu+), such a way that copper ion binding regulates the activity of the transcription factor in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter." [GOC:txnOH, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. is_a: GO:0001202 ! copper ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity is_a: GO:0001213 ! metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity involved in positive regulation of transcription created_by: kchris creation_date: 2012-04-04T03:03:00Z [Term] id: GO:0001212 name: zinc ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity involved in positive regulation of transcription namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) and interacting selectively and non-covalently with zinc (Zn) ion(s) and responding, e.g. by conformational change, to changes in the cellular level of zinc (Zn), such a way that copper ion binding regulates the activity of the transcription factor in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter." [GOC:txnOH] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. is_a: GO:0001203 ! zinc ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity is_a: GO:0001213 ! metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity involved in positive regulation of transcription created_by: kchris creation_date: 2012-04-04T03:13:34Z [Term] id: GO:0001213 name: metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity involved in positive regulation of transcription namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) and interacting selectively and non-covalently with metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of metal ion, such a way that metal ion binding regulates the activity of the transcription factor in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter." [GOC:txnOH, PMID:22084422, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. is_a: GO:0001077 ! RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription is_a: GO:0001201 ! metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity created_by: kchris creation_date: 2012-04-04T03:18:43Z [Term] id: GO:0001214 name: metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity involved in negative regulation of transcription namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) and interacting selectively and non-covalently with metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of metal ion, such a way that metal ion binding regulates the activity of the transcription factor in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:txnOH, PMID:22084422, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. is_a: GO:0001078 ! RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription is_a: GO:0001201 ! metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity created_by: kchris creation_date: 2012-04-04T03:33:08Z [Term] id: GO:0001215 name: metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in positive regulation of transcription namespace: molecular_function def: "Interacting selectively and non-covalently with a specific bacterial-type transcription regulatory DNA sequence and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor in order to activate or increase the frequency, rate or extent of cellular DNA-dependent transcription by a bacterial-type RNA polymerase. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist." [GOC:txnOH, PMID:12829264, PMID:12829265, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. is_a: GO:0001204 ! metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity is_a: GO:0001209 ! metal ion regulated sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription created_by: kchris creation_date: 2012-04-04T03:47:42Z [Term] id: GO:0001216 name: sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in positive regulation of transcription namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:krc] is_a: GO:0001130 ! sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity relationship: part_of GO:0045893 ! positive regulation of transcription, DNA-dependent created_by: kchris creation_date: 2012-04-04T03:55:59Z [Term] id: GO:0001217 name: sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in negative regulation of transcription namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:krc] is_a: GO:0001130 ! sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity relationship: part_of GO:0045892 ! negative regulation of transcription, DNA-dependent created_by: kchris creation_date: 2012-04-04T03:57:16Z [Term] id: GO:0001218 name: metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in negative regulation of transcription namespace: molecular_function def: "Interacting selectively and non-covalently with a specific bacterial-type transcription regulatory DNA sequence and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor in order to stop, prevent, or reduce the frequency, rate or extent of cellular DNA-dependent transcription by a bacterial-type RNA polymerase. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist." [GOC:txnOH, PMID:12829264, PMID:12829265, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. is_a: GO:0001204 ! metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity is_a: GO:0001210 ! metal ion regulated sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription created_by: kchris creation_date: 2012-04-05T10:46:50Z [Term] id: GO:0001219 name: copper ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in negative regulation of transcription namespace: molecular_function def: "Interacting selectively and non-covalently with a specific bacterial-type transcription regulatory DNA sequence and interacting selectively and non-covalently with copper(I) (Cu+) ion(s) and responding, e.g. by conformational change, to changes in the cellular level of copper(I) (Cu+), in such a way that copper ion binding regulates the activity of the transcription factor in order to stop, prevent, or reduce the frequency, rate or extent of cellular DNA-dependent transcription by a bacterial-type RNA polymerase." [GOC:krc, PMID:12829264, PMID:12829265, PMID:19928961] synonym: "copper ion sensor" RELATED [] is_a: GO:0001218 ! metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in negative regulation of transcription created_by: kchris creation_date: 2012-04-05T11:13:34Z [Term] id: GO:0001220 name: cadmium ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in negative regulation of transcription namespace: molecular_function def: "Interacting selectively and non-covalently with a specific bacterial-type transcription regulatory DNA sequence and interacting selectively and non-covalently with cadmium (Cd) ion(s) and responding, e.g. by conformational change, to changes in the cellular level of cadmium (Cd), in such a way that cadmium (Cd) ion binding regulates the activity of the transcription factor in order to stop, prevent, or reduce the frequency, rate or extent of cellular DNA-dependent transcription by a bacterial-type RNA polymerase." [GOC:krc, PMID:12829264, PMID:12829265, PMID:19456862] synonym: "cadmium ion sensor" RELATED [] is_a: GO:0001218 ! metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in negative regulation of transcription created_by: kchris creation_date: 2012-04-05T11:46:06Z [Term] id: GO:0001227 name: RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in the regulatory region for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:krc] is_a: GO:0000981 ! sequence-specific DNA binding RNA polymerase II transcription factor activity relationship: part_of GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: kchris creation_date: 2012-04-16T04:41:29Z [Term] id: GO:0001228 name: RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in the transcription regulatory region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter." [GOC:krc] is_a: GO:0000981 ! sequence-specific DNA binding RNA polymerase II transcription factor activity relationship: part_of GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: kchris creation_date: 2012-04-16T04:44:21Z [Term] id: GO:0001308 name: negative regulation of chromatin silencing involved in replicative cell aging namespace: biological_process def: "The process, which occurs as a dividing cell ages, leading to expression of genes that are typically not expressed due to silencing by regulatory proteins." [GOC:jh, PMID:12044934] synonym: "loss of chromatin silencing during replicative cell ageing" RELATED [] synonym: "loss of chromatin silencing involved in replicative cell aging" EXACT [] is_a: GO:0031936 ! negative regulation of chromatin silencing intersection_of: negatively_regulates GO:0006342 ! chromatin silencing [Term] id: GO:0001514 name: selenocysteine incorporation namespace: biological_process def: "The incorporation of selenocysteine into a peptide; uses a special tRNA that recognizes the UGA codon as selenocysteine, rather than as a termination codon. Selenocysteine is synthesized from serine before its incorporation; it is not a posttranslational modification of peptidyl-cysteine." [RESID:AA0022] subset: gosubset_prok xref: RESID:AA0022 is_a: GO:0006451 ! translational readthrough [Term] id: GO:0001677 name: formation of translation initiation ternary complex namespace: biological_process def: "Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator)." [GOC:hjd] subset: gosubset_prok synonym: "translation initiation ternary complex assembly" EXACT [] relationship: part_of GO:0006413 ! translational initiation [Term] id: GO:0001680 name: tRNA 3'-terminal CCA addition namespace: biological_process def: "Post-transcriptional addition of the terminal 3' CCA sequence to a tRNA which does not encode this sequence within the primary transcript. CCA addition proceeds by the sequential addition of CTP, CTP, and then ATP to the 3' end of the tRNA, yielding a diphosphate with each nucleotide addition." [EC:2.7.7.72, GOC:go_curators] subset: gosubset_prok synonym: "-C-C-A pyrophosphorylase activity" RELATED [EC:2.7.7.72] synonym: "ATP(CTP)-tRNA nucleotidyltransferase activity" BROAD [EC:2.7.7.72] synonym: "ATP(CTP):tRNA nucleotidyltransferase activity" BROAD [EC:2.7.7.72] synonym: "CCA tRNA nucleotidyltransferase activity" BROAD [EC:2.7.7.72] synonym: "CCA-adding enzyme activity" EXACT [EC:2.7.7.72] synonym: "CCA-adding enzyme, tRNA adenylyltransferase, tRNA cytidylyltransferase, tRNA CCA-pyrophosphorylase activity" EXACT [EC:2.7.7.72] synonym: "CTP(ATP):tRNA nucleotidyltransferase activity" BROAD [EC:2.7.7.72] synonym: "CTP:tRNA cytidylyltransferase activity" NARROW [EC:2.7.7.72] synonym: "ribonucleic cytidylic cytidylic adenylic pyrophosphorylase activity" EXACT [EC:2.7.7.72] synonym: "ribonucleic cytidylyltransferase activity" NARROW [EC:2.7.7.72] synonym: "transfer ribonucleate adenyltransferase activity" NARROW [EC:2.7.7.72] synonym: "transfer ribonucleate adenylyltransferase activity" NARROW [EC:2.7.7.72] synonym: "transfer ribonucleate cytidylyltransferase activity" NARROW [EC:2.7.7.72] synonym: "transfer ribonucleate nucleotidyltransferase activity" BROAD [EC:2.7.7.72] synonym: "transfer ribonucleic acid nucleotidyl transferase activity" BROAD [EC:2.7.7.72] synonym: "transfer ribonucleic adenylyl (cytidylyl) transferase activity" RELATED [EC:2.7.7.72] synonym: "transfer ribonucleic-terminal trinucleotide nucleotidyltransferase activity" BROAD [EC:2.7.7.72] synonym: "transfer RNA adenylyltransferase activity" NARROW [EC:2.7.7.72] synonym: "transfer-RNA nucleotidyltransferase activity" BROAD [EC:2.7.7.72] synonym: "tRNA adenylyl(cytidylyl)transferase activity" BROAD [EC:2.7.7.72] synonym: "tRNA CCA-diphosphorylase activity" RELATED [EC:2.7.7.72] synonym: "tRNA cytidylyltransferase activity" NARROW [EC:2.7.7.72] synonym: "tRNA-nucleotidyltransferase activity" BROAD [EC:2.7.7.72] xref: EC:2.7.7.72 xref: KEGG:R09382 xref: MetaCyc:TRNA-CYTIDYLYLTRANSFERASE-RXN is_a: GO:0042780 ! tRNA 3'-end processing [Term] id: GO:0001682 name: tRNA 5'-leader removal namespace: biological_process def: "Generation of the mature 5'-end of the tRNA, usually via an endonucleolytic cleavage by RNase P." [PMID:11592395] subset: gosubset_prok synonym: "tRNA 5' leader removal" EXACT [] is_a: GO:0008033 ! tRNA processing [Term] id: GO:0001717 name: conversion of seryl-tRNAsec to selenocys-tRNAsec namespace: biological_process def: "The modification process that results in the conversion of serine, carried by a specialized tRNA(ser) (which can read a UGA anticodon), to selenocysteine." [ISBN:155581073X] subset: gosubset_prok is_a: GO:0019988 ! charged-tRNA amino acid modification [Term] id: GO:0001720 name: conversion of lysyl-tRNA to pyrrolysyl-tRNA namespace: biological_process def: "The modification process that results in the conversion of lysine, carried by a specialized lysine-accepting tRNA (possessing a CUA anticodon), to pyrrolysine (a lysine with an amide linkage to a (4R,5R)-4-substituted pyrroline-5-carboxylate)." [PMID:12029131, PMID:12029132, PMID:12121639] subset: gosubset_prok is_a: GO:0019988 ! charged-tRNA amino acid modification [Term] id: GO:0001731 name: formation of translation preinitiation complex namespace: biological_process def: "The joining of the small ribosomal subunit, ternary complex, and mRNA." [GOC:hjd] comment: See also the cellular component terms 'eukaryotic 43S preinitiation complex ; GO:0016282', 'eukaryotic 48S initiation complex ; GO:0033290', and their children. subset: gosubset_prok synonym: "formation of translation pre-initiation complex" EXACT [] synonym: "translation preinitiation complex assembly" EXACT [] relationship: part_of GO:0006413 ! translational initiation [Term] id: GO:0001732 name: formation of translation initiation complex namespace: biological_process def: "Joining of the large subunit, with release of IF2/eIF2 and IF3/eIF3. This leaves the functional ribosome at the AUG, with the methionyl/formyl-methionyl-tRNA positioned at the P site." [GOC:hjd] subset: gosubset_prok synonym: "translation initiation complex assembly" EXACT [] relationship: part_of GO:0006413 ! translational initiation [Term] id: GO:0001750 name: photoreceptor outer segment namespace: cellular_component def: "The outer segment of a vertebrate photoreceptor that contains discs of photoreceptive membranes." [ISBN:0824072820] is_a: GO:0097458 ! neuron part [Term] id: GO:0001868 name: regulation of complement activation, lectin pathway namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the lectin pathway of complement activation." [GOC:add, ISBN:0781735149] synonym: "regulation of complement cascade, lectin pathway" EXACT [GOC:add] is_a: GO:0030449 ! regulation of complement activation [Term] id: GO:0001869 name: negative regulation of complement activation, lectin pathway namespace: biological_process def: "Any process that stops, prevents, or reduces the rate of complement activation by the lectin pathway." [GOC:add, ISBN:0781735149] synonym: "down regulation of complement activation, lectin pathway" EXACT [] synonym: "down-regulation of complement activation, lectin pathway" EXACT [] synonym: "downregulation of complement activation, lectin pathway" EXACT [] synonym: "inhibition of complement activation, lectin pathway" NARROW [] synonym: "negative regulation of complement cascade, lectin pathway" EXACT [GOC:add] is_a: GO:0001868 ! regulation of complement activation, lectin pathway is_a: GO:0045916 ! negative regulation of complement activation [Term] id: GO:0001870 name: positive regulation of complement activation, lectin pathway namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of complement activation by the lectin pathway." [GOC:add, ISBN:0781735149] synonym: "activation of complement activation, lectin pathway" NARROW [] synonym: "positive regulation of complement cascade, lectin pathway" EXACT [GOC:add] synonym: "stimulation of complement activation, lectin pathway" NARROW [] synonym: "up regulation of complement activation, lectin pathway" EXACT [] synonym: "up-regulation of complement activation, lectin pathway" EXACT [] synonym: "upregulation of complement activation, lectin pathway" EXACT [] is_a: GO:0001868 ! regulation of complement activation, lectin pathway is_a: GO:0045917 ! positive regulation of complement activation [Term] id: GO:0001917 name: photoreceptor inner segment namespace: cellular_component def: "The inner segment of a vertebrate photoreceptor containing mitochondria, ribosomes and membranes where opsin molecules are assembled and passed to be part of the outer segment discs." [GOC:add, PMID:12019563] subset: goslim_pir is_a: GO:0097458 ! neuron part [Term] id: GO:0001969 name: regulation of activation of membrane attack complex namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the activation of the membrane attack complex components of the complement cascade." [GOC:hjd] synonym: "regulation of activation of MAC" EXACT [GOC:mah] synonym: "regulation of activation of TCC" NARROW [GOC:mah] synonym: "regulation of activation of terminal complement complex" NARROW [GOC:add] synonym: "regulation of activation of the terminal complement cascade" NARROW [GOC:mah] synonym: "regulation of MAC assembly" EXACT [GOC:rl] synonym: "regulation of MAC formation" EXACT [GOC:rl] synonym: "regulation of membrane attack complex assembly" EXACT [GOC:rl] synonym: "regulation of membrane attack complex formation" EXACT [GOC:rl] is_a: GO:0030449 ! regulation of complement activation [Term] id: GO:0001970 name: positive regulation of activation of membrane attack complex namespace: biological_process def: "Any process that activates, maintains or increases the frequency, rate or extent of the activation of the membrane attack complex components of the complement cascade." [GOC:hjd] synonym: "activation of activation of membrane attack complex" NARROW [] synonym: "positive regulation of activation of MAC" EXACT [GOC:mah] synonym: "positive regulation of activation of TCC" NARROW [GOC:mah] synonym: "positive regulation of activation of terminal complement complex" NARROW [GOC:add] synonym: "positive regulation of activation of the terminal complement cascade" NARROW [GOC:mah] synonym: "positive regulation of MAC assembly" EXACT [GOC:rl] synonym: "positive regulation of MAC formation" EXACT [GOC:rl] synonym: "positive regulation of membrane attack complex assembly" EXACT [GOC:rl] synonym: "positive regulation of membrane attack complex formation" EXACT [GOC:rl] synonym: "stimulation of activation of membrane attack complex" NARROW [] synonym: "up regulation of activation of membrane attack complex" EXACT [] synonym: "up-regulation of activation of membrane attack complex" EXACT [] synonym: "upregulation of activation of membrane attack complex" EXACT [] is_a: GO:0001969 ! regulation of activation of membrane attack complex is_a: GO:0045917 ! positive regulation of complement activation [Term] id: GO:0001971 name: negative regulation of activation of membrane attack complex namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the activation of the membrane attack complex components of the complement cascade." [GOC:hjd] synonym: "down regulation of activation of membrane attack complex" EXACT [] synonym: "down-regulation of activation of membrane attack complex" EXACT [] synonym: "downregulation of activation of membrane attack complex" EXACT [] synonym: "inhibition of activation of membrane attack complex" NARROW [] synonym: "negative regulation of activation of MAC" EXACT [GOC:mah] synonym: "negative regulation of activation of TCC" NARROW [GOC:mah] synonym: "negative regulation of activation of terminal complement complex" NARROW [GOC:add] synonym: "negative regulation of activation of the terminal complement cascade" NARROW [GOC:mah] synonym: "negative regulation of MAC assembly" EXACT [GOC:rl] synonym: "negative regulation of MAC formation" EXACT [GOC:rl] synonym: "negative regulation of membrane attack complex assembly" EXACT [GOC:rl] synonym: "negative regulation of membrane attack complex formation" EXACT [GOC:rl] is_a: GO:0001969 ! regulation of activation of membrane attack complex is_a: GO:0045916 ! negative regulation of complement activation [Term] id: GO:0002003 name: angiotensin maturation namespace: biological_process def: "The process leading to the attainment of the full functional capacity of angiotensin by conversion of renin substrate into mature angiotensin in the blood." [ISBN:0721643949] is_a: GO:0016486 ! peptide hormone processing [Term] id: GO:0002097 name: tRNA wobble base modification namespace: biological_process def: "The process in which the nucleotide at position 34 in the anticodon of a tRNA is post-transcriptionally modified." [GOC:hjd, ISBN:155581073X] is_a: GO:0006400 ! tRNA modification [Term] id: GO:0002098 name: tRNA wobble uridine modification namespace: biological_process def: "The process in which a uridine in position 34 of a tRNA is post-transcriptionally modified." [GOC:hjd, ISBN:155581073X] is_a: GO:0002097 ! tRNA wobble base modification [Term] id: GO:0002099 name: tRNA wobble guanine modification namespace: biological_process def: "The process in which a guanine in t position 34 of a tRNA is post-transcriptionally modified." [GOC:hjd, ISBN:155581073X] is_a: GO:0002097 ! tRNA wobble base modification [Term] id: GO:0002100 name: tRNA wobble adenosine to inosine editing namespace: biological_process def: "The process in which an adenosine in position 34 of a tRNA is post-transcriptionally converted to inosine." [GOC:hjd, ISBN:155581073X] is_a: GO:0002097 ! tRNA wobble base modification [Term] id: GO:0002101 name: tRNA wobble cytosine modification namespace: biological_process def: "The process in which a cytosine in position 34 of a tRNA is post-transcriptionally modified." [GOC:hjd, ISBN:155581073X] is_a: GO:0002097 ! tRNA wobble base modification [Term] id: GO:0002103 name: endonucleolytic cleavage of tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA) namespace: biological_process def: "Endonucleolytic cleavage of a pre-rRNA molecule originally produced as a tetracistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, Large Subunit (LSU) the 4.5S rRNA, and the 5S rRNA in that order from 5' to 3' along the primary transcript. Primary ribosomal RNA transcripts with four genes, in this order, are produced in the chloroplasts of vascular plants. Note that the use of the word tetracistronic refers only to the number of mature rRNA molecules which will be produced from the primary transcript and ignores tRNAs that may also be present within the primary transcript." [GOC:curators] is_a: GO:0000478 ! endonucleolytic cleavage involved in rRNA processing [Term] id: GO:0002104 name: endonucleolytic cleaveage between 4.5S rRNA and 5S rRNA of tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA) namespace: biological_process def: "Endonucleolytic cleavage between the 5S rRNA and the 4.5S rRNA of an rRNA molecule originally produced as a tetracistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, Large Subunit (LSU) the 4.5S rRNA, and the 5S rRNA in that order from 5' to 3' along the primary transcript. Note that the use of the word tetracistronic refers only to the number of mature rRNA molecules which will be produced from the primary transcript and ignores tRNAs that may also be present within the primary transcript." [GOC:curators] is_a: GO:0002103 ! endonucleolytic cleavage of tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA) [Term] id: GO:0002105 name: endonucleolytic cleaveage between LSU-rRNA and 4.5S rRNA of tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA) namespace: biological_process def: "Endonucleolytic cleavage between the LSU-rRNA and the 4.5S rRNA of an rRNA molecule originally produced as a tetracistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, Large Subunit (LSU) the 4.5S rRNA, and the 5S rRNA in that order from 5' to 3' along the primary transcript. Note that the use of the word tetracistronic refers only to the number of mature rRNA molecules which will be produced from the primary transcript and ignores tRNAs that may also be present within the primary transcript." [GOC:curators] is_a: GO:0002103 ! endonucleolytic cleavage of tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA) [Term] id: GO:0002106 name: endonucleolytic cleaveage between SSU-rRNA and LSU-rRNA of tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA) namespace: biological_process def: "Endonucleolytic cleavages between the SSU-rRNA and the LSU-rRNA of an rRNA molecule originally produced as a tetracistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, Large Subunit (LSU) the 4.5S rRNA, and the 5S rRNA in that order from 5' to 3' along the primary transcript. These cleavages liberate tRNAs from the polycistronic transcript as well as separating the SSU and LSU containing transcript. Note that the use of the word tetracistronic refers only to the number of mature rRNA molecules which will be produced from the primary transcript and ignores tRNAs that may also be present within the primary transcript." [GOC:curators] is_a: GO:0002103 ! endonucleolytic cleavage of tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA) [Term] id: GO:0002107 name: generation of mature 3'-end of 5S rRNA generated by RNA polymerase III namespace: biological_process def: "The removal of extra uridine residues from the 3' end of a 5S pre-rRNA generated by transcription by RNA polymerase III to generate the mature 3'-end." [GOC:hjd, PMID:16387655, PMID:1748637, PMID:1902221, PMID:8389357] is_a: GO:0000481 ! maturation of 5S rRNA is_a: GO:0031125 ! rRNA 3'-end processing [Term] id: GO:0002108 name: maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) namespace: biological_process def: "Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule from the pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, Large Subunit (LSU) the 5S rRNA in that order from 5' to 3' along the primary transcript." [GOC:curators] is_a: GO:0000470 ! maturation of LSU-rRNA [Term] id: GO:0002109 name: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) namespace: biological_process def: "Any process involved in the maturation of a precursor Small SubUnit (SSU) ribosomal RNA (rRNA) molecule into a mature SSU-rRNA molecule from the pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, Large Subunit (LSU) the 5S rRNA in that order from 5' to 3' along the primary transcript." [GOC:curators] is_a: GO:0030490 ! maturation of SSU-rRNA [Term] id: GO:0002110 name: cotranscriptional mitochondrial rRNA nucleotide insertion namespace: biological_process def: "The insertion of one or two non-coded nucleotides during the transcription of a mitochondrial rRNA. Such additions are known to occur in myxomycetes such as Physarum, Didymium, and Stemonitis." [GOC:curators, ISBN:1555811337, PMID:8306965] is_a: GO:0000154 ! rRNA modification [Term] id: GO:0002127 name: wobble base cytosine methylation namespace: biological_process def: "The process in which the base of cytosine at position 34 in the anticodon of a tRNA is post-transcriptionally methylated at the C5 position." [GOC:hjd, ISBN:155581073X] synonym: "wobble position m5C biosynthesis" EXACT [] is_a: GO:0002101 ! tRNA wobble cytosine modification is_a: GO:0002946 ! tRNA C5-cytosine methylation [Term] id: GO:0002128 name: tRNA nucleoside ribose methylation namespace: biological_process def: "The process that results in the modification of the sugar of a nucleoside in tRNA at the 2'O position." [GOC:hjd, ISBN:155581073X] is_a: GO:0030488 ! tRNA methylation [Term] id: GO:0002129 name: wobble position guanine ribose methylation namespace: biological_process def: "The process in which the ribose of guanosine at position 34 in the anticodon of a tRNA is post-transcriptionally methylated at the 2'-O position." [GOC:hjd, ISBN:155581073X] is_a: GO:0002130 ! wobble position ribose methylation is_a: GO:0002938 ! tRNA guanine ribose methylation [Term] id: GO:0002130 name: wobble position ribose methylation namespace: biological_process def: "The process in which the ribose base of the nucleotide at position 34 in the anticodon of a tRNA is post-transcriptionally methylated at the 2'O position." [GOC:hjd, ISBN:155581073X] is_a: GO:0002128 ! tRNA nucleoside ribose methylation [Term] id: GO:0002131 name: wobble position cytosine ribose methylation namespace: biological_process def: "The process in which the ribose of cytidine at position 34 in the anticodon of a tRNA is post-transcriptionally methylated at the 2'-O position." [GOC:hjd, ISBN:155581073X] is_a: GO:0002130 ! wobble position ribose methylation [Term] id: GO:0002132 name: wobble position uridine ribose methylation namespace: biological_process def: "The process in which the ribose of uridine at position 34 in the anticodon of a tRNA is post-transcriptionally methylated at the 2'-O position." [GOC:hjd, ISBN:155581073X] is_a: GO:0002130 ! wobble position ribose methylation [Term] id: GO:0002136 name: wobble base lysidine biosynthesis namespace: biological_process def: "The process in which the carbonyl of cytosine at position 34 of a tRNA is post-transcriptionally replaced by lysine." [PMID:15894617] comment: Exclusively located at the anticodon wobble position (i.e., position 34) of eubacterial and some organellar tRNAIle2. This modification converts the codon specificity from AUG to AUA, and it also converts the aminoacylation specificity of the tRNA from methionine to isoleucine. Requires ATP. is_a: GO:0002101 ! tRNA wobble cytosine modification [Term] id: GO:0002143 name: tRNA wobble position uridine thiolation namespace: biological_process def: "The process in which a uridine residue at position 34 in the anticodon of a tRNA is post-transcriptionally thiolated at the C2 position. This process involves transfer of a sulfur from cysteine to position C2 by several steps." [PMID:16871210] comment: In E. coli, the first step of the reaction is reductive elimination of sulfur from L-cysteine by IscS cysteine desulfurase to form an enzyme-bound cysteine-persulfide intermediate. Then, five essential gene products, TusA, TusB, TusC, TusD and TusE, mediate a sulfur relay that delivers the terminal sulfur of persulfide from IscS to MnmA12. The last protein, MnmA catalyzes the transfer of the sulfur from IscS to an ATP activated U34 of the tRNA. synonym: "tRNA wobble uridine thiolation" EXACT [GOC:mah] synonym: "wobble position s2U biosynthesis" EXACT [] is_a: GO:0002098 ! tRNA wobble uridine modification is_a: GO:0034227 ! tRNA thio-modification created_by: hjd creation_date: 2009-05-06T05:05:40Z [Term] id: GO:0002161 name: aminoacyl-tRNA editing activity namespace: molecular_function def: "The hydrolysis of an incorrectly aminoacylated tRNA." [GOC:hjd, PMID:14663147, PMID:16087889] synonym: "amino acid proofreading activity" RELATED [] synonym: "aminoacyl-tRNA hydrolysis activity" RELATED [] relationship: part_of GO:0006450 ! regulation of translational fidelity created_by: hjd creation_date: 2010-02-12T03:06:56Z [Term] id: GO:0002181 name: cytoplasmic translation namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein." [GOC:hjd] subset: goslim_pombe subset: goslim_yeast is_a: GO:0006412 ! translation created_by: hjd creation_date: 2011-06-09T03:11:53Z [Term] id: GO:0002182 name: cytoplasmic translational elongation namespace: biological_process def: "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis in the cytoplasm." [GOC:hjd] is_a: GO:0006414 ! translational elongation relationship: part_of GO:0002181 ! cytoplasmic translation created_by: hjd creation_date: 2011-06-09T03:14:42Z [Term] id: GO:0002183 name: cytoplasmic translational initiation namespace: biological_process def: "The process preceding formation of the peptide bond between the first two amino acids of a protein in the cytoplasm. This includes the formation of a complex of the ribosome, mRNA, and an initiation complex that contains the first aminoacyl-tRNA." [GOC:hjd] is_a: GO:0006413 ! translational initiation relationship: part_of GO:0002181 ! cytoplasmic translation created_by: hjd creation_date: 2011-06-09T03:15:48Z [Term] id: GO:0002184 name: cytoplasmic translational termination namespace: biological_process def: "The process resulting in the release of a polypeptide chain from the ribosome in the cytoplasm, usually in response to a termination codon." [GOC:hjd] is_a: GO:0006415 ! translational termination relationship: part_of GO:0002181 ! cytoplasmic translation created_by: hjd creation_date: 2011-06-09T03:17:13Z [Term] id: GO:0002188 name: translation reinitiation namespace: biological_process def: "A gene-specific translational control mechanism where the small ribosomal subunit remains attached to the mRNA following termination of translation, then resumes scanning on the same mRNA molecule and initiates again at a downstream start site. Reinitiation depends on de novo recruitment of the ternary complex that is required to recognize the next AUG codon." [PMID:18056426, PMID:18765792] is_a: GO:0002183 ! cytoplasmic translational initiation created_by: hjd creation_date: 2011-06-22T12:31:13Z [Term] id: GO:0002190 name: cap-independent translational initiation namespace: biological_process def: "The process where translation initiation recruits the 40S ribosomal subunits in a Cap and 5' end independent fashion before an AUG codon is encountered in an appropriate sequence context to initiate mRNA translation." [PMID:17284590] is_a: GO:0002183 ! cytoplasmic translational initiation created_by: hjd creation_date: 2011-08-11T02:16:05Z [Term] id: GO:0002191 name: cap-dependent translational initiation namespace: biological_process def: "The process where the \"Cap structure\" (composed of a 7- methylguanosine (m7G) group and associated cap-binding proteins) located at the 5' end of an mRNA molecule, which serves as a \"molecular tag\" that marks the spot where the 40S ribosomal subunit is recruited and will then scan in a 5' to 3' direction until an AUG codon is encountered in an appropriate sequence context to initiate mRNA translation." [PMID:17284590, PMID:19604130] is_a: GO:0002183 ! cytoplasmic translational initiation created_by: hjd creation_date: 2011-08-11T02:20:24Z [Term] id: GO:0002192 name: IRES-dependent translational initiation namespace: biological_process def: "The process where translation initiation recruits the 40S ribosomal subunits via an internal ribosome entry segment (IRES) before an AUG codon is encountered in an appropriate sequence context to initiate mRNA translation." [PMID:17284590] is_a: GO:0002190 ! cap-independent translational initiation created_by: hjd creation_date: 2011-08-11T02:32:45Z [Term] id: GO:0002195 name: 2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine-tRNA biosynthesis namespace: biological_process def: "The chemical reactions and pathways involved in the biosynthesis of 2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine (ms2io6A), a modified nucleoside present in position 37 (adjacent to and 3' of the anticodon) of tRNAs." [UniPathway:UPA00729] comment: In Salmonella typhimurium, 2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine (ms2io6A; also referred to as 2-methylthio cis-ribozeatin) is found in tRNA, most likely in the species that have ms2i6A in E. coli. is_a: GO:0006400 ! tRNA modification created_by: hjd creation_date: 2011-08-31T02:20:06Z [Term] id: GO:0002196 name: Ser-tRNA(Ala) hydrolase activity namespace: molecular_function def: "Catalysis of the hydrolysis of misacylated Ser-tRNA(Ala)." [GOC:hjd, PMID:21285375] is_a: GO:0002161 ! aminoacyl-tRNA editing activity created_by: hjd creation_date: 2011-09-30T02:18:50Z [Term] id: GO:0002330 name: pre-B cell receptor expression namespace: biological_process def: "The process leading up to expression of the pre-B cell receptor on the surface of pre-B cells, including expression of the surrogate light chain, association of the surrogate light chain with heavy chain, and expression of the complete pre-B cell receptor on the cell surface." [GOC:add, GOC:jal, ISBN:0781735149] is_a: GO:0010467 ! gene expression [Term] id: GO:0002331 name: pre-B cell allelic exclusion namespace: biological_process def: "Expression of a single heavy chain allele during pre-B cell differentiation." [GOC:add, GOC:jal, ISBN:0781735149] synonym: "pre-B lymphocyte allelic exclusion" EXACT [] is_a: GO:0010468 ! regulation of gene expression [Term] id: GO:0002541 name: activation of plasma proteins involved in acute inflammatory response namespace: biological_process def: "Any process activating plasma proteins by proteolysis as part of an acute inflammatory response." [GOC:jal, ISBN:0781735149] is_a: GO:0016485 ! protein processing [Term] id: GO:0002542 name: Factor XII activation namespace: biological_process def: "Any process that activates Factor XII (Hageman factor). Factor XII is a protein synthesized by the liver that circulates in an inactive form until it encounters collagen or basement membrane or activated platelets (as occurs at the site of endothelial injury). Factor XII then undergoes a conformational change (becoming factor XIIa), exposing an active serine center that can subsequently cleave protein substrates and activate a variety of mediator systems. Factor XII is a participant in the clotting cascade as well as the kinin cascade." [GOC:jal, ISBN:0721601871] synonym: "Hageman factor activation" EXACT [] is_a: GO:0010954 ! positive regulation of protein processing relationship: positively_regulates GO:0002541 ! activation of plasma proteins involved in acute inflammatory response [Term] id: GO:0002926 name: tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridine biosynthesis. namespace: biological_process def: "The process whereby a wobble base uridine residue in a tRNA is modified to 5-methoxycarbonylmethyl-2-thiouridine." [GOC:hjd, UniPathway:UPA00988] synonym: "mcm5s2U34 biosynthesis" EXACT [] is_a: GO:0002098 ! tRNA wobble uridine modification created_by: hjd creation_date: 2012-01-17T02:50:54Z [Term] id: GO:0002927 name: archaeosine-tRNA biosynthetic process namespace: biological_process def: "The chemical reactions and pathways involved in the biosynthesis of archaeosine, an archaea-specific modified base found at position 15 in the D-loop of certain archaeal tRNAs." [GOC:hjd, UniPathway:UPA00393] comment: Archaeosine (7-formamidino-7-deazaguanosine) is a structural variant of the hypermodified nucleoside 7-deazaguanosine. The biosynthesis pathway starts with archaeosine tRNA-guanine transglycosylase (ArcTGT) which catalyzes the exchange of guanine at position 15 in the D-loop of archaeal tRNAs with a free 7-cyano-7-deazaguanine. is_a: GO:0006400 ! tRNA modification created_by: hjd creation_date: 2012-01-18T03:06:27Z [Term] id: GO:0002935 name: tRNA (adenine-C2-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: 2 S-adenosyl-L-methionine + adenine(37) in tRNA = S-adenosyl-L-homocysteine + 5'-deoxyadenosine + L-methionine + C2-methyladenine(37) in a tRNA." [PMID:22891362] is_a: GO:0016426 ! tRNA (adenine) methyltransferase activity created_by: hjd creation_date: 2012-09-04T14:39:56Z [Term] id: GO:0002937 name: tRNA 4-thiouridine biosynthesis namespace: biological_process def: "The processes whereby a uridine residue in a tRNA is converted to 4-thiouridine. Typically 4-thiouridine is found at position 8, in many transfer RNAs." [ISBN:155581073X] comment: In E. coli, two genes are involved, nuvA (aka Thi) and NuvC (aka iscS) . NuvA converts the trNA into an unidentified intermediate in an ATP dependent manner. NucC catalyzes the second step, transferring the sulfur from cysteine to he unidentified intermediate. NuvC also participate sin thiamine synthesis. is_a: GO:0034227 ! tRNA thio-modification created_by: hjd creation_date: 2012-10-19T15:26:28Z [Term] id: GO:0002938 name: tRNA guanine ribose methylation namespace: biological_process def: "The process whereby a guanosine residue in a tRNA is methylated on the 2'-hydroxyl group of the ribose moiety." [ISBN:155581075X, ISBN:1555811337] is_a: GO:0002128 ! tRNA nucleoside ribose methylation created_by: hjd creation_date: 2012-11-02T15:55:55Z [Term] id: GO:0002939 name: tRNA N1-guanine methylation namespace: biological_process def: "The process whereby a guanine in tRNA is methylated at position N1 of the guanine." [ISBN:155581073X, ISBN:1555811337] synonym: "tRNA m1-guanine biosynthesis" RELATED [] is_a: GO:0030488 ! tRNA methylation created_by: hjd creation_date: 2012-11-09T16:18:41Z [Term] id: GO:0002940 name: tRNA N2-guanine methylation namespace: biological_process def: "The process whereby a guanine in a tRNA is methylated at the N2 position of guanine." [ISBN:155581073X, ISBN:1555811337] synonym: "tRNA m2-guanine biosynthesis" RELATED [] is_a: GO:0030488 ! tRNA methylation created_by: hjd creation_date: 2012-11-09T16:23:41Z [Term] id: GO:0002942 name: tRNA m2,2-guanine biosynthesis namespace: biological_process def: "The process whereby a guanine residue in a transfer RNA is methylated twice at the N2 position." [GOC:hjd, ISBN:1-55581-073-x] is_a: GO:0030488 ! tRNA methylation created_by: hjd creation_date: 2012-11-16T16:07:20Z [Term] id: GO:0002943 name: tRNA dihydrouridine synthesis namespace: biological_process def: "The process whereby a uridine in a transfer RNA is converted to dihydrouridine." [GOC:hjd, ISBN:1-55581-073-x] comment: Dihydrouridine is found in numerous positions within loop I, the so called dihydrouridine loop, of many transfer RNAs. Most often found at positions 16 and 17, but also sometimes at positions 20, 20a, and 20b. is_a: GO:0006400 ! tRNA modification created_by: hjd creation_date: 2012-11-16T16:20:37Z [Term] id: GO:0002946 name: tRNA C5-cytosine methylation namespace: biological_process def: "The process whereby a cytosine in a tRNA is methylated at position 5 of the cytosine." [ISBN:1-55581-073-x] synonym: "tRNA 5-methylcytosine biosynthesis" RELATED [] is_a: GO:0030488 ! tRNA methylation created_by: hjd creation_date: 2012-12-07T14:23:13Z [Term] id: GO:0003130 name: BMP signaling pathway involved in heart induction namespace: biological_process def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to heart induction." [GOC:mtg_heart] synonym: "BMP signalling pathway involved in heart induction" EXACT [GOC:mah] is_a: GO:0060850 ! regulation of transcription involved in cell fate commitment is_a: GO:0061312 ! BMP signaling pathway involved in heart development intersection_of: GO:0030509 ! BMP signaling pathway created_by: tanyaberardini creation_date: 2009-09-22T03:02:00Z [Term] id: GO:0003154 name: BMP signaling pathway involved in determination of left/right symmetry namespace: biological_process def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the determination of left/right symmetry." [GOC:mtg_heart, GOC:signaling] synonym: "BMP signaling pathway involved in determination of left/right asymmetry" EXACT [GOC:dph] synonym: "BMP signalling pathway involved in determination of left/right symmetry" EXACT [GOC:mah] is_a: GO:0030509 ! BMP signaling pathway is_a: GO:1900094 ! regulation of transcription from RNA polymerase II promoter involved in determination of left/right symmetry intersection_of: GO:0030509 ! BMP signaling pathway created_by: tanyaberardini creation_date: 2009-09-24T05:34:57Z [Term] id: GO:0003155 name: BMP signaling pathway involved in determination of lateral mesoderm left/right asymmetry namespace: biological_process def: "A series of molecular signals generated as a consequence of any member of the BMP (bone morphogenetic protein) family binding to a cell surface receptor that contributes to the determination of lateral mesoderm left/right asymmetry." [GOC:mtg_heart] synonym: "BMP signaling pathway involved in lateral mesoderm left/right asymmetry determination" EXACT [] synonym: "BMP signalling pathway involved in determination of lateral mesoderm left/right asymmetry" EXACT [GOC:mah] is_a: GO:0003154 ! BMP signaling pathway involved in determination of left/right symmetry intersection_of: GO:0030509 ! BMP signaling pathway created_by: tanyaberardini creation_date: 2009-09-24T05:42:17Z [Term] id: GO:0003256 name: regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the differentiation of a myocardial precursor cell." [GOC:mtg_heart] is_a: GO:1901213 ! regulation of transcription from RNA polymerase II promoter involved in heart development intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2009-10-15T01:01:25Z [Term] id: GO:0003257 name: positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the differentiation of a myocardial precursor cell." [GOC:mtg_heart] is_a: GO:0003256 ! regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation is_a: GO:1901228 ! positive regulation of transcription from RNA polymerase II promoter involved in heart development intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2009-10-15T01:07:25Z [Term] id: GO:0003258 name: regulation of transcription from RNA polymerase II promoter involved in endocardial precursor cell differentiation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the differentiation of an endocardial precursor cell." [GOC:mtg_heart] is_a: GO:1901213 ! regulation of transcription from RNA polymerase II promoter involved in heart development intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2009-10-15T01:10:34Z [Term] id: GO:0003269 name: BMP signaling pathway involved in regulation of secondary heart field cardioblast proliferation namespace: biological_process def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the modulation of the frequency, rate or extent of cardioblast proliferation in the secondary heart field. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:mtg_heart] synonym: "BMP signaling pathway involved in regulation of second heart field cardioblast proliferation" EXACT [GOC:dph] synonym: "BMP signalling pathway involved in regulation of secondary heart field cardioblast proliferation" EXACT [GOC:mah] is_a: GO:0061312 ! BMP signaling pathway involved in heart development intersection_of: GO:0061312 ! BMP signaling pathway involved in heart development created_by: dph creation_date: 2009-10-15T02:45:28Z [Term] id: GO:0003303 name: BMP signaling pathway involved in heart jogging namespace: biological_process def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the process of heart jogging." [GOC:mtg_heart] synonym: "BMP signalling pathway involved in heart jogging" EXACT [GOC:mah] is_a: GO:0003154 ! BMP signaling pathway involved in determination of left/right symmetry is_a: GO:0061312 ! BMP signaling pathway involved in heart development intersection_of: GO:0030509 ! BMP signaling pathway created_by: dph creation_date: 2009-10-22T11:00:58Z [Term] id: GO:0003434 name: BMP signaling pathway involved in growth plate cartilage chondrocyte development namespace: biological_process def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the progression of a growth plate cartilage chondrocyte over time." [GOC:ascb_2009, GOC:dph, GOC:tb] synonym: "BMP signalling pathway involved in growth plate cartilage chondrocyte development" EXACT [GOC:mah] is_a: GO:0030509 ! BMP signaling pathway intersection_of: GO:0030509 ! BMP signaling pathway created_by: dph creation_date: 2009-12-22T12:50:17Z [Term] id: GO:0003700 name: sequence-specific DNA binding transcription factor activity namespace: molecular_function alt_id: GO:0000130 def: "Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:curators, GOC:txnOH] subset: goslim_plant subset: gosubset_prok synonym: "transcription factor activity" BROAD [] relationship: part_of GO:0006355 ! regulation of transcription, DNA-dependent [Term] id: GO:0003705 name: RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II." [GOC:jl, GOC:txnOH] synonym: "sequence-specific distal enhancer binding RNA polymerase II transcription factor activity" EXACT [] is_a: GO:0000981 ! sequence-specific DNA binding RNA polymerase II transcription factor activity [Term] id: GO:0003708 name: retinoic acid receptor activity namespace: molecular_function def: "Combining with retinoic acid and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. Retinoic acid is one of the forms of vitamin A." [GOC:signaling, PMID:1328967] synonym: "vitamin A receptor activity" BROAD [] is_a: GO:0004879 ! ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity [Term] id: GO:0003743 name: translation initiation factor activity namespace: molecular_function alt_id: GO:0003744 alt_id: GO:0003745 def: "Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide." [ISBN:0198506732] subset: gosubset_prok xref: Reactome:REACT_102411 "eIF2 activation, Arabidopsis thaliana" xref: Reactome:REACT_102747 "Ribosomal scanning, Plasmodium falciparum" xref: Reactome:REACT_104592 "Ribosomal scanning, Xenopus tropicalis" xref: Reactome:REACT_104947 "Start codon recognition, Arabidopsis thaliana" xref: Reactome:REACT_105336 "Ribosomal scanning, Danio rerio" xref: Reactome:REACT_105545 "eIF2 activation, Schizosaccharomyces pombe" xref: Reactome:REACT_105772 "Ribosomal scanning, Caenorhabditis elegans" xref: Reactome:REACT_106049 "Ribosomal scanning, Schizosaccharomyces pombe" xref: Reactome:REACT_107324 "eIF2 activation, Taeniopygia guttata" xref: Reactome:REACT_108980 "Ribosomal scanning, Canis familiaris" xref: Reactome:REACT_112013 "Start codon recognition, Gallus gallus" xref: Reactome:REACT_114676 "Ribosomal scanning, Gallus gallus" xref: Reactome:REACT_115071 "Ribosomal scanning, Rattus norvegicus" xref: Reactome:REACT_115079 "Start codon recognition, Rattus norvegicus" xref: Reactome:REACT_115451 "Start codon recognition, Bos taurus" xref: Reactome:REACT_1401 "eIF2 activation, Homo sapiens" xref: Reactome:REACT_1516 "Ribosomal scanning, Homo sapiens" xref: Reactome:REACT_29285 "eIF2 activation, Danio rerio" xref: Reactome:REACT_31248 "Ribosomal scanning, Drosophila melanogaster" xref: Reactome:REACT_31637 "Start codon recognition, Saccharomyces cerevisiae" xref: Reactome:REACT_32686 "eIF2 activation, Oryza sativa" xref: Reactome:REACT_33398 "Start codon recognition, Oryza sativa" xref: Reactome:REACT_33544 "Start codon recognition, Xenopus tropicalis" xref: Reactome:REACT_57036 "Start codon recognition, Plasmodium falciparum" xref: Reactome:REACT_60464 "eIF2 activation, Caenorhabditis elegans" xref: Reactome:REACT_656 "Start codon recognition, Homo sapiens" xref: Reactome:REACT_78159 "Start codon recognition, Caenorhabditis elegans" xref: Reactome:REACT_78773 "eIF2 activation, Plasmodium falciparum" xref: Reactome:REACT_79007 "Start codon recognition, Danio rerio" xref: Reactome:REACT_81171 "Start codon recognition, Mus musculus" xref: Reactome:REACT_82224 "eIF2 activation, Gallus gallus" xref: Reactome:REACT_83059 "eIF2 activation, Bos taurus" xref: Reactome:REACT_83547 "eIF2 activation, Rattus norvegicus" xref: Reactome:REACT_83592 "eIF2 activation, Saccharomyces cerevisiae" xref: Reactome:REACT_88632 "eIF2 activation, Mus musculus" xref: Reactome:REACT_88913 "Ribosomal scanning, Bos taurus" xref: Reactome:REACT_88955 "eIF2 activation, Xenopus tropicalis" xref: Reactome:REACT_91084 "Ribosomal scanning, Arabidopsis thaliana" xref: Reactome:REACT_91415 "Start codon recognition, Dictyostelium discoideum" xref: Reactome:REACT_91967 "Ribosomal scanning, Dictyostelium discoideum" xref: Reactome:REACT_91979 "Ribosomal scanning, Taeniopygia guttata" xref: Reactome:REACT_93372 "Start codon recognition, Schizosaccharomyces pombe" xref: Reactome:REACT_93678 "eIF2 activation, Canis familiaris" xref: Reactome:REACT_95840 "Ribosomal scanning, Saccharomyces cerevisiae" xref: Reactome:REACT_96533 "Ribosomal scanning, Oryza sativa" xref: Reactome:REACT_96726 "eIF2 activation, Dictyostelium discoideum" xref: Reactome:REACT_99607 "Ribosomal scanning, Mus musculus" is_a: GO:0008135 ! translation factor activity, nucleic acid binding relationship: part_of GO:0006413 ! translational initiation [Term] id: GO:0003746 name: translation elongation factor activity namespace: molecular_function alt_id: GO:0008182 alt_id: GO:0008183 def: "Functions in chain elongation during polypeptide synthesis at the ribosome." [ISBN:0198506732] subset: gosubset_prok xref: Reactome:REACT_9514 "Viral Protein Synthesis, Homo sapiens" xref: Reactome:REACT_9524 "Synthesis of PB1-F2, Homo sapiens" is_a: GO:0008135 ! translation factor activity, nucleic acid binding relationship: part_of GO:0006414 ! translational elongation [Term] id: GO:0003747 name: translation release factor activity namespace: molecular_function alt_id: GO:0003748 alt_id: GO:0003749 def: "Involved in catalyzing the release of a nascent polypeptide chain from a ribosome." [ISBN:0198547684] subset: gosubset_prok is_a: GO:0008079 ! translation termination factor activity [Term] id: GO:0003886 name: DNA (cytosine-5-)-methyltransferase activity namespace: molecular_function alt_id: GO:0008326 def: "Catalysis of the reaction: S-adenosyl-L-methionine + DNA containing cytosine = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine." [EC:2.1.1.37] comment: Note that EC:2.1.1.73 was deleted from EC as the reaction is performed by DNA (cytosine-5-)-methyltransferase (EC:2.1.1.37). subset: gosubset_prok synonym: "cytosine 5-methyltransferase activity" EXACT [EC:2.1.1.37] synonym: "cytosine DNA methylase activity" BROAD [EC:2.1.1.37] synonym: "cytosine DNA methyltransferase activity" BROAD [EC:2.1.1.37] synonym: "cytosine-specific DNA methyltransferase activity" EXACT [EC:2.1.1.37] synonym: "deoxyribonucleic (cytosine-5-)-methyltransferase activity" EXACT [EC:2.1.1.37] synonym: "deoxyribonucleic acid (cytosine-5-)-methyltransferase activity" EXACT [EC:2.1.1.37] synonym: "deoxyribonucleic methylase activity" BROAD [EC:2.1.1.37] synonym: "DNA 5-cytosine methylase activity" EXACT [EC:2.1.1.37] synonym: "DNA cytosine C(5) methylase activity" EXACT [EC:2.1.1.37] synonym: "DNA cytosine C5 methylase activity" EXACT [EC:2.1.1.37] synonym: "DNA cytosine methylase activity" BROAD [EC:2.1.1.37] synonym: "DNA-cytosine 5-methylase activity" EXACT [EC:2.1.1.37] synonym: "DNA-cytosine methyltransferase activity" BROAD [EC:2.1.1.37] synonym: "methylphosphotriester-DNA methyltransferase activity" RELATED [EC:2.1.1.37] synonym: "modification methylase activity" RELATED [EC:2.1.1.37] synonym: "restriction-modification system activity" RELATED [EC:2.1.1.37] synonym: "S-adenosyl-L-methionine:DNA (cytosine-5-)-methyltransferase activity" EXACT [EC:2.1.1.37] synonym: "site-specific DNA-methyltransferase (cytosine-specific) activity" NARROW [EC:2.1.1.37] synonym: "type II DNA methylase activity" RELATED [EC:2.1.1.37] xref: EC:2.1.1.37 xref: MetaCyc:2.1.1.73-RXN is_a: GO:0009008 ! DNA-methyltransferase activity relationship: part_of GO:0090116 ! C-5 methylation of cytosine [Term] id: GO:0004479 name: methionyl-tRNA formyltransferase activity namespace: molecular_function alt_id: GO:0001718 alt_id: GO:0070128 def: "Catalysis of the reaction: 10-formyltetrahydrofolate + L-methionyl-tRNA + H2O = tetrahydrofolate + N-formylmethionyl-tRNA." [EC:2.1.2.9] subset: gosubset_prok synonym: "10-formyltetrahydrofolate:L-methionyl-tRNA N-formyltransferase activity" EXACT [EC:2.1.2.9] synonym: "conversion of met-tRNAf to fmet-tRNA" RELATED [GO:curators] synonym: "conversion of mitochondrial met-tRNAf to fmet-tRNA" RELATED [GO:curators] synonym: "formylmethionyl-transfer ribonucleic synthetase activity" EXACT [EC:2.1.2.9] synonym: "methionyl ribonucleic formyltransferase activity" EXACT [EC:2.1.2.9] synonym: "methionyl-transfer ribonucleate methyltransferase activity" RELATED [EC:2.1.2.9] synonym: "methionyl-transfer ribonucleic transformylase activity" EXACT [EC:2.1.2.9] synonym: "methionyl-transfer RNA transformylase activity" EXACT [EC:2.1.2.9] synonym: "methionyl-tRNA Met formyltransferase activity" EXACT [EC:2.1.2.9] synonym: "methionyl-tRNA transformylase activity" EXACT [EC:2.1.2.9] synonym: "mitochondrial N-terminal peptidyl-methionine N-formylation" RELATED [GO:curators] synonym: "N(10)-formyltetrahydrofolic-methionyl-transfer ribonucleic transformylase activity" EXACT [EC:2.1.2.9] synonym: "N-terminal peptidyl-methionine N-formylation" RELATED [GO:curators] synonym: "N10-formyltetrahydrofolic-methionyl-transfer ribonucleic transformylase activity" EXACT [EC:2.1.2.9] xref: EC:2.1.2.9 xref: MetaCyc:METHIONYL-TRNA-FORMYLTRANSFERASE-RXN relationship: part_of GO:0006413 ! translational initiation relationship: part_of GO:0071951 ! conversion of methionyl-tRNA to N-formyl-methionyl-tRNA [Term] id: GO:0004482 name: mRNA (guanine-N7-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + G(5')pppR-RNA = S-adenosyl-L-homocysteine + m7G(5')pppR-RNA. m7G(5')pppR-RNA is mRNA containing an N7-methylguanine cap; R may be guanosine or adenosine." [EC:2.1.1.56] synonym: "guanine-7-methyltransferase activity" EXACT [EC:2.1.1.56] synonym: "messenger ribonucleate guanine 7-methyltransferase activity" EXACT [EC:2.1.1.56] synonym: "messenger RNA guanine 7-methyltransferase activity" EXACT [EC:2.1.1.56] synonym: "S-adenosyl-L-methionine:mRNA (guanine-7-N-)-methyltransferase activity" EXACT [EC:2.1.1.56] synonym: "S-adenosyl-L-methionine:mRNA (guanine-N7-)-methyltransferase activity" EXACT [EC:2.1.1.56] xref: EC:2.1.1.56 xref: MetaCyc:MRNA-GUANINE-N7--METHYLTRANSFERASE-RXN xref: Reactome:REACT_109033 "Methylation of GMP-cap by RNA Methyltransferase, Gallus gallus" xref: Reactome:REACT_30939 "Methylation of GMP-cap by RNA Methyltransferase, Rattus norvegicus" xref: Reactome:REACT_34170 "Methylation of GMP-cap by RNA Methyltransferase, Caenorhabditis elegans" xref: Reactome:REACT_404 "Methylation of GMP-cap by RNA Methyltransferase, Homo sapiens" xref: Reactome:REACT_84965 "Methylation of GMP-cap by RNA Methyltransferase, Xenopus tropicalis" xref: Reactome:REACT_87975 "Methylation of GMP-cap by RNA Methyltransferase, Mus musculus" xref: Reactome:REACT_93915 "Methylation of GMP-cap by RNA Methyltransferase, Drosophila melanogaster" xref: Reactome:REACT_96650 "Methylation of GMP-cap by RNA Methyltransferase, Oryza sativa" xref: Reactome:REACT_97203 "Methylation of GMP-cap by RNA Methyltransferase, Danio rerio" xref: Reactome:REACT_97945 "Methylation of GMP-cap by RNA Methyltransferase, Arabidopsis thaliana" relationship: part_of GO:0006370 ! 7-methylguanosine mRNA capping relationship: part_of GO:0036265 ! RNA (guanine-N7)-methylation [Term] id: GO:0004704 name: NF-kappaB-inducing kinase activity namespace: molecular_function def: "Catalysis of the phosphorylation of the alpha or beta subunit of the inhibitor of kappaB kinase complex (IKK)." [PMID:20685151] synonym: "NIK" EXACT [] xref: EC:2.7.11.- relationship: part_of GO:0038061 ! NIK/NF-kappaB cascade [Term] id: GO:0004808 name: tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity namespace: molecular_function alt_id: GO:0016425 def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing 5-methylaminomethyl-2-thiouridylate." [EC:2.1.1.61] subset: gosubset_prok synonym: "S-adenosyl-L-methionine:tRNA (5-methylaminomethyl-2-thio-uridylate)-methyltransferase activity" EXACT [EC:2.1.1.61] synonym: "transfer ribonucleate 5-methylaminomethyl-2-thiouridylate 5-methyltransferase activity" EXACT [EC:2.1.1.61] synonym: "tRNA 5-methylaminomethyl-2-thiouridylate 5'-methyltransferase activity" EXACT [EC:2.1.1.61] xref: EC:2.1.1.61 xref: MetaCyc:2.1.1.61-RXN is_a: GO:0008175 ! tRNA methyltransferase activity [Term] id: GO:0004809 name: tRNA (guanine-N2-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA containing guanine = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine." [EC:2.1.1.32] subset: gosubset_prok synonym: "guanine-N2-methylase activity" EXACT [EC:2.1.1.32] synonym: "N(2),N(2)-dimethylguanine tRNA methyltransferase activity" EXACT [EC:2.1.1.32] synonym: "N2,N2-dimethylguanine tRNA methyltransferase activity" EXACT [EC:2.1.1.32] synonym: "S-adenosyl-L-methionine:tRNA (guanine-2-N-)-methyltransferase activity" EXACT [EC:2.1.1.32] synonym: "S-adenosyl-L-methionine:tRNA (guanine-N2-)-methyltransferase activity" EXACT [EC:2.1.1.32] synonym: "transfer ribonucleate guanine 2-methyltransferase activity" EXACT [EC:2.1.1.32] synonym: "transfer ribonucleate guanine N2-methyltransferase activity" EXACT [EC:2.1.1.32] synonym: "transfer RNA guanine 2-methyltransferase activity" EXACT [EC:2.1.1.32] synonym: "tRNA 2,2-dimethylguanosine-26 methyltransferase activity" EXACT [EC:2.1.1.32] synonym: "tRNA(guanine-26,N(2)-N(2)) methyltransferase activity" EXACT [EC:2.1.1.32] synonym: "tRNA(guanine-26,N2-N2) methyltransferase activity" EXACT [EC:2.1.1.32] synonym: "tRNA(m(2,2)G26)dimethyltransferase activity" EXACT [EC:2.1.1.32] xref: EC:2.1.1.- is_a: GO:0016423 ! tRNA (guanine) methyltransferase activity [Term] id: GO:0004879 name: ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity namespace: molecular_function def: "Combining with a signal and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II." [GOC:signaling, GOC:txnOH] comment: GO:0004879 is intended for annotation of nuclear receptors that regulate transcription by binding directly to DNA. When the nuclear receptor functions by binding to other transcription factors or transcription factor complexes, consider instead annotating to 'ligand-activated RNA polymerase II transcription factor binding transcription factor activity ; GO:0038049'. synonym: "ligand-dependent nuclear receptor activity" RELATED [GOC:bf] synonym: "ligand-dependent transcription factor activity" RELATED [GOC:bf] synonym: "nuclear hormone receptor" NARROW [] synonym: "nuclear receptor activity" RELATED [GOC:bf] is_a: GO:0000981 ! sequence-specific DNA binding RNA polymerase II transcription factor activity [Term] id: GO:0004880 name: juvenile hormone receptor activity namespace: molecular_function def: "Combining with juvenile hormone and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II." [GOC:signaling, PMID:15475158] is_a: GO:0004879 ! ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity [Term] id: GO:0004882 name: androgen receptor activity namespace: molecular_function def: "Combining with an androgen and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with an androgen response element in DNA in order to modulate transcription by RNA polymerase II." [GOC:signaling, PMID:19372015] synonym: "androgen response element binding" NARROW [GOC:yaf] is_a: GO:0004879 ! ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity [Term] id: GO:0004884 name: ecdysteroid hormone receptor activity namespace: molecular_function def: "Combining with an ecdysteroid hormone and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II." [GOC:signaling, PMID:1653701] is_a: GO:0004879 ! ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity [Term] id: GO:0004886 name: 9-cis retinoic acid receptor activity namespace: molecular_function def: "Combining with 9-cis retinoic acid and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II." [GOC:signaling, PMID:17132853] synonym: "retinoid-X receptor activity" EXACT [GOC:bf] synonym: "RXR" EXACT [] is_a: GO:0003708 ! retinoic acid receptor activity [Term] id: GO:0004887 name: thyroid hormone receptor activity namespace: molecular_function def: "Combining with thyroid hormone and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II." [GOC:signaling] is_a: GO:0004879 ! ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity [Term] id: GO:0005575 name: cellular_component namespace: cellular_component alt_id: GO:0008372 def: "The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together." [GOC:go_curators] comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "cellular component" EXACT [] synonym: "cellular component unknown" NARROW [] xref: NIF_Subcellular:sao1337158144 is_a: snap:Object ! object disjoint_from: GO:0008150 ! biological_process [Term] id: GO:0005623 name: cell namespace: cellular_component def: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:go_curators] subset: goslim_generic subset: goslim_plant subset: gosubset_prok xref: NIF_Subcellular:sao1813327414 xref: Wikipedia:Cell_(biology) is_a: GO:0005575 ! cellular_component relationship: OMIT:geneExpressedln SO:0001867 ! candidate_gene [Term] id: GO:0005883 name: neurofilament namespace: cellular_component def: "A type of intermediate filament found in the core of neuronal axons. Neurofilaments are heteropolymers composed of three type IV polypeptides: NF-L, NF-M, and NF-H (for low, middle, and high molecular weight). Neurofilaments are responsible for the radial growth of an axon and determine axonal diameter." [ISBN:0198506732, ISBN:0716731363, ISBN:0815316194] synonym: "type IV intermediate filament" EXACT [] xref: NIF_Subcellular:sao1316272517 xref: Wikipedia:Neurofilament is_a: GO:0033267 ! axon part intersection_of: part_of GO:0030424 ! axon relationship: part_of GO:0060053 ! neurofilament cytoskeleton [Term] id: GO:0006306 name: DNA methylation namespace: biological_process def: "The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine." [GOC:ems, ISBN:0198506732] subset: gosubset_prok xref: Wikipedia:DNA_methylation is_a: GO:0040029 ! regulation of gene expression, epigenetic [Term] id: GO:0006342 name: chromatin silencing namespace: biological_process alt_id: GO:0016440 def: "Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin." [GOC:mah, PMID:10219245] comment: Note that this process is the opposite of chromatin-mediated maintenance of transcription. This regulation is exemplified by members of the Polycomb group, which maintain the inactive state of homeotic gene transcription. synonym: "chromatin-mediated maintenance of transcriptional inactivation" EXACT [] synonym: "chromatin-mediated silencing" EXACT [] synonym: "heterochromatic silencing" RELATED [] synonym: "TGS" EXACT [] synonym: "transcriptional gene silencing" EXACT [] is_a: GO:0016458 ! gene silencing is_a: GO:0045814 ! negative regulation of gene expression, epigenetic is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent [Term] id: GO:0006343 name: establishment of chromatin silencing namespace: biological_process def: "The initial formation of a transcriptionally silent chromatin structure such as heterochromatin." [GOC:mah] synonym: "establishment of heterochromatic silencing" RELATED [] relationship: part_of GO:0006342 ! chromatin silencing [Term] id: GO:0006344 name: maintenance of chromatin silencing namespace: biological_process def: "The maintenance of chromatin in a transcriptionally silent state such as heterochromatin." [GOC:mah] synonym: "maintenance of heterochromatic silencing" RELATED [] relationship: part_of GO:0006342 ! chromatin silencing [Term] id: GO:0006346 name: methylation-dependent chromatin silencing namespace: biological_process def: "Repression of transcription by methylation of DNA, leading to the formation of heterochromatin." [GOC:mah] synonym: "methylation-dependent heterochromatic silencing" EXACT [] is_a: GO:0006342 ! chromatin silencing [Term] id: GO:0006348 name: chromatin silencing at telomere namespace: biological_process def: "Repression of transcription of telomeric DNA by altering the structure of chromatin." [PMID:10219245] synonym: "heterochromatic silencing at telomere" EXACT [] synonym: "telomere chromatin silencing" EXACT [GOC:mah] synonym: "telomeric silencing" EXACT [GOC:bf] is_a: GO:0006342 ! chromatin silencing [Term] id: GO:0006349 name: regulation of gene expression by genetic imprinting namespace: biological_process def: "Heritable alterations in the activity of a gene that depend on whether it passed through the paternal or the maternal germline, but that are not encoded by DNA itself." [GOC:ems, ISBN:0198506732, PMID:11498578] synonym: "regulation of gene expression by DNA imprinting" EXACT [GOC:mah] xref: Wikipedia:Genomic_imprinting is_a: GO:0040029 ! regulation of gene expression, epigenetic intersection_of: results_in GO:0010468 ! regulation of gene expression [Term] id: GO:0006351 name: transcription, DNA-dependent namespace: biological_process alt_id: GO:0006350 alt_id: GO:0061018 alt_id: GO:0061022 def: "The cellular synthesis of RNA on a template of DNA." [GOC:jl, GOC:txnOH] subset: goslim_aspergillus subset: goslim_metagenomics subset: goslim_pombe subset: gosubset_prok synonym: "cellular transcription" BROAD [] synonym: "cellular transcription, DNA-dependent" EXACT [] synonym: "DNA-dependent transcription" EXACT [] synonym: "transcription" BROAD [] synonym: "transcription regulator activity" RELATED [] xref: Wikipedia:Transcription_(genetics) relationship: part_of GO:0010467 ! gene expression [Term] id: GO:0006352 name: DNA-dependent transcription, initiation namespace: biological_process def: "Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription." [GOC:jid, GOC:txnOH, PMID:18280161] comment: Note that promoter clearance is represented as a separate step, not part_of either initiation or elongation. subset: goslim_yeast subset: gosubset_prok synonym: "DNA-dependent RNA polymerase complex assembly at promoter" EXACT [] synonym: "initiation of DNA-dependent transcription" EXACT [GOC:jh2] synonym: "initiation of transcription, DNA-dependent" EXACT [GOC:mah] synonym: "transcription initiation factor activity" RELATED [] synonym: "transcription initiation, DNA-dependent" RELATED [GOC:jh2] relationship: part_of GO:0006351 ! transcription, DNA-dependent [Term] id: GO:0006353 name: DNA-dependent transcription, termination namespace: biological_process def: "The cellular process that completes DNA-dependent transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA." [GOC:txnOH, ISBN:0716720094, PMID:15020047, PMID:18280161] subset: goslim_yeast subset: gosubset_prok synonym: "termination of DNA-dependent transcription" EXACT [GOC:jh2] synonym: "termination of transcription, DNA-dependent" EXACT [GOC:mah] synonym: "transcription termination factor activity" RELATED [] synonym: "transcription termination, DNA-dependent" RELATED [GOC:jh2] synonym: "transcriptional complex disassembly" BROAD [] relationship: part_of GO:0006351 ! transcription, DNA-dependent [Term] id: GO:0006354 name: DNA-dependent transcription, elongation namespace: biological_process def: "The extension of an RNA molecule after transcription initiation and promoter clearance at a DNA-dependent RNA polymerase promoter by the addition of ribonucleotides catalyzed by an RNA polymerase." [GOC:mah, GOC:txnOH, PMID:15020047, PMID:18280161] subset: goslim_pir subset: goslim_yeast subset: gosubset_prok synonym: "RNA elongation" BROAD [] synonym: "transcription elongation, DNA-dependent" EXACT [GOC:jh2] synonym: "transcriptional elongation, DNA-dependent" EXACT [] relationship: part_of GO:0006351 ! transcription, DNA-dependent [Term] id: GO:0006355 name: regulation of transcription, DNA-dependent namespace: biological_process alt_id: GO:0032583 alt_id: GO:0045449 alt_id: GO:0061019 def: "Any process that modulates the frequency, rate or extent of cellular DNA-dependent transcription." [GOC:go_curators, GOC:txnOH] subset: goslim_pombe subset: gosubset_prok synonym: "regulation of cellular transcription, DNA-dependent" EXACT [] synonym: "regulation of gene-specific transcription" RELATED [] synonym: "transcriptional control" BROAD [] is_a: GO:0010468 ! regulation of gene expression intersection_of: regulates GO:0006351 ! transcription, DNA-dependent relationship: regulates GO:0006351 ! transcription, DNA-dependent [Term] id: GO:0006356 name: regulation of transcription from RNA polymerase I promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase I promoter." [GOC:go_curators] synonym: "regulation of transcription from Pol I promoter" EXACT [] is_a: GO:0006355 ! regulation of transcription, DNA-dependent intersection_of: regulates GO:0006360 ! transcription from RNA polymerase I promoter relationship: regulates GO:0006360 ! transcription from RNA polymerase I promoter [Term] id: GO:0006357 name: regulation of transcription from RNA polymerase II promoter namespace: biological_process alt_id: GO:0006358 alt_id: GO:0010551 def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:go_curators, GOC:txnOH] synonym: "global transcription regulation from Pol II promoter" RELATED [] synonym: "regulation of gene-specific transcription from RNA polymerase II promoter" RELATED [] synonym: "regulation of global transcription from Pol II promoter" RELATED [] synonym: "regulation of transcription from Pol II promoter" EXACT [] synonym: "regulation of transcription from RNA polymerase II promoter, global" RELATED [] is_a: GO:0006355 ! regulation of transcription, DNA-dependent intersection_of: regulates GO:0006366 ! transcription from RNA polymerase II promoter relationship: regulates GO:0006366 ! transcription from RNA polymerase II promoter [Term] id: GO:0006359 name: regulation of transcription from RNA polymerase III promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA ploymerase III promoter." [GOC:go_curators] synonym: "regulation of transcription from Pol III promoter" EXACT [] is_a: GO:0006355 ! regulation of transcription, DNA-dependent intersection_of: regulates GO:0006383 ! transcription from RNA polymerase III promoter relationship: regulates GO:0006383 ! transcription from RNA polymerase III promoter [Term] id: GO:0006360 name: transcription from RNA polymerase I promoter namespace: biological_process def: "The synthesis of RNA from a DNA template by RNA polymerase I (RNAP I), originating at an RNAP I promoter." [GOC:jl, GOC:txnOH] subset: goslim_yeast synonym: "RNA polymerase I transcription factor activity" RELATED [] synonym: "transcription from Pol I promoter" EXACT [] xref: Reactome:REACT_100735 "RNA Polymerase I Transcription, Mus musculus" xref: Reactome:REACT_100886 "RNA Polymerase I Transcription, Xenopus tropicalis" xref: Reactome:REACT_110611 "RNA Polymerase I Transcription, Saccharomyces cerevisiae" xref: Reactome:REACT_110625 "RNA Polymerase I Transcription, Drosophila melanogaster" xref: Reactome:REACT_1309 "RNA Polymerase I Transcription, Homo sapiens" xref: Reactome:REACT_28615 "RNA Polymerase I Transcription, Taeniopygia guttata" xref: Reactome:REACT_28661 "RNA Polymerase I Transcription, Canis familiaris" xref: Reactome:REACT_30029 "RNA Polymerase I Transcription, Caenorhabditis elegans" xref: Reactome:REACT_31383 "RNA Polymerase I Transcription, Gallus gallus" xref: Reactome:REACT_32101 "RNA Polymerase I Transcription, Bos taurus" xref: Reactome:REACT_39475 "RNA Polymerase I Transcription, Rattus norvegicus" xref: Reactome:REACT_77153 "RNA Polymerase I Transcription, Sus scrofa" xref: Reactome:REACT_78975 "RNA Polymerase I Transcription, Danio rerio" xref: Reactome:REACT_84230 "RNA Polymerase I Transcription, Oryza sativa" xref: Reactome:REACT_92088 "RNA Polymerase I Transcription, Dictyostelium discoideum" xref: Reactome:REACT_95034 "RNA Polymerase I Transcription, Schizosaccharomyces pombe" xref: Reactome:REACT_95463 "RNA Polymerase I Transcription, Arabidopsis thaliana" is_a: GO:0006351 ! transcription, DNA-dependent [Term] id: GO:0006361 name: transcription initiation from RNA polymerase I promoter namespace: biological_process def: "Any process involved in the assembly of the RNA polymerase I preinitiation complex (PIC) at an RNA polymerase I promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription." [GOC:mah, GOC:txnOH] comment: Note that promoter clearance is represented as a separate step, not part_of either initiation or elongation. synonym: "transcription initiation from Pol I promoter" EXACT [] xref: Reactome:REACT_102820 "RNA Polymerase I Promoter Escape, Danio rerio" xref: Reactome:REACT_103321 "RNA Polymerase I Promoter Opening, Xenopus tropicalis" xref: Reactome:REACT_104294 "RNA Polymerase I Promoter Clearance, Gallus gallus" xref: Reactome:REACT_104732 "RNA Polymerase I Transcription Initiation, Arabidopsis thaliana" xref: Reactome:REACT_107761 "RNA Polymerase I Promoter Opening, Bos taurus" xref: Reactome:REACT_108121 "RNA Polymerase I Promoter Clearance, Xenopus tropicalis" xref: Reactome:REACT_108556 "RNA Polymerase I Promoter Clearance, Dictyostelium discoideum" xref: Reactome:REACT_109608 "RNA Polymerase I Promoter Clearance, Danio rerio" xref: Reactome:REACT_109713 "RNA Polymerase I Promoter Opening, Canis familiaris" xref: Reactome:REACT_109923 "RNA Polymerase I Transcription Initiation, Bos taurus" xref: Reactome:REACT_110381 "RNA Polymerase I Promoter Clearance, Mus musculus" xref: Reactome:REACT_112001 "RNA Polymerase I Promoter Escape, Oryza sativa" xref: Reactome:REACT_112095 "RNA Polymerase I Promoter Opening, Rattus norvegicus" xref: Reactome:REACT_113247 "RNA Polymerase I Promoter Escape, Gallus gallus" xref: Reactome:REACT_114933 "RNA Polymerase I Promoter Escape, Rattus norvegicus" xref: Reactome:REACT_1913 "RNA Polymerase I Promoter Escape, Homo sapiens" xref: Reactome:REACT_1974 "RNA Polymerase I Promoter Clearance, Homo sapiens" xref: Reactome:REACT_2232 "RNA Polymerase I Promoter Opening, Homo sapiens" xref: Reactome:REACT_28247 "RNA Polymerase I Transcription Initiation, Sus scrofa" xref: Reactome:REACT_28672 "RNA Polymerase I Promoter Clearance, Sus scrofa" xref: Reactome:REACT_29421 "RNA Polymerase I Promoter Escape, Taeniopygia guttata" xref: Reactome:REACT_32043 "RNA Polymerase I Promoter Clearance, Oryza sativa" xref: Reactome:REACT_32220 "RNA Polymerase I Promoter Clearance, Canis familiaris" xref: Reactome:REACT_32256 "RNA Polymerase I Transcription Initiation, Taeniopygia guttata" xref: Reactome:REACT_32967 "RNA Polymerase I Promoter Clearance, Arabidopsis thaliana" xref: Reactome:REACT_33565 "RNA Polymerase I Promoter Opening, Danio rerio" xref: Reactome:REACT_52895 "RNA Polymerase I Promoter Clearance, Caenorhabditis elegans" xref: Reactome:REACT_70483 "RNA Polymerase I Transcription Initiation, Mus musculus" xref: Reactome:REACT_78359 "RNA Polymerase I Promoter Escape, Caenorhabditis elegans" xref: Reactome:REACT_78467 "RNA Polymerase I Transcription Initiation, Dictyostelium discoideum" xref: Reactome:REACT_78822 "RNA Polymerase I Transcription Initiation, Drosophila melanogaster" xref: Reactome:REACT_80187 "RNA Polymerase I Transcription Initiation, Xenopus tropicalis" xref: Reactome:REACT_80295 "RNA Polymerase I Promoter Opening, Sus scrofa" xref: Reactome:REACT_80486 "RNA Polymerase I Promoter Clearance, Drosophila melanogaster" xref: Reactome:REACT_82342 "RNA Polymerase I Promoter Clearance, Schizosaccharomyces pombe" xref: Reactome:REACT_82716 "RNA Polymerase I Transcription Initiation, Caenorhabditis elegans" xref: Reactome:REACT_84081 "RNA Polymerase I Transcription Initiation, Schizosaccharomyces pombe" xref: Reactome:REACT_85798 "RNA Polymerase I Transcription Initiation, Canis familiaris" xref: Reactome:REACT_86090 "RNA Polymerase I Promoter Opening, Mus musculus" xref: Reactome:REACT_86119 "RNA Polymerase I Promoter Opening, Taeniopygia guttata" xref: Reactome:REACT_86887 "RNA Polymerase I Transcription Initiation, Oryza sativa" xref: Reactome:REACT_88016 "RNA Polymerase I Promoter Clearance, Rattus norvegicus" xref: Reactome:REACT_88842 "RNA Polymerase I Transcription Initiation, Saccharomyces cerevisiae" xref: Reactome:REACT_89345 "RNA Polymerase I Promoter Clearance, Saccharomyces cerevisiae" xref: Reactome:REACT_89969 "RNA Polymerase I Transcription Initiation, Rattus norvegicus" xref: Reactome:REACT_90628 "RNA Polymerase I Transcription Initiation, Danio rerio" xref: Reactome:REACT_90876 "RNA Polymerase I Transcription Initiation, Gallus gallus" xref: Reactome:REACT_91155 "RNA Polymerase I Promoter Escape, Mus musculus" xref: Reactome:REACT_92356 "RNA Polymerase I Promoter Clearance, Bos taurus" xref: Reactome:REACT_94173 "RNA Polymerase I Promoter Escape, Drosophila melanogaster" xref: Reactome:REACT_953 "RNA Polymerase I Transcription Initiation, Homo sapiens" xref: Reactome:REACT_97336 "RNA Polymerase I Promoter Escape, Schizosaccharomyces pombe" xref: Reactome:REACT_97424 "RNA Polymerase I Promoter Clearance, Taeniopygia guttata" xref: Reactome:REACT_97947 "RNA Polymerase I Promoter Escape, Xenopus tropicalis" is_a: GO:0006352 ! DNA-dependent transcription, initiation relationship: part_of GO:0006360 ! transcription from RNA polymerase I promoter [Term] id: GO:0006362 name: transcription elongation from RNA polymerase I promoter namespace: biological_process def: "The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase I specific promoter by the addition of ribonucleotides catalyzed by RNA polymerase I." [GOC:mah, GOC:txnOH] synonym: "RNA elongation from Pol I promoter" EXACT [] synonym: "RNA polymerase I transcription elongation factor activity" RELATED [] xref: Reactome:REACT_100733 "RNA Polymerase I Chain Elongation, Caenorhabditis elegans" xref: Reactome:REACT_105916 "RNA Polymerase I Chain Elongation, Canis familiaris" xref: Reactome:REACT_112721 "RNA Polymerase I Chain Elongation, Oryza sativa" xref: Reactome:REACT_115044 "RNA Polymerase I Chain Elongation, Gallus gallus" xref: Reactome:REACT_2204 "RNA Polymerase I Chain Elongation, Homo sapiens" xref: Reactome:REACT_28877 "RNA Polymerase I Chain Elongation, Schizosaccharomyces pombe" xref: Reactome:REACT_79758 "RNA Polymerase I Chain Elongation, Xenopus tropicalis" xref: Reactome:REACT_80680 "RNA Polymerase I Chain Elongation, Taeniopygia guttata" xref: Reactome:REACT_81860 "RNA Polymerase I Chain Elongation, Rattus norvegicus" xref: Reactome:REACT_85058 "RNA Polymerase I Chain Elongation, Mus musculus" xref: Reactome:REACT_86256 "RNA Polymerase I Chain Elongation, Drosophila melanogaster" xref: Reactome:REACT_88778 "RNA Polymerase I Chain Elongation, Danio rerio" xref: Reactome:REACT_89996 "RNA Polymerase I Chain Elongation, Sus scrofa" xref: Reactome:REACT_90748 "RNA Polymerase I Chain Elongation, Bos taurus" is_a: GO:0006354 ! DNA-dependent transcription, elongation relationship: part_of GO:0006360 ! transcription from RNA polymerase I promoter [Term] id: GO:0006363 name: termination of RNA polymerase I transcription namespace: biological_process alt_id: GO:0019223 def: "The process in which the synthesis of an RNA molecule by RNA polymerase I using a DNA template is completed. RNAP I termination requires binding of a terminator protein so specific sequences downstream of the transcription unit." [GOC:mah, GOC:txnOH, PMID:10684922] synonym: "RNA polymerase I transcription termination" EXACT [] synonym: "RNA polymerase I transcription termination factor activity" RELATED [] synonym: "transcription termination from Pol I promoter" EXACT [] synonym: "transcription termination from RNA polymerase I promoter" EXACT [] xref: Reactome:REACT_101118 "RNA Polymerase I Transcription Termination, Danio rerio" xref: Reactome:REACT_104744 "RNA Polymerase I Transcription Termination, Canis familiaris" xref: Reactome:REACT_1074 "RNA Polymerase I Transcription Termination, Homo sapiens" xref: Reactome:REACT_113509 "RNA Polymerase I Transcription Termination, Gallus gallus" xref: Reactome:REACT_32721 "RNA Polymerase I Transcription Termination, Taeniopygia guttata" xref: Reactome:REACT_78534 "RNA Polymerase I Transcription Termination, Mus musculus" xref: Reactome:REACT_80987 "RNA Polymerase I Transcription Termination, Bos taurus" xref: Reactome:REACT_86818 "RNA Polymerase I Transcription Termination, Oryza sativa" xref: Reactome:REACT_87748 "RNA Polymerase I Transcription Termination, Arabidopsis thaliana" xref: Reactome:REACT_89655 "RNA Polymerase I Transcription Termination, Rattus norvegicus" xref: Reactome:REACT_89930 "RNA Polymerase I Transcription Termination, Sus scrofa" xref: Reactome:REACT_98009 "RNA Polymerase I Transcription Termination, Xenopus tropicalis" is_a: GO:0006353 ! DNA-dependent transcription, termination relationship: part_of GO:0006360 ! transcription from RNA polymerase I promoter [Term] id: GO:0006364 name: rRNA processing namespace: biological_process alt_id: GO:0006365 def: "Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules." [GOC:curators] subset: goslim_yeast subset: gosubset_prok synonym: "35S primary transcript processing" NARROW [] is_a: GO:0034470 ! ncRNA processing [Term] id: GO:0006366 name: transcription from RNA polymerase II promoter namespace: biological_process alt_id: GO:0032568 alt_id: GO:0032569 def: "The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs)." [GOC:jl, GOC:txnOH, ISBN:0321000382] subset: goslim_yeast synonym: "gene-specific transcription from RNA polymerase II promoter" RELATED [] synonym: "general transcription from RNA polymerase II promoter" RELATED [] synonym: "RNA polymerase II transcription factor activity" RELATED [] synonym: "specific transcription from RNA polymerase II promoter" RELATED [GOC:mah] synonym: "transcription from Pol II promoter" EXACT [] xref: Reactome:REACT_105738 "RNA Polymerase II Transcription, Bos taurus" xref: Reactome:REACT_106213 "RNA Polymerase II Transcription, Caenorhabditis elegans" xref: Reactome:REACT_108012 "RNA Polymerase II Transcription, Canis familiaris" xref: Reactome:REACT_109421 "RNA Polymerase II Transcription, Xenopus tropicalis" xref: Reactome:REACT_1366 "RNA Polymerase II Transcription, Homo sapiens" xref: Reactome:REACT_31558 "RNA Polymerase II Transcription, Taeniopygia guttata" xref: Reactome:REACT_32943 "RNA Polymerase II Transcription, Danio rerio" xref: Reactome:REACT_33538 "RNA Polymerase II Transcription, Rattus norvegicus" xref: Reactome:REACT_33583 "RNA Polymerase II Transcription, Sus scrofa" xref: Reactome:REACT_34720 "RNA Polymerase II Transcription, Schizosaccharomyces pombe" xref: Reactome:REACT_79747 "RNA Polymerase II Transcription, Plasmodium falciparum" xref: Reactome:REACT_89454 "RNA Polymerase II Transcription, Oryza sativa" xref: Reactome:REACT_89916 "RNA Polymerase II Transcription, Mus musculus" xref: Reactome:REACT_97471 "RNA Polymerase II Transcription, Arabidopsis thaliana" xref: Reactome:REACT_97536 "RNA Polymerase II Transcription, Gallus gallus" xref: Reactome:REACT_99228 "RNA Polymerase II Transcription, Drosophila melanogaster" xref: Reactome:REACT_99748 "RNA Polymerase II Transcription, Dictyostelium discoideum" xref: Reactome:REACT_99950 "RNA Polymerase II Transcription, Saccharomyces cerevisiae" is_a: GO:0006351 ! transcription, DNA-dependent [Term] id: GO:0006367 name: transcription initiation from RNA polymerase II promoter namespace: biological_process def: "Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription." [GOC:mah, GOC:txnOH] comment: Note that promoter clearance is represented as a separate step, not part_of either initiation or elongation. synonym: "transcription initiation from Pol II promoter" EXACT [] xref: Reactome:REACT_100392 "RNA Polymerase II Transcription Initiation, Dictyostelium discoideum" xref: Reactome:REACT_101175 "RNA Polymerase II Transcription Initiation, Canis familiaris" xref: Reactome:REACT_101341 "RNA Polymerase II Transcription Initiation, Danio rerio" xref: Reactome:REACT_102266 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Canis familiaris" xref: Reactome:REACT_103457 "RNA Polymerase II Transcription Initiation, Mus musculus" xref: Reactome:REACT_104036 "RNA Polymerase II Transcription Initiation, Drosophila melanogaster" xref: Reactome:REACT_104646 "RNA Polymerase II Transcription Initiation, Caenorhabditis elegans" xref: Reactome:REACT_104707 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Danio rerio" xref: Reactome:REACT_105389 "RNA Polymerase II Transcription Initiation, Oryza sativa" xref: Reactome:REACT_1655 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Homo sapiens" xref: Reactome:REACT_1851 "RNA Polymerase II Transcription Initiation, Homo sapiens" xref: Reactome:REACT_28862 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Oryza sativa" xref: Reactome:REACT_31702 "RNA Polymerase II Transcription Initiation, Gallus gallus" xref: Reactome:REACT_32920 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Bos taurus" xref: Reactome:REACT_6332 "HIV-1 Transcription Initiation, Homo sapiens" xref: Reactome:REACT_77736 "RNA Polymerase II Transcription Initiation, Xenopus tropicalis" xref: Reactome:REACT_79444 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Drosophila melanogaster" xref: Reactome:REACT_79812 "RNA Polymerase II Transcription Initiation, Rattus norvegicus" xref: Reactome:REACT_80956 "RNA Polymerase II Transcription Initiation, Schizosaccharomyces pombe" xref: Reactome:REACT_81703 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Dictyostelium discoideum" xref: Reactome:REACT_82794 "RNA Polymerase II Transcription Initiation, Bos taurus" xref: Reactome:REACT_83749 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Saccharomyces cerevisiae" xref: Reactome:REACT_84134 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Mus musculus" xref: Reactome:REACT_85783 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Schizosaccharomyces pombe" xref: Reactome:REACT_85917 "RNA Polymerase II Transcription Initiation, Taeniopygia guttata" xref: Reactome:REACT_85990 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Xenopus tropicalis" xref: Reactome:REACT_87429 "RNA Polymerase II Transcription Initiation, Saccharomyces cerevisiae" xref: Reactome:REACT_87559 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Caenorhabditis elegans" xref: Reactome:REACT_88340 "RNA Polymerase II Transcription Initiation, Arabidopsis thaliana" xref: Reactome:REACT_88353 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Gallus gallus" xref: Reactome:REACT_92769 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Rattus norvegicus" xref: Reactome:REACT_95808 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Taeniopygia guttata" xref: Reactome:REACT_98915 "RNA Polymerase II Transcription Pre-Initiation And Promoter Opening, Arabidopsis thaliana" is_a: GO:0006352 ! DNA-dependent transcription, initiation relationship: part_of GO:0006366 ! transcription from RNA polymerase II promoter [Term] id: GO:0006368 name: transcription elongation from RNA polymerase II promoter namespace: biological_process def: "The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II." [GOC:mah, GOC:txnOH] synonym: "RNA elongation from Pol II promoter" EXACT [] synonym: "RNA polymerase II transcription elongation factor activity" RELATED [] xref: Reactome:REACT_100066 "RNA Polymerase II Transcription Elongation, Rattus norvegicus" xref: Reactome:REACT_100727 "Formation of the Early Elongation Complex, Gallus gallus" xref: Reactome:REACT_101279 "Formation of the Early Elongation Complex, Caenorhabditis elegans" xref: Reactome:REACT_101816 "Formation of the Early Elongation Complex, Schizosaccharomyces pombe" xref: Reactome:REACT_104824 "RNA Polymerase II Promoter Escape, Xenopus tropicalis" xref: Reactome:REACT_104937 "RNA Polymerase II Transcription Elongation, Mus musculus" xref: Reactome:REACT_106139 "RNA Polymerase II Promoter Escape, Danio rerio" xref: Reactome:REACT_106149 "RNA Polymerase II Promoter Escape, Oryza sativa" xref: Reactome:REACT_107633 "RNA Polymerase II Transcription Elongation, Arabidopsis thaliana" xref: Reactome:REACT_107789 "RNA Polymerase II Promoter Escape, Saccharomyces cerevisiae" xref: Reactome:REACT_108831 "Formation of RNA Pol II elongation complex, Xenopus tropicalis" xref: Reactome:REACT_109274 "RNA Polymerase II Promoter Escape, Caenorhabditis elegans" xref: Reactome:REACT_109291 "Formation of the Early Elongation Complex, Mus musculus" xref: Reactome:REACT_110182 "Formation of RNA Pol II elongation complex, Mus musculus" xref: Reactome:REACT_110507 "RNA Polymerase II Transcription Elongation, Danio rerio" xref: Reactome:REACT_112408 "Formation of RNA Pol II elongation complex, Drosophila melanogaster" xref: Reactome:REACT_112630 "Formation of RNA Pol II elongation complex, Schizosaccharomyces pombe" xref: Reactome:REACT_113325 "Formation of RNA Pol II elongation complex, Caenorhabditis elegans" xref: Reactome:REACT_115524 "Formation of RNA Pol II elongation complex, Danio rerio" xref: Reactome:REACT_1845 "Formation of RNA Pol II elongation complex, Homo sapiens" xref: Reactome:REACT_2089 "RNA Polymerase II Promoter Escape, Homo sapiens" xref: Reactome:REACT_28524 "Formation of RNA Pol II elongation complex, Bos taurus" xref: Reactome:REACT_28692 "Formation of the Early Elongation Complex, Danio rerio" xref: Reactome:REACT_28768 "RNA Polymerase II Transcription Elongation, Xenopus tropicalis" xref: Reactome:REACT_29367 "RNA Polymerase II Transcription Elongation, Taeniopygia guttata" xref: Reactome:REACT_29380 "Formation of the Early Elongation Complex, Arabidopsis thaliana" xref: Reactome:REACT_31308 "Formation of the Early Elongation Complex, Rattus norvegicus" xref: Reactome:REACT_31396 "RNA Polymerase II Promoter Escape, Mus musculus" xref: Reactome:REACT_31533 "RNA Polymerase II Transcription Elongation, Canis familiaris" xref: Reactome:REACT_32311 "RNA Polymerase II Transcription Elongation, Bos taurus" xref: Reactome:REACT_32712 "Formation of RNA Pol II elongation complex, Canis familiaris" xref: Reactome:REACT_32829 "RNA Polymerase II Promoter Escape, Arabidopsis thaliana" xref: Reactome:REACT_55595 "RNA Polymerase II Promoter Escape, Schizosaccharomyces pombe" xref: Reactome:REACT_6274 "HIV-1 Transcription Elongation, Homo sapiens" xref: Reactome:REACT_66965 "RNA Polymerase II Promoter Escape, Dictyostelium discoideum" xref: Reactome:REACT_77610 "RNA Polymerase II Promoter Escape, Bos taurus" xref: Reactome:REACT_78366 "Formation of RNA Pol II elongation complex, Rattus norvegicus" xref: Reactome:REACT_81662 "RNA Polymerase II Promoter Escape, Drosophila melanogaster" xref: Reactome:REACT_81750 "RNA Polymerase II Transcription Elongation, Saccharomyces cerevisiae" xref: Reactome:REACT_81845 "RNA Polymerase II Promoter Escape, Rattus norvegicus" xref: Reactome:REACT_833 "RNA Polymerase II Transcription Elongation, Homo sapiens" xref: Reactome:REACT_83871 "Formation of the Early Elongation Complex, Dictyostelium discoideum" xref: Reactome:REACT_84247 "Formation of the Early Elongation Complex, Taeniopygia guttata" xref: Reactome:REACT_84349 "Formation of the Early Elongation Complex, Oryza sativa" xref: Reactome:REACT_846 "Formation of the Early Elongation Complex, Homo sapiens" xref: Reactome:REACT_87946 "RNA Polymerase II Transcription Elongation, Caenorhabditis elegans" xref: Reactome:REACT_89781 "RNA Polymerase II Transcription Elongation, Gallus gallus" xref: Reactome:REACT_90242 "RNA Polymerase II Promoter Escape, Gallus gallus" xref: Reactome:REACT_91644 "Formation of the Early Elongation Complex, Xenopus tropicalis" xref: Reactome:REACT_92647 "Formation of the Early Elongation Complex, Canis familiaris" xref: Reactome:REACT_92836 "RNA Polymerase II Transcription Elongation, Drosophila melanogaster" xref: Reactome:REACT_93156 "Formation of the Early Elongation Complex, Bos taurus" xref: Reactome:REACT_93741 "RNA Polymerase II Transcription Elongation, Schizosaccharomyces pombe" xref: Reactome:REACT_94090 "RNA Polymerase II Transcription Elongation, Oryza sativa" xref: Reactome:REACT_96685 "RNA Polymerase II Promoter Escape, Canis familiaris" xref: Reactome:REACT_97522 "Formation of the Early Elongation Complex, Drosophila melanogaster" xref: Reactome:REACT_99278 "RNA Polymerase II Transcription Elongation, Dictyostelium discoideum" xref: Reactome:REACT_99528 "Formation of the Early Elongation Complex, Saccharomyces cerevisiae" is_a: GO:0006354 ! DNA-dependent transcription, elongation relationship: part_of GO:0006366 ! transcription from RNA polymerase II promoter [Term] id: GO:0006369 name: termination of RNA polymerase II transcription namespace: biological_process alt_id: GO:0019224 def: "The process in which the synthesis of an RNA molecule by RNA polymerase II using a DNA template is completed." [GOC:mah, GOC:txnOH] synonym: "RNA 3'-end formation by RNA polymerase II" EXACT [] synonym: "RNA polymerase II transcription termination" EXACT [] synonym: "RNA polymerase II transcription termination factor activity" RELATED [] synonym: "transcription termination from Pol II promoter" EXACT [] synonym: "transcription termination from RNA polymerase II promoter" EXACT [] xref: Reactome:REACT_102337 "Cleavage of Growing Transcript in the Termination Region, Bos taurus" xref: Reactome:REACT_108223 "RNA Polymerase II Transcription Termination, Gallus gallus" xref: Reactome:REACT_109258 "RNA Polymerase II Transcription Termination, Canis familiaris" xref: Reactome:REACT_112978 "RNA Polymerase II Transcription Termination, Drosophila melanogaster" xref: Reactome:REACT_113157 "RNA Polymerase II Transcription Termination, Arabidopsis thaliana" xref: Reactome:REACT_113171 "Cleavage of Growing Transcript in the Termination Region, Drosophila melanogaster" xref: Reactome:REACT_114593 "Cleavage of Growing Transcript in the Termination Region, Danio rerio" xref: Reactome:REACT_114998 "RNA Polymerase II Transcription Termination, Danio rerio" xref: Reactome:REACT_115466 "Cleavage of Growing Transcript in the Termination Region, Arabidopsis thaliana" xref: Reactome:REACT_33376 "RNA Polymerase II Transcription Termination, Mus musculus" xref: Reactome:REACT_33730 "Cleavage of Growing Transcript in the Termination Region, Caenorhabditis elegans" xref: Reactome:REACT_34293 "Cleavage of Growing Transcript in the Termination Region, Rattus norvegicus" xref: Reactome:REACT_387 "Cleavage of Growing Transcript in the Termination Region, Homo sapiens" xref: Reactome:REACT_53836 "RNA Polymerase II Transcription Termination, Caenorhabditis elegans" xref: Reactome:REACT_6241 "HIV-1 Transcription Termination, Human immunodeficiency virus 1" xref: Reactome:REACT_86797 "RNA Polymerase II Transcription Termination, Xenopus tropicalis" xref: Reactome:REACT_894 "RNA Polymerase II Transcription Termination, Homo sapiens" xref: Reactome:REACT_89456 "Cleavage of Growing Transcript in the Termination Region, Taeniopygia guttata" xref: Reactome:REACT_89598 "RNA Polymerase II Transcription Termination, Bos taurus" xref: Reactome:REACT_92795 "Cleavage of Growing Transcript in the Termination Region, Mus musculus" xref: Reactome:REACT_94319 "Cleavage of Growing Transcript in the Termination Region, Xenopus tropicalis" xref: Reactome:REACT_95051 "RNA Polymerase II Transcription Termination, Taeniopygia guttata" xref: Reactome:REACT_97415 "Cleavage of Growing Transcript in the Termination Region, Gallus gallus" xref: Reactome:REACT_97704 "Cleavage of Growing Transcript in the Termination Region, Canis familiaris" xref: Reactome:REACT_99283 "RNA Polymerase II Transcription Termination, Rattus norvegicus" is_a: GO:0006353 ! DNA-dependent transcription, termination relationship: part_of GO:0006366 ! transcription from RNA polymerase II promoter [Term] id: GO:0006370 name: 7-methylguanosine mRNA capping namespace: biological_process def: "Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript." [GOC:mah, PMID:9266685] synonym: "5' end capping" BROAD [] synonym: "5' mRNA capping" EXACT [] synonym: "5'-end mRNA processing" EXACT [] synonym: "5'-end processing" BROAD [] synonym: "mRNA capping" EXACT [GOC:bf, GOC:krc, GOC:mah] xref: Reactome:REACT_101832 "mRNA Capping, Canis familiaris" xref: Reactome:REACT_102770 "mRNA Capping, Saccharomyces cerevisiae" xref: Reactome:REACT_110937 "mRNA Capping, Xenopus tropicalis" xref: Reactome:REACT_114999 "mRNA Capping, Plasmodium falciparum" xref: Reactome:REACT_1470 "mRNA Capping, Homo sapiens" xref: Reactome:REACT_31827 "mRNA Capping, Mus musculus" xref: Reactome:REACT_79473 "mRNA Capping, Taeniopygia guttata" xref: Reactome:REACT_81603 "mRNA Capping, Oryza sativa" xref: Reactome:REACT_84705 "mRNA Capping, Bos taurus" xref: Reactome:REACT_85081 "mRNA Capping, Drosophila melanogaster" xref: Reactome:REACT_85562 "mRNA Capping, Caenorhabditis elegans" xref: Reactome:REACT_85971 "mRNA Capping, Gallus gallus" xref: Reactome:REACT_86299 "mRNA Capping, Rattus norvegicus" xref: Reactome:REACT_87055 "mRNA Capping, Danio rerio" xref: Reactome:REACT_89815 "mRNA Capping, Schizosaccharomyces pombe" xref: Reactome:REACT_93735 "mRNA Capping, Arabidopsis thaliana" xref: Reactome:REACT_95432 "mRNA Capping, Sus scrofa" xref: Reactome:REACT_96579 "mRNA Capping, Dictyostelium discoideum" is_a: GO:0006397 ! mRNA processing is_a: GO:0009452 ! 7-methylguanosine RNA capping [Term] id: GO:0006376 name: mRNA splice site selection namespace: biological_process def: "Selection of a splice site by components of the assembling spliceosome." [GOC:krc, ISBN:0879695897] synonym: "spliceosomal commitment complex biosynthesis" NARROW [] synonym: "spliceosomal commitment complex formation" NARROW [] synonym: "spliceosomal E complex biosynthesis" NARROW [] synonym: "spliceosomal E complex formation" NARROW [] relationship: part_of GO:0000245 ! spliceosomal complex assembly [Term] id: GO:0006378 name: mRNA polyadenylation namespace: biological_process def: "The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript." [ISBN:0198506732] subset: gosubset_prok synonym: "cleavage and polyadenylylation specificity factor activity" NARROW [] synonym: "mRNA polyadenylylation" EXACT [] is_a: GO:0031124 ! mRNA 3'-end processing is_a: GO:0043631 ! RNA polyadenylation [Term] id: GO:0006379 name: mRNA cleavage namespace: biological_process def: "Any process in which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner." [GOC:mah] subset: gosubset_prok synonym: "cleavage and polyadenylylation specificity factor activity" RELATED [] synonym: "cleavage stimulation factor activity" RELATED [] synonym: "pre-mRNA cleavage factor activity" RELATED [] is_a: GO:0006397 ! mRNA processing [Term] id: GO:0006383 name: transcription from RNA polymerase III promoter namespace: biological_process def: "The synthesis of RNA from a DNA template by RNA polymerase III, originating at an RNAP III promoter." [GOC:jl, GOC:txnOH] subset: goslim_yeast subset: gosubset_prok synonym: "RNA polymerase III transcription factor activity" RELATED [] synonym: "transcription from Pol III promoter" EXACT [] xref: Reactome:REACT_100945 "Initiation of RNA Polymerase III Productive Transcription, Schizosaccharomyces pombe" xref: Reactome:REACT_101038 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Rattus norvegicus" xref: Reactome:REACT_101551 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Canis familiaris" xref: Reactome:REACT_101656 "RNA Polymerase III Abortive Initiation At Type 3 Open Promoters, Rattus norvegicus" xref: Reactome:REACT_101661 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Mus musculus" xref: Reactome:REACT_101700 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Sus scrofa" xref: Reactome:REACT_101771 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Gallus gallus" xref: Reactome:REACT_101901 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Danio rerio" xref: Reactome:REACT_102138 "RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters, Bos taurus" xref: Reactome:REACT_102603 "RNA Polymerase III Transcription, Gallus gallus" xref: Reactome:REACT_102683 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Rattus norvegicus" xref: Reactome:REACT_103091 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Caenorhabditis elegans" xref: Reactome:REACT_103169 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Taeniopygia guttata" xref: Reactome:REACT_103226 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Drosophila melanogaster" xref: Reactome:REACT_103412 "RNA Polymerase III Abortive Initiation At Type 3 Open Promoters, Mus musculus" xref: Reactome:REACT_103650 "RNA Polymerase III Transcription, Taeniopygia guttata" xref: Reactome:REACT_103786 "RNA Polymerase III Abortive Initiation At Type 3 Open Promoters, Sus scrofa" xref: Reactome:REACT_104805 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Schizosaccharomyces pombe" xref: Reactome:REACT_105112 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Sus scrofa" xref: Reactome:REACT_105558 "Resumption of RNA Polymerase III Productive Transcription, Dictyostelium discoideum" xref: Reactome:REACT_105661 "RNA Polymerase III Transcription, Schizosaccharomyces pombe" xref: Reactome:REACT_106059 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Caenorhabditis elegans" xref: Reactome:REACT_1061 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Homo sapiens" xref: Reactome:REACT_106142 "Initiation of RNA Polymerase III Productive Transcription, Gallus gallus" xref: Reactome:REACT_106447 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Caenorhabditis elegans" xref: Reactome:REACT_106560 "Initiation of RNA Polymerase III Productive Transcription, Sus scrofa" xref: Reactome:REACT_106688 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Bos taurus" xref: Reactome:REACT_106837 "Resumption of RNA Polymerase III Productive Transcription, Mus musculus" xref: Reactome:REACT_107790 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Taeniopygia guttata" xref: Reactome:REACT_107815 "RNA Polymerase III Transcription, Saccharomyces cerevisiae" xref: Reactome:REACT_108150 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Gallus gallus" xref: Reactome:REACT_108254 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Mus musculus" xref: Reactome:REACT_108736 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Sus scrofa" xref: Reactome:REACT_108779 "Initiation of RNA Polymerase III Productive Transcription, Canis familiaris" xref: Reactome:REACT_109038 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Xenopus tropicalis" xref: Reactome:REACT_109056 "Resumption of RNA Polymerase III Productive Transcription, Schizosaccharomyces pombe" xref: Reactome:REACT_109134 "Initiation of RNA Polymerase III Productive Transcription, Drosophila melanogaster" xref: Reactome:REACT_109293 "RNA Polymerase III Productive Transcription, Mus musculus" xref: Reactome:REACT_109350 "Resumption of RNA Polymerase III Productive Transcription, Drosophila melanogaster" xref: Reactome:REACT_109707 "RNA Polymerase III Productive Transcription, Xenopus tropicalis" xref: Reactome:REACT_109747 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Drosophila melanogaster" xref: Reactome:REACT_109934 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Drosophila melanogaster" xref: Reactome:REACT_109938 "Initiation of RNA Polymerase III Productive Transcription, Oryza sativa" xref: Reactome:REACT_110233 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Taeniopygia guttata" xref: Reactome:REACT_110354 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Drosophila melanogaster" xref: Reactome:REACT_110533 "RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters, Rattus norvegicus" xref: Reactome:REACT_110624 "Initiation of RNA Polymerase III Productive Transcription, Danio rerio" xref: Reactome:REACT_112623 "RNA Polymerase III Abortive Initiation At Type 3 Open Promoters, Drosophila melanogaster" xref: Reactome:REACT_112804 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Dictyostelium discoideum" xref: Reactome:REACT_113692 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Dictyostelium discoideum" xref: Reactome:REACT_114988 "RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters, Drosophila melanogaster" xref: Reactome:REACT_1179 "Initiation of RNA Polymerase III Productive Transcription, Homo sapiens" xref: Reactome:REACT_118261 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Caenorhabditis elegans" xref: Reactome:REACT_118310 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Caenorhabditis elegans" xref: Reactome:REACT_118481 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Caenorhabditis elegans" xref: Reactome:REACT_1241 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Homo sapiens" xref: Reactome:REACT_1371 "RNA Polymerase III Transcription, Homo sapiens" xref: Reactome:REACT_1374 "Resumption of RNA Polymerase III Productive Transcription, Homo sapiens" xref: Reactome:REACT_1616 "RNA Polymerase III Abortive Initiation At Type 3 Open Promoters, Homo sapiens" xref: Reactome:REACT_2178 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Homo sapiens" xref: Reactome:REACT_2210 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Homo sapiens" xref: Reactome:REACT_2248 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Homo sapiens" xref: Reactome:REACT_2251 "RNA Polymerase III Productive Transcription, Homo sapiens" xref: Reactome:REACT_251 "RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters, Homo sapiens" xref: Reactome:REACT_28871 "RNA Polymerase III Productive Transcription, Canis familiaris" xref: Reactome:REACT_28926 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Xenopus tropicalis" xref: Reactome:REACT_29249 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Bos taurus" xref: Reactome:REACT_29589 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Canis familiaris" xref: Reactome:REACT_30206 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Canis familiaris" xref: Reactome:REACT_30383 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Taeniopygia guttata" xref: Reactome:REACT_30530 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Canis familiaris" xref: Reactome:REACT_30710 "RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters, Taeniopygia guttata" xref: Reactome:REACT_30749 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Rattus norvegicus" xref: Reactome:REACT_30852 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Drosophila melanogaster" xref: Reactome:REACT_30868 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Canis familiaris" xref: Reactome:REACT_31576 "Resumption of RNA Polymerase III Productive Transcription, Xenopus tropicalis" xref: Reactome:REACT_31708 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Drosophila melanogaster" xref: Reactome:REACT_32551 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Mus musculus" xref: Reactome:REACT_32580 "RNA Polymerase III Abortive Initiation At Type 3 Open Promoters, Canis familiaris" xref: Reactome:REACT_34048 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Bos taurus" xref: Reactome:REACT_43442 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Bos taurus" xref: Reactome:REACT_50555 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Bos taurus" xref: Reactome:REACT_76991 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Rattus norvegicus" xref: Reactome:REACT_77583 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Gallus gallus" xref: Reactome:REACT_77734 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Rattus norvegicus" xref: Reactome:REACT_77763 "RNA Polymerase III Productive Transcription, Rattus norvegicus" xref: Reactome:REACT_77942 "Initiation of RNA Polymerase III Productive Transcription, Mus musculus" xref: Reactome:REACT_78034 "Resumption of RNA Polymerase III Productive Transcription, Taeniopygia guttata" xref: Reactome:REACT_78101 "Resumption of RNA Polymerase III Productive Transcription, Danio rerio" xref: Reactome:REACT_78330 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Xenopus tropicalis" xref: Reactome:REACT_78526 "RNA Polymerase III Productive Transcription, Taeniopygia guttata" xref: Reactome:REACT_79030 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Rattus norvegicus" xref: Reactome:REACT_79212 "Resumption of RNA Polymerase III Productive Transcription, Rattus norvegicus" xref: Reactome:REACT_79230 "RNA Polymerase III Transcription, Caenorhabditis elegans" xref: Reactome:REACT_796 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Homo sapiens" xref: Reactome:REACT_79674 "RNA Polymerase III Transcription, Xenopus tropicalis" xref: Reactome:REACT_79928 "RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters, Canis familiaris" xref: Reactome:REACT_80506 "RNA Polymerase III Productive Transcription, Gallus gallus" xref: Reactome:REACT_80530 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Danio rerio" xref: Reactome:REACT_80924 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Arabidopsis thaliana" xref: Reactome:REACT_81033 "RNA Polymerase III Productive Transcription, Schizosaccharomyces pombe" xref: Reactome:REACT_81681 "Resumption of RNA Polymerase III Productive Transcription, Canis familiaris" xref: Reactome:REACT_82476 "RNA Polymerase III Productive Transcription, Sus scrofa" xref: Reactome:REACT_82823 "RNA Polymerase III Transcription, Bos taurus" xref: Reactome:REACT_82958 "RNA Polymerase III Transcription, Rattus norvegicus" xref: Reactome:REACT_83072 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Gallus gallus" xref: Reactome:REACT_83162 "Resumption of RNA Polymerase III Productive Transcription, Gallus gallus" xref: Reactome:REACT_83237 "RNA Polymerase III Transcription, Danio rerio" xref: Reactome:REACT_83573 "RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters, Danio rerio" xref: Reactome:REACT_83679 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Mus musculus" xref: Reactome:REACT_83791 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Taeniopygia guttata" xref: Reactome:REACT_84005 "RNA Polymerase III Transcription, Sus scrofa" xref: Reactome:REACT_84052 "RNA Polymerase III Abortive Initiation At Type 3 Open Promoters, Xenopus tropicalis" xref: Reactome:REACT_84174 "RNA Polymerase III Transcription, Canis familiaris" xref: Reactome:REACT_84770 "RNA Polymerase III Transcription, Arabidopsis thaliana" xref: Reactome:REACT_85321 "RNA Polymerase III Abortive Initiation At Type 3 Open Promoters, Gallus gallus" xref: Reactome:REACT_85665 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Danio rerio" xref: Reactome:REACT_85700 "RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters, Sus scrofa" xref: Reactome:REACT_85938 "RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters, Gallus gallus" xref: Reactome:REACT_86188 "Initiation of RNA Polymerase III Productive Transcription, Dictyostelium discoideum" xref: Reactome:REACT_86214 "RNA Polymerase III Productive Transcription, Danio rerio" xref: Reactome:REACT_86477 "Resumption of RNA Polymerase III Productive Transcription, Sus scrofa" xref: Reactome:REACT_86680 "RNA Polymerase III Productive Transcription, Bos taurus" xref: Reactome:REACT_87495 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Danio rerio" xref: Reactome:REACT_88180 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Canis familiaris" xref: Reactome:REACT_88328 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Taeniopygia guttata" xref: Reactome:REACT_89113 "Initiation of RNA Polymerase III Productive Transcription, Bos taurus" xref: Reactome:REACT_89159 "RNA Polymerase III Productive Transcription, Drosophila melanogaster" xref: Reactome:REACT_89744 "RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters, Mus musculus" xref: Reactome:REACT_90232 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Mus musculus" xref: Reactome:REACT_90884 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Sus scrofa" xref: Reactome:REACT_90929 "Initiation of RNA Polymerase III Productive Transcription, Taeniopygia guttata" xref: Reactome:REACT_90945 "Initiation of RNA Polymerase III Productive Transcription, Arabidopsis thaliana" xref: Reactome:REACT_90947 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Danio rerio" xref: Reactome:REACT_91182 "RNA Polymerase III Transcription, Drosophila melanogaster" xref: Reactome:REACT_91223 "RNA Polymerase III Abortive Initiation At Type 3 Open Promoters, Taeniopygia guttata" xref: Reactome:REACT_91433 "Initiation of RNA Polymerase III Productive Transcription, Rattus norvegicus" xref: Reactome:REACT_92510 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Bos taurus" xref: Reactome:REACT_92565 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Gallus gallus" xref: Reactome:REACT_92674 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Sus scrofa" xref: Reactome:REACT_92814 "RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters, Xenopus tropicalis" xref: Reactome:REACT_92970 "RNA Polymerase III Transcription, Oryza sativa" xref: Reactome:REACT_93003 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Xenopus tropicalis" xref: Reactome:REACT_93041 "RNA Polymerase III Productive Transcription, Oryza sativa" xref: Reactome:REACT_93262 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Oryza sativa" xref: Reactome:REACT_93305 "Resumption of RNA Polymerase III Productive Transcription, Arabidopsis thaliana" xref: Reactome:REACT_93548 "RNA Polymerase III Transcription, Dictyostelium discoideum" xref: Reactome:REACT_93709 "RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites, Dictyostelium discoideum" xref: Reactome:REACT_93754 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Gallus gallus" xref: Reactome:REACT_93859 "RNA Polymerase III Productive Transcription, Arabidopsis thaliana" xref: Reactome:REACT_94189 "RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters, Xenopus tropicalis" xref: Reactome:REACT_94421 "RNA Polymerase III Transcription, Mus musculus" xref: Reactome:REACT_94567 "RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters, Xenopus tropicalis" xref: Reactome:REACT_94753 "Resumption of RNA Polymerase III Productive Transcription, Oryza sativa" xref: Reactome:REACT_96798 "Resumption of RNA Polymerase III Productive Transcription, Caenorhabditis elegans" xref: Reactome:REACT_97406 "Initiation of RNA Polymerase III Productive Transcription, Xenopus tropicalis" xref: Reactome:REACT_97559 "RNA Polymerase III Abortive Initiation At Type 2 Open Promoters, Sus scrofa" xref: Reactome:REACT_98079 "RNA Polymerase III Productive Transcription, Dictyostelium discoideum" xref: Reactome:REACT_98254 "RNA Polymerase III Abortive Initiation At Type 3 Open Promoters, Bos taurus" xref: Reactome:REACT_98466 "RNA Polymerase III Abortive Initiation At Type 3 Open Promoters, Danio rerio" xref: Reactome:REACT_98470 "Resumption of RNA Polymerase III Productive Transcription, Bos taurus" xref: Reactome:REACT_98660 "RNA Polymerase III Abortive Initiation At Type 1 Open Promoters, Mus musculus" xref: Reactome:REACT_98770 "RNA Polymerase III Productive Transcription, Caenorhabditis elegans" xref: Reactome:REACT_99332 "RNA Polymerase III Promoter Opening at Type 1 Promoters, Danio rerio" xref: Reactome:REACT_99492 "Initiation of RNA Polymerase III Productive Transcription, Caenorhabditis elegans" is_a: GO:0006351 ! transcription, DNA-dependent [Term] id: GO:0006384 name: transcription initiation from RNA polymerase III promoter namespace: biological_process def: "Any process involved in the assembly of the RNA polymerase III preinitiation complex (PIC) at an RNA polymerase III promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription." [GOC:mah, GOC:txnOH] comment: Note that promoter clearance is represented as a separate step, not part_of either initiation or elongation. synonym: "transcription initiation from Pol III promoter" EXACT [] is_a: GO:0006352 ! DNA-dependent transcription, initiation relationship: part_of GO:0006383 ! transcription from RNA polymerase III promoter [Term] id: GO:0006385 name: transcription elongation from RNA polymerase III promoter namespace: biological_process def: "The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase III promoter by the addition of ribonucleotides catalyzed by RNA polymerase III." [GOC:mah, GOC:txnOH] synonym: "RNA elongation from Pol III promoter" EXACT [] synonym: "RNA polymerase III transcription elongation factor activity" RELATED [] xref: Reactome:REACT_100029 "RNA Polymerase III Chain Elongation, Danio rerio" xref: Reactome:REACT_104942 "RNA Polymerase III Chain Elongation, Caenorhabditis elegans" xref: Reactome:REACT_109063 "RNA Polymerase III Chain Elongation, Taeniopygia guttata" xref: Reactome:REACT_28198 "RNA Polymerase III Chain Elongation, Bos taurus" xref: Reactome:REACT_33298 "RNA Polymerase III Chain Elongation, Oryza sativa" xref: Reactome:REACT_33917 "RNA Polymerase III Chain Elongation, Arabidopsis thaliana" xref: Reactome:REACT_756 "RNA Polymerase III Chain Elongation, Homo sapiens" xref: Reactome:REACT_77630 "RNA Polymerase III Chain Elongation, Dictyostelium discoideum" xref: Reactome:REACT_78831 "RNA Polymerase III Chain Elongation, Saccharomyces cerevisiae" xref: Reactome:REACT_78988 "RNA Polymerase III Chain Elongation, Xenopus tropicalis" xref: Reactome:REACT_79358 "RNA Polymerase III Chain Elongation, Canis familiaris" xref: Reactome:REACT_83012 "RNA Polymerase III Chain Elongation, Drosophila melanogaster" xref: Reactome:REACT_89687 "RNA Polymerase III Chain Elongation, Rattus norvegicus" xref: Reactome:REACT_91878 "RNA Polymerase III Chain Elongation, Mus musculus" xref: Reactome:REACT_94842 "RNA Polymerase III Chain Elongation, Schizosaccharomyces pombe" xref: Reactome:REACT_94891 "RNA Polymerase III Chain Elongation, Gallus gallus" xref: Reactome:REACT_97511 "RNA Polymerase III Chain Elongation, Sus scrofa" is_a: GO:0006354 ! DNA-dependent transcription, elongation relationship: part_of GO:0006383 ! transcription from RNA polymerase III promoter [Term] id: GO:0006386 name: termination of RNA polymerase III transcription namespace: biological_process alt_id: GO:0019225 def: "The process in which transcription by RNA polymerase III is terminated; Pol III has an intrinsic ability to terminate transcription upon incorporation of 4 to 6 contiguous U residues." [GOC:mah, PMID:12944462] synonym: "RNA polymerase III transcription termination" EXACT [] synonym: "RNA polymerase III transcription termination factor activity" RELATED [] synonym: "transcription termination from Pol III promoter" EXACT [] synonym: "transcription termination from RNA polymerase III promoter" EXACT [] xref: Reactome:REACT_101346 "RNA Polymerase III Termination and release of transcribed mRNA, Oryza sativa" xref: Reactome:REACT_103761 "RNA Polymerase III Transcription Termination, Canis familiaris" xref: Reactome:REACT_104517 "RNA Polymerase III Transcription Termination, Drosophila melanogaster" xref: Reactome:REACT_106285 "RNA Polymerase III Transcription Termination, Dictyostelium discoideum" xref: Reactome:REACT_107620 "RNA Polymerase III Termination and release of transcribed mRNA, Rattus norvegicus" xref: Reactome:REACT_107641 "RNA Polymerase III Termination and release of transcribed mRNA, Sus scrofa" xref: Reactome:REACT_110732 "RNA Polymerase III Termination and release of transcribed mRNA, Schizosaccharomyces pombe" xref: Reactome:REACT_1301 "RNA Polymerase III Termination and release of transcribed mRNA, Homo sapiens" xref: Reactome:REACT_30092 "RNA Polymerase III Termination and release of transcribed mRNA, Caenorhabditis elegans" xref: Reactome:REACT_32584 "RNA Polymerase III Termination and release of transcribed mRNA, Mus musculus" xref: Reactome:REACT_33507 "RNA Polymerase III Transcription Termination, Schizosaccharomyces pombe" xref: Reactome:REACT_473 "RNA Polymerase III Transcriptional Pause at Terminator Sequence, Saccharomyces cerevisiae" xref: Reactome:REACT_63 "RNA Polymerase III Transcription Termination, Homo sapiens" xref: Reactome:REACT_76992 "RNA Polymerase III Termination and release of transcribed mRNA, Arabidopsis thaliana" xref: Reactome:REACT_78944 "RNA Polymerase III Transcription Termination, Danio rerio" xref: Reactome:REACT_79014 "RNA Polymerase III Transcription Termination, Saccharomyces cerevisiae" xref: Reactome:REACT_81629 "RNA Polymerase III Transcription Termination, Taeniopygia guttata" xref: Reactome:REACT_82545 "RNA Polymerase III Transcription Termination, Rattus norvegicus" xref: Reactome:REACT_84701 "RNA Polymerase III Transcription Termination, Caenorhabditis elegans" xref: Reactome:REACT_84717 "RNA Polymerase III Termination and release of transcribed mRNA, Taeniopygia guttata" xref: Reactome:REACT_84919 "RNA Polymerase III Transcription Termination, Sus scrofa" xref: Reactome:REACT_84942 "RNA Polymerase III Termination and release of transcribed mRNA, Danio rerio" xref: Reactome:REACT_85666 "RNA Polymerase III Transcription Termination, Gallus gallus" xref: Reactome:REACT_86112 "RNA Polymerase III Transcription Termination, Arabidopsis thaliana" xref: Reactome:REACT_86418 "RNA Polymerase III Transcription Termination, Xenopus tropicalis" xref: Reactome:REACT_878 "RNA Polymerase III Termination and release of transcribed mRNA, Saccharomyces cerevisiae" xref: Reactome:REACT_88719 "RNA Polymerase III Termination and release of transcribed mRNA, Gallus gallus" xref: Reactome:REACT_89703 "RNA Polymerase III Transcription Termination, Bos taurus" xref: Reactome:REACT_90819 "RNA Polymerase III Termination and release of transcribed mRNA, Bos taurus" xref: Reactome:REACT_92558 "RNA Polymerase III Termination and release of transcribed mRNA, Dictyostelium discoideum" xref: Reactome:REACT_94195 "RNA Polymerase III Termination and release of transcribed mRNA, Xenopus tropicalis" xref: Reactome:REACT_95268 "RNA Polymerase III Transcription Termination, Mus musculus" xref: Reactome:REACT_95372 "RNA Polymerase III Termination and release of transcribed mRNA, Drosophila melanogaster" xref: Reactome:REACT_97380 "RNA Polymerase III Transcription Termination, Oryza sativa" xref: Reactome:REACT_99081 "RNA Polymerase III Termination and release of transcribed mRNA, Canis familiaris" is_a: GO:0006353 ! DNA-dependent transcription, termination relationship: part_of GO:0006383 ! transcription from RNA polymerase III promoter [Term] id: GO:0006388 name: tRNA splicing, via endonucleolytic cleavage and ligation namespace: biological_process def: "Splicing of tRNA substrates via recognition of the folded RNA structure that brings the 5' and 3' splice sites into proximity and cleavage of the RNA at both the 3' and 5' splice sites by an endonucleolytic mechanism, followed by ligation of the exons." [GOC:krc, ISBN:0879695897, PMID:9582290] comment: Note that while typically associated with tRNA splicing, splicing via endonucleolytic cleavages and subsequent ligation of the free exon ends is known to be used for some non-tRNA substrates, e.g. HAC1 (YFL031W) in S. cerevisiae and an intron in the 23S rRNA of the Archaeal species Desulfurococcus mobilis. subset: gosubset_prok synonym: "tRNA-Y splicing" NARROW [] is_a: GO:0000394 ! RNA splicing, via endonucleolytic cleavage and ligation is_a: GO:0008033 ! tRNA processing [Term] id: GO:0006390 name: transcription from mitochondrial promoter namespace: biological_process def: "The synthesis of RNA from a mitochondrial DNA template, usually by a specific mitochondrial RNA polymerase." [GOC:jl] synonym: "mitochondrial transcription" EXACT [] xref: Reactome:REACT_105472 "Transcription from mitochondrial promoters, Rattus norvegicus" xref: Reactome:REACT_107715 "Transcription from mitochondrial promoters, Bos taurus" xref: Reactome:REACT_1484 "Transcription from mitochondrial promoters, Homo sapiens" xref: Reactome:REACT_32274 "Transcription from mitochondrial promoters, Sus scrofa" xref: Reactome:REACT_34725 "Transcription from mitochondrial promoters, Drosophila melanogaster" xref: Reactome:REACT_78264 "Transcription from mitochondrial promoters, Taeniopygia guttata" xref: Reactome:REACT_82329 "Transcription from mitochondrial promoters, Danio rerio" xref: Reactome:REACT_88757 "Transcription from mitochondrial promoters, Caenorhabditis elegans" xref: Reactome:REACT_91390 "Transcription from mitochondrial promoters, Xenopus tropicalis" xref: Reactome:REACT_95939 "Transcription from mitochondrial promoters, Canis familiaris" xref: Reactome:REACT_97569 "Transcription from mitochondrial promoters, Gallus gallus" xref: Reactome:REACT_97823 "Transcription from mitochondrial promoters, Mus musculus" is_a: GO:0006351 ! transcription, DNA-dependent intersection_of: GO:0006351 ! transcription, DNA-dependent [Term] id: GO:0006391 name: transcription initiation from mitochondrial promoter namespace: biological_process def: "A transcription initiation process that takes place at a promoter on the mitochondrial chromosome, and results in RNA synthesis by a mitochondrial RNA polymerase." [GOC:mah] xref: Reactome:REACT_110103 "Mitochondrial transcription initiation, Drosophila melanogaster" xref: Reactome:REACT_29893 "Mitochondrial transcription initiation, Taeniopygia guttata" xref: Reactome:REACT_31772 "Mitochondrial transcription initiation, Bos taurus" xref: Reactome:REACT_33467 "Mitochondrial transcription initiation, Canis familiaris" xref: Reactome:REACT_367 "Mitochondrial transcription initiation, Homo sapiens" xref: Reactome:REACT_61705 "Mitochondrial transcription initiation, Gallus gallus" xref: Reactome:REACT_85305 "Mitochondrial transcription initiation, Sus scrofa" xref: Reactome:REACT_86086 "Mitochondrial transcription initiation, Rattus norvegicus" xref: Reactome:REACT_87798 "Mitochondrial transcription initiation, Xenopus tropicalis" xref: Reactome:REACT_88905 "Mitochondrial transcription initiation, Mus musculus" xref: Reactome:REACT_90633 "Mitochondrial transcription initiation, Caenorhabditis elegans" xref: Reactome:REACT_91065 "Mitochondrial transcription initiation, Danio rerio" is_a: GO:0006352 ! DNA-dependent transcription, initiation relationship: part_of GO:0006390 ! transcription from mitochondrial promoter [Term] id: GO:0006392 name: transcription elongation from mitochondrial promoter namespace: biological_process def: "The extension of an RNA molecule after transcription initiation and promoter clearance at mitochondrial promoter by the addition of ribonucleotides catalyzed by a mitchondrial RNA polymerase." [GOC:mah, GOC:txnOH] synonym: "RNA elongation from mitochondrial promoter" EXACT [] is_a: GO:0006354 ! DNA-dependent transcription, elongation relationship: part_of GO:0006390 ! transcription from mitochondrial promoter [Term] id: GO:0006393 name: termination of mitochondrial transcription namespace: biological_process def: "The process in which the synthesis of an RNA molecule using a mitochondrial DNA template is completed." [GOC:mah] synonym: "mitochondrial transcription termination" EXACT [] synonym: "RNA transcription termination from mitochondrial promoter" EXACT [] xref: Reactome:REACT_28906 "Mitochondrial transcription termination, Rattus norvegicus" xref: Reactome:REACT_610 "Mitochondrial transcription termination, Homo sapiens" xref: Reactome:REACT_78733 "Mitochondrial transcription termination, Canis familiaris" xref: Reactome:REACT_83191 "Mitochondrial transcription termination, Sus scrofa" xref: Reactome:REACT_84941 "Mitochondrial transcription termination, Mus musculus" xref: Reactome:REACT_87729 "Mitochondrial transcription termination, Danio rerio" xref: Reactome:REACT_89280 "Mitochondrial transcription termination, Xenopus tropicalis" is_a: GO:0006353 ! DNA-dependent transcription, termination intersection_of: GO:0006353 ! DNA-dependent transcription, termination relationship: part_of GO:0006390 ! transcription from mitochondrial promoter [Term] id: GO:0006396 name: RNA processing namespace: biological_process alt_id: GO:0006394 def: "Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules." [GOC:mah] subset: goslim_pir subset: gosubset_prok xref: Wikipedia:Post-transcriptional_modification relationship: part_of GO:0010467 ! gene expression [Term] id: GO:0006397 name: mRNA processing namespace: biological_process def: "Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide." [GOC:mah] subset: goslim_generic subset: goslim_yeast subset: gosubset_prok synonym: "mRNA maturation" RELATED [] xref: Reactome:REACT_100203 "Processing of Capped Intronless Pre-mRNA, Dictyostelium discoideum" xref: Reactome:REACT_107308 "Processing of Capped Intronless Pre-mRNA, Xenopus tropicalis" xref: Reactome:REACT_109953 "Processing of Capped Intronless Pre-mRNA, Canis familiaris" xref: Reactome:REACT_113864 "Processing of Capped Intronless Pre-mRNA, Saccharomyces cerevisiae" xref: Reactome:REACT_114358 "Processing of Capped Intronless Pre-mRNA, Schizosaccharomyces pombe" xref: Reactome:REACT_115262 "Processing of Capped Intronless Pre-mRNA, Arabidopsis thaliana" xref: Reactome:REACT_1768 "Processing of Capped Intronless Pre-mRNA, Homo sapiens" xref: Reactome:REACT_32742 "Processing of Capped Intronless Pre-mRNA, Bos taurus" xref: Reactome:REACT_33642 "Processing of Capped Intronless Pre-mRNA, Caenorhabditis elegans" xref: Reactome:REACT_82691 "Processing of Capped Intronless Pre-mRNA, Gallus gallus" xref: Reactome:REACT_90366 "Processing of Capped Intronless Pre-mRNA, Drosophila melanogaster" xref: Reactome:REACT_91511 "Processing of Capped Intronless Pre-mRNA, Danio rerio" xref: Reactome:REACT_93186 "Processing of Capped Intronless Pre-mRNA, Sus scrofa" xref: Reactome:REACT_94083 "Processing of Capped Intronless Pre-mRNA, Taeniopygia guttata" xref: Reactome:REACT_96661 "Processing of Capped Intronless Pre-mRNA, Oryza sativa" xref: Reactome:REACT_97412 "Processing of Capped Intronless Pre-mRNA, Rattus norvegicus" xref: Reactome:REACT_97436 "Processing of Capped Intronless Pre-mRNA, Mus musculus" is_a: GO:0006396 ! RNA processing [Term] id: GO:0006398 name: histone mRNA 3'-end processing namespace: biological_process def: "Any process involved in forming the mature 3' end of a histone mRNA molecule." [GOC:mah] synonym: "histone mRNA 3' end processing" EXACT [] is_a: GO:0031124 ! mRNA 3'-end processing [Term] id: GO:0006400 name: tRNA modification namespace: biological_process alt_id: GO:0016549 def: "The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically." [GOC:curators] comment: The term 'RNA editing' (GO:0016547) was merged into 'RNA modification' (GO:0009451) on the basis of statements in the preface of Modification and Editing of RNA (ISBN:1555811337) that there is no clear distinction between modification and editing. Parallel changes were made for substrate (e.g. tRNA, rRNA, etc.) specific child terms of 'RNA editing'. subset: gosubset_prok synonym: "tRNA editing" NARROW [GOC:hjd] is_a: GO:0008033 ! tRNA processing [Term] id: GO:0006412 name: translation namespace: biological_process alt_id: GO:0006416 alt_id: GO:0006453 alt_id: GO:0043037 def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators] subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "protein anabolism" EXACT [] synonym: "protein biosynthesis" EXACT [] synonym: "protein biosynthetic process" EXACT [GOC:curators] synonym: "protein formation" EXACT [] synonym: "protein synthesis" EXACT [] synonym: "protein translation" EXACT [] xref: Reactome:REACT_100338 "Translation, Sus scrofa" xref: Reactome:REACT_100851 "Translation, Saccharomyces cerevisiae" xref: Reactome:REACT_101045 "Translation, Dictyostelium discoideum" xref: Reactome:REACT_101324 "Translation, Canis familiaris" xref: Reactome:REACT_1014 "Translation, Homo sapiens" xref: Reactome:REACT_103420 "Translation, Plasmodium falciparum" xref: Reactome:REACT_105544 "Translation, Arabidopsis thaliana" xref: Reactome:REACT_29980 "Translation, Bos taurus" xref: Reactome:REACT_33559 "Translation, Rattus norvegicus" xref: Reactome:REACT_77710 "Translation, Drosophila melanogaster" xref: Reactome:REACT_79784 "Translation, Danio rerio" xref: Reactome:REACT_81734 "Translation, Schizosaccharomyces pombe" xref: Reactome:REACT_81833 "Translation, Caenorhabditis elegans" xref: Reactome:REACT_82171 "Translation, Xenopus tropicalis" xref: Reactome:REACT_83429 "Translation, Taeniopygia guttata" xref: Reactome:REACT_83530 "Translation, Gallus gallus" xref: Reactome:REACT_86996 "Translation, Oryza sativa" xref: Reactome:REACT_95535 "Translation, Mus musculus" xref: Reactome:REACT_96394 "Translation, Escherichia coli" xref: Wikipedia:Translation_(genetics) relationship: part_of GO:0010467 ! gene expression [Term] id: GO:0006413 name: translational initiation namespace: biological_process alt_id: GO:0006440 alt_id: GO:0006454 def: "The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA, and an initiation complex that contains the first aminoacyl-tRNA." [ISBN:019879276X] subset: goslim_yeast subset: gosubset_prok synonym: "biopolymerisation" BROAD [] synonym: "biopolymerization" BROAD [] synonym: "protein synthesis initiation" BROAD [] synonym: "translation initiation" EXACT [] xref: Reactome:REACT_101789 "Eukaryotic Translation Initiation, Gallus gallus" xref: Reactome:REACT_104290 "Eukaryotic Translation Initiation, Xenopus tropicalis" xref: Reactome:REACT_2159 "Eukaryotic Translation Initiation, Homo sapiens" xref: Reactome:REACT_29447 "Eukaryotic Translation Initiation, Dictyostelium discoideum" xref: Reactome:REACT_30389 "Eukaryotic Translation Initiation, Oryza sativa" xref: Reactome:REACT_33969 "Eukaryotic Translation Initiation, Caenorhabditis elegans" xref: Reactome:REACT_34354 "Eukaryotic Translation Initiation, Taeniopygia guttata" xref: Reactome:REACT_77252 "Eukaryotic Translation Initiation, Drosophila melanogaster" xref: Reactome:REACT_79705 "Eukaryotic Translation Initiation, Rattus norvegicus" xref: Reactome:REACT_85780 "Eukaryotic Translation Initiation, Bos taurus" xref: Reactome:REACT_88031 "Eukaryotic Translation Initiation, Schizosaccharomyces pombe" xref: Reactome:REACT_91066 "Eukaryotic Translation Initiation, Arabidopsis thaliana" xref: Reactome:REACT_95293 "Eukaryotic Translation Initiation, Plasmodium falciparum" xref: Reactome:REACT_95552 "Eukaryotic Translation Initiation, Mus musculus" xref: Reactome:REACT_95685 "Eukaryotic Translation Initiation, Canis familiaris" xref: Reactome:REACT_97707 "Eukaryotic Translation Initiation, Sus scrofa" xref: Reactome:REACT_98138 "Eukaryotic Translation Initiation, Saccharomyces cerevisiae" xref: Reactome:REACT_99004 "Eukaryotic Translation Initiation, Danio rerio" relationship: part_of GO:0006412 ! translation [Term] id: GO:0006414 name: translational elongation namespace: biological_process alt_id: GO:0006442 alt_id: GO:0006455 def: "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis." [GOC:ems] subset: goslim_yeast subset: gosubset_prok synonym: "protein synthesis elongation" BROAD [] synonym: "translation elongation" EXACT [] xref: Reactome:REACT_100207 "Eukaryotic Translation Elongation, Dictyostelium discoideum" xref: Reactome:REACT_100561 "Eukaryotic Translation Elongation, Canis familiaris" xref: Reactome:REACT_101290 "Eukaryotic Translation Elongation, Gallus gallus" xref: Reactome:REACT_101737 "Eukaryotic Translation Elongation, Escherichia coli" xref: Reactome:REACT_102082 "Eukaryotic Translation Elongation, Mus musculus" xref: Reactome:REACT_103580 "Eukaryotic Translation Elongation, Danio rerio" xref: Reactome:REACT_108124 "Eukaryotic Translation Elongation, Xenopus tropicalis" xref: Reactome:REACT_108677 "Eukaryotic Translation Elongation, Taeniopygia guttata" xref: Reactome:REACT_108858 "Eukaryotic Translation Elongation, Caenorhabditis elegans" xref: Reactome:REACT_1477 "Eukaryotic Translation Elongation, Homo sapiens" xref: Reactome:REACT_30678 "Eukaryotic Translation Elongation, Arabidopsis thaliana" xref: Reactome:REACT_31079 "Eukaryotic Translation Elongation, Sus scrofa" xref: Reactome:REACT_80015 "Eukaryotic Translation Elongation, Bos taurus" xref: Reactome:REACT_80831 "Eukaryotic Translation Elongation, Rattus norvegicus" xref: Reactome:REACT_81624 "Eukaryotic Translation Elongation, Drosophila melanogaster" xref: Reactome:REACT_82124 "Eukaryotic Translation Elongation, Saccharomyces cerevisiae" xref: Reactome:REACT_88049 "Eukaryotic Translation Elongation, Schizosaccharomyces pombe" xref: Reactome:REACT_93503 "Eukaryotic Translation Elongation, Oryza sativa" xref: Reactome:REACT_96070 "Eukaryotic Translation Elongation, Plasmodium falciparum" relationship: part_of GO:0006412 ! translation [Term] id: GO:0006415 name: translational termination namespace: biological_process alt_id: GO:0006443 alt_id: GO:0006456 def: "The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code)." [GOC:hjd, ISBN:019879276X] subset: gosubset_prok synonym: "protein synthesis termination" BROAD [] synonym: "translation termination" EXACT [] synonym: "translational complex disassembly" EXACT [] xref: Reactome:REACT_100227 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Taeniopygia guttata" xref: Reactome:REACT_100585 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Dictyostelium discoideum" xref: Reactome:REACT_100730 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Danio rerio" xref: Reactome:REACT_1034 "Eukaryotic Translation Termination, Saccharomyces cerevisiae" xref: Reactome:REACT_103749 "Eukaryotic Translation Termination, Oryza sativa" xref: Reactome:REACT_104420 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Caenorhabditis elegans" xref: Reactome:REACT_104616 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Taeniopygia guttata" xref: Reactome:REACT_106326 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Plasmodium falciparum" xref: Reactome:REACT_107138 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Schizosaccharomyces pombe" xref: Reactome:REACT_107171 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Danio rerio" xref: Reactome:REACT_107771 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Oryza sativa" xref: Reactome:REACT_107964 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Schizosaccharomyces pombe" xref: Reactome:REACT_109127 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Caenorhabditis elegans" xref: Reactome:REACT_109494 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Plasmodium falciparum" xref: Reactome:REACT_110009 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Mus musculus" xref: Reactome:REACT_112381 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Gallus gallus" xref: Reactome:REACT_112559 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Rattus norvegicus" xref: Reactome:REACT_112632 "Eukaryotic Translation Termination, Rattus norvegicus" xref: Reactome:REACT_113540 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Gallus gallus" xref: Reactome:REACT_114287 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Gallus gallus" xref: Reactome:REACT_114807 "Eukaryotic Translation Termination, Gallus gallus" xref: Reactome:REACT_1152 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Saccharomyces cerevisiae" xref: Reactome:REACT_115292 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Rattus norvegicus" xref: Reactome:REACT_1654 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Homo sapiens" xref: Reactome:REACT_1986 "Eukaryotic Translation Termination, Homo sapiens" xref: Reactome:REACT_227 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Homo sapiens" xref: Reactome:REACT_28115 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Canis familiaris" xref: Reactome:REACT_28238 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Xenopus tropicalis" xref: Reactome:REACT_28773 "Eukaryotic Translation Termination, Danio rerio" xref: Reactome:REACT_29257 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Drosophila melanogaster" xref: Reactome:REACT_31194 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Canis familiaris" xref: Reactome:REACT_31222 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Oryza sativa" xref: Reactome:REACT_32804 "Eukaryotic Translation Termination, Drosophila melanogaster" xref: Reactome:REACT_33545 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Dictyostelium discoideum" xref: Reactome:REACT_34123 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Mus musculus" xref: Reactome:REACT_34462 "Eukaryotic Translation Termination, Saccharomyces cerevisiae" xref: Reactome:REACT_389 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Homo sapiens" xref: Reactome:REACT_393 "GTP bound eRF3:eRF1 complex binds the peptidyl-tRNA:mRNA:Ribosome complex, Saccharomyces cerevisiae" xref: Reactome:REACT_716 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Saccharomyces cerevisiae" xref: Reactome:REACT_78279 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Arabidopsis thaliana" xref: Reactome:REACT_78389 "Eukaryotic Translation Termination, Schizosaccharomyces pombe" xref: Reactome:REACT_78823 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Dictyostelium discoideum" xref: Reactome:REACT_80339 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Xenopus tropicalis" xref: Reactome:REACT_81067 "Eukaryotic Translation Termination, Canis familiaris" xref: Reactome:REACT_81196 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Arabidopsis thaliana" xref: Reactome:REACT_81882 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Caenorhabditis elegans" xref: Reactome:REACT_83324 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Xenopus tropicalis" xref: Reactome:REACT_83432 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Drosophila melanogaster" xref: Reactome:REACT_84537 "Eukaryotic Translation Termination, Plasmodium falciparum" xref: Reactome:REACT_84840 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Plasmodium falciparum" xref: Reactome:REACT_84975 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Arabidopsis thaliana" xref: Reactome:REACT_86647 "Eukaryotic Translation Termination, Xenopus tropicalis" xref: Reactome:REACT_86888 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Taeniopygia guttata" xref: Reactome:REACT_87882 "Eukaryotic Translation Termination, Dictyostelium discoideum" xref: Reactome:REACT_88395 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Canis familiaris" xref: Reactome:REACT_88662 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Danio rerio" xref: Reactome:REACT_91109 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Oryza sativa" xref: Reactome:REACT_92456 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Schizosaccharomyces pombe" xref: Reactome:REACT_92895 "Eukaryotic Translation Termination, Taeniopygia guttata" xref: Reactome:REACT_93205 "Eukaryotic Translation Termination, Caenorhabditis elegans" xref: Reactome:REACT_93556 "Eukaryotic Translation Termination, Mus musculus" xref: Reactome:REACT_94459 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Drosophila melanogaster" xref: Reactome:REACT_94463 "Eukaryotic Translation Termination, Arabidopsis thaliana" xref: Reactome:REACT_97483 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Mus musculus" relationship: part_of GO:0006412 ! translation [Term] id: GO:0006417 name: regulation of translation namespace: biological_process alt_id: GO:0006445 def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA." [GOC:isa_complete] subset: goslim_yeast subset: gosubset_prok synonym: "regulation of protein anabolism" EXACT [] synonym: "regulation of protein biosynthesis" EXACT [] synonym: "regulation of protein formation" EXACT [] synonym: "regulation of protein synthesis" EXACT [] is_a: GO:0010608 ! posttranscriptional regulation of gene expression intersection_of: regulates GO:0006412 ! translation relationship: regulates GO:0006412 ! translation [Term] id: GO:0006418 name: tRNA aminoacylation for protein translation namespace: biological_process def: "The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis." [GOC:ma] subset: goslim_yeast subset: gosubset_prok synonym: "tRNA charging" NARROW [] xref: MetaCyc:TRNA-CHARGING-PWY xref: Reactome:REACT_100041 "Mitochondrial tRNA aminoacylation, Escherichia coli" xref: Reactome:REACT_100416 "Cytosolic tRNA aminoacylation, Sus scrofa" xref: Reactome:REACT_100487 "Mitochondrial tRNA aminoacylation, Drosophila melanogaster" xref: Reactome:REACT_102312 "tRNA Aminoacylation, Plasmodium falciparum" xref: Reactome:REACT_103116 "tRNA Aminoacylation, Canis familiaris" xref: Reactome:REACT_103136 "Mitochondrial tRNA aminoacylation, Taeniopygia guttata" xref: Reactome:REACT_103575 "tRNA Aminoacylation, Arabidopsis thaliana" xref: Reactome:REACT_103831 "Mitochondrial tRNA aminoacylation, Oryza sativa" xref: Reactome:REACT_104381 "Cytosolic tRNA aminoacylation, Staphylococcus aureus N315" xref: Reactome:REACT_106785 "Cytosolic tRNA aminoacylation, Schizosaccharomyces pombe" xref: Reactome:REACT_107047 "tRNA Aminoacylation, Escherichia coli" xref: Reactome:REACT_107203 "Cytosolic tRNA aminoacylation, Plasmodium falciparum" xref: Reactome:REACT_107248 "tRNA Aminoacylation, Danio rerio" xref: Reactome:REACT_107617 "Mitochondrial tRNA aminoacylation, Rattus norvegicus" xref: Reactome:REACT_107708 "tRNA Aminoacylation, Schizosaccharomyces pombe" xref: Reactome:REACT_109699 "tRNA Aminoacylation, Xenopus tropicalis" xref: Reactome:REACT_111025 "Cytosolic tRNA aminoacylation, Caenorhabditis elegans" xref: Reactome:REACT_15302 "Mitochondrial tRNA aminoacylation, Homo sapiens" xref: Reactome:REACT_15306 "Cytosolic tRNA aminoacylation, Homo sapiens" xref: Reactome:REACT_15482 "tRNA Aminoacylation, Homo sapiens" xref: Reactome:REACT_28311 "tRNA Aminoacylation, Staphylococcus aureus N315" xref: Reactome:REACT_28868 "tRNA Aminoacylation, Bos taurus" xref: Reactome:REACT_29481 "tRNA Aminoacylation, Mycobacterium tuberculosis" xref: Reactome:REACT_30365 "Cytosolic tRNA aminoacylation, Dictyostelium discoideum" xref: Reactome:REACT_31574 "Cytosolic tRNA aminoacylation, Oryza sativa" xref: Reactome:REACT_31839 "Cytosolic tRNA aminoacylation, Bos taurus" xref: Reactome:REACT_33855 "tRNA Aminoacylation, Caenorhabditis elegans" xref: Reactome:REACT_34656 "Mitochondrial tRNA aminoacylation, Caenorhabditis elegans" xref: Reactome:REACT_40380 "tRNA Aminoacylation, Rattus norvegicus" xref: Reactome:REACT_59282 "Cytosolic tRNA aminoacylation, Mus musculus" xref: Reactome:REACT_78082 "tRNA Aminoacylation, Mus musculus" xref: Reactome:REACT_79804 "Mitochondrial tRNA aminoacylation, Dictyostelium discoideum" xref: Reactome:REACT_80723 "tRNA Aminoacylation, Drosophila melanogaster" xref: Reactome:REACT_81425 "tRNA Aminoacylation, Sus scrofa" xref: Reactome:REACT_81996 "Mitochondrial tRNA aminoacylation, Saccharomyces cerevisiae" xref: Reactome:REACT_82393 "Cytosolic tRNA aminoacylation, Escherichia coli" xref: Reactome:REACT_82791 "Cytosolic tRNA aminoacylation, Danio rerio" xref: Reactome:REACT_84562 "Mitochondrial tRNA aminoacylation, Bos taurus" xref: Reactome:REACT_84847 "Cytosolic tRNA aminoacylation, Xenopus tropicalis" xref: Reactome:REACT_85758 "tRNA Aminoacylation, Taeniopygia guttata" xref: Reactome:REACT_85924 "Cytosolic tRNA aminoacylation, Taeniopygia guttata" xref: Reactome:REACT_86341 "Mitochondrial tRNA aminoacylation, Mycobacterium tuberculosis" xref: Reactome:REACT_87556 "Cytosolic tRNA aminoacylation, Drosophila melanogaster" xref: Reactome:REACT_88061 "Cytosolic tRNA aminoacylation, Rattus norvegicus" xref: Reactome:REACT_88111 "Mitochondrial tRNA aminoacylation, Arabidopsis thaliana" xref: Reactome:REACT_88297 "Cytosolic tRNA aminoacylation, Gallus gallus" xref: Reactome:REACT_89110 "Cytosolic tRNA aminoacylation, Canis familiaris" xref: Reactome:REACT_89459 "tRNA Aminoacylation, Oryza sativa" xref: Reactome:REACT_89892 "Mitochondrial tRNA aminoacylation, Xenopus tropicalis" xref: Reactome:REACT_91438 "Mitochondrial tRNA aminoacylation, Staphylococcus aureus N315" xref: Reactome:REACT_91939 "Mitochondrial tRNA aminoacylation, Mus musculus" xref: Reactome:REACT_93083 "Mitochondrial tRNA aminoacylation, Danio rerio" xref: Reactome:REACT_93096 "tRNA Aminoacylation, Gallus gallus" xref: Reactome:REACT_93590 "Cytosolic tRNA aminoacylation, Saccharomyces cerevisiae" xref: Reactome:REACT_95057 "Cytosolic tRNA aminoacylation, Mycobacterium tuberculosis" xref: Reactome:REACT_95362 "Mitochondrial tRNA aminoacylation, Plasmodium falciparum" xref: Reactome:REACT_95636 "Mitochondrial tRNA aminoacylation, Gallus gallus" xref: Reactome:REACT_95656 "tRNA Aminoacylation, Dictyostelium discoideum" xref: Reactome:REACT_97943 "Mitochondrial tRNA aminoacylation, Sus scrofa" xref: Reactome:REACT_98561 "Mitochondrial tRNA aminoacylation, Schizosaccharomyces pombe" xref: Reactome:REACT_98686 "Cytosolic tRNA aminoacylation, Arabidopsis thaliana" xref: Reactome:REACT_99090 "tRNA Aminoacylation, Saccharomyces cerevisiae" xref: Reactome:REACT_99901 "Mitochondrial tRNA aminoacylation, Canis familiaris" relationship: part_of GO:0006412 ! translation [Term] id: GO:0006419 name: alanyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling alanine to alanyl-tRNA, catalyzed by alanyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mcc, ISBN:0716730510] subset: gosubset_prok is_a: GO:0006418 ! tRNA aminoacylation for protein translation [Term] id: GO:0006420 name: arginyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling arginine to arginyl-tRNA, catalyzed by arginyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mcc, ISBN:0716730510] subset: gosubset_prok is_a: GO:0006418 ! tRNA aminoacylation for protein translation [Term] id: GO:0006421 name: asparaginyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling asparagine to asparaginyl-tRNA, catalyzed by asparaginyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mcc, ISBN:0716730510] subset: gosubset_prok is_a: GO:0006418 ! tRNA aminoacylation for protein translation [Term] id: GO:0006422 name: aspartyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling aspartate to aspartyl-tRNA, catalyzed by aspartyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, ISBN:0716730510] subset: gosubset_prok is_a: GO:0006418 ! tRNA aminoacylation for protein translation [Term] id: GO:0006423 name: cysteinyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling cysteine to cysteinyl-tRNA, catalyzed by cysteinyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mcc, ISBN:0716730510] subset: gosubset_prok is_a: GO:0006418 ! tRNA aminoacylation for protein translation [Term] id: GO:0006424 name: glutamyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling glutamate to glutamyl-tRNA, catalyzed by glutamyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'- adenosine residue of the tRNA." [GOC:mcc, ISBN:0716730510] subset: gosubset_prok is_a: GO:0006418 ! tRNA aminoacylation for protein translation [Term] id: GO:0006425 name: glutaminyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling glutamine to glutaminyl-tRNA, catalyzed by glutaminyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'- adenosine residue of the tRNA." [GOC:mcc, ISBN:0716730510] subset: gosubset_prok is_a: GO:0006418 ! tRNA aminoacylation for protein translation [Term] id: GO:0006426 name: glycyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling glycine to glycyl-tRNA, catalyzed by glycyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mcc, ISBN:0716730510] subset: gosubset_prok is_a: GO:0006418 ! tRNA aminoacylation for protein translation [Term] id: GO:0006427 name: histidyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling histidine to histidyl-tRNA, catalyzed by histidyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mcc, ISBN:0716730510] subset: gosubset_prok is_a: GO:0006418 ! tRNA aminoacylation for protein translation [Term] id: GO:0006428 name: isoleucyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling isoleucine to isoleucyl-tRNA, catalyzed by isoleucyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mcc, ISBN:0716730510] subset: gosubset_prok is_a: GO:0006418 ! tRNA aminoacylation for protein translation [Term] id: GO:0006429 name: leucyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling leucine to leucyl-tRNA, catalyzed by leucyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mcc, ISBN:0716730510] subset: gosubset_prok is_a: GO:0006418 ! tRNA aminoacylation for protein translation [Term] id: GO:0006430 name: lysyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling lysine to lysyl-tRNA, catalyzed by lysyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mcc, ISBN:0716730510] subset: gosubset_prok is_a: GO:0006418 ! tRNA aminoacylation for protein translation [Term] id: GO:0006431 name: methionyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling methionine to methionyl-tRNA, catalyzed by methionyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mcc, ISBN:0716730510] subset: gosubset_prok is_a: GO:0006418 ! tRNA aminoacylation for protein translation [Term] id: GO:0006432 name: phenylalanyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling phenylalanine to phenylalanyl-tRNA, catalyzed by phenylalanyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mcc, ISBN:0716730510] subset: gosubset_prok is_a: GO:0006418 ! tRNA aminoacylation for protein translation [Term] id: GO:0006433 name: prolyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling proline to prolyl-tRNA, catalyzed by prolyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, ISBN:0716730510] subset: gosubset_prok is_a: GO:0006418 ! tRNA aminoacylation for protein translation [Term] id: GO:0006434 name: seryl-tRNA aminoacylation namespace: biological_process def: "The process of coupling serine to seryl-tRNA, catalyzed by seryl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mcc, ISBN:0716730510] subset: gosubset_prok is_a: GO:0006418 ! tRNA aminoacylation for protein translation [Term] id: GO:0006435 name: threonyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling threonine to threonyl-tRNA, catalyzed by threonyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mcc, ISBN:0716730510] subset: gosubset_prok is_a: GO:0006418 ! tRNA aminoacylation for protein translation [Term] id: GO:0006436 name: tryptophanyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling tryptophan to tryptophanyl-tRNA, catalyzed by tryptophanyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mcc, ISBN:0716730510] subset: gosubset_prok is_a: GO:0006418 ! tRNA aminoacylation for protein translation [Term] id: GO:0006437 name: tyrosyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling tyrosine to tyrosyl-tRNA, catalyzed by tyrosyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mcc, ISBN:0716730510] subset: gosubset_prok is_a: GO:0006418 ! tRNA aminoacylation for protein translation [Term] id: GO:0006438 name: valyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling valine to valyl-tRNA, catalyzed by valyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mcc, ISBN:0716730510] subset: gosubset_prok is_a: GO:0006418 ! tRNA aminoacylation for protein translation [Term] id: GO:0006446 name: regulation of translational initiation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of translational initiation." [GOC:go_curators] subset: gosubset_prok is_a: GO:0006417 ! regulation of translation intersection_of: regulates GO:0006413 ! translational initiation relationship: regulates GO:0006413 ! translational initiation [Term] id: GO:0006447 name: regulation of translational initiation by iron namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the translation of certain mRNAs involved in iron metabolism; regulated by the concentration of iron." [GOC:jl] subset: gosubset_prok is_a: GO:0006446 ! regulation of translational initiation [Term] id: GO:0006448 name: regulation of translational elongation namespace: biological_process def: "Any process that modulates the frequency, rate, extent or accuracy of translational elongation." [GOC:go_curators] subset: gosubset_prok is_a: GO:0006417 ! regulation of translation intersection_of: regulates GO:0006414 ! translational elongation relationship: regulates GO:0006414 ! translational elongation [Term] id: GO:0006449 name: regulation of translational termination namespace: biological_process def: "Any process that modulates the frequency, rate or extent of translational termination." [GOC:go_curators] subset: gosubset_prok is_a: GO:0006417 ! regulation of translation intersection_of: regulates GO:0006415 ! translational termination relationship: regulates GO:0006415 ! translational termination [Term] id: GO:0006450 name: regulation of translational fidelity namespace: biological_process alt_id: GO:0000029 def: "Any process that modulates the ability of the translational apparatus to interpret the genetic code." [GOC:dph, GOC:tb] subset: gosubset_prok synonym: "regulation of translational accuracy" EXACT [] is_a: GO:0006448 ! regulation of translational elongation [Term] id: GO:0006451 name: translational readthrough namespace: biological_process def: "The continuation of translation beyond a stop codon by the use of a special tRNA that recognizes the UAG and UGA codons as modified amino acids, rather than as termination codons." [GOC:jsg] subset: gosubset_prok synonym: "natural nonsense suppression" RELATED [] is_a: GO:0006414 ! translational elongation is_a: GO:0006417 ! regulation of translation [Term] id: GO:0006452 name: translational frameshifting namespace: biological_process def: "A mechanism whereby different proteins may result from a single mRNA molecule, due to a change in the parsing of three nucleotides per codon relative to an initiating AUG codon." [GOC:hjd, ISBN:0195094425] subset: gosubset_prok xref: Wikipedia:Translational_frameshift is_a: GO:0006414 ! translational elongation [Term] id: GO:0006465 name: signal peptide processing namespace: biological_process def: "The proteolytic removal of a signal peptide from a protein during or after transport to a specific location in the cell." [GOC:mah, ISBN:0815316194] subset: gosubset_prok synonym: "leader peptide processing" EXACT [] is_a: GO:0016485 ! protein processing [Term] id: GO:0006614 name: SRP-dependent cotranslational protein targeting to membrane namespace: biological_process def: "The targeting of proteins to a membrane that occurs during translation and is dependent upon two key components, the signal-recognition particle (SRP) and the SRP receptor. SRP is a cytosolic particle that transiently binds to the endoplasmic reticulum (ER) signal sequence in a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane." [ISBN:0716731363] synonym: "ER translocation" BROAD [] synonym: "SRP-dependent cotranslational membrane targeting" EXACT [] synonym: "SRP-dependent cotranslational protein-membrane targeting" EXACT [] xref: Reactome:REACT_115902 "SRP-dependent cotranslational protein targeting to membrane, Homo sapiens" xref: Reactome:REACT_118153 "SRP-dependent cotranslational protein targeting to membrane, Drosophila melanogaster" xref: Reactome:REACT_118173 "SRP-dependent cotranslational protein targeting to membrane, Bos taurus" xref: Reactome:REACT_118175 "SRP-dependent cotranslational protein targeting to membrane, Plasmodium falciparum" xref: Reactome:REACT_118177 "SRP-dependent cotranslational protein targeting to membrane, Oryza sativa" xref: Reactome:REACT_118247 "SRP-dependent cotranslational protein targeting to membrane, Xenopus tropicalis" xref: Reactome:REACT_118289 "SRP-dependent cotranslational protein targeting to membrane, Schizosaccharomyces pombe" xref: Reactome:REACT_118393 "SRP-dependent cotranslational protein targeting to membrane, Mus musculus" xref: Reactome:REACT_118417 "SRP-dependent cotranslational protein targeting to membrane, Taeniopygia guttata" xref: Reactome:REACT_118424 "SRP-dependent cotranslational protein targeting to membrane, Canis familiaris" xref: Reactome:REACT_118427 "SRP-dependent cotranslational protein targeting to membrane, Dictyostelium discoideum" xref: Reactome:REACT_118436 "SRP-dependent cotranslational protein targeting to membrane, Caenorhabditis elegans" xref: Reactome:REACT_118486 "SRP-dependent cotranslational protein targeting to membrane, Saccharomyces cerevisiae" xref: Reactome:REACT_118502 "SRP-dependent cotranslational protein targeting to membrane, Arabidopsis thaliana" xref: Reactome:REACT_118521 "SRP-dependent cotranslational protein targeting to membrane, Rattus norvegicus" xref: Reactome:REACT_118548 "SRP-dependent cotranslational protein targeting to membrane, Danio rerio" xref: Reactome:REACT_118553 "SRP-dependent cotranslational protein targeting to membrane, Gallus gallus" relationship: has_part GO:0006412 ! translation [Term] id: GO:0006615 name: SRP-dependent cotranslational protein targeting to membrane, docking namespace: biological_process def: "The process in which an SRP-bound ribosome forms a complex with the SRP receptor in the ER membrane, allowing the ribosome to bind to the membrane, during cotranslational membrane targeting." [ISBN:0815316194] synonym: "protein docking during SRP-dependent cotranslational protein targeting to membrane" EXACT [] synonym: "SRP-dependent cotranslational membrane targeting, docking" EXACT [] synonym: "SRP-dependent cotranslational protein-membrane targeting, docking" EXACT [] relationship: part_of GO:0006614 ! SRP-dependent cotranslational protein targeting to membrane [Term] id: GO:0006616 name: SRP-dependent cotranslational protein targeting to membrane, translocation namespace: biological_process def: "The process during cotranslational membrane targeting wherein proteins move across a membrane. SRP and its receptor initiate the transfer of the nascent chain across the endoplasmic reticulum (ER) membrane; they then dissociate from the chain, which is transferred to a set of transmembrane proteins, collectively called the translocon. Once the nascent chain translocon complex is assembled, the elongating chain passes directly from the large ribosomal subunit into the centers of the translocon, a protein-lined channel within the membrane. The growing chain is never exposed to the cytosol and does not fold until it reaches the ER lumen." [ISBN:0716731363] synonym: "ER translocation" BROAD [] synonym: "SRP-dependent cotranslational membrane targeting, translocation" EXACT [] synonym: "SRP-dependent cotranslational protein-membrane targeting, translocation" EXACT [] synonym: "translocation during SRP-dependent cotranslational protein targeting to membrane" EXACT [] relationship: part_of GO:0006614 ! SRP-dependent cotranslational protein targeting to membrane [Term] id: GO:0006617 name: SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition namespace: biological_process def: "The process in which SRP binds to the signal peptide in a nascent protein, causing protein elongation to pause, during cotranslational membrane targeting." [ISBN:0815316194] synonym: "signal sequence recognition during SRP-dependent cotranslational protein targeting to membrane" EXACT [] synonym: "SRP-dependent cotranslational membrane targeting, signal sequence recognition" EXACT [] synonym: "SRP-dependent cotranslational protein-membrane targeting, signal sequence recognition" EXACT [] relationship: part_of GO:0006614 ! SRP-dependent cotranslational protein targeting to membrane [Term] id: GO:0006618 name: SRP-dependent cotranslational protein targeting to membrane, signal sequence processing namespace: biological_process def: "The removal of the signal peptide from a nascent protein during cotranslational membrane targeting." [ISBN:0815316194] synonym: "signal sequence processing during SRP-dependent cotranslational protein targeting to membrane" EXACT [] synonym: "SRP-dependent cotranslational membrane targeting, signal sequence processing" EXACT [] synonym: "SRP-dependent cotranslational protein-membrane targeting, signal sequence processing" EXACT [] is_a: GO:0006465 ! signal peptide processing relationship: part_of GO:0006614 ! SRP-dependent cotranslational protein targeting to membrane [Term] id: GO:0006624 name: vacuolar protein processing namespace: biological_process def: "Protein processing that takes place in the vacuole. Most protein processing in the vacuole represents proteolytic cleavage of precursors to form active enzymes." [GOC:mah] synonym: "vacuolar protein maturation" RELATED [] synonym: "vacuolar proteolysis" RELATED [] is_a: GO:0016485 ! protein processing intersection_of: GO:0016485 ! protein processing [Term] id: GO:0006627 name: protein processing involved in protein targeting to mitochondrion namespace: biological_process def: "The cleavage of peptide bonds in proteins, usually near the N terminus, contributing to the process of import into the mitochondrion. Several different peptidases mediate cleavage of proteins destined for different mitochondrial compartments." [GOC:mcc, PMID:12191769] synonym: "mitochondrial processing" BROAD [] synonym: "mitochondrial protein processing during import" RELATED [GOC:dph, GOC:tb] is_a: GO:0034982 ! mitochondrial protein processing intersection_of: GO:0016485 ! protein processing [Term] id: GO:0006985 name: positive regulation of NF-kappaB transcription factor activity by ER overload response namespace: biological_process def: "The conversion of inactive NF-kappaB to the active form, thereby allowing it to activate transcription of target genes, as a result of signaling from the endoplasmic reticulum." [GOC:dph, GOC:mah, GOC:tb, PMID:10390516] synonym: "EOR-mediated activation of NF-kappaB " EXACT [GOC:dph, GOC:tb] synonym: "EOR-mediated NF-kappaB activation" EXACT [] synonym: "positive regulation of NF-kappaB transcription factor activity by EOR" EXACT [GOC:dph, GOC:tb] is_a: GO:0051092 ! positive regulation of NF-kappaB transcription factor activity intersection_of: results_in GO:0051092 ! positive regulation of NF-kappaB transcription factor activity [Term] id: GO:0006990 name: positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response namespace: biological_process def: "The activation of genes whose promoters contain a specific sequence elements such as the unfolded protein response element (UPRE; consensus CAGCGTG) or the ER stress-response element (ERSE; CCAAN(N)9CCACG), as a result of signaling via the unfolded protein response." [GOC:dph, GOC:mah, GOC:tb, GOC:txnOH, PMID:12042763] synonym: "positive regulation of transcription of target genes involved in unfolded protein response" EXACT [GOC:dph, GOC:tb] synonym: "unfolded protein response, activation of target gene transcription" NARROW [] synonym: "unfolded protein response, positive regulation of target gene transcription" EXACT [GOC:tb] synonym: "unfolded protein response, stimulation of target gene transcription" NARROW [] synonym: "unfolded protein response, target gene transcriptional activation" BROAD [] synonym: "unfolded protein response, up regulation of target gene transcription" EXACT [] synonym: "unfolded protein response, up-regulation of target gene transcription" EXACT [] synonym: "unfolded protein response, upregulation of target gene transcription" EXACT [] is_a: GO:1901522 ! positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter [Term] id: GO:0007068 name: negative regulation of transcription during mitosis namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription during mitosis." [GOC:go_curators] synonym: "down regulation of transcription during mitosis" EXACT [GOC:mah] synonym: "down-regulation of transcription during mitosis" EXACT [GOC:mah] synonym: "downregulation of transcription during mitosis" EXACT [GOC:mah] synonym: "inhibition of transcription during mitosis" NARROW [GOC:mah] synonym: "mitotic repression of transcription" EXACT [] synonym: "negative regulation of transcription, mitotic" EXACT [GOC:mah] is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent is_a: GO:0045896 ! regulation of transcription during mitosis [Term] id: GO:0007069 name: negative regulation of transcription from RNA polymerase I promoter during mitosis namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase I promoter during mitosis." [GOC:go_curators] synonym: "down regulation of transcription from RNA polymerase I promoter during mitosis" EXACT [GOC:mah] synonym: "down-regulation of transcription from RNA polymerase I promoter during mitosis" EXACT [GOC:mah] synonym: "downregulation of transcription from RNA polymerase I promoter during mitosis" EXACT [GOC:mah] synonym: "inhibition of transcription from RNA polymerase I promoter during mitosis" NARROW [GOC:mah] synonym: "mitotic repression of transcription from Pol I promoter" EXACT [] synonym: "negative regulation of transcription from Pol I promoter during mitosis" EXACT [GOC:mah] synonym: "negative regulation of transcription from RNA polymerase I promoter, mitotic" EXACT [GOC:mah] is_a: GO:0007068 ! negative regulation of transcription during mitosis is_a: GO:0016479 ! negative regulation of transcription from RNA polymerase I promoter is_a: GO:0046017 ! regulation of transcription from RNA polymerase I promoter, mitotic [Term] id: GO:0007070 name: negative regulation of transcription from RNA polymerase II promoter during mitosis namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter during mitosis." [GOC:go_curators] synonym: "down regulation of transcription from RNA polymerase II promoter during mitosis" EXACT [GOC:mah] synonym: "down-regulation of transcription from RNA polymerase II promoter during mitosis" EXACT [GOC:mah] synonym: "downregulation of transcription from RNA polymerase II promoter during mitosis" EXACT [GOC:mah] synonym: "inhibition of transcription from RNA polymerase II promoter during mitosis" NARROW [GOC:mah] synonym: "mitotic repression of transcription from Pol II promoter" EXACT [] synonym: "negative regulation of transcription from Pol II promoter during mitosis" EXACT [GOC:mah] synonym: "negative regulation of transcription from RNA polymerase II promoter, mitotic" EXACT [GOC:mah] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter is_a: GO:0007068 ! negative regulation of transcription during mitosis is_a: GO:0046021 ! regulation of transcription from RNA polymerase II promoter, mitotic [Term] id: GO:0007071 name: negative regulation of transcription from RNA polymerase III promoter during mitosis namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase III promoter during mitosis." [GOC:go_curators] synonym: "down regulation of transcription from RNA polymerase III promoter during mitosis" EXACT [GOC:mah] synonym: "down-regulation of transcription from RNA polymerase III promoter during mitosis" EXACT [GOC:mah] synonym: "downregulation of transcription from RNA polymerase III promoter during mitosis" EXACT [GOC:mah] synonym: "inhibition of transcription from RNA polymerase III promoter during mitosis" NARROW [GOC:mah] synonym: "mitotic repression of transcription from Pol III promoter" EXACT [] synonym: "negative regulation of transcription from Pol III promoter during mitosis" EXACT [GOC:mah] synonym: "negative regulation of transcription from RNA polymerase III promoter, mitotic" EXACT [GOC:mah] is_a: GO:0007068 ! negative regulation of transcription during mitosis is_a: GO:0016480 ! negative regulation of transcription from RNA polymerase III promoter is_a: GO:0046023 ! regulation of transcription from RNA polymerase III promoter, mitotic [Term] id: GO:0007072 name: positive regulation of transcription on exit from mitosis namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription as the cell leaves M phase. M phase is the part of the mitotic cell cycle during which mitosis and cytokinesis take place." [GOC:dph, GOC:isa_complete, GOC:tb] synonym: "activation of transcription on exit from mitosis" NARROW [GOC:dph, GOC:tb] is_a: GO:0045897 ! positive regulation of transcription during mitosis intersection_of: GO:0045893 ! positive regulation of transcription, DNA-dependent [Term] id: GO:0007073 name: positive regulation of transcription on exit from mitosis, from RNA polymerase I promoter namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase I promoter as the cell leaves M phase. M phase is the part of the mitotic cell cycle during which mitosis and cytokinesis take place." [GOC:dph, GOC:tb] synonym: "activation of transcription on exit from mitosis, from Pol I promoter" NARROW [GOC:dph, GOC:tb] synonym: "activation of transcription on exit from mitosis, from RNA polymerase I promoter" NARROW [] is_a: GO:0007072 ! positive regulation of transcription on exit from mitosis [Term] id: GO:0007074 name: positive regulation of transcription on exit from mitosis, from RNA polymerase II promoter namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as the cell leaves M phase. M phase is the part of the mitotic cell cycle during which mitosis and cytokinesis take place." [GOC:dph, GOC:tb] synonym: "activation of transcription on exit from mitosis, from Pol II promoter" NARROW [] synonym: "activation of transcription on exit from mitosis, from RNA polymerase II promoter" NARROW [] is_a: GO:0007072 ! positive regulation of transcription on exit from mitosis [Term] id: GO:0007075 name: positive regulation of transcription on exit from mitosis, from RNA polymerase III promoter namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase III promoter as the cell leaves M phase. M phase is the part of the mitotic cell cycle during which mitosis and cytokinesis take place." [GOC:dph, GOC:tb] synonym: "activation of transcription on exit from mitosis, from Pol III promoter" NARROW [] synonym: "activation of transcription on exit from mitosis, from RNA polymerase III promoter" NARROW [GOC:dph, GOC:tb] is_a: GO:0007072 ! positive regulation of transcription on exit from mitosis [Term] id: GO:0007221 name: positive regulation of transcription of Notch receptor target namespace: biological_process def: "The activation of transcription of specific genes as a result of Notch signaling, mediated by the Notch intracellular domain." [PMID:12651094] synonym: "N receptor target transcription factor activation" RELATED [] synonym: "Notch receptor target transcription factor activation" RELATED [] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter [Term] id: GO:0007225 name: patched ligand maturation namespace: biological_process def: "The posttranslational modification of members of the Hedgehog family of signaling proteins in order for Hedgehog to exert its biological activity. These modifications include cleavage of its signal sequence, autocatalytic protein cleavage and the attachment of sterol groups." [PMID:15057936] synonym: "Hedgehog protein processing" NARROW [] synonym: "hh protein processing" EXACT [] synonym: "patched ligand processing" RELATED [] is_a: GO:0051604 ! protein maturation [Term] id: GO:0007228 name: positive regulation of hh target transcription factor activity namespace: biological_process def: "Any process that increases the activity of a transcription factor that activates transcription of Hedgehog-target genes in response to Smoothened signaling. In Drosophila, Cubitus interruptus (Ci) is the only identified transcription factor so far in the Hedgehog signaling pathway. In vertebrates, members of the Gli protein family are activated in this way. Activation of the Gli/Ci transcription factor is distinct from its stabilization, when proteolytic cleavage is inhibited." [GOC:dph, GOC:tb, PMID:11912487, PMID:15057936] synonym: "activation of hh target transcription factor" EXACT [GOC:dph, GOC:tb] synonym: "positive regulation of hedgehog target transcription factor" EXACT [GOC:bf, GOC:ecd] is_a: GO:0051091 ! positive regulation of sequence-specific DNA binding transcription factor activity [Term] id: GO:0007249 name: I-kappaB kinase/NF-kappaB cascade namespace: biological_process def: "The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription." [GOC:bf, GOC:jl, PMID:12773372, Reactome:REACT_13696.1] synonym: "activation of the inhibitor of kappa kinase" RELATED [] synonym: "canonical NF-kappaB signaling cascade" EXACT [GOC:bf] synonym: "NF-kappaB cascade" BROAD [] synonym: "p50-dependent NF-kappaB signaling" RELATED [PMID:18292232] xref: Reactome:REACT_13696.1 "NF-kB is activated and signals survival, Homo sapiens" xref: Reactome:REACT_25351 "TRAF6 mediated induction of TAK1 complex, Homo sapiens" relationship: has_part GO:0051092 ! positive regulation of NF-kappaB transcription factor activity [Term] id: GO:0007250 name: activation of NF-kappaB-inducing kinase activity namespace: biological_process def: "The stimulation of the activity of NF-kappaB-inducing kinase through phosphorylation at specific residues." [GOC:jl, PMID:12773372] synonym: "activation of NIK activity" EXACT [GOC:bf] synonym: "positive regulation of NF-kappaB-inducing kinase activity" BROAD [] xref: Reactome:REACT_25145 "TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Gallus gallus" xref: Reactome:REACT_75885 "Caspase-8 and -10 mediated induction of NF-kB, Gallus gallus" xref: Reactome:REACT_75895 "TRAF6 mediated NF-kB activation, Gallus gallus" is_a: GO:1901222 ! regulation of NIK/NF-kappaB cascade intersection_of: positively_regulates GO:0004704 ! NF-kappaB-inducing kinase activity relationship: part_of GO:0038061 ! NIK/NF-kappaB cascade relationship: positively_regulates GO:0004704 ! NF-kappaB-inducing kinase activity [Term] id: GO:0007252 name: I-kappaB phosphorylation namespace: biological_process def: "The process of introducing a phosphate group into an inhibitor of kappa B (I-kappaB) protein. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing bound NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription." [GOC:bf, GOC:jl, PMID:21772278, PMID:7594468] synonym: "IkappaB phosphorylation" EXACT [GOC:bf] synonym: "IKB phosphorylation" EXACT [GOC:bf] synonym: "inhibitor of kappaB phosphorylation" EXACT [GOC:bf] synonym: "inhibitor of NF-kappaB phosphorylation" EXACT [GOC:bf] relationship: part_of GO:0007249 ! I-kappaB kinase/NF-kappaB cascade [Term] id: GO:0007253 name: cytoplasmic sequestering of NF-kappaB namespace: biological_process def: "The selective interaction of the transcription factor NF-kappaB with specific molecules in the cytoplasm, thereby inhibiting its translocation into the nucleus." [GOC:jl] synonym: "cytoplasmic NF-kappaB retention" EXACT [] synonym: "cytoplasmic NF-kappaB sequestration" EXACT [] synonym: "cytoplasmic NF-kappaB storage" EXACT [] synonym: "cytoplasmic retention of NF-kappaB" EXACT [] synonym: "cytoplasmic sequestration of NF-kappaB" EXACT [] synonym: "cytoplasmic storage of NF-kappaB" EXACT [] synonym: "maintenance of NF-kappaB location in cytoplasm" EXACT [GOC:dph, GOC:tb] is_a: GO:0042347 ! negative regulation of NF-kappaB import into nucleus relationship: part_of GO:0043124 ! negative regulation of I-kappaB kinase/NF-kappaB cascade [Term] id: GO:0007319 name: negative regulation of oskar mRNA translation namespace: biological_process def: "Any process that stops, prevents or reduces the rate that oskar mRNAs are effectively translated into protein." [GOC:ems] synonym: "down regulation of oskar mRNA translation" EXACT [] synonym: "down-regulation of oskar mRNA translation" EXACT [] synonym: "downregulation of oskar mRNA translation" EXACT [] synonym: "inhibition of oskar mRNA translation" NARROW [] is_a: GO:0017148 ! negative regulation of translation is_a: GO:0046011 ! regulation of oskar mRNA translation [Term] id: GO:0007323 name: peptide pheromone maturation namespace: biological_process alt_id: GO:0007324 alt_id: GO:0007326 alt_id: GO:0046613 def: "The generation of a mature, active peptide pheromone via processes unique to its processing and modification. An example of this process is found in Saccharomyces cerevisiae." [GOC:elh] subset: gosubset_prok synonym: "pheromone processing" EXACT [] is_a: GO:0051604 ! protein maturation [Term] id: GO:0007329 name: positive regulation of transcription from RNA polymerase II promoter by pheromones namespace: biological_process def: "Any process involving pheromones that activates or increases the rate of transcription from an RNA polymerase II promoter." [GOC:go_curators] synonym: "activation of transcription from RNA polymerase II promoter by pheromones" NARROW [] synonym: "positive regulation of transcription from Pol II promoter by pheromones" EXACT [] synonym: "stimulation of transcription from RNA polymerase II promoter by pheromones" NARROW [] synonym: "up regulation of transcription from RNA polymerase II promoter by pheromones" EXACT [] synonym: "up-regulation of transcription from RNA polymerase II promoter by pheromones" EXACT [] synonym: "upregulation of transcription from RNA polymerase II promoter by pheromones" EXACT [] is_a: GO:0009371 ! positive regulation of transcription by pheromones is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter is_a: GO:0046019 ! regulation of transcription from RNA polymerase II promoter by pheromones [Term] id: GO:0007357 name: positive regulation of central gap gene transcription namespace: biological_process def: "The activation of genes encoding transcription factors in the central region of an insect embryo by a combination of maternal regulatory signals and interactions among themselves; exemplified by the activation of expression of the Drosophila Kruppel gene by the hunchback and bicoid gene products." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238] synonym: "activation of central gap gene" BROAD [] synonym: "activation of central gap gene transcription" NARROW [] synonym: "stimulation of central gap gene transcription" NARROW [] synonym: "up regulation of central gap gene transcription" EXACT [] synonym: "up-regulation of central gap gene transcription" EXACT [] synonym: "upregulation of central gap gene transcription" EXACT [] is_a: GO:0044324 ! regulation of transcription involved in anterior/posterior axis specification is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter [Term] id: GO:0007360 name: positive regulation of posterior gap gene transcription namespace: biological_process def: "The activation of genes encoding transcription factors in the posterior region of an insect embryo by a combination of maternal regulatory signals and interactions among themselves; exemplified by the activation of expression of the Drosophila knirps gene." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238] synonym: "activation of posterior gap gene" BROAD [] synonym: "activation of posterior gap gene transcription" NARROW [] synonym: "knirps activation" NARROW [] synonym: "stimulation of posterior gap gene transcription" NARROW [] synonym: "up regulation of posterior gap gene transcription" EXACT [] synonym: "up-regulation of posterior gap gene transcription" EXACT [] synonym: "upregulation of posterior gap gene transcription" EXACT [] is_a: GO:0044324 ! regulation of transcription involved in anterior/posterior axis specification is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter [Term] id: GO:0007363 name: positive regulation of terminal gap gene transcription namespace: biological_process def: "The activation of genes encoding transcription factors at the anterior and posterior ends of an insect embryo by a combination of maternal regulatory signals and interactions among themselves; exemplified by the activation of expression of the Drosophila tailless and huckebein genes." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238] synonym: "activation of terminal gap gene" BROAD [] synonym: "activation of terminal gap gene transcription" NARROW [] synonym: "stimulation of terminal gap gene transcription" NARROW [] synonym: "up regulation of terminal gap gene transcription" EXACT [] synonym: "up-regulation of terminal gap gene transcription" EXACT [] synonym: "upregulation of terminal gap gene transcription" EXACT [] is_a: GO:0044324 ! regulation of transcription involved in anterior/posterior axis specification is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter [Term] id: GO:0007468 name: regulation of rhodopsin gene expression namespace: biological_process def: "Any process that modulates the frequency, rate or extent of rhodopsin gene expression. This includes transcriptional, translational, or posttranslational regulation." [GOC:dph, GOC:go_curators, GOC:tb] synonym: "regulation of rhodopsin gene activity" EXACT [GOC:dph, GOC:tb] is_a: GO:0010468 ! regulation of gene expression [Term] id: GO:0007532 name: regulation of mating-type specific transcription, DNA-dependent namespace: biological_process def: "Any mating-type specific process that modulates the frequency, rate or extent of cellular DNA-dependent transcription." [GOC:go_curators, GOC:txnOH] synonym: "mating-type specific transcriptional control" EXACT [] is_a: GO:0006355 ! regulation of transcription, DNA-dependent [Term] id: GO:0007549 name: dosage compensation namespace: biological_process def: "Compensating for the two-fold variation in X:autosome chromosome ratios between sexes by a global activation or inactivation of all, or most of, genes on one or both of the X chromosomes." [GOC:ems, ISBN:0140512888, PMID:11498577] xref: Wikipedia:Dosage_compensation is_a: GO:0040029 ! regulation of gene expression, epigenetic [Term] id: GO:0008033 name: tRNA processing namespace: biological_process def: "The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group." [GOC:jl, PMID:12533506] subset: goslim_yeast subset: gosubset_prok synonym: "tRNA maturation" EXACT [GOC:vw] is_a: GO:0034470 ! ncRNA processing [Term] id: GO:0008079 name: translation termination factor activity namespace: molecular_function def: "Functions in the termination of translation." [GOC:ma] subset: gosubset_prok is_a: GO:0008135 ! translation factor activity, nucleic acid binding relationship: part_of GO:0006415 ! translational termination [Term] id: GO:0008135 name: translation factor activity, nucleic acid binding namespace: molecular_function def: "Functions during translation by interacting selectively and non-covalently with nucleic acids during polypeptide synthesis at the ribosome." [GOC:ai, GOC:vw] subset: goslim_generic subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "translation factor activity, RNA binding" EXACT [GOC:mah] relationship: part_of GO:0006412 ! translation [Term] id: GO:0008150 name: biological_process namespace: biological_process alt_id: GO:0000004 alt_id: GO:0007582 def: "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." [GOC:go_curators, GOC:isa_complete] comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok synonym: "biological process" EXACT [] synonym: "biological process unknown" NARROW [] synonym: "physiological process" EXACT [] xref: Wikipedia:Biological_process is_a: span:Process ! process [Term] id: GO:0008152 name: metabolic process namespace: biological_process def: "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "metabolic process resulting in cell growth" NARROW [] synonym: "metabolism" EXACT [] synonym: "metabolism resulting in cell growth" NARROW [] xref: Wikipedia:Metabolism is_a: GO:0008150 ! biological_process [Term] id: GO:0008175 name: tRNA methyltransferase activity namespace: molecular_function def: "Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in a tRNA molecule." [GOC:mah] subset: gosubset_prok xref: EC:2.1.1.- relationship: part_of GO:0030488 ! tRNA methylation [Term] id: GO:0008176 name: tRNA (guanine-N7-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N7-methylguanine." [EC:2.1.1.33] subset: gosubset_prok synonym: "7-methylguanine transfer ribonucleate methylase activity" EXACT [EC:2.1.1.33] synonym: "N7-methylguanine methylase activity" EXACT [EC:2.1.1.33] synonym: "S-adenosyl-L-methionine:tRNA (guanine-7-N-)-methyltransferase activity" EXACT [EC:2.1.1.33] synonym: "S-adenosyl-L-methionine:tRNA (guanine-N7-)-methyltransferase activity" EXACT [EC:2.1.1.33] synonym: "transfer ribonucleate guanine 7-methyltransferase activity" EXACT [EC:2.1.1.33] synonym: "tRNA guanine 7-methyltransferase activity" EXACT [EC:2.1.1.33] xref: EC:2.1.1.33 xref: MetaCyc:TRNA-GUANINE-N7--METHYLTRANSFERASE-RXN is_a: GO:0016423 ! tRNA (guanine) methyltransferase activity relationship: part_of GO:0036265 ! RNA (guanine-N7)-methylation [Term] id: GO:0008293 name: torso signaling pathway namespace: biological_process def: "A series of molecular signals initiated by the binding of an extracellular ligand to torso (a receptor tyrosine kinase) on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:go_curators, PMID:8343949] synonym: "torso signalling pathway" EXACT [] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter [Term] id: GO:0008380 name: RNA splicing namespace: biological_process alt_id: GO:0006395 def: "The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA." [GOC:krc, GOC:mah] subset: goslim_yeast subset: gosubset_prok synonym: "pre-mRNA splicing factor activity" RELATED [] xref: Reactome:REACT_107090 "mRNA Splicing, Gallus gallus" xref: Reactome:REACT_107348 "mRNA Splicing, Dictyostelium discoideum" xref: Reactome:REACT_107931 "mRNA Splicing, Caenorhabditis elegans" xref: Reactome:REACT_108122 "mRNA Splicing, Schizosaccharomyces pombe" xref: Reactome:REACT_113880 "mRNA Splicing, Taeniopygia guttata" xref: Reactome:REACT_1735 "mRNA Splicing, Homo sapiens" xref: Reactome:REACT_34200 "mRNA Splicing, Plasmodium falciparum" xref: Reactome:REACT_81581 "mRNA Splicing, Oryza sativa" xref: Reactome:REACT_82520 "mRNA Splicing, Rattus norvegicus" xref: Reactome:REACT_91201 "mRNA Splicing, Canis familiaris" xref: Reactome:REACT_94469 "mRNA Splicing, Drosophila melanogaster" xref: Reactome:REACT_96521 "mRNA Splicing, Bos taurus" xref: Reactome:REACT_97651 "mRNA Splicing, Xenopus tropicalis" xref: Reactome:REACT_98240 "mRNA Splicing, Danio rerio" xref: Reactome:REACT_98753 "mRNA Splicing, Mus musculus" xref: Reactome:REACT_98879 "mRNA Splicing, Arabidopsis thaliana" xref: Wikipedia:RNA_splicing is_a: GO:0006396 ! RNA processing [Term] id: GO:0008384 name: IkappaB kinase activity namespace: molecular_function def: "Catalysis of the reaction: ATP + IkappaB protein = ADP + IkappaB phosphoprotein." [EC:2.7.11.10] comment: Note that phosphorylation of IkappaB targets it for proteasomal degradation and allows the nuclear translocation of kB. synonym: "ATP:IkappaB protein phosphotransferase activity" EXACT [EC:2.7.11.10] synonym: "CHUK" RELATED [EC:2.7.11.10] synonym: "ikappaB kinase activity" EXACT [EC:2.7.11.10] synonym: "IKBKA" RELATED [EC:2.7.11.10] synonym: "IKBKB" RELATED [EC:2.7.11.10] synonym: "IKK" RELATED [EC:2.7.11.10] synonym: "IKK-1" RELATED [EC:2.7.11.10] synonym: "IKK-2" RELATED [EC:2.7.11.10] synonym: "inhibitor of NF-kappaB kinase activity" EXACT [EC:2.7.11.10] synonym: "inhibitor of NFkappaB kinase activity" EXACT [EC:2.7.11.10] synonym: "STK12" RELATED [EC:2.7.11.10] synonym: "TANK-binding kinase 1 activity" NARROW [EC:2.7.11.10] synonym: "TBK1" RELATED [EC:2.7.11.10] xref: EC:2.7.11.10 xref: MetaCyc:2.7.11.10-RXN xref: Reactome:REACT_22418 "The IKKB complex phosphorylates NFkB p105, Homo sapiens" relationship: part_of GO:0007252 ! I-kappaB phosphorylation [Term] id: GO:0008434 name: calcitriol receptor activity namespace: molecular_function def: "Combining with calcitriol, the hormonally active form of vitamin D3, and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II." [CHEBI:17823, GOC:bf, GOC:signaling, PMID:16549446, PMID:17082781, Wikipedia:Calcitriol_receptor] comment: Note that this term represents a function and not a gene product. Consider also annotating to the molecular function term 'transcription regulator activity ; GO:0030528'. synonym: " 1alpha,25(OH)2D3 receptor activity" EXACT [PMID:16549446] synonym: "1,25-(OH)2D3 receptor activity" EXACT [Wikipedia:Calcitriol] synonym: "1,25-dihydroxycholecalciferol receptor activity" EXACT [Wikipedia:Calcitriol] synonym: "1,25-dihydroxyvitamin D3 receptor activity" EXACT [Wikipedia:Calcitriol] synonym: "1alpha,25-dihydroxyvitamin D3 receptor activity" EXACT [CHEBI:17823] synonym: "vitamin D3 receptor activity" RELATED [GOC:bf, Wikipedia:Calcitriol_receptor] is_a: GO:0004879 ! ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity [Term] id: GO:0008494 name: translation activator activity namespace: molecular_function def: "Any of a group of soluble proteins functioning in the activation of ribosome-mediated translation of mRNA into a polypeptide." [GOC:ai] is_a: GO:0090079 ! translation regulator activity, nucleic acid binding relationship: part_of GO:0045727 ! positive regulation of translation [Term] id: GO:0008588 name: release of cytoplasmic sequestered NF-kappaB namespace: biological_process def: "The release of NF-kappaB from specific molecules in the cytoplasm to which it was bound, thereby allowing its translocation into the nucleus." [GOC:jl] synonym: "activation of NF-kappa B" RELATED [] synonym: "negative regulation of cytoplasmic NF-kappaB retention" RELATED [] synonym: "negative regulation of cytoplasmic NF-kappaB sequestering" RELATED [] synonym: "negative regulation of cytoplasmic NF-kappaB sequestration" RELATED [] synonym: "negative regulation of cytoplasmic NF-kappaB storage" RELATED [] synonym: "release of NF-kappaB sequestered in cytoplasm" EXACT [] synonym: "release of NF-kappaB stored in cytoplasm" EXACT [] is_a: GO:0042346 ! positive regulation of NF-kappaB import into nucleus relationship: negatively_regulates GO:0007253 ! cytoplasmic sequestering of NF-kappaB relationship: part_of GO:0007249 ! I-kappaB kinase/NF-kappaB cascade [Term] id: GO:0008616 name: queuosine biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of queuosines, any of a series of nucleosides found in tRNA and having an additional pentenyl ring added via an NH group to the methyl group of 7-methylguanosine. The pentenyl ring may carry other substituents." [GOC:go_curators, ISBN:0198506732] subset: gosubset_prok synonym: "queuosine anabolism" EXACT [] synonym: "queuosine biosynthesis" EXACT [] synonym: "queuosine formation" EXACT [] synonym: "queuosine synthesis" EXACT [] is_a: GO:0006400 ! tRNA modification [Term] id: GO:0008649 name: rRNA methyltransferase activity namespace: molecular_function def: "Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an rRNA molecule." [GOC:mah] subset: gosubset_prok xref: EC:2.1.1.- relationship: part_of GO:0031167 ! rRNA methylation [Term] id: GO:0008650 name: rRNA (uridine-2'-O-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing 2'-O-methyluridine." [GOC:mah] subset: gosubset_prok xref: EC:2.1.1.- is_a: GO:0016436 ! rRNA (uridine) methyltransferase activity [Term] id: GO:0008988 name: rRNA (adenine-N6-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N6-methyladenine." [EC:2.1.1.48] subset: gosubset_prok synonym: "ErmC 23S rRNA methyltransferase" NARROW [EC:2.1.1.48] synonym: "gene ksgA methyltransferase" NARROW [EC:2.1.1.48] synonym: "ribonucleic acid-adenine (N(6)) methylase activity" EXACT [EC:2.1.1.48] synonym: "ribonucleic acid-adenine (N6) methylase activity" EXACT [EC:2.1.1.48] synonym: "ribosomal ribonucleate adenine 6-methyltransferase activity" EXACT [EC:2.1.1.48] synonym: "S-adenosyl-L-methionine:rRNA (adenine-6-N-)-methyltransferase activity" EXACT [EC:2.1.1.48] synonym: "S-adenosyl-L-methionine:rRNA (adenine-N6-)-methyltransferase activity" EXACT [EC:2.1.1.48] xref: EC:2.1.1.- is_a: GO:0016433 ! rRNA (adenine) methyltransferase activity [Term] id: GO:0008989 name: rRNA (guanine-N1-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N1-methylguanine." [EC:2.1.1.51] subset: gosubset_prok synonym: "ribosomal ribonucleate guanine 1-methyltransferase activity" EXACT [EC:2.1.1.51] synonym: "S-adenosyl-L-methionine:rRNA (guanine-1-N-)-methyltransferase activity" EXACT [EC:2.1.1.51] synonym: "S-adenosyl-L-methionine:rRNA (guanine-N1-)-methyltransferase activity" EXACT [EC:2.1.1.51] xref: EC:2.1.1.51 xref: MetaCyc:RRNA-GUANINE-N1--METHYLTRANSFERASE-RXN is_a: GO:0016435 ! rRNA (guanine) methyltransferase activity [Term] id: GO:0008990 name: rRNA (guanine-N2-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N2-methylguanine." [EC:2.1.1.52] subset: gosubset_prok synonym: "ribosomal ribonucleate guanine-2-methyltransferase activity" EXACT [EC:2.1.1.52] synonym: "S-adenosyl-L-methionine:rRNA (guanine-2-N-)-methyltransferase activity" EXACT [EC:2.1.1.52] synonym: "S-adenosyl-L-methionine:rRNA (guanine-N2-)-methyltransferase activity" EXACT [EC:2.1.1.52] xref: EC:2.1.1.52 xref: MetaCyc:RRNA-GUANINE-N2--METHYLTRANSFERASE-RXN is_a: GO:0016435 ! rRNA (guanine) methyltransferase activity [Term] id: GO:0009007 name: site-specific DNA-methyltransferase (adenine-specific) activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + DNA adenine = S-adenosyl-L-homocysteine + DNA 6-methylaminopurine." [EC:2.1.1.72] subset: gosubset_prok synonym: "DNA adenine methylase" BROAD [] synonym: "EcoRI methylase" NARROW [EC:2.1.1.37, EC:2.1.1.72] synonym: "modification methylase activity" RELATED [EC:2.1.1.72] synonym: "N-6 adenine-specific DNA methylase activity" EXACT [EC:2.1.1.72] synonym: "restriction-modification system activity" RELATED [EC:2.1.1.72] xref: EC:2.1.1.72 xref: MetaCyc:2.1.1.72-RXN is_a: GO:0009008 ! DNA-methyltransferase activity relationship: part_of GO:0032775 ! DNA methylation on adenine [Term] id: GO:0009008 name: DNA-methyltransferase activity namespace: molecular_function def: "Catalysis of the transfer of a methyl group to a DNA molecule." [GOC:jl, ISBN:0198506732] subset: gosubset_prok synonym: "deoxyribonucleate methylase activity" EXACT [EC:2.1.1.-] synonym: "deoxyribonucleate methyltransferase activity" EXACT [EC:2.1.1.-] synonym: "deoxyribonucleic acid methylase activity" EXACT [EC:2.1.1.-] synonym: "deoxyribonucleic acid methyltransferase activity" EXACT [EC:2.1.1.-] synonym: "deoxyribonucleic acid modification methylase activity" RELATED [EC:2.1.1.-] synonym: "DNA methylase" BROAD [] synonym: "DNA methyltransferase activity" EXACT [] synonym: "DNA transmethylase activity" EXACT [EC:2.1.1.-] synonym: "Type II DNA methylase" RELATED [EC:2.1.1.37] xref: EC:2.1.1.- relationship: part_of GO:0006306 ! DNA methylation [Term] id: GO:0009019 name: tRNA (guanine-N1-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N1-methylguanine." [EC:2.1.1.31] subset: gosubset_prok synonym: "S-adenosyl-L-methionine:tRNA (guanine-1-N-)-methyltransferase activity" EXACT [EC:2.1.1.31] synonym: "S-adenosyl-L-methionine:tRNA (guanine-N1-)-methyltransferase activity" EXACT [EC:2.1.1.31] synonym: "transfer ribonucleate guanine 1-methyltransferase activity" EXACT [EC:2.1.1.31] synonym: "tRNA guanine 1-methyltransferase activity" EXACT [EC:2.1.1.31] xref: EC:2.1.1.- is_a: GO:0016423 ! tRNA (guanine) methyltransferase activity [Term] id: GO:0009020 name: tRNA (guanosine-2'-O-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing 2'-O-methylguanosine." [EC:2.1.1.34] subset: gosubset_prok synonym: "S-adenosyl-L-methionine:tRNA (guanosine-2'-O-)-methyltransferase activity" EXACT [EC:2.1.1.34] synonym: "S-adenosyl-L-methionine:tRNA guanosine-2'-O-methyltransferase activity" EXACT [EC:2.1.1.34] synonym: "transfer ribonucleate guanosine 2'-methyltransferase activity" EXACT [EC:2.1.1.34] synonym: "tRNA (Gm18) 2'-O-methyltransferase activity" EXACT [EC:2.1.1.34] synonym: "tRNA (Gm18) methyltransferase activity" EXACT [EC:2.1.1.34] synonym: "tRNA (guanosine 2')-methyltransferase activity" EXACT [EC:2.1.1.34] synonym: "tRNA guanosine 2'-methyltransferase activity" EXACT [EC:2.1.1.34] synonym: "tRNA guanosine-2'-O-methyltransferase activity" EXACT [EC:2.1.1.34] xref: EC:2.1.1.34 xref: MetaCyc:2.1.1.34-RXN is_a: GO:0016423 ! tRNA (guanine) methyltransferase activity [Term] id: GO:0009047 name: dosage compensation by hyperactivation of X chromosome namespace: biological_process def: "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global hyperactivation of all, or most of, the genes on the X-chromosome in the heterogametic sex, leading to a two-fold increase in gene expression from this chromosome. An example of this is found in Drosophila melanogaster." [GOC:jl, ISBN:0140512888, PMID:11498577] is_a: GO:0007549 ! dosage compensation [Term] id: GO:0009048 name: dosage compensation by inactivation of X chromosome namespace: biological_process def: "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex." [GOC:jl, ISBN:0140512888, PMID:11498577] synonym: "Barr body formation" RELATED [] synonym: "chromosome inactivation" BROAD [] synonym: "X chromosome inactivation" EXACT [] xref: Wikipedia:X-inactivation is_a: GO:0007549 ! dosage compensation [Term] id: GO:0009299 name: mRNA transcription namespace: biological_process alt_id: GO:0061023 def: "The cellular synthesis of messenger RNA (mRNA) from a DNA template." [GOC:jl] subset: gosubset_prok synonym: "cellular mRNA transcription" EXACT [] synonym: "mRNA biosynthesis" BROAD [] synonym: "mRNA biosynthetic process" BROAD [] synonym: "mRNA synthesis" BROAD [] is_a: GO:0006351 ! transcription, DNA-dependent [Term] id: GO:0009300 name: antisense RNA transcription namespace: biological_process def: "The synthesis of antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis, on a template of DNA." [GOC:jl] subset: gosubset_prok is_a: GO:0006351 ! transcription, DNA-dependent [Term] id: GO:0009301 name: snRNA transcription namespace: biological_process def: "The synthesis of small nuclear RNA (snRNA) from a DNA template." [GOC:jl, ISBN:0321000382] is_a: GO:0006351 ! transcription, DNA-dependent [Term] id: GO:0009302 name: snoRNA transcription namespace: biological_process def: "The synthesis of small nucleolar RNA (snoRNA) from a DNA template." [GOC:jl] is_a: GO:0006351 ! transcription, DNA-dependent [Term] id: GO:0009303 name: rRNA transcription namespace: biological_process def: "The synthesis of ribosomal RNA (rRNA), any RNA that forms part of the ribosomal structure, from a DNA template." [GOC:jl, ISBN:0198506732] subset: gosubset_prok synonym: "rRNA biosynthesis" BROAD [] synonym: "rRNA biosynthetic process" BROAD [] synonym: "rRNA synthesis" BROAD [] is_a: GO:0006351 ! transcription, DNA-dependent [Term] id: GO:0009304 name: tRNA transcription namespace: biological_process def: "The synthesis of transfer RNA (tRNA) from a DNA template." [GOC:jl] subset: gosubset_prok synonym: "tRNA biosynthesis" BROAD [] synonym: "tRNA biosynthetic process" BROAD [] synonym: "tRNA synthesis" BROAD [] is_a: GO:0006351 ! transcription, DNA-dependent [Term] id: GO:0009371 name: positive regulation of transcription by pheromones namespace: biological_process def: "Any process involving pheromones that activates or increases the rate of transcription." [GOC:go_curators] subset: gosubset_prok synonym: "activation of transcription by pheromones" NARROW [] synonym: "stimulation of transcription by pheromones" NARROW [] synonym: "up regulation of transcription by pheromones" EXACT [] synonym: "up-regulation of transcription by pheromones" EXACT [] synonym: "upregulation of transcription by pheromones" EXACT [] is_a: GO:0009373 ! regulation of transcription by pheromones is_a: GO:0045893 ! positive regulation of transcription, DNA-dependent [Term] id: GO:0009373 name: regulation of transcription by pheromones namespace: biological_process def: "Any process involving pheromones that modulates the frequency, rate or extent of transcription." [GOC:go_curators] subset: gosubset_prok is_a: GO:0006355 ! regulation of transcription, DNA-dependent [Term] id: GO:0009383 name: rRNA (cytosine-C5-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to cytosine to form 5-methylcytosine in small subunit ribosomal RNA." [GOC:imk, PMID:10026269, PMID:18786544] synonym: "rRNA (cytosine-C5-967)-methyltransferase activity" NARROW [] synonym: "rRNA m5C967 methyltransferase activity" NARROW [] xref: EC:2.1.1.- is_a: GO:0016434 ! rRNA (cytosine) methyltransferase activity [Term] id: GO:0009386 name: translational attenuation namespace: biological_process def: "Translational attenuation is a regulatory mechanism analogous to ribosome-mediated transcriptional attenuation. The system requires the presence of a short ORF, called a leader peptide, encoded in the mRNA upstream of the ribosome-binding site and start codon of the gene whose translation is to be regulated. Certain conditions, such as presence of the antibiotic tetracycline in bacteria or amino acid starvation, may cause slowing or stalling of the ribosome translating the leader peptide. The stalled ribosome masks a region of the mRNA and affects which of two alternative mRNA folded structures will form, therefore controlling whether or not a ribosome will bind and initiate translation of the downstream gene. Translational attenuation is analogous to ribosome-mediated transcriptional attenuation, in which mRNA remodeling caused by ribosome stalling regulates transcriptional termination rather than translational initiation." [PMID:15694341, PMID:15805513] subset: gosubset_prok is_a: GO:0006417 ! regulation of translation [Term] id: GO:0009452 name: 7-methylguanosine RNA capping namespace: biological_process def: "The sequence of enzymatic reactions by which the 5' cap structure, an inverted 7-methylguanosine linked via a 5'-5' triphosphate bridge (m7G(5')ppp(5')X) to the first transcribed residue, is added to a nascent RNA polymerase II transcript." [PMID:9266685] synonym: "m(7)G RNA capping" EXACT [GOC:bf, GOC:krc, GOC:mah] synonym: "RNA capping" BROAD [GOC:krc, GOC:mah] is_a: GO:0036260 ! RNA capping [Term] id: GO:0010216 name: maintenance of DNA methylation namespace: biological_process def: "Any process involved in maintaining the methylation state of a nucleotide sequence." [PMID:11898023] relationship: part_of GO:0006306 ! DNA methylation [Term] id: GO:0010239 name: chloroplast mRNA processing namespace: biological_process def: "Steps involved in processing precursor RNAs arising from transcription of operons in the chloroplast genome into mature mRNAs." [GOC:tb, PMID:9648738] is_a: GO:0006397 ! mRNA processing is_a: GO:0031425 ! chloroplast RNA processing [Term] id: GO:0010267 name: production of ta-siRNAs involved in RNA interference namespace: biological_process def: "Cleavage of double-stranded RNA to form trans-acting small interfering RNA molecules (siRNAs) of 21-23 nucleotides. ta-siRNAs arise from PolII genes and function like miRNAs to guide cleavage of target mRNAs." [GOC:tb, PMID:16129836] synonym: "RNA interference, production of ta-siRNAs" EXACT [GOC:mah] is_a: GO:0030422 ! production of siRNA involved in RNA interference [Term] id: GO:0010424 name: DNA methylation on cytosine within a CG sequence namespace: biological_process def: "The covalent transfer of a methyl group to C-5 or N-4 of a cytosine located within a CG sequence in a DNA molecule." [GOC:dph, GOC:tb, PMID:17239600] synonym: "cytosine methylation within a CG sequence" EXACT [GOC:dph, GOC:tb] is_a: GO:0032776 ! DNA methylation on cytosine [Term] id: GO:0010425 name: DNA methylation on cytosine within a CNG sequence namespace: biological_process def: "The covalent transfer of a methyl group, to C-5 or N-4, of a cytosine located within a CNG sequence in a DNA molecule. N stands for any nucleotide." [GOC:dph, GOC:tb, PMID:17239600] synonym: "cytosine methylation within a CNG sequence" EXACT [GOC:dph, GOC:tb] is_a: GO:0032776 ! DNA methylation on cytosine [Term] id: GO:0010426 name: DNA methylation on cytosine within a CHH sequence namespace: biological_process def: "The covalent transfer of a methyl group, to C-5 or N-4, of a cytosine located within an asymmetric CHH sequence in a DNA molecule. H stands for an adenine, cytosine, or thymine nucleotide." [GOC:dph, GOC:mah, GOC:tb, PMID:15861207, PMID:17239600] synonym: "cytosine methylation within a CHH sequence" EXACT [GOC:mah] synonym: "cytosine methylation within a CNN sequence" EXACT [GOC:dph, GOC:tb] synonym: "DNA methylation on cytosine within a CNN sequence" EXACT [GOC:mah] is_a: GO:0032776 ! DNA methylation on cytosine [Term] id: GO:0010467 name: gene expression namespace: biological_process def: "The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb] subset: gosubset_prok xref: Reactome:REACT_100537 "Gene Expression, Xenopus tropicalis" xref: Reactome:REACT_101147 "Gene Expression, Danio rerio" xref: Reactome:REACT_101952 "Gene Expression, Sus scrofa" xref: Reactome:REACT_105649 "Gene Expression, Drosophila melanogaster" xref: Reactome:REACT_108313 "Gene Expression, Caenorhabditis elegans" xref: Reactome:REACT_29068 "Gene Expression, Escherichia coli" xref: Reactome:REACT_34240 "Gene Expression, Staphylococcus aureus N315" xref: Reactome:REACT_71 "Gene Expression, Homo sapiens" xref: Reactome:REACT_78136 "Gene Expression, Mus musculus" xref: Reactome:REACT_78959 "Gene Expression, Taeniopygia guttata" xref: Reactome:REACT_79662 "Gene Expression, Plasmodium falciparum" xref: Reactome:REACT_85241 "Gene Expression, Oryza sativa" xref: Reactome:REACT_85359 "Gene Expression, Gallus gallus" xref: Reactome:REACT_86357 "Gene Expression, Canis familiaris" xref: Reactome:REACT_89816 "Gene Expression, Mycobacterium tuberculosis" xref: Reactome:REACT_91657 "Gene Expression, Arabidopsis thaliana" xref: Reactome:REACT_91965 "Gene Expression, Rattus norvegicus" xref: Reactome:REACT_93586 "Gene Expression, Dictyostelium discoideum" xref: Reactome:REACT_93968 "Gene Expression, Bos taurus" xref: Reactome:REACT_94814 "Gene Expression, Schizosaccharomyces pombe" xref: Reactome:REACT_98256 "Gene Expression, Saccharomyces cerevisiae" xref: Wikipedia:Gene_expression is_a: GO:0043170 ! macromolecule metabolic process [Term] id: GO:0010468 name: regulation of gene expression namespace: biological_process def: "Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb] subset: gosubset_prok synonym: "regulation of gene product expression" RELATED [GOC:curators] synonym: "regulation of protein expression" NARROW [GOC:curators] xref: Wikipedia:Regulation_of_gene_expression intersection_of: regulates GO:0010467 ! gene expression relationship: regulates GO:0010467 ! gene expression [Term] id: GO:0010495 name: long-distance posttranscriptional gene silencing namespace: biological_process def: "A posttranscriptional gene silencing process in which the silencing signal originates in a tissue separate from the tissue in which the silencing takes place." [GOC:dph, GOC:tb, PMID:11590235, PMID:17785412] synonym: "long-distance propagation of posttranscriptional gene silencing" EXACT [GOC:dph, GOC:tb] is_a: GO:0016441 ! posttranscriptional gene silencing [Term] id: GO:0010599 name: production of lsiRNA involved in RNA interference namespace: biological_process def: "Cleavage of double-stranded RNA to form lsiRNA (long small interfering RNA), a class of siRNAs 30 to 40 nt in length. lsiRNAs are induced by pathogen infection or under specific growth conditions." [PMID:18003861] synonym: "RNA interference, production of lsiRNA" EXACT [GOC:mah] is_a: GO:0070918 ! production of small RNA involved in gene silencing by RNA relationship: part_of GO:0016246 ! RNA interference [Term] id: GO:0010608 name: posttranscriptional regulation of gene expression namespace: biological_process def: "Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript." [GOC:dph, GOC:tb] is_a: GO:0010468 ! regulation of gene expression [Term] id: GO:0010609 name: mRNA localization resulting in posttranscriptional regulation of gene expression namespace: biological_process def: "Any process that modulates the frequency, rate or extent of gene expression after the production of a mRNA transcript by its transport into, or maintainance in, a specific location within the cell." [GOC:dph, GOC:tb] synonym: "mRNA localisation resulting in posttranscriptional regulation of gene expression" EXACT [] synonym: "posttranscriptional regulation of gene expression by mRNA localisation" EXACT [GOC:mah] synonym: "posttranscriptional regulation of gene expression by mRNA localization" EXACT [] is_a: GO:0010608 ! posttranscriptional regulation of gene expression intersection_of: results_in GO:0010608 ! posttranscriptional regulation of gene expression [Term] id: GO:0010610 name: regulation of mRNA stability involved in response to stress namespace: biological_process def: "Any process that modulates the propensity of mRNA molecules to degradation that is part of a change in state or activity of a cell as a result of an exogenous disturbance." [GOC:dph, GOC:tb] is_a: GO:0043488 ! regulation of mRNA stability intersection_of: GO:0043488 ! regulation of mRNA stability [Term] id: GO:0010620 name: negative regulation of transcription by transcription factor catabolism namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA-dependent transcription using a mechanism that involves the catabolism of a sequence-specific DNA binding transcription factor by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome." [GOC:bf, GOC:dph, GOC:tb] is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent intersection_of: results_in GO:0045892 ! negative regulation of transcription, DNA-dependent [Term] id: GO:0010621 name: negative regulation of transcription by transcription factor localization namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA-dependent transcription using a mechanism that involves the localization of a transcription factor." [GOC:dph, GOC:tb] synonym: "negative regulation of transcription by transcription factor localisation" EXACT [GOC:mah] is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent [Term] id: GO:0010628 name: positive regulation of gene expression namespace: biological_process def: "Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb] is_a: GO:0010468 ! regulation of gene expression intersection_of: positively_regulates GO:0010467 ! gene expression relationship: positively_regulates GO:0010467 ! gene expression [Term] id: GO:0010629 name: negative regulation of gene expression namespace: biological_process def: "Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb] is_a: GO:0010468 ! regulation of gene expression intersection_of: negatively_regulates GO:0010467 ! gene expression relationship: negatively_regulates GO:0010467 ! gene expression [Term] id: GO:0010672 name: regulation of transcription from RNA polymerase II promoter during meiosis namespace: biological_process def: "A cell cycle process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter during meiosis." [GOC:dph, GOC:tb] synonym: "regulation of transcription from RNA polymerase II promoter, meiotic" EXACT [GOC:mah] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter is_a: GO:0051037 ! regulation of transcription during meiosis [Term] id: GO:0010673 name: positive regulation of transcription from RNA polymerase II promoter during meiosis namespace: biological_process def: "A cell cycle process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter during meiosis." [GOC:dph, GOC:tb] synonym: "positive regulation of transcription from RNA polymerase II promoter, meiotic" EXACT [GOC:mah] is_a: GO:0010672 ! regulation of transcription from RNA polymerase II promoter during meiosis is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter is_a: GO:0051039 ! positive regulation of transcription during meiosis [Term] id: GO:0010674 name: negative regulation of transcription from RNA polymerase II promoter during meiosis namespace: biological_process def: "A cell cycle process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter during meiosis." [GOC:dph, GOC:tb] synonym: "negative regulation of transcription from RNA polymerase II promoter, meiotic" EXACT [GOC:mah] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter is_a: GO:0010672 ! regulation of transcription from RNA polymerase II promoter during meiosis is_a: GO:0051038 ! negative regulation of transcription during meiosis [Term] id: GO:0010678 name: negative regulation of cellular carbohydrate metabolic process by negative regulation of transcription, DNA-dependent namespace: biological_process def: "Any cellular process that decreases the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates carried out by repression of transcription." [GOC:dph, GOC:tb] synonym: "negative regulation of cellular carbohydrate metabolic process by repression of transcription" EXACT [GOC:bf, GOC:vw] synonym: "negative regulation of cellular carbohydrate metabolic process by transcriptional repression" EXACT [GOC:dph, GOC:tb] is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent intersection_of: negatively_regulates GO:0006351 ! transcription, DNA-dependent [Term] id: GO:0010688 name: negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that decreases the frequency, rate or extent of the synthesis of RNA from ribosomal protein genes by RNA polymerase II, originating at an RNA polymerase II promoter." [GOC:dph, GOC:tb, GOC:txnOH] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter is_a: GO:0060962 ! regulation of ribosomal protein gene transcription from RNA polymerase II promoter [Term] id: GO:0010689 name: negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter in response to chemical stimulus namespace: biological_process def: "Any process that decreases the frequency, rate or extent of the synthesis of RNA from ribosomal protein genes by RNA polymerase II, originating at an RNA polymerase II promoter, as a result of a chemical stimulus." [GOC:dph, GOC:tb, GOC:txnOH] is_a: GO:0010688 ! negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter [Term] id: GO:0010690 name: negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter in response to stress namespace: biological_process def: "Any process that decreases the frequency, rate or extent of the synthesis of RNA from ribosomal protein genes by RNA polymerase II, originating at an RNA polymerase II promoter, as a result of a disturbance in organismal or cellular homeostasis." [GOC:dph, GOC:tb, GOC:txnOH] is_a: GO:0010688 ! negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter [Term] id: GO:0010691 name: negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter in response to nutrient levels namespace: biological_process def: "Any process that decreases the frequency, rate or extent of the synthesis of RNA from ribosomal protein genes by RNA polymerase II, originating at an RNA polymerase II promoter, as a result of a stimulus reflecting the presence, absence, or concentration of nutrients." [GOC:dph, GOC:tb, GOC:txnOH] is_a: GO:0010688 ! negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter [Term] id: GO:0010723 name: positive regulation of transcription from RNA polymerase II promoter in response to iron namespace: biological_process def: "Any process that increases the rate of transcription from an RNA polymerase II promoter in response to an iron stimulus." [GOC:dph, GOC:tb] is_a: GO:0034395 ! regulation of transcription from RNA polymerase II promoter in response to iron is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter [Term] id: GO:0010735 name: positive regulation of transcription via serum response element binding namespace: biological_process def: "Any process that increases the frequency, rate or extent of the specifically regulated synthesis of RNA from DNA encoding a specific set of genes as a result of a transcription factor interacting with a serum response element (SRE). A serum response element is a short sequence with dyad symmetry found in the promoters of some of the cellular immediate-early genes, regulated by serum." [GOC:BHF, GOC:dph, GOC:rl, GOC:tb] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter [Term] id: GO:0010755 name: regulation of plasminogen activation namespace: biological_process def: "Any process that modulates the rate, frequency or extent of plasminogen activation. Plasminogen activation is the process in which plasminogen is processed to plasmin." [GOC:BHF, GOC:dph, GOC:tb] is_a: GO:0070613 ! regulation of protein processing intersection_of: regulates GO:0031639 ! plasminogen activation relationship: regulates GO:0031639 ! plasminogen activation [Term] id: GO:0010756 name: positive regulation of plasminogen activation namespace: biological_process def: "Any process that increases the rate, frequency or extent of plasminogen activation. Plasminogen activation is the process in which plasminogen is processed to plasmin." [GOC:BHF, GOC:dph, GOC:tb] is_a: GO:0010755 ! regulation of plasminogen activation is_a: GO:0010954 ! positive regulation of protein processing intersection_of: positively_regulates GO:0031639 ! plasminogen activation relationship: positively_regulates GO:0031639 ! plasminogen activation [Term] id: GO:0010757 name: negative regulation of plasminogen activation namespace: biological_process def: "Any process that decreases the rate, frequency or extent of plasminogen activation. Plasminogen activation is the process in which plasminogen is processed to plasmin." [GOC:BHF, GOC:dph, GOC:tb] synonym: "inhibition of plasminogen activation" NARROW [GOC:dph, GOC:tb] is_a: GO:0010755 ! regulation of plasminogen activation is_a: GO:0010955 ! negative regulation of protein processing intersection_of: negatively_regulates GO:0031639 ! plasminogen activation relationship: negatively_regulates GO:0031639 ! plasminogen activation [Term] id: GO:0010767 name: regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a UV damage stimulus." [GOC:dph, GOC:tb] is_a: GO:0043618 ! regulation of transcription from RNA polymerase II promoter in response to stress [Term] id: GO:0010768 name: negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a UV damage stimulus." [GOC:dph, GOC:tb] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter is_a: GO:0010767 ! regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage [Term] id: GO:0010892 name: positive regulation of mitochondrial translation in response to stress namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of mitochondrial translation as a result of a stimulus indicating the organism is under stress." [GOC:dph, GOC:jp, GOC:tb, PMID:8830768] is_a: GO:0032056 ! positive regulation of translation in response to stress is_a: GO:0070131 ! positive regulation of mitochondrial translation [Term] id: GO:0010944 name: negative regulation of transcription by competitive promoter binding namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA-dependent transcription using a mechanism that involves direct competition for interaction with a promoter binding site." [GOC:tb] is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent [Term] id: GO:0010954 name: positive regulation of protein processing namespace: biological_process def: "Any process that increases the rate, frequency or extent of protein maturation by peptide bond cleavage." [GOC:dph, GOC:mah, GOC:tb] synonym: "positive regulation of protein maturation by peptide bond cleavage" EXACT [GOC:bf] is_a: GO:0070613 ! regulation of protein processing intersection_of: positively_regulates GO:0016485 ! protein processing relationship: positively_regulates GO:0016485 ! protein processing created_by: tanyaberardini creation_date: 2009-04-27T12:09:13Z [Term] id: GO:0010955 name: negative regulation of protein processing namespace: biological_process def: "Any process that decreases the rate, frequency or extent of protein maturation by peptide bond cleavage." [GOC:dph, GOC:mah, GOC:tb] synonym: "negative regulation of protein maturation by peptide bond cleavage" EXACT [GOC:bf] is_a: GO:0070613 ! regulation of protein processing intersection_of: negatively_regulates GO:0016485 ! protein processing relationship: negatively_regulates GO:0016485 ! protein processing created_by: tanyaberardini creation_date: 2009-04-27T12:10:19Z [Term] id: GO:0010964 name: regulation of chromatin silencing by small RNA namespace: biological_process def: "Any process that modulates the frequency, rate or extent of chromatin silencing by small RNA. Chromatin silencing by small RNA is the repression of transcription by conversion of large regions of DNA into heterochromatin, directed by small RNAs sharing sequence identity to the repressed region." [GOC:dph, GOC:tb] is_a: GO:0031935 ! regulation of chromatin silencing is_a: GO:0060966 ! regulation of gene silencing by RNA intersection_of: regulates GO:0031048 ! chromatin silencing by small RNA relationship: regulates GO:0031048 ! chromatin silencing by small RNA created_by: tanyaberardini creation_date: 2009-05-20T11:25:42Z [Term] id: GO:0010978 name: gene silencing involved in chronological cell aging namespace: biological_process def: "Any transcriptional or post-transcriptional process, arising in non-dividing cells as they age, carried out at the cellular level that results in long-term gene inactivation." [GOC:dph, GOC:jp, GOC:tb] is_a: GO:0016458 ! gene silencing intersection_of: GO:0016458 ! gene silencing created_by: tanyaberardini creation_date: 2009-06-01T11:39:42Z [Term] id: GO:0010998 name: regulation of translational initiation by eIF2 alpha phosphorylation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of translation initiation in response to stress by the phosphorylation of eIF2 alpha." [GOC:BHF, GOC:dph, GOC:hjd, GOC:tb] is_a: GO:0043558 ! regulation of translational initiation in response to stress created_by: tanyaberardini creation_date: 2009-06-10T11:27:47Z [Term] id: GO:0010999 name: regulation of eIF2 alpha phosphorylation by heme namespace: biological_process def: "Any process that modulates the rate, frequency, or extent of eIF2 alpha phosphorylation as a result of heme levels." [GOC:BHF, GOC:dph, GOC:tb] relationship: regulates GO:0010998 ! regulation of translational initiation by eIF2 alpha phosphorylation created_by: tanyaberardini creation_date: 2009-06-10T11:42:10Z [Term] id: GO:0015667 name: site-specific DNA-methyltransferase (cytosine-N4-specific) activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + DNA cytosine = S-adenosyl-L-homocysteine + DNA N4-methylcytosine." [EC:2.1.1.113] subset: gosubset_prok synonym: "DNA[cytosine-N4]methyltransferase activity" EXACT [EC:2.1.1.113] synonym: "m4C-forming MTase activity" EXACT [EC:2.1.1.113] synonym: "modification methylase activity" RELATED [EC:2.1.1.113] synonym: "N(4)-cytosine-specific DNA methylase activity" EXACT [EC:2.1.1.113] synonym: "N4-cytosine-specific DNA methylase activity" EXACT [EC:2.1.1.113] synonym: "restriction-modification system activity" RELATED [EC:2.1.1.113] synonym: "S-adenosyl-L-methionine:DNA-cytosine 4-N-methyltransferase activity" EXACT [EC:2.1.1.113] synonym: "S-adenosyl-L-methionine:DNA-cytosine N4-methyltransferase activity" EXACT [EC:2.1.1.113] xref: EC:2.1.1.113 xref: MetaCyc:2.1.1.113-RXN is_a: GO:0009008 ! DNA-methyltransferase activity relationship: part_of GO:0090124 ! N-4 methylation of cytosine [Term] id: GO:0016149 name: translation release factor activity, codon specific namespace: molecular_function def: "A translation release factor that is specific for one or more particular termination codons; acts at the ribosomal A-site and require polypeptidyl-tRNA at the P-site." [ISBN:0198547684] subset: gosubset_prok is_a: GO:0003747 ! translation release factor activity [Term] id: GO:0016150 name: translation release factor activity, codon nonspecific namespace: molecular_function def: "A translation release factor that is not specific to particular codons; binds to guanine nucleotides." [ISBN:0198547684] is_a: GO:0003747 ! translation release factor activity [Term] id: GO:0016180 name: snRNA processing namespace: biological_process def: "Any process involved in the conversion of a primary small nuclear RNA (snRNA) transcript into a mature snRNA molecule." [GOC:jl] is_a: GO:0034470 ! ncRNA processing [Term] id: GO:0016246 name: RNA interference namespace: biological_process def: "The process in which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes." [GOC:ems, PMID:11201747, PMID:11713190, PMID:18771919] comment: Note that this term refers specifically to posttranscriptional mechanisms by which small interfering RNAs down-regulate gene expression. Also consider annotating to other descendants of 'gene silencing by RNA ; GO:0031047'. synonym: "posttranscriptional gene silencing by siRNA" EXACT [GOC:mah] synonym: "RNAi" EXACT [] xref: Wikipedia:RNA_interference is_a: GO:0035194 ! posttranscriptional gene silencing by RNA [Term] id: GO:0016300 name: tRNA (uracil) methyltransferase activity namespace: molecular_function alt_id: GO:0016431 def: "Catalysis of the transfer of a methyl group from a donor to a uracil residue in a tRNA molecule." [GOC:mah] comment: Note that the methyl donor is usually S-adenosyl-L-methionine, but there is at least one exception (see GO:0030698). subset: gosubset_prok synonym: "tRNA (uridine) methyltransferase activity" EXACT [] xref: EC:2.1.1.- is_a: GO:0008175 ! tRNA methyltransferase activity [Term] id: GO:0016423 name: tRNA (guanine) methyltransferase activity namespace: molecular_function alt_id: GO:0016424 def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing methylguanine." [EC:2.1.1.-] subset: gosubset_prok synonym: "tRNA (guanosine) methyltransferase activity" EXACT [] xref: EC:2.1.1.- is_a: GO:0008175 ! tRNA methyltransferase activity [Term] id: GO:0016426 name: tRNA (adenine) methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing methyladenine." [EC:2.1.1.-] subset: gosubset_prok xref: EC:2.1.1.- is_a: GO:0008175 ! tRNA methyltransferase activity [Term] id: GO:0016427 name: tRNA (cytosine) methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing methylcytosine." [EC:2.1.1.-] xref: EC:2.1.1.- is_a: GO:0008175 ! tRNA methyltransferase activity [Term] id: GO:0016428 name: tRNA (cytosine-5-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing 5-methylcytosine." [EC:2.1.1.29] synonym: "S-adenosyl-L-methionine:tRNA (cytosine-5-)-methyltransferase activity" EXACT [EC:2.1.1.29] synonym: "transfer ribonucleate cytosine 5-methyltransferase activity" EXACT [EC:2.1.1.29] synonym: "transfer RNA cytosine 5-methyltransferase activity" EXACT [EC:2.1.1.29] xref: EC:2.1.1.- is_a: GO:0016427 ! tRNA (cytosine) methyltransferase activity [Term] id: GO:0016429 name: tRNA (adenine-N1-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N1-methyladenine." [EC:2.1.1.36] subset: gosubset_prok synonym: "1-methyladenine transfer RNA methyltransferase activity" EXACT [EC:2.1.1.36] synonym: "adenine-1-methylase activity" EXACT [EC:2.1.1.36] synonym: "S-adenosyl-L-methionine:tRNA (adenine-1-N-)-methyltransferase activity" EXACT [EC:2.1.1.36] synonym: "S-adenosyl-L-methionine:tRNA (adenine-N1-)-methyltransferase activity" EXACT [EC:2.1.1.36] synonym: "transfer ribonucleate adenine 1-methyltransferase activity" EXACT [EC:2.1.1.36] synonym: "transfer RNA (adenine-1) methyltransferase activity" EXACT [EC:2.1.1.36] xref: EC:2.1.1.- is_a: GO:0016426 ! tRNA (adenine) methyltransferase activity [Term] id: GO:0016430 name: tRNA (adenine-N6-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N6-methyladenine." [EC:2.1.1.55] synonym: "S-adenosyl-L-methionine:tRNA (adenine-6-N-)-methyltransferase activity" EXACT [EC:2.1.1.55] synonym: "S-adenosyl-L-methionine:tRNA (adenine-N6-)-methyltransferase activity" EXACT [EC:2.1.1.55] xref: EC:2.1.1.55 xref: MetaCyc:TRNA-ADENINE-N6--METHYLTRANSFERASE-RXN is_a: GO:0016426 ! tRNA (adenine) methyltransferase activity [Term] id: GO:0016433 name: rRNA (adenine) methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing methyladenine." [EC:2.1.1.-] subset: gosubset_prok xref: EC:2.1.1.- is_a: GO:0008649 ! rRNA methyltransferase activity [Term] id: GO:0016434 name: rRNA (cytosine) methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing methylcytosine." [EC:2.1.1.-] subset: gosubset_prok xref: EC:2.1.1.- is_a: GO:0008649 ! rRNA methyltransferase activity [Term] id: GO:0016435 name: rRNA (guanine) methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing methylguanine." [EC:2.1.1.-] subset: gosubset_prok xref: EC:2.1.1.- is_a: GO:0008649 ! rRNA methyltransferase activity [Term] id: GO:0016436 name: rRNA (uridine) methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing methyluridine." [EC:2.1.1.-] subset: gosubset_prok xref: EC:2.1.1.- is_a: GO:0008649 ! rRNA methyltransferase activity [Term] id: GO:0016441 name: posttranscriptional gene silencing namespace: biological_process def: "The inactivation of gene expression by a posttranscriptional mechanism." [GOC:mah, PMID:15020054] synonym: "cosuppression" RELATED [] synonym: "post-transcriptional gene silencing" EXACT [GOC:vw] synonym: "PTGS" EXACT [] synonym: "quelling" EXACT [] xref: Wikipedia:Post_transcriptional_gene_silencing is_a: GO:0010608 ! posttranscriptional regulation of gene expression is_a: GO:0016458 ! gene silencing is_a: GO:0040029 ! regulation of gene expression, epigenetic [Term] id: GO:0016457 name: dosage compensation complex assembly involved in dosage compensation by hyperactivation of X chromosome namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins on DNA to form the complex that mediates dosage compensation on the X chromosome of the heterogametic sex, ultimately resulting in a two-fold increase in transcription from this chromosome. An example of this is found in Drosophila melanogaster." [GOC:jl] synonym: "dosage compensation complex assembly during dosage compensation by hyperactivation of X chromosome" RELATED [GOC:dph, GOC:tb] is_a: GO:0042714 ! dosage compensation complex assembly intersection_of: GO:0042714 ! dosage compensation complex assembly intersection_of: part_of GO:0009047 ! dosage compensation by hyperactivation of X chromosome relationship: part_of GO:0009047 ! dosage compensation by hyperactivation of X chromosome [Term] id: GO:0016458 name: gene silencing namespace: biological_process def: "Any transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation." [GOC:dph, GOC:jid, GOC:tb] comment: Note that this process is the opposite of long-term maintenance of gene activation. subset: goslim_pir synonym: "long-term maintenance of gene inactivation" RELATED [] xref: Wikipedia:Gene_silencing is_a: GO:0010629 ! negative regulation of gene expression [Term] id: GO:0016479 name: negative regulation of transcription from RNA polymerase I promoter namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase I promoter." [GOC:go_curators] synonym: "down regulation of transcription from RNA polymerase I promoter" EXACT [] synonym: "down-regulation of transcription from RNA polymerase I promoter" EXACT [] synonym: "downregulation of transcription from RNA polymerase I promoter" EXACT [] synonym: "inhibition of transcription from RNA polymerase I promoter" NARROW [] synonym: "negative regulation of transcription from Pol I promoter" EXACT [] is_a: GO:0006356 ! regulation of transcription from RNA polymerase I promoter is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent intersection_of: negatively_regulates GO:0006360 ! transcription from RNA polymerase I promoter relationship: negatively_regulates GO:0006360 ! transcription from RNA polymerase I promoter [Term] id: GO:0016480 name: negative regulation of transcription from RNA polymerase III promoter namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase III promoter." [GOC:go_curators] synonym: "down regulation of transcription from RNA polymerase III promoter" EXACT [] synonym: "down-regulation of transcription from RNA polymerase III promoter" EXACT [] synonym: "downregulation of transcription from RNA polymerase III promoter" EXACT [] synonym: "inhibition of transcription from RNA polymerase III promoter" NARROW [] synonym: "negative regulation of transcription from Pol III promoter" EXACT [] is_a: GO:0006359 ! regulation of transcription from RNA polymerase III promoter is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent intersection_of: negatively_regulates GO:0006383 ! transcription from RNA polymerase III promoter relationship: negatively_regulates GO:0006383 ! transcription from RNA polymerase III promoter [Term] id: GO:0016485 name: protein processing namespace: biological_process alt_id: GO:0051605 def: "Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein." [GOC:curators, GOC:jl, GOC:jsg] subset: gosubset_prok synonym: "peptidolysis during protein maturation" RELATED [GOC:mah] synonym: "protein maturation by peptide bond cleavage" EXACT [GOC:bf] synonym: "protein maturation by peptide bond hydrolysis" EXACT [GOC:mah] synonym: "protein maturation by proteolysis" RELATED [GOC:mah] is_a: GO:0051604 ! protein maturation [Term] id: GO:0016486 name: peptide hormone processing namespace: biological_process def: "The generation of a mature peptide hormone by posttranslational processing of a prohormone." [GOC:mah] xref: Reactome:REACT_100567 "Peptide hormone biosynthesis, Canis familiaris" xref: Reactome:REACT_100961 "Peptide hormone biosynthesis, Bos taurus" xref: Reactome:REACT_109010 "Peptide hormone biosynthesis, Gallus gallus" xref: Reactome:REACT_109092 "Peptide hormone biosynthesis, Xenopus tropicalis" xref: Reactome:REACT_15452 "Peptide hormone biosynthesis, Homo sapiens" xref: Reactome:REACT_30665 "Peptide hormone biosynthesis, Sus scrofa" xref: Reactome:REACT_34278 "Peptide hormone biosynthesis, Taeniopygia guttata" xref: Reactome:REACT_91994 "Peptide hormone biosynthesis, Mus musculus" xref: Reactome:REACT_93420 "Peptide hormone biosynthesis, Rattus norvegicus" xref: Reactome:REACT_96896 "Peptide hormone biosynthesis, Danio rerio" is_a: GO:0016485 ! protein processing [Term] id: GO:0016539 name: intein-mediated protein splicing namespace: biological_process def: "The removal of an internal amino acid sequence (an intein) from a protein during protein maturation; the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues." [GOC:ma, http://www.neb.com/neb/inteins.html] subset: gosubset_prok synonym: "intein" RELATED [] is_a: GO:0030908 ! protein splicing [Term] id: GO:0016540 name: protein autoprocessing namespace: biological_process def: "Processing which a protein carries out itself. This involves actions such as the autolytic removal of residues to generate the mature form of the protein." [GOC:ai, PMID:9335337] subset: gosubset_prok is_a: GO:0016485 ! protein processing [Term] id: GO:0017055 name: negative regulation of RNA polymerase II transcriptional preinitiation complex assembly namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly." [GOC:go_curators] synonym: "down regulation of RNA polymerase II transcriptional preinitiation complex assembly" EXACT [] synonym: "down-regulation of RNA polymerase II transcriptional preinitiation complex assembly" EXACT [] synonym: "downregulation of RNA polymerase II transcriptional preinitiation complex assembly" EXACT [] synonym: "inhibition of RNA polymerase II transcriptional preinitiation complex assembly" NARROW [] synonym: "negative regulation of RNA polymerase II transcriptional pre-initiation complex assembly" EXACT [] synonym: "negative regulation of RNA polymerase II transcriptional pre-initiation complex biosynthesis" EXACT [] synonym: "negative regulation of RNA polymerase II transcriptional preinitiation complex formation" EXACT [] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter is_a: GO:0045898 ! regulation of RNA polymerase II transcriptional preinitiation complex assembly intersection_of: negatively_regulates GO:0051123 ! RNA polymerase II transcriptional preinitiation complex assembly relationship: negatively_regulates GO:0051123 ! RNA polymerase II transcriptional preinitiation complex assembly [Term] id: GO:0017082 name: mineralocorticoid receptor activity namespace: molecular_function def: "Combining with a mineralocorticoid and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II." [GOC:signaling, PMID:20932876] synonym: "aldosterone receptor" NARROW [] is_a: GO:0004879 ! ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity [Term] id: GO:0017148 name: negative regulation of translation namespace: biological_process alt_id: GO:0016478 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA." [GOC:isa_complete] subset: gosubset_prok synonym: "down regulation of protein biosynthetic process" EXACT [] synonym: "down-regulation of protein biosynthetic process" EXACT [] synonym: "downregulation of protein biosynthetic process" EXACT [] synonym: "inhibition of protein biosynthetic process" NARROW [] synonym: "negative regulation of protein anabolism" EXACT [] synonym: "negative regulation of protein biosynthesis" EXACT [] synonym: "negative regulation of protein biosynthetic process" EXACT [] synonym: "negative regulation of protein formation" EXACT [] synonym: "negative regulation of protein synthesis" EXACT [] synonym: "protein biosynthesis inhibitor activity" RELATED [] synonym: "protein biosynthetic process inhibitor activity" RELATED [] is_a: GO:0006417 ! regulation of translation intersection_of: negatively_regulates GO:0006412 ! translation relationship: negatively_regulates GO:0006412 ! translation [Term] id: GO:0017150 name: tRNA dihydrouridine synthase activity namespace: molecular_function def: "Catalysis of the reaction: tRNA-uracil + acceptor = tRNA-dihydrouridine + reduced acceptor." [PMID:11983710] subset: gosubset_prok relationship: part_of GO:0002943 ! tRNA dihydrouridine synthesis [Term] id: GO:0019056 name: modulation by virus of host transcription namespace: biological_process def: "The modulation by viral gene products of host RNA polymerase II facilitated transcription." [ISBN:0781718325] synonym: "modification by virus of host transcription" EXACT [] synonym: "viral perturbation of host cell transcription" EXACT [] is_a: GO:0006355 ! regulation of transcription, DNA-dependent is_a: GO:0039656 ! modulation by virus of host gene expression [Term] id: GO:0019057 name: modulation by virus of host translation namespace: biological_process def: "Any process in which a virus modulates the frequency, rate or extent of translation of host mRNA." [ISBN:0781718325] synonym: "host cell protein synthesis shutoff" BROAD [] synonym: "host cell shutoff" BROAD [] synonym: "modification by virus of host cell mRNA translation" EXACT [] synonym: "modulation of host translation by virus" EXACT [GOC:bf] synonym: "regulation of host mRNA translation by virus" EXACT [] synonym: "regulation of host translation by virus" EXACT [] synonym: "regulation of translation in host by virus" EXACT [] synonym: "viral host shutoff protein" RELATED [] synonym: "viral perturbation of host cell mRNA translation" EXACT [] is_a: GO:0039656 ! modulation by virus of host gene expression is_a: GO:0044073 ! modulation by symbiont of host translation [Term] id: GO:0019080 name: viral genome expression namespace: biological_process def: "A process by which a viral genome is converted into a mature gene product or products (proteins or RNA). This includes viral transcription, processing to produce a mature RNA product, and viral translation." [GOC:bf, GOC:jl, ISBN:0121585336] subset: virus_checked synonym: "viral gene expression" EXACT [GOC:jl] is_a: GO:0010467 ! gene expression [Term] id: GO:0019081 name: viral translation namespace: biological_process def: "A process by which viral mRNA is translated into viral protein, using the host cellular machinery." [GOC:bf, GOC:jl, ISBN:0781702534] subset: virus_checked synonym: "viral protein anabolism" EXACT [] synonym: "viral protein biosynthesis" EXACT [] synonym: "viral protein biosynthetic process" EXACT [ISBN:0781702534] synonym: "viral protein formation" EXACT [] synonym: "viral protein synthesis" EXACT [] is_a: GO:0006412 ! translation relationship: part_of GO:0019080 ! viral genome expression [Term] id: GO:0019082 name: viral protein processing namespace: biological_process def: "Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a viral protein." [GOC:bf, GOC:jl, ISBN:0781702534] subset: virus_checked xref: Reactome:REACT_6141 "Trimerization of HA, Homo sapiens" xref: Reactome:REACT_6187 "Palmitoylation of cysteine residues on HA in the cis-Golgi network, Homo sapiens" is_a: GO:0016485 ! protein processing relationship: part_of GO:0019080 ! viral genome expression [Term] id: GO:0019083 name: viral transcription namespace: biological_process def: "The process by which a viral genome is transcribed into messenger RNA (mRNA) within the host cell." [GOC:jl, ISBN:0781702534] xref: Reactome:REACT_6142 "Assembly of an Active Transcription Complex, Homo sapiens" xref: Reactome:REACT_6152 "Influenza Viral RNA Transcription and Replication, Homo sapiens" xref: Reactome:REACT_6210 "Elongation of viral mRNA, Homo sapiens" xref: Reactome:REACT_6233 "Transcription of the HIV genome, Homo sapiens" xref: Reactome:REACT_6239 "Priming and Initiation of Transcription, Homo sapiens" xref: Reactome:REACT_6264 "Polyadenylation and Termination, Homo sapiens" xref: Reactome:REACT_6354 "Viral Messenger RNA Synthesis, Homo sapiens" relationship: part_of GO:0019080 ! viral genome expression [Term] id: GO:0019084 name: (delayed) early viral mRNA transcription namespace: biological_process def: "The second round of viral gene transcription; most genes transcribed in this round are necessary for genome replication." [ISBN:0781702534] synonym: "beta protein" RELATED [] is_a: GO:0009299 ! mRNA transcription is_a: GO:0019083 ! viral transcription [Term] id: GO:0019085 name: immediate early viral mRNA transcription namespace: biological_process def: "The transcriptional period of the earliest expressed viral genes, mainly encoding transcriptional regulators." [ISBN:0781702534] synonym: "alpha protein" BROAD [] is_a: GO:0009299 ! mRNA transcription is_a: GO:0019083 ! viral transcription [Term] id: GO:0019086 name: late viral mRNA transcription namespace: biological_process def: "The last group of viral genes to be transcribed during the viral life cycle; genes consist mainly of those encoding structural proteins." [ISBN:0781702534] synonym: "gamma protein" RELATED [] is_a: GO:0009299 ! mRNA transcription is_a: GO:0019083 ! viral transcription [Term] id: GO:0019801 name: cyclization of asparagine involved in intein-mediated protein splicing namespace: biological_process def: "The cyclization of asparagine to yield an L-aspartimide (otherwise known as alpha-aminosuccinimide) residue at the C-terminus of an excised intein during protein splicing." [RESID:AA0302] comment: See also the biological process term 'intein-mediated protein splicing ; GO:0016539'. subset: gosubset_prok synonym: "cyclization of asparagine, during protein splicing" RELATED [GOC:dph, GOC:tb] xref: RESID:AA0302 relationship: part_of GO:0016539 ! intein-mediated protein splicing [Term] id: GO:0019802 name: cyclization of glutamine involved in intein-mediated protein splicing namespace: biological_process def: "The cyclization of glutamine to yield an L-glutamimide residue at the C-terminus of an excised intein during protein splicing." [GOC:dph, GOC:tb, RESID:AA0303] comment: Note that this term should not be confused with 'peptidyl-pyroglutamic acid biosynthesis, using glutaminyl-peptide cyclotransferase ; GO:0017186'. See also the biological process term 'intein-mediated protein splicing ; GO:0016539'. subset: gosubset_prok synonym: "cyclization of glutamine, during protein splicing" RELATED [GOC:dph, GOC:tb] xref: RESID:AA0303 relationship: part_of GO:0016539 ! intein-mediated protein splicing [Term] id: GO:0019988 name: charged-tRNA amino acid modification namespace: biological_process alt_id: GO:0030630 def: "The covalent alteration of an amino acid charged on a tRNA before it is incorporated into a protein, as in N-formylmethionine, selenocysteine or pyrrolysine." [GOC:jsg] subset: gosubset_prok synonym: "charged tRNA amino acid modification" EXACT [] synonym: "charged tRNA modification" EXACT [] synonym: "charged-tRNA modification" RELATED [] synonym: "pre-translational amino acid modification" EXACT [] synonym: "pre-translational protein modification" EXACT [] synonym: "pretranslation protein modification" EXACT [] synonym: "pretranslational amino acid modification" EXACT [] is_a: GO:0006400 ! tRNA modification [Term] id: GO:0021777 name: BMP signaling pathway involved in spinal cord association neuron specification namespace: biological_process def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to its commitment to an association neuron fate." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12593981] comment: This term was added by GO_REF:0000021. synonym: "BMP signalling pathway involved in spinal cord association neuron specification" EXACT [] synonym: "bone morphogenetic protein signaling pathway involved in spinal cord association neuron specification" EXACT [] synonym: "bone morphogenetic protein signalling pathway involved in spinal cord association neuron specification" EXACT [] is_a: GO:0021919 ! BMP signaling pathway involved in spinal cord dorsal/ventral patterning is_a: GO:0021920 ! regulation of transcription from RNA polymerase II promoter involved in spinal cord association neuron specification intersection_of: GO:0030509 ! BMP signaling pathway [Term] id: GO:0021882 name: regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the commitment of a neuroblast to a neuronal fate. The neuron will reside in the forebrain." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:16226447] comment: This term was added by GO_REF:0000021. is_a: GO:0060850 ! regulation of transcription involved in cell fate commitment intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter [Term] id: GO:0021909 name: regulation of transcription from RNA polymerase II promoter involved in spinal cord anterior-posterior patterning namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that results in the spatial identity of regions along the anterior-posterior axis of the spinal cord." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:11262869] comment: This term was added by GO_REF:0000021. is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter [Term] id: GO:0021912 name: regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that results the commitment of a cell to become a motor neuron in the ventral spinal cord." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:11262869] comment: This term was added by GO_REF:0000021. is_a: GO:0060850 ! regulation of transcription involved in cell fate commitment [Term] id: GO:0021913 name: regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that results in the commitment of a cell to become an interneuron in the ventral spinal cord." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:11262869] comment: This term was added by GO_REF:0000021. is_a: GO:0060850 ! regulation of transcription involved in cell fate commitment intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter [Term] id: GO:0021918 name: regulation of transcription from RNA polymerase II promoter involved in somatic motor neuron fate commitment namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the commitment of spinal cord motor neurons to specific motor neuron types along the anterior-posterior axis." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:11262869] comment: This term was added by GO_REF:0000021. is_a: GO:0060850 ! regulation of transcription involved in cell fate commitment intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter [Term] id: GO:0021919 name: BMP signaling pathway involved in spinal cord dorsal/ventral patterning namespace: biological_process def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the spatial identity of regions along the dorsal-ventral axis of the spinal cord." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12593981] comment: This term was added by GO_REF:0000021. synonym: "BMP signaling pathway in spinal cord dorsoventral patterning" EXACT [GOC:mah] synonym: "BMP signaling pathway involved in spinal cord dorsal-ventral patterning" EXACT [GOC:mah] synonym: "BMP signalling pathway involved in spinal cord dorsal-ventral patterning" EXACT [] synonym: "bone morphogenetic protein signaling pathway in spinal cord dorsal-ventral patterning" EXACT [] synonym: "bone morphogenetic protein signalling pathway involved in spinal cord dorsal-ventral patterning" EXACT [] is_a: GO:0030509 ! BMP signaling pathway intersection_of: GO:0030509 ! BMP signaling pathway [Term] id: GO:0021920 name: regulation of transcription from RNA polymerase II promoter involved in spinal cord association neuron specification namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the commitment of neuronal precursors to association neurons in the dorsal spinal cord." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12593981] comment: This term was added by GO_REF:0000021. is_a: GO:0060850 ! regulation of transcription involved in cell fate commitment intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter [Term] id: GO:0022024 name: BMP signaling pathway involved in forebrain neuron fate commitment namespace: biological_process def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the commitment of a neuroblast to a neuronal fate. The neuron will reside in the forebrain." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] comment: This term was added by GO_REF:0000021. synonym: "BMP signalling pathway involved in forebrain neuron fate commitment" EXACT [] synonym: "bone morphogenetic protein signaling pathway involved in forebrain neuron fate commitment" EXACT [] synonym: "bone morphogenetic protein signalling pathway involved in forebrain neuron fate commitment" EXACT [] is_a: GO:0021882 ! regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment is_a: GO:0030509 ! BMP signaling pathway intersection_of: GO:0030509 ! BMP signaling pathway [Term] id: GO:0022417 name: protein maturation by protein folding namespace: biological_process def: "The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that results in the attainment of the full functional capacity of a protein." [GOC:isa_complete] is_a: GO:0051604 ! protein maturation [Term] id: GO:0023019 name: signal transduction involved in regulation of gene expression namespace: biological_process def: "Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process in which a signal is released and/or conveyed from one location to another." [GOC:mtg_signal] synonym: "regulation of gene expression as a consequence of signal transmission" RELATED [GOC:bf] intersection_of: part_of GO:0010468 ! regulation of gene expression relationship: part_of GO:0010468 ! regulation of gene expression creation_date: 2010-02-16T09:30:50Z [Term] id: GO:0030070 name: insulin processing namespace: biological_process def: "The formation of mature insulin by proteolysis of the precursor preproinsulin. The signal sequence is first cleaved from preproinsulin to form proinsulin; proinsulin is then cleaved to release the C peptide, leaving the A and B chains of mature insulin linked by disulfide bridges." [ISBN:0198506732] is_a: GO:0016486 ! peptide hormone processing [Term] id: GO:0030371 name: translation repressor activity namespace: molecular_function def: "Antagonizes ribosome-mediated translation of mRNA into a polypeptide." [GOC:ai, GOC:clt] is_a: GO:0045182 ! translation regulator activity relationship: part_of GO:0017148 ! negative regulation of translation [Term] id: GO:0030422 name: production of siRNA involved in RNA interference namespace: biological_process def: "Cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of RNA interference." [GOC:mah, PMID:11524674] synonym: "production of guide RNAs involved in RNA interference" EXACT [GOC:mah] synonym: "RNA interference, production of guide RNAs" EXACT [] synonym: "RNA interference, production of siRNA" EXACT [GOC:mah] is_a: GO:0070918 ! production of small RNA involved in gene silencing by RNA relationship: part_of GO:0016246 ! RNA interference [Term] id: GO:0030423 name: targeting of mRNA for destruction involved in RNA interference namespace: biological_process def: "The process in which small interfering RNAs target cognate mRNA molecules for degradation." [PMID:11524674] synonym: "RNA interference, targeting of mRNA for destruction" EXACT [GOC:mah] relationship: part_of GO:0016246 ! RNA interference [Term] id: GO:0030424 name: axon namespace: cellular_component def: "The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter." [GOC:nln, ISBN:0198506732] xref: NIF_Subcellular:sao1770195789 xref: Wikipedia:Axon is_a: GO:0043005 ! neuron projection [Term] id: GO:0030425 name: dendrite namespace: cellular_component def: "A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body." [GOC:dos, GOC:mah, GOC:nln, ISBN:0198506732] xref: NIF_Subcellular:sao1211023249 xref: Wikipedia:Dendrite is_a: GO:0043005 ! neuron projection [Term] id: GO:0030426 name: growth cone namespace: cellular_component def: "The migrating motile tip of a growing nerve cell axon or dendrite." [ISBN:0815316194] xref: Wikipedia:Growth_cone is_a: GO:0097458 ! neuron part relationship: part_of GO:0043005 ! neuron projection [Term] id: GO:0030449 name: regulation of complement activation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of complement activation." [GOC:go_curators] synonym: "regulation of complement cascade" EXACT [GOC:add] is_a: GO:0070613 ! regulation of protein processing [Term] id: GO:0030450 name: regulation of complement activation, classical pathway namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the classical pathway of complement activation." [GOC:go_curators] synonym: "regulation of complement cascade, classical pathway" EXACT [GOC:add] is_a: GO:0030449 ! regulation of complement activation [Term] id: GO:0030451 name: regulation of complement activation, alternative pathway namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the alternative pathway of complement activation." [GOC:go_curators] synonym: "regulation of complement cascade, alternative pathway" EXACT [GOC:add] is_a: GO:0030449 ! regulation of complement activation [Term] id: GO:0030466 name: chromatin silencing at silent mating-type cassette namespace: biological_process alt_id: GO:0006347 def: "Repression of transcription at silent mating-type loci by alteration of the structure of chromatin." [GOC:mcc] synonym: "aging-dependent sterility" NARROW [] synonym: "chromatin silencing at HML and HMR" NARROW [] synonym: "heterochromatic silencing at silent mating-type cassette" EXACT [] synonym: "silent mating-type cassette chromatin silencing" EXACT [GOC:mah] is_a: GO:0006342 ! chromatin silencing [Term] id: GO:0030488 name: tRNA methylation namespace: biological_process def: "The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule." [GOC:mah] subset: gosubset_prok is_a: GO:0006400 ! tRNA modification [Term] id: GO:0030490 name: maturation of SSU-rRNA namespace: biological_process def: "Any process involved in the maturation of a precursor Small SubUnit (SSU) ribosomal RNA (rRNA) molecule into a mature SSU-rRNA molecule." [GOC:curators] synonym: "processing of 20S pre-rRNA" NARROW [] synonym: "SSU-rRNA maturation" EXACT [GOC:dph, GOC:tb] is_a: GO:0006364 ! rRNA processing [Term] id: GO:0030509 name: BMP signaling pathway namespace: biological_process def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, ISBN:0878932437, PR:000000034] synonym: "BMP receptor signaling pathway" RELATED [] synonym: "BMP signalling pathway" EXACT [] synonym: "bone morphogenetic protein signaling pathway" EXACT [] synonym: "bone morphogenetic protein signalling pathway" EXACT [] xref: Reactome:REACT_105000 "Signaling by BMP, Mus musculus" xref: Reactome:REACT_107332 "Signaling by BMP, Bos taurus" xref: Reactome:REACT_12034 "Signaling by BMP, Homo sapiens" xref: Reactome:REACT_28579 "Signaling by BMP, Sus scrofa" xref: Reactome:REACT_31763 "Signaling by BMP, Taeniopygia guttata" xref: Reactome:REACT_77157 "Signaling by BMP, Gallus gallus" xref: Reactome:REACT_79322 "Signaling by BMP, Drosophila melanogaster" xref: Reactome:REACT_80158 "Signaling by BMP, Rattus norvegicus" xref: Reactome:REACT_81213 "Signaling by BMP, Xenopus tropicalis" xref: Reactome:REACT_86022 "Signaling by BMP, Canis familiaris" xref: Reactome:REACT_96139 "Signaling by BMP, Danio rerio" is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter [Term] id: GO:0030510 name: regulation of BMP signaling pathway namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the activity of any BMP receptor signaling pathway." [GOC:mah] synonym: "regulation of BMP receptor signaling pathway" RELATED [] synonym: "regulation of BMP signalling pathway" EXACT [] synonym: "regulation of bone morphogenetic protein signaling pathway" EXACT [] synonym: "regulation of bone morphogenetic protein signalling pathway" EXACT [] intersection_of: regulates GO:0030509 ! BMP signaling pathway relationship: regulates GO:0030509 ! BMP signaling pathway [Term] id: GO:0030513 name: positive regulation of BMP signaling pathway namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of BMP signaling pathway activity." [GOC:go_curators] synonym: "activation of BMP signaling pathway" NARROW [] synonym: "positive regulation of BMP receptor signaling pathway" RELATED [] synonym: "positive regulation of BMP signalling pathway" EXACT [] synonym: "positive regulation of bone morphogenetic protein signaling pathway" EXACT [] synonym: "positive regulation of bone morphogenetic protein signalling pathway" EXACT [] synonym: "stimulation of BMP signaling pathway" NARROW [] synonym: "up regulation of BMP signaling pathway" EXACT [] synonym: "up-regulation of BMP signaling pathway" EXACT [] synonym: "upregulation of BMP signaling pathway" EXACT [] is_a: GO:0030510 ! regulation of BMP signaling pathway intersection_of: positively_regulates GO:0030509 ! BMP signaling pathway relationship: positively_regulates GO:0030509 ! BMP signaling pathway [Term] id: GO:0030514 name: negative regulation of BMP signaling pathway namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the BMP signaling pathway." [GOC:go_curators] synonym: "down regulation of BMP signaling pathway" EXACT [] synonym: "down-regulation of BMP signaling pathway" EXACT [] synonym: "downregulation of BMP signaling pathway" EXACT [] synonym: "inhibition of BMP signaling pathway" NARROW [] synonym: "negative regulation of BMP receptor signaling pathway" RELATED [] synonym: "negative regulation of BMP signalling pathway" EXACT [] synonym: "negative regulation of bone morphogenetic protein signaling pathway" EXACT [] synonym: "negative regulation of bone morphogenetic protein signalling pathway" EXACT [] is_a: GO:0030510 ! regulation of BMP signaling pathway intersection_of: negatively_regulates GO:0030509 ! BMP signaling pathway relationship: negatively_regulates GO:0030509 ! BMP signaling pathway [Term] id: GO:0030533 name: triplet codon-amino acid adaptor activity namespace: molecular_function def: "The codon binding activity of a tRNA that positions an activated amino acid, mediating its insertion at the correct point in the sequence of a nascent polypeptide chain during protein synthesis." [GOC:hjd, GOC:mtg_MIT_16mar07, ISBN:0198506732] comment: Note that this term can be used in place of the obsolete term 'transfer RNA ; GO:0005563'. subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_yeast synonym: "transfer RNA" RELATED [] synonym: "tRNA" RELATED [] relationship: part_of GO:0006412 ! translation [Term] id: GO:0030631 name: pyrrolysine incorporation namespace: biological_process def: "The incorporation of pyrrolysine, also known as lysine methylamine methyltransferase cofactor adduct, into a peptide; uses a special tRNA that recognizes the UAG codon as a modified lysine, rather than as a termination codon. Pyrrolysine may be synthesized as a free amino acid or synthesized from a lysine charged tRNA before its incorporation; it is not a posttranslational modification of peptidyl-lysine; this modification is found in several Methanosarcina methylamine methyltransferases." [PMID:11435424, PMID:17204561, RESID:AA0321] subset: gosubset_prok synonym: "lysine methylamine methyltransferase cofactor adduct incorporation" EXACT [RESID:AA0321] synonym: "monomethylamine methyltransferase cofactor lysine adduct incorporation" EXACT [CHEBI:21860] xref: RESID:AA0321 is_a: GO:0006451 ! translational readthrough [Term] id: GO:0030673 name: axolemma namespace: cellular_component def: "The portion of the plasma membrane surrounding an axon; it is a specialized trilaminar random mosaic of protein molecules floating within a fluid matrix of highly mobile phospholipid molecules, 7-8 nm in thickness." [http://www.medik.sk/clanky/bio_jun.htm, ISBN:0124325653] synonym: "axonal membrane" EXACT [GOC:vk] xref: NIF_Subcellular:sao250772229 xref: Wikipedia:Axolemma is_a: GO:0032589 ! neuron projection membrane is_a: GO:0033267 ! axon part relationship: part_of GO:0044304 ! main axon [Term] id: GO:0030696 name: tRNA (m5U54) methyltransferase activity namespace: molecular_function def: "Catalysis of the transfer of a methyl group from a donor to the C5 atom of the uridine residue at position 54 in a tRNA molecule." [ISBN:1555811337] comment: Note that the term name mentions a specific position within a tRNA because no other names have yet arisen for this activity, and because the position is conserved in nearly all tRNAs. The term nevertheless can be used for activities that methylase an analogous residue at a position other than 54, if such is found, and synonyms that mention positions applicable to other tRNAs or species may also be added. synonym: "RUMT" EXACT [] is_a: GO:0016300 ! tRNA (uracil) methyltransferase activity [Term] id: GO:0030697 name: S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity namespace: molecular_function alt_id: GO:0009021 def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing thymine at position U54 of a transfer RNA. This occurs in most Gram-negative bacteria, some archae, and eukaryotes." [GOC:hjd, ISBN:1555811337] synonym: "M5U-methyltransferase activity" EXACT [EC:2.1.1.35] synonym: "ribothymidyl synthase activity" BROAD [EC:2.1.1.35] synonym: "RUMT" BROAD [] synonym: "RUMT activity" EXACT [EC:2.1.1.35] synonym: "S-adenosyl methionine-dependent tRNA (m5U54) methyltransferase activity" EXACT [] synonym: "S-adenosyl-L-methionine:tRNA (uracil-5-)-methyltransferase activity" EXACT [EC:2.1.1.35] synonym: "transfer RNA uracil 5-methyltransferase activity" EXACT [EC:2.1.1.35] synonym: "transfer RNA uracil methylase activity" EXACT [EC:2.1.1.35] synonym: "tRNA (uracil-5-)-methyltransferase activity" EXACT [] synonym: "tRNA uracil 5-methyltransferase activity" EXACT [EC:2.1.1.35] synonym: "tRNA:m(5)U54-methyltransferase activity" EXACT [EC:2.1.1.35] synonym: "tRNA:m5U54-methyltransferase activity" EXACT [EC:2.1.1.35] xref: EC:2.1.1.35 xref: MetaCyc:TRNA-URACIL-5--METHYLTRANSFERASE-RXN is_a: GO:0030696 ! tRNA (m5U54) methyltransferase activity [Term] id: GO:0030698 name: 5,10-methylenetetrahydrofolate-dependent tRNA (m5U54) methyltransferase activity namespace: molecular_function def: "Catalysis of the transfer of a methyl group from 5,10-methylenetetrahydrofolate to the C5 atom of the uridine residue at position 54 in a tRNA molecule. This occurs in most Gram-positive bacteria and some Gram-negative bacteria." [GOC:hjd, ISBN:1555811337] synonym: "RUMT" BROAD [] is_a: GO:0030696 ! tRNA (m5U54) methyltransferase activity [Term] id: GO:0030702 name: chromatin silencing at centromere namespace: biological_process def: "Repression of transcription of centromeric DNA by altering the structure of chromatin." [GOC:mah] synonym: "centromere chromatin silencing" EXACT [GOC:mah] synonym: "centromeric silencing" EXACT [GOC:vw] synonym: "heterochromatic silencing at centromere" EXACT [] is_a: GO:0006342 ! chromatin silencing [Term] id: GO:0030743 name: rRNA (adenosine-2'-O-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing a single residue of 2'-O-methyladenosine." [EC:2.1.1.66] subset: gosubset_prok synonym: "ribosomal ribonucleate adenosine 2'-methyltransferase activity" EXACT [EC:2.1.1.66] synonym: "RNA-pentose methylase activity" RELATED [EC:2.1.1.66] synonym: "rRNA adenosine 2'-methylase activity" EXACT [EC:2.1.1.66] synonym: "S-adenosyl-L-methionine:rRNA (adenosine-2'-O)-methyltransferase activity" EXACT [EC:2.1.1.66] synonym: "thiostrepton-resistance methylase activity" NARROW [EC:2.1.1.66] xref: EC:2.1.1.66 xref: MetaCyc:2.1.1.66-RXN is_a: GO:0016433 ! rRNA (adenine) methyltransferase activity [Term] id: GO:0030846 name: termination of RNA polymerase II transcription, poly(A)-coupled namespace: biological_process def: "The process in which transcription of polyadenylated RNA polymerase II transcripts is terminated; cleavage and polyadenylylation of the mRNA 3' end is coupled to transcription termination." [GOC:txnOH, PMID:12944462, PMID:18679429] synonym: "termination of RNA polymerase II transcription, polyadenylation-coupled" RELATED [] synonym: "transcription termination from Pol II promoter, poly(A) coupled" RELATED [] synonym: "transcription termination from Pol II promoter, RNA polymerase(A) coupled" RELATED [] is_a: GO:0006369 ! termination of RNA polymerase II transcription [Term] id: GO:0030847 name: termination of RNA polymerase II transcription, exosome-dependent namespace: biological_process def: "The process in which transcription of nonpolyadenylated RNA polymerase II transcripts is terminated; coupled to the maturation of the RNA 3'-end." [GOC:txnOH, PMID:12944462, PMID:18679429] synonym: "termination of RNA polymerase II transcription, poly(A)-independent" EXACT [] synonym: "transcription termination from Pol II promoter, poly(A)-independent" EXACT [] synonym: "transcription termination from Pol II promoter, RNA polymerase(A)-independent" EXACT [] is_a: GO:0006369 ! termination of RNA polymerase II transcription [Term] id: GO:0030908 name: protein splicing namespace: biological_process def: "The post-translational removal of peptide sequences from within a protein sequence." [GOC:mah] subset: gosubset_prok xref: Wikipedia:Protein_splicing is_a: GO:0016485 ! protein processing [Term] id: GO:0030909 name: non-intein-mediated protein splicing namespace: biological_process def: "The post-translational removal of peptide sequences from within a protein sequence, by a process not involving inteins." [GOC:mah] subset: gosubset_prok is_a: GO:0030908 ! protein splicing [Term] id: GO:0030969 name: UFP-specific transcription factor mRNA processing involved in endoplasmic reticulum unfolded protein response namespace: biological_process def: "The spliceosome-independent cleavage and ligation of the mRNA encoding a UFP-specific transcription factor to remove a single intron, thereby increasing both the translational efficiency of the processed mRNA and the activity of the protein it encodes." [GOC:mah, PMID:12042763] synonym: "UFP-specific transcription factor mRNA processing during unfolded protein response" RELATED [GOC:dph, GOC:tb] synonym: "unfolded protein response, cleavage of primary transcript encoding UFP-specific transcription factor" RELATED [] synonym: "unfolded protein response, ligation of mRNA encoding UFP-specific transcription factor by RNA ligase" RELATED [] is_a: GO:0006397 ! mRNA processing [Term] id: GO:0031047 name: gene silencing by RNA namespace: biological_process def: "Any process in which RNA molecules inactivate expression of target genes." [GOC:dph, GOC:mah, GOC:tb, PMID:15020054] synonym: "RNA-mediated gene silencing" EXACT [GOC:dph, GOC:tb] is_a: GO:0016458 ! gene silencing [Term] id: GO:0031048 name: chromatin silencing by small RNA namespace: biological_process def: "Repression of transcription by conversion of large regions of DNA into heterochromatin, directed by small RNAs sharing sequence identity to the repressed region." [GOC:dph, GOC:mtg_lung, GOC:ns] synonym: "RNA interference-like chromatin silencing" EXACT [] synonym: "RNA-mediated chromatin silencing" EXACT [GOC:dph, GOC:tb] synonym: "RNA-mediated TGS" BROAD [] synonym: "RNA-mediated transcriptional silencing" EXACT [] synonym: "RNAi-directed chromatin silencing" EXACT [GOC:vw] synonym: "RNAi-like chromatin silencing" EXACT [] synonym: "small RNA-mediated heterochromatic silencing" EXACT [] is_a: GO:0006342 ! chromatin silencing is_a: GO:0031047 ! gene silencing by RNA [Term] id: GO:0031050 name: dsRNA fragmentation namespace: biological_process def: "Cleavage of double-stranded RNA molecules by an RNaseIII-family enzyme to produce small RNAs (generally 20-30 nucleotides, depending on species) with biological function." [GOC:ns] synonym: "double-stranded RNA fragmentation" EXACT [] is_a: GO:0006396 ! RNA processing [Term] id: GO:0031051 name: scnRNA production namespace: biological_process def: "Cleavage of noncoding, double-stranded RNAs transcribed from the micronuclear genome to produce scnRNAs, small RNAs (~28 nucleotides) that direct the deletion of micronuclear-limited sequences from the developing macronuclear genome." [PMID:15196465] is_a: GO:0031050 ! dsRNA fragmentation [Term] id: GO:0031053 name: primary miRNA processing namespace: biological_process def: "Any process involved in the conversion of a primary microRNA transcript into a pre-microRNA molecule." [GOC:sl, PMID:15211354] synonym: "pri-miRNA processing" EXACT [] synonym: "primary microRNA processing" EXACT [] is_a: GO:0034470 ! ncRNA processing relationship: part_of GO:0035196 ! production of miRNAs involved in gene silencing by miRNA [Term] id: GO:0031054 name: pre-miRNA processing namespace: biological_process def: "Any process involved in the conversion of a pre-microRNA transcript into a mature microRNA molecule." [GOC:sl, PMID:15211354] synonym: "pre-microRNA processing" EXACT [] is_a: GO:0034470 ! ncRNA processing relationship: part_of GO:0035196 ! production of miRNAs involved in gene silencing by miRNA [Term] id: GO:0031070 name: intronic snoRNA processing namespace: biological_process def: "The biogenesis of a snoRNA molecule which resides within, and is processed from, the intron of a pre-mRNA." [GOC:vw] is_a: GO:0043144 ! snoRNA processing [Term] id: GO:0031118 name: rRNA pseudouridine synthesis namespace: biological_process def: "The intramolecular conversion of uridine to pseudouridine in an rRNA molecule." [GOC:mah] is_a: GO:0000154 ! rRNA modification [Term] id: GO:0031119 name: tRNA pseudouridine synthesis namespace: biological_process def: "The intramolecular conversion of uridine to pseudouridine in a tRNA molecule." [GOC:mah] is_a: GO:0006400 ! tRNA modification [Term] id: GO:0031123 name: RNA 3'-end processing namespace: biological_process def: "Any process involved in forming the mature 3' end of an RNA molecule." [GOC:mah] subset: gosubset_prok synonym: "RNA 3' end processing" EXACT [] is_a: GO:0006396 ! RNA processing [Term] id: GO:0031124 name: mRNA 3'-end processing namespace: biological_process def: "Any process involved in forming the mature 3' end of an mRNA molecule." [GOC:mah] subset: gosubset_prok synonym: "mRNA 3' end processing" EXACT [] xref: Reactome:REACT_102358 "mRNA 3'-end processing, Bos taurus" xref: Reactome:REACT_105982 "mRNA 3'-end processing, Xenopus tropicalis" xref: Reactome:REACT_112683 "mRNA 3'-end processing, Drosophila melanogaster" xref: Reactome:REACT_113053 "mRNA 3'-end processing, Caenorhabditis elegans" xref: Reactome:REACT_114937 "mRNA 3'-end processing, Arabidopsis thaliana" xref: Reactome:REACT_115007 "mRNA 3'-end processing, Oryza sativa" xref: Reactome:REACT_1849 "mRNA 3'-end processing, Homo sapiens" xref: Reactome:REACT_29064 "mRNA 3'-end processing, Danio rerio" xref: Reactome:REACT_76994 "mRNA 3'-end processing, Taeniopygia guttata" xref: Reactome:REACT_85883 "mRNA 3'-end processing, Mus musculus" xref: Reactome:REACT_99251 "mRNA 3'-end processing, Canis familiaris" is_a: GO:0006397 ! mRNA processing is_a: GO:0031123 ! RNA 3'-end processing [Term] id: GO:0031125 name: rRNA 3'-end processing namespace: biological_process def: "Any process involved in forming the mature 3' end of an rRNA molecule." [GOC:mah] synonym: "rRNA 3' end processing" EXACT [] is_a: GO:0006364 ! rRNA processing is_a: GO:0043628 ! ncRNA 3'-end processing [Term] id: GO:0031126 name: snoRNA 3'-end processing namespace: biological_process def: "Any process involved in forming the mature 3' end of a snoRNA molecule." [GOC:mah] synonym: "snoRNA 3' end processing" EXACT [] is_a: GO:0043144 ! snoRNA processing is_a: GO:0043628 ! ncRNA 3'-end processing [Term] id: GO:0031167 name: rRNA methylation namespace: biological_process def: "The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule." [GOC:mah] is_a: GO:0000154 ! rRNA modification [Term] id: GO:0031425 name: chloroplast RNA processing namespace: biological_process def: "The conversion of a primary RNA molecule transcribed from a chloroplast genome into one or more mature RNA molecules." [GOC:mah] is_a: GO:0006396 ! RNA processing [Term] id: GO:0031426 name: polycistronic mRNA processing namespace: biological_process def: "The conversion of a primary mRNA transcript containing more than one complete protein-coding region into individual mature mRNA molecules." [GOC:mah] is_a: GO:0006397 ! mRNA processing [Term] id: GO:0031437 name: regulation of mRNA cleavage namespace: biological_process def: "Any process that modulates the frequency, rate or extent of mRNA cleavage, any process in which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner." [GOC:mah] is_a: GO:0050684 ! regulation of mRNA processing intersection_of: regulates GO:0006379 ! mRNA cleavage relationship: regulates GO:0006379 ! mRNA cleavage [Term] id: GO:0031438 name: negative regulation of mRNA cleavage namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of mRNA cleavage." [GOC:mah] synonym: "down regulation of mRNA cleavage" EXACT [] synonym: "down-regulation of mRNA cleavage" EXACT [] synonym: "downregulation of mRNA cleavage" EXACT [] synonym: "inhibition of mRNA cleavage" NARROW [] is_a: GO:0031437 ! regulation of mRNA cleavage is_a: GO:0050686 ! negative regulation of mRNA processing intersection_of: negatively_regulates GO:0006379 ! mRNA cleavage relationship: negatively_regulates GO:0006379 ! mRNA cleavage [Term] id: GO:0031439 name: positive regulation of mRNA cleavage namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of mRNA cleavage." [GOC:mah] synonym: "activation of mRNA cleavage" NARROW [] synonym: "stimulation of mRNA cleavage" NARROW [] synonym: "up regulation of mRNA cleavage" EXACT [] synonym: "up-regulation of mRNA cleavage" EXACT [] synonym: "upregulation of mRNA cleavage" EXACT [] is_a: GO:0031437 ! regulation of mRNA cleavage is_a: GO:0050685 ! positive regulation of mRNA processing intersection_of: positively_regulates GO:0006379 ! mRNA cleavage relationship: positively_regulates GO:0006379 ! mRNA cleavage [Term] id: GO:0031440 name: regulation of mRNA 3'-end processing namespace: biological_process def: "Any process that modulates the frequency, rate or extent of mRNA 3'-end processing, any process involved in forming the mature 3' end of an mRNA molecule." [GOC:mah] is_a: GO:0050684 ! regulation of mRNA processing intersection_of: regulates GO:0031124 ! mRNA 3'-end processing relationship: regulates GO:0031124 ! mRNA 3'-end processing [Term] id: GO:0031441 name: negative regulation of mRNA 3'-end processing namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of mRNA 3'-end processing." [GOC:mah] synonym: "down regulation of mRNA 3'-end processing" EXACT [] synonym: "down-regulation of mRNA 3'-end processing" EXACT [] synonym: "downregulation of mRNA 3'-end processing" EXACT [] synonym: "inhibition of mRNA 3'-end processing" NARROW [] is_a: GO:0031440 ! regulation of mRNA 3'-end processing is_a: GO:0050686 ! negative regulation of mRNA processing intersection_of: negatively_regulates GO:0031124 ! mRNA 3'-end processing relationship: negatively_regulates GO:0031124 ! mRNA 3'-end processing [Term] id: GO:0031442 name: positive regulation of mRNA 3'-end processing namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of mRNA 3'-end processing." [GOC:mah] synonym: "activation of mRNA 3'-end processing" NARROW [] synonym: "stimulation of mRNA 3'-end processing" NARROW [] synonym: "up regulation of mRNA 3'-end processing" EXACT [] synonym: "up-regulation of mRNA 3'-end processing" EXACT [] synonym: "upregulation of mRNA 3'-end processing" EXACT [] is_a: GO:0031440 ! regulation of mRNA 3'-end processing is_a: GO:0050685 ! positive regulation of mRNA processing intersection_of: positively_regulates GO:0031124 ! mRNA 3'-end processing relationship: positively_regulates GO:0031124 ! mRNA 3'-end processing [Term] id: GO:0031554 name: regulation of DNA-dependent transcription, termination namespace: biological_process def: "Any process that modulates the frequency, rate, extent, or location of DNA-dependent transcription termination, the process in which transcription is completed; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA." [GOC:mlg, GOC:txnOH] synonym: "regulation of termination of DNA-dependent transcription" EXACT [GOC:jh2] synonym: "regulation of transcription termination, DNA-dependent" EXACT [GOC:jh2] synonym: "transcription antiterminator activity" RELATED [] is_a: GO:0006355 ! regulation of transcription, DNA-dependent intersection_of: regulates GO:0006353 ! DNA-dependent transcription, termination relationship: regulates GO:0006353 ! DNA-dependent transcription, termination [Term] id: GO:0031555 name: transcriptional attenuation namespace: biological_process def: "Regulation of transcription through variation in where transcription termination occurs." [GOC:dh, GOC:mlg, ISBN:0198542682] xref: Wikipedia:Attenuator_(genetics) is_a: GO:0031554 ! regulation of DNA-dependent transcription, termination [Term] id: GO:0031556 name: transcriptional attenuation by ribosome namespace: biological_process def: "A type of transcriptional regulation at the level of early termination. This process can occur only in prokaryotes, where transcription of an operon into messenger RNA and translation of that mRNA into polypeptides occur simultaneously. The general principle is that alternative mRNA secondary structures occur under different physiological conditions such as available amount of a particular amino acid. One set of conditions favors early termination of transcription. In the classic example of the trp biosynthesis operon, translation of the gene for a short, trp-containing polypeptide called the trp operon leader peptide pauses either at a trp codon (if tryptophan is scarce) or the stop codon (if trp is readily available). In the former situation transcription continues, but in the latter a Rho-independent terminator forms and reduces, or attenuates, expression of the tryptophan biosynthesis genes. Although the polypeptides encoded by leader peptide genes appear not to be stable once their translation is complete, it is suggested by recent studies that their nascent polypeptide chains interact specifically with ribosomes, specific uncharged tRNAs, or other cellular components to inhibit release at the stop codon and improve the function of transcriptional attenuation as a regulatory switch." [GOC:dh, GOC:mlg, ISBN:0198542682] synonym: "ribosome-mediated transcriptional attenuation" EXACT [GOC:dph, GOC:tb] is_a: GO:0031555 ! transcriptional attenuation [Term] id: GO:0031564 name: transcription antitermination namespace: biological_process def: "Regulation of transcription by a mechanism that allows RNA polymerase to continue transcription beyond a termination site." [ISBN:0198577788, PMID:12456320] synonym: "transcriptional readthrough" EXACT [] is_a: GO:0031555 ! transcriptional attenuation [Term] id: GO:0031591 name: wybutosine biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of wybutosine, 3H-imidazo[1,2-alpha]purine-7-butanoic acid, 4,9-dihydro- alpha-[(methoxycarbonyl)amino]- 4,6-dimethyl-9-oxo- 3-beta-D-ribofuranosyl methyl ester, a modified nucleoside found in some tRNA molecules." [GOC:hjd, GOC:mah, RNAmods:037] comment: Note that wybutosine is a hypermodified G-residue, formerly called the Y-base, and its derivatives are exclusively found at position 37 (anticodon loop) of tRNAPhe. synonym: "yW biosynthesis" EXACT [] synonym: "yW biosynthetic process" EXACT [] is_a: GO:0006400 ! tRNA modification [Term] id: GO:0031638 name: zymogen activation namespace: biological_process def: "The proteolytic processing of an inactive enzyme to an active form." [GOC:hjd] synonym: "zymogen activation by proteolytic cleavage" EXACT [] is_a: GO:0016485 ! protein processing [Term] id: GO:0031639 name: plasminogen activation namespace: biological_process def: "The process in which inactive plasminogen is processed to active plasmin. This process includes cleavage at an internal Arg-Val site to form an N-terminal A-chain and C-terminal B-chain held together by a disulfide bond, and can include further proteolytic cleavage events to remove the preactivation peptide." [PMID:9548733] synonym: "cleavage of plasminogen to plasmin" EXACT [] is_a: GO:0031638 ! zymogen activation [Term] id: GO:0031647 name: regulation of protein stability namespace: biological_process def: "Any process that affects the structure and integrity of a protein by altering the likelihood of its degradation or aggregation." [GOC:dph, GOC:mah, GOC:tb] subset: goslim_pir subset: gosubset_prok is_a: GO:0010608 ! posttranscriptional regulation of gene expression [Term] id: GO:0031648 name: protein destabilization namespace: biological_process def: "Any process that decreases the stability of a protein, making it more vulnerable to degradative processes or aggregation." [GOC:mah] synonym: "negative regulation of protein stability" EXACT [] is_a: GO:0031647 ! regulation of protein stability [Term] id: GO:0031935 name: regulation of chromatin silencing namespace: biological_process def: "Any process that affects the rate, extent or location of chromatin silencing." [GOC:mah] synonym: "regulation of heterochromatic silencing" RELATED [] is_a: GO:0006355 ! regulation of transcription, DNA-dependent is_a: GO:0060968 ! regulation of gene silencing intersection_of: regulates GO:0006342 ! chromatin silencing relationship: regulates GO:0006342 ! chromatin silencing [Term] id: GO:0031936 name: negative regulation of chromatin silencing namespace: biological_process alt_id: GO:0006345 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of chromatin silencing." [GOC:mah] synonym: "down regulation of chromatin silencing" EXACT [] synonym: "down-regulation of chromatin silencing" EXACT [] synonym: "downregulation of chromatin silencing" EXACT [] synonym: "inhibition of chromatin silencing" NARROW [] synonym: "loss of chromatin silencing" EXACT [] synonym: "negative regulation of heterochromatic silencing" EXACT [] is_a: GO:0031935 ! regulation of chromatin silencing is_a: GO:0045815 ! positive regulation of gene expression, epigenetic is_a: GO:0045893 ! positive regulation of transcription, DNA-dependent is_a: GO:0060969 ! negative regulation of gene silencing intersection_of: negatively_regulates GO:0006342 ! chromatin silencing relationship: negatively_regulates GO:0006342 ! chromatin silencing [Term] id: GO:0031937 name: positive regulation of chromatin silencing namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of chromatin silencing." [GOC:mah] synonym: "activation of chromatin silencing" NARROW [] synonym: "positive regulation of heterochromatic silencing" EXACT [] synonym: "stimulation of chromatin silencing" NARROW [] synonym: "up regulation of chromatin silencing" EXACT [] synonym: "up-regulation of chromatin silencing" EXACT [] synonym: "upregulation of chromatin silencing" EXACT [] is_a: GO:0031935 ! regulation of chromatin silencing intersection_of: positively_regulates GO:0006342 ! chromatin silencing relationship: positively_regulates GO:0006342 ! chromatin silencing [Term] id: GO:0031938 name: regulation of chromatin silencing at telomere namespace: biological_process def: "Any process that affects the rate, extent or location of chromatin silencing at telomeres." [GOC:mah] synonym: "regulation of heterochromatic silencing at telomere" EXACT [] is_a: GO:0031935 ! regulation of chromatin silencing intersection_of: regulates GO:0006348 ! chromatin silencing at telomere relationship: regulates GO:0006348 ! chromatin silencing at telomere [Term] id: GO:0031939 name: negative regulation of chromatin silencing at telomere namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of chromatin silencing at telomeres." [GOC:mah] synonym: "down regulation of chromatin silencing at telomere" EXACT [] synonym: "down-regulation of chromatin silencing at telomere" EXACT [] synonym: "downregulation of chromatin silencing at telomere" EXACT [] synonym: "inhibition of chromatin silencing at telomere" NARROW [] synonym: "negative regulation of heterochromatic silencing at telomere" EXACT [] is_a: GO:0031936 ! negative regulation of chromatin silencing is_a: GO:0031938 ! regulation of chromatin silencing at telomere intersection_of: negatively_regulates GO:0006348 ! chromatin silencing at telomere relationship: negatively_regulates GO:0006348 ! chromatin silencing at telomere [Term] id: GO:0031940 name: positive regulation of chromatin silencing at telomere namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of chromatin silencing at telomeres." [GOC:mah] synonym: "activation of chromatin silencing at telomere" NARROW [] synonym: "positive regulation of heterochromatic silencing at telomere" EXACT [] synonym: "stimulation of chromatin silencing at telomere" NARROW [] synonym: "up regulation of chromatin silencing at telomere" EXACT [] synonym: "up-regulation of chromatin silencing at telomere" EXACT [] synonym: "upregulation of chromatin silencing at telomere" EXACT [] is_a: GO:0031937 ! positive regulation of chromatin silencing is_a: GO:0031938 ! regulation of chromatin silencing at telomere intersection_of: positively_regulates GO:0006348 ! chromatin silencing at telomere relationship: positively_regulates GO:0006348 ! chromatin silencing at telomere [Term] id: GO:0032023 name: trypsinogen activation namespace: biological_process def: "The proteolytic processing of trypsinogen to the active form, trypsin." [GOC:mah] synonym: "cleavage of trypsinogen to trypsin" EXACT [] is_a: GO:0031638 ! zymogen activation [Term] id: GO:0032055 name: negative regulation of translation in response to stress namespace: biological_process def: "Any process that stops, prevents or reduces the rate of translation as a result of a stimulus indicating the organism is under stress." [GOC:mah] synonym: "down regulation of translation in response to stress" EXACT [] synonym: "down-regulation of translation in response to stress" EXACT [] synonym: "downregulation of translation in response to stress" EXACT [] synonym: "inhibition of translation in response to stress" NARROW [] is_a: GO:0017148 ! negative regulation of translation is_a: GO:0043555 ! regulation of translation in response to stress [Term] id: GO:0032056 name: positive regulation of translation in response to stress namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of translation as a result of a stimulus indicating the organism is under stress." [GOC:mah] synonym: "activation of translation in response to stress" NARROW [] synonym: "stimulation of translation in response to stress" NARROW [] synonym: "up regulation of translation in response to stress" EXACT [] synonym: "up-regulation of translation in response to stress" EXACT [] synonym: "upregulation of translation in response to stress" EXACT [] is_a: GO:0043555 ! regulation of translation in response to stress is_a: GO:0045727 ! positive regulation of translation [Term] id: GO:0032057 name: negative regulation of translational initiation in response to stress namespace: biological_process def: "Any process that stops, prevents or reduces the rate of translation initiation as a result of a stimulus indicating the organism is under stress." [GOC:mah] synonym: "down regulation of translation initiation in response to stress" EXACT [] synonym: "down-regulation of translation initiation in response to stress" EXACT [] synonym: "downregulation of translation initiation in response to stress" EXACT [] synonym: "inhibition of translation initiation in response to stress" NARROW [] is_a: GO:0032055 ! negative regulation of translation in response to stress is_a: GO:0043558 ! regulation of translational initiation in response to stress is_a: GO:0045947 ! negative regulation of translational initiation [Term] id: GO:0032058 name: positive regulation of translational initiation in response to stress namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of translation initiation as a result of a stimulus indicating the organism is under stress." [GOC:mah] synonym: "activation of translation initiation in response to stress" NARROW [] synonym: "stimulation of translation initiation in response to stress" NARROW [] synonym: "up regulation of translation initiation in response to stress" EXACT [] synonym: "up-regulation of translation initiation in response to stress" EXACT [] synonym: "upregulation of translation initiation in response to stress" EXACT [] is_a: GO:0032056 ! positive regulation of translation in response to stress is_a: GO:0043558 ! regulation of translational initiation in response to stress is_a: GO:0045948 ! positive regulation of translational initiation [Term] id: GO:0032061 name: negative regulation of translation in response to osmotic stress namespace: biological_process def: "Any process that stops, prevents or reduces the rate of translation as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell." [GOC:mah] synonym: "down regulation of translation in response to osmotic stress" EXACT [] synonym: "down-regulation of translation in response to osmotic stress" EXACT [] synonym: "downregulation of translation in response to osmotic stress" EXACT [] synonym: "inhibition of translation in response to osmotic stress" NARROW [] is_a: GO:0032055 ! negative regulation of translation in response to stress is_a: GO:0043557 ! regulation of translation in response to osmotic stress [Term] id: GO:0032062 name: positive regulation of translation in response to osmotic stress namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of translation as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell." [GOC:mah] synonym: "activation of translation in response to osmotic stress" NARROW [] synonym: "stimulation of translation in response to osmotic stress" NARROW [] synonym: "up regulation of translation in response to osmotic stress" EXACT [] synonym: "up-regulation of translation in response to osmotic stress" EXACT [] synonym: "upregulation of translation in response to osmotic stress" EXACT [] is_a: GO:0032056 ! positive regulation of translation in response to stress is_a: GO:0043557 ! regulation of translation in response to osmotic stress [Term] id: GO:0032063 name: negative regulation of translational initiation in response to osmotic stress namespace: biological_process def: "Any process that stops, prevents or reduces the rate of translation initiation, as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell." [GOC:mah] synonym: "down regulation of translation initiation in response to osmotic stress" EXACT [] synonym: "down-regulation of translation initiation in response to osmotic stress" EXACT [] synonym: "downregulation of translation initiation in response to osmotic stress" EXACT [] synonym: "inhibition of translation initiation in response to osmotic stress" NARROW [] is_a: GO:0032057 ! negative regulation of translational initiation in response to stress is_a: GO:0032061 ! negative regulation of translation in response to osmotic stress is_a: GO:0043561 ! regulation of translational initiation in response to osmotic stress [Term] id: GO:0032064 name: positive regulation of translational initiation in response to osmotic stress namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of translation initiation, as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell." [GOC:mah] synonym: "activation of translation initiation in response to osmotic stress" NARROW [] synonym: "stimulation of translation initiation in response to osmotic stress" NARROW [] synonym: "up regulation of translation initiation in response to osmotic stress" EXACT [] synonym: "up-regulation of translation initiation in response to osmotic stress" EXACT [] synonym: "upregulation of translation initiation in response to osmotic stress" EXACT [] is_a: GO:0032058 ! positive regulation of translational initiation in response to stress is_a: GO:0032062 ! positive regulation of translation in response to osmotic stress is_a: GO:0043561 ! regulation of translational initiation in response to osmotic stress [Term] id: GO:0032088 name: negative regulation of NF-kappaB transcription factor activity namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB." [GOC:dph, GOC:rl, GOC:tb] synonym: "inhibition of NF-kappaB transcription factor" EXACT [GOC:dph, GOC:tb] synonym: "NF-kappaB inhibitor" RELATED [] is_a: GO:0043433 ! negative regulation of sequence-specific DNA binding transcription factor activity [Term] id: GO:0032258 name: CVT pathway namespace: biological_process def: "A constitutive biosynthetic process that occurs under nutrient-rich conditions, in which two resident vacuolar hydrolases, aminopeptidase I and alpha-mannosidase, are sequestered into vesicles; these vesicles are transported to, and then fuse with, the vacuole. This pathway is mostly observed in yeast." [PMID:12865942, PMID:15659643] synonym: "cytoplasm to vacuole targeting" EXACT [] synonym: "cytoplasm-to-vacuole targeting" EXACT [] relationship: has_part GO:0006624 ! vacuolar protein processing [Term] id: GO:0032455 name: nerve growth factor processing namespace: biological_process def: "The generation of a mature nerve growth factor (NGF) by proteolysis of a precursor." [GOC:mah, PMID:8615794] synonym: "beta-nerve growth factor processing" EXACT [PR:000011194] synonym: "NGF processing" EXACT [PR:000011194] xref: Reactome:REACT_105501 "NGF processing, Taeniopygia guttata" xref: Reactome:REACT_107921 "NGF processing, Gallus gallus" xref: Reactome:REACT_110528 "NGF processing, Bos taurus" xref: Reactome:REACT_11062 "NGF processing, Homo sapiens" xref: Reactome:REACT_34185 "NGF processing, Sus scrofa" xref: Reactome:REACT_80539 "NGF processing, Canis familiaris" xref: Reactome:REACT_83522 "NGF processing, Mus musculus" xref: Reactome:REACT_85976 "NGF processing, Rattus norvegicus" xref: Reactome:REACT_88690 "NGF processing, Xenopus tropicalis" xref: Reactome:REACT_96202 "NGF processing, Danio rerio" is_a: GO:0016486 ! peptide hormone processing [Term] id: GO:0032543 name: mitochondrial translation namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of a protein in a mitochondrion. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein; the mitochondrion has its own ribosomes and transfer RNAs, and uses a genetic code that differs from the nuclear code." [GOC:go_curators] subset: goslim_yeast synonym: "mitochondrial protein anabolism" EXACT [] synonym: "mitochondrial protein biosynthesis" EXACT [] synonym: "mitochondrial protein formation" EXACT [] synonym: "mitochondrial protein synthesis" EXACT [] synonym: "mitochondrial protein translation" EXACT [] is_a: GO:0006412 ! translation intersection_of: GO:0006412 ! translation [Term] id: GO:0032544 name: plastid translation namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of a protein in a plastid. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein; the plastid has its own ribosomes and transfer RNAs, and uses a genetic code that differs from the nuclear code." [GOC:go_curators] synonym: "plastid protein anabolism" EXACT [] synonym: "plastid protein biosynthesis" EXACT [] synonym: "plastid protein formation" EXACT [] synonym: "plastid protein synthesis" EXACT [] synonym: "plastid protein translation" EXACT [] is_a: GO:0006412 ! translation intersection_of: GO:0006412 ! translation [Term] id: GO:0032584 name: growth cone membrane namespace: cellular_component def: "The portion of the plasma membrane surrounding a growth cone." [GOC:mah] is_a: GO:0097458 ! neuron part relationship: part_of GO:0030426 ! growth cone [Term] id: GO:0032589 name: neuron projection membrane namespace: cellular_component def: "The portion of the plasma membrane surrounding a neuron projection." [GOC:mah] is_a: GO:0097458 ! neuron part relationship: part_of GO:0043005 ! neuron projection [Term] id: GO:0032590 name: dendrite membrane namespace: cellular_component def: "The portion of the plasma membrane surrounding a dendrite." [GOC:mah] is_a: GO:0032589 ! neuron projection membrane [Term] id: GO:0032591 name: dendritic spine membrane namespace: cellular_component def: "The portion of the plasma membrane surrounding a dendritic spine." [GOC:mah] is_a: GO:0032589 ! neuron projection membrane relationship: part_of GO:0043197 ! dendritic spine [Term] id: GO:0032775 name: DNA methylation on adenine namespace: biological_process def: "The covalent transfer of a methyl group to N-6 of adenine in a DNA molecule." [GOC:pf] synonym: "adenine methylation" RELATED [] is_a: GO:0006306 ! DNA methylation [Term] id: GO:0032776 name: DNA methylation on cytosine namespace: biological_process def: "The covalent transfer of a methyl group to C-5 or N-4 of cytosine in a DNA molecule." [GOC:pf] synonym: "cytosine methylation" BROAD [] is_a: GO:0006306 ! DNA methylation [Term] id: GO:0032784 name: regulation of DNA-dependent transcription, elongation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase." [GOC:mah, GOC:txnOH] synonym: "regulation of RNA elongation" BROAD [] synonym: "regulation of transcription elongation, DNA-dependent" EXACT [GOC:jh2] synonym: "regulation of transcriptional elongation" BROAD [] synonym: "transcription elongation regulator activity" RELATED [] is_a: GO:0006355 ! regulation of transcription, DNA-dependent intersection_of: regulates GO:0006354 ! DNA-dependent transcription, elongation relationship: regulates GO:0006354 ! DNA-dependent transcription, elongation [Term] id: GO:0032785 name: negative regulation of DNA-dependent transcription, elongation namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase." [GOC:mah, GOC:txnOH] synonym: "down regulation of RNA elongation" BROAD [] synonym: "down-regulation of RNA elongation" BROAD [] synonym: "downregulation of RNA elongation" BROAD [] synonym: "inhibition of RNA elongation" BROAD [] synonym: "negative regulation of transcription elongation" BROAD [] synonym: "negative regulation of transcription elongation, DNA-dependent" EXACT [GOC:jh2] synonym: "negative regulation of transcriptional elongation" BROAD [] synonym: "negative transcription elongation regulator activity" RELATED [] is_a: GO:0032784 ! regulation of DNA-dependent transcription, elongation intersection_of: negatively_regulates GO:0006354 ! DNA-dependent transcription, elongation relationship: negatively_regulates GO:0006354 ! DNA-dependent transcription, elongation [Term] id: GO:0032786 name: positive regulation of DNA-dependent transcription, elongation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase." [GOC:mah, GOC:txnOH] synonym: "activation of RNA elongation" BROAD [] synonym: "positive regulation of transcription elongation" BROAD [] synonym: "positive regulation of transcription elongation, DNA-dependent" EXACT [GOC:jh2] synonym: "positive regulation of transcriptional elongation" BROAD [] synonym: "positive transcription elongation regulator activity" RELATED [] synonym: "stimulation of RNA elongation" BROAD [] synonym: "up regulation of RNA elongation" BROAD [] synonym: "up-regulation of RNA elongation" BROAD [] synonym: "upregulation of RNA elongation" BROAD [] is_a: GO:0032784 ! regulation of DNA-dependent transcription, elongation intersection_of: positively_regulates GO:0006354 ! DNA-dependent transcription, elongation relationship: positively_regulates GO:0006354 ! DNA-dependent transcription, elongation [Term] id: GO:0032792 name: negative regulation of CREB transcription factor activity namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor CREB." [GOC:dph, GOC:ecd, GOC:tb] synonym: "CREB inhibitor" RELATED [] synonym: "inhibition of CREB transcription factor" EXACT [GOC:dph, GOC:tb] is_a: GO:0043433 ! negative regulation of sequence-specific DNA binding transcription factor activity [Term] id: GO:0032793 name: positive regulation of CREB transcription factor activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of activity of the transcription factor CREB." [GOC:dph, GOC:ecd, GOC:tb] synonym: "activation of CREB" EXACT [] synonym: "activation of CREB transcription factor" EXACT [GOC:dph, GOC:tb] synonym: "CREB activator" RELATED [] is_a: GO:0051091 ! positive regulation of sequence-specific DNA binding transcription factor activity [Term] id: GO:0032809 name: neuronal cell body membrane namespace: cellular_component def: "The plasma membrane of a neuron cell body - excludes the plasma membrane of cell projections such as axons and dendrites." [GOC:jl] synonym: "neuron cell body membrane" EXACT [] synonym: "neuronal cell soma membrane" EXACT [] is_a: GO:0097458 ! neuron part relationship: part_of GO:0043025 ! neuronal cell body [Term] id: GO:0032839 name: dendrite cytoplasm namespace: cellular_component def: "All of the contents of a dendrite, excluding the surrounding plasma membrane." [GOC:mah] synonym: "dendritic cytoplasm" EXACT [] is_a: GO:0097458 ! neuron part relationship: part_of GO:0030425 ! dendrite [Term] id: GO:0032897 name: negative regulation of viral transcription namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of viral transcription." [GOC:mah] synonym: "down regulation of viral transcription" EXACT [] synonym: "down-regulation of viral transcription" EXACT [] synonym: "downregulation of viral transcription" EXACT [] synonym: "inhibition of viral transcription" NARROW [] is_a: GO:0046782 ! regulation of viral transcription intersection_of: negatively_regulates GO:0019083 ! viral transcription relationship: negatively_regulates GO:0019083 ! viral transcription [Term] id: GO:0032922 name: circadian regulation of gene expression namespace: biological_process def: "Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours." [GOC:mah] synonym: "circadian regulation of protein expression" RELATED [] synonym: "diurnal variation of gene expression" RELATED [] synonym: "diurnal variation of protein expression" RELATED [] is_a: GO:0010468 ! regulation of gene expression [Term] id: GO:0032933 name: SREBP signaling pathway namespace: biological_process alt_id: GO:0006994 alt_id: GO:0030967 alt_id: GO:0035104 def: "A series of molecular signals from the endoplasmic reticulum to the nucleus generated as a consequence of decreased levels of one or more sterols (and in some yeast, changes in oxygen levels) and which proceeds through activation of a sterol response element binding transcription factor (SREBP) to result in up-regulation of target gene transcription." [GOC:bf, GOC:mah, GOC:signaling, GOC:vw, PMID:12923525, PMID:22017871] synonym: "activation of sterol regulatory element binding protein target gene transcription" NARROW [] synonym: "endoplasmic reticulum to nucleus sterol response pathway" EXACT [] synonym: "endoplasmic reticulum-nuclear sterol response pathway" EXACT [] synonym: "ER to nucleus sterol response pathway" EXACT [] synonym: "ER-nuclear sterol response pathway" EXACT [] synonym: "positive regulation of sterol regulatory element binding protein target gene transcription" EXACT [GOC:dph, GOC:tb] synonym: "positive regulation of sterol regulatory element binding protein target gene transcription involved in sterol depletion response" EXACT [GOC:dph, GOC:tb] synonym: "positive regulation of transcription via sterol regulatory element binding" NARROW [GOC:vw] synonym: "positive regulation of transcription via sterol regulatory element binding involved in ER-nuclear sterol response pathway" NARROW [GOC:vw] synonym: "SREBP signalling" EXACT [GOC:bf] synonym: "SREBP target gene transcriptional activation" EXACT [] synonym: "SREBP-mediated signaling pathway" RELATED [] synonym: "SREBP-mediated signalling pathway" EXACT [] synonym: "sterol depletion response, SREBP target gene transcriptional activation" EXACT [GOC:dph, GOC:mtg_lung] synonym: "sterol regulatory element binding protein target gene transcriptional activation" BROAD [] synonym: "sterol response element binding protein signaling pathway" EXACT [GOC:bf] synonym: "stimulation of sterol regulatory element binding protein target gene transcription" NARROW [] synonym: "up regulation of sterol regulatory element binding protein target gene transcription" EXACT [] synonym: "up-regulation of sterol regulatory element binding protein target gene transcription" EXACT [] synonym: "upregulation of sterol regulatory element binding protein target gene transcription" EXACT [] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter [Term] id: GO:0032938 name: negative regulation of translation in response to oxidative stress namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of translation as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals." [GOC:mah] is_a: GO:0032055 ! negative regulation of translation in response to stress is_a: GO:0043556 ! regulation of translation in response to oxidative stress [Term] id: GO:0032939 name: positive regulation of translation in response to oxidative stress namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of translation as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals." [GOC:mah] synonym: "activation of translation in response to oxidative stress" NARROW [] synonym: "stimulation of translation in response to oxidative stress" NARROW [] synonym: "up regulation of translation in response to oxidative stress" EXACT [] synonym: "up-regulation of translation in response to oxidative stress" EXACT [] synonym: "upregulation of translation in response to oxidative stress" EXACT [] is_a: GO:0032056 ! positive regulation of translation in response to stress is_a: GO:0043556 ! regulation of translation in response to oxidative stress [Term] id: GO:0032968 name: positive regulation of transcription elongation from RNA polymerase II promoter namespace: biological_process alt_id: GO:0090040 def: "Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II." [GOC:mah, GOC:txnOH] synonym: "positive regulation of gene-specific transcription elongation from RNA polymerase II promoter" RELATED [] synonym: "positive regulation of RNA elongation from RNA polymerase II promoter" EXACT [] is_a: GO:0032786 ! positive regulation of DNA-dependent transcription, elongation is_a: GO:0034243 ! regulation of transcription elongation from RNA polymerase II promoter intersection_of: positively_regulates GO:0006368 ! transcription elongation from RNA polymerase II promoter relationship: positively_regulates GO:0006368 ! transcription elongation from RNA polymerase II promoter [Term] id: GO:0033119 name: negative regulation of RNA splicing namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of RNA splicing." [GOC:mah] is_a: GO:0043484 ! regulation of RNA splicing intersection_of: negatively_regulates GO:0008380 ! RNA splicing relationship: negatively_regulates GO:0008380 ! RNA splicing [Term] id: GO:0033120 name: positive regulation of RNA splicing namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of RNA splicing." [GOC:mah] is_a: GO:0043484 ! regulation of RNA splicing intersection_of: positively_regulates GO:0008380 ! RNA splicing relationship: positively_regulates GO:0008380 ! RNA splicing [Term] id: GO:0033168 name: conversion of ds siRNA to ss siRNA involved in RNA interference namespace: biological_process def: "The process in which double-stranded siRNA molecules are converted to single-stranded siRNAs; required for the formation of a mature RITS complex during RNA interference." [GOC:mah, PMID:17310250] synonym: "RNA interference, conversion of ds siRNA to ss siRNA" EXACT [GOC:mah] is_a: GO:0036404 ! conversion of ds siRNA to ss siRNA intersection_of: GO:0036404 ! conversion of ds siRNA to ss siRNA intersection_of: part_of GO:0016246 ! RNA interference relationship: part_of GO:0030422 ! production of siRNA involved in RNA interference [Term] id: GO:0033217 name: regulation of transcription from RNA polymerase II promoter in response to iron ion starvation namespace: biological_process def: "Modulation of the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of deprivation of iron ions." [GOC:mah] synonym: "regulation of transcription from RNA polymerase II promoter in response to iron deficiency" EXACT [] is_a: GO:0043618 ! regulation of transcription from RNA polymerase II promoter in response to stress [Term] id: GO:0033267 name: axon part namespace: cellular_component def: "A part of an axon, a cell projection of a neuron." [GOC:jl] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate xref: NIF_Subcellular:sao280355188 is_a: GO:0097458 ! neuron part intersection_of: GO:0005575 ! cellular_component intersection_of: part_of GO:0030424 ! axon relationship: part_of GO:0030424 ! axon [Term] id: GO:0033268 name: node of Ranvier namespace: cellular_component def: "An axon part that is a gap in the myelin where voltage-gated sodium channels cluster and saltatory conduction is executed." [GOC:mh] xref: NIF_Subcellular:birnlex_1152_2 xref: Wikipedia:Nodes_of_Ranvier is_a: GO:0033267 ! axon part relationship: part_of GO:0044304 ! main axon [Term] id: GO:0033269 name: internode region of axon namespace: cellular_component def: "An axon part that is located between the nodes of Ranvier and surrounded by compact myelin sheath." [GOC:mah, GOC:mh] synonym: "internode" EXACT [] xref: NIF_Subcellular:sao206157942 is_a: GO:0033267 ! axon part relationship: part_of GO:0044304 ! main axon [Term] id: GO:0033270 name: paranode region of axon namespace: cellular_component def: "An axon part that is located adjacent to the nodes of Ranvier and surrounded by lateral loop portions of myelin sheath." [GOC:mah, GOC:mh] synonym: "paranode" EXACT [] xref: NIF_Subcellular:sao234066064 is_a: GO:0033267 ! axon part relationship: part_of GO:0044304 ! main axon [Term] id: GO:0033401 name: UUU codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a UUU codon." [GOC:mah] comment: Note that in the standard genetic code, TTT codes for phenylalanine. synonym: "phenylalanine tRNA" RELATED [GOC:hjd, GOC:mah] synonym: "TTT codon-amino acid adaptor activity" EXACT [GOC:hjd] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033402 name: UUC codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a UUC codon." [GOC:mah] comment: Note that in the standard genetic code, TTC codes for phenylalanine. synonym: "phenylalanine tRNA" RELATED [GOC:hjd, GOC:mah] synonym: "TTC codon-amino acid adaptor activity" EXACT [GOC:hjd] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033403 name: UUA codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a UUA codon." [GOC:mah] comment: Note that in the standard genetic code, TTA codes for leucine. synonym: "leucine tRNA" RELATED [GOC:hjd, GOC:mah] synonym: "TTA codon-amino acid adaptor activity" EXACT [GOC:hjd] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033404 name: UUG codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a UUG codon." [GOC:mah] comment: Note that in the standard genetic code, TTG codes for leucine. synonym: "leucine tRNA" RELATED [GOC:hjd, GOC:mah] synonym: "TTG codon-amino acid adaptor activity" EXACT [GOC:hjd] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033405 name: UCU codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a UCU codon." [GOC:mah] comment: Note that in the standard genetic code, TCT codes for serine. synonym: "serine tRNA" RELATED [GOC:hjd, GOC:mah] synonym: "TCT codon-amino acid adaptor activity" EXACT [GOC:hjd] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033406 name: UCC codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a UCC codon." [GOC:mah] comment: Note that in the standard genetic code, TCC codes for serine. synonym: "serine tRNA" RELATED [GOC:hjd, GOC:mah] synonym: "TCC codon-amino acid adaptor activity" EXACT [GOC:hjd] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033407 name: UCA codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a UCA codon." [GOC:mah] comment: Note that in the standard genetic code, TCA codes for serine. synonym: "serine tRNA" RELATED [GOC:hjd, GOC:mah] synonym: "TCA codon-amino acid adaptor activity" EXACT [GOC:hjd] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033408 name: UCG codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a UCG codon." [GOC:mah] comment: Note that in the standard genetic code, TCG codes for serine. synonym: "serine tRNA" RELATED [GOC:hjd, GOC:mah] synonym: "TCG codon-amino acid adaptor activity" EXACT [GOC:hjd] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033409 name: UAU codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a UAU codon." [GOC:mah] comment: Note that in the standard genetic code, TAT codes for tyrosine. synonym: "TAT codon-amino acid adaptor activity" EXACT [GOC:hjd] synonym: "tyrosine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033410 name: UAC codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a UAC codon." [GOC:mah] comment: Note that in the standard genetic code, TAC codes for tyrosine. synonym: "TAC codon-amino acid adaptor activity" EXACT [GOC:hjd] synonym: "tyrosine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033411 name: UAA codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a UAA codon." [GOC:mah] comment: Note that in the standard genetic code, TAA is a stop codon (ochre) and is not normally read by a tRNA. synonym: "TAA codon-amino acid adaptor activity" EXACT [GOC:hjd] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033412 name: UAG codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a UAG codon." [GOC:mah] comment: Note that in the standard genetic code, TAG is a stop codon (amber) and is not normally read by a tRNA. synonym: "TAG codon-amino acid adaptor activity" EXACT [GOC:hjd] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033413 name: UGU codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a UGU codon." [GOC:mah] comment: Note that in the standard genetic code, TGT codes for cysteine. synonym: "cysteine tRNA" RELATED [GOC:hjd, GOC:mah] synonym: "TGT codon-amino acid adaptor activity" EXACT [GOC:hjd] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033414 name: UGC codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a UGC codon." [GOC:mah] comment: Note that in the standard genetic code, TGC codes for cysteine. synonym: "cysteine tRNA" RELATED [GOC:hjd, GOC:mah] synonym: "TGC codon-amino acid adaptor activity" EXACT [GOC:hjd] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033415 name: UGA codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a UGA codon." [GOC:mah] comment: Note that in the standard genetic code, TGA is a stop codon (opal) and is not normally read by a tRNA. synonym: "TGA codon-amino acid adaptor activity" EXACT [GOC:hjd] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033416 name: UGG codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a UGG codon." [GOC:mah] comment: Note that in the standard genetic code, TGG codes for tryptophan. synonym: "TGG codon-amino acid adaptor activity" EXACT [GOC:hjd] synonym: "tryptophan tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033417 name: CUU codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a CUU codon." [GOC:mah] comment: Note that in the standard genetic code, CTT codes for leucine. synonym: "CTT codon-amino acid adaptor activity" EXACT [GOC:mah] synonym: "leucine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033418 name: CUC codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a CUC codon." [GOC:mah] comment: Note that in the standard genetic code, CTC codes for leucine. synonym: "CTC codon-amino acid adaptor activity" EXACT [GOC:hjd] synonym: "leucine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033419 name: CUA codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a CUA codon." [GOC:mah] comment: Note that in the standard genetic code, CTA codes for leucine. synonym: "CTA codon-amino acid adaptor activity" EXACT [GOC:mah] synonym: "leucine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033420 name: CUG codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a CUG codon." [GOC:mah] comment: Note that in the standard genetic code, CTG codes for leucine. synonym: "CTG codon-amino acid adaptor activity" EXACT [GOC:hjd] synonym: "leucine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033421 name: CCU codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a CCU codon." [GOC:mah] comment: Note that in the standard genetic code, CCT codes for proline. synonym: "CCT codon-amino acid adaptor activity" EXACT [GOC:hjd] synonym: "proline tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033422 name: CCC codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a CCC codon." [GOC:mah] comment: Note that in the standard genetic code, CCC codes for proline. synonym: "proline tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033423 name: CCA codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a CCA codon." [GOC:mah] comment: Note that in the standard genetic code, CCA codes for proline. synonym: "proline tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033424 name: CCG codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a CCG codon." [GOC:mah] comment: Note that in the standard genetic code, CCG codes for proline. synonym: "proline tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033425 name: CAU codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a CAU codon." [GOC:mah] comment: Note that in the standard genetic code, CAT codes for histidine. synonym: "CAT codon-amino acid adaptor activity" EXACT [GOC:hjd] synonym: "histidine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033426 name: CAC codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a CAC codon." [GOC:mah] comment: Note that in the standard genetic code, CAC codes for histidine. synonym: "histidine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033427 name: CAA codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a CAA codon." [GOC:mah] comment: Note that in the standard genetic code, CAA codes for glutamine. synonym: "glutamine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033428 name: CAG codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a CAG codon." [GOC:mah] comment: Note that in the standard genetic code, CAG codes for glutamine. synonym: "glutamine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033429 name: CGU codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a CGU codon." [GOC:mah] comment: Note that in the standard genetic code, CGT codes for arginine. synonym: "arginine tRNA" RELATED [GOC:hjd, GOC:mah] synonym: "CGT codon-amino acid adaptor activity" EXACT [GOC:hjd] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033430 name: CGC codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a CGC codon." [GOC:mah] comment: Note that in the standard genetic code, CGC codes for arginine. synonym: "arginine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033431 name: CGA codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a CGA codon." [GOC:mah] comment: Note that in the standard genetic code, CGA codes for arginine. synonym: "arginine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033432 name: CGG codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a CGG codon." [GOC:mah] comment: Note that in the standard genetic code, CGG codes for arginine. synonym: "arginine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033433 name: AUU codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes an AUU codon." [GOC:mah] comment: Note that in the standard genetic code, ATT codes for isoleucine. synonym: "ATT codon-amino acid adaptor activity" EXACT [GOC:hjd] synonym: "isoleucine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033434 name: AUC codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes an AUC codon." [GOC:mah] comment: Note that in the standard genetic code, ATC codes for isoleucine. synonym: "ATC codon-amino acid adaptor activity" EXACT [GOC:hjd] synonym: "isoleucine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033435 name: AUA codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes an AUA codon." [GOC:mah] comment: Note that in the standard genetic code, ATA codes for isoleucine. synonym: "ATA codon-amino acid adaptor activity" EXACT [GOC:hjd] synonym: "isoleucine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033436 name: AUG codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes an AUG codon." [GOC:mah] comment: Note that in the standard genetic code, ATG codes for methionine, and is the initiator codon. synonym: "ATG codon-amino acid adaptor activity" EXACT [GOC:mah] synonym: "initiator methionine tRNA" RELATED [GOC:hjd, GOC:mah] synonym: "methionine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033437 name: ACU codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes an ACU codon." [GOC:mah] comment: Note that in the standard genetic code, ACT codes for threonine. synonym: "ACT codon-amino acid adaptor activity" EXACT [GOC:mah] synonym: "threonine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033438 name: ACC codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes an ACC codon." [GOC:mah] comment: Note that in the standard genetic code, ACC codes for threonine. synonym: "threonine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033439 name: ACA codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes an ACA codon." [GOC:mah] comment: Note that in the standard genetic code, ACA codes for threonine. synonym: "threonine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033440 name: ACG codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes an ACG codon." [GOC:mah] comment: Note that in the standard genetic code, ACG codes for threonine. synonym: "threonine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033441 name: AAU codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes an AAU codon." [GOC:mah] comment: Note that in the standard genetic code, AAT codes for asparagine. synonym: "AAT codon-amino acid adaptor activity" EXACT [GOC:hjd] synonym: "asparagine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033442 name: AAC codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes an AAC codon." [GOC:mah] comment: Note that in the standard genetic code, AAC codes for asparagine. synonym: "asparagine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033443 name: AAA codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes an AAA codon." [GOC:mah] comment: Note that in the standard genetic code, AAA codes for lysine. synonym: "lysine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033444 name: AAG codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes an AAG codon." [GOC:mah] comment: Note that in the standard genetic code, AAG codes for lysine. synonym: "lysine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033445 name: AGU codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes an AGU codon." [GOC:mah] comment: Note that in the standard genetic code, AGT codes for serine. synonym: "AGT codon-amino acid adaptor activity" EXACT [GOC:mah] synonym: "serine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033446 name: AGC codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes an AGC codon." [GOC:mah] comment: Note that in the standard genetic code, AGC codes for serine. synonym: "serine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033447 name: AGA codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes an AGA codon." [GOC:mah] comment: Note that in the standard genetic code, AGA codes for arginine. synonym: "arginine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033448 name: AGG codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes an AGG codon." [GOC:mah] comment: Note that in the standard genetic code, AGG codes for arginine. synonym: "arginine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033449 name: GUU codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a GUU codon." [GOC:mah] comment: Note that in the standard genetic code, GTT codes for valine. synonym: "GTT codon-amino acid adaptor activity" EXACT [GOC:hjd] synonym: "valine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033450 name: GUC codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a GUC codon." [GOC:mah] comment: Note that in the standard genetic code, GTC codes for valine. synonym: "GTC codon-amino acid adaptor activity" EXACT [GOC:hjd] synonym: "valine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033451 name: GUA codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a GUA codon." [GOC:mah] comment: Note that in the standard genetic code, GTA codes for valine. synonym: "GTA codon-amino acid adaptor activity" EXACT [GOC:hjd] synonym: "valine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033452 name: GUG codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a GUG codon." [GOC:mah] comment: Note that in the standard genetic code, GTG codes for valine. synonym: "GTG codon-amino acid adaptor activity" EXACT [GOC:hjd] synonym: "valine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033453 name: GCU codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a GCU codon." [GOC:mah] comment: Note that in the standard genetic code, GCT codes for alanine. synonym: "alanine tRNA" RELATED [GOC:hjd, GOC:mah] synonym: "GCT codon-amino acid adaptor activity" EXACT [GOC:hjd] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033454 name: GCC codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a GCC codon." [GOC:mah] comment: Note that in the standard genetic code, GCC codes for alanine. synonym: "alanine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033455 name: GCA codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a GCA codon." [GOC:mah] comment: Note that in the standard genetic code, GCA codes for alanine. synonym: "alanine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033456 name: GCG codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a GCG codon." [GOC:mah] comment: Note that in the standard genetic code, GCG codes for alanine. synonym: "alanine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033457 name: GAU codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a GAU codon." [GOC:mah] comment: Note that in the standard genetic code, GAT codes for aspartic acid. synonym: "aspartic acid tRNA" RELATED [GOC:hjd, GOC:mah] synonym: "GAT codon-amino acid adaptor activity" EXACT [GOC:hjd] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033458 name: GAC codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a GAC codon." [GOC:mah] comment: Note that in the standard genetic code, GAC codes for aspartic acid. synonym: "aspartic acid tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033459 name: GAA codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a GAA codon." [GOC:mah] comment: Note that in the standard genetic code, GAA codes for glutamic acid. synonym: "glutamic acid tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033460 name: GAG codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a GAG codon." [GOC:mah] comment: Note that in the standard genetic code, GAG codes for glutamic acid. synonym: "glutamic acid tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033461 name: GGU codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a GGU codon." [GOC:mah] comment: Note that in the standard genetic code, GGT codes for glycine. synonym: "GGT codon-amino acid adaptor activity" EXACT [GOC:hjd] synonym: "glycine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033462 name: GGC codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a GGC codon." [GOC:mah] comment: Note that in the standard genetic code, GGC codes for glycine. synonym: "glycine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033463 name: GGA codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a GGA codon." [GOC:mah] comment: Note that in the standard genetic code, GGA codes for glycine. synonym: "glycine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033464 name: GGG codon-amino acid adaptor activity namespace: molecular_function def: "A triplet codon-amino acid adaptor activity that recognizes a GGG codon." [GOC:mah] comment: Note that in the standard genetic code, GGG codes for glycine. synonym: "glycine tRNA" RELATED [GOC:hjd, GOC:mah] is_a: GO:0030533 ! triplet codon-amino acid adaptor activity [Term] id: GO:0033562 name: co-transcriptional gene silencing by RNA interference machinery namespace: biological_process def: "A process in which the RNAi machinery mediates the degradation of nascent transcripts in association with chromatin." [GOC:mah, GOC:vw, PMID:17512405, PMID:21151114, PMID:22431512] synonym: "co-transcriptional gene silencing by small RNA" EXACT [GOC:vw] synonym: "cotranscriptional gene silencing by RNA interference machinery" RELATED [] synonym: "cotranscriptional gene silencing by small RNA" RELATED [] synonym: "RNAi-mediated CTGS" EXACT [GOC:vw] synonym: "small RNA-mediated cotranscriptional gene silencing" EXACT [GOC:dph, GOC:tb] is_a: GO:0031047 ! gene silencing by RNA [Term] id: GO:0034225 name: regulation of transcription from RNA polymerase II promoter in response to zinc ion starvation namespace: biological_process def: "Modulation of the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is deprived of zinc ions." [GOC:mah] synonym: "regulation of transcription from RNA polymerase II promoter in response to zinc deficiency" EXACT [] synonym: "regulation of transcription from RNA polymerase II promoter in response to zinc ion limitation" EXACT [] is_a: GO:0043618 ! regulation of transcription from RNA polymerase II promoter in response to stress [Term] id: GO:0034227 name: tRNA thio-modification namespace: biological_process def: "The addition a sulfur atom to a nucleotide in a tRNA molecule." [GOC:mcc, PMID:12549933, PMID:14722066] subset: gosubset_prok synonym: "tRNA sulfurtransferase activity" RELATED [GOC:mah] is_a: GO:0006400 ! tRNA modification [Term] id: GO:0034230 name: enkephalin processing namespace: biological_process def: "The formation of mature enkephalin, a pentapeptide hormone involved in regulating pain and nociception in the body by proteolytic processing of enkephalin propeptide." [GOC:BHF, GOC:mah, GOC:rl, PMID:8262946] synonym: "enkephalin formation" EXACT [] synonym: "peptide enkephalin formation" EXACT [] synonym: "peptide enkephalin processing" EXACT [] is_a: GO:0016486 ! peptide hormone processing [Term] id: GO:0034231 name: islet amyloid polypeptide processing namespace: biological_process def: "The formation of mature islet amyloid polypeptide (IAPP) by posttranslational processing of pro-islet amyloid polypeptide (pro-IAPP)." [GOC:BHF, GOC:rl, PMID:15983213, PMID:8262946] synonym: "IAPP formation" EXACT [] synonym: "IAPP processing" EXACT [] synonym: "islet amyloid peptide formation" EXACT [] synonym: "islet amyloid peptide processing" EXACT [] synonym: "islet amyloid polypeptide formation" RELATED [] is_a: GO:0016486 ! peptide hormone processing [Term] id: GO:0034243 name: regulation of transcription elongation from RNA polymerase II promoter namespace: biological_process alt_id: GO:0090039 def: "Any process that modulates the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II." [GOC:mah, GOC:txnOH] synonym: "regulation of gene-specific transcription elongation from RNA polymerase II promoter" RELATED [] synonym: "regulation of RNA elongation from RNA polymerase II promoter" EXACT [] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter is_a: GO:0032784 ! regulation of DNA-dependent transcription, elongation intersection_of: regulates GO:0006368 ! transcription elongation from RNA polymerase II promoter relationship: regulates GO:0006368 ! transcription elongation from RNA polymerase II promoter [Term] id: GO:0034244 name: negative regulation of transcription elongation from RNA polymerase II promoter namespace: biological_process alt_id: GO:0090041 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II." [GOC:mah, GOC:txnOH] synonym: "negative regulation of gene-specific transcription elongation from RNA polymerase II promoter" RELATED [] synonym: "negative regulation of RNA elongation from RNA polymerase II promoter" EXACT [] is_a: GO:0032785 ! negative regulation of DNA-dependent transcription, elongation is_a: GO:0034243 ! regulation of transcription elongation from RNA polymerase II promoter intersection_of: negatively_regulates GO:0006368 ! transcription elongation from RNA polymerase II promoter relationship: negatively_regulates GO:0006368 ! transcription elongation from RNA polymerase II promoter [Term] id: GO:0034246 name: mitochondrial RNA polymerase binding promoter specificity activity namespace: molecular_function alt_id: GO:0000998 def: "Interacting selectively and non-covalently with a mitochondrial RNA polymerase to form a holoenzyme complex and also, while present in the holoenzyme, interacting with promoter sequences in order to confer sequence specific recognition of mitochondrial promoter DNA sequence motifs." [GOC:txnOH] synonym: "mitochondrial polymerase transcription factor activity" EXACT [] synonym: "mitochondrial transcription factor activity" RELATED [] synonym: "mitochondrial transcription initiation factor activity" EXACT [] relationship: part_of GO:0006391 ! transcription initiation from mitochondrial promoter [Term] id: GO:0034247 name: snoRNA splicing namespace: biological_process def: "The process of removing sections of a primary snoRNA transcript to remove sequences not present in the mature form of the snoRNA and joining the remaining sections to form the mature form of the snoRNA." [GOC:mah] is_a: GO:0008380 ! RNA splicing is_a: GO:0043144 ! snoRNA processing [Term] id: GO:0034395 name: regulation of transcription from RNA polymerase II promoter in response to iron namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter in response to an iron stimulus." [GO_REF:0000021, GOC:mah] comment: This term was added by GO_REF:0000021. synonym: "regulation of specific transcription from RNA polymerase II promoter in response to iron" EXACT [] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter [Term] id: GO:0034396 name: negative regulation of transcription from RNA polymerase II promoter in response to iron namespace: biological_process def: "Any process that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter in response to an iron stimulus." [GOC:mah] synonym: "down regulation of transcription from RNA polymerase II promoter in response to iron" EXACT [] synonym: "down-regulation of transcription from RNA polymerase II promoter in response to iron" EXACT [] synonym: "downregulation of transcription from RNA polymerase II promoter in response to iron" EXACT [] synonym: "inhibition of transcription from RNA polymerase II promoter in response to iron" NARROW [] synonym: "negative regulation of transcription from Pol II promoter in response to iron" EXACT [] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter is_a: GO:0034395 ! regulation of transcription from RNA polymerase II promoter in response to iron [Term] id: GO:0034401 name: regulation of transcription by chromatin organization namespace: biological_process def: "Any cellular process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin that modulates the rate, frequency or extent of DNA-dependent transcription." [GOC:curators] synonym: "establishment or maintenance of chromatin architecture during transcription" EXACT [GOC:mah] synonym: "regulation of transcription by chromatin organisation" EXACT [GOC:mah] is_a: GO:0006355 ! regulation of transcription, DNA-dependent intersection_of: part_of GO:0006351 ! transcription, DNA-dependent [Term] id: GO:0034402 name: recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex namespace: biological_process def: "The process in which proteins required for 3'-end transcript processing become associated with the RNA polymerase II holoenzyme complex and the 3' end of a transcript." [PMID:18195044] relationship: part_of GO:0031124 ! mRNA 3'-end processing [Term] id: GO:0034403 name: alignment of 3' and 5' splice sites of mRNA namespace: biological_process def: "Recognition of both the 5' and 3'-splice sites and positioning them in the correct alignment with respect to each other so that the second catalytic step of nuclear mRNA splicing can occur." [GOC:krc, PMID:9430647] synonym: "alignment of 3' and 5' splice sites of nuclear mRNA" EXACT [GOC:vw] is_a: GO:0000389 ! mRNA 3'-splice site recognition is_a: GO:0000395 ! mRNA 5'-splice site recognition relationship: part_of GO:0000350 ! generation of catalytic spliceosome for second transesterification step [Term] id: GO:0034414 name: tRNA 3'-trailer cleavage, endonucleolytic namespace: biological_process def: "Endonucleolytic cleavage of the 3'-end of the pre-tRNA as part of the process of generating the mature 3'-end of the tRNA." [GOC:mah] synonym: "endonucleolytic tRNA 3'-end cleavage" EXACT [] synonym: "endonucleolytic tRNA 3'-trailer cleavage" RELATED [] synonym: "tRNA 3'-end cleavage, endonucleolytic" EXACT [] is_a: GO:0042779 ! tRNA 3'-trailer cleavage [Term] id: GO:0034415 name: tRNA 3'-trailer cleavage, exonucleolytic namespace: biological_process def: "Exonucleolytic cleavage of the 3'-end of the pre-tRNA as part of the process of generating the mature 3'-end of the tRNA." [GOC:mah] synonym: "exonucleolytic tRNA 3'-end cleavage" EXACT [] synonym: "exonucleolytic tRNA 3'-trailer cleavage" EXACT [] synonym: "tRNA 3'-end cleavage, exonucleolytic" EXACT [] is_a: GO:0042779 ! tRNA 3'-trailer cleavage [Term] id: GO:0034470 name: ncRNA processing namespace: biological_process def: "Any process that results in the conversion of one or more primary non-coding RNA (ncRNA) transcripts into one or more mature ncRNA molecules." [GOC:mah] is_a: GO:0006396 ! RNA processing [Term] id: GO:0034471 name: ncRNA 5'-end processing namespace: biological_process def: "Any process involved in forming the mature 5' end of a non-coding RNA molecule." [GOC:mah] synonym: "ncRNA 5' end processing" EXACT [] is_a: GO:0000966 ! RNA 5'-end processing is_a: GO:0034470 ! ncRNA processing [Term] id: GO:0034472 name: snRNA 3'-end processing namespace: biological_process def: "Any process involved in forming the mature 3' end of an snRNA molecule." [GOC:mah] synonym: "snRNA 3' end processing" EXACT [] is_a: GO:0016180 ! snRNA processing is_a: GO:0043628 ! ncRNA 3'-end processing [Term] id: GO:0034473 name: U1 snRNA 3'-end processing namespace: biological_process def: "Any process involved in forming the mature 3' end of a U1 snRNA molecule." [GOC:mah] synonym: "U1 snRNA 3' end processing" EXACT [] is_a: GO:0034472 ! snRNA 3'-end processing [Term] id: GO:0034474 name: U2 snRNA 3'-end processing namespace: biological_process def: "Any process involved in forming the mature 3' end of a U2 snRNA molecule." [GOC:mah] synonym: "U2 snRNA 3' end processing" EXACT [] is_a: GO:0034472 ! snRNA 3'-end processing [Term] id: GO:0034475 name: U4 snRNA 3'-end processing namespace: biological_process def: "Any process involved in forming the mature 3' end of a U4 snRNA molecule." [GOC:mah] synonym: "U4 snRNA 3' end processing" EXACT [] is_a: GO:0034472 ! snRNA 3'-end processing [Term] id: GO:0034476 name: U5 snRNA 3'-end processing namespace: biological_process def: "Any process involved in forming the mature 3' end of a U5 snRNA molecule." [GOC:mah] synonym: "U5 snRNA 3' end processing" EXACT [] is_a: GO:0034472 ! snRNA 3'-end processing [Term] id: GO:0034477 name: U6 snRNA 3'-end processing namespace: biological_process def: "Any process involved in forming the mature 3' end of a U6 snRNA molecule." [GOC:mah] synonym: "U6 snRNA 3' end processing" EXACT [] is_a: GO:0034472 ! snRNA 3'-end processing [Term] id: GO:0034959 name: endothelin maturation namespace: biological_process def: "The process leading to the attainment of the full functional capacity of endothelin by conversion of Big-endothelin substrate into mature endothelin." [GOC:BHF, GOC:rl] is_a: GO:0016486 ! peptide hormone processing [Term] id: GO:0034963 name: box C/D snoRNA processing namespace: biological_process def: "Any process involved in the conversion of a primary box C/D type small nucleolar RNA (snoRNA) transcript into a mature box C/D snoRNA." [GOC:mah] is_a: GO:0043144 ! snoRNA processing [Term] id: GO:0034964 name: box H/ACA snoRNA processing namespace: biological_process def: "Any process involved in the conversion of a primary box H/ACA type small nucleolar RNA (snoRNA) transcript into a mature box H/ACA snoRNA." [GOC:mah] is_a: GO:0043144 ! snoRNA processing [Term] id: GO:0034965 name: intronic box C/D snoRNA processing namespace: biological_process def: "Any process involved in the conversion of a primary box C/D type small nucleolar RNA (snoRNA) transcript that resides within, and is processed from, the intron of a pre-mRNA into a mature box C/D snoRNA." [GOC:mah] is_a: GO:0031070 ! intronic snoRNA processing is_a: GO:0034963 ! box C/D snoRNA processing [Term] id: GO:0034966 name: intronic box H/ACA snoRNA processing namespace: biological_process def: "Any process involved in the conversion of a primary box H/ACA type small nucleolar RNA (snoRNA) transcript that resides within, and is processed from, the intron of a pre-mRNA into a mature box H/ACA snoRNA." [GOC:mah] is_a: GO:0031070 ! intronic snoRNA processing is_a: GO:0034964 ! box H/ACA snoRNA processing [Term] id: GO:0034982 name: mitochondrial protein processing namespace: biological_process def: "The peptide cleavage of mitochondrial proteins, including cleavage contributing to their import." [GOC:curators] synonym: "mitochondrial protein modification" RELATED [] is_a: GO:0016485 ! protein processing [Term] id: GO:0035087 name: siRNA loading onto RISC involved in RNA interference namespace: biological_process def: "The transfer of small interfering RNA molecules (siRNAs) from the Dicer family of enzymes that cleave the double-stranded RNA, onto the nuclease-containing RNA-initiated silencing complex (RISC), in the context of RNA interference." [GOC:bf, GOC:mah, PMID:14512631] synonym: "RNA interference, siRNA loading onto RISC" EXACT [GOC:mah] is_a: GO:0070922 ! small RNA loading onto RISC relationship: part_of GO:0016246 ! RNA interference [Term] id: GO:0035103 name: sterol regulatory element binding protein cleavage namespace: biological_process alt_id: GO:0006992 def: "The proteolytic release of a transcriptionally active sterol regulatory element binding protein (SREBP) from intracellular membranes, freeing it to move to the nucleus to upregulate transcription of target genes, in response to altered levels of one or more lipids." [GOC:bf, GOC:vw, PMID:12923525] synonym: "SREBP cleavage" EXACT [] synonym: "sterol depletion response, SREBP cleavage" EXACT [] synonym: "sterol regulatory element binding protein cleavage involved in ER-nuclear sterol response pathway" NARROW [GOC:vw] is_a: GO:0016485 ! protein processing relationship: part_of GO:0032933 ! SREBP signaling pathway [Term] id: GO:0035105 name: sterol regulatory element binding protein import into nucleus namespace: biological_process alt_id: GO:0006993 def: "The transfer of a sterol regulatory element binding protein (SREBP) into the nucleus, across the nuclear membrane, in response to altered levels of one or more lipids. SREBPs are transcription factors that bind sterol regulatory elements (SREs), DNA motifs found in the promoters of target genes." [GOC:bf, GOC:vw, PMID:12923525] comment: Note that 'translocation' is sometimes used in the literature to refer to the entire process of protein import into the nucleus, but in GO refers specifically to the step in which a cargo-carrier protein complex moves through the nuclear pore complex. synonym: "SREBP import into nucleus" EXACT [GOC:mah] synonym: "SREBP import into nucleus involved in sterol depletion response" EXACT [GOC:mah] synonym: "SREBP nuclear translocation" NARROW [GOC:mah] synonym: "sterol depletion response, SREBP import into nucleus" EXACT [GOC:mah] synonym: "sterol depletion response, SREBP nuclear translocation" NARROW [GOC:mah] synonym: "sterol depletion response, sterol regulatory element binding protein import into nucleus" EXACT [] synonym: "sterol depletion response, sterol regulatory element binding protein nuclear translocation" NARROW [GOC:dph, GOC:mah, GOC:tb] synonym: "sterol regulatory element binding protein import into nucleus involved in sterol depletion response" NARROW [GOC:vw] synonym: "sterol regulatory element binding protein nuclear translocation" NARROW [GOC:mah] synonym: "sterol regulatory element binding protein nuclear translocation involved in sterol depletion response" NARROW [GOC:mah] relationship: part_of GO:0032933 ! SREBP signaling pathway [Term] id: GO:0035194 name: posttranscriptional gene silencing by RNA namespace: biological_process def: "Any process of posttranscriptional gene inactivation (silencing) mediated by small RNA molecules that may trigger mRNA degradation or negatively regulate translation." [GOC:mah, PMID:15020054, PMID:15066275, PMID:15066283] synonym: "RNA-mediated posttranscriptional gene silencing" EXACT [GOC:dph, GOC:tb] synonym: "sense-PTGS" RELATED [] is_a: GO:0016441 ! posttranscriptional gene silencing is_a: GO:0031047 ! gene silencing by RNA [Term] id: GO:0035195 name: gene silencing by miRNA namespace: biological_process def: "Downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: mRNA cleavage or translational repression." [PMID:14744438, PMID:15066275, PMID:15066283] synonym: "gene silencing by microRNA" EXACT [GOC:pr] synonym: "microRNA-mediated gene silencing" EXACT [] synonym: "miRNA-mediated gene silencing" EXACT [GOC:dph, GOC:tb] is_a: GO:0035194 ! posttranscriptional gene silencing by RNA [Term] id: GO:0035196 name: production of miRNAs involved in gene silencing by miRNA namespace: biological_process alt_id: GO:0030918 def: "Cleavage of stem-loop RNA precursors into microRNAs (miRNAs), a class of small RNAs that primarily silence genes by blocking the translation of mRNA transcripts into protein." [GOC:dph, GOC:tb, PMID:15066275, PMID:15066283] synonym: "gene silencing by miRNA, production of miRNAs" EXACT [GOC:mah] synonym: "microRNA biogenesis" RELATED [GOC:tb] synonym: "microRNA biosynthesis" RELATED [] synonym: "microRNA biosynthetic process" RELATED [] synonym: "microRNA metabolic process" RELATED [] synonym: "microRNA metabolism" RELATED [] synonym: "microRNA processing" BROAD [] synonym: "microRNA-mediated gene silencing, production of microRNAs" EXACT [] synonym: "miRNA biogenesis" RELATED [GOC:tb] synonym: "miRNA processing" EXACT [] synonym: "miRNA-mediated gene silencing, production of miRNAs" EXACT [GOC:dph, GOC:tb] synonym: "production of microRNAs involved in gene silencing by microRNA" EXACT [GOC:pr] is_a: GO:0070918 ! production of small RNA involved in gene silencing by RNA relationship: part_of GO:0035195 ! gene silencing by miRNA [Term] id: GO:0035278 name: negative regulation of translation involved in gene silencing by miRNA namespace: biological_process def: "The process in which microRNAs (miRNAs) block the translation of target mRNAs into proteins. Once incorporated into a RNA-induced silencing complex (RISC), a miRNA will typically repress translation if the miRNA imperfectly base-pairs with the 3' untranslated regions of target mRNAs." [PMID:14744438, PMID:15196554] synonym: "down regulation of translation involved in gene silencing by miRNA" EXACT [GOC:mah] synonym: "down-regulation of translation involved in gene silencing by miRNA" EXACT [GOC:mah] synonym: "downregulation of translation involved in gene silencing by miRNA" EXACT [GOC:mah] synonym: "gene silencing by miRNA, negative regulation of translation" EXACT [GOC:mah] synonym: "inhibition of translation involved in gene silencing by miRNA" NARROW [GOC:mah] synonym: "miRNA-mediated gene silencing, negative regulation of translation" RELATED [GOC:dph, GOC:tb] synonym: "negative regulation of translation involved in gene silencing by microRNA" EXACT [GOC:pr] is_a: GO:0040033 ! negative regulation of translation, ncRNA-mediated intersection_of: GO:0017148 ! negative regulation of translation intersection_of: part_of GO:0035195 ! gene silencing by miRNA relationship: part_of GO:0035195 ! gene silencing by miRNA [Term] id: GO:0035279 name: mRNA cleavage involved in gene silencing by miRNA namespace: biological_process def: "The process in which microRNAs (miRNAs) direct the cleavage of target mRNAs. Once incorporated into a RNA-induced silencing complex (RISC), a miRNA will typically direct cleavage by base pairing with near-perfect complementarity to the target mRNA. Many plant miRNAs downregulate gene expression through this mechanism." [GOC:dph, GOC:mtg_lung, PMID:14744438, PMID:15196554] synonym: "gene silencing by miRNA, mRNA cleavage" EXACT [GOC:mah] synonym: "miRNA-mediated gene silencing, mRNA cleavage" EXACT [GOC:dph, GOC:tb] synonym: "mRNA cleavage involved in gene silencing by microRNA" EXACT [GOC:pr] is_a: GO:0006379 ! mRNA cleavage intersection_of: GO:0006379 ! mRNA cleavage intersection_of: part_of GO:0035195 ! gene silencing by miRNA relationship: part_of GO:0035195 ! gene silencing by miRNA [Term] id: GO:0035280 name: miRNA loading onto RISC involved in gene silencing by miRNA namespace: biological_process def: "The transfer of a microRNA (miRNA) strand from a miRNA:miRNA duplex onto the RNA-initiated silencing complex (RISC)." [PMID:14744438] synonym: "gene silencing by miRNA, miRNA loading onto RISC" EXACT [GOC:mah] synonym: "microRNA loading onto RISC involved in gene silencing by microRNA" EXACT [GOC:pr] synonym: "miRISC assembly" BROAD [] synonym: "miRNA-mediated gene silencing, miRNA loading onto RISC" EXACT [GOC:dph, GOC:tb] is_a: GO:0070922 ! small RNA loading onto RISC relationship: part_of GO:0035195 ! gene silencing by miRNA [Term] id: GO:0035281 name: pre-miRNA export from nucleus namespace: biological_process def: "Transport of pre-microRNAs (pre-miRNAs) from the nucleus to the cytoplasm. Pre-miRNAs are a ~60-70 nucleotide stem loop intermediate in miRNA production, produced by the nuclear cleavage of a primary miRNA (pri-mRNA) transcript. Pre-miRNAs are transported from the nucleus to the cytoplasm where further cleavage occurs to produce a mature miRNA product." [GOC:sl, PMID:14744438] synonym: "pre-microRNA export from cell nucleus" EXACT [] synonym: "pre-microRNA export from nucleus" RELATED [] synonym: "pre-microRNA export out of nucleus" EXACT [] synonym: "pre-microRNA transport from nucleus to cytoplasm" EXACT [] synonym: "pre-microRNA-nucleus export" EXACT [] relationship: part_of GO:0035195 ! gene silencing by miRNA [Term] id: GO:0035334 name: Notch receptor processing, ligand-independent namespace: biological_process def: "The proteolytic cleavages to the Notch protein that occur prior to ligand binding. A primary cleavage event within the extracellular domain whilst the Notch protein in still in the secretory pathway, leads to the transportation of a processed heterodimer to the cell surface." [GOC:bf, PMID:12651094] synonym: "Notch S1 cleavage" NARROW [PMID:12651094] is_a: GO:0016485 ! protein processing created_by: rfoulger creation_date: 2010-02-26T02:32:46Z [Term] id: GO:0035389 name: establishment of chromatin silencing at silent mating-type cassette namespace: biological_process def: "The initial formation of a transcriptionally silent chromatin structure such as heterochromatin at silent mating-type loci." [GOC:vw] is_a: GO:0006343 ! establishment of chromatin silencing relationship: part_of GO:0030466 ! chromatin silencing at silent mating-type cassette created_by: rfoulger creation_date: 2010-03-22T10:23:14Z [Term] id: GO:0035390 name: establishment of chromatin silencing at telomere namespace: biological_process def: "The initial formation of a transcriptionally silent chromatin structure such as heterochromatin at the telomere." [GOC:vw] is_a: GO:0006343 ! establishment of chromatin silencing relationship: part_of GO:0006348 ! chromatin silencing at telomere created_by: rfoulger creation_date: 2010-03-22T10:24:07Z [Term] id: GO:0035391 name: maintenance of chromatin silencing at silent mating-type cassette namespace: biological_process def: "The maintenance of chromatin in a transcriptionally silent state such as heterochromatin at silent mating-type loci." [GOC:vw] is_a: GO:0006344 ! maintenance of chromatin silencing relationship: part_of GO:0030466 ! chromatin silencing at silent mating-type cassette created_by: rfoulger creation_date: 2010-03-22T10:25:14Z [Term] id: GO:0035392 name: maintenance of chromatin silencing at telomere namespace: biological_process def: "The maintenance of chromatin in a transcriptionally silent state such as heterochromatin at the telomere." [GOC:vw] is_a: GO:0006344 ! maintenance of chromatin silencing relationship: part_of GO:0006348 ! chromatin silencing at telomere created_by: rfoulger creation_date: 2010-03-22T10:25:57Z [Term] id: GO:0035511 name: oxidative DNA demethylation namespace: biological_process def: "Removal of the methyl group from one or more nucleotides within a DNA molecule involving the oxidation (i.e. electron loss) of one or more atoms." [PMID:12594517, PMID:16482161, PMID:18775698] is_a: GO:0080111 ! DNA demethylation created_by: rfoulger creation_date: 2010-04-30T02:22:44Z [Term] id: GO:0035512 name: hydrolytic DNA demethylation namespace: biological_process def: "The hydrolytic removal of the methyl group from one or more nucleotides within a DNA molecule." [GOC:bf] is_a: GO:0080111 ! DNA demethylation created_by: rfoulger creation_date: 2010-04-30T02:24:21Z [Term] id: GO:0035514 name: DNA demethylase activity namespace: molecular_function def: "Catalysis of the removal of a methyl group from one or more nucleosides within a DNA molecule." [GOC:bf] relationship: part_of GO:0080111 ! DNA demethylation created_by: rfoulger creation_date: 2010-04-30T02:36:43Z [Term] id: GO:0035516 name: oxidative DNA demethylase activity namespace: molecular_function def: "Catalysis of the removal of the methyl group from one or more nucleotides within a DNA molecule involving the oxidation (i.e. electron loss) of one or more atoms." [PMID:12594517, PMID:16482161, PMID:18775698] synonym: "2-oxoglutarate-dependent DNA demethylase" EXACT [PMID:17991826] is_a: GO:0035514 ! DNA demethylase activity relationship: part_of GO:0035511 ! oxidative DNA demethylation created_by: rfoulger creation_date: 2010-04-30T02:38:16Z [Term] id: GO:0035551 name: protein initiator methionine removal involved in protein maturation namespace: biological_process def: "Removal of the initiating methionine or formylmethionine residue from a protein that contributes to protein maturation, the attainment of the full functional capacity of a protein." [GOC:bf, GOC:hjd, GOC:vw] is_a: GO:0016485 ! protein processing intersection_of: part_of GO:0051604 ! protein maturation created_by: rfoulger creation_date: 2010-05-13T04:29:05Z [Term] id: GO:0035552 name: oxidative single-stranded DNA demethylation namespace: biological_process def: "Removal of the methyl group from one or more nucleotides within a single-stranded DNA molecule involving the oxidation (i.e. electron loss) of one or more atoms." [GOC:rl, PMID:18775698] synonym: "oxidative ssDNA demethylation" EXACT [] is_a: GO:0035511 ! oxidative DNA demethylation created_by: rfoulger creation_date: 2010-05-14T11:03:55Z [Term] id: GO:0035582 name: sequestering of BMP in extracellular matrix namespace: biological_process def: "Confining a bone morphogenetic protein (BMP) to the extracellular matrix (ECM), such that it is separated from other components of the signaling pathway, including its cell surface receptor. Bone morphogenetic proteins (BMPs) are secreted as homodimers, non-covalently associated with N-terminal pro-peptides, and are targeted to the extracellular matrix through interaction with matrix proteins." [GOC:BHF, PMID:20855508] comment: Confining BMP in the extracellular matrix may be achieved by binding BMP directly, or by binding to members of a BMP-containing complex. synonym: "BMP sequestration in the ECM" EXACT [PMID:20855508] synonym: "negative regulation of BMP signaling pathway by extracellular sequestering of BMP" EXACT [GOC:bf] synonym: "negative regulation of BMP signalling pathway by extracellular matrix sequestering of BMP" EXACT [GOC:mah] synonym: "negative regulation of bone morphogenetic protein signaling pathway by extracellular matrix sequestering of bone morphogenetic protein" EXACT [] is_a: GO:0030514 ! negative regulation of BMP signaling pathway created_by: rfoulger creation_date: 2010-10-12T03:12:45Z [Term] id: GO:0035597 name: N6-isopentenyladenosine methylthiotransferase activity namespace: molecular_function def: "Catalysis of the methylthiolation (-SCH3 addition) at the C2 of the adenosine ring of N6-isopentenyladenosine (i6A) in tRNA, to form 2-methylthio-N6-isopentenyladenosine (ms2i6A)." [PMID:20472640] synonym: "i6A methylthiotransferase activity" EXACT [PMID:20472640] relationship: part_of GO:0035600 ! tRNA methylthiolation created_by: rfoulger creation_date: 2010-11-12T01:26:58Z [Term] id: GO:0035598 name: N6-threonylcarbomyladenosine methylthiotransferase activity namespace: molecular_function def: "Catalysis of the methylthiolation (-SCH3 addition) at the C2 of the adenosine ring of N6-threonylcarbomyladenosine (t6A) in tRNA, to form 2-methylthio-N6-threonylcarbamoyladenosine (ms2t6A)." [PMID:20472640, PMID:20584901] synonym: "t6A methylthiotransferase activity" EXACT [PMID:20472640] relationship: part_of GO:0035600 ! tRNA methylthiolation created_by: rfoulger creation_date: 2010-11-12T01:28:32Z [Term] id: GO:0035600 name: tRNA methylthiolation namespace: biological_process def: "The addition of a methylthioether group (-SCH3) to a nucleotide in a tRNA molecule." [PMID:20472640] is_a: GO:0006400 ! tRNA modification created_by: rfoulger creation_date: 2010-11-12T01:34:02Z [Term] id: GO:0035760 name: cytoplasmic polyadenylation-dependent rRNA catabolic process namespace: biological_process def: "The chemical reactions and pathways occurring in the cytoplasm and resulting in the breakdown of a ribosomal RNA (rRNA) molecule, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target rRNA truncated degradation intermediate." [PMID:20368444] synonym: "cytoplasmic poly(A)-dependent rRNA catabolic process" RELATED [GOC:vw] is_a: GO:0043634 ! polyadenylation-dependent ncRNA catabolic process created_by: rfoulger creation_date: 2011-03-25T02:14:50Z [Term] id: GO:0035947 name: regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of gluconeogenesis, by regulation of transcription from an RNA polymerase II promoter." [GOC:dgf, PMID:11024040, PMID:17875938, PMID:19686338] synonym: "regulation of gluconeogenesis by regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "regulation of glucose biosynthesis by regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "regulation of glucose biosynthesis by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "regulation of glucose biosynthetic process by regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "regulation of glucose biosynthetic process by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] is_a: GO:0072364 ! regulation of cellular ketone metabolic process by regulation of transcription from RNA polymerase II promoter intersection_of: regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: rfoulger [Term] id: GO:0035948 name: positive regulation of gluconeogenesis by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of gluconeogenesis by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, PMID:17875938] synonym: "regulation of gluconeogenesis by activation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "regulation of gluconeogenesis by positive regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "regulation of gluconeogenesis by stimulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "regulation of gluconeogenesis by up regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "regulation of gluconeogenesis by up-regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "regulation of gluconeogenesis by upregulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "regulation of glucose biosynthesis by positive regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "regulation of glucose biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "regulation of glucose biosynthesis by up regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "regulation of glucose biosynthesis by up-regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "regulation of glucose biosynthesis by upregulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "regulation of glucose biosynthetic process by positive regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "regulation of glucose biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" RELATED [GOC:obol] synonym: "regulation of glucose biosynthetic process by up regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "regulation of glucose biosynthetic process by up-regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "regulation of glucose biosynthetic process by upregulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] is_a: GO:0035947 ! regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter is_a: GO:0072366 ! regulation of cellular ketone metabolic process by positive regulation of transcription from RNA polymerase II promoter intersection_of: positively_regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: rfoulger [Term] id: GO:0035949 name: positive regulation of gluconeogenesis by negative regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of gluconeogenesis by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, PMID:17875938] synonym: "positive regulation of gluconeogenesis by down regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of gluconeogenesis by down-regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of gluconeogenesis by downregulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of gluconeogenesis by inhibition of transcription from RNA polymerase II promoter" NARROW [GOC:obol] synonym: "positive regulation of gluconeogenesis by negative regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "positive regulation of glucose biosynthesis by down regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of glucose biosynthesis by down-regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of glucose biosynthesis by downregulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of glucose biosynthesis by negative regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "positive regulation of glucose biosynthesis by negative regulation of transcription from RNA polymerase II promoter" RELATED [GOC:obol] synonym: "positive regulation of glucose biosynthetic process by down regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of glucose biosynthetic process by down-regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of glucose biosynthetic process by downregulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of glucose biosynthetic process by negative regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "positive regulation of glucose biosynthetic process by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] is_a: GO:0035947 ! regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter is_a: GO:0072365 ! regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter intersection_of: negatively_regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: rfoulger [Term] id: GO:0035950 name: regulation of oligopeptide transport by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of oligopeptide transport, by regulation of transcription from an RNA polymerase II promoter." [GOC:dgf, PMID:17005992] synonym: "regulation of oligopeptide transport by regulation of transcription from Pol II promoter" EXACT [GOC:obol] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: rfoulger [Term] id: GO:0035951 name: positive regulation of oligopeptide transport by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of oligopeptide transport by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf] synonym: "positive regulation of oligopeptide transport by activation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of oligopeptide transport by positive regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "positive regulation of oligopeptide transport by stimulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of oligopeptide transport by up regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of oligopeptide transport by up-regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of oligopeptide transport by upregulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] is_a: GO:0035950 ! regulation of oligopeptide transport by regulation of transcription from RNA polymerase II promoter is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: positively_regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: rfoulger [Term] id: GO:0035952 name: negative regulation of oligopeptide transport by negative regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of oligopeptide transport by stopping, preventing or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, PMID:17005992] synonym: "negative regulation of oligopeptide transport by down regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "negative regulation of oligopeptide transport by down-regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "negative regulation of oligopeptide transport by downregulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "negative regulation of oligopeptide transport by inhibition of transcription from RNA polymerase II promoter" NARROW [GOC:obol] synonym: "negative regulation of oligopeptide transport by negative regulation of transcription from Pol II promoter" EXACT [GOC:obol] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter is_a: GO:0035950 ! regulation of oligopeptide transport by regulation of transcription from RNA polymerase II promoter intersection_of: negatively_regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: rfoulger [Term] id: GO:0035953 name: regulation of dipeptide transport by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of dipeptide transport, by regulation of transcription from an RNA polymerase II promoter." [GOC:dgf, PMID:17005992] synonym: "regulation of dipeptide transport by regulation of transcription from Pol II promoter" EXACT [GOC:obol] is_a: GO:0035950 ! regulation of oligopeptide transport by regulation of transcription from RNA polymerase II promoter intersection_of: regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: rfoulger [Term] id: GO:0035954 name: positive regulation of dipeptide transport by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of dipeptide transport by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf] synonym: "positive regulation of dipeptide transport by activation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of dipeptide transport by positive regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "positive regulation of dipeptide transport by stimulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of dipeptide transport by up regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of dipeptide transport by up-regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of dipeptide transport by upregulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] is_a: GO:0035951 ! positive regulation of oligopeptide transport by positive regulation of transcription from RNA polymerase II promoter is_a: GO:0035953 ! regulation of dipeptide transport by regulation of transcription from RNA polymerase II promoter intersection_of: positively_regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: rfoulger [Term] id: GO:0035955 name: negative regulation of dipeptide transport by negative regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of dipeptide transport by stopping, preventing or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, PMID:10850718, PMID:17005992, PMID:9427760] synonym: "negative regulation of dipeptide transport by down regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "negative regulation of dipeptide transport by down-regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "negative regulation of dipeptide transport by downregulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "negative regulation of dipeptide transport by inhibition of transcription from RNA polymerase II promoter" NARROW [GOC:obol] synonym: "negative regulation of dipeptide transport by negative regulation of transcription from Pol II promoter" EXACT [GOC:obol] is_a: GO:0035952 ! negative regulation of oligopeptide transport by negative regulation of transcription from RNA polymerase II promoter is_a: GO:0035953 ! regulation of dipeptide transport by regulation of transcription from RNA polymerase II promoter intersection_of: negatively_regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: rfoulger [Term] id: GO:0035956 name: regulation of starch catabolic process by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the breakdown of starch, by modulating the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, PMID:9342405] synonym: "regulation of starch breakdown by regulation of transcription from Pol II promoter" EXACT [GGOC:obol] synonym: "regulation of starch breakdown by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "regulation of starch catabolic process by regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "regulation of starch catabolism by regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "regulation of starch catabolism by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "regulation of starch degradation by regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "regulation of starch degradation by regulation of transcription from RNA polymerase II promoter" RELATED [GOC:obol] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: rfoulger [Term] id: GO:0035957 name: positive regulation of starch catabolic process by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the breakdown of starch, by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf] synonym: "positive regulation of starch breakdown by regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "positive regulation of starch breakdown by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of starch catabolic process by regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "positive regulation of starch catabolism by regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "positive regulation of starch catabolism by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of starch degradation by regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "positive regulation of starch degradation by regulation of transcription from RNA polymerase II promoter" RELATED [GOC:obol] is_a: GO:0035956 ! regulation of starch catabolic process by regulation of transcription from RNA polymerase II promoter is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: positively_regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: rfoulger [Term] id: GO:0035958 name: regulation of glyoxylate cycle by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the glyoxylate cycle by modulating the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, PMID:11024040, PMID:17875938, PMID:19686338] synonym: "regulation of glyoxylate bypass by regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "regulation of glyoxylate bypass by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "regulation of glyoxylate cycle by regulation of transcription from Pol II promoter" RELATED [GOC:obol] is_a: GO:0072364 ! regulation of cellular ketone metabolic process by regulation of transcription from RNA polymerase II promoter intersection_of: regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: rfoulger [Term] id: GO:0035959 name: positive regulation of glyoxylate cycle by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the glyoxylate cycle by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, PMID:11024040, PMID:17875938, PMID:19686338] synonym: "positive regulation of glyoxylate bypass by positive regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "positive regulation of glyoxylate bypass by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of glyoxylate bypass by up regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of glyoxylate bypass by up-regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of glyoxylate bypass by upregulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of glyoxylate cycle by activation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of glyoxylate cycle by positive regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "positive regulation of glyoxylate cycle by stimulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of glyoxylate cycle by up regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of glyoxylate cycle by up-regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of glyoxylate cycle by upregulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] is_a: GO:0035958 ! regulation of glyoxylate cycle by regulation of transcription from RNA polymerase II promoter is_a: GO:0072366 ! regulation of cellular ketone metabolic process by positive regulation of transcription from RNA polymerase II promoter intersection_of: positively_regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: rfoulger [Term] id: GO:0035960 name: regulation of ergosterol biosynthetic process by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of ergosterol biosynthetic process by modulating the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, PMID:11533229, PMID:16055745] synonym: "regulation of ergosterol anabolism by regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "regulation of ergosterol anabolism by regulation of transcription from RNA polymerase II promoter" RELATED [GOC:obol] synonym: "regulation of ergosterol biosynthesis by regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "regulation of ergosterol biosynthesis by regulation of transcription from RNA polymerase II promoter" RELATED [GOC:obol] synonym: "regulation of ergosterol biosynthetic process by regulation of transcription from Pol II promoter" RELATED [GOC:obol] synonym: "regulation of ergosterol formation by regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "regulation of ergosterol formation by regulation of transcription from RNA polymerase II promoter" RELATED [GOC:obol] synonym: "regulation of ergosterol synthesis by regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "regulation of ergosterol synthesis by regulation of transcription from RNA polymerase II promoter" RELATED [GOC:obol] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: rfoulger [Term] id: GO:0035961 name: positive regulation of ergosterol biosynthetic process by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of ergosterol biosynthesis by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, PMID:11533229] synonym: "positive regulation of ergosterol anabolism by positive regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "positive regulation of ergosterol anabolism by positive regulation of transcription from RNA polymerase II promoter" RELATED [GOC:obol] synonym: "positive regulation of ergosterol anabolism by up regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of ergosterol anabolism by up-regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of ergosterol anabolism by upregulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of ergosterol biosynthesis by positive regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "positive regulation of ergosterol biosynthesis by positive regulation of transcription from RNA polymerase II promoter" RELATED [GOC:obol] synonym: "positive regulation of ergosterol biosynthesis by up regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of ergosterol biosynthesis by up-regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of ergosterol biosynthesis by upregulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of ergosterol biosynthetic process by activation of transcription from RNA polymerase II promoter" RELATED [GOC:obol] synonym: "positive regulation of ergosterol biosynthetic process by positive regulation of transcription from Pol II promoter" RELATED [GOC:obol] synonym: "positive regulation of ergosterol biosynthetic process by stimulation of transcription from RNA polymerase II promoter" RELATED [GOC:obol] synonym: "positive regulation of ergosterol biosynthetic process by up regulation of transcription from RNA polymerase II promoter" RELATED [GOC:obol] synonym: "positive regulation of ergosterol biosynthetic process by up-regulation of transcription from RNA polymerase II promoter" RELATED [GOC:obol] synonym: "positive regulation of ergosterol biosynthetic process by upregulation of transcription from RNA polymerase II promoter" RELATED [GOC:obol] synonym: "positive regulation of ergosterol formation by positive regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "positive regulation of ergosterol formation by positive regulation of transcription from RNA polymerase II promoter" RELATED [GOC:obol] synonym: "positive regulation of ergosterol formation by up regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of ergosterol formation by up-regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of ergosterol formation by upregulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of ergosterol synthesis by positive regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "positive regulation of ergosterol synthesis by positive regulation of transcription from RNA polymerase II promoter" RELATED [GOC:obol] synonym: "positive regulation of ergosterol synthesis by up regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of ergosterol synthesis by up-regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of ergosterol synthesis by upregulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] is_a: GO:0035960 ! regulation of ergosterol biosynthetic process by regulation of transcription from RNA polymerase II promoter is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: positively_regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: rfoulger [Term] id: GO:0035968 name: regulation of sterol import by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of sterol import, by regulation of transcription from an RNA polymerase II promoter." [GOC:dgf, PMID:12077145] synonym: "regulation of sterol import by regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "regulation of sterol influx by regulation of transcription from Pol II promoter" EXACT [GOC:bf] synonym: "regulation of sterol influx by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:bf] synonym: "regulation of sterol uptake by regulation of transcription from Pol II promoter" EXACT [GOC:bf] synonym: "regulation of sterol uptake by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:bf] is_a: GO:0072367 ! regulation of lipid transport by regulation of transcription from RNA polymerase II promoter intersection_of: regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: rfoulger [Term] id: GO:0035969 name: positive regulation of sterol import by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of sterol import by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, PMID:11533229] synonym: "positive regulation of sterol import by activation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of sterol import by positive regulation of transcription from Pol II promoter" EXACT [GOC:obol] synonym: "positive regulation of sterol import by stimulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of sterol import by up regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of sterol import by up-regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of sterol import by upregulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of sterol influx by activation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of sterol influx by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of sterol influx by stimulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of sterol influx by up regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of sterol influx by up-regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of sterol influx by upregulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of sterol uptake by activation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of sterol uptake by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of sterol uptake by stimulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of sterol uptake by up regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of sterol uptake by up-regulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] synonym: "positive regulation of sterol uptake by upregulation of transcription from RNA polymerase II promoter" EXACT [GOC:obol] is_a: GO:0035968 ! regulation of sterol import by regulation of transcription from RNA polymerase II promoter is_a: GO:0072369 ! regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter intersection_of: positively_regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: rfoulger [Term] id: GO:0036003 name: positive regulation of transcription from RNA polymerase II promoter in response to stress namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mcc] is_a: GO:0043618 ! regulation of transcription from RNA polymerase II promoter in response to stress is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: rfoulger creation_date: 2011-09-19T03:00:18Z [Term] id: GO:0036031 name: recruitment of mRNA capping enzyme to RNA polymerase II holoenzyme complex namespace: biological_process def: "The process in which the guanylyltransferase enzyme responsible for adding a 7-methylguanosine cap on pre-mRNA becomes associated with the RNA polymerase II holoenzyme complex and the 5' end of a transcript." [GOC:bf, GOC:rb, PMID:10594013] synonym: "capping enzyme targeting to RNA polymerase II" EXACT [PMID:10594013] synonym: "recruitment of guanylyltransferase to RNA polymerase II holoenzyme complex" EXACT [GOC:bf] relationship: part_of GO:0006370 ! 7-methylguanosine mRNA capping created_by: rfoulger creation_date: 2011-10-24T10:56:46Z [Term] id: GO:0036083 name: positive regulation of unsaturated fatty acid biosynthetic process by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of unsaturated fatty acid biosynthetic process by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, PMID:9927444] is_a: GO:0072366 ! regulation of cellular ketone metabolic process by positive regulation of transcription from RNA polymerase II promoter is_a: GO:2000531 ! regulation of fatty acid biosynthetic process by regulation of transcription from RNA polymerase II promoter intersection_of: positively_regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: rfoulger creation_date: 2011-12-20T04:52:36Z [Term] id: GO:0036086 name: positive regulation of transcription from RNA polymerase II promoter in response to iron ion starvation namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of deprivation of iron ions." [GOC:cjk] synonym: "positive regulation of transcription from RNA polymerase II promoter in response to iron deficiency" EXACT [GOC:bf] is_a: GO:0033217 ! regulation of transcription from RNA polymerase II promoter in response to iron ion starvation is_a: GO:0036003 ! positive regulation of transcription from RNA polymerase II promoter in response to stress created_by: rfoulger creation_date: 2012-01-05T01:45:26Z [Term] id: GO:0036091 name: positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals." [GOC:rn, PMID:14978214, PMID:18439143] is_a: GO:0036003 ! positive regulation of transcription from RNA polymerase II promoter in response to stress is_a: GO:0043619 ! regulation of transcription from RNA polymerase II promoter in response to oxidative stress created_by: rfoulger creation_date: 2012-01-10T02:54:43Z [Term] id: GO:0036095 name: positive regulation of invasive growth in response to glucose limitation by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of invasive growth as a result of deprivation of glucose, by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:jh, PMID:14668363] synonym: "transcriptional activation of genes involved in invasive growth" RELATED [GOC:bf] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: positively_regulates GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: rfoulger creation_date: 2012-01-24T10:53:28Z [Term] id: GO:0036129 name: negative regulation of transcription from RNA polymerase II promoter in response to hydrogen peroxide namespace: biological_process def: "Any process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hydrogen peroxide (H2O2) stimulus." [GOC:al] is_a: GO:0061417 ! negative regulation of transcription from RNA polymerase II promoter in response to oxidative stress created_by: rfoulger creation_date: 2012-03-02T10:36:39Z [Term] id: GO:0036206 name: regulation of histone gene expression namespace: biological_process def: "Any process that modulates the frequency, rate or extent of expression of a histone-encoding gene. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein." [GOC:bf, GOC:krc] comment: This term was created even though it describes a process relating to a group of gene products, because histones are highly conserved proteins that are essential components of cellular chromatin in eukaryotic cells. synonym: "regulation of expression of histone-encoding gene" EXACT [GOC:bf] is_a: GO:0010468 ! regulation of gene expression created_by: rfoulger creation_date: 2012-04-24T05:01:28Z [Term] id: GO:0036207 name: positive regulation of histone gene expression namespace: biological_process def: "Any process that increases the frequency, rate or extent of expression of a histone-encoding gene. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein." [GOC:bf, GOC:krc] comment: This term was created even though it describes a process relating to a group of gene products, because histones are highly conserved proteins that are essential components of cellular chromatin in eukaryotic cells. synonym: "activation of histone gene expression" NARROW [GOC:bf] synonym: "positive regulation of expression of histone-encoding gene" EXACT [GOC:bf] synonym: "up-regulation of histone gene expression" EXACT [GOC:bf] synonym: "upregulation of histone gene expression" EXACT [GOC:bf] is_a: GO:0010628 ! positive regulation of gene expression is_a: GO:0036206 ! regulation of histone gene expression created_by: rfoulger creation_date: 2012-04-25T09:27:42Z [Term] id: GO:0036208 name: negative regulation of histone gene expression namespace: biological_process def: "Any process that decreases the frequency, rate or extent of expression of a histone-encoding gene. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein." [GOC:bf, GOC:krc] comment: This term was created even though it describes a process relating to a group of gene products, because histones are highly conserved proteins that are essential components of cellular chromatin in eukaryotic cells. synonym: "down-regulation of histone gene expression" EXACT [GOC:bf] synonym: "downregulation of histone gene expression" EXACT [GOC:bf] synonym: "inhibition of histone gene expression" NARROW [GOC:bf] synonym: "negative regulation of expression of histone-encoding gene" EXACT [GOC:bf] is_a: GO:0010629 ! negative regulation of gene expression is_a: GO:0036206 ! regulation of histone gene expression created_by: rfoulger creation_date: 2012-04-25T09:29:43Z [Term] id: GO:0036251 name: positive regulation of transcription from RNA polymerase II promoter in response to salt stress namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under salt stress. The stress is usually an increase or decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment." [GOC:al] is_a: GO:0061393 ! positive regulation of transcription from RNA polymerase II promoter in response to osmotic stress is_a: GO:0061416 ! regulation of transcription from RNA polymerase II promoter in response to salt stress created_by: rfoulger creation_date: 2012-06-12T11:38:22Z [Term] id: GO:0036252 name: positive regulation of transcription from RNA polymerase II promoter in response to menadione namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a menadione stimulus. Menadione (also called vitamin K3) is a naphthoquinone having a methyl substituent at the 2-position." [CHEBI:28869, GOC:al] synonym: "positive regulation of transcription from RNA polymerase II promoter in response to menadione stress" NARROW [GOC:al] is_a: GO:0036003 ! positive regulation of transcription from RNA polymerase II promoter in response to stress created_by: rfoulger creation_date: 2012-06-12T11:40:58Z [Term] id: GO:0036260 name: RNA capping namespace: biological_process def: "The sequence of enzymatic reactions by which a cap structure is added to the 5' end of a nascent RNA polymerase II transcript. All RNA polymerase II transcripts receive a 7-methyl-G cap. Then for (at least) small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs), the7-methyl-G cap is hypermethylated to become a 2,2,7-trimethylguanosine (TMG) cap." [GOC:bf, GOC:krc, GOC:mah, PMID:18775984] is_a: GO:0006396 ! RNA processing created_by: rfoulger creation_date: 2012-06-15T02:10:23Z [Term] id: GO:0036261 name: 7-methylguanosine cap hypermethylation namespace: biological_process def: "Hypermethylation of the 7-(mono)methylguanosine (m(7)G) cap structure at the 2' position of the guanosine residue to convert a mono-methylated cap to a 2,2,7-trimethylguanosine cap structure. This type of cap modification occurs on small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs) and is dependent on prior guanine-N7 methylation." [GOC:bf, GOC:BHF, GOC:krc, GOC:mah, GOC:rl, PMID:11983179, PMID:18775984] synonym: "2,2,7-trimethylguanosine cap formation" EXACT [PMID:11983179] synonym: "conversion of m(7)G to m(3)G" EXACT [PMID:11983179] synonym: "hypermethylation of snoRNA cap" NARROW [GOC:bf, GOC:krc, GOC:mah] synonym: "hypermethylation of snRNA cap" NARROW [GOC:bf, GOC:krc, GOC:mah] synonym: "m(7)G cap hypermethylation" EXACT [GOC:bf] synonym: "snoRNA capping" NARROW [GOC:rl] synonym: "snRNA capping" NARROW [GOC:rl] synonym: "TMG cap formation" EXACT [PMID:11983179] is_a: GO:0036260 ! RNA capping created_by: rfoulger creation_date: 2012-06-15T02:21:39Z [Term] id: GO:0036265 name: RNA (guanine-N7)-methylation namespace: biological_process def: "The addition of a methyl group to the N7 atom in the base portion of a guanine nucleotide residue in an RNA molecule." [GOC:BHF, GOC:rl] relationship: part_of GO:0009452 ! 7-methylguanosine RNA capping created_by: rfoulger creation_date: 2012-06-25T10:28:25Z [Term] id: GO:0036278 name: positive regulation of transcription from RNA polymerase II promoter in response to nitrogen starvation namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a deprivation of nitrogen." [GOC:al, PMID:21118960] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: rfoulger creation_date: 2012-07-11T11:02:55Z [Term] id: GO:0036307 name: 23S rRNA (adenine(2030)-N(6))-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + adenine(2030) in 23S rRNA = S-adenosyl-L-homocysteine + rRNA containing N(6)-methyladenine(2030) in 23S rRNA." [GOC:imk, PMID:22847818] is_a: GO:0008988 ! rRNA (adenine-N6-)-methyltransferase activity created_by: rfoulger creation_date: 2012-08-08T14:15:48Z [Term] id: GO:0036308 name: 16S rRNA (guanine(1516)-N(2))-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + guanosine(1516) in 16S rRNA = N(2)-methylguanosine(1516) in 16S rRNA + S-adenosyl-L-homocysteine." [GOC:imk, PMID:22079366] is_a: GO:0008990 ! rRNA (guanine-N2-)-methyltransferase activity created_by: rfoulger creation_date: 2012-08-08T14:17:44Z [Term] id: GO:0036316 name: SREBP-SCAP complex retention in endoplasmic reticulum namespace: biological_process def: "Any process in which the SREBP-SCAP complex is maintained in the endoplasmic reticulum and prevented from moving elsewhere. The SREBP-SCAP complex is formed by the association of sterol regulatory element binding protein (SREBP) and SREBP-cleavage-activating protein (SCAP). In the absence of sterols, the SREBP-SCAP complex is packaged into COPII vesicles and travels to the Golgi apparatus to be processed. In the presence of sterols, the complex binds ER-resident proteins such as INSIG, which retain the complex in the ER." [GOC:bf, PMID:16525117] comment: Consider also annotating to the cellular component term: SREBP-SCAP-Insig complex ; GO:0032937. is_a: GO:2000639 ! negative regulation of SREBP signaling pathway created_by: rfoulger creation_date: 2012-08-21T14:53:08Z [Term] id: GO:0036404 name: conversion of ds siRNA to ss siRNA namespace: biological_process def: "The process in which double-stranded small interfering RNA (ds siRNA) molecules are converted to single-stranded small interfering RNA (ss siRNA)." [GOC:vw] synonym: "conversion of double-stranded small interfering RNA to single-stranded small interfering RNA." RELATED [GOC:bf] is_a: GO:0006396 ! RNA processing relationship: part_of GO:0031050 ! dsRNA fragmentation created_by: rfoulger creation_date: 2013-08-14T14:24:19Z [Term] id: GO:0036415 name: regulation of tRNA stability namespace: biological_process def: "Any process that modulates the propensity of transfer RNA (tRNA) molecules to degradation. Includes processes that both stabilize and destabilize tRNAs." [GOC:aa, PMID:21502523, PMID:23572593] is_a: GO:0043487 ! regulation of RNA stability created_by: rfoulger creation_date: 2013-08-22T15:22:13Z [Term] id: GO:0036416 name: tRNA stabilization namespace: biological_process def: "Prevention of degradation of tRNA molecules." [GOC:aa, GOC:bf, PMID:20459084] is_a: GO:0036415 ! regulation of tRNA stability is_a: GO:0043489 ! RNA stabilization created_by: rfoulger creation_date: 2013-08-22T15:41:26Z [Term] id: GO:0036417 name: tRNA destabilization namespace: biological_process def: "Any process that decreases the stability of a tRNA molecule, making it more vulnerable to degradative processes." [GOC:aa, GOC:bf] is_a: GO:0036415 ! regulation of tRNA stability is_a: GO:0050779 ! RNA destabilization created_by: rfoulger creation_date: 2013-08-22T15:43:13Z [Term] id: GO:0038004 name: epidermal growth factor receptor ligand maturation namespace: biological_process def: "Any process leading to the attainment of the full functional capacity of a ligand for an epidermal growth factor receptor. The ligand is functional when it can bind to and activate an epidermal growth factor receptor." [GOC:signaling, PMID:11672524] synonym: "EGFR ligand maturation" EXACT [GOC:bf] is_a: GO:0051604 ! protein maturation created_by: rfoulger creation_date: 2011-06-07T03:06:41Z [Term] id: GO:0038005 name: peptide bond cleavage involved in epidermal growth factor receptor ligand maturation namespace: biological_process def: "The hydrolysis of a peptide bond or bonds within a ligand for the epidermal growth factor receptor, as part of protein maturation, the process leading to the attainment of the full functional capacity of a protein. In Drosophila for example, in the Golgi apparatus of the signal producing cell, Spitz is cleaved within its transmembrane domain to release a functional soluble extracellular fragment." [GOC:signaling, PMID:11672524, PMID:11672525] synonym: "EGFR ligand maturation by peptide bond cleavage" EXACT [GOC:bf] synonym: "EGFR ligand processing" EXACT [GOC:bf] synonym: "epidermal growth factor receptor ligand processing" EXACT [GOC:bf] synonym: "peptide bond cleavage involved in EGFR ligand maturation" EXACT [GOC:bf] is_a: GO:0016485 ! protein processing intersection_of: GO:0016485 ! protein processing intersection_of: part_of GO:0038004 ! epidermal growth factor receptor ligand maturation relationship: part_of GO:0038004 ! epidermal growth factor receptor ligand maturation created_by: rfoulger creation_date: 2011-06-07T03:08:41Z [Term] id: GO:0038049 name: ligand-activated RNA polymerase II transcription factor binding transcription factor activity namespace: molecular_function def: "Combining with a signal and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. For example, some steroid hormone receptors bind to transcription factor complexes to regulate transcription of genes whose promoters do not contain hormone response elements." [GOC:signaling, GOC:txnOH] comment: GO:0038049 is intended for annotation of nuclear receptors that regulate transcription by binding to transcription factors or transcription factor complexes. When the nuclear receptor functions by binding directly to DNA response elements, consider instead annotating to 'ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity ; GO:0004879'. synonym: "ligand-activated nuclear receptor activity" RELATED [GOC:bf] synonym: "ligand-dependent transcription factor activity" RELATED [GOC:bf] is_a: GO:0001076 ! RNA polymerase II transcription factor binding transcription factor activity created_by: rfoulger creation_date: 2011-11-29T01:53:30Z [Term] id: GO:0038050 name: glucocorticoid-activated sequence-specific DNA binding RNA polymerase II transcription factor activity namespace: molecular_function def: "Combining with a glucocorticoid and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II." [GOC:signaling, PMID:17689856] comment: For glucocorticoid receptors that function by binding to other transcription factors, consider instead annotating to 'glucocorticoid-activated RNA polymerase II transcription factor binding transcription factor activity ; GO:0038051'. synonym: "glucocorticoid receptor activity" BROAD [GOC:bf] is_a: GO:0004879 ! ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity created_by: rfoulger creation_date: 2011-11-29T02:29:18Z [Term] id: GO:0038051 name: glucocorticoid-activated RNA polymerase II transcription factor binding transcription factor activity namespace: molecular_function def: "Combining with a glucocorticoid and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. For example, glucocorticoid-bound receptors can bind to transcription factor complexes to regulate transcription of genes whose promoters do not contain glucocorticoid response elements." [GOC:signaling, PMID:17689856] comment: For glucocorticoid receptors that function by binding response elements in DNA, consider instead annotating to 'glucocorticoid-activated sequence-specific DNA binding RNA polymerase II transcription factor activity ; GO:0038050'. synonym: "glucocorticoid receptor activity" BROAD [GOC:bf] is_a: GO:0038049 ! ligand-activated RNA polymerase II transcription factor binding transcription factor activity created_by: rfoulger creation_date: 2011-11-29T02:30:46Z [Term] id: GO:0038052 name: estrogen-activated sequence-specific DNA binding RNA polymerase II transcription factor activity namespace: molecular_function def: "Combining with estrogen and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II." [GOC:signaling, PMID:17615392] comment: For estrogen receptors that function by binding to other transcription factors, consider instead annotating to 'estrogen-activated RNA polymerase II transcription factor binding transcription factor activity ; GO:0038053'. synonym: "estrogen nuclear receptor activity" BROAD [GOC:bf] is_a: GO:0004879 ! ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity created_by: rfoulger creation_date: 2011-11-29T02:41:48Z [Term] id: GO:0038053 name: estrogen-activated RNA polymerase II transcription factor binding transcription factor activity namespace: molecular_function def: "Combining with estrogen and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. For example, estrogen-bound receptors can bind to transcription factor complexes to regulate transcription of genes whose promoters do not contain estrogen response elements." [GOC:signaling, PMID:17615392] comment: For estrogen receptors that function by binding response elements in DNA, consider instead annotating to 'estrogen-activated sequence-specific DNA binding RNA polymerase II transcription factor activity ; GO:0038052'. synonym: "estrogen nuclear receptor activity" BROAD [GOC:bf] is_a: GO:0038049 ! ligand-activated RNA polymerase II transcription factor binding transcription factor activity created_by: rfoulger creation_date: 2011-11-29T02:42:22Z [Term] id: GO:0038056 name: negative regulation of BMP signaling pathway by negative regulation of BMP secretion namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the BMP signaling pathway by stopping, preventing or reducing the frequency, rate or extent of secretion of a member of the BMP family of proteins from the signaling cell." [GOC:bf, GOC:sart, PMID:21750037] synonym: "negative regulation of BMP signaling pathway by negative regulation of bone morphogenetic protein secretion" EXACT [GOC:bf] synonym: "negative regulation of BMP signalling pathway by negative regulation of BMP secretion" EXACT [GOC:bf] is_a: GO:0030514 ! negative regulation of BMP signaling pathway intersection_of: negatively_regulates GO:0030509 ! BMP signaling pathway created_by: rfoulger creation_date: 2011-12-19T10:55:47Z [Term] id: GO:0038061 name: NIK/NF-kappaB cascade namespace: biological_process def: "The process in which a signal is passed on to downstream components within the cell through the NIK-dependent processing and activation of NF-KappaB. The cascade begins with activation of the NF-KappaB-inducing kinase (NIK), which in turn phosphorylates and activates IkappaB kinase alpha (IKKalpha). IKKalpha phosphorylates the NF-Kappa B2 protein (p100) leading to p100 processing and release of an active NF-KappaB (p52)." [GOC:bf, GOC:mg2, GOC:signaling, GOC:vs, PMID:11239468, PMID:15140882] synonym: "non-canonical NF-KB signaling" BROAD [PMID:21173796] synonym: "noncanonical NF-kappaB signaling" BROAD [PMID:20501935] synonym: "noncanonical nuclear factor kappaB (NF-kappaB) pathway" BROAD [PMID:20501935] synonym: "p52-dependent NF-kappaB signaling" NARROW [PMID:18292232] relationship: has_part GO:0051092 ! positive regulation of NF-kappaB transcription factor activity created_by: rfoulger creation_date: 2012-01-16T05:44:46Z [Term] id: GO:0038098 name: sequestering of BMP from receptor via BMP binding namespace: biological_process def: "Binding to a bone morphogenetic protein (BMP) in the extracellular region, and inhibiting BMP signaling by preventing BMP from binding to its cell surface receptor." [GOC:bf, GOC:signaling, PMID:19855014] synonym: "extracellular sequestering of BMP" BROAD [GOC:bf] synonym: "extracellular sequestering of bone morphogenetic protein" BROAD [GOC:bf] is_a: GO:0030514 ! negative regulation of BMP signaling pathway created_by: rfoulger creation_date: 2012-02-22T11:28:54Z [Term] id: GO:0038107 name: nodal signaling pathway involved in determination of left/right asymmetry namespace: biological_process def: "A series of molecular signals initiated by the binding of a nodal protein to an activin receptor on the surface of a target cell, which contributes to the establishment of an organism's body plan or part of an organism with respect to the left and right halves." [GOC:BHF, GOC:vk, PMID:12857784, PMID:17287255, PMID:20413706] synonym: "nodal signalling pathway involved in determination of left/right asymmetry" EXACT [GOC:mah] synonym: "regulation of transcription from RNA polymerase II promoter by nodal signaling pathway, involved in determination of left/right symmetry" EXACT [GOC:bf] is_a: GO:1900094 ! regulation of transcription from RNA polymerase II promoter involved in determination of left/right symmetry created_by: rfoulger creation_date: 2012-02-29T10:18:59Z [Term] id: GO:0038167 name: epidermal growth factor receptor signaling pathway via positive regulation of NF-kappaB transcription factor activity namespace: biological_process def: "The series of molecular signals generated as a consequence of an epidermal growth factor receptor binding to one of its physiological ligands, where the signal is passed on within the cell via activation of the transcription factor NF-kappaB." [GOC:signaling, GOC:uh, PMID:21229383, PMID:21518868, PMID:22132240] synonym: "EGFR signaling pathway via activation of NF-kappaB" EXACT [GOC:bf] relationship: has_part GO:0051092 ! positive regulation of NF-kappaB transcription factor activity created_by: rfoulger creation_date: 2012-05-15T11:49:30Z [Term] id: GO:0038168 name: epidermal growth factor receptor signaling pathway via I-kappaB kinase/NF-kappaB cascade namespace: biological_process def: "The series of molecular signals generated as a consequence of an epidermal growth factor receptor binding to one of its physiological ligands, where the signal is passed on within the cell via I-kappaB-kinase (IKK)-dependent activation of the transcription factor NF-kappaB." [GOC:bf, PMID:22132240] synonym: "EGFR signaling pathway via IKK-dependent activation of NF-kappaB" EXACT [GOC:bf] synonym: "EGFR signaling pathway via IKK/NF-kappaB cascade" EXACT [GOC:bf] is_a: GO:0038167 ! epidermal growth factor receptor signaling pathway via positive regulation of NF-kappaB transcription factor activity relationship: has_part GO:0007249 ! I-kappaB kinase/NF-kappaB cascade created_by: rfoulger creation_date: 2012-05-15T12:01:09Z [Term] id: GO:0038175 name: negative regulation of SREBP signaling pathway in response to increased oxygen levels namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of the SREBP signaling pathway in response to an increase in oxygen levels." [GOC:al, PMID:22017871] synonym: "negative regulation of SREBP-mediated signaling pathway in presence of oxygen" RELATED [PMID:22017871] synonym: "negative regulation of SREBP-mediated signaling pathway in response to increased oxygen levels" EXACT [GOC:bf, GOC:vw] is_a: GO:2000639 ! negative regulation of SREBP signaling pathway created_by: rfoulger creation_date: 2012-07-20T01:28:59Z [Term] id: GO:0038176 name: positive regulation of SREBP signaling pathway in response to decreased oxygen levels namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the SREBP signaling pathway in response to a decrease in oxygen levels." [GOC:al, PMID:22017871] synonym: "positive regulation of SREBP-mediated signaling pathway in absence of oxygen" RELATED [PMID:22017871] synonym: "positive regulation of SREBP-mediated signaling pathway in response to decreased oxygen levels" EXACT [GOC:bf, GOC:vw] is_a: GO:2000640 ! positive regulation of SREBP signaling pathway created_by: rfoulger creation_date: 2012-07-20T01:30:25Z [Term] id: GO:0039523 name: suppression by virus of host RNA polymerase II activity namespace: biological_process def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host RNA polymerase II activity." [GOC:bf, GOC:sp, UniProtKB-KW:KW-1104, VZ:905] subset: virus_checked synonym: "inhibition of host RNA polymerase II activity by virus" EXACT [GOC:bf] synonym: "inhibition of host RNA polymerase II by virus" EXACT [UniProtKB-KW:KW-1104] synonym: "negative regulation by virus of host RNA polymerase II activity" BROAD [GOC:bf] xref: VZ:905 "Inhibition of host RNA polymerase II by virus" is_a: GO:0039653 ! suppression by virus of host transcription created_by: rfoulger creation_date: 2011-06-22T04:38:59Z [Term] id: GO:0039524 name: suppression by virus of host mRNA processing namespace: biological_process def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of mRNA processing in the host cell. mRNA processing is the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide." [GOC:bf, GOC:sp, UniProtKB-KW:KW-1103, VZ:903] subset: virus_checked synonym: "inhibition by virus of host mRNA processing" EXACT [GOC:bf] synonym: "inhibition of host mRNA processing by virus" EXACT [GOC:bf] synonym: "inhibition of host pre-mRNA processing by virus" EXACT [UniProtKB-KW:KW-1103, VZ:903] synonym: "negative regulation by virus of host mRNA processing" BROAD [GOC:bf] xref: VZ:903 "Inhibition of host pre-mRNA processing by virus" is_a: GO:0039657 ! suppression by virus of host gene expression is_a: GO:0046778 ! modification by virus of host mRNA processing created_by: rfoulger creation_date: 2011-06-22T04:51:55Z [Term] id: GO:0039548 name: suppression by virus of host IRF3 activity namespace: biological_process def: "Any process in which a virus stops, prevents, or reduces the activity of host IRF3 (interferon regulatory factor-3), a transcription factor in the RIG-I/MDA-5 signaling pathway. Viral infection triggers phosphorylation of cytoplasmic IRF3, which allows IRF3 to form a homodimer, migrate to the nucleus, and activate transcription of IFN-alpha and IFN-beta genes." [PMID:21632562, UniProtKB-KW:KW-1092, VZ:757] comment: This term is for annotation of viral proteins that counteract the host anti-viral innate immune response. subset: virus_checked synonym: "inhibition of host IRF3 by virus" EXACT [UniProtKB-KW:KW-1092] synonym: "Inhibition of IRF3-dependent antiviral response" BROAD [PMID:19125153] xref: VZ:757 "Inhibition of host IRF3 by virus" is_a: GO:0039653 ! suppression by virus of host transcription created_by: rfoulger creation_date: 2012-01-19T04:04:26Z [Term] id: GO:0039549 name: suppression by virus of host IRF3 activity by inhibition of IRF3 phosphorylation namespace: biological_process def: "Any process in which a virus stops, prevents, or reduces the rate or extent of the phosphorylation of IRF3 (interferon regulatory factor-3), thereby inhibiting IRF3 activation. In response to signaling from RIG-1/MDA-5 receptors, IRF3 is phosphorylated on multiple serine and threonine residues; phosphorylation results in the cytoplasm-to-nucleus translocation of IRF3, DNA binding, and increased transcriptional activation of interferon-encoding genes." [PMID:11124948, PMID:12829834, PMID:20631144, PMID:9566918] comment: This term is for annotation of viral proteins that counteract the host anti-viral innate immune response. subset: virus_checked synonym: "inhibition of phosphorylation-induced activation of host IRF3" RELATED [PMID:11124948] synonym: "inhibition of virus-induced IRF-3 phosphorylation" BROAD [PMID:12829834] is_a: GO:0039548 ! suppression by virus of host IRF3 activity created_by: rfoulger creation_date: 2012-01-19T04:27:06Z [Term] id: GO:0039550 name: suppression by virus of host IRF3 activity by inhibition of DNA binding namespace: biological_process def: "Any process in which a virus stops, prevents, or reduces IRF3-dependent gene transcription, by preventing or reducing IRF3 binding to promoter sites." [PMID:21632562] comment: This term is for annotation of viral proteins that counteract the host anti-viral innate immune response. subset: virus_checked synonym: "inhibition by virus of host IRF3-DNA binding" EXACT [GOC:bf] is_a: GO:0039548 ! suppression by virus of host IRF3 activity created_by: rfoulger creation_date: 2012-01-19T04:27:25Z [Term] id: GO:0039551 name: suppression by virus of host IRF3 activity by positive regulation of IRF3 catabolic process namespace: biological_process def: "Any process in which a virus stops, prevents, or reduces the activity of host IRF3 (interferon regulatory factor-3) by promoting the ubiquitin-dependent degradation of IRF3, mediated by the proteasome." [VZ:757] comment: This term is for annotation of viral proteins that counteract the host anti-viral innate immune response. subset: virus_checked synonym: "promotion by virus of proteosome-dependent IRF3 degradation" EXACT [VZ:757] is_a: GO:0039548 ! suppression by virus of host IRF3 activity created_by: rfoulger creation_date: 2012-01-20T11:35:33Z [Term] id: GO:0039557 name: suppression by virus of host IRF7 activity namespace: biological_process def: "Any process in which a virus stops, prevents, or reduces the activity of host IRF7 (interferon regulatory factor-7), a transcription factor in the RIG-I/MDA-5 signaling pathway. Viral infection triggers phosphorylation of cytoplasmic IRF7, which allows IRF7 to form a homodimer, migrate to the nucleus, and activate transcription of IFN-alpha and IFN-beta genes." [UniProtKB-KW:KW-1093, VZ:653] comment: This term is for annotation of viral proteins that counteract the host anti-viral innate immune response. subset: virus_checked synonym: "inhibition of host interferon regulatory factor-7 by virus" EXACT [VZ:653] synonym: "inhibition of host IRF7 by virus" EXACT [UniProtKB-KW:KW-1093] xref: VZ:653 "Inhibition of host IRF7 by virus" is_a: GO:0039653 ! suppression by virus of host transcription created_by: rfoulger creation_date: 2012-03-09T04:17:46Z [Term] id: GO:0039558 name: suppression by virus of host IRF7 activity by positive regulation of IRF7 sumoylation namespace: biological_process def: "Any process in which a virus stops, prevents, or reduces IRF7-dependent gene transcription, by promoting the sumoylation of IRF7, thereby disabling its activity." [PMID:18635538, PMID:19694547, VZ:653] comment: This term is for annotation of viral proteins that counteract the host anti-viral innate immune response. subset: virus_checked synonym: "promotion of IRF-7 SUMOylation" EXACT [PMID:19694547] synonym: "suppression by virus of host interferon regulatory factor-7 activity by positive regulation of IRF7 sumoylation" RELATED [GOC:bf] is_a: GO:0039557 ! suppression by virus of host IRF7 activity created_by: rfoulger creation_date: 2012-03-09T04:27:57Z [Term] id: GO:0039559 name: suppression by virus of host IRF7 activity by positive regulation of IRF7 catabolic process namespace: biological_process def: "Any process in which a virus stops, prevents, or reduces the activity of host IRF7 (interferon regulatory factor-7) by promoting the ubiquitin-dependent degradation of IRF7, mediated by the proteasome." [PMID:17301153, VZ:653] comment: This term is for annotation of viral proteins that counteract the host anti-viral innate immune response. subset: virus_checked synonym: "promotion by virus of proteosome-dependent IRF7 degradation" EXACT [VZ:653] is_a: GO:0039557 ! suppression by virus of host IRF7 activity created_by: rfoulger creation_date: 2012-03-09T04:38:58Z [Term] id: GO:0039560 name: suppression by virus of host IRF9 activity namespace: biological_process def: "Any process in which a virus stops, prevents, or reduces the activity of host IRF9 (interferon regulatory factor-9), a transcription factor involved in the innate immune response. Viral infection triggers binding of IRF9 to phosphorylated STAT1 and STAT2, forming the ISGF3 complex. The ISGF3 complex migrates to the nucleus and activates transcription of IFN-responsive genes." [UniProtKB-KW:KW-1094, VZ:683] comment: This term is for annotation of viral proteins that counteract the host anti-viral innate immune response. subset: virus_checked synonym: "inhibition of host interferon regulatory factor-9 by virus" EXACT [GOC:bf] synonym: "inhibition of host IRF9 by virus" EXACT [UniProtKB-KW:KW-1094] xref: VZ:683 "Inhibition of host IRF9 by virus" is_a: GO:0039653 ! suppression by virus of host transcription created_by: rfoulger creation_date: 2012-03-09T04:42:08Z [Term] id: GO:0039561 name: suppression by virus of host IRF9 activity by positive regulation of IRF9 localization to nucleus namespace: biological_process def: "Any process in which a virus stops, prevents, or reduces the activity of host IRF9 (interferon regulatory factor-9) by promoting the nuclear accumulation of IRF9. For example, the reovirus mu2 protein promotes nuclear accumulation of host IRF9 by an as yet unconfirmed-mechanism." [PMID:19109390] comment: This term is for annotation of viral proteins that counteract the host anti-viral innate immune response. subset: virus_checked synonym: "suppression by virus of host IRF9 activity by nuclear localization of IRF9" RELATED [PMID:19109390] synonym: "suppression of interferon signaling by nuclear accumulation of IRF9" RELATED [PMID:19109390] is_a: GO:0039560 ! suppression by virus of host IRF9 activity created_by: rfoulger creation_date: 2012-03-09T04:53:44Z [Term] id: GO:0039573 name: suppression by virus of host complement activation namespace: biological_process def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of complement activation. The activation of complement involves the sequential proteolysis of proteins to generate enzymes with catalytic activities. The biological functions of the complement include opsonization, inflammation, lysis of immune complexes, or enhancement of the humoral immune response. For example, the virus complement control protein (VCP) of vaccinia virus, and the complement control protein of herpesvirus inhibit C3 convertase." [PMID:21191012, PMID:7745740, UniProtKB-KW:KW-1087, VZ:811] subset: virus_checked synonym: "inhibition of host complement activation by virus" EXACT [GOC:bf] synonym: "inhibition of host complement cascade by virus" EXACT [GOC:bf] synonym: "inhibition of host complement factors by virus" BROAD [UniProtKB-KW:KW-1087] xref: VZ:811 "Inhibition of host complement factors by virus" is_a: GO:0045916 ! negative regulation of complement activation created_by: rfoulger [Term] id: GO:0039594 name: endoribonuclease activity involved in viral induction of host mRNA catabolic process namespace: molecular_function def: "Any endoribonuclease activity that contributes to the viral-induced catabolism of host mRNA." [GOC:bf, PMID:22046136] comment: GO:0039594 can be used to annotate a host or viral endoribonuclease activity that cleaves host mRNA in response to a viral infection. subset: virus_checked relationship: part_of GO:0039599 ! cleavage by virus of host mRNA created_by: rfoulger creation_date: 2012-07-05T11:21:26Z [Term] id: GO:0039599 name: cleavage by virus of host mRNA namespace: biological_process def: "Any process in which a host pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner by a viral endoribonuclease." [PMID:22046136] subset: virus_checked synonym: "host mRNA cleavage by viral endoribonuclease" EXACT [GOC:bf] synonym: "viral endoribonuclease activity involved in degradation of host mRNA" RELATED [GOC:bf] is_a: GO:0006379 ! mRNA cleavage created_by: rfoulger creation_date: 2012-07-04T05:09:08Z [Term] id: GO:0039602 name: suppression by virus of host transcription initiation from RNA polymerase II promoter namespace: biological_process alt_id: GO:0039601 def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a host DNA template." [UniProtKB-KW:KW-1111, VZ:904] subset: virus_checked synonym: "inhibition of host transcription initiation by virus" EXACT [GOC:bf] synonym: "suppression by virus of host DNA-dependent transcription, initiation" EXACT [] xref: VZ:904 "Inhibition of host transcription initiation by virus" is_a: GO:0039653 ! suppression by virus of host transcription created_by: rfoulger creation_date: 2012-07-05T03:29:34Z [Term] id: GO:0039603 name: TBP-class protein binding involved in viral suppression of host transcription initiation from RNA polymerase II promoter namespace: molecular_function def: "Selective and non-covalent interaction of a viral protein with a member of the class of TATA-binding proteins (TBP) in the host, including any of the TBP-related factors (TRFs), which contributes to the viral-suppression of assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a host DNA template." [GOC:vw, PMID:11968006] subset: virus_checked relationship: part_of GO:0039602 ! suppression by virus of host transcription initiation from RNA polymerase II promoter created_by: rfoulger creation_date: 2012-07-05T04:00:15Z [Term] id: GO:0039604 name: suppression by virus of host translation namespace: biological_process def: "Any process in which a virus prevents or reduces the frequency, rate or extent of translation of host mRNA." [UniProtKB-KW:KW-1193, VZ:1579] subset: virus_checked synonym: "host translation shutoff by virus" EXACT [UniProtKB-KW:KW-1193, VZ:1579] synonym: "viral inhibition of cellular protein synthesis" EXACT [VZ:1579] synonym: "viral shutoff of host protein synthesis" EXACT [PMID:8643618] xref: VZ:1579 "Translation shutoff" is_a: GO:0019057 ! modulation by virus of host translation is_a: GO:0039657 ! suppression by virus of host gene expression created_by: rfoulger creation_date: 2012-07-05T04:25:22Z [Term] id: GO:0039605 name: TFIIB-class transcription factor binding involved in viral suppression of host transcription initiation from RNA polymerase II promoter namespace: molecular_function def: "Selective and non-covalent interaction of a viral protein with a member of the TFIIB-class of host transcription factors, which contributes to the viral-suppression of assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a host DNA template." [GOC:vw, PMID:18768974] subset: virus_checked relationship: part_of GO:0039602 ! suppression by virus of host transcription initiation from RNA polymerase II promoter created_by: rfoulger creation_date: 2012-07-05T04:16:45Z [Term] id: GO:0039606 name: suppression by virus of host translation initiation namespace: biological_process def: "Any process in which a virus prevents or reduces the frequency, rate or extent of host translation initiation, the host process preceding formation of the peptide bond between the first two amino acids of a protein." [GOC:bf] subset: virus_checked is_a: GO:0039604 ! suppression by virus of host translation created_by: rfoulger creation_date: 2012-07-05T04:44:10Z [Term] id: GO:0039607 name: proteolysis by virus of host translation initiation factor namespace: biological_process def: "The chemical reactions and pathways performed by a virus resulting in the hydrolysis of a host translation initiation factor by cleavage of its peptide bonds." [PMID:18572216] subset: virus_checked synonym: "cleavage of host translation initiation factor by viral protease" EXACT [GOC:bf] synonym: "cleavage of host translation initiation factor by virus" RELATED [GOC:sp] synonym: "proteolytic cleavage by virus of host translation initiation factor" EXACT [GOC:bf] synonym: "suppression by virus of host translation initiation factor activity by proteolysis" EXACT [GOC:bf] is_a: GO:0039611 ! suppression by virus of host translation initiation factor activity created_by: rfoulger creation_date: 2012-07-05T04:46:21Z [Term] id: GO:0039608 name: suppression by virus of host translation initiation factor activity by induction of host protein dephosphorylation namespace: biological_process def: "Any process in which a virus prevents or reduces the frequency, rate or extent of activity of a host translation initiation factor by promoting dephosphorylation of a host protein." [PMID:12239292, PMID:8643618] comment: GO:0039608 can be used to annotate viral proteins which promote dephosphorylation of a host translation initiation factor itself (e.g. eIF4E) or promote dephosphorylation of a host protein that, when un-phosphorylated, inactivates a translation initiation factor. For example, the transcriptional repressor and eIF4E-binding protein 4E-BP1 is activated by dephosphorylation upon EMCV and poliovirus infections. subset: virus_checked is_a: GO:0039611 ! suppression by virus of host translation initiation factor activity created_by: rfoulger creation_date: 2012-07-06T10:30:57Z [Term] id: GO:0039611 name: suppression by virus of host translation initiation factor activity namespace: biological_process def: "Any process in which a virus prevents or reduces the frequency, rate or extent of activity of a host translation initiation factor." [GOC:bf, UniProtKB-KW:KW-1075] subset: virus_checked synonym: "inactivation of eIF2 activity" NARROW [PMID:12239292] synonym: "inhibition of activity of host translation initiation factor" EXACT [PMID:12239292] synonym: "Inhibition of host translation factors by virus" BROAD [UniProtKB-KW:KW-1075] synonym: "suppression by virus of host EIF-4E activity" EXACT [GOC:bf] is_a: GO:0039606 ! suppression by virus of host translation initiation created_by: rfoulger creation_date: 2012-07-06T10:27:16Z [Term] id: GO:0039644 name: suppression by virus of host NF-kappaB transcription factor activity namespace: biological_process def: "Any process in which a virus stops, prevents, or reduces the activity of host NF-kappaB activity." [UniProtKB-KW:KW-1100, VZ:695] synonym: "inhibition of host NF-kappa-B by virus " EXACT [UniProtKB-KW:KW-1100, VZ:695] xref: VZ:695 "Inhibition of host NF-kappa-B by virus" is_a: GO:0039653 ! suppression by virus of host transcription created_by: rfoulger creation_date: 2012-10-09T15:04:27Z [Term] id: GO:0039647 name: suppression by virus of host poly(A)-binding protein activity namespace: biological_process def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host poly(A)-binding protein (PABP) activity. PABP binds to the poly(A) tail of mRNA to facilitate translation." [UniProtKB-KW:KW-1101] synonym: "inhibition of host poly(A)-binding protein by virus" EXACT [UniProtKB-KW:KW-1101] synonym: "suppression by virus of host PABP activity" EXACT [Wikipedia:Poly(A)-binding_protein] is_a: GO:0039604 ! suppression by virus of host translation created_by: rfoulger creation_date: 2012-10-09T15:14:07Z [Term] id: GO:0039652 name: activation by virus of host NF-kappaB transcription factor activity namespace: biological_process def: "Any process in which a virus starts, promotes, or enhances the activity of the host transcription factor NF-kappaB." [UniProtKB-KW:KW-1074] subset: virus_checked synonym: "activation of host NF-kappa-B by virus" EXACT [UniProtKB-KW:KW-1074] xref: VZ:841 "Activation of host NF-kappa-B by virus" is_a: GO:0019056 ! modulation by virus of host transcription created_by: rfoulger creation_date: 2012-10-11T16:04:31Z [Term] id: GO:0039653 name: suppression by virus of host transcription namespace: biological_process def: "Any process in which a virus stops, prevents, or reduces the activity of host DNA-dependent transcription; the cellular synthesis of RNA on a template of DNA. Viral proteins can interfere with either host RNA polymerase or with transcription factors." [UniProtKB-KW:KW-1191, VZ:1577] synonym: "host transcription shutoff by virus " NARROW [UniProtKB-KW:KW-1191, VZ:1577] synonym: "suppression by virus of host DNA-dependent transcription" EXACT [GOC:bf] xref: VZ:1577 "Host transcription shutoff by virus" is_a: GO:0019056 ! modulation by virus of host transcription is_a: GO:0039657 ! suppression by virus of host gene expression created_by: rfoulger creation_date: 2012-10-11T16:11:17Z [Term] id: GO:0039656 name: modulation by virus of host gene expression namespace: biological_process def: "The process in which a virus effects a change in gene expression in its host organism. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form." [GOC:bf] subset: virus_checked synonym: "regulation by virus of host gene expression" RELATED [GOC:bf] is_a: GO:0010468 ! regulation of gene expression created_by: rfoulger creation_date: 2013-06-20T15:28:26Z [Term] id: GO:0039657 name: suppression by virus of host gene expression namespace: biological_process def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form." [UniProtKB-KW:KW-1190, VZ:1582] synonym: "host gene expression shutoff by virus" EXACT [UniProtKB-KW:KW-1190, VZ:1582] xref: VZ:1582 "Host gene expression shutoff by virus" is_a: GO:0010629 ! negative regulation of gene expression is_a: GO:0039656 ! modulation by virus of host gene expression created_by: rfoulger creation_date: 2013-06-20T15:29:55Z [Term] id: GO:0040029 name: regulation of gene expression, epigenetic namespace: biological_process def: "Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence." [PMID:10521337, PMID:11498582] subset: goslim_plant subset: gosubset_prok is_a: GO:0010468 ! regulation of gene expression [Term] id: GO:0040033 name: negative regulation of translation, ncRNA-mediated namespace: biological_process def: "Any process, mediated by small non-coding RNAs, that stops, prevents or reduces the rate that mRNAs are effectively translated into protein." [GOC:dph, GOC:ems, GOC:tb] synonym: "down regulation of mRNA translation, ncRNA-mediated" EXACT [] synonym: "down-regulation of mRNA translation, ncRNA-mediated" EXACT [] synonym: "downregulation of mRNA translation, ncRNA-mediated" EXACT [] synonym: "inhibition of mRNA translation, ncRNA-mediated" NARROW [] is_a: GO:0017148 ! negative regulation of translation is_a: GO:0045974 ! regulation of translation, ncRNA-mediated [Term] id: GO:0042345 name: regulation of NF-kappaB import into nucleus namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the transfer of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane." [GOC:jl, ISBN:0198506732] synonym: "regulation of NF-kappaB import into cell nucleus" EXACT [] synonym: "regulation of NF-kappaB transport from cytoplasm to nucleus" EXACT [] synonym: "regulation of NF-kappaB-nucleus import" EXACT [] is_a: GO:0043122 ! regulation of I-kappaB kinase/NF-kappaB cascade intersection_of: regulates GO:0042348 ! NF-kappaB import into nucleus relationship: regulates GO:0042348 ! NF-kappaB import into nucleus [Term] id: GO:0042346 name: positive regulation of NF-kappaB import into nucleus namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transfer of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane." [GOC:jl, ISBN:0198506732] synonym: "activation of NF-kappaB import into nucleus" NARROW [] synonym: "positive regulation of NF-kappaB import into cell nucleus" EXACT [] synonym: "positive regulation of NF-kappaB transport from cytoplasm to nucleus" EXACT [] synonym: "positive regulation of NF-kappaB-nucleus import" EXACT [] synonym: "stimulation of NF-kappaB import into nucleus" NARROW [] synonym: "up regulation of NF-kappaB import into nucleus" EXACT [] synonym: "up-regulation of NF-kappaB import into nucleus" EXACT [] synonym: "upregulation of NF-kappaB import into nucleus" EXACT [] is_a: GO:0042345 ! regulation of NF-kappaB import into nucleus intersection_of: positively_regulates GO:0042348 ! NF-kappaB import into nucleus relationship: positively_regulates GO:0042348 ! NF-kappaB import into nucleus [Term] id: GO:0042347 name: negative regulation of NF-kappaB import into nucleus namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the transfer of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane." [GOC:jl, ISBN:0198506732] synonym: "down regulation of NF-kappaB import into nucleus" EXACT [] synonym: "down-regulation of NF-kappaB import into nucleus" EXACT [] synonym: "downregulation of NF-kappaB import into nucleus" EXACT [] synonym: "inhibition of NF-kappaB import into nucleus" NARROW [] synonym: "negative regulation of NF-kappaB import into cell nucleus" EXACT [] synonym: "negative regulation of NF-kappaB transport from cytoplasm to nucleus" EXACT [] synonym: "negative regulation of NF-kappaB-nucleus import" EXACT [] is_a: GO:0042345 ! regulation of NF-kappaB import into nucleus intersection_of: negatively_regulates GO:0042348 ! NF-kappaB import into nucleus relationship: negatively_regulates GO:0042348 ! NF-kappaB import into nucleus [Term] id: GO:0042348 name: NF-kappaB import into nucleus namespace: biological_process def: "The directed movement of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane." [GOC:jl, ISBN:0198506732] synonym: "NF-kappaB import into cell nucleus" EXACT [] synonym: "NF-kappaB protein-nucleus import" EXACT [] synonym: "NF-kappaB transport from cytoplasm to nucleus" EXACT [] synonym: "NF-kappaB-nucleus import" EXACT [] synonym: "NF-KB import into nucleus" EXACT [GOC:bf] relationship: part_of GO:0007249 ! I-kappaB kinase/NF-kappaB cascade [Term] id: GO:0042464 name: dosage compensation by hypoactivation of X chromosome namespace: biological_process def: "Compensating for the two-fold variation in X:autosome chromosome ratios between sexes by an inactivation of a proportion of genes on both of the X chromosomes of the XX sex, leading to a decrease, of half, of the levels of gene expression from these chromosomes. An example of this process is found in Caenorhabditis elegans." [GOC:jl, PMID:11102361] is_a: GO:0007549 ! dosage compensation [Term] id: GO:0042622 name: photoreceptor outer segment membrane namespace: cellular_component def: "The membrane surrounding the outer segment of a vertebrate photoreceptor." [GOC:jl] is_a: GO:0097458 ! neuron part relationship: part_of GO:0001750 ! photoreceptor outer segment [Term] id: GO:0042714 name: dosage compensation complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins on DNA or RNA to form the complex that mediates dosage compensation on one or more X chromosomes." [GOC:jl, PMID:11102361, PMID:12672493] relationship: part_of GO:0007549 ! dosage compensation [Term] id: GO:0042715 name: dosage compensation complex assembly involved in dosage compensation by hypoactivation of X chromosome namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins on DNA to form the complex that mediates dosage compensation on both X chromosomes in the monogametic sex, ultimately resulting in a two-fold reduction in transcription from these chromosomes. An example of this process is found in Caenorhabditis elegans." [GOC:jl, PMID:11102361, PMID:12672493] synonym: "dosage compensation complex assembly during dosage compensation by hypoactivation of X chromosome" RELATED [GOC:dph, GOC:tb] is_a: GO:0042714 ! dosage compensation complex assembly intersection_of: GO:0042714 ! dosage compensation complex assembly intersection_of: part_of GO:0042464 ! dosage compensation by hypoactivation of X chromosome relationship: part_of GO:0042464 ! dosage compensation by hypoactivation of X chromosome [Term] id: GO:0042734 name: presynaptic membrane namespace: cellular_component def: "A specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane." [GOC:jl, ISBN:0815316194] synonym: "pre-synaptic membrane" EXACT [] is_a: GO:0097458 ! neuron part [Term] id: GO:0042757 name: giant axon namespace: cellular_component def: "Extremely large, unmyelinated axon found in invertebrates. Has high conduction speeds and is usually involved in panic or escape responses." [GOC:jl, PMID:9705477] is_a: GO:0030424 ! axon [Term] id: GO:0042779 name: tRNA 3'-trailer cleavage namespace: biological_process def: "Cleavage of the 3'-end of the pre-tRNA as part of the process of generating the mature 3'-end of the tRNA; may involve endonucleolytic or exonucleolytic cleavage, or both." [GOC:go_curators] subset: gosubset_prok synonym: "removal of tRNA 3'-trailer sequence" EXACT [] synonym: "tRNA 3'-end cleavage" EXACT [] is_a: GO:0042780 ! tRNA 3'-end processing [Term] id: GO:0042780 name: tRNA 3'-end processing namespace: biological_process def: "The process in which the 3' end of a pre-tRNA molecule is converted to that of a mature tRNA." [GOC:go_curators] subset: gosubset_prok synonym: "tRNA 3' processing" EXACT [] is_a: GO:0008033 ! tRNA processing is_a: GO:0043628 ! ncRNA 3'-end processing [Term] id: GO:0042789 name: mRNA transcription from RNA polymerase II promoter namespace: biological_process def: "The cellular synthesis of messenger RNA (mRNA) from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter." [GOC:jl, ISBN:0321000382] synonym: "mRNA transcription from Pol II promoter" EXACT [] is_a: GO:0006366 ! transcription from RNA polymerase II promoter is_a: GO:0009299 ! mRNA transcription [Term] id: GO:0042790 name: transcription of nuclear large rRNA transcript from RNA polymerase I promoter namespace: biological_process def: "The synthesis of the large ribosomal RNA (rRNA) transcript which encodes several rRNAs, e.g. in mammals 28S, 18S and 5.8S, from a nuclear DNA template transcribed by RNA polymerase I." [GOC:jl, GOC:txnOH, ISBN:0321000382] synonym: "transcription of nuclear rRNA large Pol I transcript" EXACT [] is_a: GO:0006360 ! transcription from RNA polymerase I promoter is_a: GO:0009303 ! rRNA transcription [Term] id: GO:0042791 name: 5S class rRNA transcription from RNA polymerase III type 1 promoter namespace: biological_process def: "The synthesis of 5S ribosomal RNA (rRNA), or an equivalent rRNA, from a DNA template by RNA polymerase III (Pol III), originating at a type 1 RNA polymerase III promoter." [GOC:jl, GOC:txnOH, ISBN:0321000382, PMID:12381659] subset: gosubset_prok synonym: "5S rRNA transcription" EXACT [] is_a: GO:0006383 ! transcription from RNA polymerase III promoter is_a: GO:0009303 ! rRNA transcription [Term] id: GO:0042792 name: rRNA transcription from mitochondrial promoter namespace: biological_process def: "The synthesis of ribosomal RNA (rRNA) from a mitochondrial DNA template." [GOC:jl, ISBN:0321000382] is_a: GO:0006390 ! transcription from mitochondrial promoter is_a: GO:0009303 ! rRNA transcription [Term] id: GO:0042793 name: transcription from plastid promoter namespace: biological_process def: "The synthesis of RNA from a plastid DNA template, usually by a specific plastid RNA polymerase." [GOC:jl, ISBN:0321000382] synonym: "plastid transcription" EXACT [] is_a: GO:0006351 ! transcription, DNA-dependent [Term] id: GO:0042794 name: rRNA transcription from plastid promoter namespace: biological_process def: "The synthesis of ribosomal RNA (rRNA) from a plastid DNA template, usually by a specific plastid RNA polymerase." [GOC:jl, ISBN:0321000382] is_a: GO:0009303 ! rRNA transcription is_a: GO:0042793 ! transcription from plastid promoter [Term] id: GO:0042795 name: snRNA transcription from RNA polymerase II promoter namespace: biological_process def: "The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase II (Pol II), originating at a Pol II promoter." [GOC:jl, ISBN:0321000382] synonym: "snRNA transcription from Pol II promoter" EXACT [] is_a: GO:0006366 ! transcription from RNA polymerase II promoter is_a: GO:0009301 ! snRNA transcription [Term] id: GO:0042796 name: snRNA transcription from RNA polymerase III promoter namespace: biological_process def: "The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase III (Pol III), originating at a Pol III promoter." [GOC:jl, ISBN:0321000382] synonym: "snRNA transcription from Pol III promoter" EXACT [] is_a: GO:0006383 ! transcription from RNA polymerase III promoter is_a: GO:0009301 ! snRNA transcription [Term] id: GO:0042797 name: tRNA transcription from RNA polymerase III promoter namespace: biological_process def: "The synthesis of transfer RNA (tRNA) from a DNA template by RNA Polymerase III (Pol III), originating at a Pol III promoter." [GOC:jl, ISBN:0321000382] synonym: "tRNA transcription from Pol III promoter" EXACT [] is_a: GO:0006383 ! transcription from RNA polymerase III promoter is_a: GO:0009304 ! tRNA transcription [Term] id: GO:0043005 name: neuron projection namespace: cellular_component def: "A prolongation or process extending from a nerve cell, e.g. an axon or dendrite." [GOC:jl, http://www.cogsci.princeton.edu/~wn/] subset: goslim_pir synonym: "neurite" NARROW [] synonym: "neuron process" EXACT [] synonym: "neuron protrusion" EXACT [] synonym: "neuronal cell projection" EXACT [] xref: NIF_Subcellular:sao-867568886 is_a: GO:0097458 ! neuron part [Term] id: GO:0043025 name: neuronal cell body namespace: cellular_component def: "The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites." [GOC:go_curators] comment: Note that 'cell body' and 'cell soma' are not used in the literature for cells that lack projections, nor for some cells (e.g. yeast with mating projections) that do have projections. subset: goslim_pir synonym: "neuron cell body" EXACT [] synonym: "neuronal cell soma" EXACT [] xref: NIF_Subcellular:sao1044911821 xref: Wikipedia:Soma_(biology) is_a: GO:0097458 ! neuron part [Term] id: GO:0043045 name: DNA methylation involved in embryo development namespace: biological_process def: "The covalent transfer of a methyl group to C-5 of cytosine that contributes to the epigenetic regulation of embryonic gene expression." [GOC:go_curators, PMID:12138111] synonym: "de novo DNA methylation" RELATED [] is_a: GO:0006306 ! DNA methylation intersection_of: GO:0006306 ! DNA methylation [Term] id: GO:0043046 name: DNA methylation involved in gamete generation namespace: biological_process def: "The covalent transfer of a methyl group to C-5 of cytosine that contributes to the establishment of DNA methylation patterns in the gamete." [GOC:go_curators, PMID:12138111] synonym: "de novo DNA methylation" RELATED [] is_a: GO:0006306 ! DNA methylation intersection_of: GO:0006306 ! DNA methylation [Term] id: GO:0043122 name: regulation of I-kappaB kinase/NF-kappaB cascade namespace: biological_process def: "Any process that modulates an I-kappaB kinase/NF-kappaB induced cascade." [GOC:jl, PMID:12773372] intersection_of: regulates GO:0007249 ! I-kappaB kinase/NF-kappaB cascade relationship: regulates GO:0007249 ! I-kappaB kinase/NF-kappaB cascade [Term] id: GO:0043123 name: positive regulation of I-kappaB kinase/NF-kappaB cascade namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of an I-kappaB kinase/NF-kappaB induced cascade." [GOC:jl] synonym: "activation of I-kappaB kinase/NF-kappaB cascade" NARROW [] synonym: "stimulation of I-kappaB kinase/NF-kappaB cascade" NARROW [] synonym: "up regulation of I-kappaB kinase/NF-kappaB cascade" EXACT [] synonym: "up-regulation of I-kappaB kinase/NF-kappaB cascade" EXACT [] synonym: "upregulation of I-kappaB kinase/NF-kappaB cascade" EXACT [] xref: Reactome:REACT_24918 "IRAK1 recruits IKK complex, Homo sapiens" is_a: GO:0043122 ! regulation of I-kappaB kinase/NF-kappaB cascade intersection_of: positively_regulates GO:0007249 ! I-kappaB kinase/NF-kappaB cascade relationship: positively_regulates GO:0007249 ! I-kappaB kinase/NF-kappaB cascade [Term] id: GO:0043124 name: negative regulation of I-kappaB kinase/NF-kappaB cascade namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of an I-kappaB kinase/NF-kappaB induced cascade." [GOC:jl] synonym: "down regulation of I-kappaB kinase/NF-kappaB cascade" EXACT [] synonym: "down-regulation of I-kappaB kinase/NF-kappaB cascade" EXACT [] synonym: "downregulation of I-kappaB kinase/NF-kappaB cascade" EXACT [] synonym: "inhibition of I-kappaB kinase/NF-kappaB cascade" NARROW [] is_a: GO:0043122 ! regulation of I-kappaB kinase/NF-kappaB cascade intersection_of: negatively_regulates GO:0007249 ! I-kappaB kinase/NF-kappaB cascade relationship: negatively_regulates GO:0007249 ! I-kappaB kinase/NF-kappaB cascade [Term] id: GO:0043143 name: regulation of translation by machinery localization namespace: biological_process def: "Any process in which proteins and protein complexes involved in translation are transported to, or maintained in, a specific location." [GOC:jl] subset: gosubset_prok synonym: "establishment and maintenance of translational machinery localization" EXACT [] synonym: "establishment and maintenance of translational protein localization" EXACT [] synonym: "regulation of translation by machinery localisation" EXACT [GOC:mah] synonym: "translational machinery localization" EXACT [GOC:dph, GOC:tb] synonym: "translational protein localization" EXACT [] is_a: GO:0006417 ! regulation of translation intersection_of: part_of GO:0006412 ! translation [Term] id: GO:0043144 name: snoRNA processing namespace: biological_process def: "Any process involved in the conversion of a primary small nucleolar RNA (snoRNA) transcript into a mature snoRNA." [GOC:go_curators, PMID:12773397] subset: goslim_yeast is_a: GO:0034470 ! ncRNA processing [Term] id: GO:0043145 name: snoRNA 3'-end cleavage namespace: biological_process def: "The endonucleolytic cleavage of snoRNA 3' ends, which is required for mature snoRNAs to be functional." [GOC:go_curators, PMID:12773397] synonym: "snoRNA 3' end cleavage" EXACT [] is_a: GO:0031126 ! snoRNA 3'-end processing [Term] id: GO:0043170 name: macromolecule metabolic process namespace: biological_process alt_id: GO:0043283 def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [CHEBI:33694, GOC:mah] subset: goslim_pir subset: gosubset_prok synonym: "biopolymer metabolic process" EXACT [GOC:mtg_chebi_dec09] synonym: "macromolecule metabolism" EXACT [] is_a: GO:0071704 ! organic substance metabolic process [Term] id: GO:0043194 name: axon initial segment namespace: cellular_component def: "Portion of the axon proximal to the neuronal cell body, at the level of the axon hillock. The action potentials that propagate along the axon are generated at the level of this initial segment." [GOC:nln, GOC:sl, PMID:1754851, PMID:21551097] synonym: "initial segment" EXACT [] xref: NIF_Subcellular:sao256000789 is_a: GO:0033267 ! axon part relationship: part_of GO:0044304 ! main axon [Term] id: GO:0043195 name: terminal bouton namespace: cellular_component def: "Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it." [GOC:dph, GOC:mc, GOC:nln, PMID:10218156, PMID:8409967] synonym: "bouton" EXACT [] synonym: "presynaptic bouton" EXACT [] synonym: "synaptic bouton" EXACT [] synonym: "terminal button" EXACT [] is_a: GO:0033267 ! axon part relationship: part_of GO:0043679 ! axon terminus [Term] id: GO:0043196 name: varicosity namespace: cellular_component def: "Non-terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters." [GOC:nln] is_a: GO:0033267 ! axon part relationship: part_of GO:0044304 ! main axon [Term] id: GO:0043197 name: dendritic spine namespace: cellular_component def: "Protrusion from a dendrite. Spines are specialised subcellular compartments involved in the synaptic transmission. They are linked to the dendritic shaft by a restriction. Because of their bulb shape, they function as a biochemical and an electrical compartment. Spine remodeling is though to be involved in synaptic plasticity." [GOC:nln] synonym: "branched dendritic spine" NARROW [NIF_Subcellular:sao-965204139] synonym: "dendrite spine" EXACT [] synonym: "mushroom dendritic spine" NARROW [NIF_Subcellular:sao-876577163] synonym: "sessile dendritic spine" NARROW [NIF_Subcellular:sao1536532595] synonym: "stubby dendritic spine" NARROW [NIF_Subcellular:sao317384566] synonym: "thin dendritic spine" NARROW [NIF_Subcellular:sao1232858786] xref: NIF_Subcellular:sao1799103720 xref: Wikipedia:Dendritic_spine is_a: GO:0044309 ! neuron spine relationship: part_of GO:0030425 ! dendrite [Term] id: GO:0043198 name: dendritic shaft namespace: cellular_component def: "Cylindric portion of the dendrite, directly stemming from the perikaryon, and carrying the dendritic spines." [GOC:nln] synonym: "trunk" RELATED [NIF_Subcellular:sao1078172392] xref: NIF_Subcellular:sao2034472720 is_a: GO:0097458 ! neuron part relationship: part_of GO:0030425 ! dendrite [Term] id: GO:0043203 name: axon hillock namespace: cellular_component def: "Portion of the neuronal cell soma from which the axon originates." [GOC:nln] xref: NIF_Subcellular:sao627227260 xref: Wikipedia:Axon_hillock is_a: GO:0033267 ! axon part relationship: part_of GO:0043025 ! neuronal cell body [Term] id: GO:0043204 name: perikaryon namespace: cellular_component def: "The portion of the cell soma (cell body) that excludes the nucleus." [GOC:jl] synonym: "cell soma cytoplasm" RELATED [] is_a: GO:0097458 ! neuron part relationship: part_of GO:0043025 ! neuronal cell body [Term] id: GO:0043433 name: negative regulation of sequence-specific DNA binding transcription factor activity namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription." [GOC:jl] synonym: "down regulation of transcription factor activity" EXACT [] synonym: "down-regulation of transcription factor activity" EXACT [] synonym: "downregulation of transcription factor activity" EXACT [] synonym: "inhibition of transcription factor activity" NARROW [] synonym: "negative regulation of transcription factor activity" BROAD [GOC:dph, GOC:tb] is_a: GO:0051090 ! regulation of sequence-specific DNA binding transcription factor activity intersection_of: negatively_regulates GO:0003700 ! sequence-specific DNA binding transcription factor activity relationship: negatively_regulates GO:0003700 ! sequence-specific DNA binding transcription factor activity [Term] id: GO:0043484 name: regulation of RNA splicing namespace: biological_process def: "Any process that modulates the frequency, rate or extent of RNA splicing, the process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA." [GOC:jl] is_a: GO:0010468 ! regulation of gene expression intersection_of: regulates GO:0008380 ! RNA splicing relationship: regulates GO:0008380 ! RNA splicing [Term] id: GO:0043487 name: regulation of RNA stability namespace: biological_process def: "Any process that modulates the propensity of RNA molecules to degradation. Includes processes that both stabilize and destabilize RNAs." [GOC:jl] subset: gosubset_prok is_a: GO:0010608 ! posttranscriptional regulation of gene expression [Term] id: GO:0043488 name: regulation of mRNA stability namespace: biological_process def: "Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs." [GOC:jl] subset: gosubset_prok is_a: GO:0043487 ! regulation of RNA stability [Term] id: GO:0043489 name: RNA stabilization namespace: biological_process def: "Prevention of degradation of RNA molecules." [GOC:go_curators] subset: gosubset_prok is_a: GO:0043487 ! regulation of RNA stability [Term] id: GO:0043555 name: regulation of translation in response to stress namespace: biological_process def: "Modulation of the frequency, rate or extent of translation as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:jl] synonym: "translational stress response" EXACT [] is_a: GO:0006417 ! regulation of translation [Term] id: GO:0043556 name: regulation of translation in response to oxidative stress namespace: biological_process def: "Any process that modulates the frequency, rate or extent of translation as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals." [GOC:jl] is_a: GO:0043555 ! regulation of translation in response to stress [Term] id: GO:0043557 name: regulation of translation in response to osmotic stress namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the frequency, rate or extent of translation as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell." [GOC:jl] is_a: GO:0043555 ! regulation of translation in response to stress [Term] id: GO:0043558 name: regulation of translational initiation in response to stress namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of translation initiation, as a result of a stimulus indicating the organism is under stress." [GOC:jl] synonym: "regulation of translation initiation in response to stress" EXACT [GOC:dph, GOC:hjd, GOC:tb] is_a: GO:0006446 ! regulation of translational initiation is_a: GO:0043555 ! regulation of translation in response to stress [Term] id: GO:0043561 name: regulation of translational initiation in response to osmotic stress namespace: biological_process def: "Any process that modulates the frequency, rate or extent of translation initiation, as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell." [GOC:dph, GOC:jl, GOC:tb] is_a: GO:0043557 ! regulation of translation in response to osmotic stress is_a: GO:0043558 ! regulation of translational initiation in response to stress [Term] id: GO:0043618 name: regulation of transcription from RNA polymerase II promoter in response to stress namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:jl] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter is_a: GO:0043620 ! regulation of DNA-dependent transcription in response to stress [Term] id: GO:0043619 name: regulation of transcription from RNA polymerase II promoter in response to oxidative stress namespace: biological_process def: "Modulation of the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals." [GOC:jl] is_a: GO:0043618 ! regulation of transcription from RNA polymerase II promoter in response to stress [Term] id: GO:0043620 name: regulation of DNA-dependent transcription in response to stress namespace: biological_process def: "Modulation of the frequency, rate or extent of transcription from a DNA template as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:jl, GOC:txnOH] is_a: GO:0006355 ! regulation of transcription, DNA-dependent [Term] id: GO:0043628 name: ncRNA 3'-end processing namespace: biological_process def: "Any process involved in forming the mature 3' end of a non-coding RNA molecule." [GOC:jl] synonym: "ncRNA 3' end processing" EXACT [] is_a: GO:0031123 ! RNA 3'-end processing is_a: GO:0034470 ! ncRNA processing [Term] id: GO:0043629 name: ncRNA polyadenylation namespace: biological_process def: "The enzymatic addition of a sequence of adenylyl residues at the 3' end of a non-coding RNA (ncRNA) molecule. In eukaryotes, substrates include nuclear non-coding RNAs such as precursors and a variety of incorrectly processed forms of snRNAs, snoRNAs, rRNAs, and tRNAs, as well as discarded RNA fragments which have been removed from ncRNA primary transcripts. Polyadenylation of precursors is often linked to termination of transcription, but polyadenylation of RNAs targeted for degradation may also occur post-transcriptionally. This polyadenylation is important both for 3'-end processing to produce mature ncRNA species and also for targeting incorrectly processed or discarded RNA molecules for degradation." [GOC:dgf, GOC:krc, GOC:rn, PMID:15828860, PMID:15935758, PMID:16374505, PMID:16431988, PMID:18951092] synonym: "non-coding RNA polyadenylation" EXACT [] is_a: GO:0043628 ! ncRNA 3'-end processing is_a: GO:0043631 ! RNA polyadenylation [Term] id: GO:0043630 name: ncRNA polyadenylation involved in polyadenylation-dependent ncRNA catabolic process namespace: biological_process def: "The enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end of a non-coding RNA, occurring as part of the process of polyadenylation-dependent non-coding RNA catabolism." [GOC:dph, GOC:jl, GOC:tb] synonym: "ncRNA polyadenylation during polyadenylation-dependent ncRNA catabolic process" RELATED [GOC:dph, GOC:tb] synonym: "ncRNA polyadenylation involved in poly(A)-dependent ncRNA catabolic process" RELATED [GOC:vw] is_a: GO:0043629 ! ncRNA polyadenylation intersection_of: GO:0043629 ! ncRNA polyadenylation intersection_of: part_of GO:0043634 ! polyadenylation-dependent ncRNA catabolic process relationship: part_of GO:0043634 ! polyadenylation-dependent ncRNA catabolic process [Term] id: GO:0043631 name: RNA polyadenylation namespace: biological_process def: "The enzymatic addition of a sequence of adenylyl residues at the 3' end of an RNA molecule." [GOC:jl] subset: gosubset_prok is_a: GO:0031123 ! RNA 3'-end processing [Term] id: GO:0043634 name: polyadenylation-dependent ncRNA catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of a noncoding RNA (ncRNA) molecule, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target ncRNA." [GOC:dgf, GOC:jl, GOC:krc] synonym: "poly(A)-dependent ncRNA catabolic process" RELATED [GOC:vw] relationship: has_part GO:0043629 ! ncRNA polyadenylation [Term] id: GO:0043679 name: axon terminus namespace: cellular_component def: "Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal button is a specialized region of it." [GOC:dph, GOC:jl] synonym: "axon terminal" EXACT [] synonym: "axon terminal specialization" RELATED [] synonym: "motor endplate" RELATED [NIF_Subcellular:nlx_subcell_20090512] synonym: "nerve ending" EXACT [] is_a: GO:0033267 ! axon part is_a: GO:0044306 ! neuron projection terminus [Term] id: GO:0043685 name: conversion of glutamyl-tRNA to glutaminyl-tRNA namespace: biological_process def: "The modification process that results in the conversion of glutamate charged on a tRNA(Gln) to glutaminyl-tRNA." [GOC:jsg, PMID:3340166, PMID:9342308] comment: Note that this process has been observed in some archaeal and bacterial species. subset: gosubset_prok is_a: GO:0019988 ! charged-tRNA amino acid modification [Term] id: GO:0043688 name: conversion of aspartyl-tRNA to asparaginyl-tRNA namespace: biological_process def: "The modification process that results in the conversion of aspartate charged on a tRNA(Asn) to asparaginyl-tRNA." [GOC:jsg, PMID:9789001] comment: Note that this process has been observed in some archeal and bacterial species. subset: gosubset_prok is_a: GO:0019988 ! charged-tRNA amino acid modification [Term] id: GO:0043766 name: Sep-tRNA:Cys-tRNA synthase activity namespace: molecular_function def: "Catalysis of the reaction: O-phospho-L-seryl-tRNACys + sulfide = L-cysteinyl-tRNACys + phosphate." [EC:2.5.1.73, IMG:00235, PMID:15790858, PMID:16380427, PMID:17110438] subset: gosubset_prok synonym: "O-phosphoseryl-tRNA:cysteinyl-tRNA synthase activity" EXACT [] synonym: "Sep-tRNA:Cys-tRNA synthetase activity" EXACT [] synonym: "SepCysS" RELATED [] xref: EC:2.5.1.73 xref: MetaCyc:RXN-10719 relationship: part_of GO:0071952 ! conversion of O-phosphoseryl-tRNA to cysteinyl-tRNA [Term] id: GO:0043827 name: tRNA (adenine-57, 58-N(1)-) methyltransferase activity namespace: molecular_function def: "Catalysis of the methylation of adenine-57 and adenine-58 in the T-loop of tRNA." [IMG:00706, PMID:14739239] subset: gosubset_prok synonym: "TrmI" RELATED [] synonym: "tRNA (adenine-57, 58 N1-) methyltransferase activity" EXACT [] synonym: "tRNA (adenine-57, 58-N1-) methyltransferase activity" EXACT [] synonym: "tRNA (m1A) MTase" BROAD [] xref: EC:2.1.1.- is_a: GO:0016429 ! tRNA (adenine-N1-)-methyltransferase activity [Term] id: GO:0043856 name: anti-sigma factor antagonist activity namespace: molecular_function def: "The function of binding to an anti-sigma factor and stopping, preventing or reducing the rate of its activity." [GOC:jl, GOC:txnOH, PMID:15576799] subset: gosubset_prok synonym: "anti-anti-sigma factor activity" EXACT [] relationship: part_of GO:0045893 ! positive regulation of transcription, DNA-dependent [Term] id: GO:0043906 name: Ala-tRNA(Pro) hydrolase activity namespace: molecular_function def: "Catalysis of the hydrolysis of misacylated Ala-tRNA(Pro)." [GOC:jl, PMID:14663147] subset: gosubset_prok synonym: "Ala-tRNAPro hydrolase activity" EXACT [] xref: EC:3.1.1.- xref: IMG:02668 is_a: GO:0002161 ! aminoacyl-tRNA editing activity [Term] id: GO:0043907 name: Cys-tRNA(Pro) hydrolase activity namespace: molecular_function def: "Catalysis of the hydrolysis of misacylated Cys-tRNA(Pro)." [GOC:jl, PMID:15886196] subset: gosubset_prok synonym: "Cys-tRNA(Pro) deacetylase activity" EXACT [] synonym: "Cys-tRNAPro hydrolase activity" EXACT [] xref: EC:3.1.1.- xref: IMG:02669 is_a: GO:0002161 ! aminoacyl-tRNA editing activity [Term] id: GO:0043921 name: modulation by host of viral transcription namespace: biological_process def: "Any process in which a host organism modulates the frequency, rate or extent of viral transcription, the synthesis of either RNA on a template of DNA or DNA on a template of RNA." [GOC:jl] synonym: "regulation by host of viral transcription" EXACT [] synonym: "regulation of viral transcription by host " EXACT [] is_a: GO:0046782 ! regulation of viral transcription [Term] id: GO:0043922 name: negative regulation by host of viral transcription namespace: biological_process def: "Any process in which a host organism stops, prevents, or reduces the frequency, rate or extent of viral transcription, the synthesis of either RNA on a template of DNA or DNA on a template of RNA." [GOC:jl] synonym: "negative regulation of viral transcription by host" EXACT [] is_a: GO:0032897 ! negative regulation of viral transcription is_a: GO:0043921 ! modulation by host of viral transcription [Term] id: GO:0043923 name: positive regulation by host of viral transcription namespace: biological_process def: "Any process is which a host organism activates or increases the frequency, rate or extent of viral transcription, the synthesis of either RNA on a template of DNA or DNA on a template of RNA." [GOC:jl] synonym: "positive regulation of viral transcription by host" EXACT [] is_a: GO:0043921 ! modulation by host of viral transcription is_a: GO:0050434 ! positive regulation of viral transcription [Term] id: GO:0044026 name: DNA hypermethylation namespace: biological_process def: "An increase in the epigenetic methylation of cytosine and adenosine residues in DNA." [GOC:jl, http://en.wiktionary.org/] is_a: GO:0044030 ! regulation of DNA methylation [Term] id: GO:0044027 name: hypermethylation of CpG island namespace: biological_process def: "An increase in the epigenetic methylation of cytosine and adenosine residues in a CpG island in DNA. CpG islands are genomic regions that contain a high frequency of the CG dinucleotide and are often associated with the transcription start site of genes." [GOC:jl, Wikipedia:Cpg_island] synonym: "DNA hypermethylation of CpG island" EXACT [] is_a: GO:0044026 ! DNA hypermethylation [Term] id: GO:0044028 name: DNA hypomethylation namespace: biological_process def: "An decrease in the epigenetic methylation of cytosine and adenosine residues in DNA." [GOC:jl, http://en.wiktionary.org/hypomethylation] is_a: GO:0044030 ! regulation of DNA methylation [Term] id: GO:0044029 name: hypomethylation of CpG island namespace: biological_process def: "An decrease in the epigenetic methylation of cytosine and adenosine residues in a CpG island in DNA. CpG islands are genomic regions that contain a high frequency of the CG dinucleotide and are often associated with the transcription start site of genes." [GOC:jl, Wikipedia:Cpg_island] synonym: "DNA hypomethylation of CpG island" EXACT [] is_a: GO:0044028 ! DNA hypomethylation [Term] id: GO:0044030 name: regulation of DNA methylation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine." [GOC:jl] intersection_of: regulates GO:0006306 ! DNA methylation relationship: regulates GO:0006306 ! DNA methylation [Term] id: GO:0044073 name: modulation by symbiont of host translation namespace: biological_process def: "The process in which a symbiont organism effects a change in translation, the chemical reactions and pathways resulting in the formation of a protein, in its host organism." [MITRE:tk] subset: gosubset_prok synonym: "modification by symbiont of host translation" EXACT [] synonym: "modulation of host translation by symbiont" EXACT [] synonym: "regulation by symbiont of host translation" EXACT [] is_a: GO:0006417 ! regulation of translation [Term] id: GO:0044074 name: negative regulation by symbiont of host translation namespace: biological_process def: "The process in which a symbiont organism stops, prevents, or reduces the frequency, rate or extent of translation, the chemical reactions and pathways resulting in the formation of a protein, in its host organism." [MITRE:tk] subset: gosubset_prok synonym: "negative regulation of host translation by symbiont" EXACT [] is_a: GO:0017148 ! negative regulation of translation is_a: GO:0044073 ! modulation by symbiont of host translation [Term] id: GO:0044224 name: juxtaparanode region of axon namespace: cellular_component def: "A region of an axon near a node of Ranvier that is between the paranode and internode regions." [GOC:BHF, GOC:jl, PMID:10624965, PMID:14682359] synonym: "juxtaparanodal region" EXACT [] synonym: "juxtaparanode" EXACT [] xref: NIF_Subcellular:sao758620702 is_a: GO:0033267 ! axon part relationship: part_of GO:0044304 ! main axon created_by: jane creation_date: 2009-11-13T12:57:36Z [Term] id: GO:0044225 name: apical pole of neuron namespace: cellular_component def: "Portion of a neuron cell soma closest to the point where the apical dendrite emerges." [NIF_Subcellular:sao1186862860] xref: NIF_Subcellular:sao1186862860 is_a: GO:0097458 ! neuron part relationship: part_of GO:0043025 ! neuronal cell body created_by: jane creation_date: 2009-11-13T03:49:14Z [Term] id: GO:0044226 name: basal pole of neuron namespace: cellular_component def: "Portion of a neuron cell soma closest to the point where the basilar dendrite emerges." [NIF_Subcellular:sao1186862860] xref: NIF_Subcellular:sao1186862860 is_a: GO:0097458 ! neuron part relationship: part_of GO:0043025 ! neuronal cell body created_by: jane creation_date: 2009-11-13T04:32:17Z [Term] id: GO:0044280 name: subplasmalemmal coating namespace: cellular_component def: "Electron dense material observed coating the cytoplasmic face of the plasma membrane in certain regions of a neuron, e.g., the axon initial segment; the nodal membrane at the Node of Ranvier." [NIF_Subcellular:sao1938587839] xref: NIF_Subcellular:sao1938587839 is_a: GO:0097458 ! neuron part created_by: jane creation_date: 2010-01-14T03:58:38Z [Term] id: GO:0044292 name: dendrite terminus namespace: cellular_component def: "A structure at the distal end of a dendrite adapted to carry out a specific function, e.g. dendriole." [GOC:jl, NIF_Subcellular:sao28175134] synonym: "dendrite terminal" EXACT [] synonym: "dendrite terminal specialization" RELATED [] synonym: "terminal specialization" RELATED [NIF_Subcellular:sao28175134] synonym: "terminal specialization of a dendrite" EXACT [] xref: NIF_Subcellular:sao28175134 is_a: GO:0097458 ! neuron part relationship: part_of GO:0030425 ! dendrite created_by: jane creation_date: 2010-02-04T03:14:37Z [Term] id: GO:0044293 name: dendriole namespace: cellular_component def: "Small dendrites that makes up a brush structure found as the terminal specialization of a dendrite of a unipolar brush cell (UBC)." [GOC:jl, NIF_Subcellular:sao28175134, PMID:8300904] xref: NIF_Subcellular:sao28175134 is_a: GO:0044292 ! dendrite terminus created_by: jane creation_date: 2010-02-04T03:32:02Z [Term] id: GO:0044294 name: dendritic growth cone namespace: cellular_component def: "The migrating motile tip of a growing nerve cell dendrite." [GOC:jl] synonym: "dendrite growth cone" EXACT [] xref: NIF_Subcellular:sao1594955670 is_a: GO:0030426 ! growth cone is_a: GO:0044292 ! dendrite terminus created_by: jane creation_date: 2010-02-04T03:45:27Z [Term] id: GO:0044295 name: axonal growth cone namespace: cellular_component def: "The migrating motile tip of a growing nerve cell axon." [GOC:jl] synonym: "axon growth cone" EXACT [] xref: NIF_Subcellular:sao1594955670 is_a: GO:0030426 ! growth cone is_a: GO:0033267 ! axon part created_by: jane creation_date: 2010-02-04T03:57:16Z [Term] id: GO:0044296 name: dendritic tuft namespace: cellular_component def: "The terminal specialization found in some types of dendrites which consists of numerous small terminal branches, giving the dendrite a tufted appearance." [NIF_Subcellular:sao1340260079] synonym: "dendrite tuft" EXACT [] xref: NIF_Subcellular:sao1340260079 is_a: GO:0044292 ! dendrite terminus created_by: jane creation_date: 2010-02-04T04:03:29Z [Term] id: GO:0044299 name: C-fiber namespace: cellular_component def: "The axon of a dorsal root ganglion cell that are responsive to pain and temperature. C-fibers are small in diameter (0.2-1.5 um) and unmyelinated." [NIF_Subcellular:nlx_subcell_20090210] synonym: "C-fibre" EXACT [] xref: NIF_Subcellular:nlx_subcell_20090210 is_a: GO:0030424 ! axon created_by: jane creation_date: 2010-02-05T11:14:51Z [Term] id: GO:0044300 name: cerebellar mossy fiber namespace: cellular_component def: "An axon arising from cerebellar projecting cells in the cochlea, vestibular nuclei, spinal cord, reticular formation, cerebellar nuclei and basilar pontine nuclei. Mossy fibers enter through all three cerebellar peduncles and send collaterals to the deep cerebellar nuclei, then branch in the white matter and terminate in the granule cell layer. Through this branching, a given mossy fiber can innervate several folia. Mossy fibers synapse on granule cells. The synaptic contacts are made at enlargements along the length of the mossy fiber called mossy fiber rosettes. The enlargements of the rosettes give the axons as \"mossy\" appearance in Golgi stained preparations." [NIF_Subcellular:nlx_subcell_20090209] synonym: "cerebellar mossy fibre" EXACT [] xref: NIF_Subcellular:nlx_subcell_20090209 is_a: GO:0030424 ! axon created_by: jane creation_date: 2010-02-05T11:16:40Z [Term] id: GO:0044301 name: climbing fiber namespace: cellular_component def: "The axon of inferior olive neuron that projects to the cerebellar cortex, largely via the inferior cerebellar peduncle. They range in diameter from 1-3 um and are myelinated until they enter the granule cell layer. They give off collaterals to the deep cerebellar nuclei. They synapse extensively with the dendrites of Purkinje cells in the molecular layer, where each fiber branches repeatedly to \"climb\" along the Purkinje cell dendritic tree. Each Purkinje cell is innervated by only a single climbing fiber." [NIF_Subcellular:nlx_subcell_20090203] synonym: "climbing fibre" EXACT [] xref: NIF_Subcellular:nlx_subcell_20090203 is_a: GO:0030424 ! axon created_by: jane creation_date: 2010-02-05T11:20:56Z [Term] id: GO:0044302 name: dentate gyrus mossy fiber namespace: cellular_component def: "Distinctive, unmyelinated axons produced by granule cells." [NIF_Subcellular:nlx_subcell_20090601, PMID:17765709] synonym: "dentate gyrus mossy fibre" EXACT [] synonym: "granule cell axon" EXACT [] xref: NIF_Subcellular:nlx_subcell_20090601 is_a: GO:0030424 ! axon created_by: jane creation_date: 2010-02-05T11:23:55Z [Term] id: GO:0044303 name: axon collateral namespace: cellular_component def: "Any of the smaller branches of an axon that emanate from the main axon cylinder." [NIF_Subcellular:sao1470140754] xref: NIF_Subcellular:sao1470140754 is_a: GO:0033267 ! axon part created_by: jane creation_date: 2010-02-05T11:29:04Z [Term] id: GO:0044304 name: main axon namespace: cellular_component def: "The main axonal trunk, as opposed to the collaterals." [NIF_Subcellular:sao1596975044] synonym: "axon trunk" EXACT [] xref: NIF_Subcellular:sao1596975044 is_a: GO:0033267 ! axon part created_by: jane creation_date: 2010-02-05T03:48:17Z [Term] id: GO:0044305 name: calyx of Held namespace: cellular_component def: "The terminal specialization of a calyciferous axon which forms large synapses in the mammalian auditory central nervous system." [NIF_Subcellular:sao1684283879, PMID:11823805] xref: NIF_Subcellular:sao1684283879 is_a: GO:0043679 ! axon terminus created_by: jane creation_date: 2010-02-05T02:33:20Z [Term] id: GO:0044306 name: neuron projection terminus namespace: cellular_component def: "The specialized, terminal region of a neuron projection such as an axon or a dendrite." [GOC:jl] synonym: "neuron projection terminal" EXACT [] synonym: "neuron terminal specialization" EXACT [] is_a: GO:0097458 ! neuron part relationship: part_of GO:0043005 ! neuron projection created_by: jane creation_date: 2010-02-05T02:44:04Z [Term] id: GO:0044307 name: dendritic branch namespace: cellular_component def: "A dendrite arising from another dendrite." [NIF_Subcellular:sao884265541] synonym: "dendrite branch" EXACT [] xref: NIF_Subcellular:sao884265541 is_a: GO:0097458 ! neuron part relationship: part_of GO:0030425 ! dendrite created_by: jane creation_date: 2010-02-05T04:18:53Z [Term] id: GO:0044308 name: axonal spine namespace: cellular_component def: "A spine that originates from the axon, usually from the initial segment." [NIF_Subcellular:sao18239917] synonym: "axon spine" EXACT [] xref: NIF_Subcellular:sao18239917 is_a: GO:0033267 ! axon part is_a: GO:0044309 ! neuron spine created_by: jane creation_date: 2010-02-05T04:22:13Z [Term] id: GO:0044309 name: neuron spine namespace: cellular_component def: "A small membranous protrusion, often ending in a bulbous head and attached to the neuron by a narrow stalk or neck." [ISBN:0198504888, NIF_Subcellular:sao1145756102] synonym: "spine" BROAD [] xref: NIF_Subcellular:sao1145756102 is_a: GO:0043005 ! neuron projection created_by: jane creation_date: 2010-02-05T04:25:10Z [Term] id: GO:0044316 name: cone cell pedicle namespace: cellular_component def: "A specialized axon terminus which is produced by retinal cone cells. Pedicles are large, conical, flat end-feet (8-10 micrometers diameter) of the retinal cone axon that lie more or less side by side on the same plane at the outer edge of the outer plexiform layer (OPL)." [http://webvision.med.utah.edu/photo2.html, PMID:10939333] synonym: "cone pedicle" EXACT [] is_a: GO:0043679 ! axon terminus created_by: jane creation_date: 2010-07-14T01:30:02Z [Term] id: GO:0044317 name: rod spherule namespace: cellular_component def: "A specialized neuron projection which is the site of synaptic transmission produced by retinal rod cells. Rod spherules are small round enlargements of the axon (3-5 micrometers diameter) or even extensions of the cell body." [http://webvision.med.utah.edu/photo2.html] synonym: "rod cell spherule" EXACT [] synonym: "rod photoreceptor spherule" EXACT [] is_a: GO:0043005 ! neuron projection created_by: jane creation_date: 2010-07-14T01:38:07Z [Term] id: GO:0044324 name: regulation of transcription involved in anterior/posterior axis specification namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription that contributes to the specification of the anterior/posterior axis." [GOC:jl] is_a: GO:0006355 ! regulation of transcription, DNA-dependent intersection_of: GO:0006355 ! regulation of transcription, DNA-dependent created_by: janelomax creation_date: 2010-08-04T12:35:41Z [Term] id: GO:0044326 name: dendritic spine neck namespace: cellular_component def: "Part of the dendritic spine that connects the dendritic shaft to the head of the dendritic spine." [GOC:nln] is_a: GO:0097458 ! neuron part relationship: part_of GO:0043197 ! dendritic spine created_by: janelomax creation_date: 2010-08-18T02:31:15Z [Term] id: GO:0044327 name: dendritic spine head namespace: cellular_component def: "Distal part of the dendritic spine, that carries the post-synaptic density." [GOC:nln] is_a: GO:0097458 ! neuron part relationship: part_of GO:0043197 ! dendritic spine created_by: janelomax creation_date: 2010-08-18T02:33:12Z [Term] id: GO:0044357 name: regulation of rRNA stability namespace: biological_process def: "Any process that modulates the propensity of rRNA molecules to degradation. Includes processes that both stabilize and destabilize rRNAs." [GOC:jl] synonym: "regulation of ribosomal RNA stability" EXACT [] is_a: GO:0043487 ! regulation of RNA stability created_by: janelomax creation_date: 2011-08-31T09:57:54Z [Term] id: GO:0044464 name: cell part namespace: cellular_component def: "Any constituent part of a cell, the basic structural and functional unit of all organisms." [GOC:jl] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_annotate subset: goslim_pir subset: gosubset_prok synonym: "protoplast" RELATED [GOC:mah] is_a: GO:0005575 ! cellular_component intersection_of: GO:0005575 ! cellular_component intersection_of: part_of GO:0005623 ! cell relationship: part_of GO:0005623 ! cell [Term] id: GO:0044528 name: regulation of mitochondrial mRNA stability namespace: biological_process def: "Any process that modulates the propensity of mitochondrial mRNA molecules to degradation. Includes processes that both stabilize and destabilize mitochondrial mRNAs." [GOC:al, GOC:jl] is_a: GO:0043488 ! regulation of mRNA stability created_by: janelomax creation_date: 2012-03-15T03:20:10Z [Term] id: GO:0044529 name: regulation of mitochondrial rRNA stability namespace: biological_process def: "Any process that modulates the propensity of mitochondrial rRNA molecules to degradation. Includes processes that both stabilize and destabilize mitochondrial rRNAs." [GOC:al, GOC:jl] subset: gosubset_prok is_a: GO:0044357 ! regulation of rRNA stability created_by: janelomax creation_date: 2012-03-15T03:22:19Z [Term] id: GO:0044541 name: zymogen activation in other organism namespace: biological_process def: "The chemical reactions and pathways performed by an organism resulting in the proteolytic processing of an inactive enzyme to an active form in another organism." [GOC:fj, GOC:jl] is_a: GO:0031638 ! zymogen activation created_by: janelomax creation_date: 2012-03-22T11:39:41Z [Term] id: GO:0044542 name: plasminogen activation in other organism namespace: biological_process def: "The chemical reactions and pathways performed by an organism resulting in the processing of inactive plasminogen to active plasmin in another organism." [GOC:fj, GOC:jl] is_a: GO:0031639 ! plasminogen activation is_a: GO:0044541 ! zymogen activation in other organism created_by: janelomax creation_date: 2012-03-22T11:40:03Z [Term] id: GO:0044543 name: envenomation resulting in zymogen activation in other organism namespace: biological_process def: "The process which begins with venom being forced into an organism by the bite or sting of another organism, and ends with the proteolytic processing of an inactive enzyme to an active form." [GOC:fj, GOC:jl] relationship: has_part GO:0044541 ! zymogen activation in other organism created_by: janelomax creation_date: 2012-03-22T11:52:56Z [Term] id: GO:0044544 name: envenomation resulting in plasminogen activation in other organism namespace: biological_process def: "The process which begins with venom being forced into an organism by the bite or sting of another organism, and ends with the activation of plasminogen into plasmin in the bitten organism. This process includes cleavage at an internal Arg-Val site to form an N-terminal A-chain and C-terminal B-chain held together by a disulfide bond, and can include further proteolytic cleavage events to remove the preactivation peptide." [GOC:fj, GOC:jl] relationship: has_part GO:0044542 ! plasminogen activation in other organism created_by: janelomax creation_date: 2012-03-22T11:54:49Z [Term] id: GO:0044627 name: modulation of complement activation, classical pathway in other organism namespace: biological_process def: "A process that modulates the frequency, rate or extent of the classical pathway of complement activation, in a different organism." [GOC:jl, PMID:20837040] synonym: "regulation of complement activation, classical pathway in other organism" EXACT [] is_a: GO:0030450 ! regulation of complement activation, classical pathway created_by: janelomax creation_date: 2012-07-05T12:55:53Z [Term] id: GO:0044628 name: positive regulation of complement activation, classical pathway in other organism namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of complement activation by the classical pathway, in a different organism." [GOC:jl, PMID:20837040] is_a: GO:0044627 ! modulation of complement activation, classical pathway in other organism is_a: GO:0045960 ! positive regulation of complement activation, classical pathway created_by: janelomax creation_date: 2012-07-05T01:00:10Z [Term] id: GO:0044629 name: negative regulation of complement activation, classical pathway in other organism namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of complement activation by the classical pathway, in a different organism." [GOC:jl, PMID:20837040] is_a: GO:0044627 ! modulation of complement activation, classical pathway in other organism is_a: GO:0045959 ! negative regulation of complement activation, classical pathway created_by: janelomax creation_date: 2012-07-05T01:03:25Z [Term] id: GO:0044630 name: modulation of complement activation, lectin pathway in other organism namespace: biological_process def: "A process that modulates the frequency, rate or extent of the lectin pathway of complement activation, in a different organism." [GOC:jl, PMID:20837040] synonym: "regulation of complement activation, lectin pathway in other organism" EXACT [] is_a: GO:0001868 ! regulation of complement activation, lectin pathway created_by: janelomax creation_date: 2012-07-05T01:10:31Z [Term] id: GO:0044631 name: positive regulation of complement activation, lectin pathway in other organism namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of complement activation by the lectin pathway, in a different organism." [GOC:jl, PMID:20837040] is_a: GO:0001870 ! positive regulation of complement activation, lectin pathway is_a: GO:0044630 ! modulation of complement activation, lectin pathway in other organism created_by: janelomax creation_date: 2012-07-05T01:17:33Z [Term] id: GO:0044632 name: negative regulation of complement activation, lectin pathway in other organism namespace: biological_process def: "Any process that stops, prevents, or reduces the rate of complement activation by the lectin pathway, in a different organism." [GOC:jl, PMID:20837040] is_a: GO:0001869 ! negative regulation of complement activation, lectin pathway is_a: GO:0044630 ! modulation of complement activation, lectin pathway in other organism created_by: janelomax creation_date: 2012-07-05T01:18:43Z [Term] id: GO:0044633 name: modulation of complement activation, alternative pathway in other organism namespace: biological_process def: "A process that modulates the frequency, rate or extent of complement activation, via the alternative pathway, in a different organism." [GOC:jl, PMID:20837040] synonym: "regulation of complement activation, alternative pathway in other organism" RELATED [] is_a: GO:0030451 ! regulation of complement activation, alternative pathway created_by: janelomax creation_date: 2012-07-05T04:24:08Z [Term] id: GO:0044634 name: negative regulation of complement activation, alternative pathway in other organism namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of complement activation by the alternative pathway, in a different organism." [GOC:jl, PMID:20837040] is_a: GO:0044633 ! modulation of complement activation, alternative pathway in other organism is_a: GO:0045957 ! negative regulation of complement activation, alternative pathway created_by: janelomax creation_date: 2012-07-05T04:32:55Z [Term] id: GO:0044635 name: positive regulation of complement activation, alternative pathway in other organism namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of complement activation by the alternative pathway, in a different organism." [GOC:jl, PMID:20837040] is_a: GO:0044633 ! modulation of complement activation, alternative pathway in other organism is_a: GO:0045958 ! positive regulation of complement activation, alternative pathway created_by: janelomax creation_date: 2012-07-05T04:36:11Z [Term] id: GO:0044636 name: envenomation resulting in modulation of complement activation, classical pathway in other organism namespace: biological_process def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the regulation of complement activation via the classical pathway of the bitten/stung organism." [GOC:fj, GOC:jl, PMID:20837040] relationship: has_part GO:0044627 ! modulation of complement activation, classical pathway in other organism created_by: janelomax creation_date: 2012-07-05T04:40:57Z [Term] id: GO:0044637 name: envenomation resulting in negative regulation of complement activation, classical pathway in other organism namespace: biological_process def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the negative regulation of complement activation via the classical pathway of the bitten/stung organism." [GOC:fj, GOC:jl, PMID:20837040] is_a: GO:0044636 ! envenomation resulting in modulation of complement activation, classical pathway in other organism relationship: has_part GO:0044629 ! negative regulation of complement activation, classical pathway in other organism created_by: janelomax creation_date: 2012-07-05T04:46:56Z [Term] id: GO:0044638 name: envenomation resulting in positive regulation of complement activation, classical pathway in other organism namespace: biological_process def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the positive regulation of complement activation via the classical pathway of the bitten/stung organism." [GOC:fj, GOC:jl, PMID:20837040] is_a: GO:0044636 ! envenomation resulting in modulation of complement activation, classical pathway in other organism relationship: has_part GO:0044628 ! positive regulation of complement activation, classical pathway in other organism created_by: janelomax creation_date: 2012-07-05T04:51:36Z [Term] id: GO:0044639 name: envenomation resulting in modulation of complement activation, lectin pathway in other organism namespace: biological_process def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of complement activation via the lectin pathway in the bitten/stung organism." [GOC:fj, GOC:jl, PMID:20837040] synonym: "envenomation resulting in regulation of complement activation, lectin pathway in other organism" EXACT [] relationship: has_part GO:0044630 ! modulation of complement activation, lectin pathway in other organism created_by: janelomax creation_date: 2012-07-05T04:53:36Z [Term] id: GO:0044640 name: envenomation resulting in negative regulation of complement activation, lectin pathway in other organism namespace: biological_process def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant negative regulation of complement activation via the lectin pathway in the bitten/stung organism." [GOC:fj, GOC:jl, PMID:20837040] is_a: GO:0044639 ! envenomation resulting in modulation of complement activation, lectin pathway in other organism relationship: has_part GO:0044632 ! negative regulation of complement activation, lectin pathway in other organism created_by: janelomax creation_date: 2012-07-05T04:56:30Z [Term] id: GO:0044641 name: envenomation resulting in positive regulation of complement activation, lectin pathway in other organism namespace: biological_process def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant positive regulation of complement activation via the lectin pathway in the bitten/stung organism." [GOC:fj, GOC:jl, PMID:20837040] is_a: GO:0044639 ! envenomation resulting in modulation of complement activation, lectin pathway in other organism relationship: has_part GO:0044631 ! positive regulation of complement activation, lectin pathway in other organism created_by: janelomax creation_date: 2012-07-11T11:50:23Z [Term] id: GO:0044642 name: envenomation resulting in modulation of complement activation, alternative pathway in other organism namespace: biological_process def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of complement activation via the alternative pathway in the bitten/stung organism." [GOC:fj, GOC:jl, PMID:20837040] synonym: "envenomation resulting in regulation of complement activation, alternative pathway in other organism" EXACT [] relationship: has_part GO:0044633 ! modulation of complement activation, alternative pathway in other organism created_by: janelomax creation_date: 2012-07-11T11:53:12Z [Term] id: GO:0044643 name: envenomation resulting in positive regulation of complement activation, alternative pathway in other organism namespace: biological_process def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant positive regulation of complement activation via the alternative pathway in the bitten/stung organism." [GOC:fj, GOC:jl, PMID:20837040] is_a: GO:0044642 ! envenomation resulting in modulation of complement activation, alternative pathway in other organism relationship: has_part GO:0044635 ! positive regulation of complement activation, alternative pathway in other organism created_by: janelomax creation_date: 2012-07-11T11:56:48Z [Term] id: GO:0044644 name: envenomation resulting in negative regulation of complement activation, alternative pathway in other organism namespace: biological_process def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant negative regulation of complement activation via the alternative pathway in the bitten/stung organism." [GOC:fj, GOC:jl, PMID:20837040] is_a: GO:0044642 ! envenomation resulting in modulation of complement activation, alternative pathway in other organism relationship: has_part GO:0044634 ! negative regulation of complement activation, alternative pathway in other organism created_by: janelomax creation_date: 2012-07-11T12:35:11Z [Term] id: GO:0044725 name: chromatin reprogramming in the zygote namespace: biological_process def: "The global reprogramming of epigenetic modifications in the zygote following fertilization. The paternal genome undergoes active DNA demethylation before the first cell division, while the adjacent maternal genome is protected from this process." [GOC:sp, PMID:22868271] is_a: GO:0043045 ! DNA methylation involved in embryo development created_by: janelomax creation_date: 2012-10-24T13:53:28Z [Term] id: GO:0044726 name: protection of DNA demethylation of female pronucleus namespace: biological_process def: "The protection of the maternal genome from DNA demethylation in the zygote following fertilization." [GOC:sp, PMID:22868271] is_a: GO:0044030 ! regulation of DNA methylation relationship: part_of GO:0044725 ! chromatin reprogramming in the zygote created_by: janelomax creation_date: 2012-10-24T14:10:36Z [Term] id: GO:0044727 name: DNA demethylation of male pronucleus namespace: biological_process def: "The active DNA demethylation of the paternal genome that takes place before the first cell division." [GOC:sp, PMID:22868271] is_a: GO:0043045 ! DNA methylation involved in embryo development relationship: part_of GO:0044725 ! chromatin reprogramming in the zygote created_by: janelomax creation_date: 2012-10-24T14:25:35Z [Term] id: GO:0044747 name: mature miRNA 3'-end processing namespace: biological_process def: "Any process involved in forming distinct miRNA isoforms from a mature miRNA that differ at their 3'-ends." [PMID:22055292, PMID:22055293] synonym: "miRNA 3' end terminal trimming" BROAD [] synonym: "miRNA 3'-end processing" BROAD [] synonym: "miRNA trimming" BROAD [] is_a: GO:0043628 ! ncRNA 3'-end processing relationship: part_of GO:0035196 ! production of miRNAs involved in gene silencing by miRNA created_by: janelomax creation_date: 2012-11-15T13:45:21Z [Term] id: GO:0044748 name: 3'-5'-exoribonuclease activity involved in mature miRNA 3'-end processing namespace: molecular_function def: "Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule that contributes to forming distinct miRNA isoforms from a mature miRNA." [GOC:sart] synonym: "exonucleolytic trimming to generate 3' end of miRNA" BROAD [] intersection_of: part_of GO:0044747 ! mature miRNA 3'-end processing relationship: part_of GO:0044747 ! mature miRNA 3'-end processing created_by: janelomax creation_date: 2012-11-20T13:48:29Z [Term] id: GO:0045013 name: carbon catabolite repression of transcription namespace: biological_process def: "A transcription regulation process in which the presence of one carbon source leads to a decrease in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources. Carbon catabolite repression is a mechanism of genetic regulation which the accumulation of catabolites of one substance in the cell represses the formation of enzymes that contribute to the catabolism of other substances." [GOC:mah, ISBN:0198506732, PMID:11018147, PMID:18359269, PMID:9618445] subset: gosubset_prok synonym: "carbon catabolite repression" EXACT [] synonym: "negative regulation of transcription by carbon catabolites" EXACT [GOC:mah] is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent is_a: GO:0045990 ! carbon catabolite regulation of transcription [Term] id: GO:0045014 name: negative regulation of transcription by glucose namespace: biological_process def: "Any process involving glucose that stops, prevents or reduces the rate of transcription. The presence of glucose in the growth medium inhibits the synthesis of certain enzymes in bacteria growing on the medium. For example, transcription of some catabolic operons is under negative control by specific repressors and glucose is an anti-inducer of xylose utilization and glycerol kinase." [ISBN:0198506732, PMID:11018147] subset: gosubset_prok synonym: "down regulation of transcription by glucose" EXACT [] synonym: "down-regulation of transcription by glucose" EXACT [] synonym: "downregulation of transcription by glucose" EXACT [] synonym: "glucose effect" EXACT [] synonym: "glucose repression" EXACT [] synonym: "inhibition of transcription by glucose" NARROW [] is_a: GO:0045013 ! carbon catabolite repression of transcription is_a: GO:0046015 ! regulation of transcription by glucose [Term] id: GO:0045182 name: translation regulator activity namespace: molecular_function def: "Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome." [GOC:ai] subset: goslim_aspergillus subset: goslim_candida subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "translation factor activity" EXACT [] relationship: part_of GO:0006417 ! regulation of translation [Term] id: GO:0045183 name: translation factor activity, non-nucleic acid binding namespace: molecular_function def: "A translation regulator activity that does not involve binding to nucleic acids." [GOC:ai, GOC:dph, GOC:tb] subset: gosubset_prok is_a: GO:0045182 ! translation regulator activity [Term] id: GO:0045291 name: mRNA trans splicing, SL addition namespace: biological_process def: "The joining together of two independently transcribed RNAs, where the one that provides the 5' portion of the final mRNA is from a splice leader RNA (SL-RNA). The SL-RNA, or mini-exon donor sequence, is added to the 5'-end of the acceptor RNA molecule which provides the mRNA body." [GOC:krc, ISBN:0879695897, PMID:2675423] synonym: "nuclear mRNA trans splicing, SL addition" EXACT [GOC:vw] synonym: "nuclear mRNA trans splicing, spliced leader addition" EXACT [] is_a: GO:0000365 ! mRNA trans splicing, via spliceosome [Term] id: GO:0045292 name: mRNA cis splicing, via spliceosome namespace: biological_process def: "The joining together, after removal of an intervening sequence composed of one or more introns, of two segments of the same RNA molecule via spliceosomal catalysis to produce an mRNA composed only of exon sequences that all came from the same primary transcript." [GOC:krc, http://calspace.ucsd.edu/origins/Glossary/C.htm, ISBN:0879695897] synonym: "nuclear mRNA cis splicing, via spliceosome" EXACT [GOC:vw] synonym: "nuclear mRNA cis splicing, via U2-type spliceosome" NARROW [] synonym: "splicing" BROAD [GOC:vw] is_a: GO:0000398 ! mRNA splicing, via spliceosome [Term] id: GO:0045301 name: tRNA-(2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine)-hydroxylase activity namespace: molecular_function def: "Catalysis of the reaction: tRNA-(2-methylthio-N-6-isopentenyl adenosine) = tRNA-(2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine) + O2. 2-methylthio-N-6-isopentenyl adenosine is also known as ms2i6A; 2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine is also known as ms2io6A and 2-methylthio-cis-ribozeatin." [GOC:mlg, PMID:8253666] subset: gosubset_prok synonym: "2-methylthio-cis-ribozeatin hydroxylase activity" EXACT [] synonym: "tRNA-(2-methylthio-N-6-(cis-hydroxy)isopentenyladenosine)-hydroxylase activity" EXACT [] synonym: "tRNA-(ms2io6A)-hydroxylase activity" EXACT [] relationship: part_of GO:0002195 ! 2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine-tRNA biosynthesis [Term] id: GO:0045727 name: positive regulation of translation namespace: biological_process alt_id: GO:0045946 def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA." [GOC:dph, GOC:go_curators, GOC:tb] subset: gosubset_prok synonym: "activation of protein biosynthetic process" NARROW [] synonym: "positive regulation of protein anabolism" EXACT [] synonym: "positive regulation of protein biosynthesis" EXACT [] synonym: "positive regulation of protein biosynthetic process" EXACT [GOC:tb] synonym: "positive regulation of protein formation" EXACT [] synonym: "positive regulation of protein synthesis" EXACT [] synonym: "stimulation of protein biosynthetic process" NARROW [] synonym: "up regulation of protein biosynthetic process" EXACT [] synonym: "up-regulation of protein biosynthetic process" EXACT [] synonym: "upregulation of protein biosynthetic process" EXACT [] xref: Reactome:REACT_6236 "Activated DTOR phosphorylates DS6K, Drosophila melanogaster" is_a: GO:0006417 ! regulation of translation intersection_of: positively_regulates GO:0006412 ! translation relationship: positively_regulates GO:0006412 ! translation [Term] id: GO:0045814 name: negative regulation of gene expression, epigenetic namespace: biological_process def: "Any epigenetic process that stops, prevents or reduces the rate of gene expression." [GOC:go_curators] subset: gosubset_prok synonym: "down regulation of gene expression, epigenetic" EXACT [] synonym: "down-regulation of gene expression, epigenetic" EXACT [] synonym: "downregulation of gene expression, epigenetic" EXACT [] synonym: "inhibition of gene expression, epigenetic" NARROW [] is_a: GO:0010629 ! negative regulation of gene expression is_a: GO:0040029 ! regulation of gene expression, epigenetic [Term] id: GO:0045815 name: positive regulation of gene expression, epigenetic namespace: biological_process def: "Any epigenetic process that activates or increases the rate of gene expression." [GOC:go_curators] synonym: "activation of gene expression, epigenetic" NARROW [] synonym: "stimulation of gene expression, epigenetic" NARROW [] synonym: "up regulation of gene expression, epigenetic" EXACT [] synonym: "up-regulation of gene expression, epigenetic" EXACT [] synonym: "upregulation of gene expression, epigenetic" EXACT [] is_a: GO:0010628 ! positive regulation of gene expression is_a: GO:0040029 ! regulation of gene expression, epigenetic [Term] id: GO:0045871 name: negative regulation of rhodopsin gene expression namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of rhodopsin gene expression." [GOC:dph, GOC:go_curators, GOC:tb] synonym: "down regulation of rhodopsin gene activity" EXACT [] synonym: "down-regulation of rhodopsin gene activity" EXACT [] synonym: "downregulation of rhodopsin gene activity" EXACT [] synonym: "inhibition of rhodopsin gene activity" NARROW [] synonym: "negative regulation of rhodopsin gene activity" EXACT [GOC:dph, GOC:tb] is_a: GO:0007468 ! regulation of rhodopsin gene expression is_a: GO:0010629 ! negative regulation of gene expression [Term] id: GO:0045872 name: positive regulation of rhodopsin gene expression namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of rhodopsin gene expression." [GOC:dph, GOC:go_curators, GOC:tb] synonym: "activation of rhodopsin gene activity" NARROW [] synonym: "positive regulation of rhodopsin gene activity" EXACT [GOC:dph, GOC:tb] synonym: "stimulation of rhodopsin gene activity" NARROW [] synonym: "up regulation of rhodopsin gene activity" EXACT [] synonym: "up-regulation of rhodopsin gene activity" EXACT [] synonym: "upregulation of rhodopsin gene activity" EXACT [] is_a: GO:0007468 ! regulation of rhodopsin gene expression is_a: GO:0010628 ! positive regulation of gene expression [Term] id: GO:0045892 name: negative regulation of transcription, DNA-dependent namespace: biological_process alt_id: GO:0016481 alt_id: GO:0032582 alt_id: GO:0061021 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-dependent transcription." [GOC:go_curators, GOC:txnOH] subset: gosubset_prok synonym: "down regulation of gene-specific transcription" RELATED [] synonym: "down regulation of transcription, DNA-dependent" EXACT [] synonym: "down-regulation of gene-specific transcription" RELATED [] synonym: "down-regulation of transcription, DNA-dependent" EXACT [] synonym: "downregulation of gene-specific transcription" RELATED [] synonym: "downregulation of transcription, DNA-dependent" EXACT [] synonym: "inhibition of gene-specific transcription" RELATED [] synonym: "inhibition of transcription, DNA-dependent" NARROW [] synonym: "negative regulation of cellular transcription, DNA-dependent" EXACT [] synonym: "negative regulation of gene-specific transcription" RELATED [] synonym: "transcription repressor activity" RELATED [] is_a: GO:0006355 ! regulation of transcription, DNA-dependent is_a: GO:0010629 ! negative regulation of gene expression intersection_of: negatively_regulates GO:0006351 ! transcription, DNA-dependent relationship: negatively_regulates GO:0006351 ! transcription, DNA-dependent [Term] id: GO:0045893 name: positive regulation of transcription, DNA-dependent namespace: biological_process alt_id: GO:0043193 alt_id: GO:0045941 alt_id: GO:0061020 def: "Any process that activates or increases the frequency, rate or extent of cellular DNA-dependent transcription." [GOC:go_curators, GOC:txnOH] subset: gosubset_prok synonym: "activation of gene-specific transcription" RELATED [] synonym: "activation of transcription, DNA-dependent" NARROW [] synonym: "positive regulation of cellular transcription, DNA-dependent" EXACT [] synonym: "positive regulation of gene-specific transcription" RELATED [] synonym: "stimulation of gene-specific transcription" NARROW [] synonym: "stimulation of transcription, DNA-dependent" NARROW [] synonym: "transcription activator activity" RELATED [] synonym: "up regulation of gene-specific transcription" RELATED [] synonym: "up regulation of transcription, DNA-dependent" EXACT [] synonym: "up-regulation of gene-specific transcription" RELATED [] synonym: "up-regulation of transcription, DNA-dependent" EXACT [] synonym: "upregulation of gene-specific transcription" RELATED [] synonym: "upregulation of transcription, DNA-dependent" EXACT [] is_a: GO:0006355 ! regulation of transcription, DNA-dependent is_a: GO:0010628 ! positive regulation of gene expression intersection_of: positively_regulates GO:0006351 ! transcription, DNA-dependent relationship: positively_regulates GO:0006351 ! transcription, DNA-dependent [Term] id: GO:0045894 name: negative regulation of mating-type specific transcription, DNA-dependent namespace: biological_process def: "Any mating-type specific process that stops, prevents or reduces the rate of cellular DNA-dependent transcription." [GOC:go_curators, GOC:txnOH] synonym: "down regulation of transcription, mating-type specific" EXACT [] synonym: "down-regulation of transcription, mating-type specific" EXACT [] synonym: "downregulation of transcription, mating-type specific" EXACT [] synonym: "inhibition of transcription, mating-type specific" NARROW [] is_a: GO:0007532 ! regulation of mating-type specific transcription, DNA-dependent is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent [Term] id: GO:0045895 name: positive regulation of mating-type specific transcription, DNA-dependent namespace: biological_process def: "Any mating-type specific process that activates or increases the rate of cellular DNA-dependent transcription." [GOC:go_curators, GOC:txnOH] synonym: "activation of transcription, mating-type specific" NARROW [] synonym: "stimulation of transcription, mating-type specific" NARROW [] synonym: "up regulation of transcription, mating-type specific" EXACT [] synonym: "up-regulation of transcription, mating-type specific" EXACT [] synonym: "upregulation of transcription, mating-type specific" EXACT [] is_a: GO:0007532 ! regulation of mating-type specific transcription, DNA-dependent is_a: GO:0045893 ! positive regulation of transcription, DNA-dependent [Term] id: GO:0045896 name: regulation of transcription during mitosis namespace: biological_process def: "A cell cycle process that modulates the frequency, rate or extent of transcription during mitosis." [GOC:go_curators] synonym: "mitotic regulation of transcription" EXACT [] synonym: "regulation of transcription, mitotic" EXACT [GOC:mah] is_a: GO:0006355 ! regulation of transcription, DNA-dependent intersection_of: GO:0006355 ! regulation of transcription, DNA-dependent [Term] id: GO:0045897 name: positive regulation of transcription during mitosis namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transcription during mitosis." [GOC:go_curators] synonym: "activation of transcription during mitosis" NARROW [GOC:mah] synonym: "mitotic activation of transcription" EXACT [] synonym: "positive regulation of transcription, mitotic" EXACT [GOC:mah] synonym: "stimulation of transcription during mitosis" NARROW [GOC:mah] synonym: "up regulation of transcription during mitosis" EXACT [GOC:mah] synonym: "up-regulation of transcription during mitosis" EXACT [GOC:mah] synonym: "upregulation of transcription during mitosis" EXACT [GOC:mah] is_a: GO:0045893 ! positive regulation of transcription, DNA-dependent is_a: GO:0045896 ! regulation of transcription during mitosis intersection_of: GO:0045893 ! positive regulation of transcription, DNA-dependent [Term] id: GO:0045898 name: regulation of RNA polymerase II transcriptional preinitiation complex assembly namespace: biological_process def: "Any process that modulates the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly." [GOC:go_curators] synonym: "regulation of RNA polymerase II transcriptional pre-initiation complex assembly" EXACT [] synonym: "regulation of RNA polymerase II transcriptional pre-initiation complex biosynthesis" EXACT [] synonym: "regulation of RNA polymerase II transcriptional preinitiation complex formation" RELATED [] is_a: GO:0060260 ! regulation of transcription initiation from RNA polymerase II promoter intersection_of: regulates GO:0051123 ! RNA polymerase II transcriptional preinitiation complex assembly relationship: regulates GO:0051123 ! RNA polymerase II transcriptional preinitiation complex assembly [Term] id: GO:0045899 name: positive regulation of RNA polymerase II transcriptional preinitiation complex assembly namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly." [GOC:go_curators] synonym: "activation of RNA polymerase II transcriptional preinitiation complex assembly" NARROW [] synonym: "positive regulation of RNA polymerase II transcriptional pre-initiation complex assembly" EXACT [] synonym: "positive regulation of RNA polymerase II transcriptional pre-initiation complex biosynthesis" EXACT [] synonym: "positive regulation of RNA polymerase II transcriptional preinitiation complex formation" EXACT [] synonym: "stimulation of RNA polymerase II transcriptional preinitiation complex assembly" NARROW [] synonym: "up regulation of RNA polymerase II transcriptional preinitiation complex assembly" EXACT [] synonym: "up-regulation of RNA polymerase II transcriptional preinitiation complex assembly" EXACT [] synonym: "upregulation of RNA polymerase II transcriptional preinitiation complex assembly" EXACT [] is_a: GO:0045898 ! regulation of RNA polymerase II transcriptional preinitiation complex assembly is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: positively_regulates GO:0051123 ! RNA polymerase II transcriptional preinitiation complex assembly relationship: positively_regulates GO:0051123 ! RNA polymerase II transcriptional preinitiation complex assembly [Term] id: GO:0045900 name: negative regulation of translational elongation namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of translational elongation." [GOC:go_curators] subset: gosubset_prok synonym: "down regulation of translational elongation" EXACT [] synonym: "down-regulation of translational elongation" EXACT [] synonym: "downregulation of translational elongation" EXACT [] synonym: "inhibition of translational elongation" NARROW [] is_a: GO:0006448 ! regulation of translational elongation is_a: GO:0017148 ! negative regulation of translation intersection_of: negatively_regulates GO:0006414 ! translational elongation relationship: negatively_regulates GO:0006414 ! translational elongation [Term] id: GO:0045901 name: positive regulation of translational elongation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of translational elongation." [GOC:go_curators] subset: gosubset_prok synonym: "activation of translational elongation" NARROW [] synonym: "stimulation of translational elongation" NARROW [] synonym: "up regulation of translational elongation" EXACT [] synonym: "up-regulation of translational elongation" EXACT [] synonym: "upregulation of translational elongation" EXACT [] is_a: GO:0006448 ! regulation of translational elongation is_a: GO:0045727 ! positive regulation of translation intersection_of: positively_regulates GO:0006414 ! translational elongation relationship: positively_regulates GO:0006414 ! translational elongation [Term] id: GO:0045902 name: negative regulation of translational fidelity namespace: biological_process def: "Any process that decreases the ability of the translational apparatus to interpret the genetic code." [GOC:dph, GOC:tb] subset: gosubset_prok synonym: "down regulation of translational fidelity" EXACT [] synonym: "down-regulation of translational fidelity" EXACT [] synonym: "downregulation of translational fidelity" EXACT [] synonym: "inhibition of translational fidelity" NARROW [] is_a: GO:0006450 ! regulation of translational fidelity is_a: GO:0017148 ! negative regulation of translation [Term] id: GO:0045903 name: positive regulation of translational fidelity namespace: biological_process def: "Any process that increases the ability of the translational apparatus to interpret the genetic code." [GOC:dph, GOC:tb] subset: gosubset_prok synonym: "activation of translational fidelity" NARROW [] synonym: "stimulation of translational fidelity" NARROW [] synonym: "up regulation of translational fidelity" EXACT [] synonym: "up-regulation of translational fidelity" EXACT [] synonym: "upregulation of translational fidelity" EXACT [] is_a: GO:0006450 ! regulation of translational fidelity is_a: GO:0045727 ! positive regulation of translation [Term] id: GO:0045904 name: negative regulation of translational termination namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of translational termination." [GOC:go_curators] subset: gosubset_prok synonym: "down regulation of translational termination" EXACT [] synonym: "down-regulation of translational termination" EXACT [] synonym: "downregulation of translational termination" EXACT [] synonym: "inhibition of translational termination" NARROW [] is_a: GO:0006449 ! regulation of translational termination is_a: GO:0017148 ! negative regulation of translation intersection_of: negatively_regulates GO:0006415 ! translational termination relationship: negatively_regulates GO:0006415 ! translational termination [Term] id: GO:0045905 name: positive regulation of translational termination namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of translational termination." [GOC:go_curators] subset: gosubset_prok synonym: "activation of translational termination" NARROW [] synonym: "stimulation of translational termination" NARROW [] synonym: "up regulation of translational termination" EXACT [] synonym: "up-regulation of translational termination" EXACT [] synonym: "upregulation of translational termination" EXACT [] is_a: GO:0006449 ! regulation of translational termination is_a: GO:0045727 ! positive regulation of translation intersection_of: positively_regulates GO:0006415 ! translational termination relationship: positively_regulates GO:0006415 ! translational termination [Term] id: GO:0045916 name: negative regulation of complement activation namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of complement activation." [GOC:go_curators] synonym: "down regulation of complement activation" EXACT [] synonym: "down-regulation of complement activation" EXACT [] synonym: "downregulation of complement activation" EXACT [] synonym: "inhibition of complement activation" NARROW [] synonym: "negative regulation of complement cascade" EXACT [GOC:add] is_a: GO:0010955 ! negative regulation of protein processing is_a: GO:0030449 ! regulation of complement activation [Term] id: GO:0045917 name: positive regulation of complement activation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of complement activation." [GOC:go_curators] synonym: "activation of complement activation" NARROW [] synonym: "positive regulation of complement cascade" EXACT [GOC:add] synonym: "stimulation of complement activation" NARROW [] synonym: "up regulation of complement activation" EXACT [] synonym: "up-regulation of complement activation" EXACT [] synonym: "upregulation of complement activation" EXACT [] is_a: GO:0010954 ! positive regulation of protein processing is_a: GO:0030449 ! regulation of complement activation [Term] id: GO:0045943 name: positive regulation of transcription from RNA polymerase I promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase I promoter." [GOC:go_curators, GOC:txnOH] synonym: "activation of transcription from RNA polymerase I promoter" NARROW [] synonym: "positive regulation of transcription from Pol I promoter" EXACT [] synonym: "stimulation of transcription from RNA polymerase I promoter" NARROW [] synonym: "up regulation of transcription from RNA polymerase I promoter" EXACT [] synonym: "up-regulation of transcription from RNA polymerase I promoter" EXACT [] synonym: "upregulation of transcription from RNA polymerase I promoter" EXACT [] is_a: GO:0006356 ! regulation of transcription from RNA polymerase I promoter is_a: GO:0045893 ! positive regulation of transcription, DNA-dependent intersection_of: positively_regulates GO:0006360 ! transcription from RNA polymerase I promoter relationship: positively_regulates GO:0006360 ! transcription from RNA polymerase I promoter [Term] id: GO:0045944 name: positive regulation of transcription from RNA polymerase II promoter namespace: biological_process alt_id: GO:0010552 alt_id: GO:0045817 def: "Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:go_curators, GOC:txnOH] synonym: "activation of global transcription from RNA polymerase II promoter" RELATED [] synonym: "activation of transcription from RNA polymerase II promoter" EXACT [] synonym: "positive regulation of gene-specific transcription from RNA polymerase II promoter" RELATED [] synonym: "positive regulation of global transcription from Pol II promoter" RELATED [] synonym: "positive regulation of transcription from Pol II promoter" EXACT [] synonym: "positive regulation of transcription from RNA polymerase II promoter, global" RELATED [] synonym: "stimulation of global transcription from RNA polymerase II promoter" NARROW [] synonym: "stimulation of transcription from RNA polymerase II promoter" EXACT [] synonym: "up regulation of global transcription from RNA polymerase II promoter" RELATED [] synonym: "up regulation of transcription from RNA polymerase II promoter" EXACT [] synonym: "up-regulation of global transcription from RNA polymerase II promoter" RELATED [] synonym: "up-regulation of transcription from RNA polymerase II promoter" EXACT [] synonym: "upregulation of global transcription from RNA polymerase II promoter" RELATED [] synonym: "upregulation of transcription from RNA polymerase II promoter" EXACT [] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter is_a: GO:0045893 ! positive regulation of transcription, DNA-dependent intersection_of: positively_regulates GO:0006366 ! transcription from RNA polymerase II promoter relationship: positively_regulates GO:0006366 ! transcription from RNA polymerase II promoter [Term] id: GO:0045945 name: positive regulation of transcription from RNA polymerase III promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase III promoter." [GOC:go_curators, GOC:txnOH] synonym: "activation of transcription from RNA polymerase III promoter" NARROW [] synonym: "positive regulation of transcription from Pol III promoter" EXACT [] synonym: "stimulation of transcription from RNA polymerase III promoter" NARROW [] synonym: "up regulation of transcription from RNA polymerase III promoter" EXACT [] synonym: "up-regulation of transcription from RNA polymerase III promoter" EXACT [] synonym: "upregulation of transcription from RNA polymerase III promoter" EXACT [] is_a: GO:0006359 ! regulation of transcription from RNA polymerase III promoter is_a: GO:0045893 ! positive regulation of transcription, DNA-dependent intersection_of: positively_regulates GO:0006383 ! transcription from RNA polymerase III promoter relationship: positively_regulates GO:0006383 ! transcription from RNA polymerase III promoter [Term] id: GO:0045947 name: negative regulation of translational initiation namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation." [GOC:go_curators] subset: gosubset_prok synonym: "down regulation of translational initiation" EXACT [] synonym: "down-regulation of translational initiation" EXACT [] synonym: "downregulation of translational initiation" EXACT [] synonym: "inhibition of translational initiation" NARROW [] is_a: GO:0006446 ! regulation of translational initiation is_a: GO:0017148 ! negative regulation of translation intersection_of: negatively_regulates GO:0006413 ! translational initiation relationship: negatively_regulates GO:0006413 ! translational initiation [Term] id: GO:0045948 name: positive regulation of translational initiation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of translational initiation." [GOC:go_curators] subset: gosubset_prok synonym: "activation of translational initiation" NARROW [] synonym: "stimulation of translational initiation" NARROW [] synonym: "up regulation of translational initiation" EXACT [] synonym: "up-regulation of translational initiation" EXACT [] synonym: "upregulation of translational initiation" EXACT [] is_a: GO:0006446 ! regulation of translational initiation is_a: GO:0045727 ! positive regulation of translation intersection_of: positively_regulates GO:0006413 ! translational initiation relationship: positively_regulates GO:0006413 ! translational initiation [Term] id: GO:0045957 name: negative regulation of complement activation, alternative pathway namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of complement activation by the alternative pathway." [GOC:go_curators] synonym: "down regulation of complement activation, alternative pathway" EXACT [] synonym: "down-regulation of complement activation, alternative pathway" EXACT [] synonym: "downregulation of complement activation, alternative pathway" EXACT [] synonym: "inhibition of complement activation, alternative pathway" NARROW [] synonym: "negative regulation of complement cascade, alternative pathway" EXACT [GOC:add] is_a: GO:0030451 ! regulation of complement activation, alternative pathway is_a: GO:0045916 ! negative regulation of complement activation [Term] id: GO:0045958 name: positive regulation of complement activation, alternative pathway namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of complement activation by the alternative pathway." [GOC:go_curators] synonym: "activation of complement activation, alternative pathway" NARROW [] synonym: "positive regulation of complement cascade, alternative pathway" EXACT [GOC:add] synonym: "stimulation of complement activation, alternative pathway" NARROW [] synonym: "up regulation of complement activation, alternative pathway" EXACT [] synonym: "up-regulation of complement activation, alternative pathway" EXACT [] synonym: "upregulation of complement activation, alternative pathway" EXACT [] is_a: GO:0030451 ! regulation of complement activation, alternative pathway is_a: GO:0045917 ! positive regulation of complement activation [Term] id: GO:0045959 name: negative regulation of complement activation, classical pathway namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of complement activation by the classical pathway." [GOC:go_curators] synonym: "down regulation of complement activation, classical pathway" EXACT [] synonym: "down-regulation of complement activation, classical pathway" EXACT [] synonym: "downregulation of complement activation, classical pathway" EXACT [] synonym: "inhibition of complement activation, classical pathway" NARROW [] synonym: "negative regulation of complement cascade, classical pathway" EXACT [GOC:add] is_a: GO:0030450 ! regulation of complement activation, classical pathway is_a: GO:0045916 ! negative regulation of complement activation [Term] id: GO:0045960 name: positive regulation of complement activation, classical pathway namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of complement activation by the classical pathway." [GOC:go_curators] synonym: "activation of complement activation, classical pathway" NARROW [] synonym: "positive regulation of complement cascade, classical pathway" EXACT [GOC:add] synonym: "stimulation of complement activation, classical pathway" NARROW [] synonym: "up regulation of complement activation, classical pathway" EXACT [] synonym: "up-regulation of complement activation, classical pathway" EXACT [] synonym: "upregulation of complement activation, classical pathway" EXACT [] is_a: GO:0030450 ! regulation of complement activation, classical pathway is_a: GO:0045917 ! positive regulation of complement activation [Term] id: GO:0045974 name: regulation of translation, ncRNA-mediated namespace: biological_process def: "Any process, mediated by small non-coding RNAs, that modulates the frequency, rate or extent that mRNAs are effectively translated into protein." [GOC:dph, GOC:go_curators, GOC:tb] is_a: GO:0006417 ! regulation of translation [Term] id: GO:0045975 name: positive regulation of translation, ncRNA-mediated namespace: biological_process def: "Any process, mediated by small non-coding RNAs, that activates or increases the rate that mRNAs are effectively translated into protein." [GOC:dph, GOC:go_curators, GOC:tb] synonym: "activation of mRNA translation, ncRNA-mediated" NARROW [] synonym: "stimulation of mRNA translation, ncRNA-mediated" NARROW [] synonym: "up regulation of mRNA translation, ncRNA-mediated" EXACT [] synonym: "up-regulation of mRNA translation, ncRNA-mediated" EXACT [] synonym: "upregulation of mRNA translation, ncRNA-mediated" EXACT [] is_a: GO:0045727 ! positive regulation of translation is_a: GO:0045974 ! regulation of translation, ncRNA-mediated [Term] id: GO:0045990 name: carbon catabolite regulation of transcription namespace: biological_process def: "A transcription regulation process in which the presence of one carbon source leads to the modulation of the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources." [GOC:go_curators, GOC:mah, PMID:18359269, PMID:9618445] subset: gosubset_prok synonym: "regulation of transcription by carbon catabolites" EXACT [GOC:mah] is_a: GO:0006355 ! regulation of transcription, DNA-dependent [Term] id: GO:0045991 name: carbon catabolite activation of transcription namespace: biological_process def: "A transcription regulation process in which the presence of one carbon source leads to an increase in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources." [GOC:mah, PMID:10559153] subset: gosubset_prok synonym: "positive regulation of transcription by carbon catabolites" EXACT [GOC:mah] is_a: GO:0045893 ! positive regulation of transcription, DNA-dependent is_a: GO:0045990 ! carbon catabolite regulation of transcription [Term] id: GO:0045993 name: negative regulation of translational initiation by iron namespace: biological_process def: "Any process involving iron that stops, prevents or reduces the rate of translational initiation." [GOC:go_curators] subset: gosubset_prok synonym: "down regulation of translational initiation by iron" EXACT [] synonym: "down-regulation of translational initiation by iron" EXACT [] synonym: "downregulation of translational initiation by iron" EXACT [] synonym: "inhibition of translational initiation by iron" NARROW [] is_a: GO:0006447 ! regulation of translational initiation by iron is_a: GO:0045947 ! negative regulation of translational initiation [Term] id: GO:0045994 name: positive regulation of translational initiation by iron namespace: biological_process def: "Any process involving iron that activates or increases the rate of translational initiation." [GOC:go_curators] subset: gosubset_prok synonym: "activation of translational initiation by iron" NARROW [] synonym: "stimulation of translational initiation by iron" NARROW [] synonym: "up regulation of translational initiation by iron" EXACT [] synonym: "up-regulation of translational initiation by iron" EXACT [] synonym: "upregulation of translational initiation by iron" EXACT [] is_a: GO:0006447 ! regulation of translational initiation by iron is_a: GO:0045948 ! positive regulation of translational initiation [Term] id: GO:0045996 name: negative regulation of transcription by pheromones namespace: biological_process def: "Any process involving pheromones that stops, prevents or reduces the rate of transcription." [GOC:go_curators] subset: gosubset_prok synonym: "down regulation of transcription by pheromones" EXACT [] synonym: "down-regulation of transcription by pheromones" EXACT [] synonym: "downregulation of transcription by pheromones" EXACT [] synonym: "inhibition of transcription by pheromones" NARROW [] is_a: GO:0009373 ! regulation of transcription by pheromones is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent [Term] id: GO:0046011 name: regulation of oskar mRNA translation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of oskar mRNA translation. To ensure the localization of Oskar protein at the posterior pole of the oocyte, translation of oskar mRNA is repressed during its transport to the posterior pole and activated upon localization of the mRNA at the posterior cortex." [GOC:go_curators, PMID:12538512] is_a: GO:0006417 ! regulation of translation [Term] id: GO:0046012 name: positive regulation of oskar mRNA translation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of oskar mRNA translation." [GOC:go_curators] synonym: "activation of oskar mRNA translation" NARROW [] synonym: "stimulation of oskar mRNA translation" NARROW [] synonym: "up regulation of oskar mRNA translation" EXACT [] synonym: "up-regulation of oskar mRNA translation" EXACT [] synonym: "upregulation of oskar mRNA translation" EXACT [] is_a: GO:0045727 ! positive regulation of translation is_a: GO:0046011 ! regulation of oskar mRNA translation [Term] id: GO:0046015 name: regulation of transcription by glucose namespace: biological_process def: "Any process involving glucose that modulates the frequency, rate or extent or transcription." [GOC:go_curators] subset: gosubset_prok is_a: GO:0045990 ! carbon catabolite regulation of transcription [Term] id: GO:0046016 name: positive regulation of transcription by glucose namespace: biological_process def: "Any process involving glucose that activates or increases the rate of transcription." [GOC:go_curators] subset: gosubset_prok synonym: "activation of transcription by glucose" NARROW [] synonym: "stimulation of transcription by glucose" NARROW [] synonym: "up regulation of transcription by glucose" EXACT [] synonym: "up-regulation of transcription by glucose" EXACT [] synonym: "upregulation of transcription by glucose" EXACT [] is_a: GO:0045991 ! carbon catabolite activation of transcription is_a: GO:0046015 ! regulation of transcription by glucose [Term] id: GO:0046017 name: regulation of transcription from RNA polymerase I promoter, mitotic namespace: biological_process def: "A cell cycle process that modulates the frequency, rate or extent of transcription from an RNA polymerase I promoter during mitosis." [GOC:go_curators] synonym: "mitotic regulation of transcription from Pol I promoter" EXACT [] synonym: "regulation of transcription from Pol I promoter during mitosis" EXACT [GOC:dph, GOC:tb] synonym: "regulation of transcription from RNA polymerase I promoter during mitosis" EXACT [GOC:dph, GOC:tb] is_a: GO:0006356 ! regulation of transcription from RNA polymerase I promoter is_a: GO:0045896 ! regulation of transcription during mitosis intersection_of: GO:0006356 ! regulation of transcription from RNA polymerase I promoter [Term] id: GO:0046018 name: positive regulation of transcription from RNA polymerase I promoter during mitosis namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase I promoter during mitosis." [GOC:go_curators] synonym: "activation of transcription from RNA polymerase I promoter during mitosis" NARROW [GOC:mah] synonym: "mitotic activation of transcription from Pol I promoter" EXACT [] synonym: "positive regulation of transcription from Pol I promoter during mitosis" EXACT [GOC:mah] synonym: "positive regulation of transcription from RNA polymerase I promoter, mitotic" EXACT [GOC:mah] synonym: "stimulation of transcription from RNA polymerase I promoter during mitosis" NARROW [GOC:mah] synonym: "up regulation of transcription from RNA polymerase I promoter during mitosis" EXACT [GOC:mah] synonym: "up-regulation of transcription from RNA polymerase I promoter during mitosis" EXACT [GOC:mah] synonym: "upregulation of transcription from RNA polymerase I promoter during mitosis" EXACT [GOC:mah] is_a: GO:0045897 ! positive regulation of transcription during mitosis is_a: GO:0045943 ! positive regulation of transcription from RNA polymerase I promoter is_a: GO:0046017 ! regulation of transcription from RNA polymerase I promoter, mitotic intersection_of: GO:0045943 ! positive regulation of transcription from RNA polymerase I promoter [Term] id: GO:0046019 name: regulation of transcription from RNA polymerase II promoter by pheromones namespace: biological_process def: "Any process involving pheromones that modulates the frequency, rate or extent or transcription from an RNA polymerase II promoter." [GOC:go_curators, GOC:txnOH] synonym: "regulation of transcription from Pol II promoter by pheromones" EXACT [] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter is_a: GO:0009373 ! regulation of transcription by pheromones [Term] id: GO:0046020 name: negative regulation of transcription from RNA polymerase II promoter by pheromones namespace: biological_process def: "Any process involving pheromones that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter." [GOC:go_curators] synonym: "down regulation of transcription from RNA polymerase II promoter by pheromones" EXACT [] synonym: "down-regulation of transcription from RNA polymerase II promoter by pheromones" EXACT [] synonym: "downregulation of transcription from RNA polymerase II promoter by pheromones" EXACT [] synonym: "inhibition of transcription from RNA polymerase II promoter by pheromones" NARROW [] synonym: "negative regulation of transcription from Pol II promoter by pheromones" EXACT [] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter is_a: GO:0045996 ! negative regulation of transcription by pheromones is_a: GO:0046019 ! regulation of transcription from RNA polymerase II promoter by pheromones [Term] id: GO:0046021 name: regulation of transcription from RNA polymerase II promoter, mitotic namespace: biological_process def: "A cell cycle process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter during mitosis." [GOC:go_curators] synonym: "mitotic regulation of transcription from Pol II promoter" EXACT [] synonym: "regulation of transcription from Pol II promoter, mitotic" EXACT [] synonym: "regulation of transcription from RNA polymerase II promoter during mitosis" EXACT [GOC:dph, GOC:tb] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter is_a: GO:0045896 ! regulation of transcription during mitosis intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter [Term] id: GO:0046022 name: positive regulation of transcription from RNA polymerase II promoter during mitosis namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter during mitosis." [GOC:go_curators] synonym: "activation of transcription from RNA polymerase II promoter during mitosis" NARROW [GOC:mah] synonym: "mitotic activation of transcription from Pol II promoter" EXACT [] synonym: "positive regulation of transcription from Pol II promoter during mitosis" EXACT [GOC:mah] synonym: "positive regulation of transcription from RNA polymerase II promoter, mitotic" EXACT [GOC:mah] synonym: "stimulation of transcription from RNA polymerase II promoter during mitosis" NARROW [GOC:mah] synonym: "up regulation of transcription from RNA polymerase II promoter during mitosis" EXACT [GOC:mah] synonym: "up-regulation of transcription from RNA polymerase II promoter during mitosis" EXACT [GOC:mah] synonym: "upregulation of transcription from RNA polymerase II promoter during mitosis" EXACT [GOC:mah] is_a: GO:0045897 ! positive regulation of transcription during mitosis is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter is_a: GO:0046021 ! regulation of transcription from RNA polymerase II promoter, mitotic intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter [Term] id: GO:0046023 name: regulation of transcription from RNA polymerase III promoter, mitotic namespace: biological_process def: "A cell cycle process that modulates the frequency, rate or extent of transcription from an RNA polymerase III promoter during mitosis." [GOC:go_curators] synonym: "mitotic regulation of transcription from Pol III promoter" EXACT [] synonym: "regulation of transcription from Pol III promoter, mitotic" EXACT [] synonym: "regulation of transcription from RNA polymerase III promoter during mitosis" EXACT [GOC:dph, GOC:tb] is_a: GO:0006359 ! regulation of transcription from RNA polymerase III promoter is_a: GO:0045896 ! regulation of transcription during mitosis intersection_of: GO:0006359 ! regulation of transcription from RNA polymerase III promoter [Term] id: GO:0046024 name: positive regulation of transcription from RNA polymerase III promoter during mitosis namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase III promoter during mitosis." [GOC:go_curators] synonym: "activation of transcription from RNA polymerase III promoter during mitosis" NARROW [GOC:mah] synonym: "mitotic activation of transcription from Pol III promoter" EXACT [] synonym: "positive regulation of transcription from Pol III promoter during mitosis" EXACT [GOC:mah] synonym: "positive regulation of transcription from RNA polymerase III promoter, mitotic" EXACT [GOC:mah] synonym: "stimulation of transcription from RNA polymerase III promoter during mitosis" NARROW [GOC:mah] synonym: "up regulation of transcription from RNA polymerase III promoter during mitosis" EXACT [GOC:mah] synonym: "up-regulation of transcription from RNA polymerase III promoter during mitosis" EXACT [GOC:mah] synonym: "upregulation of transcription from RNA polymerase III promoter during mitosis" EXACT [GOC:mah] is_a: GO:0045897 ! positive regulation of transcription during mitosis is_a: GO:0045945 ! positive regulation of transcription from RNA polymerase III promoter is_a: GO:0046023 ! regulation of transcription from RNA polymerase III promoter, mitotic intersection_of: GO:0045945 ! positive regulation of transcription from RNA polymerase III promoter [Term] id: GO:0046773 name: suppression by virus of host termination of protein biosynthetic process namespace: biological_process def: "Any viral process that inhibits the termination of host cell protein biosynthesis that occurs in response to viral infection." [ISBN:0781718325] synonym: "negative regulation by virus of host cell protein biosynthesis shutoff" EXACT [] synonym: "negative regulation by virus of host cell protein biosynthetic process shutoff" EXACT [] synonym: "viral inhibition of host cell protein biosynthesis shutoff" EXACT [] synonym: "viral inhibition of host cell protein biosynthetic process shutoff" EXACT [] synonym: "viral inhibition of termination of host cell protein biosynthesis" EXACT [] synonym: "viral inhibition of termination of host cell protein biosynthetic process" EXACT [] synonym: "viral suppression of termination by host of host cell protein biosynthesis" EXACT [] synonym: "viral suppression of termination by host of host cell protein biosynthetic process" EXACT [] is_a: GO:0045904 ! negative regulation of translational termination [Term] id: GO:0046778 name: modification by virus of host mRNA processing namespace: biological_process def: "Any viral process that interferes with the processing of mRNA in the host cell." [ISBN:0781718325] synonym: "viral perturbation of host mRNA processing" EXACT [] xref: Reactome:REACT_6168 "Binding of NS1 to cleavage and host polyadenylation specificity factor (CPSF), Homo sapiens" xref: Reactome:REACT_6173 "Inhibition of Host mRNA Processing and RNA Silencing, Homo sapiens" xref: Reactome:REACT_6287 "Binding of NS1 to poly(A)-binding protein II (PABII), Homo sapiens" is_a: GO:0039656 ! modulation by virus of host gene expression [Term] id: GO:0046779 name: suppression by virus of expression of host genes with introns namespace: biological_process def: "Any viral process that discriminates against and subsequently inhibits host transcripts containing introns, thus allowing only intronless viral mRNA to be fully processed." [PMID:11598019] synonym: "negative regulation by virus of expression of host genes with introns" EXACT [] synonym: "viral inhibition of expression of host genes with introns" EXACT [] is_a: GO:0039653 ! suppression by virus of host transcription [Term] id: GO:0046780 name: suppression by virus of host mRNA splicing namespace: biological_process def: "Any viral process that inhibits the splicing of host mRNA, thus reducing host protein production." [ISBN:0781718325] synonym: "negative regulation by virus of host mRNA splicing" EXACT [] synonym: "viral inhibition of host mRNA splicing" EXACT [] is_a: GO:0039524 ! suppression by virus of host mRNA processing [Term] id: GO:0046781 name: dispersion by virus of host splicing factors namespace: biological_process def: "Any viral process that disperses host splicing factors (snRNPs) to prevent host mRNA splicing, thus reducing host protein production." [ISBN:0781718325] synonym: "viral dispersion of host splicing factors" EXACT [] is_a: GO:0046778 ! modification by virus of host mRNA processing [Term] id: GO:0046782 name: regulation of viral transcription namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the transcription of the viral genome." [GOC:ai] is_a: GO:0010468 ! regulation of gene expression intersection_of: regulates GO:0019083 ! viral transcription relationship: regulates GO:0019083 ! viral transcription [Term] id: GO:0046783 name: modification by virus of host polysomes namespace: biological_process def: "Any viral process that interferes with and inhibits the assembly and function of polysomes." [PMID:10438802] comment: See also the cellular component term 'polysome ; GO:0005844'. synonym: "viral perturbation of polysomes" EXACT [] is_a: GO:0019057 ! modulation by virus of host translation [Term] id: GO:0046793 name: induction by virus of modification of host RNA polymerase II namespace: biological_process def: "The viral induction of modification to the host RNA polymerase II." [PMID:7637000] synonym: "virus-induced modification of host RNA polymerase II" EXACT [] is_a: GO:0019056 ! modulation by virus of host transcription [Term] id: GO:0048024 name: regulation of mRNA splicing, via spliceosome namespace: biological_process alt_id: GO:0035055 def: "Any process that modulates the frequency, rate or extent of mRNA splicing via a spliceosomal mechanism." [GOC:jid] synonym: "regulation of nuclear mRNA splicing via U2-type spliceosome" NARROW [] synonym: "regulation of nuclear mRNA splicing, via spliceosome" EXACT [GOC:vw] synonym: "regulation of pre-mRNA splicing" BROAD [] is_a: GO:0043484 ! regulation of RNA splicing is_a: GO:0050684 ! regulation of mRNA processing intersection_of: regulates GO:0000398 ! mRNA splicing, via spliceosome relationship: regulates GO:0000398 ! mRNA splicing, via spliceosome [Term] id: GO:0048025 name: negative regulation of mRNA splicing, via spliceosome namespace: biological_process alt_id: GO:0035056 def: "Any process that stops, prevents or reduces the rate or extent of mRNA splicing via a spliceosomal mechanism." [GOC:jid] synonym: "down regulation of nuclear mRNA splicing via U2-type spliceosome" NARROW [] synonym: "down regulation of nuclear mRNA splicing, via spliceosome" EXACT [] synonym: "down-regulation of nuclear mRNA splicing via U2-type spliceosome" NARROW [] synonym: "down-regulation of nuclear mRNA splicing, via spliceosome" EXACT [] synonym: "downregulation of nuclear mRNA splicing via U2-type spliceosome" NARROW [] synonym: "downregulation of nuclear mRNA splicing, via spliceosome" EXACT [] synonym: "inhibition of nuclear mRNA splicing via U2-type spliceosome" NARROW [] synonym: "inhibition of nuclear mRNA splicing, via spliceosome" NARROW [] synonym: "negative regulation of nuclear mRNA splicing via U2-type spliceosome" NARROW [] synonym: "negative regulation of nuclear mRNA splicing, via spliceosome" EXACT [GOC:vw] synonym: "negative regulation of pre-mRNA splicing" BROAD [] is_a: GO:0033119 ! negative regulation of RNA splicing is_a: GO:0048024 ! regulation of mRNA splicing, via spliceosome is_a: GO:0050686 ! negative regulation of mRNA processing intersection_of: negatively_regulates GO:0000398 ! mRNA splicing, via spliceosome relationship: negatively_regulates GO:0000398 ! mRNA splicing, via spliceosome [Term] id: GO:0048026 name: positive regulation of mRNA splicing, via spliceosome namespace: biological_process alt_id: GO:0035057 def: "Any process that activates or increases the rate or extent of mRNA splicing via a spliceosomal mechanism." [GOC:jid] synonym: "activation of nuclear mRNA splicing via U2-type spliceosome" NARROW [] synonym: "activation of nuclear mRNA splicing, via spliceosome" NARROW [] synonym: "positive regulation of nuclear mRNA splicing via U2-type spliceosome" NARROW [] synonym: "positive regulation of nuclear mRNA splicing, via spliceosome" EXACT [GOC:vw] synonym: "positive regulation of pre-mRNA splicing" BROAD [] synonym: "stimulation of nuclear mRNA splicing via U2-type spliceosome" NARROW [] synonym: "stimulation of nuclear mRNA splicing, via spliceosome" NARROW [] synonym: "up regulation of nuclear mRNA splicing via U2-type spliceosome" NARROW [] synonym: "up regulation of nuclear mRNA splicing, via spliceosome" EXACT [] synonym: "up-regulation of nuclear mRNA splicing via U2-type spliceosome" NARROW [] synonym: "up-regulation of nuclear mRNA splicing, via spliceosome" EXACT [] synonym: "upregulation of nuclear mRNA splicing via U2-type spliceosome" NARROW [] synonym: "upregulation of nuclear mRNA splicing, via spliceosome" EXACT [] is_a: GO:0033120 ! positive regulation of RNA splicing is_a: GO:0048024 ! regulation of mRNA splicing, via spliceosome is_a: GO:0050685 ! positive regulation of mRNA processing intersection_of: positively_regulates GO:0000398 ! mRNA splicing, via spliceosome relationship: positively_regulates GO:0000398 ! mRNA splicing, via spliceosome [Term] id: GO:0048096 name: chromatin-mediated maintenance of transcription namespace: biological_process def: "Maintenance of transcription by remodelling of chromatin into an 'open configuration'. Once established, this regulation is mitotically stable and is maintained over many cell divisions. It is also heritable." [GOC:jid] comment: Note that this process is the opposite of chromatin silencing. This regulation is exemplified by members of the trithorax group, which maintain the active state of homeotic gene transcription. is_a: GO:0045815 ! positive regulation of gene expression, epigenetic is_a: GO:0045893 ! positive regulation of transcription, DNA-dependent [Term] id: GO:0048097 name: long-term maintenance of gene activation namespace: biological_process def: "Any mechanism, at the level of transcription or post-transcription, maintaining gene activation in the long-term." [GOC:jid] comment: Note that this process is the opposite of gene silencing. is_a: GO:0045815 ! positive regulation of gene expression, epigenetic [Term] id: GO:0048255 name: mRNA stabilization namespace: biological_process def: "Prevention of degradation of mRNA molecules. In the absence of compensating changes in other processes, the slowing of mRNA degradation can result in an overall increase in the population of active mRNA molecules." [GOC:jid] subset: gosubset_prok is_a: GO:0043488 ! regulation of mRNA stability is_a: GO:0043489 ! RNA stabilization [Term] id: GO:0048786 name: presynaptic active zone namespace: cellular_component def: "A specialized region of the plasma membrane and cell cortex of a presynaptic neuron; encompasses a region of the plasma membrane where synaptic vesicles dock and fuse, synaptic vesicles, and a specialized cortical cytoskeletal matrix." [GOC:dh, GOC:dl, GOC:ef, GOC:jid, PMID:3152289] synonym: "pre-synaptic active zone" EXACT [] xref: NIF_Subcellular:sao792027222 is_a: GO:0097458 ! neuron part [Term] id: GO:0048787 name: presynaptic active zone membrane namespace: cellular_component def: "The membrane portion of the presynaptic active zone; it is the site where docking and fusion of synaptic vesicles occurs for the release of neurotransmitters." [PMID:12812759, PMID:12923177, PMID:3152289] synonym: "active zone plasma membrane" EXACT [] synonym: "active zone pre-synaptic plasma membrane" EXACT [] synonym: "active zone presynaptic plasma membrane" EXACT [] synonym: "pre-synaptic active zone membrane" EXACT [] is_a: GO:0042734 ! presynaptic membrane relationship: part_of GO:0048786 ! presynaptic active zone [Term] id: GO:0048788 name: presynaptic cytoskeletal matrix assembled at active zones namespace: cellular_component def: "The specialized cytoskeletal matrix assembled at the active zones of the presynaptic nerve terminal. The cytoskeletal matrix is a proteinaceous structure involved in organizing synaptic events such as immobilisation or translocation of synaptic vesicles, and assembling active zone components. The cytomatrix protein exclusively assembled at active zones, is thought to form a molecular scaffold that organizes neurotransmitter release sites." [GOC:dh, GOC:dl, GOC:ef, GOC:jid, NIF_Subcellular:sao1470121605, PMID:10944438] synonym: "active zone cytomatrix" EXACT [] synonym: "CAZ" NARROW [] synonym: "pre-synaptic cytoskeletal matrix assembled at active zones" RELATED [] synonym: "pre-synaptic dense body" NARROW [NIF_Subcellular:sao1111202255, PMID:12575947] synonym: "pre-synaptic ribbon" RELATED [ISBN:0716723808, NIF_Subcellular:sao1488888179] synonym: "presynaptic cytomatrix assembled at active zones" EXACT [] synonym: "presynaptic dense body" NARROW [PMID:16709774] synonym: "presynaptic ribbon" RELATED [ISBN:0716723808, NIF_Subcellular:sao1488888179] synonym: "ribbon" RELATED [NIF_Subcellular:sao1111202255, PMID:12575947] synonym: "synaptic ribbon" NARROW [PMID:19264728] synonym: "T-bar" NARROW [PMID:20127822] synonym: "T-bar ribbon" NARROW [PMID:16384719] is_a: GO:0097458 ! neuron part intersection_of: part_of GO:0048786 ! presynaptic active zone relationship: part_of GO:0048786 ! presynaptic active zone [Term] id: GO:0050434 name: positive regulation of viral transcription namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of viral transcription." [GOC:ai] synonym: "activation of viral transcription" NARROW [] synonym: "stimulation of viral transcription" NARROW [] synonym: "up regulation of viral transcription" EXACT [] synonym: "up-regulation of viral transcription" EXACT [] synonym: "upregulation of viral transcription" EXACT [] xref: Reactome:REACT_6162 "Tat-mediated elongation of the HIV-1 transcript, Homo sapiens" is_a: GO:0046782 ! regulation of viral transcription intersection_of: positively_regulates GO:0019083 ! viral transcription relationship: positively_regulates GO:0019083 ! viral transcription [Term] id: GO:0050684 name: regulation of mRNA processing namespace: biological_process def: "Any process that modulates the frequency, rate or extent of mRNA processing, those processes involved in the conversion of a primary mRNA transcript into a mature mRNA prior to its translation into polypeptide." [GOC:ai] subset: gosubset_prok is_a: GO:0010468 ! regulation of gene expression intersection_of: regulates GO:0006397 ! mRNA processing relationship: regulates GO:0006397 ! mRNA processing [Term] id: GO:0050685 name: positive regulation of mRNA processing namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of mRNA processing." [GOC:ai] subset: gosubset_prok synonym: "activation of mRNA processing" NARROW [] synonym: "stimulation of mRNA processing" NARROW [] synonym: "up regulation of mRNA processing" EXACT [] synonym: "up-regulation of mRNA processing" EXACT [] synonym: "upregulation of mRNA processing" EXACT [] is_a: GO:0050684 ! regulation of mRNA processing intersection_of: positively_regulates GO:0006397 ! mRNA processing relationship: positively_regulates GO:0006397 ! mRNA processing [Term] id: GO:0050686 name: negative regulation of mRNA processing namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of mRNA processing." [GOC:ai] subset: gosubset_prok synonym: "down regulation of mRNA processing" EXACT [] synonym: "down-regulation of mRNA processing" EXACT [] synonym: "downregulation of mRNA processing" EXACT [] synonym: "inhibition of mRNA processing" NARROW [] is_a: GO:0050684 ! regulation of mRNA processing intersection_of: negatively_regulates GO:0006397 ! mRNA processing relationship: negatively_regulates GO:0006397 ! mRNA processing [Term] id: GO:0050779 name: RNA destabilization namespace: biological_process def: "Any process that decreases the stability of an RNA molecule, making it more vulnerable to degradative processes." [GOC:ai] subset: gosubset_prok is_a: GO:0043487 ! regulation of RNA stability [Term] id: GO:0050821 name: protein stabilization namespace: biological_process def: "Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation." [GOC:ai] subset: gosubset_prok synonym: "lysosomal protein stabilization" NARROW [] synonym: "positive regulation of protein stability" EXACT [] synonym: "protein sequestering" RELATED [] synonym: "protein stabilization activity" RELATED [] is_a: GO:0031647 ! regulation of protein stability [Term] id: GO:0051037 name: regulation of transcription during meiosis namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription during meiosis." [GOC:go_curators] synonym: "meiotic regulation of transcription" EXACT [] synonym: "regulation of transcription, meiotic" EXACT [GOC:mah] is_a: GO:0006355 ! regulation of transcription, DNA-dependent intersection_of: GO:0006355 ! regulation of transcription, DNA-dependent [Term] id: GO:0051038 name: negative regulation of transcription during meiosis namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription during meiosis." [GOC:ai] synonym: "down regulation of transcription during meiosis" EXACT [GOC:mah] synonym: "down-regulation of transcription during meiosis" EXACT [GOC:mah] synonym: "downregulation of transcription during meiosis" EXACT [GOC:mah] synonym: "inhibition of transcription during meiosis" NARROW [GOC:mah] synonym: "meiotic repression of transcription" EXACT [] synonym: "negative regulation of meiotic transcription" EXACT [] synonym: "negative regulation of transcription, meiotic" EXACT [GOC:mah] is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent is_a: GO:0051037 ! regulation of transcription during meiosis [Term] id: GO:0051039 name: positive regulation of transcription during meiosis namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transcription during meiosis." [GOC:ai] synonym: "activation of transcription during meiosis" NARROW [GOC:mah] synonym: "positive regulation of meiotic transcription" EXACT [] synonym: "positive regulation of transcription, meiotic" EXACT [GOC:mah] synonym: "stimulation of transcription during meiosis" NARROW [GOC:mah] synonym: "up regulation of transcription during meiosis" EXACT [GOC:mah] synonym: "up-regulation of transcription during meiosis" EXACT [GOC:mah] synonym: "upregulation of transcription during meiosis" EXACT [GOC:mah] is_a: GO:0045893 ! positive regulation of transcription, DNA-dependent is_a: GO:0051037 ! regulation of transcription during meiosis [Term] id: GO:0051090 name: regulation of sequence-specific DNA binding transcription factor activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription." [GOC:ai] subset: gosubset_prok synonym: "regulation of transcription factor activity" BROAD [GOC:dph, GOC:tb] xref: Reactome:REACT_104536 "Activation of the AP-1 family of transcription factors, Bos taurus" xref: Reactome:REACT_107559 "Activation of the AP-1 family of transcription factors, Danio rerio" xref: Reactome:REACT_109535 "Activation of the AP-1 family of transcription factors, Schizosaccharomyces pombe" xref: Reactome:REACT_110257 "Activation of the AP-1 family of transcription factors, Drosophila melanogaster" xref: Reactome:REACT_110693 "Activation of the AP-1 family of transcription factors, Gallus gallus" xref: Reactome:REACT_21326 "Activation of the AP-1 family of transcription factors, Homo sapiens" xref: Reactome:REACT_82719 "Activation of the AP-1 family of transcription factors, Xenopus tropicalis" xref: Reactome:REACT_83365 "Activation of the AP-1 family of transcription factors, Sus scrofa" xref: Reactome:REACT_90659 "Activation of the AP-1 family of transcription factors, Taeniopygia guttata" xref: Reactome:REACT_92725 "Activation of the AP-1 family of transcription factors, Canis familiaris" xref: Reactome:REACT_96476 "Activation of the AP-1 family of transcription factors, Rattus norvegicus" xref: Reactome:REACT_99415 "Activation of the AP-1 family of transcription factors, Mus musculus" is_a: GO:0006355 ! regulation of transcription, DNA-dependent intersection_of: regulates GO:0003700 ! sequence-specific DNA binding transcription factor activity relationship: regulates GO:0003700 ! sequence-specific DNA binding transcription factor activity [Term] id: GO:0051091 name: positive regulation of sequence-specific DNA binding transcription factor activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription." [GOC:ai] subset: gosubset_prok synonym: "activation of transcription factor activity" NARROW [] synonym: "positive regulation of transcription factor activity" BROAD [GOC:dph, GOC:tb] synonym: "stimulation of transcription factor activity" NARROW [] synonym: "up regulation of transcription factor activity" EXACT [] synonym: "up-regulation of transcription factor activity" EXACT [] synonym: "upregulation of transcription factor activity" EXACT [] is_a: GO:0051090 ! regulation of sequence-specific DNA binding transcription factor activity intersection_of: positively_regulates GO:0003700 ! sequence-specific DNA binding transcription factor activity relationship: positively_regulates GO:0003700 ! sequence-specific DNA binding transcription factor activity [Term] id: GO:0051092 name: positive regulation of NF-kappaB transcription factor activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB." [GOC:dph, GOC:tb, PMID:15087454, PMID:15170030] synonym: "activation of NF-kappaB" EXACT [] synonym: "activation of NF-kappaB transcription factor" EXACT [GOC:dph, GOC:tb] synonym: "NF-kappaB activation" EXACT [] xref: Reactome:REACT_107873 "TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Rattus norvegicus" xref: Reactome:REACT_113398 "TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Taeniopygia guttata" xref: Reactome:REACT_113766 "TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Drosophila melanogaster" xref: Reactome:REACT_21281 "TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Homo sapiens" xref: Reactome:REACT_31084 "TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Canis familiaris" xref: Reactome:REACT_33907 "TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Danio rerio" xref: Reactome:REACT_34168 "TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Sus scrofa" xref: Reactome:REACT_34256 "TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Bos taurus" xref: Reactome:REACT_87914 "TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Xenopus tropicalis" xref: Reactome:REACT_95400 "TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Mus musculus" is_a: GO:0051091 ! positive regulation of sequence-specific DNA binding transcription factor activity [Term] id: GO:0051123 name: RNA polymerase II transcriptional preinitiation complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase." [GOC:txnOH, PMID:10882737, PMID:15020047] synonym: "RNA polymerase II transcription PIC biosynthesis" EXACT [] synonym: "RNA polymerase II transcription PIC formation" EXACT [] synonym: "RNA polymerase II transcriptional preinitiation complex formation" EXACT [] is_a: GO:0070897 ! DNA-dependent transcriptional preinitiation complex assembly relationship: part_of GO:0006367 ! transcription initiation from RNA polymerase II promoter [Term] id: GO:0051391 name: tRNA acetylation namespace: biological_process def: "The modification of tRNA structure by addition of an acetyl group to tRNA. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid." [GOC:ai] is_a: GO:0006400 ! tRNA modification [Term] id: GO:0051604 name: protein maturation namespace: biological_process def: "Any process leading to the attainment of the full functional capacity of a protein." [GOC:ai] subset: goslim_generic subset: goslim_pir subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok relationship: part_of GO:0010467 ! gene expression [Term] id: GO:0051718 name: DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + CpG (in DNA) = S-adenosyl-L-homocysteine + 5-MeCpG (in DNA)." [EC:2.1.1.37, PMID:15689527] synonym: "HpaII methylase" NARROW [EC:2.1.1.37] synonym: "HpaII' methylase" NARROW [EC:2.1.1.37] synonym: "M.BsuRIa" NARROW [EC:2.1.1.37] synonym: "M.BsuRIb" NARROW [EC:2.1.1.37] is_a: GO:0003886 ! DNA (cytosine-5-)-methyltransferase activity [Term] id: GO:0051719 name: DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + DNA containing CpN = S-adenosyl-L-homocysteine + DNA containing 5-MeCpN." [EC:2.1.1.37, PMID:15689527] is_a: GO:0003886 ! DNA (cytosine-5-)-methyltransferase activity [Term] id: GO:0051720 name: DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + DNA containing CpNpG = S-adenosyl-L-homocysteine + DNA containing 5-MeCpNpG." [EC:2.1.1.37, PMID:15689527] is_a: GO:0003886 ! DNA (cytosine-5-)-methyltransferase activity [Term] id: GO:0051747 name: cytosine C-5 DNA demethylase activity namespace: molecular_function def: "Catalysis of the reaction: methyl-dCpdG DNA + H2O = dCpdG DNA + methanol. This reaction is the hydrolytic removal of the methyl group on the 5 position of cytosine in DNA." [PMID:10050851] synonym: "DNA demethylase activity" BROAD [PMID:10050851] synonym: "DNA methyltransferase activity acting on cytosine C-5" EXACT [] synonym: "hydrolytic DNA demethylase activity" BROAD [] is_a: GO:0035514 ! DNA demethylase activity [Term] id: GO:0052665 name: tRNA (uracil-2'-O-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing 2'-O-methyluracil." [EC:2.1.1.34] subset: gosubset_prok synonym: "S-adenosyl-L-methionine:tRNA (uracil-2'-O-)-methyltransferase activity" EXACT [EC:2.1.1.34] synonym: "S-adenosyl-L-methionine:tRNA uracil-2'-O-methyltransferase activity" EXACT [EC:2.1.1.34] synonym: "transfer ribonucleate uracil 2'-methyltransferase activity" EXACT [EC:2.1.1.34] synonym: "tRNA (uracil 2')-methyltransferase activity" EXACT [EC:2.1.1.34] synonym: "tRNA uracil 2'-methyltransferase activity" EXACT [EC:2.1.1.34] synonym: "tRNA uracil-2'-O-methyltransferase activity" EXACT [EC:2.1.1.34] xref: EC:2.1.1.- xref: MetaCyc:RXN0-5143 is_a: GO:0016300 ! tRNA (uracil) methyltransferase activity created_by: gwg creation_date: 2010-10-11T01:05:35Z [Term] id: GO:0052666 name: tRNA (cytosine-2'-O-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing 2'-O-methylcytosine." [EC:2.1.1.34] subset: gosubset_prok synonym: "S-adenosyl-L-methionine:tRNA (cytosine-2'-O-)-methyltransferase activity" EXACT [EC:2.1.1.34] synonym: "S-adenosyl-L-methionine:tRNA cytosine-2'-O-methyltransferase activity" EXACT [EC:2.1.1.34] synonym: "transfer ribonucleate cytosine 2'-methyltransferase activity" EXACT [EC:2.1.1.34] synonym: "tRNA (cytosine 2')-methyltransferase activity" EXACT [EC:2.1.1.34] synonym: "tRNA cytosine 2'-methyltransferase activity" EXACT [EC:2.1.1.34] synonym: "tRNA cytosine-2'-O-methyltransferase activity" EXACT [EC:2.1.1.34] xref: EC:2.1.1.- xref: MetaCyc:RXN0-5143 is_a: GO:0016427 ! tRNA (cytosine) methyltransferase activity created_by: gwg creation_date: 2010-10-11T01:05:47Z [Term] id: GO:0052735 name: tRNA (cytosine-3-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing 3-methylcytosine." [PMID:21518804, PMID:21518805] synonym: "S-adenosyl-L-methionine:tRNA (cytosine-3-)-methyltransferase activity" EXACT [] synonym: "S-adenosyl-L-methionine:tRNA cytosine-3-methyltransferase activity" EXACT [] synonym: "transfer ribonucleate cytosine 3-methyltransferase activity" EXACT [] synonym: "tRNA (cytosine 3)-methyltransferase activity" EXACT [] synonym: "tRNA cytosine 3-methyltransferase activity" EXACT [] synonym: "tRNA cytosine-3-methyltransferase activity" EXACT [] xref: EC:2.1.1.- is_a: GO:0016427 ! tRNA (cytosine) methyltransferase activity [Term] id: GO:0052905 name: tRNA (guanine(9)-N(1))-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + guanine(9) in tRNA = N(1)-methylguanine(9) in tRNA + S-adenosyl-L-homocysteine." [EC:2.1.1.221] synonym: "tRNA (guanine-N(1)-)-methyltransferase activity" EXACT [EC:2.1.1.221] synonym: "tRNA m(1)G(9) Mtase activity" EXACT [EC:2.1.1.221] synonym: "tRNA m(1)G(9)-methyltransferase activity" EXACT [EC:2.1.1.221] synonym: "tRNA(m(1)G(9)/m(1)A(9))-methyltransferase activity" EXACT [EC:2.1.1.221] synonym: "tRNA(m(1)G(9)/m(1)A(9))Mtase activity" EXACT [EC:2.1.1.221] xref: EC:2.1.1.221 xref: MetaCyc:RXN-12459 is_a: GO:0009019 ! tRNA (guanine-N1-)-methyltransferase activity [Term] id: GO:0052906 name: tRNA (guanine(37)-N(1))-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + guanine(37) in tRNA = N(1)-methylguanine(37) in tRNA + S-adenosyl-L-homocysteine." [EC:2.1.1.228] synonym: "transfer RNA (m(1)G(37)) methyltransferase activity" EXACT [EC:2.1.1.228] synonym: "tRNA (m(1)G(37)) methyltransferase activity" EXACT [EC:2.1.1.228] synonym: "tRNA-(N(1)G37) methyltransferase activity" EXACT [EC:2.1.1.228] xref: EC:2.1.1.228 xref: MetaCyc:RXN-12458 is_a: GO:0009019 ! tRNA (guanine-N1-)-methyltransferase activity [Term] id: GO:0052907 name: 23S rRNA (adenine(1618)-N(6))-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + adenine(1618) in 23S rRNA = S-adenosyl-L-homocysteine + rRNA containing N(6)-methyladenine(1618) in 23S rRNA." [EC:2.1.1.181] synonym: "M(6)A(1618) activity" BROAD [EC:2.1.1.181] synonym: "rRNA large subunit methyltransferase F activity" RELATED [EC:2.1.1.181] xref: EC:2.1.1.181 xref: KEGG:R07232 xref: MetaCyc:RXN-11596 is_a: GO:0008988 ! rRNA (adenine-N6-)-methyltransferase activity [Term] id: GO:0052908 name: 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: 4 S-adenosyl-L-methionine + adenine(1518)/adenine(1519) in 16S rRNA = 4 S-adenosyl-L-homocysteine + N(6)-dimethyladenine(1518)/N(6)-dimethyladenine(1519) in 16S rRNA." [EC:2.1.1.182] synonym: "S-adenosylmethionine-6-N',N'-adenosyl (rRNA) dimethyltransferase activity" EXACT [EC:2.1.1.182] xref: EC:2.1.1.182 xref: MetaCyc:RXN-11633 is_a: GO:0008988 ! rRNA (adenine-N6-)-methyltransferase activity [Term] id: GO:0052909 name: 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: 4 S-adenosyl-L-methionine + adenine(1779)/adenine(1780) in 18S rRNA = 4 S-adenosyl-L-homocysteine + N(6)-dimethyladenine(1779)/N(6)-dimethyladenine(1780) in 18S rRNA." [EC:2.1.1.183] synonym: "M(6)(2)A dimethylase activity" BROAD [EC:2.1.1.183] xref: EC:2.1.1.183 xref: MetaCyc:RXN-11634 is_a: GO:0008988 ! rRNA (adenine-N6-)-methyltransferase activity [Term] id: GO:0052910 name: 23S rRNA (adenine(2085)-N(6))-dimethyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: 2 S-adenosyl-L-methionine + adenine(2085) in 23S rRNA = 2 S-adenosyl-L-homocysteine + N(6)-dimethyladenine(2085) in 23S rRNA." [EC:2.1.1.184] synonym: "ermC 23S rRNA methyltransferase activity" RELATED [EC:2.1.1.184] synonym: "rRNA methyltransferase ermC' activity" RELATED [EC:2.1.1.184] synonym: "rRNA:m(6)A methyltransferase ermC' activity" RELATED [EC:2.1.1.184] xref: EC:2.1.1.184 xref: MetaCyc:RXN-11597 is_a: GO:0008988 ! rRNA (adenine-N6-)-methyltransferase activity [Term] id: GO:0052911 name: 23S rRNA (guanine(745)-N(1))-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + guanine(745) in 23S rRNA = N(1)-methylguanine(745) in 23S rRNA + S-adenosyl-L-homocysteine." [EC:2.1.1.187] synonym: "23S rRNA m(1)G(745) methyltransferase activity" EXACT [EC:2.1.1.187] synonym: "ribosomal ribonucleate guanine 1-methyltransferase activity" BROAD [EC:2.1.1.187] synonym: "ribosomal RNA(m(1)G)-methylase activity" BROAD [EC:2.1.1.187] synonym: "rlmA(I) methyltransferase activity" BROAD [EC:2.1.1.187] synonym: "rRNA(m(1)G)methylase activity" BROAD [EC:2.1.1.187] synonym: "S-adenosyl-L-methionine:rRNA (guanine-1-N-)-methyltransferase activity" BROAD [EC:2.1.1.187] xref: EC:2.1.1.187 xref: KEGG:R07233 xref: MetaCyc:RXN-11573 is_a: GO:0008989 ! rRNA (guanine-N1-)-methyltransferase activity [Term] id: GO:0052912 name: 23S rRNA (guanine(748)-N(1))-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + guanine(748) in 23S rRNA = N(1)-methylguanine(748) in 23S rRNA + S-adenosyl-L-homocysteine." [EC:2.1.1.188] synonym: "23S rRNA m(1)G(748) methyltransferase activity" BROAD [EC:2.1.1.188] xref: EC:2.1.1.188 xref: KEGG:R07233 xref: MetaCyc:RXN-11599 is_a: GO:0008989 ! rRNA (guanine-N1-)-methyltransferase activity [Term] id: GO:0052913 name: 16S rRNA (guanine(966)-N(2))-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + guanosine(966) in 16S rRNA = N(2)-methylguanosine(966) in 16S rRNA + S-adenosyl-L-homocysteine." [EC:2.1.1.171] xref: EC:2.1.1.171 xref: KEGG:R07234 xref: MetaCyc:RXN0-6515 is_a: GO:0008990 ! rRNA (guanine-N2-)-methyltransferase activity [Term] id: GO:0052914 name: 16S rRNA (guanine(1207)-N(2))-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + guanosine(1207) in 16S rRNA = N(2)-methylguanosine(1207) in 16S rRNA + S-adenosyl-L-homocysteine." [EC:2.1.1.172] synonym: "M(2)G1207 methyltransferase activity" EXACT [EC:2.1.1.172] xref: EC:2.1.1.172 xref: KEGG:R07234 xref: MetaCyc:RXN-11576 is_a: GO:0008990 ! rRNA (guanine-N2-)-methyltransferase activity [Term] id: GO:0052915 name: 23S rRNA (guanine(2445)-N(2))-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + guanosine(2445) in 23S rRNA = N(2)-methylguanosine(2445) in 23S rRNA + S-adenosyl-L-homocysteine." [EC:2.1.1.173] xref: EC:2.1.1.173 xref: KEGG:R07234 xref: MetaCyc:RXN-11574 is_a: GO:0008990 ! rRNA (guanine-N2-)-methyltransferase activity [Term] id: GO:0052916 name: 23S rRNA (guanine(1835)-N(2))-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + guanosine(1835) in 23S rRNA = N(2)-methylguanosine(1835) in 23S rRNA + S-adenosyl-L-homocysteine." [EC:2.1.1.174] xref: EC:2.1.1.174 xref: KEGG:R07234 xref: MetaCyc:RXN-11635 is_a: GO:0008990 ! rRNA (guanine-N2-)-methyltransferase activity [Term] id: GO:0060053 name: neurofilament cytoskeleton namespace: cellular_component def: "Intermediate filament cytoskeletal structure that is made up of neurofilaments. Neurofilaments are specialized intermediate filaments found in neurons." [GOC:dph] is_a: GO:0097458 ! neuron part [Term] id: GO:0060145 name: viral gene silencing in virus induced gene silencing namespace: biological_process def: "The posttranscriptional gene silencing of viral genes after viral infection." [GOC:dph] is_a: GO:0016441 ! posttranscriptional gene silencing [Term] id: GO:0060146 name: host gene silencing in virus induced gene silencing namespace: biological_process def: "The posttranscriptional gene silencing of host genes that are homologous to viral genes after viral infection." [GOC:dph] is_a: GO:0016441 ! posttranscriptional gene silencing [Term] id: GO:0060147 name: regulation of posttranscriptional gene silencing namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism." [GOC:dph] is_a: GO:0060968 ! regulation of gene silencing intersection_of: regulates GO:0016441 ! posttranscriptional gene silencing relationship: regulates GO:0016441 ! posttranscriptional gene silencing [Term] id: GO:0060148 name: positive regulation of posttranscriptional gene silencing namespace: biological_process def: "Any process that increases the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism." [GOC:dph] is_a: GO:0060147 ! regulation of posttranscriptional gene silencing intersection_of: positively_regulates GO:0016441 ! posttranscriptional gene silencing relationship: positively_regulates GO:0016441 ! posttranscriptional gene silencing [Term] id: GO:0060149 name: negative regulation of posttranscriptional gene silencing namespace: biological_process def: "Any process that decreases the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism." [GOC:dph] is_a: GO:0060147 ! regulation of posttranscriptional gene silencing is_a: GO:0060969 ! negative regulation of gene silencing intersection_of: negatively_regulates GO:0016441 ! posttranscriptional gene silencing relationship: negatively_regulates GO:0016441 ! posttranscriptional gene silencing [Term] id: GO:0060150 name: viral triggering of virus induced gene silencing namespace: biological_process def: "Any process that increases the frequency, rate or extent of the inactivation of gene expression of both viral genes and host homologues to those genes by a posttranscriptional mechanism in a virally infected cell." [GOC:dph] is_a: GO:0060148 ! positive regulation of posttranscriptional gene silencing [Term] id: GO:0060194 name: regulation of antisense RNA transcription namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the synthesis of antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis, on a template of DNA." [GOC:dph, GOC:jp, GOC:tb, PMID:18075583] is_a: GO:0006355 ! regulation of transcription, DNA-dependent intersection_of: regulates GO:0009300 ! antisense RNA transcription relationship: regulates GO:0009300 ! antisense RNA transcription [Term] id: GO:0060195 name: negative regulation of antisense RNA transcription namespace: biological_process def: "Any process that decreases the frequency, rate or extent of the synthesis of antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis, on a template of DNA." [GOC:dph, GOC:tb, PMID:18075583] is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent is_a: GO:0060194 ! regulation of antisense RNA transcription intersection_of: negatively_regulates GO:0009300 ! antisense RNA transcription relationship: negatively_regulates GO:0009300 ! antisense RNA transcription [Term] id: GO:0060196 name: positive regulation of antisense RNA transcription namespace: biological_process def: "Any process that increases the frequency, rate or extent of the synthesis of antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis, on a template of DNA." [GOC:dph, GOC:tb, PMID:18075583] is_a: GO:0045893 ! positive regulation of transcription, DNA-dependent is_a: GO:0060194 ! regulation of antisense RNA transcription intersection_of: positively_regulates GO:0009300 ! antisense RNA transcription relationship: positively_regulates GO:0009300 ! antisense RNA transcription [Term] id: GO:0060211 name: regulation of nuclear-transcribed mRNA poly(A) tail shortening namespace: biological_process def: "Any process that modulates the frequency, rate or extent of poly(A) tail shortening of a nuclear-transcribed mRNA. Poly(A) tail shortening is the decrease in length of the poly(A) tail of an mRNA from full length to an oligo(A) length." [GOC:dph, GOC:tb] synonym: "regulation of 3' to 5' mRNA deadenylation" RELATED [] synonym: "regulation of mRNA deadenylation" RELATED [] synonym: "regulation of nuclear mRNA poly(A) tail shortening" RELATED [] is_a: GO:0031440 ! regulation of mRNA 3'-end processing intersection_of: regulates GO:0000289 ! nuclear-transcribed mRNA poly(A) tail shortening relationship: regulates GO:0000289 ! nuclear-transcribed mRNA poly(A) tail shortening [Term] id: GO:0060212 name: negative regulation of nuclear-transcribed mRNA poly(A) tail shortening namespace: biological_process def: "Any process that decreases the frequency, rate or extent of poly(A) tail shortening of a nuclear-transcribed mRNA. Poly(A) tail shortening is the decrease in length of the poly(A) tail of an mRNA from full length to an oligo(A) length." [GOC:dph, GOC:tb] synonym: "negative regulation of 3' to 5' mRNA deadenylation" RELATED [GOC:dph, GOC:tb] synonym: "negative regulation of mRNA deadenylation" RELATED [GOC:dph, GOC:tb] synonym: "negative regulation of nuclear mRNA poly(A) tail shortening" RELATED [] is_a: GO:0031441 ! negative regulation of mRNA 3'-end processing is_a: GO:0060211 ! regulation of nuclear-transcribed mRNA poly(A) tail shortening intersection_of: negatively_regulates GO:0000289 ! nuclear-transcribed mRNA poly(A) tail shortening relationship: negatively_regulates GO:0000289 ! nuclear-transcribed mRNA poly(A) tail shortening [Term] id: GO:0060213 name: positive regulation of nuclear-transcribed mRNA poly(A) tail shortening namespace: biological_process def: "Any process that increases the frequency, rate or extent of poly(A) tail shortening of a nuclear-transcribed mRNA. Poly(A) tail shortening is the decrease in length of the poly(A) tail of an mRNA from full length to an oligo(A) length." [GOC:dph, GOC:tb] synonym: "positive regulation of 3' to 5' mRNA deadenylation" RELATED [GOC:dph, GOC:tb] synonym: "positive regulation of mRNA deadenylation" RELATED [GOC:dph, GOC:tb] synonym: "positive regulation of nuclear mRNA poly(A) tail shortening" RELATED [] is_a: GO:0031442 ! positive regulation of mRNA 3'-end processing is_a: GO:0060211 ! regulation of nuclear-transcribed mRNA poly(A) tail shortening intersection_of: positively_regulates GO:0000289 ! nuclear-transcribed mRNA poly(A) tail shortening relationship: positively_regulates GO:0000289 ! nuclear-transcribed mRNA poly(A) tail shortening [Term] id: GO:0060260 name: regulation of transcription initiation from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter." [GOC:dph, GOC:tb, GOC:txnOH] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter is_a: GO:2000142 ! regulation of DNA-dependent transcription, initiation intersection_of: regulates GO:0006367 ! transcription initiation from RNA polymerase II promoter relationship: regulates GO:0006367 ! transcription initiation from RNA polymerase II promoter [Term] id: GO:0060261 name: positive regulation of transcription initiation from RNA polymerase II promoter namespace: biological_process def: "Any process that increases the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter." [GOC:dph, GOC:tb, GOC:txnOH] is_a: GO:0060260 ! regulation of transcription initiation from RNA polymerase II promoter is_a: GO:2000144 ! positive regulation of DNA-dependent transcription, initiation intersection_of: positively_regulates GO:0006367 ! transcription initiation from RNA polymerase II promoter relationship: positively_regulates GO:0006367 ! transcription initiation from RNA polymerase II promoter [Term] id: GO:0060342 name: photoreceptor inner segment membrane namespace: cellular_component def: "The membrane surrounding the outer segment of a vertebrate photoreceptor. The photoreceptor inner segment contains mitochondria, ribosomes and membranes where opsin molecules are assembled and passed to be part of the outer segment discs." [GOC:dph] is_a: GO:0097458 ! neuron part relationship: part_of GO:0001917 ! photoreceptor inner segment [Term] id: GO:0060469 name: positive regulation of transcription involved in egg activation namespace: biological_process def: "Any process that increases the rate, frequency or extent of transcription as a part of the process of egg activation." [GOC:dph] synonym: "activation of the egg genome" RELATED [GOC:dph] synonym: "activation of the maternal genome" RELATED [GOC:dph] is_a: GO:0045893 ! positive regulation of transcription, DNA-dependent intersection_of: GO:0045893 ! positive regulation of transcription, DNA-dependent [Term] id: GO:0060500 name: regulation of transcription from RNA polymerase II promoter involved in lung bud formation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the branching morphogenesis by which the initial primordium of the lung is formed." [GOC:dph, GOC:mtg_lung] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter [Term] id: GO:0060566 name: positive regulation of DNA-dependent transcription, termination namespace: biological_process def: "Any process that increases the rate, frequency or extent of DNA-dependent transcription termination, the process in which transcription is completed; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA." [GOC:dph, GOC:tb, GOC:txnOH] synonym: "positive regulation of termination of DNA-dependent transcription " EXACT [GOC:jh2] synonym: "positive regulation of transcription termination, DNA-dependent" EXACT [GOC:jh2] is_a: GO:0031554 ! regulation of DNA-dependent transcription, termination is_a: GO:0045893 ! positive regulation of transcription, DNA-dependent intersection_of: positively_regulates GO:0006353 ! DNA-dependent transcription, termination relationship: positively_regulates GO:0006353 ! DNA-dependent transcription, termination created_by: dph creation_date: 2009-04-29T02:54:50Z [Term] id: GO:0060567 name: negative regulation of DNA-dependent transcription, termination namespace: biological_process def: "Any process that decreases the rate, frequency or extent of DNA-dependent transcription termination, the process in which transcription is completed; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA." [GOC:dph, GOC:tb, GOC:txnOH] synonym: "negative regulation of termination of DNA-dependent transcription " EXACT [GOC:jh2] synonym: "negative regulation of transcription termination, DNA-dependent" EXACT [GOC:jh2] is_a: GO:0031554 ! regulation of DNA-dependent transcription, termination is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent intersection_of: negatively_regulates GO:0006353 ! DNA-dependent transcription, termination relationship: negatively_regulates GO:0006353 ! DNA-dependent transcription, termination created_by: dph creation_date: 2009-04-29T02:59:12Z [Term] id: GO:0060568 name: regulation of peptide hormone processing namespace: biological_process def: "Any process that modulates the rate, frequency or extent of peptide hormone processing. Peptide hormone processing is the generation of a mature peptide hormone by posttranslational processing of a prohormone." [GOC:dph, GOC:tb] is_a: GO:0070613 ! regulation of protein processing intersection_of: regulates GO:0016486 ! peptide hormone processing relationship: regulates GO:0016486 ! peptide hormone processing created_by: dph creation_date: 2009-04-29T03:16:05Z [Term] id: GO:0060569 name: positive regulation of peptide hormone processing namespace: biological_process def: "Any process that increases the rate, frequency or extent of peptide hormone processing. Peptide hormone processing is the generation of a mature peptide hormone by posttranslational processing of a prohormone." [GOC:dph, GOC:tb] is_a: GO:0010954 ! positive regulation of protein processing is_a: GO:0060568 ! regulation of peptide hormone processing intersection_of: positively_regulates GO:0016486 ! peptide hormone processing relationship: positively_regulates GO:0016486 ! peptide hormone processing created_by: dph creation_date: 2009-04-29T03:22:05Z [Term] id: GO:0060570 name: negative regulation of peptide hormone processing namespace: biological_process def: "Any process that decreases the rate, frequency or extent of peptide hormone processing. Peptide hormone processing is the generation of a mature peptide hormone by posttranslational processing of a prohormone." [GOC:dph, GOC:tb] is_a: GO:0010955 ! negative regulation of protein processing is_a: GO:0060568 ! regulation of peptide hormone processing intersection_of: negatively_regulates GO:0016486 ! peptide hormone processing relationship: negatively_regulates GO:0016486 ! peptide hormone processing created_by: dph creation_date: 2009-04-29T03:24:55Z [Term] id: GO:0060597 name: regulation of transcription from RNA polymerase II promoter involved in mammary gland formation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the formation of the mammary line, placode or bud." [GOC:dph, PMID:16168142] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2009-05-13T12:04:53Z [Term] id: GO:0060633 name: negative regulation of transcription initiation from RNA polymerase II promoter namespace: biological_process def: "Any process that decreases the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter." [GOC:dph, GOC:tb, GOC:txnOH] is_a: GO:0060260 ! regulation of transcription initiation from RNA polymerase II promoter is_a: GO:2000143 ! negative regulation of DNA-dependent transcription, initiation intersection_of: negatively_regulates GO:0006367 ! transcription initiation from RNA polymerase II promoter relationship: negatively_regulates GO:0006367 ! transcription initiation from RNA polymerase II promoter created_by: dph creation_date: 2009-05-18T03:11:26Z [Term] id: GO:0060733 name: regulation of eIF2 alpha phosphorylation by amino acid starvation namespace: biological_process def: "Any process that modulates the rate, frequency, or extent of eIF2 alpha phosphorylation as a cellular response to amino acid starvation." [GOC:dph, GOC:tb] relationship: regulates GO:0010998 ! regulation of translational initiation by eIF2 alpha phosphorylation created_by: dph creation_date: 2009-06-12T02:08:50Z [Term] id: GO:0060734 name: regulation of eIF2 alpha phosphorylation by endoplasmic reticulum stress namespace: biological_process def: "Any process that modulates the rate, frequency, or extent of eIF2 alpha phosphorylation as a cellular response to endoplasmic reticulum stress." [GOC:dph, GOC:tb] synonym: "regulation of eIF2 alpha phosphorylation by ER stress" EXACT [GOC:dph, GOC:tb] relationship: regulates GO:0010998 ! regulation of translational initiation by eIF2 alpha phosphorylation created_by: dph creation_date: 2009-06-12T02:15:16Z [Term] id: GO:0060735 name: regulation of eIF2 alpha phosphorylation by dsRNA namespace: biological_process def: "Any process that modulates the rate, frequency, or extent of eIF2 alpha phosphorylation as a cellular response to double-stranded RNA." [GOC:dph, GOC:tb] synonym: "regulation of eIF2 alpha phosphorylation by double-stranded RNA" EXACT [GOC:dph] synonym: "regulation of eIF2 alpha phosphorylation by PKR" NARROW [GOC:dph, GOC:tb] relationship: regulates GO:0010998 ! regulation of translational initiation by eIF2 alpha phosphorylation created_by: dph creation_date: 2009-06-12T02:27:14Z [Term] id: GO:0060796 name: regulation of transcription involved in primary germ layer cell fate commitment namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that results in cells adopting an endoderm, ectoderm or mesoderm cell fate." [GOC:dph, GOC:sdb_2009, GOC:tb] is_a: GO:0060850 ! regulation of transcription involved in cell fate commitment intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2009-08-04T03:40:21Z [Term] id: GO:0060803 name: BMP signaling pathway involved in mesodermal cell fate specification namespace: biological_process def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to a cell becoming specified to adopt a mesodermal fate." [GOC:dph, GOC:sdb_2009, GOC:tb] synonym: "BMP signalling pathway involved in mesodermal cell fate specification" EXACT [GOC:mah] is_a: GO:0030509 ! BMP signaling pathway is_a: GO:0060796 ! regulation of transcription involved in primary germ layer cell fate commitment intersection_of: GO:0030509 ! BMP signaling pathway created_by: dph creation_date: 2009-08-06T01:47:39Z [Term] id: GO:0060804 name: positive regulation of Wnt receptor signaling pathway by BMP signaling pathway namespace: biological_process def: "A series of molecular signals generated as a consequence of any member of the BMP (bone morphogenetic protein) family binding to a cell surface receptor that results in an increase in the rate, frequency or extent of a Wnt receptor signaling pathway." [GOC:dph, GOC:sdb_2009, GOC:tb] synonym: "positive regulation of WNT receptor signaling pathway by BMP signaling pathway" EXACT [GOC:bf] synonym: "positive regulation of WNT receptor signalling pathway by BMP signalling pathway" EXACT [GOC:mah] is_a: GO:0030509 ! BMP signaling pathway intersection_of: GO:0030509 ! BMP signaling pathway created_by: dph creation_date: 2009-08-06T01:52:48Z [Term] id: GO:0060807 name: regulation of transcription from RNA polymerase II promoter involved in definitive endodermal cell fate specification namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that ultimately results in a cell being specified to adopt a definitive endodermal cell fate." [GOC:dph, GOC:sdb_2009, GOC:tb] is_a: GO:0060796 ! regulation of transcription involved in primary germ layer cell fate commitment created_by: dph creation_date: 2009-08-06T02:14:09Z [Term] id: GO:0060815 name: regulation of translation involved in anterior/posterior axis specification namespace: biological_process def: "Any process that modulates the frequency, rate or extent of translation of mRNAs that contribute to the specification of the anterior/posterior axis." [GOC:dph, GOC:sdb_2009, GOC:tb] is_a: GO:0006417 ! regulation of translation intersection_of: GO:0006417 ! regulation of translation created_by: dph creation_date: 2009-08-07T10:02:31Z [Term] id: GO:0060816 name: random inactivation of X chromosome namespace: biological_process def: "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on either the paternal or maternal X-chromosome in the XX sex." [GOC:dph, GOC:sdb_2009, GOC:tb] is_a: GO:0009048 ! dosage compensation by inactivation of X chromosome created_by: dph creation_date: 2009-08-11T10:47:30Z [Term] id: GO:0060817 name: inactivation of paternal X chromosome namespace: biological_process def: "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes specifically on the paternal X-chromosome in the XX sex." [GOC:dph, GOC:sdb_2009, GOC:tb] is_a: GO:0009048 ! dosage compensation by inactivation of X chromosome created_by: dph creation_date: 2009-08-11T10:50:20Z [Term] id: GO:0060818 name: inactivation of paternal X chromosome by genetic imprinting namespace: biological_process def: "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on the paternal X-chromosome in the XX sex by genetic imprinting." [GOC:dph, GOC:sdb_2009, GOC:tb] is_a: GO:0060817 ! inactivation of paternal X chromosome is_a: GO:0060819 ! inactivation of X chromosome by genetic imprinting created_by: dph creation_date: 2009-08-11T10:52:31Z [Term] id: GO:0060819 name: inactivation of X chromosome by genetic imprinting namespace: biological_process def: "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex by genetic imprinting." [GOC:dph, GOC:sdb_2009, GOC:tb] is_a: GO:0006349 ! regulation of gene expression by genetic imprinting is_a: GO:0009048 ! dosage compensation by inactivation of X chromosome created_by: dph creation_date: 2009-08-11T10:56:06Z [Term] id: GO:0060820 name: inactivation of X chromosome by heterochromatin assembly namespace: biological_process def: "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex by the mechanism of heterochromatin formation." [GOC:dph, GOC:sdb_2009, GOC:tb] synonym: "inactivation of X chromosome by heterochromatin formation" EXACT [] is_a: GO:0009048 ! dosage compensation by inactivation of X chromosome created_by: dph creation_date: 2009-08-11T10:58:06Z [Term] id: GO:0060821 name: inactivation of X chromosome by DNA methylation namespace: biological_process def: "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex by a mechanism of DNA methylation." [GOC:dph, GOC:sdb_2009, GOC:tb] is_a: GO:0009048 ! dosage compensation by inactivation of X chromosome created_by: dph creation_date: 2009-08-11T11:02:19Z [Term] id: GO:0060849 name: regulation of transcription involved in lymphatic endothelial cell fate commitment namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the commitment of a venous endothelial cell to a lymphatic endothelial cell." [GOC:dph, GOC:sdb_2009, GOC:tb] is_a: GO:0060850 ! regulation of transcription involved in cell fate commitment intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2009-08-12T11:19:14Z [Term] id: GO:0060850 name: regulation of transcription involved in cell fate commitment namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the commitment of a cell to a specific fate." [GOC:dph, GOC:sdb_2009, GOC:tb] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2009-08-12T11:40:09Z [Term] id: GO:0060852 name: regulation of transcription involved in venous endothelial cell fate commitment namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the commitment of a cell to a specific fate and contributes to a cell adopting a venous endothelial cell fate." [GOC:dph, GOC:sdb_2009, GOC:tb] is_a: GO:0060850 ! regulation of transcription involved in cell fate commitment intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2009-08-12T11:49:49Z [Term] id: GO:0060899 name: regulation of transcription involved in eye field cell fate commitment of camera-type eye namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the commitment of a neurectodermal cell to a specialized neurectodermal cell that will give rise to the optic vesicle." [GOC:dph, GOC:sdb_2009, GOC:tb] is_a: GO:0060850 ! regulation of transcription involved in cell fate commitment intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2009-08-13T02:11:48Z [Term] id: GO:0060902 name: regulation of hair cycle by BMP signaling pathway namespace: biological_process def: "A series of molecular signals generated as a consequence of any member of the BMP (bone morphogenetic protein) family binding to a cell surface receptor that modulates the rate, frequency or extent of the hair cycle." [GOC:dph, GOC:sdb_2009, GOC:tb] synonym: "regulation of hair cycle by BMP signalling pathway" EXACT [GOC:mah] is_a: GO:0030509 ! BMP signaling pathway intersection_of: GO:0030509 ! BMP signaling pathway created_by: dph creation_date: 2009-08-13T02:45:12Z [Term] id: GO:0060906 name: negative regulation of chromatin silencing by small RNA namespace: biological_process def: "Any process that decreases the frequency, rate or extent of chromatin silencing by small RNA. Chromatin silencing by small RNA is the repression of transcription by conversion of large regions of DNA into heterochromatin, directed by small RNAs sharing sequence identity to the repressed region." [GOC:dph, GOC:tb] is_a: GO:0010964 ! regulation of chromatin silencing by small RNA is_a: GO:0031936 ! negative regulation of chromatin silencing is_a: GO:0060967 ! negative regulation of gene silencing by RNA intersection_of: negatively_regulates GO:0031048 ! chromatin silencing by small RNA relationship: negatively_regulates GO:0031048 ! chromatin silencing by small RNA created_by: dph creation_date: 2009-08-14T01:22:24Z [Term] id: GO:0060962 name: regulation of ribosomal protein gene transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the synthesis of RNA from ribosomal protein genes by RNA polymerase II, originating at an RNA polymerase II promoter." [GOC:dph, GOC:tb, GOC:txnOH] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2009-10-05T03:00:40Z [Term] id: GO:0060963 name: positive regulation of ribosomal protein gene transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that increases the frequency, rate or extent of the synthesis of RNA from ribosomal protein genes by RNA polymerase II, originating at an RNA polymerase II promoter." [GOC:dph, GOC:tb, GOC:txnOH] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter is_a: GO:0060962 ! regulation of ribosomal protein gene transcription from RNA polymerase II promoter created_by: dph creation_date: 2009-10-05T03:04:05Z [Term] id: GO:0060964 name: regulation of gene silencing by miRNA namespace: biological_process def: "Any process that modulates the rate, frequency, or extent of the downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: mRNA cleavage or translational repression." [GOC:dph, GOC:tb] synonym: "regulation of gene silencing by microRNA" EXACT [GOC:pr] is_a: GO:0060147 ! regulation of posttranscriptional gene silencing is_a: GO:0060966 ! regulation of gene silencing by RNA intersection_of: regulates GO:0035195 ! gene silencing by miRNA relationship: regulates GO:0035195 ! gene silencing by miRNA created_by: dph creation_date: 2009-10-05T03:10:28Z [Term] id: GO:0060965 name: negative regulation of gene silencing by miRNA namespace: biological_process def: "Any process that decreases the rate, frequency, or extent of the downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: mRNA cleavage or translational repression." [GOC:dph, GOC:tb] synonym: "negative regulation of gene silencing by microRNA" EXACT [GOC:bf, GOC:pr] is_a: GO:0060149 ! negative regulation of posttranscriptional gene silencing is_a: GO:0060964 ! regulation of gene silencing by miRNA is_a: GO:0060967 ! negative regulation of gene silencing by RNA intersection_of: negatively_regulates GO:0035195 ! gene silencing by miRNA relationship: negatively_regulates GO:0035195 ! gene silencing by miRNA created_by: dph creation_date: 2009-10-05T03:14:14Z [Term] id: GO:0060966 name: regulation of gene silencing by RNA namespace: biological_process def: "Any process that regulates the rate, frequency, or extent of gene silencing by RNA. Gene silencing by RNA is the process in which RNA molecules inactivate expression of target genes." [GOC:dph, GOC:tb] is_a: GO:0060968 ! regulation of gene silencing intersection_of: regulates GO:0031047 ! gene silencing by RNA relationship: regulates GO:0031047 ! gene silencing by RNA created_by: dph creation_date: 2009-10-05T03:17:02Z [Term] id: GO:0060967 name: negative regulation of gene silencing by RNA namespace: biological_process def: "Any process that decreases the rate, frequency, or extent of gene silencing by RNA. Gene silencing by RNA is the process in which RNA molecules inactivate expression of target genes." [GOC:dph, GOC:tb] is_a: GO:0060966 ! regulation of gene silencing by RNA is_a: GO:0060969 ! negative regulation of gene silencing intersection_of: negatively_regulates GO:0031047 ! gene silencing by RNA relationship: negatively_regulates GO:0031047 ! gene silencing by RNA created_by: dph creation_date: 2009-10-05T03:21:05Z [Term] id: GO:0060968 name: regulation of gene silencing namespace: biological_process def: "Any process that modulates the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation." [GOC:dph, GOC:tb] intersection_of: regulates GO:0016458 ! gene silencing relationship: regulates GO:0016458 ! gene silencing created_by: dph creation_date: 2009-10-05T03:23:56Z [Term] id: GO:0060969 name: negative regulation of gene silencing namespace: biological_process def: "Any process that decreases the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation." [GOC:dph, GOC:tb] is_a: GO:0060968 ! regulation of gene silencing intersection_of: negatively_regulates GO:0016458 ! gene silencing relationship: negatively_regulates GO:0016458 ! gene silencing created_by: dph creation_date: 2009-10-05T03:26:19Z [Term] id: GO:0060994 name: regulation of transcription from RNA polymerase II promoter involved in kidney development namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the branching morphogenesis by which the kidney progresses from its initial formation to the mature state." [GOC:dph, GOC:mtg_kidney_jan10] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2010-01-19T08:24:46Z [Term] id: GO:0061149 name: BMP signaling pathway involved in ureter morphogenesis namespace: biological_process def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the shaping of the ureter. The ureter is a tube that extends from the kidney to the bladder." [GOC:dph, GOC:mtg_kidney_jan10] synonym: "BMP signalling pathway involved in ureter morphogenesis" EXACT [GOC:mah] is_a: GO:0030509 ! BMP signaling pathway intersection_of: GO:0030509 ! BMP signaling pathway created_by: dph creation_date: 2010-06-02T09:11:46Z [Term] id: GO:0061151 name: BMP signaling pathway involved in renal system segmentation namespace: biological_process def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the segmentation of the renal system." [GOC:dph, GOC:yaf] synonym: "BMP signalling pathway involved in renal system segmentation" EXACT [GOC:mah] is_a: GO:0030509 ! BMP signaling pathway intersection_of: GO:0030509 ! BMP signaling pathway created_by: dph creation_date: 2010-06-02T09:29:43Z [Term] id: GO:0061157 name: mRNA destabilization namespace: biological_process def: "Any process that decreases the stability of an mRNA molecule, making it more vulnerable to degradative processes. Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [GOC:dph, GOC:jh] is_a: GO:0043488 ! regulation of mRNA stability is_a: GO:0050779 ! RNA destabilization created_by: dph creation_date: 2010-06-22T08:42:10Z [Term] id: GO:0061158 name: 3'-UTR-mediated mRNA destabilization namespace: biological_process def: "An mRNA destabilization process in which one or more RNA-binding proteins associate with the 3'-untranslated region (UTR) of an mRNA." [GOC:dph, GOC:jh] is_a: GO:0061157 ! mRNA destabilization created_by: dph creation_date: 2010-06-22T08:44:39Z [Term] id: GO:0061174 name: type I terminal bouton namespace: cellular_component def: "Terminal inflated portion of the axon of a glutamatergic neuron, containing the specialized apparatus necessary to release neurotransmitters that will induce the contraction of muscle. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it." [GOC:dph, GOC:mc] synonym: "type I terminal button" EXACT [GOC:dph] is_a: GO:0043195 ! terminal bouton created_by: dph creation_date: 2010-07-13T09:13:05Z [Term] id: GO:0061175 name: type II terminal bouton namespace: cellular_component def: "Terminal inflated portion of the axon of a non-glutamatergic neuron, containing the specialized apparatus necessary to release neurotransmitters at a regulatory synapse. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it." [GOC:dph, GOC:mc] synonym: "type II terminal button" EXACT [GOC:dph] is_a: GO:0043195 ! terminal bouton created_by: dph creation_date: 2010-07-13T09:18:01Z [Term] id: GO:0061176 name: type Ib terminal bouton namespace: cellular_component def: "Terminal inflated portion of the axon of a glutamatergic neuron, containing the specialized apparatus necessary for the tonic release neurotransmitters that will induce the contraction of muscle. Type Ib terminal boutons are larger than type Is terminal boutons." [GOC:dph, GOC:mc] synonym: "type Ib terminal button" EXACT [GOC:dph] is_a: GO:0061174 ! type I terminal bouton created_by: dph creation_date: 2010-07-13T09:20:04Z [Term] id: GO:0061177 name: type Is terminal bouton namespace: cellular_component def: "Terminal inflated portion of the axon of a glutamatergic neuron, containing the specialized apparatus necessary for the phasic release neurotransmitters that will induce the contraction of muscle. Type Is terminal boutons are smaller than type Ib terminal boutons." [GOC:dph, GOC:mc] synonym: "type Is terminal button" RELATED [GOC:dph] is_a: GO:0061174 ! type I terminal bouton created_by: dph creation_date: 2010-07-13T09:25:15Z [Term] id: GO:0061186 name: negative regulation of chromatin silencing at silent mating-type cassette namespace: biological_process def: "Any process that decreases the frequency, rate, or extent of chromatin silencing at silent mating-type cassette. Chromatin silencing at silent mating-type cassette is the repression of transcription at silent mating-type loci by altering the structure of chromatin." [GOC:dph, PMID:10388812] is_a: GO:0031936 ! negative regulation of chromatin silencing is_a: GO:0090054 ! regulation of chromatin silencing at silent mating-type cassette intersection_of: negatively_regulates GO:0030466 ! chromatin silencing at silent mating-type cassette relationship: negatively_regulates GO:0030466 ! chromatin silencing at silent mating-type cassette created_by: dph creation_date: 2010-07-14T08:59:11Z [Term] id: GO:0061187 name: regulation of chromatin silencing at rDNA namespace: biological_process def: "Any process that modulates the rate, frequency, or extent of the repression of transcription of ribosomal DNA by altering the structure of chromatin." [GOC:dph, PMID:10388812] is_a: GO:0031935 ! regulation of chromatin silencing intersection_of: regulates GO:0000183 ! chromatin silencing at rDNA relationship: regulates GO:0000183 ! chromatin silencing at rDNA created_by: dph creation_date: 2010-07-14T09:04:16Z [Term] id: GO:0061188 name: negative regulation of chromatin silencing at rDNA namespace: biological_process def: "Any process that decreases the rate, frequency, or extent of the repression of transcription of ribosomal DNA by altering the structure of chromatin." [GOC:dph, PMID:10388812] is_a: GO:0031936 ! negative regulation of chromatin silencing is_a: GO:0061187 ! regulation of chromatin silencing at rDNA intersection_of: negatively_regulates GO:0000183 ! chromatin silencing at rDNA relationship: negatively_regulates GO:0000183 ! chromatin silencing at rDNA created_by: dph creation_date: 2010-07-14T09:07:59Z [Term] id: GO:0061216 name: regulation of transcription from RNA polymerase II promoter involved in mesonephros development namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the mesonephros progressing from its initial formation to the mature state." [GOC:mtg_kidney_jan10] is_a: GO:0060994 ! regulation of transcription from RNA polymerase II promoter involved in kidney development intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2010-08-17T03:32:27Z [Term] id: GO:0061312 name: BMP signaling pathway involved in heart development namespace: biological_process def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the progression of the heart over time." [GOC:dph, GOC:mtg_heart] synonym: "BMP signalling pathway involved in heart development" EXACT [GOC:mah] is_a: GO:0030509 ! BMP signaling pathway is_a: GO:1901213 ! regulation of transcription from RNA polymerase II promoter involved in heart development intersection_of: GO:0030509 ! BMP signaling pathway created_by: dph creation_date: 2010-09-23T11:02:14Z [Term] id: GO:0061353 name: BMP signaling pathway involved in Malpighian tubule cell chemotaxis namespace: biological_process def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the directed movement of a Malpighian tubule cell toward a stimulus, thereby contributing to the shaping of the tubule." [GOC:dph, GOC:mtg_kidney_jan10, PMID:19783135] synonym: "bone morphogenic protein receptor signalling pathway involved in Malpighian tubule cell chemotaxis" EXACT [GOC:mah] is_a: GO:0030509 ! BMP signaling pathway intersection_of: GO:0030509 ! BMP signaling pathway created_by: dph creation_date: 2010-10-01T12:01:00Z [Term] id: GO:0061392 name: regulation of transcription from RNA polymerase II promoter in response to osmotic stress namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell." [GOC:dph, PMID:12086627, PMID:9858577] is_a: GO:0043618 ! regulation of transcription from RNA polymerase II promoter in response to stress created_by: dph creation_date: 2011-12-13T08:52:04Z [Term] id: GO:0061393 name: positive regulation of transcription from RNA polymerase II promoter in response to osmotic stress namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell." [GOC:dph, PMID:12086627, PMID:9858577] is_a: GO:0036003 ! positive regulation of transcription from RNA polymerase II promoter in response to stress is_a: GO:0061392 ! regulation of transcription from RNA polymerase II promoter in response to osmotic stress created_by: dph creation_date: 2011-12-13T08:58:20Z [Term] id: GO:0061394 name: regulation of transcription from RNA polymerase II promoter in response to arsenic-containing substance namespace: biological_process def: "Modulation of the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of an arsenic stimulus from compounds containing arsenic, including arsenates, arsenites, and arsenides." [GOC:dph] is_a: GO:0043618 ! regulation of transcription from RNA polymerase II promoter in response to stress created_by: dph creation_date: 2011-12-14T08:48:36Z [Term] id: GO:0061395 name: positive regulation of transcription from RNA polymerase II promoter in response to arsenic-containing substance namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of an arsenic stimulus from compounds containing arsenic, including arsenates, arsenites, and arsenides." [GOC:dph] is_a: GO:0036003 ! positive regulation of transcription from RNA polymerase II promoter in response to stress is_a: GO:0061394 ! regulation of transcription from RNA polymerase II promoter in response to arsenic-containing substance created_by: dph creation_date: 2011-12-14T08:53:20Z [Term] id: GO:0061396 name: regulation of transcription from RNA polymerase II promoter in response to copper ion namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter in response to an copper ion stimulus." [GOC:dph] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2012-01-10T09:07:08Z [Term] id: GO:0061397 name: positive regulation of transcription from RNA polymerase II promoter in response to copper ion namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter in response to an copper ion stimulus." [GOC:dph] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter is_a: GO:0061396 ! regulation of transcription from RNA polymerase II promoter in response to copper ion created_by: dph creation_date: 2012-01-10T09:14:51Z [Term] id: GO:0061398 name: negative regulation of transcription from RNA polymerase II promoter in response to copper ion namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter in response to an copper ion stimulus." [GOC:dph] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter is_a: GO:0061396 ! regulation of transcription from RNA polymerase II promoter in response to copper ion created_by: dph creation_date: 2012-01-10T09:17:02Z [Term] id: GO:0061399 name: positive regulation of transcription from RNA polymerase II promoter in response to cobalt ion namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter in response to a cobalt ion stimulus." [GOC:dph] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2012-01-10T09:28:52Z [Term] id: GO:0061400 name: positive regulation of transcription from RNA polymerase II promoter in response to calcium ion namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter in response to a calcium ion stimulus." [GOC:dph] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2012-01-10T09:36:02Z [Term] id: GO:0061401 name: positive regulation of transcription from RNA polymerase II promoter in response to a hypotonic environment namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of detection of, or exposure to, a decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment." [GOC:dph] is_a: GO:0061393 ! positive regulation of transcription from RNA polymerase II promoter in response to osmotic stress created_by: dph creation_date: 2012-01-10T09:43:08Z [Term] id: GO:0061402 name: positive regulation of transcription from RNA polymerase II promoter in response to acidity namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a pH stimulus with pH < 7." [GOC:dph] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2012-01-10T03:06:32Z [Term] id: GO:0061403 name: positive regulation of transcription from RNA polymerase II promoter in response to nitrosative stress namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a nitrosative stress stimulus. Nitrosative stress is a state often resulting from exposure to high levels of nitric oxide (NO) or the highly reactive oxidant peroxynitrite, which is produced following interaction of NO with superoxide anions." [GOC:dph] is_a: GO:0036003 ! positive regulation of transcription from RNA polymerase II promoter in response to stress created_by: dph creation_date: 2012-01-10T03:15:30Z [Term] id: GO:0061404 name: positive regulation of transcription from RNA polymerase II promoter in response to increased salt namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of detection of, or exposure to, an increase in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment." [GOC:dph] is_a: GO:0036251 ! positive regulation of transcription from RNA polymerase II promoter in response to salt stress created_by: dph creation_date: 2012-01-10T03:20:40Z [Term] id: GO:0061405 name: positive regulation of transcription from RNA polymerase II promoter in response to hydrostatic pressure namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hydrostatic pressure stimulus. Hydrostatic pressure is the force acting on an object in a system where the fluid is at rest (as opposed to moving). The weight of the fluid above the object creates pressure on it." [GOC:dph] is_a: GO:0036003 ! positive regulation of transcription from RNA polymerase II promoter in response to stress created_by: dph creation_date: 2012-01-10T03:24:51Z [Term] id: GO:0061406 name: positive regulation of transcription from RNA polymerase II promoter in response to glucose starvation namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of deprivation of glucose." [GOC:dph] is_a: GO:0036003 ! positive regulation of transcription from RNA polymerase II promoter in response to stress created_by: dph creation_date: 2012-01-12T11:16:10Z [Term] id: GO:0061407 name: positive regulation of transcription from RNA polymerase II promoter in response to hydrogen peroxide namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hydrogen peroxide (H2O2) stimulus." [GOC:dph] is_a: GO:0036091 ! positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress created_by: dph creation_date: 2012-01-12T11:39:10Z [Term] id: GO:0061408 name: positive regulation of transcription from RNA polymerase II promoter in response to heat stress namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism." [GOC:dph] is_a: GO:0036003 ! positive regulation of transcription from RNA polymerase II promoter in response to stress created_by: dph creation_date: 2012-01-12T11:50:30Z [Term] id: GO:0061409 name: positive regulation of transcription from RNA polymerase II promoter in response to freezing namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a freezing stimulus, temperatures below 0 degrees Celsius." [GOC:dph] is_a: GO:0061411 ! positive regulation of transcription from RNA polymerase II promoter in response to cold created_by: dph creation_date: 2012-01-12T12:11:06Z [Term] id: GO:0061410 name: positive regulation of transcription from RNA polymerase II promoter in response to ethanol namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of an ethanol stimulus." [GOC:dph] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2012-01-12T12:17:35Z [Term] id: GO:0061411 name: positive regulation of transcription from RNA polymerase II promoter in response to cold namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism." [GOC:dph] is_a: GO:0036003 ! positive regulation of transcription from RNA polymerase II promoter in response to stress created_by: dph creation_date: 2012-01-12T12:31:33Z [Term] id: GO:0061412 name: positive regulation of transcription from RNA polymerase II promoter in response to amino acid starvation namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of deprivation of amino acids." [GOC:dph] is_a: GO:0036003 ! positive regulation of transcription from RNA polymerase II promoter in response to stress created_by: dph creation_date: 2012-01-12T12:54:05Z [Term] id: GO:0061413 name: regulation of transcription from RNA polymerase II promoter by a nonfermentable carbon source namespace: biological_process def: "A transcription regulation process in which the presence of a nonfermentable carbon source leads to the modulation of the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other carbon sources." [GOC:dph, PMID:19686338] is_a: GO:0000429 ! carbon catabolite regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2012-01-23T11:13:06Z [Term] id: GO:0061414 name: positive regulation of transcription from RNA polymerase II promoter by a nonfermentable carbon source namespace: biological_process def: "A transcription regulation process in which the presence of a nonfermentable carbon source leads to an increase of the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other carbon sources." [GOC:dph, PMID:19686338] is_a: GO:0000436 ! carbon catabolite activation of transcription from RNA polymerase II promoter is_a: GO:0061413 ! regulation of transcription from RNA polymerase II promoter by a nonfermentable carbon source created_by: dph creation_date: 2012-01-23T11:31:27Z [Term] id: GO:0061415 name: negative regulation of transcription from RNA polymerase II promoter by a nonfermentable carbon source namespace: biological_process def: "A transcription regulation process in which the presence of a nonfermentable carbon source leads to a decrease of the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other carbon sources." [GOC:dph, PMID:19686338] is_a: GO:0000437 ! carbon catabolite repression of transcription from RNA polymerase II promoter is_a: GO:0061413 ! regulation of transcription from RNA polymerase II promoter by a nonfermentable carbon source created_by: dph creation_date: 2012-01-23T11:33:08Z [Term] id: GO:0061416 name: regulation of transcription from RNA polymerase II promoter in response to salt stress namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under salt stress. The stress is usually an increase or decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment." [GOC:dph, PMID:18667581] is_a: GO:0061392 ! regulation of transcription from RNA polymerase II promoter in response to osmotic stress created_by: dph creation_date: 2012-01-23T12:56:36Z [Term] id: GO:0061417 name: negative regulation of transcription from RNA polymerase II promoter in response to oxidative stress namespace: biological_process def: "Any process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals." [GOC:dph, PMID:9767597] is_a: GO:0043619 ! regulation of transcription from RNA polymerase II promoter in response to oxidative stress is_a: GO:0097201 ! negative regulation of transcription from RNA polymerase II promoter in response to stress created_by: dph creation_date: 2012-01-23T01:02:10Z [Term] id: GO:0061418 name: regulation of transcription from RNA polymerase II promoter in response to hypoxia namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus." [GOC:dph, PMID:12511571] is_a: GO:0043618 ! regulation of transcription from RNA polymerase II promoter in response to stress created_by: dph creation_date: 2012-01-23T01:05:59Z [Term] id: GO:0061419 name: positive regulation of transcription from RNA polymerase II promoter in response to hypoxia namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus." [GOC:dph] is_a: GO:0036003 ! positive regulation of transcription from RNA polymerase II promoter in response to stress is_a: GO:0061418 ! regulation of transcription from RNA polymerase II promoter in response to hypoxia created_by: dph creation_date: 2012-01-23T01:07:43Z [Term] id: GO:0061420 name: regulation of transcription from RNA polymerase II promoter in response to biotin starvation namespace: biological_process def: "Modulation of the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of deprivation of biotin." [GOC:dph, PMID:16533810] is_a: GO:0043618 ! regulation of transcription from RNA polymerase II promoter in response to stress created_by: dph creation_date: 2012-01-25T09:55:39Z [Term] id: GO:0061421 name: positive regulation of transcription by oleic acid namespace: biological_process def: "Any process involving oleic acid that activates or increases the rate of transcription." [GOC:dph, PMID:20395639] is_a: GO:0045991 ! carbon catabolite activation of transcription created_by: dph creation_date: 2012-01-25T10:11:39Z [Term] id: GO:0061422 name: positive regulation of transcription from RNA polymerase II promoter in response to alkalinity namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a pH >7.0." [GOC:dph, PMID:11523797, PMID:15299026, PMID:21749328] is_a: GO:0036003 ! positive regulation of transcription from RNA polymerase II promoter in response to stress created_by: dph creation_date: 2012-01-26T12:42:21Z [Term] id: GO:0061423 name: positive regulation of sodium ion transport by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter resulting in the increased frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:dph, PMID:11523797] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2012-01-26T12:52:05Z [Term] id: GO:0061424 name: positive regulation of peroxisome organization by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter and activates or increases the frequency, rate or extent of peroxisome organization." [GOC:dph, PMID:7500953] synonym: "positive regulation of peroxisome organisation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:mah] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2012-02-02T12:50:36Z [Term] id: GO:0061425 name: positive regulation of ethanol catabolic process by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter and activates or increases the frequency, rate or extent of an ethanol catabolic process." [GOC:dph, PMID:10608811, PMID:7760841] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2012-02-02T01:12:36Z [Term] id: GO:0061426 name: positive regulation of sulfite transport by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter and activates or increases the frequency, rate or extent of sulfite transport." [GOC:dph, PMID:10234785, PMID:10870099] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2012-02-02T01:21:46Z [Term] id: GO:0061427 name: negative regulation of ceramide biosynthetic process by negative regulation of transcription from RNA Polymerase II promoter namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter and stops, prevents or reduces the frequency, rate or extent of a ceramide biosynthetic process." [GOC:dph, PMID:15302821] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter intersection_of: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2012-02-02T01:30:41Z [Term] id: GO:0061428 name: negative regulation of transcription from RNA polymerase II promoter in response to hypoxia namespace: biological_process def: "Any process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus." [GOC:dph, PMID:17785431] is_a: GO:0061418 ! regulation of transcription from RNA polymerase II promoter in response to hypoxia is_a: GO:0097201 ! negative regulation of transcription from RNA polymerase II promoter in response to stress created_by: dph creation_date: 2012-02-06T09:26:05Z [Term] id: GO:0061429 name: positive regulation of transcription from RNA polymerase II promoter by oleic acid namespace: biological_process def: "Any process involving oleic acid that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dph, PMID:20395639] is_a: GO:0000436 ! carbon catabolite activation of transcription from RNA polymerase II promoter is_a: GO:0061421 ! positive regulation of transcription by oleic acid created_by: dph creation_date: 2012-02-07T09:54:49Z [Term] id: GO:0061432 name: regulation of transcription from RNA polymerase II promoter in response to methionine namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a methionine stimulus." [GOC:dph, PMID:7891681] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2012-02-07T10:33:35Z [Term] id: GO:0061434 name: regulation of replicative cell aging by regulation of transcription from RNA polymerase II promoter in response to caloric restriction namespace: biological_process def: "Any process that modulates the frequency, rate or extent of replicative cell aging through a mechanism that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a caloric restriction stimulus." [GOC:dph, PMID:17914901] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2012-02-09T09:06:09Z [Term] id: GO:0061435 name: positive regulation of transcription from a mobile element promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transcription from a mobile element promoter." [GOC:dph, PMID:12230120, PMID:9271107] is_a: GO:0045893 ! positive regulation of transcription, DNA-dependent created_by: dph creation_date: 2012-02-09T10:01:33Z [Term] id: GO:0061475 name: cytosolic valyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling valine to valyl-tRNA in the cytosol, catalyzed by valyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:dph] is_a: GO:0006438 ! valyl-tRNA aminoacylation intersection_of: GO:0006438 ! valyl-tRNA aminoacylation created_by: dph creation_date: 2012-11-06T12:29:42Z [Term] id: GO:0061504 name: cyclic threonylcarbamoyladenosine biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of cyclic threonylcarbamoyladenosine, a modified nucleoside found in some tRNA molecules." [PMID:23242255] is_a: GO:0006400 ! tRNA modification created_by: dph creation_date: 2013-01-22T14:25:00Z [Term] id: GO:0070028 name: regulation of transcription by carbon monoxide namespace: biological_process def: "Any process involving carbon monoxide that modulates the frequency, rate or extent of transcription." [GOC:ecd] subset: gosubset_prok synonym: "regulation of transcription by CO" EXACT [] is_a: GO:0006355 ! regulation of transcription, DNA-dependent [Term] id: GO:0070037 name: rRNA (pseudouridine) methyltransferase activity namespace: molecular_function def: "Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a pseudouridine residue in an rRNA molecule." [GOC:imk, GOC:mah] subset: gosubset_prok is_a: GO:0008649 ! rRNA methyltransferase activity [Term] id: GO:0070038 name: rRNA (pseudouridine-N3-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N3-methylpseudouridine." [GOC:imk, GOC:mah] subset: gosubset_prok is_a: GO:0070037 ! rRNA (pseudouridine) methyltransferase activity [Term] id: GO:0070039 name: rRNA (guanosine-2'-O-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing 2'-O-methylguanosine." [GOC:imk, GOC:mah] subset: gosubset_prok is_a: GO:0016435 ! rRNA (guanine) methyltransferase activity relationship: part_of GO:0000451 ! rRNA 2'-O-methylation [Term] id: GO:0070040 name: rRNA (adenine-C2-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: 2 S-adenosyl-L-methionine + adenine(2503) in 23S rRNA = S-adenosyl-L-homocysteine + 5'-deoxyadenosine + L-methionine + rRNA containing C2-methyladenine(2503) in 23S rRNA." [GOC:imk, PMID:20007606, PMID:20184321, PMID:21368151, PMID:21415317, PMID:21527678] subset: gosubset_prok xref: EC:2.1.1.192 xref: MetaCyc:RXN-11586 is_a: GO:0016433 ! rRNA (adenine) methyltransferase activity [Term] id: GO:0070041 name: rRNA (uridine-C5-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing C5-methyluridine." [GOC:imk, GOC:mah] subset: gosubset_prok is_a: GO:0016436 ! rRNA (uridine) methyltransferase activity [Term] id: GO:0070042 name: rRNA (uridine-N3-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N3-methyluridine." [GOC:imk, GOC:mah] subset: gosubset_prok is_a: GO:0016436 ! rRNA (uridine) methyltransferase activity [Term] id: GO:0070043 name: rRNA (guanine-N7-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N7-methylguanine." [GOC:imk, GOC:mah] subset: gosubset_prok is_a: GO:0016435 ! rRNA (guanine) methyltransferase activity relationship: part_of GO:0070476 ! rRNA (guanine-N7)-methylation [Term] id: GO:0070054 name: mRNA splicing, via endonucleolytic cleavage and ligation namespace: biological_process alt_id: GO:0061012 def: "Splicing of mRNA substrates via recognition of the folded RNA structure that brings the 5' and 3' splice sites into proximity and cleavage of the RNA at both the 3' and 5' splice sites by an endonucleolytic mechanism, followed by ligation of the exons." [GOC:krc, GOC:mah] comment: Note that while typically associated with tRNA splicing, splicing via endonucleolytic cleavages and subsequent ligation of the free exon ends is known to be used for some non-tRNA substrates, e.g. HAC1 (YFL031W) in S. cerevisiae and an intron in the 23S rRNA of the Archaeal species Desulfurococcus mobilis. subset: gosubset_prok synonym: "cytosolic mRNA splicing" RELATED [GOC:curators] is_a: GO:0000394 ! RNA splicing, via endonucleolytic cleavage and ligation is_a: GO:0006397 ! mRNA processing [Term] id: GO:0070055 name: HAC1-type intron splice site recognition and cleavage namespace: biological_process def: "The process in which the tertiary structure of a HAC1 type intron is recognized, and the endonucleolytic cleavage of the RNA at both the 5' and 3' splice sites occurs." [GOC:krc, GOC:mah, PMID:10357823] subset: gosubset_prok is_a: GO:0006396 ! RNA processing relationship: part_of GO:0070054 ! mRNA splicing, via endonucleolytic cleavage and ligation [Term] id: GO:0070124 name: mitochondrial translational initiation namespace: biological_process def: "The process preceding formation of the peptide bond between the first two amino acids of a protein in a mitochondrion. This includes the formation of a complex of the ribosome, mRNA, and an initiation complex that contains the first aminoacyl-tRNA." [GOC:mah] synonym: "mitochondrial translation initiation" EXACT [GOC:mah] is_a: GO:0006413 ! translational initiation intersection_of: GO:0006413 ! translational initiation relationship: part_of GO:0032543 ! mitochondrial translation [Term] id: GO:0070125 name: mitochondrial translational elongation namespace: biological_process def: "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis in a mitochondrion." [GOC:mah] synonym: "mitochondrial translation elongation" EXACT [GOC:mah] is_a: GO:0006414 ! translational elongation intersection_of: GO:0006414 ! translational elongation relationship: part_of GO:0032543 ! mitochondrial translation [Term] id: GO:0070126 name: mitochondrial translational termination namespace: biological_process def: "The process resulting in the release of a polypeptide chain from the ribosome in a mitochondrion, usually in response to a termination codon (note that mitochondria use variants of the universal genetic code that differ between different taxa)." [GOC:mah, http://mitogenome.org/index.php/Genetic_Code_of_mitochondria] synonym: "mitochondrial translation termination" EXACT [GOC:mah] is_a: GO:0006415 ! translational termination intersection_of: GO:0006415 ! translational termination relationship: part_of GO:0032543 ! mitochondrial translation [Term] id: GO:0070127 name: tRNA aminoacylation for mitochondrial protein translation namespace: biological_process def: "The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis in a mitochondrion." [GOC:mah] is_a: GO:0006418 ! tRNA aminoacylation for protein translation relationship: part_of GO:0032543 ! mitochondrial translation [Term] id: GO:0070129 name: regulation of mitochondrial translation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA in a mitochondrion." [GOC:mah] synonym: "regulation of mitochondrial protein anabolism" EXACT [GOC:mah] synonym: "regulation of mitochondrial protein biosynthesis" EXACT [GOC:mah] synonym: "regulation of mitochondrial protein formation" EXACT [GOC:mah] synonym: "regulation of mitochondrial protein synthesis" EXACT [GOC:mah] is_a: GO:0006417 ! regulation of translation intersection_of: regulates GO:0032543 ! mitochondrial translation relationship: regulates GO:0032543 ! mitochondrial translation [Term] id: GO:0070130 name: negative regulation of mitochondrial translation namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA in a mitochondrion." [GOC:mah] synonym: "negative regulation of mitochondrial protein anabolism" EXACT [GOC:mah] synonym: "negative regulation of mitochondrial protein biosynthesis" EXACT [GOC:mah] synonym: "negative regulation of mitochondrial protein formation" EXACT [GOC:mah] synonym: "negative regulation of mitochondrial protein synthesis" EXACT [GOC:mah] is_a: GO:0017148 ! negative regulation of translation is_a: GO:0070129 ! regulation of mitochondrial translation intersection_of: negatively_regulates GO:0032543 ! mitochondrial translation relationship: negatively_regulates GO:0032543 ! mitochondrial translation [Term] id: GO:0070131 name: positive regulation of mitochondrial translation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA in a mitochondrion." [GOC:mah] synonym: "positive regulation of mitochondrial protein anabolism" EXACT [GOC:mah] synonym: "positive regulation of mitochondrial protein biosynthesis" EXACT [GOC:mah] synonym: "positive regulation of mitochondrial protein formation" EXACT [GOC:mah] synonym: "positive regulation of mitochondrial protein synthesis" EXACT [GOC:mah] is_a: GO:0045727 ! positive regulation of translation is_a: GO:0070129 ! regulation of mitochondrial translation intersection_of: positively_regulates GO:0032543 ! mitochondrial translation relationship: positively_regulates GO:0032543 ! mitochondrial translation [Term] id: GO:0070132 name: regulation of mitochondrial translational initiation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the process preceding formation of the peptide bond between the first two amino acids of a protein in a mitochondrion." [GOC:mah] synonym: "regulation of mitochondrial translation initiation" EXACT [GOC:mah] is_a: GO:0006446 ! regulation of translational initiation is_a: GO:0070129 ! regulation of mitochondrial translation intersection_of: regulates GO:0070124 ! mitochondrial translational initiation relationship: regulates GO:0070124 ! mitochondrial translational initiation [Term] id: GO:0070133 name: negative regulation of mitochondrial translational initiation namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the process preceding formation of the peptide bond between the first two amino acids of a protein in a mitochondrion." [GOC:mah] synonym: "negative regulation of mitochondrial translation initiation" EXACT [GOC:mah] is_a: GO:0045947 ! negative regulation of translational initiation is_a: GO:0070132 ! regulation of mitochondrial translational initiation intersection_of: negatively_regulates GO:0070124 ! mitochondrial translational initiation relationship: negatively_regulates GO:0070124 ! mitochondrial translational initiation [Term] id: GO:0070134 name: positive regulation of mitochondrial translational initiation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the process preceding formation of the peptide bond between the first two amino acids of a protein in a mitochondrion." [GOC:mah] synonym: "positive regulation of mitochondrial translation initiation" EXACT [GOC:mah] is_a: GO:0045948 ! positive regulation of translational initiation is_a: GO:0070132 ! regulation of mitochondrial translational initiation intersection_of: positively_regulates GO:0070124 ! mitochondrial translational initiation relationship: positively_regulates GO:0070124 ! mitochondrial translational initiation [Term] id: GO:0070143 name: mitochondrial alanyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling alanine to alanyl-tRNA in a mitochondrion, catalyzed by alanyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc] is_a: GO:0006419 ! alanyl-tRNA aminoacylation is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation intersection_of: GO:0006419 ! alanyl-tRNA aminoacylation [Term] id: GO:0070144 name: mitochondrial arginyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling arginine to arginyl-tRNA in a mitochondrion, catalyzed by arginyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc] is_a: GO:0006420 ! arginyl-tRNA aminoacylation is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation intersection_of: GO:0006420 ! arginyl-tRNA aminoacylation [Term] id: GO:0070145 name: mitochondrial asparaginyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling asparagine to asparaginyl-tRNA in a mitochondrion, catalyzed by asparaginyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc] is_a: GO:0006421 ! asparaginyl-tRNA aminoacylation is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation intersection_of: GO:0006421 ! asparaginyl-tRNA aminoacylation [Term] id: GO:0070146 name: mitochondrial aspartyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling aspartate to aspartyl-tRNA in a mitochondrion, catalyzed by aspartyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc] is_a: GO:0006422 ! aspartyl-tRNA aminoacylation is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation intersection_of: GO:0006422 ! aspartyl-tRNA aminoacylation [Term] id: GO:0070147 name: mitochondrial cysteinyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling cysteine to cysteinyl-tRNA in a mitochondrion, catalyzed by cysteinyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc] is_a: GO:0006423 ! cysteinyl-tRNA aminoacylation is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation intersection_of: GO:0006423 ! cysteinyl-tRNA aminoacylation [Term] id: GO:0070148 name: mitochondrial glutaminyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling glutamine to glutaminyl-tRNA in a mitochondrion, catalyzed by glutaminyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc] is_a: GO:0006425 ! glutaminyl-tRNA aminoacylation is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation intersection_of: GO:0006425 ! glutaminyl-tRNA aminoacylation [Term] id: GO:0070149 name: mitochondrial glutamyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling glutamate to glutamyl-tRNA in a mitochondrion, catalyzed by glutamyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc] is_a: GO:0006424 ! glutamyl-tRNA aminoacylation is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation intersection_of: GO:0006424 ! glutamyl-tRNA aminoacylation [Term] id: GO:0070150 name: mitochondrial glycyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling glycine to glycyl-tRNA in a mitochondrion, catalyzed by glycyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc] is_a: GO:0006426 ! glycyl-tRNA aminoacylation is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation intersection_of: GO:0006426 ! glycyl-tRNA aminoacylation [Term] id: GO:0070151 name: mitochondrial histidyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling histidine to histidyl-tRNA in a mitochondrion, catalyzed by histidyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc] is_a: GO:0006427 ! histidyl-tRNA aminoacylation is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation intersection_of: GO:0006427 ! histidyl-tRNA aminoacylation [Term] id: GO:0070152 name: mitochondrial isoleucyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling isoleucine to isoleucyl-tRNA in a mitochondrion, catalyzed by isoleucyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc] is_a: GO:0006428 ! isoleucyl-tRNA aminoacylation is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation intersection_of: GO:0006428 ! isoleucyl-tRNA aminoacylation [Term] id: GO:0070153 name: mitochondrial leucyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling leucine to leucyl-tRNA in a mitochondrion, catalyzed by leucyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc] is_a: GO:0006429 ! leucyl-tRNA aminoacylation is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation intersection_of: GO:0006429 ! leucyl-tRNA aminoacylation [Term] id: GO:0070154 name: mitochondrial lysyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling lysine to lysyl-tRNA in a mitochondrion, catalyzed by lysyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc] is_a: GO:0006430 ! lysyl-tRNA aminoacylation is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation intersection_of: GO:0006430 ! lysyl-tRNA aminoacylation [Term] id: GO:0070155 name: mitochondrial methionyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling methionine to methionyl-tRNA in a mitochondrion, catalyzed by methionyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc] is_a: GO:0006431 ! methionyl-tRNA aminoacylation is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation intersection_of: GO:0006431 ! methionyl-tRNA aminoacylation [Term] id: GO:0070156 name: mitochondrial phenylalanyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling phenylalanine to phenylalanyl-tRNA in a mitochondrion, catalyzed by phenylalanyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc] is_a: GO:0006432 ! phenylalanyl-tRNA aminoacylation is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation intersection_of: GO:0006432 ! phenylalanyl-tRNA aminoacylation [Term] id: GO:0070157 name: mitochondrial prolyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling proline to prolyl-tRNA in a mitochondrion, catalyzed by prolyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc] is_a: GO:0006433 ! prolyl-tRNA aminoacylation is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation intersection_of: GO:0006433 ! prolyl-tRNA aminoacylation [Term] id: GO:0070158 name: mitochondrial seryl-tRNA aminoacylation namespace: biological_process def: "The process of coupling serine to seryl-tRNA in a mitochondrion, catalyzed by seryl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc] is_a: GO:0006434 ! seryl-tRNA aminoacylation is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation intersection_of: GO:0006434 ! seryl-tRNA aminoacylation [Term] id: GO:0070159 name: mitochondrial threonyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling threonine to threonyl-tRNA in a mitochondrion, catalyzed by threonyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc] is_a: GO:0006435 ! threonyl-tRNA aminoacylation is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation intersection_of: GO:0006435 ! threonyl-tRNA aminoacylation [Term] id: GO:0070183 name: mitochondrial tryptophanyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling tryptophan to tryptophanyl-tRNA in a mitochondrion, catalyzed by tryptophanyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc] is_a: GO:0006436 ! tryptophanyl-tRNA aminoacylation is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation intersection_of: GO:0006436 ! tryptophanyl-tRNA aminoacylation [Term] id: GO:0070184 name: mitochondrial tyrosyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling threonine to tyrosyl-tRNA in a mitochondrion, catalyzed by tyrosyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc] is_a: GO:0006437 ! tyrosyl-tRNA aminoacylation is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation intersection_of: GO:0006437 ! tyrosyl-tRNA aminoacylation [Term] id: GO:0070185 name: mitochondrial valyl-tRNA aminoacylation namespace: biological_process def: "The process of coupling valine to valyl-tRNA in a mitochondrion, catalyzed by valyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc] is_a: GO:0006438 ! valyl-tRNA aminoacylation is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation intersection_of: GO:0006438 ! valyl-tRNA aminoacylation [Term] id: GO:0070321 name: regulation of translation in response to nitrogen starvation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the frequency, rate or extent of translation as a result of a stimulus indicating deprivation of nitrogen." [GOC:mah] is_a: GO:0043555 ! regulation of translation in response to stress [Term] id: GO:0070322 name: negative regulation of translation in response to nitrogen starvation namespace: biological_process def: "Any process that stops, prevents or reduces the rate of translation as a result of a stimulus indicating deprivation of nitrogen." [GOC:mah] synonym: "down regulation of translation in response to nitrogen starvation" EXACT [GOC:mah] synonym: "down-regulation of translation in response to nitrogen starvation" EXACT [GOC:mah] synonym: "downregulation of translation in response to nitrogen starvation" EXACT [GOC:mah] synonym: "inhibition of translation in response to nitrogen starvation" NARROW [GOC:mah] is_a: GO:0032055 ! negative regulation of translation in response to stress is_a: GO:0070321 ! regulation of translation in response to nitrogen starvation [Term] id: GO:0070323 name: positive regulation of translation in response to nitrogen starvation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of translation as a result of a stimulus indicating deprivation of nitrogen." [GOC:mah] synonym: "activation of translation in response to nitrogen starvation" NARROW [GOC:mah] synonym: "stimulation of translation in response to nitrogen starvation" NARROW [GOC:mah] synonym: "up regulation of translation in response to nitrogen starvation" EXACT [GOC:mah] synonym: "up-regulation of translation in response to nitrogen starvation" EXACT [GOC:mah] synonym: "upregulation of translation in response to nitrogen starvation" EXACT [GOC:mah] is_a: GO:0032056 ! positive regulation of translation in response to stress is_a: GO:0070321 ! regulation of translation in response to nitrogen starvation [Term] id: GO:0070329 name: tRNA seleno-modification namespace: biological_process def: "The substitution of a selenium atom for a sulfur atom in a ribonucleotide in a tRNA molecule." [GOC:jsg, PMID:14594807] subset: gosubset_prok synonym: "tRNA base modification to selenouridine" EXACT [GOC:mah] is_a: GO:0006400 ! tRNA modification [Term] id: GO:0070475 name: rRNA base methylation namespace: biological_process def: "The addition of a methyl group to an atom in the nucleoside base portion of a nucleotide residue in an rRNA molecule." [GOC:mah] is_a: GO:0031167 ! rRNA methylation [Term] id: GO:0070476 name: rRNA (guanine-N7)-methylation namespace: biological_process def: "The addition of a methyl group to the N7 atom in the base portion of a guanine nucleotide residue in an rRNA molecule." [GOC:mah] is_a: GO:0036265 ! RNA (guanine-N7)-methylation is_a: GO:0070475 ! rRNA base methylation [Term] id: GO:0070526 name: threonylcarbamoyladenosine biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of threonylcarbamoyladenosine, a modified nucleoside found in some tRNA molecules." [GOC:imk, GOC:mah, PMID:19287007] synonym: "t6A biosynthesis" EXACT [PMID:19287007] synonym: "t6A biosynthetic process" EXACT [PMID:19287007] synonym: "threonylcarbamoyladenosine anabolism" EXACT [GOC:mah] synonym: "threonylcarbamoyladenosine biosynthesis" EXACT [GOC:mah] synonym: "threonylcarbamoyladenosine formation" EXACT [GOC:mah] synonym: "threonylcarbamoyladenosine synthesis" EXACT [GOC:mah] is_a: GO:0006400 ! tRNA modification [Term] id: GO:0070549 name: negative regulation of translation involved in RNA interference namespace: biological_process def: "A process of negative regulation of translation that is mediated by the association of small interfering RNAs (siRNAs) with a cognate target mRNA." [GOC:mah, PMID:18771919] synonym: "down regulation of translation involved in RNA interference" EXACT [GOC:mah] synonym: "down-regulation of translation involved in RNA interference" EXACT [GOC:mah] synonym: "downregulation of translation involved in RNA interference" EXACT [GOC:mah] synonym: "inhibition of translation involved in RNA interference" NARROW [GOC:mah] synonym: "RNA interference, negative regulation of translation" EXACT [GOC:mah] is_a: GO:0040033 ! negative regulation of translation, ncRNA-mediated intersection_of: GO:0017148 ! negative regulation of translation intersection_of: part_of GO:0016246 ! RNA interference relationship: part_of GO:0016246 ! RNA interference [Term] id: GO:0070575 name: peptide mating pheromone maturation involved in pheromone-induced unidirectional conjugation namespace: biological_process def: "The formation of a mature peptide mating pheromone by proteolysis and/or modification of a peptide precursor, occurring in the context of pheromone-induced unidirectional conjugation." [GOC:mah] synonym: "peptide mating pheromone formation involved in pheromone-induced unidirectional conjugation" EXACT [GOC:mah] synonym: "peptide mating pheromone processing involved in pheromone-induced unidirectional conjugation" EXACT [GOC:mah] is_a: GO:0007323 ! peptide pheromone maturation created_by: midori creation_date: 2009-04-20T04:32:07Z [Term] id: GO:0070613 name: regulation of protein processing namespace: biological_process alt_id: GO:0010953 def: "Any process that modulates the frequency, rate or extent of protein processing, any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein." [GOC:mah] synonym: "regulation of protein maturation by peptide bond cleavage" EXACT [] is_a: GO:0010468 ! regulation of gene expression intersection_of: regulates GO:0016485 ! protein processing relationship: regulates GO:0016485 ! protein processing created_by: midori creation_date: 2009-04-29T02:49:14Z [Term] id: GO:0070677 name: rRNA (cytosine-2'-O-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing 2'-O-methylcytosine." [GOC:mah, PMID:19400805] subset: gosubset_prok xref: EC:2.1.1.- is_a: GO:0016434 ! rRNA (cytosine) methyltransferase activity created_by: midori creation_date: 2009-05-29T03:37:53Z [Term] id: GO:0070816 name: phosphorylation of RNA polymerase II C-terminal domain namespace: biological_process alt_id: GO:0016245 def: "The process of introducing a phosphate group on to an amino acid residue in the C-terminal domain of RNA polymerase II. Typically, this occurs during the transcription cycle and results in production of an RNA polymerase II enzyme where the carboxy-terminal domain (CTD) of the largest subunit is extensively phosphorylated, often referred to as hyperphosphorylated or the II(0) form. Specific types of phosphorylation within the CTD are usually associated with specific regions of genes, though there are exceptions. The phosphorylation state regulates the association of specific complexes such as the capping enzyme or 3'-RNA processing machinery to the elongating RNA polymerase complex." [GOC:krc, GOC:mah, PMID:17079683] synonym: "CTD domain phosphorylation of RNA polymerase II" EXACT [GOC:mah] synonym: "generation of hyperphosphorylated CTD of RNA polymerase II" EXACT [GOC:krc] synonym: "generation of II(0) form of RNA polymerase II" EXACT [GOC:krc] synonym: "hyperphosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:krc] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: midori creation_date: 2009-07-13T04:01:19Z [Term] id: GO:0070852 name: cell body fiber namespace: cellular_component def: "A neuron projection that is found in unipolar neurons and corresponds to the region between the cell body and the point at which the single projection branches." [GOC:dos, GOC:mah] synonym: "cell body fibre" EXACT [] synonym: "primary neurite" RELATED [GOC:dos, GOC:mah] is_a: GO:0043005 ! neuron projection created_by: midori creation_date: 2009-08-11T04:38:53Z [Term] id: GO:0070868 name: heterochromatin organization involved in chromatin silencing namespace: biological_process def: "Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic heterochromatin and contributes to chromatin silencing." [GOC:mah] synonym: "heterochromatin organisation involved in chromatin silencing" EXACT [GOC:mah] intersection_of: part_of GO:0006342 ! chromatin silencing relationship: part_of GO:0006342 ! chromatin silencing created_by: midori creation_date: 2009-08-20T12:45:52Z [Term] id: GO:0070869 name: heterochromatin assembly involved in chromatin silencing namespace: biological_process def: "Any process that results in the assembly of chromatin into heterochromatin and contributes to chromatin silencing." [GOC:mah] synonym: "heterochromatin formation involved in chromatin silencing" EXACT [] is_a: GO:0070868 ! heterochromatin organization involved in chromatin silencing intersection_of: part_of GO:0006342 ! chromatin silencing created_by: midori creation_date: 2009-08-20T01:04:27Z [Term] id: GO:0070870 name: heterochromatin maintenance involved in chromatin silencing namespace: biological_process def: "A chromatin organization process that preserves heterochromatin in a stable functional or structural state, and that contributes to chromatin silencing." [GOC:mah] is_a: GO:0070868 ! heterochromatin organization involved in chromatin silencing intersection_of: part_of GO:0006342 ! chromatin silencing created_by: midori creation_date: 2009-08-20T01:08:43Z [Term] id: GO:0070897 name: DNA-dependent transcriptional preinitiation complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins on promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription." [GOC:jp, GOC:txnOH] synonym: "transcription PIC biosynthesis" BROAD [GOC:mah] synonym: "transcription PIC formation" BROAD [GOC:mah] synonym: "transcriptional preinitiation complex formation" BROAD [GOC:mah] relationship: part_of GO:0006352 ! DNA-dependent transcription, initiation created_by: midori creation_date: 2009-09-01T04:33:47Z [Term] id: GO:0070898 name: RNA polymerase III transcriptional preinitiation complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins on promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from an RNA polymerase III promoter." [GOC:jp, GOC:txnOH, PMID:11387215] synonym: "RNA polymerase III transcription PIC biosynthesis" EXACT [GOC:mah] synonym: "RNA polymerase III transcription PIC formation" EXACT [GOC:mah] synonym: "RNA polymerase III transcriptional preinitiation complex formation" EXACT [GOC:mah] is_a: GO:0070897 ! DNA-dependent transcriptional preinitiation complex assembly relationship: part_of GO:0006384 ! transcription initiation from RNA polymerase III promoter created_by: midori creation_date: 2009-09-01T04:47:18Z [Term] id: GO:0070899 name: mitochondrial tRNA wobble uridine modification namespace: biological_process def: "The process in which a uridine in position 34 of a mitochondrial tRNA is post-transcriptionally modified." [GOC:mah, GOC:mcc] is_a: GO:0002098 ! tRNA wobble uridine modification is_a: GO:0070900 ! mitochondrial tRNA modification intersection_of: GO:0002098 ! tRNA wobble uridine modification created_by: midori creation_date: 2009-09-02T03:14:13Z [Term] id: GO:0070900 name: mitochondrial tRNA modification namespace: biological_process def: "The covalent alteration of one or more nucleotides within a mitochondrial tRNA molecule to produce a mitochondrial tRNA molecule with a sequence that differs from that coded genetically." [GOC:mah, GOC:mcc] is_a: GO:0000963 ! mitochondrial RNA processing is_a: GO:0006400 ! tRNA modification intersection_of: GO:0006400 ! tRNA modification created_by: midori creation_date: 2009-09-02T03:16:53Z [Term] id: GO:0070901 name: mitochondrial tRNA methylation namespace: biological_process def: "The posttranscriptional addition of methyl groups to specific residues in a mitochondrial tRNA molecule." [GOC:mah, GOC:mcc] is_a: GO:0030488 ! tRNA methylation is_a: GO:0070900 ! mitochondrial tRNA modification intersection_of: GO:0030488 ! tRNA methylation created_by: midori creation_date: 2009-09-02T04:08:00Z [Term] id: GO:0070902 name: mitochondrial tRNA pseudouridine synthesis namespace: biological_process def: "The intramolecular conversion of uridine to pseudouridine in a mitochondrial tRNA molecule." [GOC:mah, GOC:mcc] is_a: GO:0031119 ! tRNA pseudouridine synthesis is_a: GO:0070900 ! mitochondrial tRNA modification intersection_of: GO:0031119 ! tRNA pseudouridine synthesis created_by: midori creation_date: 2009-09-02T04:09:48Z [Term] id: GO:0070903 name: mitochondrial tRNA thio-modification namespace: biological_process def: "The addition a sulfur atom to a nucleotide in a mitochondrial tRNA molecule." [GOC:mah, GOC:mcc] is_a: GO:0034227 ! tRNA thio-modification is_a: GO:0070900 ! mitochondrial tRNA modification intersection_of: GO:0034227 ! tRNA thio-modification created_by: midori creation_date: 2009-09-02T04:11:17Z [Term] id: GO:0070918 name: production of small RNA involved in gene silencing by RNA namespace: biological_process def: "The process in which a double-stranded RNA precursor is processed into short (20-30 nt) fragments. RNA cleavage is catalyzed by a Dicer endonuclease." [GOC:mah, PMID:19239886] synonym: "gene silencing by RNA, production of guide RNA" EXACT [GOC:mah] synonym: "gene silencing by RNA, production of small RNA" EXACT [GOC:mah] is_a: GO:0031050 ! dsRNA fragmentation relationship: part_of GO:0031047 ! gene silencing by RNA created_by: midori creation_date: 2009-09-11T03:32:19Z [Term] id: GO:0070919 name: production of siRNA involved in chromatin silencing by small RNA namespace: biological_process def: "Cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of chromatin silencing by small RNA." [GOC:mah, PMID:19239886] synonym: "chromatin silencing by small RNA, production of guide RNAs" EXACT [] synonym: "chromatin silencing by small RNA, production of siRNA" EXACT [GOC:mah] synonym: "production of guide RNAs involved in chromatin silencing by small RNA" EXACT [GOC:mah] is_a: GO:0070918 ! production of small RNA involved in gene silencing by RNA relationship: part_of GO:0031048 ! chromatin silencing by small RNA created_by: midori creation_date: 2009-09-11T03:39:18Z [Term] id: GO:0070920 name: regulation of production of small RNA involved in gene silencing by RNA namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the production of small RNA involved in gene silencing by RNA." [GOC:mah] synonym: "regulation of gene silencing by RNA, production of guide RNA" EXACT [GOC:mah] synonym: "regulation of gene silencing by RNA, production of small RNA" EXACT [GOC:mah] is_a: GO:0010468 ! regulation of gene expression is_a: GO:0060966 ! regulation of gene silencing by RNA intersection_of: regulates GO:0070918 ! production of small RNA involved in gene silencing by RNA relationship: regulates GO:0070918 ! production of small RNA involved in gene silencing by RNA created_by: midori creation_date: 2009-09-11T03:41:59Z [Term] id: GO:0070921 name: regulation of production of siRNA involved in chromatin silencing by small RNA namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the production of siRNA, the cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of chromatin silencing by small RNA." [GOC:mah] synonym: "regulation of chromatin silencing by small RNA, production of siRNA" EXACT [GOC:mah] is_a: GO:0010964 ! regulation of chromatin silencing by small RNA is_a: GO:0070920 ! regulation of production of small RNA involved in gene silencing by RNA intersection_of: regulates GO:0070919 ! production of siRNA involved in chromatin silencing by small RNA relationship: regulates GO:0070919 ! production of siRNA involved in chromatin silencing by small RNA created_by: midori creation_date: 2009-09-11T03:42:51Z [Term] id: GO:0070922 name: small RNA loading onto RISC namespace: biological_process def: "The process in which a single-stranded small RNA associates with the RNA-initiated silencing complex (RISC); occurs as part of a process of gene silencing by small RNA." [GOC:mah, PMID:19239886] synonym: "gene silencing by RNA, small RNA loading onto RISC" EXACT [GOC:mah] synonym: "RISC assembly" RELATED [GOC:mah] relationship: part_of GO:0031047 ! gene silencing by RNA created_by: midori creation_date: 2009-09-11T03:57:38Z [Term] id: GO:0070923 name: siRNA loading onto RISC involved in chromatin silencing by small RNA namespace: biological_process def: "The process in which a single-stranded small RNA associates with the RNA-initiated silencing complex (RISC); occurs as part of a process of chromatin silencing by small RNA." [GOC:mah, PMID:19239886] synonym: "chromatin silencing by small RNA, siRNA loading onto RISC" EXACT [GOC:mah] is_a: GO:0070922 ! small RNA loading onto RISC relationship: part_of GO:0031048 ! chromatin silencing by small RNA created_by: midori creation_date: 2009-09-11T04:01:44Z [Term] id: GO:0070924 name: heterochromatin assembly involved in chromatin silencing by small RNA namespace: biological_process def: "The process in which an siRNA-associated RNA-induced silencing complex (siRISC) associates with nascent transcripts and RNA polymerase to induce the formation of heterochromatin." [GOC:mah, PMID:19239886] synonym: "chromatin silencing by small RNA, heterochromatin formation" EXACT [GOC:mah] synonym: "heterochromatin formation involved in chromatin silencing by small RNA" EXACT [] synonym: "small RNA-mediated heterochromatin biosynthesis" EXACT [GOC:mah] synonym: "small RNA-mediated heterochromatin formation" EXACT [GOC:mah] is_a: GO:0070869 ! heterochromatin assembly involved in chromatin silencing intersection_of: part_of GO:0031048 ! chromatin silencing by small RNA relationship: part_of GO:0031048 ! chromatin silencing by small RNA created_by: midori creation_date: 2009-09-11T04:10:51Z [Term] id: GO:0070928 name: regulation of mRNA stability, ncRNA-mediated namespace: biological_process def: "Any process, mediated by small non-coding RNAs, that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs." [GOC:jh2] synonym: "ncRNA-mediated regulation of mRNA stability" EXACT [GOC:mah] synonym: "regulation of mRNA stability, non-coding RNA-mediated" EXACT [GOC:mah] is_a: GO:0043488 ! regulation of mRNA stability created_by: midori creation_date: 2009-09-16T03:26:21Z [Term] id: GO:0070929 name: trans-translation namespace: biological_process def: "A translational elongation process in which transfer of a translating ribosome from one mRNA to another RNA template takes place. Trans-translation occurs during tmRNA release of stalled ribosomes." [GOC:jh2, GOC:mah] is_a: GO:0006414 ! translational elongation created_by: midori creation_date: 2009-09-16T04:06:12Z [Term] id: GO:0070930 name: trans-translation-dependent protein tagging namespace: biological_process def: "A protein modification process in which a polypeptide is added to a nascent polypeptide cotranslationally by trans-translation." [GOC:jh2, GOC:jsg, GOC:mah] comment: Note that this term is not a child of 'co-translational protein modification process ; GO:0043686' because co-translational protein modification implies modification of a previously incorporated amino acid in a nascent chain, rather than addition of new sequence to the C-terminus. synonym: "co-translational protein tagging" EXACT [GOC:jh2, GOC:jsg] synonym: "cotranslational protein tagging" EXACT [GOC:mah] synonym: "protein modification by trans-translation" EXACT [GOC:mah] relationship: has_part GO:0070929 ! trans-translation created_by: midori creation_date: 2009-09-16T04:10:49Z [Term] id: GO:0070934 name: CRD-mediated mRNA stabilization namespace: biological_process def: "An mRNA stabilization process in which one or more RNA-binding proteins associate with a sequence in the open reading frame called the coding region instability determinant (CRD)." [GOC:mah, PMID:19029303] synonym: "coding region determinant-mediated mRNA stabilization" EXACT [GOC:mah] is_a: GO:0048255 ! mRNA stabilization created_by: midori creation_date: 2009-09-21T02:57:06Z [Term] id: GO:0070935 name: 3'-UTR-mediated mRNA stabilization namespace: biological_process def: "An mRNA stabilization process in which one or more RNA-binding proteins associate with the 3'-untranslated region (UTR) of an mRNA." [GOC:mah, PMID:19029303] synonym: "3'-untranslated region-mediated mRNA stabilization" EXACT [GOC:mah] is_a: GO:0048255 ! mRNA stabilization created_by: midori creation_date: 2009-09-21T03:08:20Z [Term] id: GO:0070940 name: dephosphorylation of RNA polymerase II C-terminal domain namespace: biological_process def: "The process of removing a phosphate group from an amino acid residue in the C-terminal domain of RNA polymerase II. Some dephosphorylation occurs during transcription while some may occur after the enzyme is released from the template in order to prepare it for the beginning of the transcription cycle again. RNA polymerase II with little or no phosphorylation is referred to as the hypophosphorylated or II(A) form." [GOC:krc, GOC:mah, PMID:17079683] synonym: "CTD domain dephosphorylation of RNA polymerase II" EXACT [GOC:mah] synonym: "generation of hypophosphorylated CTD of RNA polymerase II" EXACT [GOC:krc] synonym: "generation of II(A) form of RNA polymerase II" EXACT [GOC:krc] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: midori creation_date: 2009-09-29T04:34:14Z [Term] id: GO:0071030 name: nuclear mRNA surveillance of spliceosomal pre-mRNA splicing namespace: biological_process def: "The set of processes involved in identifying and degrading incorrectly spliced pre-mRNAs within the nucleus." [GOC:dgf, GOC:krc, PMID:18644474] synonym: "nuclear mRNA quality control of incorrectly spliced pre-mRNA" EXACT [GOC:dgf, GOC:krc] synonym: "nuclear RNA catabolic process of incorrectly spliced pre-mRNA" EXACT [GOC:dgf, GOC:krc] relationship: has_part GO:0071042 ! nuclear polyadenylation-dependent mRNA catabolic process created_by: kchris creation_date: 2009-07-28T04:24:04Z [Term] id: GO:0071031 name: nuclear mRNA surveillance of mRNA 3'-end processing namespace: biological_process def: "The set of processes involved in identifying and degrading mRNAs with incorrectly formed 3'-ends within the nucleus." [GOC:dgf, GOC:krc, PMID:18644474] synonym: "nuclear mRNA catabolic process of mRNA with aberrant 3'-ends" EXACT [GOC:dgf, GOC:krc] synonym: "nuclear mRNA quality control of mRNAs with aberrant 3'-ends" EXACT [GOC:dgf, GOC:krc] relationship: has_part GO:0071042 ! nuclear polyadenylation-dependent mRNA catabolic process created_by: kchris creation_date: 2009-07-28T04:29:17Z [Term] id: GO:0071035 name: nuclear polyadenylation-dependent rRNA catabolic process namespace: biological_process def: "The chemical reactions and pathways occurring in the nucleus and resulting in the breakdown of a ribosomal RNA (rRNA) molecule, including RNA fragments released as part of processing the primary transcript into multiple mature rRNA species, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target rRNA." [GOC:dgf, GOC:krc, PMID:15173578, PMID:15572680, PMID:15935758, PMID:17652137, PMID:18591258] synonym: "nuclear poly(A)-dependent rRNA catabolic process" RELATED [GOC:vw] is_a: GO:0071046 ! nuclear polyadenylation-dependent ncRNA catabolic process created_by: kchris creation_date: 2009-07-29T12:42:39Z [Term] id: GO:0071036 name: nuclear polyadenylation-dependent snoRNA catabolic process namespace: biological_process def: "The chemical reactions and pathways occurring in the nucleus and resulting in the breakdown of a small nucleolar RNA (snoRNA) molecule, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target snoRNA." [GOC:dgf, GOC:krc, PMID:15935758] synonym: "nuclear poly(A)-dependent snoRNA catabolic process" RELATED [GOC:tb] is_a: GO:0071046 ! nuclear polyadenylation-dependent ncRNA catabolic process relationship: has_part GO:0071050 ! snoRNA polyadenylation created_by: kchris creation_date: 2009-07-29T01:04:44Z [Term] id: GO:0071037 name: nuclear polyadenylation-dependent snRNA catabolic process namespace: biological_process def: "The chemical reactions and pathways occurring in the nucleus and resulting in the breakdown of a small nuclear RNA (snRNA) molecule, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target snRNA." [GOC:dgf, GOC:krc] synonym: "nuclear poly(A)-dependent snRNA catabolic process" RELATED [GOC:vw] is_a: GO:0071046 ! nuclear polyadenylation-dependent ncRNA catabolic process created_by: kchris creation_date: 2009-07-29T01:07:18Z [Term] id: GO:0071038 name: nuclear polyadenylation-dependent tRNA catabolic process namespace: biological_process def: "The chemical reactions and pathways occurring in the nucleus and resulting in the breakdown of an aberrant or incorrectly modified transfer RNA (tRNA) molecule, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target tRNA." [GOC:dgf, GOC:krc] synonym: "nuclear poly(A)-dependent tRNA catabolic process" RELATED [GOC:vw] is_a: GO:0071046 ! nuclear polyadenylation-dependent ncRNA catabolic process created_by: kchris creation_date: 2009-07-29T01:08:14Z [Term] id: GO:0071039 name: nuclear polyadenylation-dependent CUT catabolic process namespace: biological_process def: "The chemical reactions and pathways occurring in the nucleus and resulting in the breakdown of a cryptic unstable transcript (CUT), initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target CUT." [GOC:dgf, GOC:krc, PMID:15935759, PMID:16973436, PMID:16973437, PMID:18007593, PMID:18591258] synonym: "nuclear poly(A)-dependent CUT catabolic process" RELATED [GOC:vw] is_a: GO:0071046 ! nuclear polyadenylation-dependent ncRNA catabolic process created_by: kchris creation_date: 2009-07-29T01:10:34Z [Term] id: GO:0071040 name: nuclear polyadenylation-dependent antisense transcript catabolic process namespace: biological_process def: "The chemical reactions and pathways occurring in the nucleus and resulting in the breakdown of an antisense transcript, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target antisense transcript." [GOC:dgf, GOC:krc, PMID:18022365] synonym: "nuclear poly(A)-dependent antisense transcript catabolic process" RELATED [GOC:vw] is_a: GO:0071046 ! nuclear polyadenylation-dependent ncRNA catabolic process created_by: kchris creation_date: 2009-07-29T01:25:21Z [Term] id: GO:0071042 name: nuclear polyadenylation-dependent mRNA catabolic process namespace: biological_process def: "The chemical reactions and pathways occurring in the nucleus and resulting in the breakdown of a messenger RNA (mRNA) molecule, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target mRNA." [GOC:dgf, GOC:krc, PMID:15145828, PMID:15828860, PMID:16431988, PMID:17643380, PMID:18000032, PMID:18644474] synonym: "nuclear poly(A)-dependent mRNA catabolic process" RELATED [GOC:vw] is_a: GO:0071047 ! polyadenylation-dependent mRNA catabolic process created_by: kchris creation_date: 2009-07-29T02:06:19Z [Term] id: GO:0071046 name: nuclear polyadenylation-dependent ncRNA catabolic process namespace: biological_process def: "The chemical reactions and pathways occurring in the nucleus and resulting in the breakdown of a noncoding RNA (ncRNA) molecule, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target ncRNA." [GOC:dgf, GOC:jl, GOC:krc, PMID:17410208] synonym: "nuclear poly(A)-dependent ncRNA catabolic process" RELATED [GOC:vw] is_a: GO:0043634 ! polyadenylation-dependent ncRNA catabolic process created_by: kchris creation_date: 2009-08-06T02:14:53Z [Term] id: GO:0071047 name: polyadenylation-dependent mRNA catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of a messenger RNA (mRNA) molecule, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target mRNA." [GOC:dgf, GOC:krc] synonym: "poly(A)-dependent mRNA catabolic process" RELATED [GOC:vw] relationship: has_part GO:0006378 ! mRNA polyadenylation created_by: kchris creation_date: 2009-08-07T09:57:56Z [Term] id: GO:0071048 name: nuclear retention of unspliced pre-mRNA at the site of transcription namespace: biological_process def: "The process involved in retention of incorrectly or incompletely spliced pre-mRNA within the nucleus at the site of transcription." [GOC:dgf, GOC:krc, PMID:14718167] relationship: part_of GO:0071030 ! nuclear mRNA surveillance of spliceosomal pre-mRNA splicing created_by: kchris creation_date: 2009-08-11T02:19:03Z [Term] id: GO:0071049 name: nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription namespace: biological_process def: "The process involved in retention of mRNAs that have incorrectly formed 3'-ends within the nucleus at the site of transcription." [GOC:dgf, GOC:krc, PMID:11586364, PMID:12417728] relationship: part_of GO:0071031 ! nuclear mRNA surveillance of mRNA 3'-end processing created_by: kchris creation_date: 2009-08-11T02:40:56Z [Term] id: GO:0071050 name: snoRNA polyadenylation namespace: biological_process def: "The enzymatic addition of a sequence of adenylyl residues at the 3' end of snoRNA molecule. In eukaryotes, this occurs in conjunction with termination of transcription of precursor snoRNA molecules and may occur post-transcriptionally on incorrectly processed molecules targeted for degradation." [GOC:dgf, GOC:krc, PMID:18951092] is_a: GO:0043629 ! ncRNA polyadenylation created_by: kchris creation_date: 2009-08-25T03:33:44Z [Term] id: GO:0071051 name: polyadenylation-dependent snoRNA 3'-end processing namespace: biological_process def: "Any process involved in forming the mature 3' end of a snoRNA molecule linked to prior polyadenylation of the 3'-end of the precursor snoRNA." [GOC:dgf, GOC:krc, PMID:18951092] synonym: "poly(A)-dependent snoRNA 3'-end processing" RELATED [GOC:vw] is_a: GO:0031126 ! snoRNA 3'-end processing relationship: has_part GO:0071050 ! snoRNA polyadenylation created_by: kchris creation_date: 2009-08-25T03:47:24Z [Term] id: GO:0071076 name: RNA 3' uridylation namespace: biological_process def: "The enzymatic addition of a sequence of uridylyl residues at the 3' end of an RNA molecule." [GOC:vw, PMID:19430462] is_a: GO:0031123 ! RNA 3'-end processing created_by: midori creation_date: 2009-11-06T02:41:23Z [Term] id: GO:0071164 name: RNA trimethylguanosine synthase activity namespace: molecular_function def: "Catalysis of two successive methyl transfer reactions from AdoMet to the N-2 atom of guanosine, thereby converting 7-methylguanosine in an RNA cap to 2,2,7 trimethylguanosine." [GOC:BHF, PMID:11983179, PMID:18775984] synonym: "cap hypermethylase activity" EXACT [PMID:11983179] synonym: "small nuclear RNA methyltransferase activity" RELATED [GOC:rl] synonym: "snRNA methyltransferase activity" RELATED [GOC:rl] relationship: part_of GO:0036261 ! 7-methylguanosine cap hypermethylation created_by: midori creation_date: 2009-11-19T03:23:20Z [Term] id: GO:0071212 name: subsynaptic reticulum namespace: cellular_component def: "An elaborate tubulolamellar membrane system that underlies the postsynaptic cell membrane." [PMID:1460464, PMID:18171947, PMID:19244343, PMID:7946331] synonym: "SSR" EXACT [PMID:19244343] is_a: GO:0033267 ! axon part relationship: part_of GO:0061174 ! type I terminal bouton created_by: midori creation_date: 2009-12-01T05:05:21Z [Term] id: GO:0071255 name: CVT vesicle assembly namespace: biological_process def: "A vesicle organization process that takes place as part of the CVT pathway, and results in the formation of a double membrane-bounded cytosolic structure that sequesters precursor aminopeptidase I (prAPI)." [GOC:rb, PMID:10966461, PMID:11085977] synonym: "CVT vesicle biosynthesis" RELATED [GOC:mah] synonym: "CVT vesicle formation" EXACT [GOC:mah] relationship: part_of GO:0032258 ! CVT pathway created_by: midori creation_date: 2009-12-04T10:39:50Z [Term] id: GO:0071262 name: regulation of translational initiation in response to starvation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of translation initiation, as a result of deprivation of nourishment." [GOC:mah] synonym: "regulation of translational initiation in response to nutrient starvation" EXACT [GOC:vw] is_a: GO:0043558 ! regulation of translational initiation in response to stress created_by: midori creation_date: 2009-12-08T05:31:05Z [Term] id: GO:0071263 name: negative regulation of translational initiation in response to starvation namespace: biological_process def: "Any process that stops, prevents or reduces the rate of translation initiation, as a result of deprivation of nourishment." [GOC:mah] synonym: "down regulation of translation initiation in response to starvation" EXACT [GOC:mah] synonym: "down-regulation of translation initiation in response to starvation" EXACT [GOC:mah] synonym: "downregulation of translation initiation in response to starvation" EXACT [GOC:mah] synonym: "inhibition of translation initiation in response to starvation" NARROW [GOC:mah] synonym: "negative regulation of translational initiation in response to nutrient starvation" EXACT [GOC:vw] is_a: GO:0032057 ! negative regulation of translational initiation in response to stress is_a: GO:0071262 ! regulation of translational initiation in response to starvation created_by: midori creation_date: 2009-12-08T05:33:12Z [Term] id: GO:0071264 name: positive regulation of translational initiation in response to starvation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of translation initiation, as a result of deprivation of nourishment." [GOC:mah] synonym: "activation of translation initiation in response to starvation" NARROW [GOC:mah] synonym: "positive regulation of translational initiation in response to nutrient starvation" EXACT [GOC:mah] synonym: "stimulation of translation initiation in response to starvation" NARROW [GOC:mah] synonym: "up regulation of translation initiation in response to starvation" EXACT [GOC:mah] synonym: "up-regulation of translation initiation in response to starvation" EXACT [GOC:mah] synonym: "upregulation of translation initiation in response to starvation" EXACT [GOC:mah] is_a: GO:0032058 ! positive regulation of translational initiation in response to stress is_a: GO:0071262 ! regulation of translational initiation in response to starvation created_by: midori creation_date: 2009-12-08T05:35:45Z [Term] id: GO:0071424 name: rRNA (cytosine-N4-)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N4-methylcytosine." [GOC:imk, PMID:19965768] subset: gosubset_prok xref: EC:2.1.1.- is_a: GO:0016434 ! rRNA (cytosine) methyltransferase activity created_by: midori creation_date: 2009-12-15T03:46:52Z [Term] id: GO:0071430 name: pre-miRNA-containing ribonucleoprotein complex export from nucleus namespace: biological_process def: "The directed movement of a ribonucleoprotein complex that contains pre-microRNA from the nucleus to the cytoplasm." [GOC:mah, GOC:sl] synonym: "pre-microRNA-containing ribonucleoprotein complex export from cell nucleus" EXACT [GOC:mah] synonym: "pre-microRNA-containing ribonucleoprotein complex export from nucleus" EXACT [] synonym: "pre-microRNA-containing ribonucleoprotein complex nucleus export" EXACT [GOC:mah] synonym: "pre-microRNA-containing ribonucleoprotein complex transport from nucleus to cytoplasm" EXACT [GOC:mah] synonym: "pre-microRNA-containing RNP export from nucleus" EXACT [GOC:mah] relationship: has_part GO:0035281 ! pre-miRNA export from nucleus created_by: midori creation_date: 2009-12-16T10:26:16Z [Term] id: GO:0071432 name: peptide mating pheromone maturation involved in conjugation with cellular fusion namespace: biological_process def: "The formation of a mature peptide mating pheromone by proteolysis and/or modification of a peptide precursor, occurring in the context of conjugation with cellular fusion." [GOC:mah] synonym: "a-factor processing (proteolytic)" NARROW [GOC:vw] synonym: "alpha-factor maturation" NARROW [GOC:vw] synonym: "mating-type peptide pheromone maturation involved in conjugation with cellular fusion" EXACT [GOC:mah] synonym: "peptide mating pheromone formation involved in conjugation with cellular fusion" EXACT [GOC:mah] synonym: "peptide mating pheromone processing involved in conjugation with cellular fusion" EXACT [GOC:mah] is_a: GO:0007323 ! peptide pheromone maturation created_by: midori creation_date: 2009-12-16T10:46:50Z [Term] id: GO:0071565 name: nBAF complex namespace: cellular_component def: "A SWI/SNF-type complex that is found in post-mitotic neurons, and in human contains actin and proteins encoded by the ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, DPF1/BAF45B, DPF3/BAF45C, ACTL6B/BAF53B genes. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth." [GOC:mah, GOC:ss, PMID:17640523] is_a: GO:0097458 ! neuron part created_by: midori creation_date: 2010-01-20T03:41:19Z [Term] id: GO:0071586 name: CAAX-box protein processing namespace: biological_process def: "The second process in a series of specific posttranslational modifications to the CAAX box region of CAAX box proteins, in which the last three amino acids of the protein (AAX) are removed by proteolysis." [GOC:mah] is_a: GO:0016485 ! protein processing relationship: part_of GO:0080120 ! CAAX-box protein maturation created_by: midori creation_date: 2010-01-28T04:42:45Z [Term] id: GO:0071587 name: CAAX-box protein modification namespace: biological_process def: "The covalent alteration of one or more amino acid residues within the CAAX box region of CAAX box proteins." [GOC:mah] relationship: part_of GO:0080120 ! CAAX-box protein maturation created_by: midori creation_date: 2010-01-28T04:48:56Z [Term] id: GO:0071598 name: neuronal ribonucleoprotein granule namespace: cellular_component def: "A ribonucleoprotein complex that is found in the cytoplasm of axons and dendrites, and transports translationally silenced mRNAs to dendritic synapses, where they are released and translated in response to specific exogenous stimuli." [GOC:BHF, GOC:go_curators, GOC:mah, PMID:19015237, PMID:20368989] synonym: "neuronal RNA granule" NARROW [] synonym: "neuronal RNP granule" EXACT [] is_a: GO:0097458 ! neuron part relationship: part_of GO:0043005 ! neuron projection created_by: midori creation_date: 2010-02-04T04:01:57Z [Term] id: GO:0071619 name: phosphorylation of RNA polymerase II C-terminal domain serine 2 residues namespace: biological_process def: "The process of introducing a phosphate group onto a serine residue at position 2 within the heptapeptide repeat (YSPTSPS) of the C-terminal domain of RNA polymerase II. Typically, phosphorylation of serine 2 (Ser2) occurs subsequent to phosphorylation of serine 5 and is thus seen in the middle and 3' ends of genes. In vivo, Ser2 phosphorylation is primarily performed by CTDK-I in S. cerevisiae or CDK9 in metazoans." [GOC:krc, PMID:17079683] is_a: GO:0070816 ! phosphorylation of RNA polymerase II C-terminal domain created_by: midori creation_date: 2010-02-09T02:37:02Z [Term] id: GO:0071620 name: phosphorylation of RNA polymerase II C-terminal domain serine 5 residues namespace: biological_process def: "The process of introducing a phosphate group onto a serine residue at position 5 within the heptapeptide repeat (YSPTSPS) of the C-terminal domain of RNA polymerase II. Typically, phosphorylation of serine 5 (Ser5) occurs near the 5' ends of genes. It is generally still observed in the middle of genes, overlapping with phosphorylation of serine 2, but is generally not present at the 3' ends of genes. In vivo, Ser5 phosphorylation occurs primarily through the action of TFIIH (KIN28 in S. cerevisiae, CKD7 in metazoans)." [GOC:krc, PMID:17079683] is_a: GO:0070816 ! phosphorylation of RNA polymerase II C-terminal domain created_by: midori creation_date: 2010-02-09T02:39:52Z [Term] id: GO:0071683 name: sensory dendrite namespace: cellular_component def: "A dendrite that is found on a sensory neuron, and directly transduces a sensory signal from the sensory neuron to another neuron." [GOC:dos, GOC:kmv, GOC:mah] is_a: GO:0030425 ! dendrite created_by: midori creation_date: 2010-02-19T04:17:05Z [Term] id: GO:0071704 name: organic substance metabolic process namespace: biological_process def: "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon." [CHEBI:50860, GOC:mah] synonym: "organic molecular entity metabolic process" EXACT [] synonym: "organic molecular entity metabolism" EXACT [] synonym: "organic substance metabolism" EXACT [] is_a: GO:0008152 ! metabolic process created_by: midori creation_date: 2010-03-08T03:32:18Z [Term] id: GO:0071733 name: transcriptional activation by promoter-enhancer looping namespace: biological_process def: "The formation and maintenance of DNA loops that juxtapose the promoter and enhancer regions of RNA polymerase II-transcribed genes and activate transcription from an RNA polymerase II promoter." [GOC:mah, PMID:15060134, PMID:19923429] synonym: "long-range enhancer-promoter communication" RELATED [PMID:15060134] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: midori creation_date: 2010-03-19T02:01:19Z [Term] id: GO:0071891 name: N-terminal peptidyl-proline dimethylation involved in translation namespace: biological_process def: "An N-terminal peptidyl-proline dimethylation process that contributes to translation." [GOC:mah] intersection_of: part_of GO:0006412 ! translation relationship: part_of GO:0006412 ! translation created_by: midori creation_date: 2010-09-14T02:19:40Z [Term] id: GO:0071893 name: BMP signaling pathway involved in nephric duct formation namespace: biological_process def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to nephric duct formation." [GOC:mah, GOC:mtg_kidney_jan10] synonym: "BMP signalling pathway involved in nephric duct formation" EXACT [GOC:mah] is_a: GO:0030509 ! BMP signaling pathway intersection_of: GO:0030509 ! BMP signaling pathway created_by: midori creation_date: 2010-09-14T03:14:59Z [Term] id: GO:0071930 name: negative regulation of transcription involved in G1/S transition of mitotic cell cycle namespace: biological_process def: "Any process that stop, prevents or decreases transcription as part of the G1/S transition of the mitotic cell cycle." [GOC:mah, GOC:vw] synonym: "negative regulation of transcription from RNA polymerase II promoter during G1/S phase of mitotic cell cycle" RELATED [GOC:mah] synonym: "negative regulation of transcription from RNA polymerase II promoter involved in G1/S transition of mitotic cell cycle" EXACT [GOC:mah] is_a: GO:0000083 ! regulation of transcription involved in G1/S transition of mitotic cell cycle is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter intersection_of: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: midori creation_date: 2010-09-29T11:12:11Z [Term] id: GO:0071931 name: positive regulation of transcription involved in G1/S transition of mitotic cell cycle namespace: biological_process def: "Any process that activates or increases transcription as part of the G1/S transition of the mitotic cell cycle." [GOC:mah, GOC:vw] synonym: "positive regulation of transcription from RNA polymerase II promoter during G1/S phase of mitotic cell cycle" RELATED [GOC:mah] synonym: "positive regulation of transcription from RNA polymerase II promoter involved in G1/S transition of mitotic cell cycle" EXACT [GOC:mah] is_a: GO:0000083 ! regulation of transcription involved in G1/S transition of mitotic cell cycle is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: midori creation_date: 2010-09-29T11:15:34Z [Term] id: GO:0071951 name: conversion of methionyl-tRNA to N-formyl-methionyl-tRNA namespace: biological_process def: "The modification process that results in the conversion of methionine charged on a tRNA(fMet) to N-formyl-methionine-tRNA(fMet)." [GOC:jsg, PMID:5337045] is_a: GO:0019988 ! charged-tRNA amino acid modification created_by: midori creation_date: 2010-10-08T11:54:38Z [Term] id: GO:0071952 name: conversion of O-phosphoseryl-tRNA to cysteinyl-tRNA namespace: biological_process def: "The modification process that results in the conversion of O-phosphoserine charged on a tRNA(Cys) to cysteinyl-tRNA." [GOC:jsg, PMID:17351629, PMID:18559341] comment: Note that this process has been observed in some archeal and bacterial species. subset: gosubset_prok is_a: GO:0019988 ! charged-tRNA amino acid modification created_by: midori creation_date: 2010-10-08T12:02:00Z [Term] id: GO:0072097 name: negative regulation of branch elongation involved in ureteric bud branching by BMP signaling pathway namespace: biological_process def: "A series of molecular signals generated as a consequence of any member of the BMP (bone morphogenetic protein) family binding to a cell surface receptor resulting in the reduction of the frequency, rate or extent of branch elongation involved in ureteric bud branching, the growth of a branch of the ureteric bud along its axis." [GOC:mtg_kidney_jan10] synonym: "negative regulation of branch elongation involved in ureteric bud branching by BMP signalling pathway" EXACT [GOC:mah] is_a: GO:0030509 ! BMP signaling pathway intersection_of: GO:0030509 ! BMP signaling pathway created_by: midori creation_date: 2010-02-10T02:00:34Z [Term] id: GO:0072101 name: specification of ureteric bud anterior/posterior symmetry by BMP signaling pathway namespace: biological_process def: "A series of molecular signals generated as a consequence of any member of the BMP (bone morphogenetic protein) family binding to a cell surface receptor that results in the establishment of the ureteric bud such that there is a similar arrangement in form and relationship of parts along its anterior/posterior axis." [GOC:mtg_kidney_jan10] synonym: "specification of ureteric bud anterior/posterior asymmetry by BMP signaling pathway" EXACT [GOC:dph] synonym: "specification of ureteric bud anterior/posterior symmetry by BMP signalling pathway" EXACT [GOC:mah] is_a: GO:0030509 ! BMP signaling pathway is_a: GO:0060994 ! regulation of transcription from RNA polymerase II promoter involved in kidney development created_by: midori creation_date: 2010-02-10T02:21:03Z [Term] id: GO:0072212 name: regulation of transcription from RNA polymerase II promoter involved in metanephros development namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the branching morphogenesis by which the metanephros progresses from its initial formation to the mature state." [GOC:mtg_kidney_jan10] is_a: GO:0060994 ! regulation of transcription from RNA polymerase II promoter involved in kidney development intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: midori creation_date: 2010-03-18T01:14:09Z [Term] id: GO:0072344 name: rescue of stalled ribosome namespace: biological_process def: "A process of translational elongation that takes place when a ribosome has stalled during translation, and results in freeing the ribosome from the stalled translation complex." [GOC:jh2, GOC:mah, PMID:18557701, PMID:19170872, PMID:20117091, PMID:20185543] subset: gosubset_prok is_a: GO:0006414 ! translational elongation is_a: GO:0006417 ! regulation of translation created_by: midori creation_date: 2010-11-10T11:54:26Z [Term] id: GO:0072361 name: regulation of glycolysis by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of glycolysis by modulating the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:BHF, GOC:mah] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: midori creation_date: 2010-11-16T02:57:18Z [Term] id: GO:0072362 name: regulation of glycolysis by negative regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of glycolysis by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:BHF, GOC:mah] synonym: "regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter" EXACT [GOC:bf] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter is_a: GO:0072361 ! regulation of glycolysis by regulation of transcription from RNA polymerase II promoter intersection_of: negatively_regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: midori creation_date: 2010-11-16T02:59:32Z [Term] id: GO:0072363 name: regulation of glycolysis by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of glycolysis by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:BHF, GOC:mah] synonym: "regulation of glycolysis by positive regulation of transcription from an RNA polymerase II promoter" EXACT [GOC:bf] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter is_a: GO:0072361 ! regulation of glycolysis by regulation of transcription from RNA polymerase II promoter intersection_of: positively_regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: midori creation_date: 2010-11-16T03:08:25Z [Term] id: GO:0072364 name: regulation of cellular ketone metabolic process by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a cellular ketone metabolic process by modulating the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:BHF, GOC:mah] synonym: "regulation of cellular ketone metabolic process by regulation of transcription from an RNA polymerase II promoter" EXACT [GOC:bf] synonym: "regulation of cellular ketone metabolism by regulation of transcription from an RNA polymerase II promoter" EXACT [GOC:mah] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: midori creation_date: 2010-11-16T03:11:39Z [Term] id: GO:0072365 name: regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a cellular ketone metabolic process by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:BHF, GOC:mah] synonym: "regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter" EXACT [GOC:bf] synonym: "regulation of cellular ketone metabolism by negative regulation of transcription from an RNA polymerase II promoter" EXACT [GOC:mah] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter is_a: GO:0072364 ! regulation of cellular ketone metabolic process by regulation of transcription from RNA polymerase II promoter intersection_of: negatively_regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: midori creation_date: 2010-11-16T03:12:09Z [Term] id: GO:0072366 name: regulation of cellular ketone metabolic process by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a cellular ketone metabolic process by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:BHF, GOC:mah] synonym: "regulation of cellular ketone metabolic process by positive regulation of transcription from an RNA polymerase II promoter" EXACT [GOC:bf] synonym: "regulation of cellular ketone metabolism by positive regulation of transcription from an RNA polymerase II promoter" EXACT [GOC:mah] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter is_a: GO:0072364 ! regulation of cellular ketone metabolic process by regulation of transcription from RNA polymerase II promoter intersection_of: positively_regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: midori creation_date: 2010-11-16T03:12:47Z [Term] id: GO:0072367 name: regulation of lipid transport by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of lipid transport by modulating the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:BHF, GOC:mah] synonym: "regulation of lipid transport by regulation of transcription from an RNA polymerase II promoter" EXACT [GOC:bf] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: midori creation_date: 2010-11-16T03:17:54Z [Term] id: GO:0072368 name: regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of lipid transport by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:BHF, GOC:mah] synonym: "regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter" EXACT [GOC:bf] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter is_a: GO:0072367 ! regulation of lipid transport by regulation of transcription from RNA polymerase II promoter intersection_of: negatively_regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: midori creation_date: 2010-11-16T03:18:13Z [Term] id: GO:0072369 name: regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of lipid transport by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:BHF, GOC:mah] synonym: "regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter" EXACT [GOC:bf] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter is_a: GO:0072367 ! regulation of lipid transport by regulation of transcription from RNA polymerase II promoter intersection_of: positively_regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: midori creation_date: 2010-11-16T03:23:53Z [Term] id: GO:0072670 name: mitochondrial tRNA threonylcarbamoyladenosine modification namespace: biological_process def: "The attachment of a carbonyl group and a threonine to the amino group of the adenine residue immediately 3' of the anticodon, in tRNAs that decode ANN codons (where N is any base)." [GOC:mcc, PMID:21183954] synonym: "mitochondrial tRNA t6A modification" EXACT [GOC:mcc] is_a: GO:0070900 ! mitochondrial tRNA modification created_by: midori creation_date: 2011-02-18T11:34:35Z [Term] id: GO:0072684 name: mitochondrial tRNA 3'-trailer cleavage, endonucleolytic namespace: biological_process def: "Endonucleolytic cleavage of the 3'-end of the pre-tRNA as part of the process of generating the mature 3'-end of the tRNA in the mitochondrion." [GOC:mah] synonym: "mitochondrial endonucleolytic tRNA 3'-end cleavage" EXACT [GOC:mah] synonym: "mitochondrial endonucleolytic tRNA 3'-trailer cleavage" RELATED [GOC:mah] synonym: "mitochondrial tRNA 3'-end cleavage, endonucleolytic" EXACT [GOC:mah] is_a: GO:0034414 ! tRNA 3'-trailer cleavage, endonucleolytic is_a: GO:1990180 ! mitochondrial tRNA 3'-end processing intersection_of: GO:0034414 ! tRNA 3'-trailer cleavage, endonucleolytic created_by: midori creation_date: 2011-02-23T01:32:52Z [Term] id: GO:0072692 name: chromatin silencing at centromere central core namespace: biological_process def: "Repression of transcription of DNA at the central core of a regional centromere by altering the structure of chromatin." [GOC:mah] synonym: "centromere central core chromatin silencing" EXACT [GOC:mah] synonym: "chromatin silencing at centromeric central core" EXACT [GOC:vw] synonym: "chromatin silencing at chromosome kinetochore domain" EXACT [GOC:vw] synonym: "heterochromatic silencing at centromere central core" EXACT [GOC:mah] is_a: GO:0030702 ! chromatin silencing at centromere created_by: midori creation_date: 2011-09-12T03:16:41Z [Term] id: GO:0075522 name: IRES-dependent viral translational initiation namespace: biological_process def: "Process by which viral mRNA translation is initiated, where a domain in the 5' untranslated region (UTR) of the viral mRNA called an internal ribosome entry site (IRES) binds the host 43S preinitiation complex, circumventing regular cap-dependent translation initiation." [GOC:bf, GOC:jl, PMID:19632368, VZ:867] subset: virus_checked xref: VZ:867 "Viral initiation of translation: IRES and DLP" is_a: GO:0002192 ! IRES-dependent translational initiation relationship: part_of GO:0019081 ! viral translation created_by: janelomax creation_date: 2011-08-03T02:25:03Z [Term] id: GO:0075523 name: viral translational frameshifting namespace: biological_process def: "A process which occurs during viral translation, which involves a translational recoding mechanism called programmed ribosomal frameshifting. This causes the ribosome to alter its reading of the mRNA to an a different open reading frame to produce alternate viral proteins." [GOC:bf, GOC:jl, PMID:8852897, VZ:860] subset: virus_checked synonym: "ribosomal frameshifting involved in viral translation" EXACT [GOC:jl] xref: VZ:860 "Ribosomal frameshifting" is_a: GO:0006452 ! translational frameshifting relationship: part_of GO:0019081 ! viral translation created_by: janelomax creation_date: 2011-08-03T02:48:46Z [Term] id: GO:0075524 name: ribosomal skipping namespace: biological_process def: "A translation process in which a specific viral peptide prevents the ribosome from covalently linking a new inserted amino acid, and lets it continue translation, thereby cleaving the nascent protein while allowing translation to continue." [GOC:bf, GOC:jl, VZ:914] subset: virus_checked xref: VZ:914 "Ribosomal skipping" relationship: part_of GO:0019081 ! viral translation created_by: janelomax creation_date: 2011-08-03T03:19:37Z [Term] id: GO:0075525 name: viral translational termination-reinitiation namespace: biological_process def: "A process which occurs as part of viral mRNA translation which allows expression of a downstream open reading frame (ORF) in a dicistronic mRNA. In this process, ribosomes translate the upstream ORF but following termination, a proportion of 40S subunits remain tethered to the mRNA and go on to re-initiate translation at the start codon of the downstream ORF." [GOC:bf, GOC:jl, PMID:18631147, VZ:858] subset: virus_checked synonym: "termination reinitiation involved in viral translation" EXACT [GO:jl] synonym: "viral translation involving termination re-initiation" EXACT [GO:jl] synonym: "viral translation involving termination-reinitiation" EXACT [GO:jl] synonym: "viral translation involving translational stop-start" EXACT [GO:jl] xref: VZ:858 "RNA termination-reinitiation" relationship: part_of GO:0019081 ! viral translation created_by: janelomax creation_date: 2011-08-04T12:01:22Z [Term] id: GO:0075526 name: cap snatching namespace: biological_process def: "A translation initiation process during which a nucleotide sequence between 10 and 20 nucleotides in size is cleaved from the 5' end of host mRNAs by a viral RNA-dependent polymerase. The capped leader sequence obtained is subsequently used to prime transcription on the viral genome, which ultimately leads to the synthesis of capped, translatable viral mRNAs." [GOC:bf, GOC:jl, VZ:839] subset: virus_checked synonym: "cap snatching involved in viral mRNA transcription" EXACT [GO:jl] xref: VZ:839 relationship: part_of GO:0019083 ! viral transcription created_by: janelomax creation_date: 2011-08-04T01:19:00Z [Term] id: GO:0075527 name: viral RNA editing namespace: biological_process def: "The process by which bases in viral mRNA are chemically altered during viral transcription. This is usually the incorporation of 1 - 6 additional nucleotides, which shifts the reading frame, allowing the generation of different protein products or through a specific nucleotide change that eliminates the termination codon." [PMID:1629949, VZ:857] subset: virus_checked synonym: "RNA editing involved in viral mRNA transcription" EXACT [GO:jl] xref: VZ:857 "RNA editing" relationship: part_of GO:0019083 ! viral transcription created_by: janelomax creation_date: 2011-08-04T02:07:03Z [Term] id: GO:0080111 name: DNA demethylation namespace: biological_process def: "The removal of a methyl group from one or more nucleotides within an DNA molecule." [PMID:17208187] is_a: GO:0040029 ! regulation of gene expression, epigenetic created_by: donghui creation_date: 2009-04-27T02:42:05Z [Term] id: GO:0080120 name: CAAX-box protein maturation namespace: biological_process def: "A series of specific posttranslational modifications to the CAAX box region of CAAX box proteins. CAAX box proteins are eukaryotic proteins that contain a CAAX motif where the C is a cysteine, the two A residues are aliphatic amino acids and the X can be one of several amino acids. The CAAX-box proteins undergo three sequential, enzymatic, post-translational modifications essential to their targeting: First, the proteins are prenylated by one of two prenyltransferases called farnesyltransferase and geranylgeranyltransferase-I. Prenylation results in the covalent attachment of either farnesyl or geranylgeranyl isoprenoid groups to the cysteine in the CAAX box motif. Prenylation is followed by proteolytic removal of the last three amino acids of the protein (AAX). Finally, the newly exposed carboxylate group of the isoprenylcysteine is methylated by an ER-associated prenyl-dependent carboxylmethyltransferase." [PMID:12039957, PMID:17114793, PMID:18641086] synonym: "CAAX-box protein processing" RELATED [] synonym: "farnesylated protein maturation" RELATED [GOC:vw] is_a: GO:0051604 ! protein maturation relationship: has_part GO:0016485 ! protein processing created_by: donghui creation_date: 2009-04-28T03:06:13Z [Term] id: GO:0080149 name: sucrose induced translational repression namespace: biological_process def: "Any process that stops, prevents or reduces the rate of translation as a result of increase in sucrose level." [PMID:19403731] synonym: "negative regulation of translation in response to sucrose" EXACT [] is_a: GO:0032055 ! negative regulation of translation in response to stress created_by: donghui creation_date: 2010-03-26T04:13:15Z [Term] id: GO:0080188 name: RNA-directed DNA methylation namespace: biological_process def: "An epigenetic RNA-based gene silencing process first elucidated in plants whereby 24-nt small interfering RNAs (siRNAs) guide DNA methyltransferases to the siRNA-generating genomic loci and other loci that are homologous to the siRNAs for de novo DNA methylation. In general this process consists of three phases: biogenesis of siRNAs, scaffold RNA production, and the formation of the guiding complex that recruits de novo DNA methyltransferases to the target loci." [PMID:21420348] synonym: "RdDM" EXACT [] is_a: GO:0006306 ! DNA methylation is_a: GO:0031047 ! gene silencing by RNA created_by: donghui creation_date: 2012-05-22T02:22:50Z [Term] id: GO:0085032 name: modulation by symbiont of host I-kappaB kinase/NF-kappaB cascade namespace: biological_process def: "Any process in which an organism modulates the frequency, rate or extent of host NF-kappaB-mediated signal transduction pathways during the host defense response. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators] synonym: "modulation by symbiont of host NF-kappaB-mediated signal transduction pathway" EXACT [] is_a: GO:0043122 ! regulation of I-kappaB kinase/NF-kappaB cascade created_by: janelomax creation_date: 2010-07-27T02:13:37Z [Term] id: GO:0085033 name: positive regulation by symbiont of host I-kappaB kinase/NF-kappaB cascade namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of host NF-kappaB-mediated signal transduction pathways during the host defense response. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators] synonym: "activation by symbiont of host I-kappaB kinase/NF-kappaB cascade" EXACT [] synonym: "induction by symbiont of host I-kappaB kinase/NF-kappaB cascade" EXACT [] synonym: "positive regulation by symbiont of host NF-kappaB-mediated signal transduction pathway" EXACT [] synonym: "positive regulation by symbiont of nuclear factor kappa-light-chain-enhancer of activated B cells mediated signal transduction pathway" EXACT [] synonym: "stimulation by symbiont of host I-kappaB kinase/NF-kappaB cascade" EXACT [] synonym: "up regulation by symbiont of host I-kappaB kinase/NF-kappaB cascade" EXACT [] synonym: "up-regulation by symbiont of host I-kappaB kinase/NF-kappaB cascade" EXACT [] synonym: "upregulation by symbiont of host I-kappaB kinase/NF-kappaB cascade" EXACT [] is_a: GO:0043123 ! positive regulation of I-kappaB kinase/NF-kappaB cascade is_a: GO:0085032 ! modulation by symbiont of host I-kappaB kinase/NF-kappaB cascade created_by: janelomax creation_date: 2010-07-27T02:47:01Z [Term] id: GO:0085034 name: negative regulation by symbiont of host I-kappaB kinase/NF-kappaB cascade namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of host NF-kappaB-mediated signal transduction pathways during the host defense response. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators] is_a: GO:0043124 ! negative regulation of I-kappaB kinase/NF-kappaB cascade created_by: janelomax creation_date: 2010-07-27T03:32:44Z [Term] id: GO:0090019 name: regulation of transcription involved in anterior neural plate formation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter contributing to the formation of the anterior neural plate." [GOC:dph, GOC:sdb_2009, GOC:tb] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: tanyaberardini creation_date: 2009-07-29T11:38:28Z [Term] id: GO:0090020 name: regulation of transcription involved in posterior neural plate formation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter contributing to the formation of the posterior neural plate." [GOC:dph, GOC:sdb_2009, GOC:tb] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: tanyaberardini creation_date: 2009-07-29T11:39:29Z [Term] id: GO:0090052 name: regulation of chromatin silencing at centromere namespace: biological_process def: "Any process that modulates the frequency, rate or extent of chromatin silencing at the centromere. Chromatin silencing at the centromere is the repression of transcription of centromeric DNA by altering the structure of chromatin." [GOC:dph, GOC:tb] is_a: GO:0031935 ! regulation of chromatin silencing intersection_of: regulates GO:0030702 ! chromatin silencing at centromere relationship: regulates GO:0030702 ! chromatin silencing at centromere created_by: tanyaberardini creation_date: 2009-08-07T10:47:41Z [Term] id: GO:0090053 name: positive regulation of chromatin silencing at centromere namespace: biological_process def: "Any process that increases the frequency, rate or extent of chromatin silencing at the centromere. Chromatin silencing at the centromere is the repression of transcription of centromeric DNA by altering the structure of chromatin." [GOC:dph, GOC:tb] is_a: GO:0031937 ! positive regulation of chromatin silencing is_a: GO:0090052 ! regulation of chromatin silencing at centromere intersection_of: positively_regulates GO:0030702 ! chromatin silencing at centromere relationship: positively_regulates GO:0030702 ! chromatin silencing at centromere created_by: tanyaberardini creation_date: 2009-08-07T10:49:40Z [Term] id: GO:0090054 name: regulation of chromatin silencing at silent mating-type cassette namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of chromatin silencing at silent mating-type cassette. Chromatin silencing at silent mating-type cassette is the repression of transcription at silent mating-type loci by altering the structure of chromatin." [GOC:dph, GOC:tb] is_a: GO:0031935 ! regulation of chromatin silencing intersection_of: regulates GO:0030466 ! chromatin silencing at silent mating-type cassette relationship: regulates GO:0030466 ! chromatin silencing at silent mating-type cassette created_by: tanyaberardini creation_date: 2009-08-07T10:52:59Z [Term] id: GO:0090055 name: positive regulation of chromatin silencing at silent mating-type cassette namespace: biological_process def: "Any process that increases the frequency, rate, or extent of chromatin silencing at silent mating-type cassette. Chromatin silencing at silent mating-type cassette is the repression of transcription at silent mating-type loci by altering the structure of chromatin." [GOC:dph, GOC:tb] is_a: GO:0031937 ! positive regulation of chromatin silencing is_a: GO:0090054 ! regulation of chromatin silencing at silent mating-type cassette intersection_of: positively_regulates GO:0030466 ! chromatin silencing at silent mating-type cassette relationship: positively_regulates GO:0030466 ! chromatin silencing at silent mating-type cassette created_by: tanyaberardini creation_date: 2009-08-07T10:54:36Z [Term] id: GO:0090065 name: regulation of production of siRNA involved in RNA interference namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the production of siRNA, the cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of RNA interference." [GOC:dph, GOC:mah, GOC:tb] synonym: "regulation of RNA interference, production of siRNA" EXACT [GOC:mah] is_a: GO:0070920 ! regulation of production of small RNA involved in gene silencing by RNA is_a: GO:1900368 ! regulation of RNA interference intersection_of: regulates GO:0030422 ! production of siRNA involved in RNA interference relationship: regulates GO:0030422 ! production of siRNA involved in RNA interference created_by: tanyaberardini creation_date: 2009-08-12T11:41:09Z [Term] id: GO:0090079 name: translation regulator activity, nucleic acid binding namespace: molecular_function def: "Any selective and non-covalent interaction with a nucleic acid involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome." [GOC:dph, GOC:tb, GOC:vw] is_a: GO:0045182 ! translation regulator activity created_by: tanyaberardini creation_date: 2009-10-19T10:19:05Z [Term] id: GO:0090115 name: C-5 methylation on cytosine involved in chromatin silencing namespace: biological_process def: "The covalent transfer of a methyl group to C-5 of cytosine in a DNA molecule that contributes to chromatin silencing." [GOC:ascb_2009, GOC:dph, GOC:tb] is_a: GO:0090116 ! C-5 methylation of cytosine relationship: part_of GO:0006346 ! methylation-dependent chromatin silencing created_by: tanyaberardini creation_date: 2009-12-07T11:55:16Z [Term] id: GO:0090116 name: C-5 methylation of cytosine namespace: biological_process def: "The covalent transfer of a methyl group to C-5 of cytosine in a DNA molecule." [GOC:ascb_2009, GOC:dph, GOC:tb] is_a: GO:0032776 ! DNA methylation on cytosine created_by: tanyaberardini creation_date: 2009-12-07T11:58:47Z [Term] id: GO:0090124 name: N-4 methylation of cytosine namespace: biological_process def: "The covalent transfer of a methyl group to N-4 of cytosine in a DNA molecule." [GOC:ascb_2009, GOC:dph, GOC:tb] is_a: GO:0032776 ! DNA methylation on cytosine created_by: tanyaberardini creation_date: 2009-12-07T02:40:38Z [Term] id: GO:0090203 name: transcriptional activation by promoter-terminator looping namespace: biological_process def: "The formation and maintenance of DNA loops that juxtapose the promoter and terminator regions of RNA polymerase II-transcribed genes and activate transcription from an RNA polymerase II promoter." [GOC:dph, GOC:rb, GOC:tb] synonym: "transcriptional activation by memory gene loops" RELATED [GOC:dph, GOC:rb, GOC:tb] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: tanyaberardini creation_date: 2009-12-18T11:58:32Z [Term] id: GO:0090236 name: regulation of transcription from RNA polymerase II promoter involved in somitogenesis namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the formation of mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo." [GOC:ascb_2009, GOC:dph, GOC:tb] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: tanyaberardini creation_date: 2010-01-20T11:12:29Z [Term] id: GO:0090282 name: positive regulation of transcription involved in G2/M transition of mitotic cell cycle namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transcription of target genes that are transcribed as part of the G2/M transition of the mitotic cell cycle." [GOC:rn, PMID:10747051, PMID:10894548, PMID:10899128, PMID:10959837] synonym: "activation of G2/M-specific transcription in the mitotic cell cycle" EXACT [GOC:rn] synonym: "activation of transcription from RNA polymerase II promoter during G2/M-phase of the mitotic cell cycle" EXACT [GOC:rn] synonym: "activation of transcription involved in G2/M transition of mitotic cell cycle" EXACT [GOC:rn] synonym: "positive regulation of G2/M-specific transcription in the mitotic cell cycle" EXACT [GOC:rn] synonym: "positive regulation of transcription from RNA polymerase II promoter during G2/M-phase of the mitotic cell cycle" EXACT [GOC:rn] synonym: "up-regulation of G2/M-specific transcription in the mitotic cell cycle" EXACT [GOC:rn] synonym: "up-regulation of transcription from RNA polymerase II promoter during G2/M transition of the mitotic cell cycle" EXACT [GOC:rn] synonym: "up-regulation of transcription involved in G2/M transition of mitotic cell cycle" EXACT [GOC:rn] is_a: GO:0000117 ! regulation of transcription involved in G2/M transition of mitotic cell cycle is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045893 ! positive regulation of transcription, DNA-dependent created_by: tanyaberardini creation_date: 2010-02-09T02:13:26Z [Term] id: GO:0090293 name: nitrogen catabolite regulation of transcription namespace: biological_process def: "A transcription regulation process in which the presence of one nitrogen source leads to the modulation of the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other nitrogen sources." [GOC:mah, GOC:rb, PMID:19104072] synonym: "regulation of transcription by nitrogen catabolites" EXACT [GOC:mah] is_a: GO:0006355 ! regulation of transcription, DNA-dependent created_by: tanyaberardini creation_date: 2010-02-24T02:31:53Z [Term] id: GO:0090294 name: nitrogen catabolite activation of transcription namespace: biological_process def: "A transcription regulation process in which the presence of one nitrogen source leads to an increase in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other nitrogen sources." [GOC:mah, GOC:rb, PMID:19104072] synonym: "positive regulation of transcription by nitrogen catabolites" EXACT [GOC:mah] is_a: GO:0045893 ! positive regulation of transcription, DNA-dependent is_a: GO:0090293 ! nitrogen catabolite regulation of transcription created_by: tanyaberardini creation_date: 2010-02-24T02:31:53Z [Term] id: GO:0090295 name: nitrogen catabolite repression of transcription namespace: biological_process def: "A transcription regulation process in which the presence of one nitrogen source leads to a decrease in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other nitrogen sources." [GOC:mah, GOC:rb, PMID:19104072] synonym: "negative regulation of transcription by nitrogen catabolites" EXACT [GOC:mah] synonym: "nitrogen catabolite repression" EXACT [GOC:mah, GOC:rb] is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent is_a: GO:0090293 ! nitrogen catabolite regulation of transcription created_by: tanyaberardini creation_date: 2010-02-24T02:31:53Z [Term] id: GO:0090308 name: regulation of methylation-dependent chromatin silencing namespace: biological_process def: "Any process that modulates the rate, frequency, or extent of the repression of transcription by methylation of DNA, leading to the formation of heterochromatin." [GOC:BHF] is_a: GO:0031935 ! regulation of chromatin silencing intersection_of: regulates GO:0006346 ! methylation-dependent chromatin silencing relationship: regulates GO:0006346 ! methylation-dependent chromatin silencing created_by: tanyaberardini creation_date: 2010-04-09T02:12:53Z [Term] id: GO:0090309 name: positive regulation of methylation-dependent chromatin silencing namespace: biological_process def: "Any process that increases the rate, frequency, or extent of the repression of transcription by methylation of DNA, leading to the formation of heterochromatin." [GOC:BHF] is_a: GO:0031937 ! positive regulation of chromatin silencing is_a: GO:0090308 ! regulation of methylation-dependent chromatin silencing intersection_of: positively_regulates GO:0006346 ! methylation-dependent chromatin silencing relationship: positively_regulates GO:0006346 ! methylation-dependent chromatin silencing created_by: tanyaberardini creation_date: 2010-04-09T02:12:53Z [Term] id: GO:0090310 name: negative regulation of methylation-dependent chromatin silencing namespace: biological_process def: "Any process that decreases the rate, frequency, or extent of the repression of transcription by methylation of DNA, leading to the formation of heterochromatin." [GOC:BHF] is_a: GO:0031936 ! negative regulation of chromatin silencing is_a: GO:0090308 ! regulation of methylation-dependent chromatin silencing intersection_of: negatively_regulates GO:0006346 ! methylation-dependent chromatin silencing relationship: negatively_regulates GO:0006346 ! methylation-dependent chromatin silencing created_by: tanyaberardini creation_date: 2010-04-09T02:12:53Z [Term] id: GO:0090375 name: negative regulation of transcription from RNA polymerase II promoter in response to iron ion starvation namespace: biological_process def: "Any process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of deprivation of iron ions." [GOC:tb] synonym: "negative regulation of transcription from RNA polymerase II promoter in response to iron deficiency" EXACT [GOC:tb] is_a: GO:0033217 ! regulation of transcription from RNA polymerase II promoter in response to iron ion starvation is_a: GO:0097201 ! negative regulation of transcription from RNA polymerase II promoter in response to stress created_by: tanyaberardini creation_date: 2010-09-01T01:22:23Z [Term] id: GO:0090419 name: negative regulation of transcription involved in G2/M transition of mitotic cell cycle namespace: biological_process def: "Any process that inhibits or decreases the frequency, rate or extent of transcription of target genes that are transcribed as part of the G2/M transition of the mitotic cell cycle." [GOC:mtg_cell_cycle, PMID:10747051] synonym: "down-regulation of transcription from RNA polymerase II promoter during the G2/M transition of the mitotic cell cycle" RELATED [] synonym: "negative regulation of transcription from RNA polymerase II promoter during G2/M transition of the mitotic cell cycle" RELATED [] is_a: GO:0000117 ! regulation of transcription involved in G2/M transition of mitotic cell cycle intersection_of: GO:0045892 ! negative regulation of transcription, DNA-dependent created_by: tanyaberardini creation_date: 2011-10-26T03:59:41Z [Term] id: GO:0090472 name: dibasic protein processing namespace: biological_process def: "Any protein processing achieved by the cleavage of a peptide bond after two basic amino acids within a protein." [GOC:al] is_a: GO:0016485 ! protein processing created_by: tanyaberardini creation_date: 2012-10-01T10:39:26Z [Term] id: GO:0090473 name: lys-arg specific dibasic protein processing namespace: biological_process def: "Any protein processing achieved by the cleavage of a peptide bond after a lysine-arginine amino acid residue combination within a protein." [GOC:al] is_a: GO:0090472 ! dibasic protein processing created_by: tanyaberardini creation_date: 2012-10-01T10:42:30Z [Term] id: GO:0090474 name: arg-arg specific dibasic protein processing namespace: biological_process def: "Any protein processing achieved by the cleavage of a peptide bond after two consecutive arginine amino acid residues within a protein." [GOC:al] is_a: GO:0090472 ! dibasic protein processing created_by: tanyaberardini creation_date: 2012-10-01T10:42:30Z [Term] id: GO:0090475 name: lys-lys specific dibasic protein processing namespace: biological_process def: "Any protein processing achieved by the cleavage of a peptide bond after two consecutive lysine amino acid residues within a protein." [GOC:al] is_a: GO:0090472 ! dibasic protein processing created_by: tanyaberardini creation_date: 2012-10-01T10:42:30Z [Term] id: GO:0097167 name: circadian regulation of translation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of mRNA translation with a regularity of approximately 24 hours." [GOC:ans, PMID:17264215] synonym: "regulation of mRNA translation in response to circadian clock" EXACT [] is_a: GO:0006417 ! regulation of translation created_by: paola creation_date: 2011-09-29T03:13:31Z [Term] id: GO:0097201 name: negative regulation of transcription from RNA polymerase II promoter in response to stress namespace: biological_process def: "Any process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:rn, PMID:11027285, PMID:15575969, PMID:16556235, PMID:18086556, PMID:18627600] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter is_a: GO:0043618 ! regulation of transcription from RNA polymerase II promoter in response to stress created_by: paola creation_date: 2011-12-14T09:16:22Z [Term] id: GO:0097222 name: mitochondrial mRNA polyadenylation namespace: biological_process def: "The enzymatic addition of a sequence of 40-60 adenylyl residues at the 3' end of a eukaryotic mitochondrial mRNA primary transcript. Mitochondria contain both stabilizing and destabilizing poly(A) tails." [GOC:ans, PMID:18083837] is_a: GO:0006378 ! mRNA polyadenylation created_by: paola creation_date: 2012-01-24T02:47:19Z [Term] id: GO:0097235 name: positive regulation of fatty acid beta-oxidation by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of fatty acid beta-oxidation by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, PMID:1899286] is_a: GO:0072366 ! regulation of cellular ketone metabolic process by positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: paola creation_date: 2012-02-01T05:07:12Z [Term] id: GO:0097236 name: positive regulation of transcription from RNA polymerase II promoter in response to zinc ion starvation namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of deprivation of zinc ions." [GOC:dgf, PMID:19702872] is_a: GO:0034225 ! regulation of transcription from RNA polymerase II promoter in response to zinc ion starvation is_a: GO:0036003 ! positive regulation of transcription from RNA polymerase II promoter in response to stress created_by: paola creation_date: 2012-02-01T09:33:11Z [Term] id: GO:0097239 name: positive regulation of transcription from RNA polymerase II promoter in response to methylglyoxal namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter in response to a methylglyoxal stimulus." [GOC:dgf, PMID:15773992] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: paola creation_date: 2012-02-02T12:28:46Z [Term] id: GO:0097301 name: regulation of potassium ion concentration by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that regulates the internal concentration of potassium ions at the level of a cell by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, PMID:20412803] synonym: "cellular potassium ion homeostasis by positive regulation of transcription from RNA polymerase II promoter" EXACT [] synonym: "potassium ion homeostasis by positive regulation of transcription from RNA polymerase II promoter" BROAD [] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: paola creation_date: 2012-05-09T09:03:02Z [Term] id: GO:0097341 name: zymogen inhibition namespace: biological_process def: "Any process that prevents the proteolytic processing of an inactive enzyme to an active form." [GOC:mtg_apoptosis, PMID:20383739] synonym: "prevention of zymogen activation" EXACT [] is_a: GO:0010955 ! negative regulation of protein processing created_by: paola creation_date: 2012-06-18T11:25:45Z [Term] id: GO:0097381 name: photoreceptor disc membrane namespace: cellular_component def: "Ovally-shaped membranous stack located inside the photoreceptor outer segment, and containing densely packed molecules of the photoreceptor protein rhodopsin that traverse the lipid bilayer. Disc membranes are apparently derived from the plasma membrane in the region of the cilium that connects the photoreceptor outer segment to the inner segment." [GOC:bj, PMID:11826267, PMID:2537204, PMID:7507907] is_a: GO:0097458 ! neuron part relationship: part_of GO:0001750 ! photoreceptor outer segment created_by: paola creation_date: 2012-10-05T11:01:22Z [Term] id: GO:0097393 name: telomeric RNA transcription namespace: biological_process def: "The synthesis of telomeric RNA from a DNA template. A telomere is a complex of DNA and proteins that seals the end of a chromosome." [GOC:al, PMID:22139915] is_a: GO:0006351 ! transcription, DNA-dependent created_by: paola creation_date: 2012-10-23T10:06:17Z [Term] id: GO:0097394 name: telomeric RNA transcription from RNA pol II promoter namespace: biological_process def: "The synthesis of telomeric RNA from a DNA template by RNA Polymerase II (Pol II), originating at a Pol II promoter." [GOC:al, PMID:22139915] synonym: "telomeric RNA transcription from Pol II promoter" EXACT [] is_a: GO:0006366 ! transcription from RNA polymerase II promoter is_a: GO:0097393 ! telomeric RNA transcription created_by: paola creation_date: 2012-10-23T10:09:15Z [Term] id: GO:0097413 name: Lewy body namespace: cellular_component def: "Cytoplasmic, spherical inclusion commonly found in damaged neurons, and composed of abnormally phosphorylated, neurofilament proteins aggregated with ubiquitin and alpha-synuclein." [NIF_Subcellular:sao4933778419] synonym: "cytoplasmic inclusion" RELATED [] is_a: GO:0097458 ! neuron part created_by: paola creation_date: 2012-11-06T16:26:08Z [Term] id: GO:0097414 name: classical Lewy body namespace: cellular_component def: "Cytoplasmic inclusion, 5 to 15 micrometers in diameter, with a dense core surrounded by a halo of 10 to 20 nm wide radially oriented alpha-synuclein fibrils." [NIF_Subcellular:sao4749542545] synonym: "brainstem Lewy body" RELATED [] is_a: GO:0097413 ! Lewy body created_by: paola creation_date: 2012-11-06T16:27:41Z [Term] id: GO:0097415 name: cortical Lewy body namespace: cellular_component def: "Cytoplasmic inclusion similar to a classical Lewy body but lacking a halo of protein fibrils." [NIF_Subcellular:sao4040591221] is_a: GO:0097413 ! Lewy body created_by: paola creation_date: 2012-11-06T16:29:11Z [Term] id: GO:0097416 name: Lewy body-like hyaline inclusion namespace: cellular_component def: "Cytoplasmic inclusion found in neurons. It consists of filaments and granular materials, exhibits a dense core with a rough peripheral halo and lacks a limiting membrane. The filaments of these inclusions are composed of approximately 15-25 nm granule-coated fibrils in association with normal 10-nm neurofilaments." [NIF_Subcellular:nlx_subcell_20090105, PMID:18026741] synonym: "LBHI" EXACT [] is_a: GO:0097458 ! neuron part created_by: paola creation_date: 2012-11-06T16:46:15Z [Term] id: GO:0097418 name: neurofibrillary tangle namespace: cellular_component def: "Intracellular mass of paired, helically wound protein filaments (also called PHF) lying in the cytoplasm of neuronal cell bodies and neuritic cell processes. Neurofibrillary tangles contain an abnormally phosphorylated form of a microtubule-associated protein, tau. The shape of these inclusions may resemble a flame or a star." [NIF_Subcellular:nlx_subcell_20090201, NIF_Subcellular:nlx_subcell_20090202, NIF_Subcellular:sao2409833926] synonym: "flame-shaped neurofibrillary tangle" NARROW [] synonym: "star-shaped neurofibrillary tangle" NARROW [] is_a: GO:0097458 ! neuron part created_by: paola creation_date: 2012-11-06T16:49:35Z [Term] id: GO:0097428 name: protein maturation by iron-sulfur cluster transfer namespace: biological_process def: "The transfer of an assembled iron-sulfur cluster from a scaffold protein to an acceptor protein that contributes to the attainment of the full functional capacity of a protein." [GOC:al, GOC:mah, PMID:11939799, PMID:18322036, PMID:21977977] is_a: GO:0051604 ! protein maturation created_by: paola creation_date: 2012-11-15T09:59:06Z [Term] id: GO:0097440 name: apical dendrite namespace: cellular_component def: "A dendrite that emerges near the apical pole of a neuron. In bipolar neurons, apical dendrites are located on the opposite side of the soma from the axon." [NIF_Subcellular:sao273773228] is_a: GO:0030425 ! dendrite created_by: paola creation_date: 2012-12-06T13:45:18Z [Term] id: GO:0097441 name: basilar dendrite namespace: cellular_component def: "A dendrite that emerges near the basal pole of a neuron. In bipolar neurons, basal dendrites are either on the same side of the soma as the axon, or project toward the axon." [NIF_Subcellular:sao1079900774] is_a: GO:0030425 ! dendrite created_by: paola creation_date: 2012-12-06T13:46:28Z [Term] id: GO:0097442 name: CA3 pyramidal cell dendrite namespace: cellular_component def: "A dendrite of a hippocampal CA3 pyramidal cell." [NIF_Subcellular:nlx_subcell_1005001] is_a: GO:0030425 ! dendrite created_by: paola creation_date: 2012-12-06T13:47:23Z [Term] id: GO:0097444 name: spine apparatus namespace: cellular_component def: "A specialization of the endomembrane system found in some classes of neuron spines consisting of two or more closely apposed lamellae with interspersed dense material." [NIF_Subcellular:sao725931194] synonym: "dense material" NARROW [NIF_Subcellular:sao1004601938] is_a: GO:0097458 ! neuron part relationship: part_of GO:0044309 ! neuron spine created_by: paola creation_date: 2012-12-06T14:05:58Z [Term] id: GO:0097445 name: presynaptic active zone dense projection namespace: cellular_component def: "Electron dense projection extending from the cytomatrix into the cytoplasm on which synaptic vesicles are tethered." [NIF_Subcellular:sao494258938, PMID:15381754] synonym: "active zone dense projection" EXACT [] synonym: "pre-synaptic active zone dense projection" EXACT [] is_a: GO:0097458 ! neuron part relationship: part_of GO:0048786 ! presynaptic active zone created_by: paola creation_date: 2012-12-06T14:08:21Z [Term] id: GO:0097447 name: dendritic tree namespace: cellular_component def: "The entire complement of dendrites for a neuron, consisting of each primary dendrite and all its branches." [NIF_Subcellular:sao172297168] is_a: GO:0097458 ! neuron part relationship: has_part GO:0030425 ! dendrite created_by: paola creation_date: 2012-12-17T12:31:49Z [Term] id: GO:0097448 name: spine mat namespace: cellular_component def: "A configuration of neuron spines found on ciliary ganglion neurons in the embryonic and adult brain consisting of patches of closely spaced spines lying flat against the soma." [NIF_Subcellular:sao2128156969, PMID:10818137] is_a: GO:0097458 ! neuron part relationship: has_part GO:0044309 ! neuron spine created_by: paola creation_date: 2012-12-17T12:34:16Z [Term] id: GO:0097457 name: hippocampal mossy fiber namespace: cellular_component def: "Axon of dentate gyrus granule cell projecting to hippocampal area CA3, characterized by expansions (mossy fiber expansions) giving the fibers a mossy appearance. These unmyelinated axons were first described by Ramon y Cajal." [NIF_Subcellular:nlx_subcell_100312, PMID:17765709] is_a: GO:0044302 ! dentate gyrus mossy fiber created_by: paola creation_date: 2012-12-19T16:51:57Z [Term] id: GO:0097458 name: neuron part namespace: cellular_component def: "Any constituent part of a neuron, the basic cellular unit of nervous tissue. A typical neuron consists of a cell body (often called the soma), an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system." [GOC:pr, http://en.wikipedia.org/wiki/Neuron] subset: gocheck_do_not_annotate is_a: GO:0044464 ! cell part created_by: paola creation_date: 2012-12-19T16:53:50Z [Term] id: GO:0097462 name: Lewy neurite namespace: cellular_component def: "Elongated neuronal process, often with side branches and more than one branching point, described in brains of patients with Parkinson's disease. Lewy neurites stain positively for ubiquitin in brainstem and forebrain regions affected in Parkinson's disease." [NIF_Subcellular:sao601362597] is_a: GO:0043005 ! neuron projection created_by: paola creation_date: 2012-12-21T07:57:58Z [Term] id: GO:0097463 name: gemmule namespace: cellular_component def: "Spine-like process found on some neurons, e.g., periglomerular cells of olfactory cortex." [NIF_Subcellular:nlx_subcell_1005003] is_a: GO:0043005 ! neuron projection created_by: paola creation_date: 2012-12-21T07:59:04Z [Term] id: GO:0097464 name: thorny excrescence namespace: cellular_component def: "Large complex spine protruding from a dendrite. Each excrescence is formed by a cluster of spine heads." [NIF_Subcellular:nlx_467, PMID:730852] is_a: GO:0043197 ! dendritic spine created_by: paola creation_date: 2012-12-21T08:00:13Z [Term] id: GO:0097465 name: somatic spine namespace: cellular_component def: "Spine emanating from the cell soma of a neuron." [NIF_Subcellular:sao2048514053] is_a: GO:0044309 ! neuron spine created_by: paola creation_date: 2012-12-21T08:02:37Z [Term] id: GO:0097467 name: type III terminal bouton namespace: cellular_component def: "Terminal inflated portion of the axon of a non-glutamatergic neuron, containing the specialized apparatus necessary to release neurotransmitters at a regulatory synapse. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it. Type III terminal boutons are larger than type II ones." [GOC:mc, PMID:10218156] synonym: "type III terminal button" EXACT [] is_a: GO:0043195 ! terminal bouton created_by: paola creation_date: 2013-02-06T09:39:18Z [Term] id: GO:0097481 name: neuronal postsynaptic density namespace: cellular_component def: "A postsynaptic density that is part of a neuron." [GOC:pr] synonym: "neuron postsynaptic density" EXACT [] is_a: GO:0097458 ! neuron part relationship: part_of GO:0044327 ! dendritic spine head created_by: paola creation_date: 2013-07-02T09:44:28Z [Term] id: GO:1900018 name: phosphorylation of RNA polymerase II C-terminal domain serine 5 residues involved in recruitment of mRNA capping enzyme to RNA polymerase II holoenzyme complex namespace: biological_process def: "Any phosphorylation of RNA polymerase II C-terminal domain serine 5 residues that is involved in recruitment of mRNA capping enzyme to RNA polymerase II holoenzyme complex." [GOC:rb, GOC:TermGenie, PMID:10594013, PMID:19666497] is_a: GO:0071620 ! phosphorylation of RNA polymerase II C-terminal domain serine 5 residues intersection_of: GO:0071620 ! phosphorylation of RNA polymerase II C-terminal domain serine 5 residues intersection_of: part_of GO:0036031 ! recruitment of mRNA capping enzyme to RNA polymerase II holoenzyme complex relationship: part_of GO:0036031 ! recruitment of mRNA capping enzyme to RNA polymerase II holoenzyme complex created_by: bf creation_date: 2012-01-11T11:40:41Z [Term] id: GO:1900094 name: regulation of transcription from RNA polymerase II promoter involved in determination of left/right symmetry namespace: biological_process def: "Any regulation of transcription from RNA polymerase II promoter that is involved in determination of left/right symmetry." [GOC:BHF, GOC:TermGenie] synonym: "global transcription regulation from Pol II promoter of determination of left/right asymmetry" RELATED [GOC:TermGenie] synonym: "global transcription regulation from Pol II promoter of determination of left/right symmetry" RELATED [GOC:TermGenie] synonym: "regulation of gene-specific transcription from RNA polymerase II promoter of determination of left/right asymmetry" RELATED [GOC:TermGenie] synonym: "regulation of gene-specific transcription from RNA polymerase II promoter of determination of left/right symmetry" RELATED [GOC:TermGenie] synonym: "regulation of global transcription from Pol II promoter of determination of left/right asymmetry" RELATED [GOC:TermGenie] synonym: "regulation of global transcription from Pol II promoter of determination of left/right symmetry" RELATED [GOC:TermGenie] synonym: "regulation of transcription from Pol II promoter of determination of left/right asymmetry" EXACT [GOC:TermGenie] synonym: "regulation of transcription from Pol II promoter of determination of left/right symmetry" EXACT [GOC:TermGenie] synonym: "regulation of transcription from RNA polymerase II promoter of determination of left/right asymmetry" EXACT [GOC:TermGenie] synonym: "regulation of transcription from RNA polymerase II promoter of determination of left/right symmetry" EXACT [GOC:TermGenie] synonym: "regulation of transcription from RNA polymerase II promoter, global of determination of left/right asymmetry" RELATED [GOC:TermGenie] synonym: "regulation of transcription from RNA polymerase II promoter, global of determination of left/right symmetry" RELATED [GOC:TermGenie] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: vk creation_date: 2012-02-14T10:58:20Z [Term] id: GO:1900095 name: regulation of dosage compensation by inactivation of X chromosome namespace: biological_process def: "Any process that modulates the frequency, rate or extent of dosage compensation, by inactivation of X chromosome." [GOC:TermGenie] synonym: "regulation of Barr body formation" RELATED [GOC:TermGenie] synonym: "regulation of chromosome inactivation" BROAD [GOC:TermGenie] synonym: "regulation of X chromosome inactivation" EXACT [GOC:TermGenie] intersection_of: regulates GO:0009048 ! dosage compensation by inactivation of X chromosome relationship: regulates GO:0009048 ! dosage compensation by inactivation of X chromosome created_by: hjd creation_date: 2012-02-14T07:29:45Z [Term] id: GO:1900096 name: negative regulation of dosage compensation by inactivation of X chromosome namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of dosage compensation, by inactivation of X chromosome." [GOC:TermGenie] synonym: "down regulation of Barr body formation" RELATED [GOC:TermGenie] synonym: "down regulation of chromosome inactivation" BROAD [GOC:TermGenie] synonym: "down regulation of dosage compensation, by inactivation of X chromosome" EXACT [GOC:TermGenie] synonym: "down regulation of X chromosome inactivation" EXACT [GOC:TermGenie] synonym: "down-regulation of Barr body formation" RELATED [GOC:TermGenie] synonym: "down-regulation of chromosome inactivation" BROAD [GOC:TermGenie] synonym: "down-regulation of dosage compensation, by inactivation of X chromosome" EXACT [GOC:TermGenie] synonym: "down-regulation of X chromosome inactivation" EXACT [GOC:TermGenie] synonym: "downregulation of Barr body formation" RELATED [GOC:TermGenie] synonym: "downregulation of chromosome inactivation" BROAD [GOC:TermGenie] synonym: "downregulation of dosage compensation, by inactivation of X chromosome" EXACT [GOC:TermGenie] synonym: "downregulation of X chromosome inactivation" EXACT [GOC:TermGenie] synonym: "inhibition of Barr body formation" RELATED [GOC:TermGenie] synonym: "inhibition of chromosome inactivation" BROAD [GOC:TermGenie] synonym: "inhibition of dosage compensation, by inactivation of X chromosome" NARROW [GOC:TermGenie] synonym: "inhibition of X chromosome inactivation" EXACT [GOC:TermGenie] synonym: "negative regulation of Barr body formation" RELATED [GOC:TermGenie] synonym: "negative regulation of chromosome inactivation" BROAD [GOC:TermGenie] synonym: "negative regulation of X chromosome inactivation" EXACT [GOC:TermGenie] is_a: GO:1900095 ! regulation of dosage compensation by inactivation of X chromosome intersection_of: negatively_regulates GO:0009048 ! dosage compensation by inactivation of X chromosome relationship: negatively_regulates GO:0009048 ! dosage compensation by inactivation of X chromosome created_by: hjd creation_date: 2012-02-14T07:29:49Z [Term] id: GO:1900097 name: positive regulation of dosage compensation by inactivation of X chromosome namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of dosage compensation, by inactivation of X chromosome." [GOC:TermGenie] synonym: "activation of Barr body formation" RELATED [GOC:TermGenie] synonym: "activation of chromosome inactivation" BROAD [GOC:TermGenie] synonym: "activation of dosage compensation, by inactivation of X chromosome" NARROW [GOC:TermGenie] synonym: "activation of X chromosome inactivation" EXACT [GOC:TermGenie] synonym: "positive regulation of Barr body formation" RELATED [GOC:TermGenie] synonym: "positive regulation of chromosome inactivation" BROAD [GOC:TermGenie] synonym: "positive regulation of X chromosome inactivation" EXACT [GOC:TermGenie] synonym: "up regulation of Barr body formation" RELATED [GOC:TermGenie] synonym: "up regulation of chromosome inactivation" BROAD [GOC:TermGenie] synonym: "up regulation of dosage compensation, by inactivation of X chromosome" EXACT [GOC:TermGenie] synonym: "up regulation of X chromosome inactivation" EXACT [GOC:TermGenie] synonym: "up-regulation of Barr body formation" RELATED [GOC:TermGenie] synonym: "up-regulation of chromosome inactivation" BROAD [GOC:TermGenie] synonym: "up-regulation of dosage compensation, by inactivation of X chromosome" EXACT [GOC:TermGenie] synonym: "up-regulation of X chromosome inactivation" EXACT [GOC:TermGenie] synonym: "upregulation of Barr body formation" RELATED [GOC:TermGenie] synonym: "upregulation of chromosome inactivation" BROAD [GOC:TermGenie] synonym: "upregulation of dosage compensation, by inactivation of X chromosome" EXACT [GOC:TermGenie] synonym: "upregulation of X chromosome inactivation" EXACT [GOC:TermGenie] is_a: GO:1900095 ! regulation of dosage compensation by inactivation of X chromosome intersection_of: positively_regulates GO:0009048 ! dosage compensation by inactivation of X chromosome relationship: positively_regulates GO:0009048 ! dosage compensation by inactivation of X chromosome created_by: hjd creation_date: 2012-02-14T07:29:52Z [Term] id: GO:1900145 name: regulation of nodal signaling pathway involved in determination of left/right asymmetry namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a nodal signaling pathway, where the nodal signaling pathway is involved in determination of left/right asymmetry." [GOC:BHF, GOC:signaling, GOC:TermGenie, GOC:vk] synonym: "regulation of nodal signalling pathway involved in determination of left/right asymmetry" EXACT [GOC:mah] intersection_of: regulates GO:0038107 ! nodal signaling pathway involved in determination of left/right asymmetry relationship: regulates GO:0038107 ! nodal signaling pathway involved in determination of left/right asymmetry created_by: bf creation_date: 2012-03-06T11:00:32Z [Term] id: GO:1900146 name: negative regulation of nodal signaling pathway involved in determination of left/right asymmetry namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of a nodal signaling pathway, where the nodal signaling pathway is involved in determination of left/right asymmetry." [GOC:BHF, GOC:signaling, GOC:TermGenie, GOC:vk] synonym: "down regulation of nodal signaling pathway involved in determination of left/right asymmetry" EXACT [GOC:TermGenie] synonym: "down-regulation of nodal signaling pathway involved in determination of left/right asymmetry" EXACT [GOC:TermGenie] synonym: "downregulation of nodal signaling pathway involved in determination of left/right asymmetry" EXACT [GOC:TermGenie] synonym: "inhibition of nodal signaling pathway involved in determination of left/right asymmetry" NARROW [GOC:TermGenie] synonym: "negative regulation of nodal signalling pathway involved in determination of left/right asymmetry" EXACT [GOC:mah] is_a: GO:1900145 ! regulation of nodal signaling pathway involved in determination of left/right asymmetry intersection_of: negatively_regulates GO:0038107 ! nodal signaling pathway involved in determination of left/right asymmetry relationship: negatively_regulates GO:0038107 ! nodal signaling pathway involved in determination of left/right asymmetry created_by: bf creation_date: 2012-03-06T11:00:36Z [Term] id: GO:1900164 name: nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry namespace: biological_process def: "A series of molecular signals initiated by the binding of a nodal protein to an activin receptor on the surface of a target cell, which contributes to the establishment of lateral mesoderm with respect to the left and right halves." [GOC:BHF, GOC:TermGenie, GOC:vk] synonym: "nodal signaling of determination of left/right asymmetry in lateral mesoderm" EXACT [GOC:TermGenie] synonym: "nodal signaling pathway of determination of left/right asymmetry in lateral mesoderm" EXACT [GOC:TermGenie] synonym: "nodal signalling pathway involved in determination of lateral mesoderm left/right asymmetry" EXACT [GOC:mah] is_a: GO:0038107 ! nodal signaling pathway involved in determination of left/right asymmetry created_by: bf creation_date: 2012-03-08T02:58:39Z [Term] id: GO:1900175 name: regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a nodal signaling pathway, where the nodal signaling pathway is involved in determination of left/right asymmetry in the lateral mesoderm." [GOC:BHF, GOC:TermGenie, GOC:vk] synonym: "regulation of nodal signalling pathway involved in determination of lateral mesoderm left/right asymmetry" EXACT [GOC:mah] is_a: GO:1900145 ! regulation of nodal signaling pathway involved in determination of left/right asymmetry intersection_of: regulates GO:1900164 ! nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry relationship: regulates GO:1900164 ! nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry created_by: bf creation_date: 2012-03-09T10:39:10Z [Term] id: GO:1900176 name: negative regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of a nodal signaling pathway, where the nodal signaling pathway is involved in determination of left/right asymmetry in the lateral mesoderm." [GOC:BHF, GOC:TermGenie, GOC:vk, PMID:15084459] synonym: "down-regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry" EXACT [GOC:TermGenie] synonym: "downregulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry" EXACT [GOC:TermGenie] synonym: "inhibition of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry" NARROW [GOC:TermGenie] synonym: "negative regulation of nodal signalling pathway involved in determination of lateral mesoderm left/right asymmetry" EXACT [GOC:mah] is_a: GO:1900146 ! negative regulation of nodal signaling pathway involved in determination of left/right asymmetry is_a: GO:1900175 ! regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry intersection_of: negatively_regulates GO:1900164 ! nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry relationship: negatively_regulates GO:1900164 ! nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry created_by: bf creation_date: 2012-03-09T10:39:14Z [Term] id: GO:1900224 name: positive regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry." [GOC:BHF, GOC:TermGenie] synonym: "activation of nodal signaling of determination of left/right asymmetry in lateral mesoderm" EXACT [GOC:TermGenie] synonym: "activation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry" NARROW [GOC:TermGenie] synonym: "activation of nodal signaling pathway of determination of left/right asymmetry in lateral mesoderm" EXACT [GOC:TermGenie] synonym: "positive regulation of nodal signaling of determination of left/right asymmetry in lateral mesoderm" EXACT [GOC:TermGenie] synonym: "positive regulation of nodal signaling pathway of determination of left/right asymmetry in lateral mesoderm" EXACT [GOC:TermGenie] synonym: "positive regulation of nodal signalling pathway involved in determination of lateral mesoderm left/right asymmetry" EXACT [GOC:mah] synonym: "up regulation of nodal signaling of determination of left/right asymmetry in lateral mesoderm" EXACT [GOC:TermGenie] synonym: "up regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry" EXACT [GOC:TermGenie] synonym: "up regulation of nodal signaling pathway of determination of left/right asymmetry in lateral mesoderm" EXACT [GOC:TermGenie] synonym: "up-regulation of nodal signaling of determination of left/right asymmetry in lateral mesoderm" EXACT [GOC:TermGenie] synonym: "up-regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry" EXACT [GOC:TermGenie] synonym: "up-regulation of nodal signaling pathway of determination of left/right asymmetry in lateral mesoderm" EXACT [GOC:TermGenie] synonym: "upregulation of nodal signaling of determination of left/right asymmetry in lateral mesoderm" EXACT [GOC:TermGenie] synonym: "upregulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry" EXACT [GOC:TermGenie] synonym: "upregulation of nodal signaling pathway of determination of left/right asymmetry in lateral mesoderm" EXACT [GOC:TermGenie] is_a: GO:1900175 ! regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry intersection_of: positively_regulates GO:1900164 ! nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry relationship: positively_regulates GO:1900164 ! nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry created_by: vk creation_date: 2012-03-22T02:30:13Z [Term] id: GO:1900247 name: regulation of cytoplasmic translational elongation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of cytoplasmic translational elongation." [GOC:TermGenie] is_a: GO:0006448 ! regulation of translational elongation is_a: GO:2000765 ! regulation of cytoplasmic translation intersection_of: regulates GO:0002182 ! cytoplasmic translational elongation relationship: regulates GO:0002182 ! cytoplasmic translational elongation created_by: vw creation_date: 2012-04-03T05:07:02Z [Term] id: GO:1900248 name: negative regulation of cytoplasmic translational elongation namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of cytoplasmic translational elongation." [GOC:TermGenie] synonym: "down regulation of cytoplasmic translational elongation" EXACT [GOC:TermGenie] synonym: "down-regulation of cytoplasmic translational elongation" EXACT [GOC:TermGenie] synonym: "downregulation of cytoplasmic translational elongation" EXACT [GOC:TermGenie] synonym: "inhibition of cytoplasmic translational elongation" NARROW [GOC:TermGenie] is_a: GO:0045900 ! negative regulation of translational elongation is_a: GO:1900247 ! regulation of cytoplasmic translational elongation intersection_of: negatively_regulates GO:0002182 ! cytoplasmic translational elongation relationship: negatively_regulates GO:0002182 ! cytoplasmic translational elongation created_by: vw creation_date: 2012-04-03T05:07:14Z [Term] id: GO:1900249 name: positive regulation of cytoplasmic translational elongation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of cytoplasmic translational elongation." [GOC:TermGenie] synonym: "activation of cytoplasmic translational elongation" NARROW [GOC:TermGenie] synonym: "up regulation of cytoplasmic translational elongation" EXACT [GOC:TermGenie] synonym: "up-regulation of cytoplasmic translational elongation" EXACT [GOC:TermGenie] synonym: "upregulation of cytoplasmic translational elongation" EXACT [GOC:TermGenie] is_a: GO:0045901 ! positive regulation of translational elongation is_a: GO:1900247 ! regulation of cytoplasmic translational elongation intersection_of: positively_regulates GO:0002182 ! cytoplasmic translational elongation relationship: positively_regulates GO:0002182 ! cytoplasmic translational elongation created_by: vw creation_date: 2012-04-03T05:07:24Z [Term] id: GO:1900363 name: regulation of mRNA polyadenylation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of mRNA polyadenylation." [GOC:se, GOC:TermGenie, PMID:15121841] synonym: "regulation of cleavage and polyadenylylation specificity factor activity" NARROW [GOC:TermGenie] synonym: "regulation of mRNA polyadenylylation" EXACT [GOC:TermGenie] is_a: GO:0031440 ! regulation of mRNA 3'-end processing intersection_of: regulates GO:0006378 ! mRNA polyadenylation relationship: regulates GO:0006378 ! mRNA polyadenylation created_by: pr creation_date: 2012-04-12T04:36:21Z [Term] id: GO:1900364 name: negative regulation of mRNA polyadenylation namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of mRNA polyadenylation." [GOC:se, GOC:TermGenie, PMID:15121841] synonym: "down regulation of cleavage and polyadenylylation specificity factor activity" NARROW [GOC:TermGenie] synonym: "down regulation of mRNA polyadenylation" EXACT [GOC:TermGenie] synonym: "down regulation of mRNA polyadenylylation" EXACT [GOC:TermGenie] synonym: "down-regulation of cleavage and polyadenylylation specificity factor activity" NARROW [GOC:TermGenie] synonym: "down-regulation of mRNA polyadenylation" EXACT [GOC:TermGenie] synonym: "down-regulation of mRNA polyadenylylation" EXACT [GOC:TermGenie] synonym: "downregulation of cleavage and polyadenylylation specificity factor activity" NARROW [GOC:TermGenie] synonym: "downregulation of mRNA polyadenylation" EXACT [GOC:TermGenie] synonym: "downregulation of mRNA polyadenylylation" EXACT [GOC:TermGenie] synonym: "inhibition of cleavage and polyadenylylation specificity factor activity" NARROW [GOC:TermGenie] synonym: "inhibition of mRNA polyadenylation" NARROW [GOC:TermGenie] synonym: "inhibition of mRNA polyadenylylation" NARROW [GOC:TermGenie] synonym: "negative regulation of cleavage and polyadenylylation specificity factor activity" NARROW [GOC:TermGenie] synonym: "negative regulation of mRNA polyadenylylation" EXACT [GOC:TermGenie] is_a: GO:0031441 ! negative regulation of mRNA 3'-end processing is_a: GO:1900363 ! regulation of mRNA polyadenylation intersection_of: negatively_regulates GO:0006378 ! mRNA polyadenylation relationship: negatively_regulates GO:0006378 ! mRNA polyadenylation created_by: pr creation_date: 2012-04-12T04:36:31Z [Term] id: GO:1900365 name: positive regulation of mRNA polyadenylation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of mRNA polyadenylation." [GOC:se, GOC:TermGenie, PMID:15121841] synonym: "activation of cleavage and polyadenylylation specificity factor activity" NARROW [GOC:TermGenie] synonym: "activation of mRNA polyadenylation" NARROW [GOC:TermGenie] synonym: "activation of mRNA polyadenylylation" NARROW [GOC:TermGenie] synonym: "positive regulation of cleavage and polyadenylylation specificity factor activity" NARROW [GOC:TermGenie] synonym: "positive regulation of mRNA polyadenylylation" EXACT [GOC:TermGenie] synonym: "up regulation of cleavage and polyadenylylation specificity factor activity" NARROW [GOC:TermGenie] synonym: "up regulation of mRNA polyadenylation" EXACT [GOC:TermGenie] synonym: "up regulation of mRNA polyadenylylation" EXACT [GOC:TermGenie] synonym: "up-regulation of cleavage and polyadenylylation specificity factor activity" NARROW [GOC:TermGenie] synonym: "up-regulation of mRNA polyadenylation" EXACT [GOC:TermGenie] synonym: "up-regulation of mRNA polyadenylylation" EXACT [GOC:TermGenie] synonym: "upregulation of cleavage and polyadenylylation specificity factor activity" NARROW [GOC:TermGenie] synonym: "upregulation of mRNA polyadenylation" EXACT [GOC:TermGenie] synonym: "upregulation of mRNA polyadenylylation" EXACT [GOC:TermGenie] is_a: GO:0031442 ! positive regulation of mRNA 3'-end processing is_a: GO:1900363 ! regulation of mRNA polyadenylation intersection_of: positively_regulates GO:0006378 ! mRNA polyadenylation relationship: positively_regulates GO:0006378 ! mRNA polyadenylation created_by: pr creation_date: 2012-04-12T04:36:39Z [Term] id: GO:1900368 name: regulation of RNA interference namespace: biological_process def: "Any process that modulates the frequency, rate or extent of RNA interference." [GOC:kmv, GOC:TermGenie, PMID:22412382] synonym: "regulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie] synonym: "regulation of RNAi" EXACT [GOC:TermGenie] is_a: GO:0060147 ! regulation of posttranscriptional gene silencing is_a: GO:0060966 ! regulation of gene silencing by RNA intersection_of: regulates GO:0016246 ! RNA interference relationship: regulates GO:0016246 ! RNA interference created_by: kmv creation_date: 2012-04-13T08:28:39Z [Term] id: GO:1900369 name: negative regulation of RNA interference namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of RNA interference." [GOC:kmv, GOC:TermGenie, PMID:22412382] synonym: "down regulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie] synonym: "down regulation of RNA interference" EXACT [GOC:TermGenie] synonym: "down regulation of RNAi" EXACT [GOC:TermGenie] synonym: "down-regulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie] synonym: "down-regulation of RNA interference" EXACT [GOC:TermGenie] synonym: "down-regulation of RNAi" EXACT [GOC:TermGenie] synonym: "downregulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie] synonym: "downregulation of RNA interference" EXACT [GOC:TermGenie] synonym: "downregulation of RNAi" EXACT [GOC:TermGenie] synonym: "inhibition of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie] synonym: "inhibition of RNA interference" NARROW [GOC:TermGenie] synonym: "inhibition of RNAi" EXACT [GOC:TermGenie] synonym: "negative regulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie] synonym: "negative regulation of RNAi" EXACT [GOC:TermGenie] is_a: GO:0060149 ! negative regulation of posttranscriptional gene silencing is_a: GO:0060967 ! negative regulation of gene silencing by RNA is_a: GO:1900368 ! regulation of RNA interference intersection_of: negatively_regulates GO:0016246 ! RNA interference relationship: negatively_regulates GO:0016246 ! RNA interference created_by: kmv creation_date: 2012-04-13T08:28:50Z [Term] id: GO:1900370 name: positive regulation of RNA interference namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of RNA interference." [GOC:kmv, GOC:TermGenie, PMID:22412382] synonym: "activation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie] synonym: "activation of RNA interference" NARROW [GOC:TermGenie] synonym: "activation of RNAi" EXACT [GOC:TermGenie] synonym: "positive regulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie] synonym: "positive regulation of RNAi" EXACT [GOC:TermGenie] synonym: "up regulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie] synonym: "up regulation of RNA interference" EXACT [GOC:TermGenie] synonym: "up regulation of RNAi" EXACT [GOC:TermGenie] synonym: "up-regulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie] synonym: "up-regulation of RNA interference" EXACT [GOC:TermGenie] synonym: "up-regulation of RNAi" EXACT [GOC:TermGenie] synonym: "upregulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie] synonym: "upregulation of RNA interference" EXACT [GOC:TermGenie] synonym: "upregulation of RNAi" EXACT [GOC:TermGenie] is_a: GO:0060148 ! positive regulation of posttranscriptional gene silencing is_a: GO:1900368 ! regulation of RNA interference intersection_of: positively_regulates GO:0016246 ! RNA interference relationship: positively_regulates GO:0016246 ! RNA interference created_by: kmv creation_date: 2012-04-13T08:29:00Z [Term] id: GO:1900374 name: positive regulation of mating type switching by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A regulation of transcription from RNA polymerase II promoter that results in positive regulation of mating type switching." [GOC:go_curators, GOC:TermGenie, PMID:8804308] synonym: "activation of mating type switching by regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "stimulation of mating type switching by regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "up regulation of mating type switching by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of mating type switching by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of mating type switching by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: krc creation_date: 2012-04-17T12:39:56Z [Term] id: GO:1900375 name: positive regulation of inositol biosynthetic process by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A positive regulation of transcription from RNA polymerase II promoter that results in positive regulation of inositol biosynthetic process." [GOC:go_curators, GOC:TermGenie, PMID:2004420] synonym: "activation of inositol anabolism by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "activation of inositol biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "activation of inositol biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "activation of inositol formation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "activation of inositol synthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "activation of myo-inositol biosynthesis by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "activation of myo-inositol biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "activation of vitamin Bh biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "activation of vitamin Bh biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "positive regulation of inositol anabolism by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "positive regulation of inositol biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "positive regulation of inositol formation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "positive regulation of inositol synthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "positive regulation of myo-inositol biosynthesis by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "positive regulation of myo-inositol biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "positive regulation of vitamin Bh biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "positive regulation of vitamin Bh biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of inositol anabolism by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of inositol biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of inositol biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of inositol formation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of inositol synthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of myo-inositol biosynthesis by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "up regulation of myo-inositol biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "up regulation of vitamin Bh biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of vitamin Bh biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of inositol anabolism by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of inositol biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of inositol biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of inositol formation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of inositol synthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of myo-inositol biosynthesis by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "up-regulation of myo-inositol biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "up-regulation of vitamin Bh biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of vitamin Bh biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of inositol anabolism by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of inositol biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of inositol biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of inositol formation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of inositol synthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of myo-inositol biosynthesis by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "upregulation of myo-inositol biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "upregulation of vitamin Bh biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of vitamin Bh biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter is_a: GO:1900402 ! regulation of carbohydrate metabolic process by regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: krc creation_date: 2012-04-17T12:45:48Z [Term] id: GO:1900382 name: regulation of thiamine biosynthetic process by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A regulation of transcription from RNA polymerase II promoter that results in regulation of thiamine biosynthetic process." [GOC:mah, GOC:TermGenie, PMID:16874521] synonym: "regulation of thiamin biosynthetic process by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "regulation of thiamine anabolism by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "regulation of thiamine biosynthesis by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "regulation of thiamine formation by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "regulation of thiamine synthesis by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: mah creation_date: 2012-04-17T04:05:24Z [Term] id: GO:1900387 name: negative regulation of cell-cell adhesion by negative regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A negative regulation of transcription from RNA polymerase II promoter that results in negative regulation of cell-cell adhesion." [GOC:BHF, GOC:TermGenie, PMID:15737616] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter intersection_of: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: pr creation_date: 2012-04-18T12:01:19Z [Term] id: GO:1900388 name: regulation of vesicle-mediated transport by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A regulation of transcription from RNA polymerase II promoter that results in regulation of vesicle-mediated transport." [GOC:mah, GOC:TermGenie, PMID:18622392] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: mah creation_date: 2012-04-18T03:52:29Z [Term] id: GO:1900389 name: regulation of glucose import by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A regulation of transcription from RNA polymerase II promoter that results in regulation of glucose import." [GOC:mah, GOC:TermGenie, PMID:18622392] synonym: "regulation of glucose uptake by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: mah creation_date: 2012-04-18T03:52:43Z [Term] id: GO:1900391 name: regulation of cAMP-mediated signaling by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A regulation of transcription from RNA polymerase II promoter that results in regulation of cAMP-mediated signaling." [GOC:mah, GOC:TermGenie, PMID:15448137] synonym: "regulation of cAMP-mediated signalling by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: mah creation_date: 2012-04-18T04:19:39Z [Term] id: GO:1900392 name: regulation of transport by negative regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A negative regulation of transcription from RNA polymerase II promoter that results in regulation of transport." [GOC:mah, GOC:TermGenie, PMID:17446861] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter intersection_of: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: mah creation_date: 2012-04-18T04:20:25Z [Term] id: GO:1900393 name: regulation of iron ion transport by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A regulation of transcription from RNA polymerase II promoter that results in regulation of iron ion transport." [GOC:mah, GOC:TermGenie, PMID:11956219] synonym: "regulation of Fe transport by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "regulation of iron transport by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: mah creation_date: 2012-04-18T04:20:39Z [Term] id: GO:1900400 name: regulation of iron ion import by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A regulation of transcription from RNA polymerase II promoter that results in regulation of iron ion import." [GOC:mah, GOC:TermGenie, PMID:18622392] synonym: "regulation of iron import by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:1900393 ! regulation of iron ion transport by regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: mah creation_date: 2012-04-20T02:34:12Z [Term] id: GO:1900401 name: regulation of meiosis by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A regulation of transcription from RNA polymerase II promoter that results in regulation of meiosis." [GOC:mah, GOC:TermGenie, PMID:12161753] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: mah creation_date: 2012-04-20T02:45:12Z [Term] id: GO:1900402 name: regulation of carbohydrate metabolic process by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A regulation of transcription from RNA polymerase II promoter that results in regulation of carbohydrate metabolic process." [GOC:mah, GOC:TermGenie, PMID:16408318] synonym: "regulation of carbohydrate metabolism by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: mah creation_date: 2012-04-20T02:45:27Z [Term] id: GO:1900403 name: negative regulation of cellular amino acid biosynthetic process by negative regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A negative regulation of transcription from RNA polymerase II promoter that results in negative regulation of cellular amino acid biosynthetic process." [GOC:mah, GOC:TermGenie, PMID:17446861] synonym: "negative regulation of amino acid biosynthetic process by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "negative regulation of cellular amino acid anabolism by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "negative regulation of cellular amino acid biosynthesis by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "negative regulation of cellular amino acid formation by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "negative regulation of cellular amino acid synthesis by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0072365 ! regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter intersection_of: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: mah creation_date: 2012-04-20T02:45:42Z [Term] id: GO:1900404 name: positive regulation of DNA repair by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A positive regulation of transcription from RNA polymerase II promoter that results in positive regulation of DNA repair." [GOC:mah, GOC:TermGenie, PMID:20299455] synonym: "activation of DNA repair by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "stimulation of DNA repair by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "up regulation of DNA repair by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of DNA repair by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of DNA repair by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: mah creation_date: 2012-04-20T02:45:56Z [Term] id: GO:1900405 name: regulation of cytokinetic cell separation by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A regulation of transcription from RNA polymerase II promoter that results in regulation of cytokinetic cell separation." [GOC:mah, GOC:TermGenie, PMID:10491317, PMID:12665550] synonym: "regulation of cell separation during cytokinesis by regulation of transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: mah creation_date: 2012-04-20T02:46:10Z [Term] id: GO:1900406 name: regulation of conjugation with cellular fusion by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A regulation of transcription from RNA polymerase II promoter that results in regulation of conjugation with cellular fusion." [GOC:mah, GOC:TermGenie, PMID:1112904] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: mah creation_date: 2012-04-20T02:46:24Z [Term] id: GO:1900410 name: regulation of histone modification by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A regulation of transcription from RNA polymerase II promoter that results in regulation of histone modification." [GOC:mah, GOC:TermGenie] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: mah creation_date: 2012-04-20T03:35:08Z [Term] id: GO:1900411 name: regulation of histone acetylation by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A regulation of transcription from RNA polymerase II promoter that results in regulation of histone acetylation." [GOC:mah, GOC:TermGenie, PMID:15218150] is_a: GO:1900410 ! regulation of histone modification by regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: mah creation_date: 2012-04-20T03:35:22Z [Term] id: GO:1900412 name: regulation of histone methylation by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A regulation of transcription from RNA polymerase II promoter that results in regulation of histone methylation." [GOC:mah, GOC:TermGenie, PMID:15218150] is_a: GO:1900410 ! regulation of histone modification by regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: mah creation_date: 2012-04-20T03:35:36Z [Term] id: GO:1900413 name: positive regulation of phospholipid biosynthetic process by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A positive regulation of transcription from RNA polymerase II promoter that results in positive regulation of phospholipid biosynthetic process." [GOC:mah, GOC:TermGenie, PMID:16537923] synonym: "positive regulation of phospholipid biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "positive regulation of phospholipid synthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: mah creation_date: 2012-04-20T03:41:58Z [Term] id: GO:1900415 name: regulation of fungal-type cell wall biogenesis by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A regulation of transcription from RNA polymerase II promoter that results in regulation of fungal-type cell wall biogenesis." [GOC:mah, GOC:TermGenie, PMID:15509866] synonym: "regulation of chitin- and beta-glucan-containing cell wall biogenesis by regulation of transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: mah creation_date: 2012-04-20T03:42:27Z [Term] id: GO:1900416 name: regulation of 4,6-pyruvylated galactose residue biosynthetic process by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A regulation of transcription from RNA polymerase II promoter that results in regulation of 4,6-pyruvylated galactose residue biosynthetic process." [GOC:mah, GOC:TermGenie, PMID:15173185] is_a: GO:1900402 ! regulation of carbohydrate metabolic process by regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: mah creation_date: 2012-04-20T03:42:41Z [Term] id: GO:1900417 name: negative regulation of transmembrane transport by negative regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A negative regulation of transcription from RNA polymerase II promoter that results in negative regulation of transmembrane transport." [GOC:mah, GOC:TermGenie, PMID:20404084] is_a: GO:1900392 ! regulation of transport by negative regulation of transcription from RNA polymerase II promoter intersection_of: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: mah creation_date: 2012-04-20T03:42:55Z [Term] id: GO:1900418 name: positive regulation of purine nucleotide biosynthetic process by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A positive regulation of transcription from RNA polymerase II promoter that results in positive regulation of purine nucleotide biosynthetic process." [GOC:curators, GOC:TermGenie, PMID:17573544] synonym: "activation of purine nucleotide anabolism by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "activation of purine nucleotide biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "activation of purine nucleotide biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "activation of purine nucleotide formation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "activation of purine nucleotide synthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "positive regulation of purine nucleotide anabolism by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "positive regulation of purine nucleotide biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "positive regulation of purine nucleotide formation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "positive regulation of purine nucleotide synthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of purine nucleotide anabolism by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of purine nucleotide biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of purine nucleotide biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of purine nucleotide formation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of purine nucleotide synthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of purine nucleotide anabolism by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of purine nucleotide biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of purine nucleotide biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of purine nucleotide formation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of purine nucleotide synthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of purine nucleotide anabolism by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of purine nucleotide biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of purine nucleotide biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of purine nucleotide formation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of purine nucleotide synthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: krc creation_date: 2012-04-20T10:13:58Z [Term] id: GO:1900422 name: positive regulation of cellular alcohol catabolic process by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A positive regulation of transcription from RNA polymerase II promoter that results in positive regulation of cellular alcohol catabolic process." [GOC:curators, GOC:TermGenie, PMID:3305157, PMID:8221926] synonym: "activation of cellular alcohol catabolic process by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "up regulation of cellular alcohol catabolic process by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of cellular alcohol catabolic process by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of cellular alcohol catabolic process by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: krc creation_date: 2012-04-24T05:13:25Z [Term] id: GO:1900423 name: positive regulation of mating type switching by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A positive regulation of transcription from RNA polymerase II promoter that results in positive regulation of mating type switching." [GOC:TermGenie, PMID:8804308] synonym: "activation of mating type switching by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "stimulation of mating type switching by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "up regulation of mating type switching by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of mating type switching by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of mating type switching by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter is_a: GO:1900374 ! positive regulation of mating type switching by regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: krc creation_date: 2012-04-24T05:50:51Z [Term] id: GO:1900427 name: regulation of cellular response to oxidative stress by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A regulation of transcription from RNA polymerase II promoter that results in regulation of cellular response to oxidative stress." [GOC:mah, GOC:TermGenie, PMID:10348908] synonym: "regulation of adaptive response to oxidative stress by regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: mah creation_date: 2012-04-25T09:11:41Z [Term] id: GO:1900446 name: negative regulation of tRNA transcription from RNA polymerase III promoter namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of tRNA transcription from RNA polymerase III promoter." [GOC:sart, GOC:TermGenie] synonym: "down regulation of tRNA transcription from Pol III promoter" EXACT [GOC:TermGenie] synonym: "down regulation of tRNA transcription from RNA polymerase III promoter" EXACT [GOC:TermGenie] synonym: "down-regulation of tRNA transcription from Pol III promoter" EXACT [GOC:TermGenie] synonym: "down-regulation of tRNA transcription from RNA polymerase III promoter" EXACT [GOC:TermGenie] synonym: "downregulation of tRNA transcription from Pol III promoter" EXACT [GOC:TermGenie] synonym: "downregulation of tRNA transcription from RNA polymerase III promoter" EXACT [GOC:TermGenie] synonym: "inhibition of tRNA transcription from Pol III promoter" EXACT [GOC:TermGenie] synonym: "inhibition of tRNA transcription from RNA polymerase III promoter" NARROW [GOC:TermGenie] synonym: "negative regulation of tRNA transcription from Pol III promoter" EXACT [GOC:TermGenie] is_a: GO:0016480 ! negative regulation of transcription from RNA polymerase III promoter intersection_of: negatively_regulates GO:0042797 ! tRNA transcription from RNA polymerase III promoter relationship: negatively_regulates GO:0042797 ! tRNA transcription from RNA polymerase III promoter created_by: sart creation_date: 2012-04-26T05:28:34Z [Term] id: GO:1900448 name: regulation of pyrimidine nucleotide biosynthetic process by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of pyrimidine nucleotide biosynthesis by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:TermGenie] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: jh creation_date: 2012-04-27T02:57:38Z [Term] id: GO:1900460 name: negative regulation of invasive growth in response to glucose limitation by negative regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of invasive growth in response to glucose limitation by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, GOC:TermGenie, PMID:12024013, PMID:15466424, PMID:9811878] synonym: "negative regulation of colony morphology by negative regulation of transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter intersection_of: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: dianna.fisk creation_date: 2012-05-01T06:09:17Z [Term] id: GO:1900461 name: positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of pseudohyphal growth by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, GOC:TermGenie, PMID:11046133, PMID:8710886, PMID:9987114] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: dianna.fisk creation_date: 2012-05-01T07:01:40Z [Term] id: GO:1900462 name: negative regulation of pseudohyphal growth by negative regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of pseudohyphal growth by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II Any process that stops, prevents, or reduces the frequency, rate or extent of pseudohyphal growth by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, GOC:TermGenie, PMID:12024012, PMID:9811878] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter intersection_of: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: dianna.fisk creation_date: 2012-05-01T07:01:54Z [Term] id: GO:1900463 name: negative regulation of cellular response to alkalinity by negative regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cellular response to alkalinity by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, GOC:TermGenie, PMID:12509465, PMID:17023428] synonym: "negative regulation of cellular response to alkaline pH by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "negative regulation of cellular response to basic pH by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter intersection_of: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: dianna.fisk creation_date: 2012-05-01T07:22:50Z [Term] id: GO:1900464 name: negative regulation of cellular hyperosmotic salinity response by negative regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cellular hyperosmotic salinity response by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, GOC:TermGenie, PMID:16278455] synonym: "negative regulation of cellular response to hyperosmotic salt stress by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter intersection_of: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: dianna.fisk creation_date: 2012-05-01T07:29:19Z [Term] id: GO:1900465 name: negative regulation of arginine catabolic process by negative regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cellular arginine catabolic process by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, GOC:TermGenie, PMID:19233144, PMID:8455631] synonym: "negative regulation of arginine breakdown by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "negative regulation of arginine catabolism by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "negative regulation of arginine degradation by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0072365 ! regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter intersection_of: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: dianna.fisk creation_date: 2012-05-01T07:38:01Z [Term] id: GO:1900466 name: positive regulation of arginine biosynthetic process by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of arginine biosynthetic process by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, GOC:TermGenie, PMID:19233144, PMID:8455631] synonym: "activation of arginine anabolism by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "activation of arginine biosynthesis by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "activation of arginine biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "activation of arginine formation by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "activation of arginine synthesis by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "positive regulation of arginine anabolism by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "positive regulation of arginine biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "positive regulation of arginine formation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "positive regulation of arginine synthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of arginine anabolism by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of arginine biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of arginine biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of arginine formation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of arginine synthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of arginine anabolism by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of arginine biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of arginine biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of arginine formation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of arginine synthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of arginine anabolism by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of arginine biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of arginine biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of arginine formation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of arginine synthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0072366 ! regulation of cellular ketone metabolic process by positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: dianna.fisk creation_date: 2012-05-01T07:38:14Z [Term] id: GO:1900471 name: negative regulation of inositol biosynthetic process by negative regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of inositol biosynthetic process by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, GOC:TermGenie, PMID:8056324, PMID:8614637] synonym: "negative regulation of inositol anabolism by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "negative regulation of inositol biosynthesis by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "negative regulation of inositol formation by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "negative regulation of inositol synthesis by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "negative regulation of myo-inositol biosynthesis by negative regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "negative regulation of myo-inositol biosynthetic process by negative regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "negative regulation of vitamin Bh biosynthesis by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "negative regulation of vitamin Bh biosynthetic process by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter is_a: GO:0010678 ! negative regulation of cellular carbohydrate metabolic process by negative regulation of transcription, DNA-dependent is_a: GO:1900402 ! regulation of carbohydrate metabolic process by regulation of transcription from RNA polymerase II promoter intersection_of: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: dianna.fisk creation_date: 2012-05-01T08:13:23Z [Term] id: GO:1900472 name: positive regulation of phosphatidylcholine biosynthetic process by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of phosphatidylcholine biosynthetic process by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, GOC:TermGenie, PMID:8056324, PMID:8614637] synonym: "positive regulation of phosphatidylcholine anabolism by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "positive regulation of phosphatidylcholine biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "positive regulation of phosphatidylcholine formation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "positive regulation of phosphatidylcholine synthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:1900413 ! positive regulation of phospholipid biosynthetic process by positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: dianna.fisk creation_date: 2012-05-01T08:13:36Z [Term] id: GO:1900473 name: negative regulation of phosphatidylcholine biosynthetic process by negative regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of phosphatidylcholine biosynthetic process by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, GOC:TermGenie, PMID:8056324] synonym: "negative regulation of phosphatidylcholine anabolism by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "negative regulation of phosphatidylcholine biosynthesis by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "negative regulation of phosphatidylcholine formation by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "negative regulation of phosphatidylcholine synthesis by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter intersection_of: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: dianna.fisk creation_date: 2012-05-01T08:13:51Z [Term] id: GO:1900474 name: negative regulation of mating type switching by negative regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of mating type switching by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, GOC:TermGenie, PMID:8625408, PMID:8625409] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter intersection_of: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: dianna.fisk creation_date: 2012-05-01T08:33:18Z [Term] id: GO:1900475 name: positive regulation of meiosis by negative regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of meiosis by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, GOC:TermGenie, PMID:8618927] synonym: "activation of meiosis by negative regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "stimulation of meiosis by negative regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "up regulation of meiosis by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of meiosis by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of meiosis by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter is_a: GO:1900401 ! regulation of meiosis by regulation of transcription from RNA polymerase II promoter intersection_of: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: dianna.fisk creation_date: 2012-05-01T08:39:58Z [Term] id: GO:1900476 name: positive regulation of meiosis by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of meiosis by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, GOC:TermGenie, PMID:8618927] synonym: "activation of meiosis by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "stimulation of meiosis by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "up regulation of meiosis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of meiosis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of meiosis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter is_a: GO:1900401 ! regulation of meiosis by regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: dianna.fisk creation_date: 2012-05-01T08:40:11Z [Term] id: GO:1900477 name: negative regulation of G1/S transition of mitotic cell cycle by negative regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of G1/S transition of mitotic cell cycle by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, GOC:TermGenie, PMID:19841732] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter intersection_of: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: dianna.fisk creation_date: 2012-05-01T09:01:04Z [Term] id: GO:1900478 name: positive regulation of sulfate assimilation by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of sulfate assimilation by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, GOC:TermGenie, PMID:7601277, PMID:7891681] synonym: "activation of sulfate assimilation by positive regulation of transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie] synonym: "activation of sulfate assimilation, phosphoadenylyl sulfate reduction by an oxidoreductase, acting on sulfur group of donors, NAD or NADP as acceptor by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "activation of sulphate assimilation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "activation of sulphate assimilation, phosphoadenylyl sulphate reduction by an oxidoreductase, acting on sulphur group of donors, NAD or NADP as acceptor by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "positive regulation of sulfate assimilation, phosphoadenylyl sulfate reduction by an oxidoreductase, acting on sulfur group of donors, NAD or NADP as acceptor by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "positive regulation of sulphate assimilation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "positive regulation of sulphate assimilation, phosphoadenylyl sulphate reduction by an oxidoreductase, acting on sulphur group of donors, NAD or NADP as acceptor by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "up regulation of sulfate assimilation by positive regulation of transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie] synonym: "up regulation of sulfate assimilation, phosphoadenylyl sulfate reduction by an oxidoreductase, acting on sulfur group of donors, NAD or NADP as acceptor by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "up regulation of sulphate assimilation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of sulphate assimilation, phosphoadenylyl sulphate reduction by an oxidoreductase, acting on sulphur group of donors, NAD or NADP as acceptor by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "up-regulation of sulfate assimilation by positive regulation of transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie] synonym: "up-regulation of sulfate assimilation, phosphoadenylyl sulfate reduction by an oxidoreductase, acting on sulfur group of donors, NAD or NADP as acceptor by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "up-regulation of sulphate assimilation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of sulphate assimilation, phosphoadenylyl sulphate reduction by an oxidoreductase, acting on sulphur group of donors, NAD or NADP as acceptor by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "upregulation of sulfate assimilation by positive regulation of transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie] synonym: "upregulation of sulfate assimilation, phosphoadenylyl sulfate reduction by an oxidoreductase, acting on sulfur group of donors, NAD or NADP as acceptor by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "upregulation of sulphate assimilation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of sulphate assimilation, phosphoadenylyl sulphate reduction by an oxidoreductase, acting on sulphur group of donors, NAD or NADP as acceptor by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: dianna.fisk creation_date: 2012-05-01T09:08:04Z [Term] id: GO:1900524 name: positive regulation of flocculation via cell wall protein-carbohydrate interaction by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of flocculation via cell wall protein-carbohydrate interaction process by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, GOC:TermGenie, PMID:10591965, PMID:15466424, PMID:16568252] synonym: "activation of flocculation via cell wall protein-carbohydrate interaction by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "up regulation of flocculation via cell wall protein-carbohydrate interaction by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of flocculation via cell wall protein-carbohydrate interaction by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of flocculation via cell wall protein-carbohydrate interaction by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: dgf creation_date: 2012-05-03T05:13:41Z [Term] id: GO:1900525 name: positive regulation of phosphatidylserine biosynthetic process by positive regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of phosphatidylserine biosynthetic process by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, GOC:TermGenie, PMID:8056324, PMID:8614637] synonym: "activation of phosphatidylserine anabolism by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "activation of phosphatidylserine biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "activation of phosphatidylserine biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "activation of phosphatidylserine formation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "activation of phosphatidylserine synthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "positive regulation of phosphatidylserine anabolism by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "positive regulation of phosphatidylserine biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "positive regulation of phosphatidylserine formation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "positive regulation of phosphatidylserine synthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of phosphatidylserine anabolism by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of phosphatidylserine biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of phosphatidylserine biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of phosphatidylserine formation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of phosphatidylserine synthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of phosphatidylserine anabolism by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of phosphatidylserine biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of phosphatidylserine biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of phosphatidylserine formation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of phosphatidylserine synthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of phosphatidylserine anabolism by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of phosphatidylserine biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of phosphatidylserine biosynthetic process by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of phosphatidylserine formation by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of phosphatidylserine synthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:0072366 ! regulation of cellular ketone metabolic process by positive regulation of transcription from RNA polymerase II promoter is_a: GO:1900413 ! positive regulation of phospholipid biosynthetic process by positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: dgf creation_date: 2012-05-03T05:13:55Z [Term] id: GO:1900526 name: negative regulation of phosphatidylserine biosynthetic process by negative regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of phosphatidylserine biosynthetic process by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, GOC:TermGenie, PMID:8056324] synonym: "negative regulation of phosphatidylserine anabolism by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "negative regulation of phosphatidylserine biosynthesis by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "negative regulation of phosphatidylserine formation by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "negative regulation of phosphatidylserine synthesis by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:1900403 ! negative regulation of cellular amino acid biosynthetic process by negative regulation of transcription from RNA polymerase II promoter intersection_of: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: dgf creation_date: 2012-05-03T05:14:10Z [Term] id: GO:1900545 name: regulation of phenotypic switching by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A regulation of transcription from RNA polymerase II promoter that results in regulation of phenotypic switching." [GOC:di, GOC:TermGenie] synonym: "regulation of phenotypic dimorphism by regulation of transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: di creation_date: 2012-05-14T11:28:41Z [Term] id: GO:1900546 name: positive regulation of phenotypic switching by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A regulation of transcription from RNA polymerase II promoter that results in positive regulation of phenotypic switching." [GOC:di, GOC:TermGenie] synonym: "activation of phenotypic dimorphism by regulation of transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie] synonym: "activation of phenotypic switching by regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie] synonym: "positive regulation of phenotypic dimorphism by regulation of transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie] synonym: "up regulation of phenotypic dimorphism by regulation of transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie] synonym: "up regulation of phenotypic switching by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of phenotypic dimorphism by regulation of transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie] synonym: "up-regulation of phenotypic switching by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of phenotypic dimorphism by regulation of transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie] synonym: "upregulation of phenotypic switching by regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie] is_a: GO:1900545 ! regulation of phenotypic switching by regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: di creation_date: 2012-05-14T11:36:05Z [Term] id: GO:1900547 name: negative regulation of phenotypic switching by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A regulation of transcription from RNA polymerase II promoter that results in negative regulation of phenotypic switching." [GOC:di, GOC:TermGenie] synonym: "negative regulation of phenotypic dimorphism by regulation of transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie] is_a: GO:1900545 ! regulation of phenotypic switching by regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: di creation_date: 2012-05-14T11:40:54Z [Term] id: GO:1900621 name: regulation of transcription from RNA polymerase II promoter by calcium-mediated signaling namespace: biological_process def: "Calcium-mediated signaling that results in regulation of transcription from an RNA polymerase II promoter." [GOC:BHF, GOC:TermGenie] synonym: "regulation of gene-specific transcription from RNA polymerase II promoter by calcium-mediated signaling" RELATED [GOC:TermGenie] synonym: "regulation of global transcription from Pol II promoter by calcium-mediated signaling" RELATED [GOC:TermGenie] synonym: "regulation of transcription from Pol II promoter by calcium-mediated signaling" EXACT [GOC:TermGenie] synonym: "regulation of transcription from RNA polymerase II promoter, global by calcium-mediated signaling" RELATED [GOC:TermGenie] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: results_in GO:0006357 ! regulation of transcription from RNA polymerase II promoter relationship: results_in GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: bf creation_date: 2012-05-18T01:00:39Z [Term] id: GO:1900622 name: positive regulation of transcription from RNA polymerase II promoter by calcium-mediated signaling namespace: biological_process def: "Calcium-mediated signaling that results in positive regulation of transcription from an RNA polymerase II promoter." [GOC:bf, GOC:BHF, GOC:dgf, GOC:TermGenie, PMID:9407035, PMID:9407036] synonym: "activation of global transcription from RNA polymerase II promoter by calcium-mediated signaling" RELATED [GOC:TermGenie] synonym: "activation of transcription from RNA polymerase II promoter by calcium-mediated signaling" EXACT [GOC:TermGenie] synonym: "calcineurin-dependent transcription activation" NARROW [PMID:9407036] synonym: "calcineurin-dependent transcriptional induction" NARROW [PMID:9407035] synonym: "calcineurin-mediated activation of transcription" NARROW [PMID:9407035] synonym: "positive regulation of gene-specific transcription from RNA polymerase II promoter by calcium-mediated signaling" RELATED [GOC:TermGenie] synonym: "positive regulation of global transcription from Pol II promoter by calcium-mediated signaling" RELATED [GOC:TermGenie] synonym: "positive regulation of transcription from Pol II promoter by calcium-mediated signaling" EXACT [GOC:TermGenie] synonym: "positive regulation of transcription from RNA polymerase II promoter, global by calcium-mediated signaling" RELATED [GOC:TermGenie] synonym: "stimulation of global transcription from RNA polymerase II promoter by calcium-mediated signaling" NARROW [GOC:TermGenie] synonym: "stimulation of transcription from RNA polymerase II promoter by calcium-mediated signaling" EXACT [GOC:TermGenie] synonym: "up regulation of global transcription from RNA polymerase II promoter by calcium-mediated signaling" RELATED [GOC:TermGenie] synonym: "up regulation of transcription from RNA polymerase II promoter by calcium-mediated signaling" EXACT [GOC:TermGenie] synonym: "up-regulation of global transcription from RNA polymerase II promoter by calcium-mediated signaling" RELATED [GOC:TermGenie] synonym: "up-regulation of transcription from RNA polymerase II promoter by calcium-mediated signaling" EXACT [GOC:TermGenie] synonym: "upregulation of global transcription from RNA polymerase II promoter by calcium-mediated signaling" RELATED [GOC:TermGenie] synonym: "upregulation of transcription from RNA polymerase II promoter by calcium-mediated signaling" EXACT [GOC:TermGenie] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter is_a: GO:1900621 ! regulation of transcription from RNA polymerase II promoter by calcium-mediated signaling intersection_of: results_in GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter relationship: results_in GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: bf creation_date: 2012-05-18T01:01:04Z [Term] id: GO:1900756 name: protein processing in phagocytic vesicle namespace: biological_process def: "Protein processing that takes place in the phagosome. Most protein processing in the phagosome represents protein degradation." [GOC:rjd, GOC:TermGenie] synonym: "peptidolysis during protein maturation in phagocytic vesicle" RELATED [GOC:TermGenie] synonym: "peptidolysis during protein maturation in phagosome" RELATED [GOC:TermGenie] synonym: "protein maturation by peptide bond cleavage in phagocytic vesicle" EXACT [GOC:TermGenie] synonym: "protein maturation by peptide bond cleavage in phagosome" EXACT [GOC:TermGenie] synonym: "protein maturation by peptide bond hydrolysis in phagocytic vesicle" EXACT [GOC:TermGenie] synonym: "protein maturation by peptide bond hydrolysis in phagosome" EXACT [GOC:TermGenie] synonym: "protein maturation by proteolysis in phagocytic vesicle" RELATED [GOC:TermGenie] synonym: "protein maturation by proteolysis in phagosome" RELATED [GOC:TermGenie] synonym: "protein processing in phagosome" EXACT [GOC:TermGenie] is_a: GO:0016485 ! protein processing intersection_of: GO:0016485 ! protein processing created_by: rjd creation_date: 2012-05-29T09:55:14Z [Term] id: GO:1901148 name: gene expression involved in extracellular matrix organization namespace: biological_process def: "Any gene expression that is involved in extracellular matrix organization. Gene expression includes both transcription to produce an RNA transcript, and the translation of that mRNA into protein." [GOC:pg, GOC:TermGenie, PMID:18668558] synonym: "expression of extracellular matrix proteins" EXACT [GOC:bf] synonym: "extracellular matrix protein production" RELATED [GOC:pg] is_a: GO:0010467 ! gene expression intersection_of: GO:0010467 ! gene expression created_by: bf creation_date: 2012-07-16T03:29:30Z [Term] id: GO:1901190 name: regulation of formation of translation initiation ternary complex namespace: biological_process def: "Any process that modulates the frequency, rate or extent of formation of translation initiation ternary complex." [GOC:TermGenie] synonym: "regulation of translation initiation ternary complex assembly" EXACT [GOC:TermGenie] is_a: GO:0006446 ! regulation of translational initiation intersection_of: regulates GO:0001677 ! formation of translation initiation ternary complex relationship: regulates GO:0001677 ! formation of translation initiation ternary complex created_by: ss creation_date: 2012-07-25T02:26:58Z [Term] id: GO:1901191 name: negative regulation of formation of translation initiation ternary complex namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of formation of translation initiation ternary complex." [GOC:TermGenie] synonym: "down regulation of formation of translation initiation ternary complex" EXACT [GOC:TermGenie] synonym: "down regulation of translation initiation ternary complex assembly" EXACT [GOC:TermGenie] synonym: "down-regulation of formation of translation initiation ternary complex" EXACT [GOC:TermGenie] synonym: "down-regulation of translation initiation ternary complex assembly" EXACT [GOC:TermGenie] synonym: "downregulation of formation of translation initiation ternary complex" EXACT [GOC:TermGenie] synonym: "downregulation of translation initiation ternary complex assembly" EXACT [GOC:TermGenie] synonym: "inhibition of formation of translation initiation ternary complex" NARROW [GOC:TermGenie] synonym: "inhibition of translation initiation ternary complex assembly" EXACT [GOC:TermGenie] synonym: "negative regulation of translation initiation ternary complex assembly" EXACT [GOC:TermGenie] is_a: GO:1901190 ! regulation of formation of translation initiation ternary complex intersection_of: negatively_regulates GO:0001677 ! formation of translation initiation ternary complex relationship: negatively_regulates GO:0001677 ! formation of translation initiation ternary complex created_by: ss creation_date: 2012-07-25T02:27:21Z [Term] id: GO:1901192 name: positive regulation of formation of translation initiation ternary complex namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of formation of translation initiation ternary complex." [GOC:TermGenie] synonym: "activation of formation of translation initiation ternary complex" NARROW [GOC:TermGenie] synonym: "activation of translation initiation ternary complex assembly" EXACT [GOC:TermGenie] synonym: "positive regulation of translation initiation ternary complex assembly" EXACT [GOC:TermGenie] synonym: "up regulation of formation of translation initiation ternary complex" EXACT [GOC:TermGenie] synonym: "up regulation of translation initiation ternary complex assembly" EXACT [GOC:TermGenie] synonym: "up-regulation of formation of translation initiation ternary complex" EXACT [GOC:TermGenie] synonym: "up-regulation of translation initiation ternary complex assembly" EXACT [GOC:TermGenie] synonym: "upregulation of formation of translation initiation ternary complex" EXACT [GOC:TermGenie] synonym: "upregulation of translation initiation ternary complex assembly" EXACT [GOC:TermGenie] is_a: GO:1901190 ! regulation of formation of translation initiation ternary complex intersection_of: positively_regulates GO:0001677 ! formation of translation initiation ternary complex relationship: positively_regulates GO:0001677 ! formation of translation initiation ternary complex created_by: ss creation_date: 2012-07-25T02:27:29Z [Term] id: GO:1901193 name: regulation of formation of translation preinitiation complex namespace: biological_process def: "Any process that modulates the frequency, rate or extent of formation of translation preinitiation complex." [GOC:TermGenie] synonym: "regulation of formation of translation pre-initiation complex" EXACT [GOC:TermGenie] synonym: "regulation of translation preinitiation complex assembly" EXACT [GOC:TermGenie] is_a: GO:0006446 ! regulation of translational initiation intersection_of: regulates GO:0001731 ! formation of translation preinitiation complex relationship: regulates GO:0001731 ! formation of translation preinitiation complex created_by: ss creation_date: 2012-07-25T02:31:20Z [Term] id: GO:1901194 name: negative regulation of formation of translation preinitiation complex namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of formation of translation preinitiation complex." [GOC:TermGenie] synonym: "down regulation of formation of translation pre-initiation complex" EXACT [GOC:TermGenie] synonym: "down regulation of formation of translation preinitiation complex" EXACT [GOC:TermGenie] synonym: "down regulation of translation preinitiation complex assembly" EXACT [GOC:TermGenie] synonym: "down-regulation of formation of translation pre-initiation complex" EXACT [GOC:TermGenie] synonym: "down-regulation of formation of translation preinitiation complex" EXACT [GOC:TermGenie] synonym: "down-regulation of translation preinitiation complex assembly" EXACT [GOC:TermGenie] synonym: "downregulation of formation of translation pre-initiation complex" EXACT [GOC:TermGenie] synonym: "downregulation of formation of translation preinitiation complex" EXACT [GOC:TermGenie] synonym: "downregulation of translation preinitiation complex assembly" EXACT [GOC:TermGenie] synonym: "inhibition of formation of translation pre-initiation complex" EXACT [GOC:TermGenie] synonym: "inhibition of formation of translation preinitiation complex" NARROW [GOC:TermGenie] synonym: "inhibition of translation preinitiation complex assembly" EXACT [GOC:TermGenie] synonym: "negative regulation of formation of translation pre-initiation complex" EXACT [GOC:TermGenie] synonym: "negative regulation of translation preinitiation complex assembly" EXACT [GOC:TermGenie] is_a: GO:1901193 ! regulation of formation of translation preinitiation complex intersection_of: negatively_regulates GO:0001731 ! formation of translation preinitiation complex relationship: negatively_regulates GO:0001731 ! formation of translation preinitiation complex created_by: ss creation_date: 2012-07-25T02:31:41Z [Term] id: GO:1901195 name: positive regulation of formation of translation preinitiation complex namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of formation of translation preinitiation complex." [GOC:TermGenie] synonym: "activation of formation of translation pre-initiation complex" EXACT [GOC:TermGenie] synonym: "activation of formation of translation preinitiation complex" NARROW [GOC:TermGenie] synonym: "activation of translation preinitiation complex assembly" EXACT [GOC:TermGenie] synonym: "positive regulation of formation of translation pre-initiation complex" EXACT [GOC:TermGenie] synonym: "positive regulation of translation preinitiation complex assembly" EXACT [GOC:TermGenie] synonym: "up regulation of formation of translation pre-initiation complex" EXACT [GOC:TermGenie] synonym: "up regulation of formation of translation preinitiation complex" EXACT [GOC:TermGenie] synonym: "up regulation of translation preinitiation complex assembly" EXACT [GOC:TermGenie] synonym: "up-regulation of formation of translation pre-initiation complex" EXACT [GOC:TermGenie] synonym: "up-regulation of formation of translation preinitiation complex" EXACT [GOC:TermGenie] synonym: "up-regulation of translation preinitiation complex assembly" EXACT [GOC:TermGenie] synonym: "upregulation of formation of translation pre-initiation complex" EXACT [GOC:TermGenie] synonym: "upregulation of formation of translation preinitiation complex" EXACT [GOC:TermGenie] synonym: "upregulation of translation preinitiation complex assembly" EXACT [GOC:TermGenie] is_a: GO:1901193 ! regulation of formation of translation preinitiation complex intersection_of: positively_regulates GO:0001731 ! formation of translation preinitiation complex relationship: positively_regulates GO:0001731 ! formation of translation preinitiation complex created_by: ss creation_date: 2012-07-25T02:31:50Z [Term] id: GO:1901213 name: regulation of transcription from RNA polymerase II promoter involved in heart development namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the development of the heart over time." [GOC:BHF, GOC:TermGenie] synonym: "global transcription regulation from Pol II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "global transcription regulation from Pol II promoter involved in dorsal vessel development" RELATED [GOC:TermGenie] synonym: "global transcription regulation from Pol II promoter involved in heart development" RELATED [GOC:TermGenie] synonym: "regulation of gene-specific transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "regulation of gene-specific transcription from RNA polymerase II promoter involved in dorsal vessel development" RELATED [GOC:TermGenie] synonym: "regulation of gene-specific transcription from RNA polymerase II promoter involved in heart development" RELATED [GOC:TermGenie] synonym: "regulation of global transcription from Pol II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "regulation of global transcription from Pol II promoter involved in dorsal vessel development" RELATED [GOC:TermGenie] synonym: "regulation of global transcription from Pol II promoter involved in heart development" RELATED [GOC:TermGenie] synonym: "regulation of transcription from Pol II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "regulation of transcription from Pol II promoter involved in dorsal vessel development" NARROW [GOC:TermGenie] synonym: "regulation of transcription from Pol II promoter involved in heart development" EXACT [GOC:TermGenie] synonym: "regulation of transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "regulation of transcription from RNA polymerase II promoter involved in dorsal vessel development" NARROW [GOC:TermGenie] synonym: "regulation of transcription from RNA polymerase II promoter, global involved in cardiac development" RELATED [GOC:TermGenie] synonym: "regulation of transcription from RNA polymerase II promoter, global involved in dorsal vessel development" RELATED [GOC:TermGenie] synonym: "regulation of transcription from RNA polymerase II promoter, global involved in heart development" RELATED [GOC:TermGenie] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: rl creation_date: 2012-07-31T07:26:45Z [Term] id: GO:1901222 name: regulation of NIK/NF-kappaB cascade namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a NIK/NF-kappaB cascade." [GOC:TermGenie] synonym: "regulation of non-canonical NF-KB signaling" BROAD [GOC:TermGenie] synonym: "regulation of noncanonical NF-kappaB signaling" BROAD [GOC:TermGenie] synonym: "regulation of noncanonical nuclear factor kappaB (NF-kappaB) pathway" BROAD [GOC:TermGenie] synonym: "regulation of p52-dependent NF-kappaB signaling" NARROW [GOC:TermGenie] intersection_of: regulates GO:0038061 ! NIK/NF-kappaB cascade relationship: regulates GO:0038061 ! NIK/NF-kappaB cascade created_by: hjd creation_date: 2012-08-06T20:27:17Z [Term] id: GO:1901223 name: negative regulation of NIK/NF-kappaB cascade namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of a NIK/NF-kappaB cascade." [GOC:TermGenie] synonym: "down regulation of NIK/NF-kappaB cascade" EXACT [GOC:TermGenie] synonym: "down regulation of non-canonical NF-KB signaling" BROAD [GOC:TermGenie] synonym: "down regulation of noncanonical NF-kappaB signaling" BROAD [GOC:TermGenie] synonym: "down regulation of noncanonical nuclear factor kappaB (NF-kappaB) pathway" BROAD [GOC:TermGenie] synonym: "down regulation of p52-dependent NF-kappaB signaling" NARROW [GOC:TermGenie] synonym: "down-regulation of NIK/NF-kappaB cascade" EXACT [GOC:TermGenie] synonym: "down-regulation of non-canonical NF-KB signaling" BROAD [GOC:TermGenie] synonym: "down-regulation of noncanonical NF-kappaB signaling" BROAD [GOC:TermGenie] synonym: "down-regulation of noncanonical nuclear factor kappaB (NF-kappaB) pathway" BROAD [GOC:TermGenie] synonym: "down-regulation of p52-dependent NF-kappaB signaling" NARROW [GOC:TermGenie] synonym: "downregulation of NIK/NF-kappaB cascade" EXACT [GOC:TermGenie] synonym: "downregulation of non-canonical NF-KB signaling" BROAD [GOC:TermGenie] synonym: "downregulation of noncanonical NF-kappaB signaling" BROAD [GOC:TermGenie] synonym: "downregulation of noncanonical nuclear factor kappaB (NF-kappaB) pathway" BROAD [GOC:TermGenie] synonym: "downregulation of p52-dependent NF-kappaB signaling" NARROW [GOC:TermGenie] synonym: "inhibition of NIK/NF-kappaB cascade" NARROW [GOC:TermGenie] synonym: "inhibition of non-canonical NF-KB signaling" BROAD [GOC:TermGenie] synonym: "inhibition of noncanonical NF-kappaB signaling" BROAD [GOC:TermGenie] synonym: "inhibition of noncanonical nuclear factor kappaB (NF-kappaB) pathway" BROAD [GOC:TermGenie] synonym: "inhibition of p52-dependent NF-kappaB signaling" NARROW [GOC:TermGenie] synonym: "negative regulation of non-canonical NF-KB signaling" BROAD [GOC:TermGenie] synonym: "negative regulation of noncanonical NF-kappaB signaling" BROAD [GOC:TermGenie] synonym: "negative regulation of noncanonical nuclear factor kappaB (NF-kappaB) pathway" BROAD [GOC:TermGenie] synonym: "negative regulation of p52-dependent NF-kappaB signaling" NARROW [GOC:TermGenie] is_a: GO:1901222 ! regulation of NIK/NF-kappaB cascade intersection_of: negatively_regulates GO:0038061 ! NIK/NF-kappaB cascade relationship: negatively_regulates GO:0038061 ! NIK/NF-kappaB cascade created_by: hjd creation_date: 2012-08-06T20:27:39Z [Term] id: GO:1901224 name: positive regulation of NIK/NF-kappaB cascade namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of a NIK/NF-kappaB cascade." [GOC:TermGenie] synonym: "activation of NIK/NF-kappaB cascade" NARROW [GOC:TermGenie] synonym: "activation of non-canonical NF-KB signaling" BROAD [GOC:TermGenie] synonym: "activation of noncanonical NF-kappaB signaling" BROAD [GOC:TermGenie] synonym: "activation of noncanonical nuclear factor kappaB (NF-kappaB) pathway" BROAD [GOC:TermGenie] synonym: "activation of p52-dependent NF-kappaB signaling" NARROW [GOC:TermGenie] synonym: "positive regulation of non-canonical NF-KB signaling" BROAD [GOC:TermGenie] synonym: "positive regulation of noncanonical NF-kappaB signaling" BROAD [GOC:TermGenie] synonym: "positive regulation of noncanonical nuclear factor kappaB (NF-kappaB) pathway" BROAD [GOC:TermGenie] synonym: "positive regulation of p52-dependent NF-kappaB signaling" NARROW [GOC:TermGenie] synonym: "up regulation of NIK/NF-kappaB cascade" EXACT [GOC:TermGenie] synonym: "up regulation of non-canonical NF-KB signaling" BROAD [GOC:TermGenie] synonym: "up regulation of noncanonical NF-kappaB signaling" BROAD [GOC:TermGenie] synonym: "up regulation of noncanonical nuclear factor kappaB (NF-kappaB) pathway" BROAD [GOC:TermGenie] synonym: "up regulation of p52-dependent NF-kappaB signaling" NARROW [GOC:TermGenie] synonym: "up-regulation of NIK/NF-kappaB cascade" EXACT [GOC:TermGenie] synonym: "up-regulation of non-canonical NF-KB signaling" BROAD [GOC:TermGenie] synonym: "up-regulation of noncanonical NF-kappaB signaling" BROAD [GOC:TermGenie] synonym: "up-regulation of noncanonical nuclear factor kappaB (NF-kappaB) pathway" BROAD [GOC:TermGenie] synonym: "up-regulation of p52-dependent NF-kappaB signaling" NARROW [GOC:TermGenie] synonym: "upregulation of NIK/NF-kappaB cascade" EXACT [GOC:TermGenie] synonym: "upregulation of non-canonical NF-KB signaling" BROAD [GOC:TermGenie] synonym: "upregulation of noncanonical NF-kappaB signaling" BROAD [GOC:TermGenie] synonym: "upregulation of noncanonical nuclear factor kappaB (NF-kappaB) pathway" BROAD [GOC:TermGenie] synonym: "upregulation of p52-dependent NF-kappaB signaling" NARROW [GOC:TermGenie] is_a: GO:1901222 ! regulation of NIK/NF-kappaB cascade intersection_of: positively_regulates GO:0038061 ! NIK/NF-kappaB cascade relationship: positively_regulates GO:0038061 ! NIK/NF-kappaB cascade created_by: hjd creation_date: 2012-08-06T20:27:47Z [Term] id: GO:1901227 name: negative regulation of transcription from RNA polymerase II promoter involved in heart development namespace: biological_process def: "Any negative regulation of transcription from RNA polymerase II promoter that is involved in heart development." [GOC:BHF, GOC:TermGenie] synonym: "down regulation of global transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "down regulation of global transcription from RNA polymerase II promoter involved in dorsal vessel development" RELATED [GOC:TermGenie] synonym: "down regulation of global transcription from RNA polymerase II promoter involved in heart development" RELATED [GOC:TermGenie] synonym: "down regulation of transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "down regulation of transcription from RNA polymerase II promoter involved in dorsal vessel development" NARROW [GOC:TermGenie] synonym: "down regulation of transcription from RNA polymerase II promoter involved in heart development" EXACT [GOC:TermGenie] synonym: "down-regulation of global transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "down-regulation of global transcription from RNA polymerase II promoter involved in dorsal vessel development" RELATED [GOC:TermGenie] synonym: "down-regulation of global transcription from RNA polymerase II promoter involved in heart development" RELATED [GOC:TermGenie] synonym: "down-regulation of transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "down-regulation of transcription from RNA polymerase II promoter involved in dorsal vessel development" NARROW [GOC:TermGenie] synonym: "down-regulation of transcription from RNA polymerase II promoter involved in heart development" EXACT [GOC:TermGenie] synonym: "downregulation of global transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "downregulation of global transcription from RNA polymerase II promoter involved in dorsal vessel development" RELATED [GOC:TermGenie] synonym: "downregulation of global transcription from RNA polymerase II promoter involved in heart development" RELATED [GOC:TermGenie] synonym: "downregulation of transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "downregulation of transcription from RNA polymerase II promoter involved in dorsal vessel development" NARROW [GOC:TermGenie] synonym: "downregulation of transcription from RNA polymerase II promoter involved in heart development" EXACT [GOC:TermGenie] synonym: "inhibition of global transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "inhibition of global transcription from RNA polymerase II promoter involved in dorsal vessel development" RELATED [GOC:TermGenie] synonym: "inhibition of global transcription from RNA polymerase II promoter involved in heart development" RELATED [GOC:TermGenie] synonym: "inhibition of transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "inhibition of transcription from RNA polymerase II promoter involved in dorsal vessel development" NARROW [GOC:TermGenie] synonym: "inhibition of transcription from RNA polymerase II promoter involved in heart development" NARROW [GOC:TermGenie] synonym: "negative regulation of gene-specific transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "negative regulation of gene-specific transcription from RNA polymerase II promoter involved in dorsal vessel development" RELATED [GOC:TermGenie] synonym: "negative regulation of gene-specific transcription from RNA polymerase II promoter involved in heart development" RELATED [GOC:TermGenie] synonym: "negative regulation of global transcription from Pol II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "negative regulation of global transcription from Pol II promoter involved in dorsal vessel development" RELATED [GOC:TermGenie] synonym: "negative regulation of global transcription from Pol II promoter involved in heart development" RELATED [GOC:TermGenie] synonym: "negative regulation of transcription from Pol II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "negative regulation of transcription from Pol II promoter involved in dorsal vessel development" NARROW [GOC:TermGenie] synonym: "negative regulation of transcription from Pol II promoter involved in heart development" EXACT [GOC:TermGenie] synonym: "negative regulation of transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "negative regulation of transcription from RNA polymerase II promoter involved in dorsal vessel development" NARROW [GOC:TermGenie] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter is_a: GO:1901213 ! regulation of transcription from RNA polymerase II promoter involved in heart development intersection_of: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: pr creation_date: 2012-08-07T12:50:30Z [Term] id: GO:1901228 name: positive regulation of transcription from RNA polymerase II promoter involved in heart development namespace: biological_process def: "Any positive regulation of transcription from RNA polymerase II promoter that is involved in heart development." [GOC:BHF, GOC:TermGenie] synonym: "activation of global transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "activation of global transcription from RNA polymerase II promoter involved in dorsal vessel development" RELATED [GOC:TermGenie] synonym: "activation of global transcription from RNA polymerase II promoter involved in heart development" RELATED [GOC:TermGenie] synonym: "activation of transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "activation of transcription from RNA polymerase II promoter involved in dorsal vessel development" NARROW [GOC:TermGenie] synonym: "activation of transcription from RNA polymerase II promoter involved in heart development" NARROW [GOC:TermGenie] synonym: "positive regulation of gene-specific transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "positive regulation of gene-specific transcription from RNA polymerase II promoter involved in dorsal vessel development" RELATED [GOC:TermGenie] synonym: "positive regulation of gene-specific transcription from RNA polymerase II promoter involved in heart development" RELATED [GOC:TermGenie] synonym: "positive regulation of global transcription from Pol II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "positive regulation of global transcription from Pol II promoter involved in dorsal vessel development" RELATED [GOC:TermGenie] synonym: "positive regulation of global transcription from Pol II promoter involved in heart development" RELATED [GOC:TermGenie] synonym: "positive regulation of transcription from Pol II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "positive regulation of transcription from Pol II promoter involved in dorsal vessel development" NARROW [GOC:TermGenie] synonym: "positive regulation of transcription from Pol II promoter involved in heart development" EXACT [GOC:TermGenie] synonym: "positive regulation of transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "positive regulation of transcription from RNA polymerase II promoter involved in dorsal vessel development" NARROW [GOC:TermGenie] synonym: "stimulation of global transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "stimulation of global transcription from RNA polymerase II promoter involved in dorsal vessel development" NARROW [GOC:TermGenie] synonym: "stimulation of global transcription from RNA polymerase II promoter involved in heart development" NARROW [GOC:TermGenie] synonym: "stimulation of transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "stimulation of transcription from RNA polymerase II promoter involved in dorsal vessel development" NARROW [GOC:TermGenie] synonym: "stimulation of transcription from RNA polymerase II promoter involved in heart development" EXACT [GOC:TermGenie] synonym: "up regulation of global transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "up regulation of global transcription from RNA polymerase II promoter involved in dorsal vessel development" RELATED [GOC:TermGenie] synonym: "up regulation of global transcription from RNA polymerase II promoter involved in heart development" RELATED [GOC:TermGenie] synonym: "up regulation of transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "up regulation of transcription from RNA polymerase II promoter involved in dorsal vessel development" NARROW [GOC:TermGenie] synonym: "up regulation of transcription from RNA polymerase II promoter involved in heart development" EXACT [GOC:TermGenie] synonym: "up-regulation of global transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "up-regulation of global transcription from RNA polymerase II promoter involved in dorsal vessel development" RELATED [GOC:TermGenie] synonym: "up-regulation of global transcription from RNA polymerase II promoter involved in heart development" RELATED [GOC:TermGenie] synonym: "up-regulation of transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "up-regulation of transcription from RNA polymerase II promoter involved in dorsal vessel development" NARROW [GOC:TermGenie] synonym: "up-regulation of transcription from RNA polymerase II promoter involved in heart development" EXACT [GOC:TermGenie] synonym: "upregulation of global transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "upregulation of global transcription from RNA polymerase II promoter involved in dorsal vessel development" RELATED [GOC:TermGenie] synonym: "upregulation of global transcription from RNA polymerase II promoter involved in heart development" RELATED [GOC:TermGenie] synonym: "upregulation of transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie] synonym: "upregulation of transcription from RNA polymerase II promoter involved in dorsal vessel development" NARROW [GOC:TermGenie] synonym: "upregulation of transcription from RNA polymerase II promoter involved in heart development" EXACT [GOC:TermGenie] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter is_a: GO:1901213 ! regulation of transcription from RNA polymerase II promoter involved in heart development intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: pr creation_date: 2012-08-07T12:53:01Z [Term] id: GO:1901244 name: positive regulation of transcription from RNA polymerase II promoter involved in defense response to fungus namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter to protect the cell or organism in response to the presence of a fungus." [GOC:kmv, GOC:TermGenie] synonym: "activation of global transcription from RNA polymerase II promoter involved in defence response to fungi" RELATED [GOC:TermGenie] synonym: "activation of global transcription from RNA polymerase II promoter involved in defence response to fungus" RELATED [GOC:TermGenie] synonym: "activation of global transcription from RNA polymerase II promoter involved in defense response to fungi" RELATED [GOC:TermGenie] synonym: "activation of global transcription from RNA polymerase II promoter involved in defense response to fungus" RELATED [GOC:TermGenie] synonym: "activation of transcription from RNA polymerase II promoter involved in defence response to fungi" NARROW [GOC:TermGenie] synonym: "activation of transcription from RNA polymerase II promoter involved in defence response to fungus" NARROW [GOC:TermGenie] synonym: "activation of transcription from RNA polymerase II promoter involved in defense response to fungi" NARROW [GOC:TermGenie] synonym: "activation of transcription from RNA polymerase II promoter involved in defense response to fungus" NARROW [GOC:TermGenie] synonym: "positive regulation of gene-specific transcription from RNA polymerase II promoter involved in defence response to fungi" RELATED [GOC:TermGenie] synonym: "positive regulation of gene-specific transcription from RNA polymerase II promoter involved in defence response to fungus" RELATED [GOC:TermGenie] synonym: "positive regulation of gene-specific transcription from RNA polymerase II promoter involved in defense response to fungi" RELATED [GOC:TermGenie] synonym: "positive regulation of gene-specific transcription from RNA polymerase II promoter involved in defense response to fungus" RELATED [GOC:TermGenie] synonym: "positive regulation of global transcription from Pol II promoter involved in defence response to fungi" RELATED [GOC:TermGenie] synonym: "positive regulation of global transcription from Pol II promoter involved in defence response to fungus" RELATED [GOC:TermGenie] synonym: "positive regulation of global transcription from Pol II promoter involved in defense response to fungi" RELATED [GOC:TermGenie] synonym: "positive regulation of global transcription from Pol II promoter involved in defense response to fungus" RELATED [GOC:TermGenie] synonym: "positive regulation of transcription from Pol II promoter involved in defence response to fungi" EXACT [GOC:TermGenie] synonym: "positive regulation of transcription from Pol II promoter involved in defence response to fungus" EXACT [GOC:TermGenie] synonym: "positive regulation of transcription from Pol II promoter involved in defense response to fungi" EXACT [GOC:TermGenie] synonym: "positive regulation of transcription from Pol II promoter involved in defense response to fungus" EXACT [GOC:TermGenie] synonym: "positive regulation of transcription from RNA polymerase II promoter involved in defence response to fungi" EXACT [GOC:TermGenie] synonym: "positive regulation of transcription from RNA polymerase II promoter involved in defence response to fungus" EXACT [GOC:TermGenie] synonym: "positive regulation of transcription from RNA polymerase II promoter involved in defense response to fungi" EXACT [GOC:TermGenie] synonym: "stimulation of global transcription from RNA polymerase II promoter involved in defence response to fungi" NARROW [GOC:TermGenie] synonym: "stimulation of global transcription from RNA polymerase II promoter involved in defence response to fungus" NARROW [GOC:TermGenie] synonym: "stimulation of global transcription from RNA polymerase II promoter involved in defense response to fungi" NARROW [GOC:TermGenie] synonym: "stimulation of global transcription from RNA polymerase II promoter involved in defense response to fungus" NARROW [GOC:TermGenie] synonym: "stimulation of transcription from RNA polymerase II promoter involved in defence response to fungi" EXACT [GOC:TermGenie] synonym: "stimulation of transcription from RNA polymerase II promoter involved in defence response to fungus" EXACT [GOC:TermGenie] synonym: "stimulation of transcription from RNA polymerase II promoter involved in defense response to fungi" EXACT [GOC:TermGenie] synonym: "stimulation of transcription from RNA polymerase II promoter involved in defense response to fungus" EXACT [GOC:TermGenie] synonym: "up regulation of global transcription from RNA polymerase II promoter involved in defence response to fungi" RELATED [GOC:TermGenie] synonym: "up regulation of global transcription from RNA polymerase II promoter involved in defence response to fungus" RELATED [GOC:TermGenie] synonym: "up regulation of global transcription from RNA polymerase II promoter involved in defense response to fungi" RELATED [GOC:TermGenie] synonym: "up regulation of global transcription from RNA polymerase II promoter involved in defense response to fungus" RELATED [GOC:TermGenie] synonym: "up regulation of transcription from RNA polymerase II promoter involved in defence response to fungi" EXACT [GOC:TermGenie] synonym: "up regulation of transcription from RNA polymerase II promoter involved in defence response to fungus" EXACT [GOC:TermGenie] synonym: "up regulation of transcription from RNA polymerase II promoter involved in defense response to fungi" EXACT [GOC:TermGenie] synonym: "up regulation of transcription from RNA polymerase II promoter involved in defense response to fungus" EXACT [GOC:TermGenie] synonym: "up-regulation of global transcription from RNA polymerase II promoter involved in defence response to fungi" RELATED [GOC:TermGenie] synonym: "up-regulation of global transcription from RNA polymerase II promoter involved in defence response to fungus" RELATED [GOC:TermGenie] synonym: "up-regulation of global transcription from RNA polymerase II promoter involved in defense response to fungi" RELATED [GOC:TermGenie] synonym: "up-regulation of global transcription from RNA polymerase II promoter involved in defense response to fungus" RELATED [GOC:TermGenie] synonym: "up-regulation of transcription from RNA polymerase II promoter involved in defence response to fungi" EXACT [GOC:TermGenie] synonym: "up-regulation of transcription from RNA polymerase II promoter involved in defence response to fungus" EXACT [GOC:TermGenie] synonym: "up-regulation of transcription from RNA polymerase II promoter involved in defense response to fungi" EXACT [GOC:TermGenie] synonym: "up-regulation of transcription from RNA polymerase II promoter involved in defense response to fungus" EXACT [GOC:TermGenie] synonym: "upregulation of global transcription from RNA polymerase II promoter involved in defence response to fungi" RELATED [GOC:TermGenie] synonym: "upregulation of global transcription from RNA polymerase II promoter involved in defence response to fungus" RELATED [GOC:TermGenie] synonym: "upregulation of global transcription from RNA polymerase II promoter involved in defense response to fungi" RELATED [GOC:TermGenie] synonym: "upregulation of global transcription from RNA polymerase II promoter involved in defense response to fungus" RELATED [GOC:TermGenie] synonym: "upregulation of transcription from RNA polymerase II promoter involved in defence response to fungi" EXACT [GOC:TermGenie] synonym: "upregulation of transcription from RNA polymerase II promoter involved in defence response to fungus" EXACT [GOC:TermGenie] synonym: "upregulation of transcription from RNA polymerase II promoter involved in defense response to fungi" EXACT [GOC:TermGenie] synonym: "upregulation of transcription from RNA polymerase II promoter involved in defense response to fungus" EXACT [GOC:TermGenie] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: kmv creation_date: 2012-08-07T18:40:02Z [Term] id: GO:1901259 name: chloroplast rRNA processing namespace: biological_process def: "Any rRNA processing that takes place in chloroplast." [GOC:TermGenie] is_a: GO:0006364 ! rRNA processing intersection_of: GO:0006364 ! rRNA processing created_by: tb creation_date: 2012-08-10T17:43:19Z [Term] id: GO:1901294 name: negative regulation of SREBP signaling pathway by negative regulation of DNA binding namespace: biological_process def: "Negative regulation of DNA binding that results in negative regulation of a SREBP signaling pathway." [GOC:TermGenie, PMID:22017871] synonym: "inhibition of SREBP-dependent transcription by blocking DNA binding" EXACT [PMID:22017871] synonym: "negative regulation of SREBP signaling pathway by down regulation of DNA binding" EXACT [GOC:TermGenie] synonym: "negative regulation of SREBP signaling pathway by down-regulation of DNA binding" EXACT [GOC:TermGenie] synonym: "negative regulation of SREBP signaling pathway by downregulation of DNA binding" EXACT [GOC:TermGenie] synonym: "negative regulation of SREBP signaling pathway by inhibition of DNA binding" NARROW [GOC:TermGenie] synonym: "negative regulation of SREBP-mediated signaling pathway by down regulation of DNA binding" EXACT [GOC:TermGenie] synonym: "negative regulation of SREBP-mediated signaling pathway by down-regulation of DNA binding" EXACT [GOC:TermGenie] synonym: "negative regulation of SREBP-mediated signaling pathway by downregulation of DNA binding" EXACT [GOC:TermGenie] synonym: "negative regulation of SREBP-mediated signaling pathway by inhibition of DNA binding" NARROW [GOC:TermGenie] synonym: "negative regulation of SREBP-mediated signaling pathway by negative regulation of DNA binding" EXACT [GOC:TermGenie] synonym: "negative regulation of SREBP-mediated signalling pathway by down regulation of DNA binding" EXACT [GOC:TermGenie] synonym: "negative regulation of SREBP-mediated signalling pathway by down-regulation of DNA binding" EXACT [GOC:TermGenie] synonym: "negative regulation of SREBP-mediated signalling pathway by downregulation of DNA binding" EXACT [GOC:TermGenie] synonym: "negative regulation of SREBP-mediated signalling pathway by inhibition of DNA binding" NARROW [GOC:TermGenie] synonym: "negative regulation of SREBP-mediated signalling pathway by negative regulation of DNA binding" EXACT [GOC:TermGenie] is_a: GO:2000639 ! negative regulation of SREBP signaling pathway intersection_of: results_in GO:2000639 ! negative regulation of SREBP signaling pathway created_by: bf creation_date: 2012-08-20T14:11:03Z [Term] id: GO:1901308 name: regulation of sterol regulatory element binding protein cleavage namespace: biological_process def: "Any process that modulates the frequency, rate or extent of sterol regulatory element binding protein cleavage." [GOC:TermGenie] synonym: "regulation of SREBP cleavage" EXACT [GOC:TermGenie] is_a: GO:0070613 ! regulation of protein processing is_a: GO:2000638 ! regulation of SREBP signaling pathway intersection_of: regulates GO:0035103 ! sterol regulatory element binding protein cleavage relationship: regulates GO:0035103 ! sterol regulatory element binding protein cleavage created_by: bf creation_date: 2012-08-21T16:43:12Z [Term] id: GO:1901309 name: negative regulation of sterol regulatory element binding protein cleavage namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of sterol regulatory element binding protein cleavage." [GOC:TermGenie, PMID:15899885, PMID:16525117] synonym: "down regulation of SREBP cleavage" EXACT [GOC:TermGenie] synonym: "down regulation of sterol regulatory element binding protein cleavage" EXACT [GOC:TermGenie] synonym: "down-regulation of SREBP cleavage" EXACT [GOC:TermGenie] synonym: "down-regulation of sterol regulatory element binding protein cleavage" EXACT [GOC:TermGenie] synonym: "downregulation of SREBP cleavage" EXACT [GOC:TermGenie] synonym: "downregulation of sterol regulatory element binding protein cleavage" EXACT [GOC:TermGenie] synonym: "inhibition of SREBP cleavage" EXACT [GOC:TermGenie] synonym: "inhibition of SREBP processing" EXACT [GOC:bf] synonym: "inhibition of sterol regulatory element binding protein cleavage" NARROW [GOC:TermGenie] synonym: "negative regulation of SREBP cleavage" EXACT [GOC:TermGenie] is_a: GO:0010955 ! negative regulation of protein processing is_a: GO:1901308 ! regulation of sterol regulatory element binding protein cleavage intersection_of: negatively_regulates GO:0035103 ! sterol regulatory element binding protein cleavage relationship: negatively_regulates GO:0035103 ! sterol regulatory element binding protein cleavage created_by: bf creation_date: 2012-08-21T16:43:32Z [Term] id: GO:1901310 name: positive regulation of sterol regulatory element binding protein cleavage namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of sterol regulatory element binding protein cleavage." [GOC:TermGenie, PMID:15899885, PMID:16525117] synonym: "activation of SREBP cleavage" EXACT [GOC:TermGenie] synonym: "activation of sterol regulatory element binding protein cleavage" NARROW [GOC:TermGenie] synonym: "positive regulation of SREBP cleavage" EXACT [GOC:TermGenie] synonym: "up regulation of SREBP cleavage" EXACT [GOC:TermGenie] synonym: "up regulation of sterol regulatory element binding protein cleavage" EXACT [GOC:TermGenie] synonym: "up-regulation of SREBP cleavage" EXACT [GOC:TermGenie] synonym: "up-regulation of sterol regulatory element binding protein cleavage" EXACT [GOC:TermGenie] synonym: "upregulation of SREBP cleavage" EXACT [GOC:TermGenie] synonym: "upregulation of sterol regulatory element binding protein cleavage" EXACT [GOC:TermGenie] is_a: GO:0010954 ! positive regulation of protein processing is_a: GO:1901308 ! regulation of sterol regulatory element binding protein cleavage intersection_of: positively_regulates GO:0035103 ! sterol regulatory element binding protein cleavage relationship: positively_regulates GO:0035103 ! sterol regulatory element binding protein cleavage created_by: bf creation_date: 2012-08-21T16:43:40Z [Term] id: GO:1901311 name: regulation of gene expression involved in extracellular matrix organization namespace: biological_process def: "Any process that modulates the frequency, rate or extent of gene expression involved in extracellular matrix organization." [GOC:BHF, GOC:TermGenie] synonym: "regulation of expression of extracellular matrix proteins" EXACT [GOC:TermGenie] synonym: "regulation of extracellular matrix protein production" RELATED [GOC:TermGenie] is_a: GO:0010468 ! regulation of gene expression intersection_of: regulates GO:1901148 ! gene expression involved in extracellular matrix organization relationship: regulates GO:1901148 ! gene expression involved in extracellular matrix organization created_by: vk creation_date: 2012-08-22T09:18:13Z [Term] id: GO:1901312 name: negative regulation of gene expression involved in extracellular matrix organization namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of gene expression involved in extracellular matrix organization." [GOC:BHF, GOC:TermGenie] synonym: "down regulation of expression of extracellular matrix proteins" EXACT [GOC:TermGenie] synonym: "down regulation of extracellular matrix protein production" RELATED [GOC:TermGenie] synonym: "down regulation of gene expression involved in extracellular matrix organization" EXACT [GOC:TermGenie] synonym: "down-regulation of expression of extracellular matrix proteins" EXACT [GOC:TermGenie] synonym: "down-regulation of extracellular matrix protein production" RELATED [GOC:TermGenie] synonym: "down-regulation of gene expression involved in extracellular matrix organization" EXACT [GOC:TermGenie] synonym: "downregulation of expression of extracellular matrix proteins" EXACT [GOC:TermGenie] synonym: "downregulation of extracellular matrix protein production" RELATED [GOC:TermGenie] synonym: "downregulation of gene expression involved in extracellular matrix organization" EXACT [GOC:TermGenie] synonym: "inhibition of expression of extracellular matrix proteins" EXACT [GOC:TermGenie] synonym: "inhibition of extracellular matrix protein production" RELATED [GOC:TermGenie] synonym: "inhibition of gene expression involved in extracellular matrix organization" NARROW [GOC:TermGenie] synonym: "negative regulation of expression of extracellular matrix proteins" EXACT [GOC:TermGenie] synonym: "negative regulation of extracellular matrix protein production" RELATED [GOC:TermGenie] is_a: GO:0010629 ! negative regulation of gene expression is_a: GO:1901311 ! regulation of gene expression involved in extracellular matrix organization intersection_of: negatively_regulates GO:1901148 ! gene expression involved in extracellular matrix organization relationship: negatively_regulates GO:1901148 ! gene expression involved in extracellular matrix organization created_by: vk creation_date: 2012-08-22T09:18:35Z [Term] id: GO:1901313 name: positive regulation of gene expression involved in extracellular matrix organization namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of gene expression involved in extracellular matrix organization." [GOC:BHF, GOC:TermGenie] synonym: "activation of expression of extracellular matrix proteins" EXACT [GOC:TermGenie] synonym: "activation of extracellular matrix protein production" RELATED [GOC:TermGenie] synonym: "activation of gene expression involved in extracellular matrix organization" NARROW [GOC:TermGenie] synonym: "positive regulation of expression of extracellular matrix proteins" EXACT [GOC:TermGenie] synonym: "positive regulation of extracellular matrix protein production" RELATED [GOC:TermGenie] synonym: "up regulation of expression of extracellular matrix proteins" EXACT [GOC:TermGenie] synonym: "up regulation of extracellular matrix protein production" RELATED [GOC:TermGenie] synonym: "up regulation of gene expression involved in extracellular matrix organization" EXACT [GOC:TermGenie] synonym: "up-regulation of expression of extracellular matrix proteins" EXACT [GOC:TermGenie] synonym: "up-regulation of extracellular matrix protein production" RELATED [GOC:TermGenie] synonym: "up-regulation of gene expression involved in extracellular matrix organization" EXACT [GOC:TermGenie] synonym: "upregulation of expression of extracellular matrix proteins" EXACT [GOC:TermGenie] synonym: "upregulation of extracellular matrix protein production" RELATED [GOC:TermGenie] synonym: "upregulation of gene expression involved in extracellular matrix organization" EXACT [GOC:TermGenie] is_a: GO:0010628 ! positive regulation of gene expression is_a: GO:1901311 ! regulation of gene expression involved in extracellular matrix organization intersection_of: positively_regulates GO:1901148 ! gene expression involved in extracellular matrix organization relationship: positively_regulates GO:1901148 ! gene expression involved in extracellular matrix organization created_by: vk creation_date: 2012-08-22T09:18:42Z [Term] id: GO:1901407 name: regulation of phosphorylation of RNA polymerase II C-terminal domain namespace: biological_process def: "Any process that modulates the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain." [GOC:TermGenie] synonym: "regulation of CTD domain phosphorylation of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "regulation of generation of hyperphosphorylated CTD of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "regulation of generation of II(0) form of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "regulation of hyperphosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:TermGenie] intersection_of: regulates GO:0070816 ! phosphorylation of RNA polymerase II C-terminal domain relationship: regulates GO:0070816 ! phosphorylation of RNA polymerase II C-terminal domain created_by: vw creation_date: 2012-10-01T14:39:50Z [Term] id: GO:1901408 name: negative regulation of phosphorylation of RNA polymerase II C-terminal domain namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain." [GOC:TermGenie] synonym: "down regulation of CTD domain phosphorylation of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "down regulation of generation of hyperphosphorylated CTD of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "down regulation of generation of II(0) form of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "down regulation of hyperphosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:TermGenie] synonym: "down regulation of phosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:TermGenie] synonym: "down-regulation of CTD domain phosphorylation of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "down-regulation of generation of hyperphosphorylated CTD of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "down-regulation of generation of II(0) form of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "down-regulation of hyperphosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:TermGenie] synonym: "down-regulation of phosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:TermGenie] synonym: "downregulation of CTD domain phosphorylation of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "downregulation of generation of hyperphosphorylated CTD of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "downregulation of generation of II(0) form of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "downregulation of hyperphosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:TermGenie] synonym: "downregulation of phosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:TermGenie] synonym: "inhibition of CTD domain phosphorylation of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "inhibition of generation of hyperphosphorylated CTD of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "inhibition of generation of II(0) form of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "inhibition of hyperphosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:TermGenie] synonym: "inhibition of phosphorylation of RNA polymerase II C-terminal domain" NARROW [GOC:TermGenie] synonym: "negative regulation of CTD domain phosphorylation of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "negative regulation of generation of hyperphosphorylated CTD of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "negative regulation of generation of II(0) form of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "negative regulation of hyperphosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:TermGenie] is_a: GO:1901407 ! regulation of phosphorylation of RNA polymerase II C-terminal domain intersection_of: negatively_regulates GO:0070816 ! phosphorylation of RNA polymerase II C-terminal domain relationship: negatively_regulates GO:0070816 ! phosphorylation of RNA polymerase II C-terminal domain created_by: vw creation_date: 2012-10-01T14:40:58Z [Term] id: GO:1901409 name: positive regulation of phosphorylation of RNA polymerase II C-terminal domain namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain." [GOC:TermGenie] synonym: "activation of CTD domain phosphorylation of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "activation of generation of hyperphosphorylated CTD of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "activation of generation of II(0) form of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "activation of hyperphosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:TermGenie] synonym: "activation of phosphorylation of RNA polymerase II C-terminal domain" NARROW [GOC:TermGenie] synonym: "positive regulation of CTD domain phosphorylation of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "positive regulation of generation of hyperphosphorylated CTD of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "positive regulation of generation of II(0) form of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "positive regulation of hyperphosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:TermGenie] synonym: "up regulation of CTD domain phosphorylation of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "up regulation of generation of hyperphosphorylated CTD of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "up regulation of generation of II(0) form of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "up regulation of hyperphosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:TermGenie] synonym: "up regulation of phosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:TermGenie] synonym: "up-regulation of CTD domain phosphorylation of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "up-regulation of generation of hyperphosphorylated CTD of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "up-regulation of generation of II(0) form of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "up-regulation of hyperphosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:TermGenie] synonym: "up-regulation of phosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:TermGenie] synonym: "upregulation of CTD domain phosphorylation of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "upregulation of generation of hyperphosphorylated CTD of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "upregulation of generation of II(0) form of RNA polymerase II" EXACT [GOC:TermGenie] synonym: "upregulation of hyperphosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:TermGenie] synonym: "upregulation of phosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:TermGenie] is_a: GO:1901407 ! regulation of phosphorylation of RNA polymerase II C-terminal domain intersection_of: positively_regulates GO:0070816 ! phosphorylation of RNA polymerase II C-terminal domain relationship: positively_regulates GO:0070816 ! phosphorylation of RNA polymerase II C-terminal domain created_by: vw creation_date: 2012-10-01T14:41:15Z [Term] id: GO:1901486 name: negative regulation of SREBP signaling pathway by positive regulation of transcription factor catabolic process namespace: biological_process def: "Positive regulation of transcription factor catabolism that results in negative regulation of the SREBP signaling pathway." [GOC:TermGenie, GOC:vw, PMID:22833559] synonym: "negative regulation of SREBP signaling pathway by positive regulation of SREBP degradation" NARROW [GOC:bf] synonym: "negative regulation of SREBP signaling pathway by positive regulation of transcription factor catabolism" EXACT [GOC:bf] synonym: "negative regulation of SREBP-mediated signaling pathway by positive regulation of transcription factor catabolic process" EXACT [GOC:TermGenie] synonym: "negative regulation of SREBP-mediated signalling pathway by positive regulation of transcription factor catabolic process" EXACT [GOC:TermGenie] is_a: GO:2000639 ! negative regulation of SREBP signaling pathway intersection_of: results_in GO:2000639 ! negative regulation of SREBP signaling pathway created_by: bf creation_date: 2012-10-09T08:23:26Z [Term] id: GO:1901487 name: negative regulation of SREBP signaling pathway by positive regulation of transcription factor catabolic process in response to increased oxygen levels namespace: biological_process def: "Positive regulation of transcription factor catabolism in response to increased oxygen levels, which results in negative regulation of the SREBP signaling pathway." [GOC:TermGenie, GOC:vw, PMID:22833559] synonym: "negative regulation of SREBP signaling by acceleration of SREBP degradation, in response to increased oxygen levels" NARROW [PMID:22833559] synonym: "negative regulation of SREBP signaling by positive regulation of transcription factor catabolism in response to increased oxygen levels" EXACT [GOC:bf] synonym: "negative regulation of SREBP signaling pathway by positive regulation of SREBP degradation, in response to elevated oxygen" NARROW [GOC:bf] synonym: "negative regulation of SREBP-mediated signaling pathway in presence of oxygen by positive regulation of transcription factor catabolic process" RELATED [GOC:TermGenie] synonym: "negative regulation of SREBP-mediated signaling pathway in response to increased oxygen levels by positive regulation of transcription factor catabolic process" EXACT [GOC:TermGenie] is_a: GO:0038175 ! negative regulation of SREBP signaling pathway in response to increased oxygen levels is_a: GO:1901486 ! negative regulation of SREBP signaling pathway by positive regulation of transcription factor catabolic process intersection_of: results_in GO:0038175 ! negative regulation of SREBP signaling pathway in response to increased oxygen levels created_by: bf creation_date: 2012-10-09T08:23:33Z [Term] id: GO:1901488 name: positive regulation of SREBP signaling pathway by negative regulation of transcription factor catabolic process namespace: biological_process def: "Negative regulation of transcription factor catabolism that results in positive regulation of the SREBP signaling pathway." [GOC:TermGenie, GOC:vw, PMID:22833559] synonym: "positive regulation of SREBP signaling pathway by inhibition of SREBP degradation" NARROW [PMID:22833559] synonym: "positive regulation of SREBP signaling pathway by negative regulation of SREBP degradation" NARROW [PMID:22833559] synonym: "positive regulation of SREBP signaling pathway by negative regulation of transcription factor catabolism" EXACT [GOC:bf] synonym: "positive regulation of SREBP-mediated signaling pathway by negative regulation of transcription factor catabolic process" EXACT [GOC:TermGenie] synonym: "positive regulation of SREBP-mediated signalling pathway by negative regulation of transcription factor catabolic process" EXACT [GOC:TermGenie] is_a: GO:2000640 ! positive regulation of SREBP signaling pathway intersection_of: results_in GO:2000640 ! positive regulation of SREBP signaling pathway created_by: bf creation_date: 2012-10-09T08:23:43Z [Term] id: GO:1901489 name: positive regulation of SREBP signaling pathway by negative regulation of transcription factor catabolic process in response to decreased oxygen levels namespace: biological_process def: "Negative regulation of transcription factor catabolism in response to decreased oxygen levels, which results in positive regulation of the SREBP signaling pathway." [GOC:TermGenie, GOC:vw, PMID:22833559] synonym: "positive regulation of SREBP signaling by inhibition of SREBP degradation in response to decreased oxygen levels" EXACT [GOC:bf] synonym: "positive regulation of SREBP signaling by negative regulation of transcription factor catabolism at low oxygen levels" EXACT [GOC:bf] synonym: "positive regulation of SREBP signaling pathway by negative regulation of SREBP degradation, in response to decreased oxygen" NARROW [PMID:22833559] synonym: "positive regulation of SREBP-mediated signaling pathway in absence of oxygen by negative regulation of transcription factor catabolic process" RELATED [GOC:TermGenie] synonym: "positive regulation of SREBP-mediated signaling pathway in response to decreased oxygen levels by negative regulation of transcription factor catabolic process" EXACT [GOC:TermGenie] is_a: GO:0038176 ! positive regulation of SREBP signaling pathway in response to decreased oxygen levels is_a: GO:1901488 ! positive regulation of SREBP signaling pathway by negative regulation of transcription factor catabolic process intersection_of: results_in GO:0038176 ! positive regulation of SREBP signaling pathway in response to decreased oxygen levels created_by: bf creation_date: 2012-10-09T08:23:50Z [Term] id: GO:1901522 name: positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus namespace: biological_process def: "Any positive regulation of transcription from RNA polymerase II promoter that is involved in cellular response to chemical stimulus." [GOC:TermGenie, PMID:22840777] synonym: "activation of global transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus" RELATED [GOC:TermGenie] synonym: "activation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus" NARROW [GOC:TermGenie] synonym: "positive regulation of gene-specific transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus" RELATED [GOC:TermGenie] synonym: "positive regulation of global transcription from Pol II promoter involved in cellular response to chemical stimulus" RELATED [GOC:TermGenie] synonym: "positive regulation of transcription from Pol II promoter involved in cellular response to chemical stimulus" EXACT [GOC:TermGenie] synonym: "stimulation of global transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus" NARROW [GOC:TermGenie] synonym: "stimulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus" EXACT [GOC:TermGenie] synonym: "up regulation of global transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus" RELATED [GOC:TermGenie] synonym: "up regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus" EXACT [GOC:TermGenie] synonym: "up-regulation of global transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus" RELATED [GOC:TermGenie] synonym: "up-regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus" EXACT [GOC:TermGenie] synonym: "upregulation of global transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus" RELATED [GOC:TermGenie] synonym: "upregulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus" EXACT [GOC:TermGenie] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: al creation_date: 2012-10-19T08:25:05Z [Term] id: GO:1901535 name: regulation of DNA demethylation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of DNA demethylation." [GOC:TermGenie] intersection_of: regulates GO:0080111 ! DNA demethylation relationship: regulates GO:0080111 ! DNA demethylation created_by: jl creation_date: 2012-10-24T13:52:50Z [Term] id: GO:1901536 name: negative regulation of DNA demethylation namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of DNA demethylation." [GOC:TermGenie] synonym: "down regulation of DNA demethylation" EXACT [GOC:TermGenie] synonym: "down-regulation of DNA demethylation" EXACT [GOC:TermGenie] synonym: "downregulation of DNA demethylation" EXACT [GOC:TermGenie] synonym: "inhibition of DNA demethylation" NARROW [GOC:TermGenie] is_a: GO:1901535 ! regulation of DNA demethylation intersection_of: negatively_regulates GO:0080111 ! DNA demethylation relationship: negatively_regulates GO:0080111 ! DNA demethylation created_by: jl creation_date: 2012-10-24T13:52:54Z [Term] id: GO:1901537 name: positive regulation of DNA demethylation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of DNA demethylation." [GOC:TermGenie] synonym: "activation of DNA demethylation" NARROW [GOC:TermGenie] synonym: "up regulation of DNA demethylation" EXACT [GOC:TermGenie] synonym: "up-regulation of DNA demethylation" EXACT [GOC:TermGenie] synonym: "upregulation of DNA demethylation" EXACT [GOC:TermGenie] is_a: GO:1901535 ! regulation of DNA demethylation intersection_of: positively_regulates GO:0080111 ! DNA demethylation relationship: positively_regulates GO:0080111 ! DNA demethylation created_by: jl creation_date: 2012-10-24T13:52:59Z [Term] id: GO:1901580 name: regulation of telomeric RNA transcription from RNA pol II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of telomeric RNA transcription from RNA pol II promoter." [GOC:TermGenie] synonym: "regulation of telomeric RNA transcription from Pol II promoter" EXACT [GOC:TermGenie] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: regulates GO:0097394 ! telomeric RNA transcription from RNA pol II promoter relationship: regulates GO:0097394 ! telomeric RNA transcription from RNA pol II promoter created_by: al creation_date: 2012-11-06T11:07:16Z [Term] id: GO:1901581 name: negative regulation of telomeric RNA transcription from RNA pol II promoter namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of telomeric RNA transcription from RNA pol II promoter." [GOC:TermGenie] synonym: "down regulation of telomeric RNA transcription from Pol II promoter" EXACT [GOC:TermGenie] synonym: "down regulation of telomeric RNA transcription from RNA pol II promoter" EXACT [GOC:TermGenie] synonym: "down-regulation of telomeric RNA transcription from Pol II promoter" EXACT [GOC:TermGenie] synonym: "down-regulation of telomeric RNA transcription from RNA pol II promoter" EXACT [GOC:TermGenie] synonym: "downregulation of telomeric RNA transcription from Pol II promoter" EXACT [GOC:TermGenie] synonym: "downregulation of telomeric RNA transcription from RNA pol II promoter" EXACT [GOC:TermGenie] synonym: "inhibition of telomeric RNA transcription from Pol II promoter" EXACT [GOC:TermGenie] synonym: "inhibition of telomeric RNA transcription from RNA pol II promoter" NARROW [GOC:TermGenie] synonym: "negative regulation of telomeric RNA transcription from Pol II promoter" EXACT [GOC:TermGenie] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter is_a: GO:1901580 ! regulation of telomeric RNA transcription from RNA pol II promoter intersection_of: negatively_regulates GO:0097394 ! telomeric RNA transcription from RNA pol II promoter relationship: negatively_regulates GO:0097394 ! telomeric RNA transcription from RNA pol II promoter created_by: al creation_date: 2012-11-06T11:07:21Z [Term] id: GO:1901582 name: positive regulation of telomeric RNA transcription from RNA pol II promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of telomeric RNA transcription from RNA pol II promoter." [GOC:TermGenie] synonym: "activation of telomeric RNA transcription from Pol II promoter" EXACT [GOC:TermGenie] synonym: "activation of telomeric RNA transcription from RNA pol II promoter" NARROW [GOC:TermGenie] synonym: "positive regulation of telomeric RNA transcription from Pol II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of telomeric RNA transcription from Pol II promoter" EXACT [GOC:TermGenie] synonym: "up regulation of telomeric RNA transcription from RNA pol II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of telomeric RNA transcription from Pol II promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of telomeric RNA transcription from RNA pol II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of telomeric RNA transcription from Pol II promoter" EXACT [GOC:TermGenie] synonym: "upregulation of telomeric RNA transcription from RNA pol II promoter" EXACT [GOC:TermGenie] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter is_a: GO:1901580 ! regulation of telomeric RNA transcription from RNA pol II promoter intersection_of: positively_regulates GO:0097394 ! telomeric RNA transcription from RNA pol II promoter relationship: positively_regulates GO:0097394 ! telomeric RNA transcription from RNA pol II promoter created_by: al creation_date: 2012-11-06T11:07:25Z [Term] id: GO:1901588 name: dendritic microtubule namespace: cellular_component def: "Any microtubule in a dendrite, a neuron projection." [GOC:TermGenie, NIF_Subcellular:sao110773650] synonym: "microtubule of dendrite" EXACT [GOC:TermGenie] synonym: "microtubulus of dendrite" EXACT [GOC:TermGenie] is_a: GO:0097458 ! neuron part intersection_of: part_of GO:0030425 ! dendrite relationship: part_of GO:0030425 ! dendrite created_by: pr creation_date: 2012-11-07T14:37:30Z [Term] id: GO:1901589 name: axon microtubule bundle namespace: cellular_component def: "An arrangement of closely apposed microtubules running parallel to each other in the axon hillock and initial segment." [GOC:TermGenie, NIF_Subcellular:sao707332678] synonym: "axon microtubule fascicle" EXACT [] synonym: "microtubule bundle of axon" EXACT [GOC:TermGenie] synonym: "microtubule fascicle of axon" EXACT [GOC:TermGenie] is_a: GO:0033267 ! axon part intersection_of: part_of GO:0030424 ! axon relationship: part_of GO:0030424 ! axon created_by: pr creation_date: 2012-11-07T15:37:12Z [Term] id: GO:1901619 name: tRNA methylation in response to nitrogen starvation namespace: biological_process def: "The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule as a result of deprivation of nitrogen." [GOC:TermGenie, PMID:23074192] is_a: GO:0030488 ! tRNA methylation intersection_of: results_in GO:0030488 ! tRNA methylation created_by: al creation_date: 2012-11-13T14:36:00Z [Term] id: GO:1901643 name: regulation of tRNA methylation in response to nitrogen starvation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of tRNA methylation in response to nitrogen starvation." [GOC:TermGenie] is_a: GO:2000235 ! regulation of tRNA processing intersection_of: regulates GO:1901619 ! tRNA methylation in response to nitrogen starvation relationship: regulates GO:1901619 ! tRNA methylation in response to nitrogen starvation created_by: al creation_date: 2012-11-16T14:44:08Z [Term] id: GO:1901644 name: positive regulation of tRNA methylation in response to nitrogen starvation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of tRNA methylation in response to nitrogen starvation." [GOC:TermGenie] synonym: "activation of tRNA methylation in response to nitrogen starvation" NARROW [GOC:TermGenie] synonym: "up regulation of tRNA methylation in response to nitrogen starvation" EXACT [GOC:TermGenie] synonym: "up-regulation of tRNA methylation in response to nitrogen starvation" EXACT [GOC:TermGenie] synonym: "upregulation of tRNA methylation in response to nitrogen starvation" EXACT [GOC:TermGenie] is_a: GO:1901643 ! regulation of tRNA methylation in response to nitrogen starvation is_a: GO:2000237 ! positive regulation of tRNA processing intersection_of: positively_regulates GO:1901619 ! tRNA methylation in response to nitrogen starvation relationship: positively_regulates GO:1901619 ! tRNA methylation in response to nitrogen starvation created_by: al creation_date: 2012-11-16T14:44:12Z [Term] id: GO:1901718 name: regulation of dipeptide transmembrane transport by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A regulation of transcription from RNA polymerase II promoter that results in regulation of dipeptide transmembrane transport." [GOC:TermGenie, GOC:vw] is_a: GO:0035953 ! regulation of dipeptide transport by regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: pr creation_date: 2012-12-19T17:04:04Z [Term] id: GO:1901836 name: regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription of nuclear large rRNA transcript from RNA polymerase I promoter." [GOC:sart, GOC:TermGenie] synonym: "regulation of transcription of nuclear rRNA large Pol I transcript" EXACT [GOC:TermGenie] is_a: GO:0006356 ! regulation of transcription from RNA polymerase I promoter intersection_of: regulates GO:0042790 ! transcription of nuclear large rRNA transcript from RNA polymerase I promoter relationship: regulates GO:0042790 ! transcription of nuclear large rRNA transcript from RNA polymerase I promoter created_by: sart creation_date: 2013-01-23T10:16:27Z [Term] id: GO:1901837 name: negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of transcription of nuclear large rRNA transcript from RNA polymerase I promoter." [GOC:sart, GOC:TermGenie] synonym: "down regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter" EXACT [GOC:TermGenie] synonym: "down regulation of transcription of nuclear rRNA large Pol I transcript" EXACT [GOC:TermGenie] synonym: "down-regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter" EXACT [GOC:TermGenie] synonym: "down-regulation of transcription of nuclear rRNA large Pol I transcript" EXACT [GOC:TermGenie] synonym: "downregulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter" EXACT [GOC:TermGenie] synonym: "downregulation of transcription of nuclear rRNA large Pol I transcript" EXACT [GOC:TermGenie] synonym: "inhibition of transcription of nuclear large rRNA transcript from RNA polymerase I promoter" NARROW [GOC:TermGenie] synonym: "inhibition of transcription of nuclear rRNA large Pol I transcript" EXACT [GOC:TermGenie] synonym: "negative regulation of transcription of nuclear rRNA large Pol I transcript" EXACT [GOC:TermGenie] is_a: GO:0016479 ! negative regulation of transcription from RNA polymerase I promoter is_a: GO:1901836 ! regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter intersection_of: negatively_regulates GO:0042790 ! transcription of nuclear large rRNA transcript from RNA polymerase I promoter relationship: negatively_regulates GO:0042790 ! transcription of nuclear large rRNA transcript from RNA polymerase I promoter created_by: sart creation_date: 2013-01-23T10:16:31Z [Term] id: GO:1901838 name: positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transcription of nuclear large rRNA transcript from RNA polymerase I promoter." [GOC:sart, GOC:TermGenie] synonym: "activation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter" NARROW [GOC:TermGenie] synonym: "activation of transcription of nuclear rRNA large Pol I transcript" EXACT [GOC:TermGenie] synonym: "positive regulation of transcription of nuclear rRNA large Pol I transcript" EXACT [GOC:TermGenie] synonym: "up regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter" EXACT [GOC:TermGenie] synonym: "up regulation of transcription of nuclear rRNA large Pol I transcript" EXACT [GOC:TermGenie] synonym: "up-regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter" EXACT [GOC:TermGenie] synonym: "up-regulation of transcription of nuclear rRNA large Pol I transcript" EXACT [GOC:TermGenie] synonym: "upregulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter" EXACT [GOC:TermGenie] synonym: "upregulation of transcription of nuclear rRNA large Pol I transcript" EXACT [GOC:TermGenie] is_a: GO:0045943 ! positive regulation of transcription from RNA polymerase I promoter is_a: GO:1901836 ! regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter intersection_of: positively_regulates GO:0042790 ! transcription of nuclear large rRNA transcript from RNA polymerase I promoter relationship: positively_regulates GO:0042790 ! transcription of nuclear large rRNA transcript from RNA polymerase I promoter created_by: sart creation_date: 2013-01-23T10:16:36Z [Term] id: GO:1901921 name: phosphorylation of RNA polymerase II C-terminal domain involved in recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex namespace: biological_process def: "Any phosphorylation of RNA polymerase II C-terminal domain that is involved in recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex." [GOC:TermGenie, PMID:10594013] synonym: "CTD domain phosphorylation of RNA polymerase II involved in recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex" EXACT [GOC:TermGenie] is_a: GO:0070816 ! phosphorylation of RNA polymerase II C-terminal domain intersection_of: GO:0070816 ! phosphorylation of RNA polymerase II C-terminal domain intersection_of: part_of GO:0034402 ! recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex relationship: part_of GO:0034402 ! recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex created_by: ramab creation_date: 2013-02-15T19:09:31Z [Term] id: GO:1902010 name: negative regulation of translation involved in response to endoplasmic reticulum stress namespace: biological_process def: "Any negative regulation of translation that is involved in response to endoplasmic reticulum stress." [GOC:dph, GOC:TermGenie, PMID:10882126] synonym: "down regulation of protein biosynthetic process involved in ER stress response" EXACT [GOC:TermGenie] synonym: "down regulation of protein biosynthetic process involved in response to endoplasmic reticulum stress" EXACT [GOC:TermGenie] synonym: "down regulation of protein biosynthetic process involved in response to ER stress" EXACT [GOC:TermGenie] synonym: "down-regulation of protein biosynthetic process involved in ER stress response" EXACT [GOC:TermGenie] synonym: "down-regulation of protein biosynthetic process involved in response to endoplasmic reticulum stress" EXACT [GOC:TermGenie] synonym: "down-regulation of protein biosynthetic process involved in response to ER stress" EXACT [GOC:TermGenie] synonym: "downregulation of protein biosynthetic process involved in ER stress response" EXACT [GOC:TermGenie] synonym: "downregulation of protein biosynthetic process involved in response to endoplasmic reticulum stress" EXACT [GOC:TermGenie] synonym: "downregulation of protein biosynthetic process involved in response to ER stress" EXACT [GOC:TermGenie] synonym: "inhibition of protein biosynthetic process involved in ER stress response" NARROW [GOC:TermGenie] synonym: "inhibition of protein biosynthetic process involved in response to endoplasmic reticulum stress" NARROW [GOC:TermGenie] synonym: "inhibition of protein biosynthetic process involved in response to ER stress" NARROW [GOC:TermGenie] synonym: "negative regulation of protein anabolism involved in ER stress response" EXACT [GOC:TermGenie] synonym: "negative regulation of protein anabolism involved in response to endoplasmic reticulum stress" EXACT [GOC:TermGenie] synonym: "negative regulation of protein anabolism involved in response to ER stress" EXACT [GOC:TermGenie] synonym: "negative regulation of protein biosynthesis involved in ER stress response" EXACT [GOC:TermGenie] synonym: "negative regulation of protein biosynthesis involved in response to endoplasmic reticulum stress" EXACT [GOC:TermGenie] synonym: "negative regulation of protein biosynthesis involved in response to ER stress" EXACT [GOC:TermGenie] synonym: "negative regulation of protein biosynthetic process involved in ER stress response" EXACT [GOC:TermGenie] synonym: "negative regulation of protein biosynthetic process involved in response to endoplasmic reticulum stress" EXACT [GOC:TermGenie] synonym: "negative regulation of protein biosynthetic process involved in response to ER stress" EXACT [GOC:TermGenie] synonym: "negative regulation of protein formation involved in ER stress response" EXACT [GOC:TermGenie] synonym: "negative regulation of protein formation involved in response to endoplasmic reticulum stress" EXACT [GOC:TermGenie] synonym: "negative regulation of protein formation involved in response to ER stress" EXACT [GOC:TermGenie] synonym: "negative regulation of protein synthesis involved in ER stress response" EXACT [GOC:TermGenie] synonym: "negative regulation of protein synthesis involved in response to endoplasmic reticulum stress" EXACT [GOC:TermGenie] synonym: "negative regulation of protein synthesis involved in response to ER stress" EXACT [GOC:TermGenie] synonym: "negative regulation of translation involved in ER stress response" EXACT [GOC:TermGenie] synonym: "negative regulation of translation involved in response to ER stress" EXACT [GOC:TermGenie] synonym: "protein biosynthesis inhibitor activity involved in ER stress response" RELATED [GOC:TermGenie] synonym: "protein biosynthesis inhibitor activity involved in response to endoplasmic reticulum stress" RELATED [GOC:TermGenie] synonym: "protein biosynthesis inhibitor activity involved in response to ER stress" RELATED [GOC:TermGenie] synonym: "protein biosynthetic process inhibitor activity involved in ER stress response" RELATED [GOC:TermGenie] synonym: "protein biosynthetic process inhibitor activity involved in response to endoplasmic reticulum stress" RELATED [GOC:TermGenie] synonym: "protein biosynthetic process inhibitor activity involved in response to ER stress" RELATED [GOC:TermGenie] is_a: GO:0017148 ! negative regulation of translation intersection_of: GO:0017148 ! negative regulation of translation created_by: dph creation_date: 2013-03-22T13:43:26Z [Term] id: GO:1902064 name: regulation of transcription from RNA polymerase II promoter involved in spermatogenesis namespace: biological_process def: "Any regulation of transcription from RNA polymerase II promoter that is involved in spermatogenesis." [GOC:kmv, GOC:TermGenie, PMID:22570621] synonym: "global transcription regulation from Pol II promoter involved in generation of spermatozoa" RELATED [GOC:TermGenie] synonym: "global transcription regulation from Pol II promoter involved in spermatogenesis" RELATED [GOC:TermGenie] synonym: "regulation of gene-specific transcription from RNA polymerase II promoter involved in generation of spermatozoa" RELATED [GOC:TermGenie] synonym: "regulation of gene-specific transcription from RNA polymerase II promoter involved in spermatogenesis" RELATED [GOC:TermGenie] synonym: "regulation of global transcription from Pol II promoter involved in generation of spermatozoa" RELATED [GOC:TermGenie] synonym: "regulation of global transcription from Pol II promoter involved in spermatogenesis" RELATED [GOC:TermGenie] synonym: "regulation of transcription from Pol II promoter involved in generation of spermatozoa" EXACT [GOC:TermGenie] synonym: "regulation of transcription from Pol II promoter involved in spermatogenesis" EXACT [GOC:TermGenie] synonym: "regulation of transcription from RNA polymerase II promoter involved in generation of spermatozoa" EXACT [GOC:TermGenie] synonym: "regulation of transcription from RNA polymerase II promoter, global involved in generation of spermatozoa" RELATED [GOC:TermGenie] synonym: "regulation of transcription from RNA polymerase II promoter, global involved in spermatogenesis" RELATED [GOC:TermGenie] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: kmv creation_date: 2013-04-16T20:27:18Z [Term] id: GO:1902097 name: positive regulation of transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacterium namespace: biological_process def: "Any positive regulation of transcription from RNA polymerase II promoter that is involved in defense response to Gram-negative bacterium." [GOC:kmv, GOC:TermGenie, PMID:17183709] synonym: "activation of global transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacteria" RELATED [GOC:TermGenie] synonym: "activation of global transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacterium" RELATED [GOC:TermGenie] synonym: "activation of global transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacteria" RELATED [GOC:TermGenie] synonym: "activation of global transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacterium" RELATED [GOC:TermGenie] synonym: "activation of global transcription from RNA polymerase II promoter involved in Gram-negative antibacterial peptide activity" RELATED [GOC:TermGenie] synonym: "activation of transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacteria" NARROW [GOC:TermGenie] synonym: "activation of transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacterium" NARROW [GOC:TermGenie] synonym: "activation of transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacteria" NARROW [GOC:TermGenie] synonym: "activation of transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacterium" NARROW [GOC:TermGenie] synonym: "activation of transcription from RNA polymerase II promoter involved in Gram-negative antibacterial peptide activity" RELATED [GOC:TermGenie] synonym: "positive regulation of gene-specific transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacteria" RELATED [GOC:TermGenie] synonym: "positive regulation of gene-specific transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacterium" RELATED [GOC:TermGenie] synonym: "positive regulation of gene-specific transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacteria" RELATED [GOC:TermGenie] synonym: "positive regulation of gene-specific transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacterium" RELATED [GOC:TermGenie] synonym: "positive regulation of gene-specific transcription from RNA polymerase II promoter involved in Gram-negative antibacterial peptide activity" RELATED [GOC:TermGenie] synonym: "positive regulation of global transcription from Pol II promoter involved in defence response to Gram-negative bacteria" RELATED [GOC:TermGenie] synonym: "positive regulation of global transcription from Pol II promoter involved in defence response to Gram-negative bacterium" RELATED [GOC:TermGenie] synonym: "positive regulation of global transcription from Pol II promoter involved in defense response to Gram-negative bacteria" RELATED [GOC:TermGenie] synonym: "positive regulation of global transcription from Pol II promoter involved in defense response to Gram-negative bacterium" RELATED [GOC:TermGenie] synonym: "positive regulation of global transcription from Pol II promoter involved in Gram-negative antibacterial peptide activity" RELATED [GOC:TermGenie] synonym: "positive regulation of transcription from Pol II promoter involved in defence response to Gram-negative bacteria" EXACT [GOC:TermGenie] synonym: "positive regulation of transcription from Pol II promoter involved in defence response to Gram-negative bacterium" EXACT [GOC:TermGenie] synonym: "positive regulation of transcription from Pol II promoter involved in defense response to Gram-negative bacteria" EXACT [GOC:TermGenie] synonym: "positive regulation of transcription from Pol II promoter involved in defense response to Gram-negative bacterium" EXACT [GOC:TermGenie] synonym: "positive regulation of transcription from Pol II promoter involved in Gram-negative antibacterial peptide activity" RELATED [GOC:TermGenie] synonym: "positive regulation of transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacteria" EXACT [GOC:TermGenie] synonym: "positive regulation of transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacterium" EXACT [GOC:TermGenie] synonym: "positive regulation of transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacteria" EXACT [GOC:TermGenie] synonym: "positive regulation of transcription from RNA polymerase II promoter involved in Gram-negative antibacterial peptide activity" RELATED [GOC:TermGenie] synonym: "stimulation of global transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacteria" NARROW [GOC:TermGenie] synonym: "stimulation of global transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacterium" NARROW [GOC:TermGenie] synonym: "stimulation of global transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacteria" NARROW [GOC:TermGenie] synonym: "stimulation of global transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacterium" NARROW [GOC:TermGenie] synonym: "stimulation of global transcription from RNA polymerase II promoter involved in Gram-negative antibacterial peptide activity" RELATED [GOC:TermGenie] synonym: "stimulation of transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacteria" EXACT [GOC:TermGenie] synonym: "stimulation of transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacterium" EXACT [GOC:TermGenie] synonym: "stimulation of transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacteria" EXACT [GOC:TermGenie] synonym: "stimulation of transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacterium" EXACT [GOC:TermGenie] synonym: "stimulation of transcription from RNA polymerase II promoter involved in Gram-negative antibacterial peptide activity" RELATED [GOC:TermGenie] synonym: "up regulation of global transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacteria" RELATED [GOC:TermGenie] synonym: "up regulation of global transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacterium" RELATED [GOC:TermGenie] synonym: "up regulation of global transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacteria" RELATED [GOC:TermGenie] synonym: "up regulation of global transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacterium" RELATED [GOC:TermGenie] synonym: "up regulation of global transcription from RNA polymerase II promoter involved in Gram-negative antibacterial peptide activity" RELATED [GOC:TermGenie] synonym: "up regulation of transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacteria" EXACT [GOC:TermGenie] synonym: "up regulation of transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacterium" EXACT [GOC:TermGenie] synonym: "up regulation of transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacteria" EXACT [GOC:TermGenie] synonym: "up regulation of transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacterium" EXACT [GOC:TermGenie] synonym: "up regulation of transcription from RNA polymerase II promoter involved in Gram-negative antibacterial peptide activity" RELATED [GOC:TermGenie] synonym: "up-regulation of global transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacteria" RELATED [GOC:TermGenie] synonym: "up-regulation of global transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacterium" RELATED [GOC:TermGenie] synonym: "up-regulation of global transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacteria" RELATED [GOC:TermGenie] synonym: "up-regulation of global transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacterium" RELATED [GOC:TermGenie] synonym: "up-regulation of global transcription from RNA polymerase II promoter involved in Gram-negative antibacterial peptide activity" RELATED [GOC:TermGenie] synonym: "up-regulation of transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacteria" EXACT [GOC:TermGenie] synonym: "up-regulation of transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacterium" EXACT [GOC:TermGenie] synonym: "up-regulation of transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacteria" EXACT [GOC:TermGenie] synonym: "up-regulation of transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacterium" EXACT [GOC:TermGenie] synonym: "up-regulation of transcription from RNA polymerase II promoter involved in Gram-negative antibacterial peptide activity" RELATED [GOC:TermGenie] synonym: "upregulation of global transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacteria" RELATED [GOC:TermGenie] synonym: "upregulation of global transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacterium" RELATED [GOC:TermGenie] synonym: "upregulation of global transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacteria" RELATED [GOC:TermGenie] synonym: "upregulation of global transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacterium" RELATED [GOC:TermGenie] synonym: "upregulation of global transcription from RNA polymerase II promoter involved in Gram-negative antibacterial peptide activity" RELATED [GOC:TermGenie] synonym: "upregulation of transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacteria" EXACT [GOC:TermGenie] synonym: "upregulation of transcription from RNA polymerase II promoter involved in defence response to Gram-negative bacterium" EXACT [GOC:TermGenie] synonym: "upregulation of transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacteria" EXACT [GOC:TermGenie] synonym: "upregulation of transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacterium" EXACT [GOC:TermGenie] synonym: "upregulation of transcription from RNA polymerase II promoter involved in Gram-negative antibacterial peptide activity" RELATED [GOC:TermGenie] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: kmv creation_date: 2013-04-30T16:54:30Z [Term] id: GO:1902352 name: negative regulation of filamentous growth of a population of unicellular organisms in response to starvation by negative regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A negative regulation of transcription from RNA polymerase II promoter that results in negative regulation of filamentous growth of a population of unicellular organisms in response to starvation." [GOC:rn, GOC:TermGenie, PMID:23223039] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter intersection_of: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: bf creation_date: 2013-08-14T09:35:43Z [Term] id: GO:1902353 name: positive regulation of induction of conjugation with cellular fusion by negative regulation of transcription from RNA polymerase II promoter by pheromones namespace: biological_process def: "A negative regulation of transcription from RNA polymerase II promoter by pheromones that results in positive regulation of induction of conjugation with cellular fusion." [GOC:rn, GOC:TermGenie, PMID:23872066] synonym: "up regulation of induction of conjugation with cellular fusion by negative regulation of transcription from RNA polymerase II promoter by pheromones" EXACT [GOC:TermGenie] synonym: "up-regulation of induction of conjugation with cellular fusion by negative regulation of transcription from RNA polymerase II promoter by pheromones" EXACT [GOC:TermGenie] synonym: "upregulation of induction of conjugation with cellular fusion by negative regulation of transcription from RNA polymerase II promoter by pheromones" EXACT [GOC:TermGenie] is_a: GO:0046020 ! negative regulation of transcription from RNA polymerase II promoter by pheromones intersection_of: GO:0046020 ! negative regulation of transcription from RNA polymerase II promoter by pheromones created_by: bf creation_date: 2013-08-14T09:45:21Z [Term] id: GO:1902360 name: conversion of ds siRNA to ss siRNA involved in chromatin silencing by small RNA namespace: biological_process def: "Any conversion of ds siRNA to ss siRNA that is involved in chromatin silencing by small RNA." [GOC:TermGenie, GOC:vw, PMID:19239886] synonym: "conversion of double-stranded small interfering RNA to single-stranded small interfering RNA. involved in chromatin silencing by small RNA" RELATED [GOC:TermGenie] synonym: "conversion of double-stranded small interfering RNA to single-stranded small interfering RNA. involved in RNA interference-like chromatin silencing" RELATED [GOC:TermGenie] synonym: "conversion of double-stranded small interfering RNA to single-stranded small interfering RNA. involved in RNA-mediated chromatin silencing" RELATED [GOC:TermGenie] synonym: "conversion of double-stranded small interfering RNA to single-stranded small interfering RNA. involved in RNA-mediated transcriptional silencing" RELATED [GOC:TermGenie] synonym: "conversion of double-stranded small interfering RNA to single-stranded small interfering RNA. involved in RNAi-directed chromatin silencing" RELATED [GOC:TermGenie] synonym: "conversion of double-stranded small interfering RNA to single-stranded small interfering RNA. involved in RNAi-like chromatin silencing" RELATED [GOC:TermGenie] synonym: "conversion of double-stranded small interfering RNA to single-stranded small interfering RNA. involved in small RNA-mediated heterochromatic silencing" RELATED [GOC:TermGenie] synonym: "conversion of ds siRNA to ss siRNA involved in RNA interference-like chromatin silencing" EXACT [GOC:TermGenie] synonym: "conversion of ds siRNA to ss siRNA involved in RNA-mediated chromatin silencing" EXACT [GOC:TermGenie] synonym: "conversion of ds siRNA to ss siRNA involved in RNA-mediated transcriptional silencing" EXACT [GOC:TermGenie] synonym: "conversion of ds siRNA to ss siRNA involved in RNAi-directed chromatin silencing" EXACT [GOC:TermGenie] synonym: "conversion of ds siRNA to ss siRNA involved in RNAi-like chromatin silencing" EXACT [GOC:TermGenie] synonym: "conversion of ds siRNA to ss siRNA involved in small RNA-mediated heterochromatic silencing" EXACT [GOC:TermGenie] is_a: GO:0036404 ! conversion of ds siRNA to ss siRNA intersection_of: GO:0036404 ! conversion of ds siRNA to ss siRNA intersection_of: part_of GO:0031048 ! chromatin silencing by small RNA relationship: part_of GO:0031048 ! chromatin silencing by small RNA created_by: bf creation_date: 2013-08-15T10:06:18Z [Term] id: GO:1902368 name: heterochromatin maintenance involved in chromatin silencing at centromere outer repeat region namespace: biological_process def: "Any heterochromatin maintenance that is involved in chromatin silencing at centromere outer repeat region." [GOC:TermGenie, GOC:vw, PMID:21289066] synonym: "heterochromatin maintenance involved in chromatin silencing at centromeric outer repeats" EXACT [GOC:vw] synonym: "heterochromatin maintenance involved in chromatin silencing at pericentric region" RELATED [GOC:TermGenie] is_a: GO:0070870 ! heterochromatin maintenance involved in chromatin silencing intersection_of: part_of GO:1990141 ! chromatin silencing at centromere outer repeat region relationship: part_of GO:1990141 ! chromatin silencing at centromere outer repeat region created_by: bf creation_date: 2013-08-21T10:13:39Z [Term] id: GO:1902375 name: nuclear tRNA 3'-trailer cleavage, endonucleolytic namespace: biological_process def: "Any tRNA 3'-trailer cleavage, endonucleolytic that takes place in nucleus." [GOC:TermGenie, PMID:23928301] synonym: "endonucleolytic tRNA 3'-end cleavage in cell nucleus" EXACT [GOC:TermGenie] synonym: "endonucleolytic tRNA 3'-end cleavage in nucleus" EXACT [GOC:TermGenie] synonym: "endonucleolytic tRNA 3'-trailer cleavage in cell nucleus" RELATED [GOC:TermGenie] synonym: "endonucleolytic tRNA 3'-trailer cleavage in nucleus" RELATED [GOC:TermGenie] synonym: "tRNA 3'-end cleavage, endonucleolytic in cell nucleus" EXACT [GOC:TermGenie] synonym: "tRNA 3'-end cleavage, endonucleolytic in nucleus" EXACT [GOC:TermGenie] synonym: "tRNA 3'-trailer cleavage, endonucleolytic in cell nucleus" EXACT [GOC:TermGenie] is_a: GO:0034414 ! tRNA 3'-trailer cleavage, endonucleolytic intersection_of: GO:0034414 ! tRNA 3'-trailer cleavage, endonucleolytic created_by: al creation_date: 2013-08-30T09:17:30Z [Term] id: GO:1990013 name: presynaptic grid namespace: cellular_component def: "A hexagonal array of electron dense particles attached to the cytoplasmic face of the presynaptic membrane." [ISBN:0716723808, NIF_Subcellular:sao1730664005] synonym: "pre-synaptic grid" EXACT [] is_a: GO:0097458 ! neuron part relationship: part_of GO:0048786 ! presynaptic active zone created_by: pr creation_date: 2012-12-13T09:00:35Z [Term] id: GO:1990020 name: recurrent axon collateral namespace: cellular_component def: "Axon collateral that ramifies in the area of the soma of the cell of origin." [NIF_Subcellular:sao1642494436] synonym: "recurrent collateral" BROAD [] is_a: GO:0044303 ! axon collateral created_by: pr creation_date: 2013-01-10T16:04:31Z [Term] id: GO:1990021 name: Schaffer axon collateral namespace: cellular_component def: "Part of axon of a CA3 pyramidal neuron that projects to hippocampal area CA1." [NIF_Subcellular:nlx_subcell_20090511] synonym: "Schaffer collateral" BROAD [] is_a: GO:0044303 ! axon collateral created_by: pr creation_date: 2013-01-10T16:06:17Z [Term] id: GO:1990024 name: C bouton namespace: cellular_component def: "Synaptic bouton found in spinal cord on the soma and proximal dendrites of motor neurons." [NIF_Subcellular:nlx_subcell_100208] is_a: GO:0043195 ! terminal bouton created_by: pr creation_date: 2013-02-06T10:27:41Z [Term] id: GO:1990025 name: F bouton namespace: cellular_component def: "Synaptic bouton found in the ventral horn of the spinal cord. F boutons range in diameter from 0.5 to 7 um and contain flattened or pleomorphic synaptic vesicles." [NIF_Subcellular:nlx_subcell_100206] is_a: GO:0043195 ! terminal bouton created_by: pr creation_date: 2013-02-06T10:29:42Z [Term] id: GO:1990026 name: hippocampal mossy fiber expansion namespace: cellular_component def: "Synaptic expansion of hippocampal mossy fiber axon that makes contact with the thorny excrescences of hippocampal CA3 pyramidal cell dendrites." [NIF_Subcellular:nlx_subcell_1005002] synonym: "dentate gyrus granule cell axonal bouton" RELATED [] synonym: "dentate gyrus mossy fiber expansion" RELATED [] synonym: "mossy fiber expansion" BROAD [] is_a: GO:0043195 ! terminal bouton created_by: pr creation_date: 2013-02-06T10:31:59Z [Term] id: GO:1990027 name: S bouton namespace: cellular_component def: "Synaptic bouton found in the ventral horn of the spinal cord. S boutons range in diameter from 0.5 to 8 um and contain spherical synaptic vesicles." [NIF_Subcellular:nlx_subcell_100207] is_a: GO:0043195 ! terminal bouton created_by: pr creation_date: 2013-02-06T10:35:12Z [Term] id: GO:1990030 name: pericellular basket namespace: cellular_component def: "Ramification of basket cell axon surrounding cell bodies, forming the characteristic pericellular baskets from which the cell class derives its name." [NIF_Subcellular:sao413722576] synonym: "peri cellular basket" EXACT [] synonym: "peri-cellular basket" EXACT [] is_a: GO:0033267 ! axon part created_by: pr creation_date: 2013-02-07T12:53:54Z [Term] id: GO:1990031 name: pinceau fiber namespace: cellular_component def: "Dense plexus formed by the descending collaterals of cerebellar basket cells that wrap around a Purkinje cell axonal initial segment." [NIF_Subcellular:sao109906988] is_a: GO:0033267 ! axon part created_by: pr creation_date: 2013-02-07T12:56:50Z [Term] id: GO:1990032 name: parallel fiber namespace: cellular_component def: "A parallel fiber results from the bifurcation of a cerebellar granule cell axon in the molecular layer into two diametrically opposed branches, that are oriented parallel to the long axis of the folium." [ISBN:0195159551, NIF_Subcellular:nlx_330] is_a: GO:0033267 ! axon part created_by: pr creation_date: 2013-02-07T12:58:43Z [Term] id: GO:1990033 name: dendritic branch point namespace: cellular_component def: "The part of a dendrite where the cell projection branches, giving rise to a dendritic branch." [NIF_Subcellular:sao-1348591767] synonym: "branch point of dendrite" EXACT [] is_a: GO:0097458 ! neuron part relationship: part_of GO:0030425 ! dendrite created_by: pr creation_date: 2013-02-07T13:01:01Z [Term] id: GO:1990037 name: Lewy body core namespace: cellular_component def: "The center portion of a Lewy body. In Parkinson's disease, it contains a matted meshwork of filaments." [NIF_Subcellular:sao6587439252] is_a: GO:0097458 ! neuron part relationship: part_of GO:0097413 ! Lewy body created_by: pr creation_date: 2013-02-08T12:56:59Z [Term] id: GO:1990038 name: Lewy body corona namespace: cellular_component def: "The periphery of a Lewy body. In Parkinson's disease, it contains spherical accumulations of filaments arranged in a loose, radiating array." [NIF_Subcellular:sao5764355747] synonym: "halo" BROAD [] is_a: GO:0097458 ! neuron part relationship: part_of GO:0097413 ! Lewy body created_by: pr creation_date: 2013-02-08T13:03:27Z [Term] id: GO:1990095 name: positive regulation of transcription from RNA polymerase II promoter in response to reactive oxygen species namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals." [GOC:kmv, PMID:16166371] is_a: GO:0036091 ! positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress created_by: pr creation_date: 2013-05-07T12:10:32Z [Term] id: GO:1990096 name: positive regulation of transcription from RNA polymerase II promoter in response to superoxide namespace: biological_process def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a superoxide stimulus. Superoxide is the anion, oxygen-, formed by addition of one electron to dioxygen (O2) or any compound containing the superoxide anion." [GOC:kmv, PMID:12869585, PMID:16166371] is_a: GO:1990095 ! positive regulation of transcription from RNA polymerase II promoter in response to reactive oxygen species created_by: pr creation_date: 2013-05-07T12:25:34Z [Term] id: GO:1990141 name: chromatin silencing at centromere outer repeat region namespace: biological_process def: "Repression of transcription of DNA at the outer repeat region of a regional centromere by altering the structure of chromatin." [PMID:21847092] synonym: "chromatin silencing at pericentric region" RELATED [GOC:mah] is_a: GO:0030702 ! chromatin silencing at centromere created_by: mah creation_date: 2013-07-17T15:21:38Z [Term] id: GO:1990145 name: maintenance of translational fidelity namespace: biological_process def: "Suppression of the occurrence of translational errors, such as codon-anticodon mis-paring, during the process of translation of a protein using an mRNA template." [GOC:hjd, ISBN:9781936113460, PMID:21841312] relationship: part_of GO:0006412 ! translation created_by: hjd creation_date: 2013-07-24T19:30:09Z [Term] id: GO:1990180 name: mitochondrial tRNA 3'-end processing namespace: biological_process def: "The process in which the 3' end of a pre-tRNA molecule is converted to that of a mature tRNA in the mitochondrion." [GOC:mah, GOC:TermGenie, PMID:23928301] synonym: "tRNA 3' processing in mitochondria" EXACT [GOC:TermGenie] synonym: "tRNA 3' processing in mitochondrion" EXACT [GOC:TermGenie] synonym: "tRNA 3'-end processing in mitochondria" EXACT [GOC:TermGenie] is_a: GO:0000965 ! mitochondrial RNA 3'-end processing is_a: GO:0042780 ! tRNA 3'-end processing intersection_of: GO:0042780 ! tRNA 3'-end processing created_by: mah creation_date: 2013-08-30T16:17:36Z [Term] id: GO:2000142 name: regulation of DNA-dependent transcription, initiation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of DNA-dependent transcription initiation." [GOC:mah, GOC:txnOH] synonym: "regulation of DNA-dependent RNA polymerase complex assembly at promoter" EXACT [GOC:obol] synonym: "regulation of initiation of DNA-dependent transcription" EXACT [GOC:jh2] synonym: "regulation of transcription initiation, DNA-dependent" EXACT [GOC:jh2] is_a: GO:0006355 ! regulation of transcription, DNA-dependent intersection_of: regulates GO:0006352 ! DNA-dependent transcription, initiation relationship: regulates GO:0006352 ! DNA-dependent transcription, initiation created_by: midori creation_date: 2010-10-01T09:11:35Z [Term] id: GO:2000143 name: negative regulation of DNA-dependent transcription, initiation namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA-dependent transcription initiation." [GOC:mah, GOC:txnOH] synonym: "negative regulation of DNA-dependent RNA polymerase complex assembly at promoter" EXACT [GOC:obol] synonym: "negative regulation of initiation of DNA-dependent transcription" EXACT [GOC:jh2] synonym: "negative regulation of transcription initiation, DNA-dependent" EXACT [GOC:jh2] is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent is_a: GO:2000142 ! regulation of DNA-dependent transcription, initiation intersection_of: negatively_regulates GO:0006352 ! DNA-dependent transcription, initiation relationship: negatively_regulates GO:0006352 ! DNA-dependent transcription, initiation created_by: midori creation_date: 2010-10-01T09:11:40Z [Term] id: GO:2000144 name: positive regulation of DNA-dependent transcription, initiation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of DNA-dependent transcription initiation." [GOC:mah, GOC:txnOH] synonym: "positive regulation of DNA-dependent RNA polymerase complex assembly at promoter" EXACT [GOC:obol] synonym: "positive regulation of initiation of DNA-dependent transcription" EXACT [GOC:jh2] synonym: "positive regulation of transcription initiation, DNA-dependent" EXACT [GOC:jh2] synonym: "transactivation" RELATED [PMID:11158542] synonym: "transcriptional transactivation" RELATED [PMID:11580863] is_a: GO:0045893 ! positive regulation of transcription, DNA-dependent is_a: GO:2000142 ! regulation of DNA-dependent transcription, initiation intersection_of: positively_regulates GO:0006352 ! DNA-dependent transcription, initiation relationship: positively_regulates GO:0006352 ! DNA-dependent transcription, initiation created_by: midori creation_date: 2010-10-01T09:11:43Z [Term] id: GO:2000223 name: regulation of BMP signaling pathway involved in heart jogging namespace: biological_process def: "Any process that modulates the frequency, rate or extent of BMP signaling pathway involved in heart jogging." [GOC:BHF] synonym: "regulation of BMP signalling pathway involved in heart jogging pathway involved in somitogenesis" EXACT [GOC:mah] is_a: GO:0030510 ! regulation of BMP signaling pathway intersection_of: regulates GO:0003303 ! BMP signaling pathway involved in heart jogging relationship: regulates GO:0003303 ! BMP signaling pathway involved in heart jogging created_by: vk creation_date: 2010-11-04T02:44:01Z [Term] id: GO:2000232 name: regulation of rRNA processing namespace: biological_process def: "Any process that modulates the frequency, rate or extent of rRNA processing." [GOC:mah] synonym: "regulation of 35S primary transcript processing" RELATED [GOC:obol] is_a: GO:0010468 ! regulation of gene expression intersection_of: regulates GO:0006364 ! rRNA processing relationship: regulates GO:0006364 ! rRNA processing created_by: midori creation_date: 2010-11-10T12:11:29Z [Term] id: GO:2000233 name: negative regulation of rRNA processing namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of rRNA processing." [GOC:mah] synonym: "negative regulation of 35S primary transcript processing" RELATED [GOC:obol] is_a: GO:2000232 ! regulation of rRNA processing intersection_of: negatively_regulates GO:0006364 ! rRNA processing relationship: negatively_regulates GO:0006364 ! rRNA processing created_by: midori creation_date: 2010-11-10T12:11:33Z [Term] id: GO:2000234 name: positive regulation of rRNA processing namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of rRNA processing." [GOC:mah] synonym: "positive regulation of 35S primary transcript processing" RELATED [GOC:obol] is_a: GO:2000232 ! regulation of rRNA processing intersection_of: positively_regulates GO:0006364 ! rRNA processing relationship: positively_regulates GO:0006364 ! rRNA processing created_by: midori creation_date: 2010-11-10T12:11:36Z [Term] id: GO:2000235 name: regulation of tRNA processing namespace: biological_process def: "Any process that modulates the frequency, rate or extent of tRNA processing." [GOC:mah] synonym: "regulation of tRNA maturation" EXACT [GOC:obol] is_a: GO:0010468 ! regulation of gene expression intersection_of: regulates GO:0008033 ! tRNA processing relationship: regulates GO:0008033 ! tRNA processing created_by: midori creation_date: 2010-11-10T12:15:08Z [Term] id: GO:2000236 name: negative regulation of tRNA processing namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of tRNA processing." [GOC:mah] synonym: "negative regulation of tRNA maturation" EXACT [GOC:obol] is_a: GO:2000235 ! regulation of tRNA processing intersection_of: negatively_regulates GO:0008033 ! tRNA processing relationship: negatively_regulates GO:0008033 ! tRNA processing created_by: midori creation_date: 2010-11-10T12:15:13Z [Term] id: GO:2000237 name: positive regulation of tRNA processing namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of tRNA processing." [GOC:mah] synonym: "positive regulation of tRNA maturation" EXACT [GOC:obol] is_a: GO:2000235 ! regulation of tRNA processing intersection_of: positively_regulates GO:0008033 ! tRNA processing relationship: positively_regulates GO:0008033 ! tRNA processing created_by: midori creation_date: 2010-11-10T12:15:17Z [Term] id: GO:2000531 name: regulation of fatty acid biosynthetic process by regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the biosynthesis of fatty acids, by modulating the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:vw] is_a: GO:0072364 ! regulation of cellular ketone metabolic process by regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: dph creation_date: 2011-03-24T12:18:33Z [Term] id: GO:2000631 name: regulation of pre-miRNA processing namespace: biological_process def: "Any process that modulates the frequency, rate or extent of pre-microRNA processing." [GOC:dph, GOC:sl] synonym: "regulation of pre-microRNA processing" EXACT [] is_a: GO:0060964 ! regulation of gene silencing by miRNA is_a: GO:0070920 ! regulation of production of small RNA involved in gene silencing by RNA intersection_of: regulates GO:0031054 ! pre-miRNA processing relationship: regulates GO:0031054 ! pre-miRNA processing created_by: dph creation_date: 2011-04-18T03:50:16Z [Term] id: GO:2000632 name: negative regulation of pre-miRNA processing namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of pre-microRNA processing." [GOC:dph, GOC:sl] synonym: "negative regulation of pre-microRNA processing" EXACT [GOC:obol] is_a: GO:2000631 ! regulation of pre-miRNA processing intersection_of: negatively_regulates GO:0031054 ! pre-miRNA processing relationship: negatively_regulates GO:0031054 ! pre-miRNA processing created_by: dph creation_date: 2011-04-18T03:50:19Z [Term] id: GO:2000633 name: positive regulation of pre-miRNA processing namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of pre-microRNA processing." [GOC:dph, GOC:sl] synonym: "positive regulation of pre-microRNA processing" EXACT [GOC:obol] is_a: GO:2000631 ! regulation of pre-miRNA processing intersection_of: positively_regulates GO:0031054 ! pre-miRNA processing relationship: positively_regulates GO:0031054 ! pre-miRNA processing created_by: dph creation_date: 2011-04-18T03:50:22Z [Term] id: GO:2000634 name: regulation of primary miRNA processing namespace: biological_process def: "Any process that modulates the frequency, rate or extent of primary microRNA processing." [GOC:dph, GOC:sl] synonym: "regulation of pri-miRNA processing" EXACT [GOC:obol] synonym: "regulation of primary microRNA processing" EXACT [GOC:obol] is_a: GO:0060964 ! regulation of gene silencing by miRNA is_a: GO:0070920 ! regulation of production of small RNA involved in gene silencing by RNA intersection_of: regulates GO:0031053 ! primary miRNA processing relationship: regulates GO:0031053 ! primary miRNA processing created_by: dph creation_date: 2011-04-18T03:50:50Z [Term] id: GO:2000635 name: negative regulation of primary miRNA processing namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of primary microRNA processing." [GOC:dph, GOC:sl] synonym: "negative regulation of pri-miRNA processing" EXACT [GOC:obol] synonym: "negative regulation of primary microRNA processing" EXACT [GOC:obol] is_a: GO:2000634 ! regulation of primary miRNA processing intersection_of: negatively_regulates GO:0031053 ! primary miRNA processing relationship: negatively_regulates GO:0031053 ! primary miRNA processing created_by: dph creation_date: 2011-04-18T03:50:53Z [Term] id: GO:2000636 name: positive regulation of primary miRNA processing namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of primary microRNA processing." [GOC:dph, GOC:sl] synonym: "positive regulation of pri-miRNA processing" EXACT [GOC:obol] synonym: "positive regulation of primary microRNA processing" EXACT [GOC:obol] is_a: GO:2000634 ! regulation of primary miRNA processing intersection_of: positively_regulates GO:0031053 ! primary miRNA processing relationship: positively_regulates GO:0031053 ! primary miRNA processing created_by: dph creation_date: 2011-04-18T03:50:56Z [Term] id: GO:2000637 name: positive regulation of gene silencing by miRNA namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of gene silencing by miRNA." [GOC:dph] synonym: "positive regulation of gene silencing by microRNA" RELATED [GOC:pr] synonym: "positive regulation of microRNA-mediated gene silencing" EXACT [GOC:obol] synonym: "positive regulation of miRNA-mediated gene silencing" EXACT [GOC:obol] is_a: GO:0060148 ! positive regulation of posttranscriptional gene silencing is_a: GO:0060964 ! regulation of gene silencing by miRNA intersection_of: positively_regulates GO:0035195 ! gene silencing by miRNA relationship: positively_regulates GO:0035195 ! gene silencing by miRNA created_by: dph creation_date: 2011-04-18T03:51:24Z [Term] id: GO:2000638 name: regulation of SREBP signaling pathway namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the SREBP signaling pathway." [GOC:BHF] synonym: "regulation of SREBP-mediated signaling pathway" EXACT [GOC:bf, GOC:vw] synonym: "regulation of SREBP-mediated signalling pathway" EXACT [GOC:obol] intersection_of: regulates GO:0032933 ! SREBP signaling pathway relationship: regulates GO:0032933 ! SREBP signaling pathway created_by: vk creation_date: 2011-04-20T02:45:59Z [Term] id: GO:2000639 name: negative regulation of SREBP signaling pathway namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of the SREBP signaling pathway." [GOC:BHF] synonym: "negative regulation of SREBP-mediated signaling pathway" EXACT [GOC:bf, GOC:vw] synonym: "negative regulation of SREBP-mediated signalling pathway" EXACT [GOC:obol] is_a: GO:2000638 ! regulation of SREBP signaling pathway intersection_of: negatively_regulates GO:0032933 ! SREBP signaling pathway relationship: negatively_regulates GO:0032933 ! SREBP signaling pathway created_by: vk creation_date: 2011-04-20T02:46:02Z [Term] id: GO:2000640 name: positive regulation of SREBP signaling pathway namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the SREBP signaling pathway." [GOC:BHF] synonym: "positive regulation of SREBP-mediated signaling pathway" EXACT [GOC:bf, GOC:vw] synonym: "positive regulation of SREBP-mediated signalling pathway" EXACT [GOC:obol] is_a: GO:2000638 ! regulation of SREBP signaling pathway intersection_of: positively_regulates GO:0032933 ! SREBP signaling pathway relationship: positively_regulates GO:0032933 ! SREBP signaling pathway created_by: vk creation_date: 2011-04-20T02:46:05Z [Term] id: GO:2000721 name: positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation namespace: biological_process def: "Any positive regulation of transcription from RNA polymerase II promoter that is involved in smooth muscle cell differentiation." [GOC:BHF] synonym: "activation of global transcription from RNA polymerase II promoter of nonstriated muscle cell differentiation" RELATED [GOC:obol] synonym: "activation of global transcription from RNA polymerase II promoter of smooth muscle cell differentiation" RELATED [GOC:obol] synonym: "activation of transcription from RNA polymerase II promoter of nonstriated muscle cell differentiation" EXACT [GOC:obol] synonym: "activation of transcription from RNA polymerase II promoter of smooth muscle cell differentiation" EXACT [GOC:obol] synonym: "positive regulation of gene-specific transcription from RNA polymerase II promoter of nonstriated muscle cell differentiation" RELATED [GOC:obol] synonym: "positive regulation of gene-specific transcription from RNA polymerase II promoter of smooth muscle cell differentiation" RELATED [GOC:obol] synonym: "positive regulation of global transcription from Pol II promoter of nonstriated muscle cell differentiation" RELATED [GOC:obol] synonym: "positive regulation of global transcription from Pol II promoter of smooth muscle cell differentiation" RELATED [GOC:obol] synonym: "positive regulation of transcription from Pol II promoter of nonstriated muscle cell differentiation" EXACT [GOC:obol] synonym: "positive regulation of transcription from Pol II promoter of smooth muscle cell differentiation" EXACT [GOC:obol] synonym: "positive regulation of transcription from RNA polymerase II promoter of nonstriated muscle cell differentiation" EXACT [GOC:obol] synonym: "positive regulation of transcription from RNA polymerase II promoter of smooth muscle cell differentiation" EXACT [GOC:obol] synonym: "positive regulation of transcription from RNA polymerase II promoter, global of nonstriated muscle cell differentiation" RELATED [GOC:obol] synonym: "positive regulation of transcription from RNA polymerase II promoter, global of smooth muscle cell differentiation" RELATED [GOC:obol] synonym: "stimulation of global transcription from RNA polymerase II promoter of nonstriated muscle cell differentiation" RELATED [GOC:obol] synonym: "stimulation of global transcription from RNA polymerase II promoter of smooth muscle cell differentiation" RELATED [GOC:obol] synonym: "stimulation of transcription from RNA polymerase II promoter of nonstriated muscle cell differentiation" EXACT [GOC:obol] synonym: "stimulation of transcription from RNA polymerase II promoter of smooth muscle cell differentiation" EXACT [GOC:obol] synonym: "up regulation of global transcription from RNA polymerase II promoter of nonstriated muscle cell differentiation" RELATED [GOC:obol] synonym: "up regulation of global transcription from RNA polymerase II promoter of smooth muscle cell differentiation" RELATED [GOC:obol] synonym: "up regulation of transcription from RNA polymerase II promoter of nonstriated muscle cell differentiation" EXACT [GOC:obol] synonym: "up regulation of transcription from RNA polymerase II promoter of smooth muscle cell differentiation" EXACT [GOC:obol] synonym: "up-regulation of global transcription from RNA polymerase II promoter of nonstriated muscle cell differentiation" RELATED [GOC:obol] synonym: "up-regulation of global transcription from RNA polymerase II promoter of smooth muscle cell differentiation" RELATED [GOC:obol] synonym: "up-regulation of transcription from RNA polymerase II promoter of nonstriated muscle cell differentiation" EXACT [GOC:obol] synonym: "up-regulation of transcription from RNA polymerase II promoter of smooth muscle cell differentiation" EXACT [GOC:obol] synonym: "upregulation of global transcription from RNA polymerase II promoter of nonstriated muscle cell differentiation" RELATED [GOC:obol] synonym: "upregulation of global transcription from RNA polymerase II promoter of smooth muscle cell differentiation" EXACT [GOC:obol] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: vk creation_date: 2011-06-08T08:34:55Z [Term] id: GO:2000730 name: regulation of termination of RNA polymerase I transcription namespace: biological_process def: "Any process that modulates the frequency, rate or extent of termination of RNA polymerase I transcription." [GOC:obol] synonym: "regulation of RNA polymerase I transcription termination" EXACT [GOC:obol] synonym: "regulation of transcription termination from Pol I promoter" EXACT [GOC:obol] synonym: "regulation of transcription termination from RNA polymerase I promoter" EXACT [GOC:obol] is_a: GO:0006356 ! regulation of transcription from RNA polymerase I promoter is_a: GO:0031554 ! regulation of DNA-dependent transcription, termination intersection_of: regulates GO:0006363 ! termination of RNA polymerase I transcription relationship: regulates GO:0006363 ! termination of RNA polymerase I transcription created_by: dph creation_date: 2011-06-10T08:43:39Z [Term] id: GO:2000731 name: negative regulation of termination of RNA polymerase I transcription namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of termination of RNA polymerase I transcription." [GOC:obol] synonym: "negative regulation of RNA polymerase I transcription termination" EXACT [GOC:obol] synonym: "negative regulation of transcription termination from Pol I promoter" EXACT [GOC:obol] synonym: "negative regulation of transcription termination from RNA polymerase I promoter" EXACT [GOC:obol] is_a: GO:0060567 ! negative regulation of DNA-dependent transcription, termination is_a: GO:2000730 ! regulation of termination of RNA polymerase I transcription intersection_of: negatively_regulates GO:0006363 ! termination of RNA polymerase I transcription relationship: negatively_regulates GO:0006363 ! termination of RNA polymerase I transcription created_by: dph creation_date: 2011-06-10T08:43:44Z [Term] id: GO:2000732 name: positive regulation of termination of RNA polymerase I transcription namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of termination of RNA polymerase I transcription." [GOC:obol] synonym: "positive regulation of RNA polymerase I transcription termination" EXACT [GOC:obol] synonym: "positive regulation of transcription termination from Pol I promoter" EXACT [GOC:obol] synonym: "positive regulation of transcription termination from RNA polymerase I promoter" EXACT [GOC:obol] is_a: GO:0060566 ! positive regulation of DNA-dependent transcription, termination is_a: GO:2000730 ! regulation of termination of RNA polymerase I transcription intersection_of: positively_regulates GO:0006363 ! termination of RNA polymerase I transcription relationship: positively_regulates GO:0006363 ! termination of RNA polymerase I transcription created_by: dph creation_date: 2011-06-10T08:43:48Z [Term] id: GO:2000749 name: positive regulation of chromatin silencing at rDNA namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of chromatin silencing at rDNA." [PMID:10899127] synonym: "positive regulation of chromatin silencing at ribosomal DNA" EXACT [GOC:obol] synonym: "positive regulation of heterochromatic silencing at rDNA" EXACT [GOC:obol] synonym: "positive regulation of rDNA chromatin silencing" EXACT [GOC:obol] is_a: GO:0031937 ! positive regulation of chromatin silencing is_a: GO:0061187 ! regulation of chromatin silencing at rDNA intersection_of: positively_regulates GO:0000183 ! chromatin silencing at rDNA relationship: positively_regulates GO:0000183 ! chromatin silencing at rDNA created_by: pr creation_date: 2011-06-16T09:43:55Z [Term] id: GO:2000763 name: positive regulation of transcription from RNA polymerase II promoter involved in norepinephrine biosynthetic process namespace: biological_process def: "Any positive regulation of transcription from RNA polymerase II promoter that is involved in norepinephrine biosynthetic process." [GOC:BHF] synonym: "positive regulation of transcription from Pol II promoter involved in levarterenol biosynthesis" EXACT [GOC:obol] synonym: "positive regulation of transcription from Pol II promoter involved in levarterenol biosynthetic process" EXACT [GOC:obol] synonym: "positive regulation of transcription from Pol II promoter involved in noradrenaline biosynthesis" EXACT [GOC:obol] synonym: "positive regulation of transcription from Pol II promoter involved in noradrenaline biosynthetic process" EXACT [GOC:obol] synonym: "positive regulation of transcription from Pol II promoter involved in norepinephrine anabolism" EXACT [GOC:obol] synonym: "positive regulation of transcription from Pol II promoter involved in norepinephrine biosynthesis" EXACT [GOC:obol] synonym: "positive regulation of transcription from Pol II promoter involved in norepinephrine biosynthetic process" EXACT [GOC:obol] synonym: "positive regulation of transcription from Pol II promoter involved in norepinephrine formation" EXACT [GOC:obol] synonym: "positive regulation of transcription from Pol II promoter involved in norepinephrine synthesis" EXACT [GOC:obol] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter intersection_of: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: vk creation_date: 2011-06-18T04:14:58Z [Term] id: GO:2000765 name: regulation of cytoplasmic translation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of cytoplasmic translation." [GOC:obol] is_a: GO:0006417 ! regulation of translation intersection_of: regulates GO:0002181 ! cytoplasmic translation relationship: regulates GO:0002181 ! cytoplasmic translation created_by: vw creation_date: 2011-06-20T10:39:19Z [Term] id: GO:2000766 name: negative regulation of cytoplasmic translation namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of cytoplasmic translation." [GOC:obol] is_a: GO:0017148 ! negative regulation of translation is_a: GO:2000765 ! regulation of cytoplasmic translation intersection_of: negatively_regulates GO:0002181 ! cytoplasmic translation relationship: negatively_regulates GO:0002181 ! cytoplasmic translation created_by: vw creation_date: 2011-06-20T10:39:23Z [Term] id: GO:2000767 name: positive regulation of cytoplasmic translation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of cytoplasmic translation." [GOC:obol] is_a: GO:0045727 ! positive regulation of translation is_a: GO:2000765 ! regulation of cytoplasmic translation intersection_of: positively_regulates GO:0002181 ! cytoplasmic translation relationship: positively_regulates GO:0002181 ! cytoplasmic translation created_by: vw creation_date: 2011-06-20T10:39:26Z [Term] id: GO:2000804 name: regulation of termination of RNA polymerase II transcription, poly(A)-coupled namespace: biological_process def: "Any process that modulates the frequency, rate or extent of termination of RNA polymerase II transcription, poly(A)-coupled." [GOC:obol] synonym: "regulation of termination of RNA polymerase II transcription, polyadenylation-coupled" RELATED [] synonym: "regulation of transcription termination from Pol II promoter, poly(A) coupled" RELATED [GOC:obol] synonym: "regulation of transcription termination from Pol II promoter, RNA polymerase(A) coupled" RELATED [GOC:obol] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter is_a: GO:0031554 ! regulation of DNA-dependent transcription, termination intersection_of: regulates GO:0030846 ! termination of RNA polymerase II transcription, poly(A)-coupled relationship: regulates GO:0030846 ! termination of RNA polymerase II transcription, poly(A)-coupled created_by: pr creation_date: 2011-07-04T08:41:27Z [Term] id: GO:2000805 name: negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of termination of RNA polymerase II transcription, poly(A)-coupled." [GOC:obol] synonym: "negative regulation of termination of RNA polymerase II transcription, polyadenylation-coupled" RELATED [] synonym: "negative regulation of transcription termination from Pol II promoter, poly(A) coupled" RELATED [GOC:obol] synonym: "negative regulation of transcription termination from Pol II promoter, RNA polymerase(A) coupled" RELATED [GOC:obol] is_a: GO:0060567 ! negative regulation of DNA-dependent transcription, termination is_a: GO:2000804 ! regulation of termination of RNA polymerase II transcription, poly(A)-coupled intersection_of: negatively_regulates GO:0030846 ! termination of RNA polymerase II transcription, poly(A)-coupled relationship: negatively_regulates GO:0030846 ! termination of RNA polymerase II transcription, poly(A)-coupled created_by: pr creation_date: 2011-07-04T08:41:34Z [Term] id: GO:2000806 name: positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of termination of RNA polymerase II transcription, poly(A)-coupled." [GOC:obol] synonym: "positive regulation of termination of RNA polymerase II transcription, polyadenylation-coupled" RELATED [] synonym: "positive regulation of transcription termination from Pol II promoter, poly(A) coupled" RELATED [GOC:obol] synonym: "positive regulation of transcription termination from Pol II promoter, RNA polymerase(A) coupled" RELATED [GOC:obol] is_a: GO:0060566 ! positive regulation of DNA-dependent transcription, termination is_a: GO:2000804 ! regulation of termination of RNA polymerase II transcription, poly(A)-coupled intersection_of: positively_regulates GO:0030846 ! termination of RNA polymerase II transcription, poly(A)-coupled relationship: positively_regulates GO:0030846 ! termination of RNA polymerase II transcription, poly(A)-coupled created_by: pr creation_date: 2011-07-04T08:41:39Z [Term] id: GO:2000815 name: regulation of mRNA stability involved in response to oxidative stress namespace: biological_process def: "A process of regulation of mRNA stability that is involved in a response to oxidative stress." [GOC:obol] is_a: GO:0010610 ! regulation of mRNA stability involved in response to stress intersection_of: GO:0043488 ! regulation of mRNA stability created_by: midori creation_date: 2011-07-11T04:40:56Z [Term] id: GO:2000820 name: negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation namespace: biological_process def: "Any negative regulation of transcription from RNA polymerase II promoter that is involved in smooth muscle cell differentiation." [GOC:BHF] synonym: "down regulation of global transcription from RNA polymerase II promoter involved in nonstriated muscle cell differentiation" RELATED [GOC:obol] synonym: "down regulation of global transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation" RELATED [GOC:obol] synonym: "down regulation of transcription from RNA polymerase II promoter involved in nonstriated muscle cell differentiation" EXACT [GOC:obol] synonym: "down regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation" EXACT [GOC:obol] synonym: "down-regulation of global transcription from RNA polymerase II promoter involved in nonstriated muscle cell differentiation" RELATED [GOC:obol] synonym: "down-regulation of global transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation" RELATED [GOC:obol] synonym: "down-regulation of transcription from RNA polymerase II promoter involved in nonstriated muscle cell differentiation" EXACT [GOC:obol] synonym: "down-regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation" EXACT [GOC:obol] synonym: "downregulation of global transcription from RNA polymerase II promoter involved in nonstriated muscle cell differentiation" RELATED [GOC:obol] synonym: "downregulation of global transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation" RELATED [GOC:obol] synonym: "downregulation of transcription from RNA polymerase II promoter involved in nonstriated muscle cell differentiation" EXACT [GOC:obol] synonym: "downregulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation" EXACT [GOC:obol] synonym: "inhibition of global transcription from RNA polymerase II promoter involved in nonstriated muscle cell differentiation" RELATED [GOC:obol] synonym: "inhibition of global transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation" RELATED [GOC:obol] synonym: "inhibition of transcription from RNA polymerase II promoter involved in nonstriated muscle cell differentiation" EXACT [GOC:obol] synonym: "inhibition of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation" EXACT [GOC:obol] synonym: "negative regulation of gene-specific transcription from RNA polymerase II promoter involved in nonstriated muscle cell differentiation" RELATED [GOC:obol] synonym: "negative regulation of gene-specific transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation" RELATED [GOC:obol] synonym: "negative regulation of global transcription from Pol II promoter involved in nonstriated muscle cell differentiation" RELATED [GOC:obol] synonym: "negative regulation of global transcription from Pol II promoter involved in smooth muscle cell differentiation" RELATED [GOC:obol] synonym: "negative regulation of transcription from Pol II promoter involved in nonstriated muscle cell differentiation" EXACT [GOC:obol] synonym: "negative regulation of transcription from Pol II promoter involved in smooth muscle cell differentiation" EXACT [GOC:obol] synonym: "negative regulation of transcription from RNA polymerase II promoter involved in nonstriated muscle cell differentiation" EXACT [GOC:obol] synonym: "negative regulation of transcription from RNA polymerase II promoter, global involved in nonstriated muscle cell differentiation" RELATED [GOC:obol] synonym: "negative regulation of transcription from RNA polymerase II promoter, global involved in smooth muscle cell differentiation" RELATED [GOC:obol] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter intersection_of: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: rfoulger creation_date: 2011-07-14T08:25:05Z [Term] id: GO:2000823 name: regulation of androgen receptor activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of androgen receptor activity." [GOC:obol] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter is_a: GO:0051090 ! regulation of sequence-specific DNA binding transcription factor activity intersection_of: regulates GO:0004882 ! androgen receptor activity relationship: regulates GO:0004882 ! androgen receptor activity created_by: yaf creation_date: 2011-07-15T10:56:08Z [Term] id: GO:2000824 name: negative regulation of androgen receptor activity namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of androgen receptor activity." [GOC:obol] is_a: GO:0043433 ! negative regulation of sequence-specific DNA binding transcription factor activity is_a: GO:2000823 ! regulation of androgen receptor activity intersection_of: negatively_regulates GO:0004882 ! androgen receptor activity relationship: negatively_regulates GO:0004882 ! androgen receptor activity created_by: yaf creation_date: 2011-07-15T10:56:12Z [Term] id: GO:2000825 name: positive regulation of androgen receptor activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of androgen receptor activity." [GOC:obol] is_a: GO:0051091 ! positive regulation of sequence-specific DNA binding transcription factor activity is_a: GO:2000823 ! regulation of androgen receptor activity intersection_of: positively_regulates GO:0004882 ! androgen receptor activity relationship: positively_regulates GO:0004882 ! androgen receptor activity created_by: yaf creation_date: 2011-07-15T10:56:14Z [Term] id: GO:2000976 name: regulation of transcription from RNA polymerase II promoter involved in detection of glucose namespace: biological_process def: "Any regulation of transcription from RNA polymerase II promoter that is involved in detection of glucose." [GOC:BHF] synonym: "global transcription regulation from Pol II promoter involved in detection of glucose" RELATED [GOC:obol] synonym: "global transcription regulation from Pol II promoter involved in glucose detection" RELATED [GOC:obol] synonym: "global transcription regulation from Pol II promoter involved in glucose perception" RELATED [GOC:obol] synonym: "global transcription regulation from Pol II promoter involved in glucose sensing" RELATED [GOC:obol] synonym: "regulation of gene-specific transcription from RNA polymerase II promoter involved in detection of glucose" RELATED [GOC:obol] synonym: "regulation of gene-specific transcription from RNA polymerase II promoter involved in glucose detection" RELATED [GOC:obol] synonym: "regulation of gene-specific transcription from RNA polymerase II promoter involved in glucose perception" RELATED [GOC:obol] synonym: "regulation of gene-specific transcription from RNA polymerase II promoter involved in glucose sensing" RELATED [GOC:obol] synonym: "regulation of global transcription from Pol II promoter involved in detection of glucose" RELATED [GOC:obol] synonym: "regulation of global transcription from Pol II promoter involved in glucose detection" RELATED [GOC:obol] synonym: "regulation of global transcription from Pol II promoter involved in glucose perception" RELATED [GOC:obol] synonym: "regulation of global transcription from Pol II promoter involved in glucose sensing" RELATED [GOC:obol] synonym: "regulation of transcription from Pol II promoter involved in detection of glucose" EXACT [GOC:obol] synonym: "regulation of transcription from Pol II promoter involved in glucose detection" EXACT [GOC:obol] synonym: "regulation of transcription from Pol II promoter involved in glucose perception" RELATED [GOC:obol] synonym: "regulation of transcription from Pol II promoter involved in glucose sensing" RELATED [GOC:obol] synonym: "regulation of transcription from RNA polymerase II promoter involved in glucose detection" EXACT [GOC:obol] synonym: "regulation of transcription from RNA polymerase II promoter involved in glucose perception" RELATED [GOC:obol] synonym: "regulation of transcription from RNA polymerase II promoter involved in glucose sensing" RELATED [GOC:obol] synonym: "regulation of transcription from RNA polymerase II promoter, global involved in detection of glucose" RELATED [GOC:obol] synonym: "regulation of transcription from RNA polymerase II promoter, global involved in glucose detection" RELATED [GOC:obol] synonym: "regulation of transcription from RNA polymerase II promoter, global involved in glucose perception" RELATED [GOC:obol] synonym: "regulation of transcription from RNA polymerase II promoter, global involved in glucose sensing" RELATED [GOC:obol] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: vk creation_date: 2011-08-02T05:06:52Z [Term] id: GO:2001124 name: regulation of translational frameshifting namespace: biological_process def: "Any process that modulates the frequency, rate or extent of translational frameshifting." [GOC:obol] is_a: GO:0006448 ! regulation of translational elongation intersection_of: regulates GO:0006452 ! translational frameshifting relationship: regulates GO:0006452 ! translational frameshifting created_by: dph creation_date: 2011-10-12T05:52:22Z [Term] id: GO:2001125 name: negative regulation of translational frameshifting namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of translational frameshifting." [GOC:obol] is_a: GO:0045900 ! negative regulation of translational elongation is_a: GO:2001124 ! regulation of translational frameshifting intersection_of: negatively_regulates GO:0006452 ! translational frameshifting relationship: negatively_regulates GO:0006452 ! translational frameshifting created_by: dph creation_date: 2011-10-12T05:52:27Z [Term] id: GO:2001126 name: positive regulation of translational frameshifting namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of translational frameshifting." [GOC:obol] is_a: GO:0045901 ! positive regulation of translational elongation is_a: GO:2001124 ! regulation of translational frameshifting intersection_of: positively_regulates GO:0006452 ! translational frameshifting relationship: positively_regulates GO:0006452 ! translational frameshifting created_by: dph creation_date: 2011-10-12T05:52:30Z [Term] id: GO:2001159 name: regulation of CVT pathway namespace: biological_process def: "Any process that modulates the frequency, rate or extent of CVT pathway." [GOC:obol] synonym: "regulation of cytoplasm to vacuole targeting" EXACT [GOC:obol] synonym: "regulation of cytoplasm-to-vacuole targeting" EXACT [GOC:obol] intersection_of: regulates GO:0032258 ! CVT pathway relationship: regulates GO:0032258 ! CVT pathway created_by: jp creation_date: 2011-10-25T10:22:24Z [Term] id: GO:2001163 name: regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues namespace: biological_process def: "Any process that modulates the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues." [PMID:15149594] is_a: GO:1901407 ! regulation of phosphorylation of RNA polymerase II C-terminal domain intersection_of: regulates GO:0071619 ! phosphorylation of RNA polymerase II C-terminal domain serine 2 residues relationship: regulates GO:0071619 ! phosphorylation of RNA polymerase II C-terminal domain serine 2 residues created_by: se creation_date: 2011-10-25T10:30:59Z [Term] id: GO:2001164 name: negative regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues." [PMID:15149594] is_a: GO:1901408 ! negative regulation of phosphorylation of RNA polymerase II C-terminal domain is_a: GO:2001163 ! regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues intersection_of: negatively_regulates GO:0071619 ! phosphorylation of RNA polymerase II C-terminal domain serine 2 residues relationship: negatively_regulates GO:0071619 ! phosphorylation of RNA polymerase II C-terminal domain serine 2 residues created_by: se creation_date: 2011-10-25T10:31:03Z [Term] id: GO:2001165 name: positive regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues." [PMID:15149594] is_a: GO:1901409 ! positive regulation of phosphorylation of RNA polymerase II C-terminal domain is_a: GO:2001163 ! regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues intersection_of: positively_regulates GO:0071619 ! phosphorylation of RNA polymerase II C-terminal domain serine 2 residues relationship: positively_regulates GO:0071619 ! phosphorylation of RNA polymerase II C-terminal domain serine 2 residues created_by: se creation_date: 2011-10-25T10:31:07Z [Term] id: GO:2001207 name: regulation of transcription elongation from RNA polymerase I promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription elongation from RNA polymerase I promoter." [PMID:20299458] synonym: "regulation of RNA elongation from Pol I promoter" EXACT [GOC:obol] is_a: GO:0006356 ! regulation of transcription from RNA polymerase I promoter is_a: GO:0032784 ! regulation of DNA-dependent transcription, elongation intersection_of: regulates GO:0006362 ! transcription elongation from RNA polymerase I promoter relationship: regulates GO:0006362 ! transcription elongation from RNA polymerase I promoter created_by: se creation_date: 2011-11-11T10:46:28Z [Term] id: GO:2001208 name: negative regulation of transcription elongation from RNA polymerase I promoter namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of transcription elongation from RNA polymerase I promoter." [PMID:20299458] synonym: "negative regulation of RNA elongation from Pol I promoter" EXACT [GOC:obol] is_a: GO:0032785 ! negative regulation of DNA-dependent transcription, elongation is_a: GO:2001207 ! regulation of transcription elongation from RNA polymerase I promoter intersection_of: negatively_regulates GO:0006362 ! transcription elongation from RNA polymerase I promoter relationship: negatively_regulates GO:0006362 ! transcription elongation from RNA polymerase I promoter created_by: se creation_date: 2011-11-11T10:46:36Z [Term] id: GO:2001209 name: positive regulation of transcription elongation from RNA polymerase I promoter namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transcription elongation from RNA polymerase I promoter." [PMID:20299458] synonym: "positive regulation of RNA elongation from Pol I promoter" EXACT [GOC:obol] is_a: GO:0032786 ! positive regulation of DNA-dependent transcription, elongation is_a: GO:2001207 ! regulation of transcription elongation from RNA polymerase I promoter intersection_of: positively_regulates GO:0006362 ! transcription elongation from RNA polymerase I promoter relationship: positively_regulates GO:0006362 ! transcription elongation from RNA polymerase I promoter created_by: se creation_date: 2011-11-11T10:46:41Z [Term] id: MOD:00030 name: N-formyl-L-methionine residue namespace: MOD synonym: "fMet" EXACT PSI-MOD-label [] is_a: PR:000002970 ! pre-translationally modified amino-acid residue [Term] id: MOD:00031 name: L-selenocysteine residue namespace: MOD synonym: "Sec" EXACT PSI-MOD-label [] is_a: PR:000002970 ! pre-translationally modified amino-acid residue [Term] id: MOD:00033 name: crosslinked residues namespace: MOD synonym: "XLNK" EXACT PSI-MOD-label [PRO:DAN] is_a: PR:000002968 ! post-translationally modified amino-acid residue [Term] id: MOD:00115 name: S-palmitoyl-L-cysteine namespace: protein def: "A protein modification that effectively converts an L-cysteine residue to S-palmitoyl-L-cysteine." [DeltaMass:303, PubMed:1872406, PubMed:3166978, PubMed:8180229, PubMed:8824274, RESID:AA0106, UniMod:47] synonym: "SPamCys" EXACT PSI-MOD-label [] is_a: PR:000002968 ! post-translationally modified amino-acid residue [Term] id: MOD:00127 name: N6-lipoyl-L-lysine namespace: MOD synonym: "LipoLys" EXACT PSI-MOD-label [PRO:DAN] is_a: PR:000002968 ! post-translationally modified amino-acid residue [Term] id: MOD:00128 name: N6-pyridoxal phosphate-L-lysine namespace: MOD synonym: "PyridLys" EXACT PSI-MOD-label [PRO:DAN] is_a: PR:000002968 ! post-translationally modified amino-acid residue [Term] id: MOD:00237 name: L-beta-methylthioaspartic acid namespace: MOD synonym: "BMeThyAsp" EXACT PSI-MOD-label [PRO:DAN] is_a: PR:000002968 ! post-translationally modified amino-acid residue [Term] id: MOD:00394 name: acetylated residue namespace: MOD synonym: "AcRes" EXACT PSI-MOD-label [] is_a: PR:000002968 ! post-translationally modified amino-acid residue [Term] id: MOD:00427 name: methylated residue namespace: MOD synonym: "MeRes" EXACT PSI-MOD-label [] is_a: PR:000002968 ! post-translationally modified amino-acid residue [Term] id: MOD:00438 name: myristoylated residue namespace: MOD synonym: "MyrRes" EXACT PSI-MOD-label [] is_a: PR:000002968 ! post-translationally modified amino-acid residue [Term] id: MOD:00448 name: N-acetylaminoglucosylated residue namespace: MOD synonym: "GlcNAcRes" EXACT PSI-MOD-label [] is_a: PR:000002968 ! post-translationally modified amino-acid residue [Term] id: MOD:00670 name: N-acylated residue namespace: MOD def: "A protein modification that effectively replaces a residue amino group with an acylamino group." [PubMed:18688235] synonym: "NAcylRes" EXACT PSI-MOD-label [] is_a: PR:000002968 ! post-translationally modified amino-acid residue [Term] id: MOD:00693 name: glycosylated residue namespace: MOD synonym: "GlycoRes" EXACT PSI-MOD-label [] is_a: PR:000002968 ! post-translationally modified amino-acid residue [Term] id: MOD:00696 name: phosphorylated residue namespace: MOD synonym: "PhosRes" EXACT PSI-MOD-label [] is_a: PR:000002968 ! post-translationally modified amino-acid residue [Term] id: MOD:00703 name: isoprenylated residue namespace: MOD synonym: "IpRes" EXACT PSI-MOD-label [] is_a: PR:000002968 ! post-translationally modified amino-acid residue [Term] id: MOD:00818 name: glycosylphosphatidylinositolated residue namespace: MOD synonym: "GPIRes" EXACT PSI-MOD-label [] is_a: PR:000002968 ! post-translationally modified amino-acid residue [Term] id: MOD:01048 name: 2-pyrrolidone-5-carboxylic acid namespace: MOD synonym: "PyrGlu" EXACT PSI-MOD-label [] is_a: PR:000002968 ! post-translationally modified amino-acid residue [Term] id: MOD:01148 name: ubiquitinylated lysine namespace: MOD synonym: "UbiqLys" EXACT PSI-MOD-label [PRO:DAN] is_a: PR:000002968 ! post-translationally modified amino-acid residue [Term] id: MOD:01149 name: sumoylated lysine namespace: MOD synonym: "SumoLys" EXACT PSI-MOD-label [PRO:DAN] is_a: PR:000002968 ! post-translationally modified amino-acid residue [Term] id: MOD:01150 name: neddylated lysine namespace: MOD synonym: "NeddLys" EXACT PSI-MOD-label [PRO:DAN] is_a: PR:000002968 ! post-translationally modified amino-acid residue [Term] id: MOD:01152 name: carboxylated residue namespace: MOD synonym: "CbxRes" EXACT PSI-MOD-label [PRO:DAN] is_a: PR:000002968 ! post-translationally modified amino-acid residue [Term] id: MOD:01187 name: L-pyrrolysine residue namespace: MOD synonym: "Pyl" EXACT PSI-MOD-label [] is_a: PR:000002970 ! pre-translationally modified amino-acid residue [Term] id: NCBITaxon:0000408 name: UnclassifiedMammalia namespace: ncbi_taxonomy def: "mammals that have not yet been given a classification" [] is_a: NCBITaxon:40674 ! Mammalia created_by: He Zhang creation_date: 2013-10-06T12:20:09Z [Term] id: NCBITaxon:0000414 name: Dipnotetrapodomorpha namespace: ncbi_taxonomy def: "undefinable" [] xref: GC_ID:1 is_a: NCBITaxon:8287 ! Sarcopterygii property_value: has_rank NCBITaxon:infraclass created_by: He Zhang creation_date: 2013-10-06T12:23:31Z [Term] id: NCBITaxon:0000430 name: UnclassifiedChordata namespace: ncbi_taxonomy is_a: NCBITaxon:7711 ! Chordata created_by: He Zhang creation_date: 2013-10-06T12:46:37Z [Term] id: NCBITaxon:0000436 name: Xenacoelomorpha namespace: ncbi_taxonomy def: "proposed grouping of the xenoturbellids and acaelomorph flatworm" [] is_a: NCBITaxon:33511 ! Deuterostomia created_by: He Zhang creation_date: 2013-10-06T12:49:16Z [Term] id: NCBITaxon:1001604 name: Nucleariidae and Fonticula group namespace: ncbi_taxonomy is_a: NCBITaxon:33154 ! Opisthokonta created_by: He Zhang creation_date: 2013-10-06T13:08:48Z [Term] id: NCBITaxon:10197 name: Ctenophora namespace: ncbi_taxonomy def: "Ctenophora is a phylum of animals that live in marine waters worldwide. Their most distinctive feature is the \"combs\", groups of cilia they use for swimming, and they are the largest animals that swim" [] xref: GC_ID:1 is_a: NCBITaxon:6072 ! Eumetazoa property_value: has_rank NCBITaxon:phylum created_by: He Zhang creation_date: 2013-10-06T12:57:07Z [Term] id: NCBITaxon:10213 name: Mesozoa namespace: ncbi_taxonomy def: "are enigmatic, minuscule, worm-like parasites of marine invertebrates. it was still unclear whether they are degenerate platyhelminthes (flatworms) or truly-primitive, basal metazoans" [] xref: GC_ID:1 is_a: NCBITaxon:33208 ! Metazoa property_value: has_rank NCBITaxon:superphylum created_by: He Zhang creation_date: 2013-10-06T12:59:38Z [Term] id: NCBITaxon:10219 name: Hemichordata namespace: ncbi_taxonomy def: "phylum of marine deuterostome animals" [] xref: GC_ID:1 is_a: NCBITaxon:33511 ! Deuterostomia property_value: has_rank NCBITaxon:phylum created_by: He Zhang creation_date: 2013-10-06T12:49:16Z [Term] id: NCBITaxon:10226 name: Placozoa namespace: ncbi_taxonomy def: "are a basal form of invertebrate. They are the simplest in structure of all non-parasitic multicellular animals" [] xref: GC_ID:1 is_a: NCBITaxon:33208 ! Metazoa property_value: has_rank NCBITaxon:phylum created_by: He Zhang creation_date: 2013-10-06T12:59:38Z [Term] id: NCBITaxon:10229 name: Chaetognatha namespace: ncbi_taxonomy def: "a group of small active transparent marine worms" [] xref: GC_ID:1 is_a: NCBITaxon:33511 ! Deuterostomia property_value: has_rank NCBITaxon:phylum created_by: He Zhang creation_date: 2013-10-06T12:49:16Z [Term] id: NCBITaxon:110814 name: Xenoturbellida namespace: ncbi_taxonomy def: "genus of bilaterian animals; it contains two marine worm-like species" [] xref: GC_ID:1 is_a: NCBITaxon:33511 ! Deuterostomia property_value: has_rank NCBITaxon:phylum created_by: He Zhang creation_date: 2013-10-06T12:49:16Z [Term] id: NCBITaxon:117565 name: Hyperotreti namespace: ncbi_taxonomy def: "are eel-shaped slime-producing marine animals" [] xref: GC_ID:1 is_a: NCBITaxon:89593 ! Craniata created_by: He Zhang creation_date: 2013-10-06T12:35:00Z [Term] id: NCBITaxon:117569 name: Hyperoartia namespace: ncbi_taxonomy def: " lampreys as distinguished from hagfishes" [] xref: GC_ID:1 is_a: NCBITaxon:7742 ! Vertebrata created_by: He Zhang creation_date: 2013-10-06T12:33:01Z [Term] id: NCBITaxon:117570 name: Teleostomi namespace: ncbi_taxonomy def: "clade of jawed vertebrates that includes the tetrapods, bony fish, and the wholly extinct acanthodian fish" [] xref: GC_ID:1 is_a: NCBITaxon:7776 ! Gnathostomata created_by: He Zhang creation_date: 2013-10-06T12:28:38Z [Term] id: NCBITaxon:117571 name: Euteleostomi namespace: ncbi_taxonomy def: "successful clade that includes more than 90% of the living species of vertebrates" [] xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi created_by: He Zhang creation_date: 2013-10-06T12:27:09Z [Term] id: NCBITaxon:118072 name: Coelacanthimorpha namespace: ncbi_taxonomy def: "rare order of fish that includes two extant species in the genus Latimeria: West Indian Ocean coelacanth (Latimeria chalumnae) and the Indonesian coelacanth" [] xref: GC_ID:1 is_a: NCBITaxon:8287 ! Sarcopterygii property_value: has_rank NCBITaxon:subclass created_by: He Zhang creation_date: 2013-10-06T12:25:27Z [Term] id: NCBITaxon:136087 name: Malawimonadidae namespace: ncbi_taxonomy def: "is a eukaryotic family" [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota property_value: has_rank NCBITaxon:family created_by: He Zhang creation_date: 2013-10-06T16:26:14Z [Term] id: NCBITaxon:190469 name: Bilateria incertae sedis namespace: ncbi_taxonomy is_a: NCBITaxon:33213 ! Bilateria created_by: He Zhang creation_date: 2013-10-06T12:53:32Z [Term] id: NCBITaxon:193537 name: Centroheliozoa namespace: ncbi_taxonomy def: "large group of heliozoan protists" [] is_a: NCBITaxon:2759 ! Eukaryota created_by: He Zhang creation_date: 2013-10-06T16:26:14Z [Term] id: NCBITaxon:207245 name: Fornicata namespace: ncbi_taxonomy def: "group of excavate protist" [] is_a: NCBITaxon:2759 ! Eukaryota created_by: He Zhang creation_date: 2013-10-06T16:26:14Z [Term] id: NCBITaxon:207598 name: Homininae namespace: ncbi_taxonomy def: "Homininae is a subfamily of Hominidae that includes humans, gorillas, chimpanzees, bonobos and some extinct relatives; it comprises all hominids that arose after the split from orangutans" [] is_a: NCBITaxon:9604 ! Hominidae created_by: He Zhang creation_date: 2013-10-06T11:31:34Z [Term] id: NCBITaxon:2759 name: Eukaryota namespace: ncbi_taxonomy xref: GC_ID:1 is_a: OMIT:0000481 ! CellularOrganism property_value: has_rank NCBITaxon:superkingdom created_by: He Zhang creation_date: 2013-10-06T13:09:14Z [Term] id: NCBITaxon:2763 name: Rhodophyta namespace: ncbi_taxonomy def: "mostly marine and littoral eukaryotic algae" [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota created_by: He Zhang creation_date: 2013-10-06T16:26:14Z [Term] id: NCBITaxon:28009 name: Choanoflagellida namespace: ncbi_taxonomy def: "Choanoflagellida" [] xref: GC_ID:1 is_a: NCBITaxon:33154 ! Opisthokonta property_value: has_rank NCBITaxon:order created_by: He Zhang creation_date: 2013-10-06T13:08:48Z [Term] id: NCBITaxon:2830 name: Haptophyceae namespace: ncbi_taxonomy def: "are a division of algae" [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota created_by: He Zhang creation_date: 2013-10-06T16:26:14Z [Term] id: NCBITaxon:3027 name: Cryptophyta namespace: ncbi_taxonomy def: "a phylum in the kingdom Protoctista" [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota property_value: has_rank NCBITaxon:class created_by: He Zhang creation_date: 2013-10-06T16:26:14Z [Term] id: NCBITaxon:30656 name: Dermoptera namespace: ncbi_taxonomy def: "flying lemurs" [] xref: GC_ID:1 is_a: NCBITaxon:314146 ! Euarchontoglires property_value: has_rank NCBITaxon:order created_by: He Zhang creation_date: 2013-10-06T12:13:45Z [Term] id: NCBITaxon:311790 name: Afrotheria namespace: ncbi_taxonomy def: "clade of mammals, the living members of which belong to groups currently living in Africa or that are of African origi" [] is_a: NCBITaxon:9347 ! Eutheria created_by: He Zhang creation_date: 2013-10-06T12:16:42Z [Term] id: NCBITaxon:314145 name: Laurasiatheria namespace: ncbi_taxonomy def: "large group of placental mammals believed to have originated on the northern supercontinent of Laurasia" [] is_a: NCBITaxon:9347 ! Eutheria created_by: He Zhang creation_date: 2013-10-06T12:16:42Z [Term] id: NCBITaxon:314146 name: Euarchontoglires namespace: ncbi_taxonomy def: "living members of which belong to one of the five following groups: rodents, lagomorphs, treeshrews, colugos and primates (including humans" [] is_a: NCBITaxon:9347 ! Eutheria creation_date: 2013-10-06T12:11:29Z [Term] id: NCBITaxon:314147 name: Glires namespace: ncbi_taxonomy def: "clade (sometimes ranked as grandorder) consisting of rodents and lagomorphs" [] is_a: NCBITaxon:314146 ! Euarchontoglires created_by: He Zhang creation_date: 2013-10-06T12:13:45Z [Term] id: NCBITaxon:314293 name: Simiiformes namespace: ncbi_taxonomy def: "\"higher primates\" familiar to most people" [] is_a: NCBITaxon:376913 ! Haplorrhini created_by: He Zhang creation_date: 2013-10-06T11:38:24Z [Term] id: NCBITaxon:314294 name: Cercopithecoidea namespace: ncbi_taxonomy def: "are a group of primates" [] is_a: NCBITaxon:9526 ! Catarrhini created_by: He Zhang creation_date: 2013-10-06T11:37:41Z [Term] id: NCBITaxon:314295 name: Hominoidea namespace: ncbi_taxonomy def: "anthropoid apes and human beings" [] is_a: NCBITaxon:9526 ! Catarrhini created_by: He Zhang creation_date: 2013-10-06T11:34:50Z [Term] id: NCBITaxon:32523 name: Tetrapoda namespace: ncbi_taxonomy def: "a vertebrate animal having four feet or legs or leglike appendages" [] xref: GC_ID:1 is_a: NCBITaxon:0000414 ! Dipnotetrapodomorpha created_by: He Zhang creation_date: 2013-10-06T12:22:11Z [Term] id: NCBITaxon:32524 name: Amniota namespace: ncbi_taxonomy def: "higher vertebrates (reptiles, birds and mammals) possessing an amnion during development" [] xref: GC_ID:1 is_a: NCBITaxon:32523 ! Tetrapoda created_by: He Zhang creation_date: 2013-10-06T12:20:38Z [Term] id: NCBITaxon:32525 name: Theria namespace: ncbi_taxonomy def: "subclass of mammals that give birth to live young without using a shelled egg" [] xref: GC_ID:1 is_a: NCBITaxon:40674 ! Mammalia created_by: He Zhang creation_date: 2013-10-06T12:17:06Z [Term] id: NCBITaxon:33090 name: Viridiplantae namespace: ncbi_taxonomy def: "are a clade comprising the embryophytes (land plants), and the related green algae which are primarily aquatic" [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota property_value: has_rank NCBITaxon:kingdom created_by: He Zhang creation_date: 2013-10-06T16:26:14Z [Term] id: NCBITaxon:33154 name: Opisthokonta namespace: ncbi_taxonomy def: "are a broad group of eukaryotes, including both the animal and fungus kingdom" [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota created_by: He Zhang creation_date: 2013-10-06T13:01:09Z [Term] id: NCBITaxon:33208 name: Metazoa namespace: ncbi_taxonomy def: "multicellular animals having cells differentiated into tissues and organs and usually a digestive cavity and nervous system" [] xref: GC_ID:1 is_a: NCBITaxon:33154 ! Opisthokonta property_value: has_rank NCBITaxon:kingdom created_by: He Zhang creation_date: 2013-10-06T12:58:07Z [Term] id: NCBITaxon:33213 name: Bilateria namespace: ncbi_taxonomy def: "all animals having a bilateral symmetry" [] xref: GC_ID:1 is_a: NCBITaxon:6072 ! Eumetazoa created_by: He Zhang creation_date: 2013-10-06T12:50:12Z [Term] id: NCBITaxon:33317 name: Protostomia namespace: ncbi_taxonomy def: "mostly comprising animals with bilateral symmetry and three germ layers" [] xref: GC_ID:1 is_a: NCBITaxon:33213 ! Bilateria created_by: He Zhang creation_date: 2013-10-06T12:52:16Z [Term] id: NCBITaxon:33511 name: Deuterostomia namespace: ncbi_taxonomy def: "Deuterostomes are distinguished by their embryonic development; in deuterostomes, the first opening (the blastopore) becomes the anus, while in protostomes it becomes the mouth. Deuterostomes are also known as enterocoelomates because their coelom develops through enterocoely" [] xref: GC_ID:1 is_a: NCBITaxon:33213 ! Bilateria created_by: He Zhang creation_date: 2013-10-06T12:47:10Z [Term] id: NCBITaxon:33630 name: Alveolata namespace: ncbi_taxonomy def: "major superphylum of protists" [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota created_by: He Zhang creation_date: 2013-10-06T16:26:14Z [Term] id: NCBITaxon:33634 name: Stramenopiles namespace: ncbi_taxonomy def: "The heterokonts or stramenopiles are a major line of eukaryotes currently containing more than 100,000 known species. Most are algae, ranging from the giant multicellular kelp to the unicellular diatoms" [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota created_by: He Zhang creation_date: 2013-10-06T16:26:14Z [Term] id: NCBITaxon:33682 name: Euglenozoa namespace: ncbi_taxonomy def: "large group of flagellate protozoa" [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota created_by: He Zhang creation_date: 2013-10-06T16:26:14Z [Term] id: NCBITaxon:33858 name: environmental samples namespace: ncbi_taxonomy def: "Samples taken from the environment" [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota is_a: NCBITaxon:33154 ! Opisthokonta is_a: NCBITaxon:33208 ! Metazoa is_a: NCBITaxon:33213 ! Bilateria is_a: NCBITaxon:40674 ! Mammalia is_a: NCBITaxon:7711 ! Chordata created_by: He Zhang creation_date: 2013-10-06T12:20:09Z [Term] id: NCBITaxon:339960 name: Katablepharidophyta namespace: ncbi_taxonomy def: "undefinable" [] is_a: NCBITaxon:2759 ! Eukaryota created_by: He Zhang creation_date: 2013-10-06T16:26:14Z [Term] id: NCBITaxon:376911 name: Strepsirrhini namespace: ncbi_taxonomy def: "suborder of primates that includes the lemuriform primates" [] is_a: NCBITaxon:9443 ! Primates created_by: He Zhang creation_date: 2013-10-06T11:42:37Z [Term] id: NCBITaxon:376912 name: Tarsiiformes namespace: ncbi_taxonomy def: "group of primates that was once ranged across Europe, northern Africa, Asia, and North America" [] is_a: NCBITaxon:376913 ! Haplorrhini created_by: He Zhang creation_date: 2013-10-06T11:40:30Z [Term] id: NCBITaxon:376913 name: Haplorrhini namespace: ncbi_taxonomy def: "\"dry-nosed\" primates" [] is_a: NCBITaxon:9443 ! Primates created_by: He Zhang creation_date: 2013-10-06T11:39:46Z [Term] id: NCBITaxon:38254 name: Glaucocystophyceae namespace: ncbi_taxonomy def: "small group of freshwater microscopic algae" [] is_a: NCBITaxon:2759 ! Eukaryota created_by: He Zhang creation_date: 2013-10-06T16:26:14Z [Term] id: NCBITaxon:40674 name: Mammalia namespace: ncbi_taxonomy def: "warm-blooded vertebrates characterized by mammary glands in the female" [] xref: GC_ID:1 is_a: NCBITaxon:32524 ! Amniota property_value: has_rank NCBITaxon:class created_by: He Zhang creation_date: 2013-10-06T12:18:41Z [Term] id: NCBITaxon:42452 name: unclassified eukaryotes namespace: ncbi_taxonomy def: "Organism whose cells contain a nucleus and other structures (organelles) enclosed within membranes" [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota created_by: He Zhang creation_date: 2013-10-06T16:26:14Z [Term] id: NCBITaxon:42461 name: Opisthokonta incertae sedis namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:33154 ! Opisthokonta created_by: He Zhang creation_date: 2013-10-06T13:08:48Z [Term] id: NCBITaxon:4751 name: Fungi namespace: ncbi_taxonomy def: "any of a group of unicellular, multicellular, or syncytial spore-producing organisms feeding on organic matte" [] xref: GC_ID:1 is_a: NCBITaxon:33154 ! Opisthokonta property_value: has_rank NCBITaxon:kingdom created_by: He Zhang creation_date: 2013-10-06T13:08:48Z [Term] id: NCBITaxon:543769 name: Rhizaria namespace: ncbi_taxonomy def: "species-rich supergroup of mostly unicellular eukaryotes" [] is_a: NCBITaxon:2759 ! Eukaryota created_by: He Zhang creation_date: 2013-10-06T16:26:14Z [Term] id: NCBITaxon:554296 name: Apusozoa namespace: ncbi_taxonomy def: "phylum comprising several genera of flagellate protozoa" [] is_a: NCBITaxon:2759 ! Eukaryota created_by: He Zhang creation_date: 2013-10-06T16:26:14Z [Term] id: NCBITaxon:554915 name: Amoebozoa namespace: ncbi_taxonomy def: "major group of amoeboid protozoa, including the majority that move by means of internal cytoplasmic flow" [] is_a: NCBITaxon:2759 ! Eukaryota created_by: He Zhang creation_date: 2013-10-06T16:26:14Z [Term] id: NCBITaxon:556282 name: Jakobida namespace: ncbi_taxonomy def: "are an order of protists in the supergroup of Excavates" [] is_a: NCBITaxon:2759 ! Eukaryota created_by: He Zhang creation_date: 2013-10-06T16:26:14Z [Term] id: NCBITaxon:57118 name: Unclassified Primates namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:9443 ! Primates created_by: He Zhang creation_date: 2013-10-06T11:42:37Z [Term] id: NCBITaxon:5719 name: Parabasalidea namespace: ncbi_taxonomy def: "The parabasalids are a group of flagellated protists within the supergroup Excavata" [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota created_by: He Zhang creation_date: 2013-10-06T16:26:14Z [Term] id: NCBITaxon:5752 name: Heterolobosea namespace: ncbi_taxonomy def: "group of colourless protozoa, including many that can transform between amoeboid, flagellate, and encysted stages" [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota property_value: has_rank NCBITaxon:class created_by: He Zhang creation_date: 2013-10-06T16:26:14Z [Term] id: NCBITaxon:590648 name: Breviatea namespace: ncbi_taxonomy def: "single-celled protis" [] is_a: NCBITaxon:2759 ! Eukaryota created_by: He Zhang creation_date: 2013-10-06T16:26:14Z [Term] id: NCBITaxon:6040 name: Porifera namespace: ncbi_taxonomy def: "sponges" [] xref: GC_ID:1 is_a: NCBITaxon:33208 ! Metazoa property_value: has_rank NCBITaxon:phylum created_by: He Zhang creation_date: 2013-10-06T12:59:38Z [Term] id: NCBITaxon:6072 name: Eumetazoa namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:33208 ! Metazoa created_by: He Zhang creation_date: 2013-10-06T12:55:38Z [Term] id: NCBITaxon:6073 name: Cnidaria namespace: ncbi_taxonomy def: "Cnidaria is a phylum containing over 10,000 species of animals found exclusively in aquatic and mostly marine environments. Their distinguishing feature is cnidocytes, specialized cells that they use mainly for capturing prey" [] xref: GC_ID:1 is_a: NCBITaxon:6072 ! Eumetazoa property_value: has_rank NCBITaxon:phylum created_by: He Zhang creation_date: 2013-10-06T12:57:07Z [Term] id: NCBITaxon:607660 name: Ponginae namespace: ncbi_taxonomy def: "Ponginae is a subfamily in the hominidae family" [] is_a: NCBITaxon:9604 ! Hominidae created_by: He Zhang creation_date: 2013-10-06T11:33:38Z [Term] id: NCBITaxon:6157 name: Platyhelminthes namespace: ncbi_taxonomy def: "flatworms" [] xref: GC_ID:1 is_a: NCBITaxon:33213 ! Bilateria property_value: has_rank NCBITaxon:phylum created_by: He Zhang creation_date: 2013-10-06T12:52:16Z [Term] id: NCBITaxon:66288 name: Oxymonadida namespace: ncbi_taxonomy def: "group of flagellated protozoa found exclusively in the intestines of termites and other wood-eating insects" [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota property_value: has_rank NCBITaxon:order created_by: He Zhang creation_date: 2013-10-06T16:26:14Z [Term] id: NCBITaxon:66780 name: Gnathostomulida namespace: ncbi_taxonomy def: "jaw worms, are a small phylum of nearly microscopic marine animals" [] xref: GC_ID:1 is_a: NCBITaxon:33213 ! Bilateria property_value: has_rank NCBITaxon:phylum created_by: He Zhang creation_date: 2013-10-06T12:52:16Z [Term] id: NCBITaxon:7586 name: Echinodermata namespace: ncbi_taxonomy def: "radially symmetrical marine invertebrates including e.g. starfish and sea urchins and sea cucumbers" [] xref: GC_ID:1 is_a: NCBITaxon:33511 ! Deuterostomia property_value: has_rank NCBITaxon:phylum created_by: He Zhang creation_date: 2013-10-06T12:49:16Z [Term] id: NCBITaxon:7711 name: Chordata namespace: ncbi_taxonomy def: "comprises true vertebrates and animals having a notochord" [] xref: GC_ID:1 is_a: NCBITaxon:33511 ! Deuterostomia property_value: has_rank NCBITaxon:phylum created_by: He Zhang creation_date: 2013-10-06T12:45:05Z [Term] id: NCBITaxon:7712 name: Tunicata namespace: ncbi_taxonomy def: "Urochordata: tunicates" [] xref: GC_ID:1 is_a: NCBITaxon:7711 ! Chordata property_value: has_rank NCBITaxon:subphylum created_by: He Zhang creation_date: 2013-10-06T12:46:37Z [Term] id: NCBITaxon:7735 name: Cephalochordata namespace: ncbi_taxonomy def: "lancelets" [] xref: GC_ID:1 is_a: NCBITaxon:7711 ! Chordata property_value: has_rank NCBITaxon:subphylum created_by: He Zhang creation_date: 2013-10-06T12:46:37Z [Term] id: NCBITaxon:7742 name: Vertebrata namespace: ncbi_taxonomy def: "animals that are members of the subphylum Vertebrata" [] xref: GC_ID:1 is_a: NCBITaxon:89593 ! Craniata created_by: He Zhang creation_date: 2013-10-06T12:32:29Z [Term] id: NCBITaxon:7776 name: Gnathostomata namespace: ncbi_taxonomy def: "comprising all vertebrates with upper and lower jaws" [] xref: GC_ID:1 is_a: NCBITaxon:7742 ! Vertebrata created_by: He Zhang creation_date: 2013-10-06T12:30:58Z [Term] id: NCBITaxon:7777 name: Chondrichthyes namespace: ncbi_taxonomy def: "cartilaginous fishes" [] xref: GC_ID:1 is_a: NCBITaxon:7776 ! Gnathostomata property_value: has_rank NCBITaxon:class created_by: He Zhang creation_date: 2013-10-06T12:31:39Z [Term] id: NCBITaxon:7878 name: Dipnoi namespace: ncbi_taxonomy def: "bony fishes of the southern hemisphere that breathe by a modified air bladder as well as gills" [] xref: GC_ID:1 is_a: NCBITaxon:0000414 ! Dipnotetrapodomorpha property_value: has_rank NCBITaxon:infraclass created_by: He Zhang creation_date: 2013-10-06T12:24:11Z [Term] id: NCBITaxon:7898 name: Actinopterygii namespace: ncbi_taxonomy def: "ray-finned fishes, constitute a class or subclass of the bony fishes" [] xref: GC_ID:1 is_a: NCBITaxon:117571 ! Euteleostomi property_value: has_rank NCBITaxon:class created_by: He Zhang creation_date: 2013-10-06T12:27:42Z [Term] id: NCBITaxon:8287 name: Sarcopterygii namespace: ncbi_taxonomy def: "lobe-finned fish" [] xref: GC_ID:1 is_a: NCBITaxon:117571 ! Euteleostomi created_by: He Zhang creation_date: 2013-10-06T12:24:47Z [Term] id: NCBITaxon:8292 name: Amphibia namespace: ncbi_taxonomy def: "a cold-blooded vertebrate animal of a class that comprises the frogs, toads, newts, and salamanders" [] xref: GC_ID:1 is_a: NCBITaxon:32523 ! Tetrapoda property_value: has_rank NCBITaxon:class created_by: He Zhang creation_date: 2013-10-06T12:22:51Z [Term] id: NCBITaxon:8457 name: Sauropsida namespace: ncbi_taxonomy def: "group of amniotes that includes all existing reptiles and birds and their fossil ancestors" [] xref: GC_ID:1 is_a: NCBITaxon:32524 ! Amniota created_by: He Zhang creation_date: 2013-10-06T12:21:14Z [Term] id: NCBITaxon:89593 name: Craniata namespace: ncbi_taxonomy def: "clade of chordate animal" [] xref: GC_ID:1 is_a: NCBITaxon:7711 ! Chordata property_value: has_rank NCBITaxon:subphylum created_by: He Zhang creation_date: 2013-10-06T12:34:29Z [Term] id: NCBITaxon:9254 name: Prototheria namespace: ncbi_taxonomy def: "echidnas; platypus" [] xref: GC_ID:1 is_a: NCBITaxon:40674 ! Mammalia created_by: He Zhang creation_date: 2013-10-06T12:20:09Z [Term] id: NCBITaxon:9263 name: Metatheria namespace: ncbi_taxonomy def: "pouched animals" [] xref: GC_ID:1 is_a: NCBITaxon:32525 ! Theria created_by: He Zhang creation_date: 2013-10-06T12:17:54Z [Term] id: NCBITaxon:9347 name: Eutheria namespace: ncbi_taxonomy def: "all mammals except monotremes and marsupials" [] xref: GC_ID:1 is_a: NCBITaxon:32525 ! Theria created_by: He Zhang creation_date: 2013-10-06T12:14:15Z [Term] id: NCBITaxon:9348 name: Xenarthra namespace: ncbi_taxonomy def: "armadillos; American anteaters; sloths" [] xref: GC_ID:1 is_a: NCBITaxon:9347 ! Eutheria created_by: He Zhang creation_date: 2013-10-06T12:16:42Z [Term] id: NCBITaxon:9392 name: Scandentia namespace: ncbi_taxonomy def: "a small order comprising only the tree shrews" [] xref: GC_ID:1 is_a: NCBITaxon:314146 ! Euarchontoglires property_value: has_rank NCBITaxon:order created_by: He Zhang creation_date: 2013-10-06T12:13:45Z [Term] id: NCBITaxon:9443 name: Primates namespace: ncbi_taxonomy def: "A primate is a mammal of the order Primates" [] xref: GC_ID:1 is_a: NCBITaxon:314146 ! Euarchontoglires property_value: has_rank NCBITaxon:order created_by: He Zhang creation_date: 2013-10-06T11:41:34Z [Term] id: NCBITaxon:9479 name: Platyrrhini namespace: ncbi_taxonomy def: "New World monkeys: capuchin; douroucouli; howler monkey; saki; spider monkey; squirrel monkey; titi; uakari; woolly monkey; marmoset; tamarin" [] xref: GC_ID:1 is_a: NCBITaxon:314293 ! Simiiformes property_value: has_rank NCBITaxon:parvorder created_by: He Zhang creation_date: 2013-10-06T11:38:58Z [Term] id: NCBITaxon:9526 name: Catarrhini namespace: ncbi_taxonomy def: "one of the two subdivisions of the higher primates" [] xref: GC_ID:1 is_a: NCBITaxon:314293 ! Simiiformes property_value: has_rank NCBITaxon:parvorder created_by: He Zhang creation_date: 2013-10-06T11:37:00Z [Term] id: NCBITaxon:9577 name: Hylobatidae namespace: ncbi_taxonomy def: "used in some classifications for the lesser apes (gibbons and siamangs); sometimes considered a subfamily of Pongidae" [] xref: GC_ID:1 is_a: NCBITaxon:314295 ! Hominoidea property_value: has_rank NCBITaxon:family created_by: He Zhang creation_date: 2013-10-06T11:35:32Z [Term] id: NCBITaxon:9592 name: Gorilla namespace: ncbi_taxonomy def: "biggest and strongest of the anthropoid apes" [] xref: GC_ID:1 is_a: NCBITaxon:207598 ! Homininae property_value: has_rank NCBITaxon:genus created_by: He Zhang creation_date: 2013-10-06T11:32:32Z [Term] id: NCBITaxon:9596 name: Pan namespace: ncbi_taxonomy def: "genus for chimpanzees" [] xref: GC_ID:1 is_a: NCBITaxon:207598 ! Homininae property_value: has_rank NCBITaxon:genus created_by: He Zhang creation_date: 2013-10-06T11:32:32Z [Term] id: NCBITaxon:9604 name: Hominidae namespace: ncbi_taxonomy def: "modern man and extinct immediate ancestors of man" [] xref: GC_ID:1 is_a: NCBITaxon:314295 ! Hominoidea property_value: has_rank NCBITaxon:family created_by: He Zhang creation_date: 2013-10-06T11:33:00Z [Term] id: NCBITaxon:9605 name: Homo namespace: ncbi_taxonomy def: "Homo is the genus of great apes that includes modern humans and species closely related to them" [] xref: GC_ID:1 is_a: NCBITaxon:207598 ! Homininae property_value: has_rank NCBITaxon:genus created_by: He Zhang creation_date: 2013-10-06T11:28:25Z [Term] id: NCBITaxon:9606 name: Homo sapiens namespace: ncbi_taxonomy def: "humans" [] xref: GC_ID:1 is_a: NCBITaxon:9605 ! Homo property_value: has_rank NCBITaxon:species created_by: He Zhang creation_date: 2013-10-06T11:27:57Z [Term] id: OMIT:0000026 name: EnvironmentalVariable def: "An experimental variable is the variable that is used in an experiment and is known as the dependent variable that can be manipulated and is being studied" [] is_a: snap:Quality ! quality created_by: He Zhang creation_date: 2013-09-28T19:15:26Z [Term] id: OMIT:0000027 name: GeneSequence is_a: snap:Quality ! quality created_by: He Zhang creation_date: 2013-09-28T19:15:26Z [Term] id: OMIT:0000028 name: Pressure def: "The ratio of force to the area over which that force is distributed" [] is_a: OMIT:0000026 ! EnvironmentalVariable created_by: He Zhang creation_date: 2013-09-28T19:16:26Z [Term] id: OMIT:0000029 name: Temperature def: "Numerical measure of hot or cold" [] is_a: OMIT:0000026 ! EnvironmentalVariable created_by: He Zhang creation_date: 2013-09-28T19:16:26Z [Term] id: OMIT:0000030 name: HighPressure is_a: OMIT:0000028 ! Pressure created_by: He Zhang creation_date: 2013-09-28T19:17:41Z [Term] id: OMIT:0000031 name: LowPressure is_a: OMIT:0000028 ! Pressure created_by: He Zhang creation_date: 2013-09-28T19:17:41Z [Term] id: OMIT:0000032 name: NormalPressure is_a: OMIT:0000028 ! Pressure created_by: He Zhang creation_date: 2013-09-28T19:17:41Z [Term] id: OMIT:0000033 name: HighTemperature is_a: OMIT:0000029 ! Temperature created_by: He Zhang creation_date: 2013-09-28T19:18:33Z [Term] id: OMIT:0000034 name: LowTemperature is_a: OMIT:0000029 ! Temperature created_by: He Zhang creation_date: 2013-09-28T19:18:33Z [Term] id: OMIT:0000035 name: NormalTemperature is_a: OMIT:0000029 ! Temperature created_by: He Zhang creation_date: 2013-09-28T19:18:33Z [Term] id: OMIT:0000040 name: HarmfulRole comment: "A harmful role or activity realizeable by some agent in the human body" is_a: snap:Role ! role created_by: He Zhang creation_date: 2013-09-29T18:27:09Z [Term] id: OMIT:0000041 name: HarmfulEnvironmentalEffect comment: "Harmful physical agents" is_a: OMIT:0000040 ! HarmfulRole created_by: He Zhang creation_date: 2013-09-29T18:29:20Z [Term] id: OMIT:0000042 name: Pathogenicity def: "The potential capacity of certain species of microbes to cause a disease" [] comment: ""Germs" -- foreign microorganisms capable of causing disease" is_a: OMIT:0000040 ! HarmfulRole created_by: He Zhang creation_date: 2013-09-29T18:29:20Z [Term] id: OMIT:0000043 name: ToxicActivity comment: "Harmful chemical agents" is_a: OMIT:0000040 ! HarmfulRole created_by: He Zhang creation_date: 2013-09-29T18:29:20Z [Term] id: OMIT:0000044 name: Carcinogenicity def: " The ability or tendency to produce cancer." [] is_a: OMIT:0000043 ! ToxicActivity created_by: He Zhang creation_date: 2013-09-29T18:30:22Z [Term] id: OMIT:0000052 name: Organism def: "Any contiguous living system (such as animal, fungus, micro-organism, or plant)" [] is_a: snap:Object ! object created_by: He Zhang creation_date: 2013-09-29T18:41:01Z [Term] id: OMIT:0000054 name: ConnectiveTissueCell def: "The stromatous or nonparenchymatous tissues of the body; that which binds together and is the ground substance of the various parts and organs of the body." [] is_a: GO:0005623 ! cell created_by: He Zhang creation_date: 2013-10-01T23:03:48Z [Term] id: OMIT:0000055 name: EpithelialTissueCell def: "Cells that cover the surface of the body and line its cavities." [] is_a: GO:0005623 ! cell created_by: He Zhang creation_date: 2013-10-01T23:03:48Z [Term] id: OMIT:0000056 name: MuscleTissueCell def: "Any of the cells of skeletal or cardiac muscle tissue. Skeletal muscle fibers are cylindrical multinucleate cells containing contracting myofibrils, across which run transverse striations. Cardiac muscle fibers have one or sometimes two nuclei, contain myofibrils, and are separated from one another by an intercalated disk; although striated, cardiac muscle fibers branch to form an interlacing network." [] is_a: GO:0005623 ! cell created_by: He Zhang creation_date: 2013-10-01T23:03:48Z [Term] id: OMIT:0000057 name: NerveTissueCell def: "Any of the conducting cells of the nervous system, consisting of a cell body, containing the nucleus and its surrounding cytoplasm, and the axon and dendrites." [] is_a: GO:0005623 ! cell created_by: He Zhang creation_date: 2013-10-01T23:03:48Z [Term] id: OMIT:0000058 name: AdiposeTissueCell def: "A connective tissue cell specialized for the synthesis and storage of fat; such cells are bloated with globules of triglycerides, the nucleus being displaced to one side and the cytoplasm seen as a thin line around the fat droplet." [] is_a: OMIT:0000054 ! ConnectiveTissueCell created_by: He Zhang creation_date: 2013-10-01T23:05:33Z [Term] id: OMIT:0000059 name: Erythrocyte def: "Blood cell of vertebrates that transports oxygen and carbon dioxide, combined with the red pigment haemoglobin, to and from the tissues; also called red blood cell" [] comment: "Red blood cells - carry oxygen to body tissues" is_a: OMIT:0000054 ! ConnectiveTissueCell created_by: He Zhang creation_date: 2013-10-01T23:05:33Z [Term] id: OMIT:0000060 name: Leukocyte def: "White blood cells of the immune system involved in defending the body against both infectious disease" [] comment: "White blood cells - these have an immune function" is_a: OMIT:0000054 ! ConnectiveTissueCell created_by: He Zhang creation_date: 2013-10-01T23:05:33Z [Term] id: OMIT:0000061 name: Thrombocyte def: "Nucleated, spindle-shaped cell of nonmammalian vertebrates that promotes blood clotting" [] comment: "Platelets - function in blood clotting" is_a: OMIT:0000054 ! ConnectiveTissueCell created_by: He Zhang creation_date: 2013-10-01T23:05:33Z [Term] id: OMIT:0000062 name: Agranulocyte def: "A white blood cell without cytoplasmic granules" [] comment: "White cell line with no granules visible under microscope" is_a: OMIT:0000060 ! Leukocyte created_by: He Zhang creation_date: 2013-10-01T23:07:10Z [Term] id: OMIT:0000063 name: Granulocyte def: "Category of white blood cells characterized by the presence of granules in their cytoplasm" [] comment: "White cell line with granules visible under microscope" is_a: OMIT:0000060 ! Leukocyte created_by: He Zhang creation_date: 2013-10-01T23:07:10Z [Term] id: OMIT:0000064 name: Lymphocytes def: "A kind of white blood cell in the vertebrate immune system" [] comment: "White cells of the lymphatic lineage" is_a: OMIT:0000062 ! Agranulocyte created_by: He Zhang creation_date: 2013-10-01T23:08:02Z [Term] id: OMIT:0000065 name: Monocytes def: "A large, circulating, phagocytic white blood cell, having a single well-defined nucleus and very fine granulation in the cytoplasm" [] comment: "White cells destined to become macrophages, which "eat" pathogens" is_a: OMIT:0000062 ! Agranulocyte created_by: He Zhang creation_date: 2013-10-01T23:08:02Z [Term] id: OMIT:0000066 name: BLymphocytes def: "A type of lymphocyte that, when stimulated by a particular antigen, differentiates into plasma cells that synthesize the antibodies that circulate in the blood and react with the specific antigens" [] comment: "White cells that produce antibodies (as plasma cells)" is_a: OMIT:0000064 ! Lymphocytes created_by: He Zhang creation_date: 2013-10-01T23:09:21Z [Term] id: OMIT:0000067 name: NK comment: "Natural killer cells thought to destroy cancerous cells" is_a: OMIT:0000064 ! Lymphocytes created_by: He Zhang creation_date: 2013-10-01T23:09:21Z [Term] id: OMIT:0000068 name: TLymphocytes def: "A mononuclear, nongranular leukocyte having a deeply staining nucleus containing dense chromatin and a pale-blue staining cytoplasm. Chiefly a product of lymphoid tissue, it participates in immunity" [] comment: "White cells involved in regulation of the immune system and destruction of virus-infected cells" is_a: OMIT:0000064 ! Lymphocytes created_by: He Zhang creation_date: 2013-10-01T23:09:21Z [Term] id: OMIT:0000069 name: CD4 def: "A glycoprotein on the surface of helper T cells that serves as a receptor for HIV." [] comment: ""Helper T cells" - Regulatory cells of the immune system" is_a: OMIT:0000068 ! TLymphocytes created_by: He Zhang creation_date: 2013-10-01T23:10:26Z [Term] id: OMIT:0000070 name: CD8 def: "A glycoprotein on the surface of killer cells that enhances binding with major histocompatibility complex molecules." [] comment: ""Cytotoxic T cells" - destroy virus-infected cells" is_a: OMIT:0000068 ! TLymphocytes created_by: He Zhang creation_date: 2013-10-01T23:10:26Z [Term] id: OMIT:0000071 name: Basophils def: "A granular leukocyte with an irregularly shaped, relatively pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm containing coarse bluish-black granules of variable size" [] comment: "White cells of unknown function; possibly become mast cells (involved in allergies and inflammatory reactions)" is_a: OMIT:0000063 ! Granulocyte created_by: He Zhang creation_date: 2013-10-01T23:12:48Z [Term] id: OMIT:0000072 name: Eosinophils def: "White blood cells of the granulocyte type that have rough, round granules of cytoplasm that stain with eosin" [] comment: "White cells that function in fighting parasitic infections" is_a: OMIT:0000063 ! Granulocyte created_by: He Zhang creation_date: 2013-10-01T23:12:48Z [Term] id: OMIT:0000073 name: Neutrophils def: "White blood cells with cytoplasmic granules that consume harmful bacteria, fungi, and other foreign materials." [] comment: "Fast-response white blood cells that "eat" pathogens" is_a: OMIT:0000063 ! Granulocyte created_by: He Zhang creation_date: 2013-10-01T23:12:48Z [Term] id: OMIT:0000074 name: GlialCell def: "Non-neuronal cells that maintain homeostasis, form myelin, and provide support and protection for neurons in the brain andperipheral nervous system" [] comment: "Supportive cells of the nervous system" is_a: OMIT:0000057 ! NerveTissueCell created_by: He Zhang creation_date: 2013-10-01T23:14:18Z [Term] id: OMIT:0000075 name: Neuron def: "An electrically excitable cell that processes and transmits information through electrical and chemical signals" [] comment: "Functional (information-processing) cells of the nervous system" is_a: OMIT:0000057 ! NerveTissueCell created_by: He Zhang creation_date: 2013-10-01T23:14:18Z [Term] id: OMIT:0000076 name: MacroglialCell comment: "Large supportive cells of the nervous system" is_a: OMIT:0000074 ! GlialCell created_by: He Zhang creation_date: 2013-10-01T23:16:02Z [Term] id: OMIT:0000077 name: MicroglialCell def: "Small nonneural cells forming part of the supporting structure of the central nervous system. They are migratory and act as phagocytes to waste products of nerve tissue" [] comment: "Macrophages of the nervous system" is_a: OMIT:0000074 ! GlialCell created_by: He Zhang creation_date: 2013-10-01T23:16:02Z [Term] id: OMIT:0000078 name: Astrocyte def: "Star-shaped glial cell, especially a neuroglial cell of nervous tissue" [] comment: "Cells that supply nutrients to neurons and maintain the electrochemical environment of the nervous system." is_a: OMIT:0000076 ! MacroglialCell created_by: He Zhang creation_date: 2013-10-01T23:19:01Z [Term] id: OMIT:0000079 name: EpendymalCell def: "Squamous-to-columnar cell lining of the spinal central canal and the four ventricles of the brain; supports the choroid plexuses" [] comment: "Cells that line the ventricles of the braina dn produce cerebrospinal-fluid" is_a: OMIT:0000076 ! MacroglialCell created_by: He Zhang creation_date: 2013-10-01T23:19:01Z [Term] id: OMIT:0000080 name: Oligodendrocyte def: "Glial cells that provide support to axons and to produce the Myelin sheath, which insulates axons" [] comment: "Cells that produce the myelin sheath in the central nervous system (speeds nerve conduction)" is_a: OMIT:0000076 ! MacroglialCell created_by: He Zhang creation_date: 2013-10-01T23:19:01Z [Term] id: OMIT:0000081 name: RadialGlialCell comment: "Glia used to guide neurons during development" is_a: OMIT:0000076 ! MacroglialCell created_by: He Zhang creation_date: 2013-10-01T23:19:01Z [Term] id: OMIT:0000082 name: SatelliteCell def: "Type of glial cell that line the exterior surface of neurons in the peripheral nervous system" [] comment: "Supportive cells found in some parts of the nervous system" is_a: OMIT:0000076 ! MacroglialCell created_by: He Zhang creation_date: 2013-10-01T23:19:01Z [Term] id: OMIT:0000083 name: SchwannCell def: "Principal glia of the peripheral nervous system" [] comment: "Cells that produce the myelin sheath in the peripheral nervous system (speeds nerve conduction)" is_a: OMIT:0000076 ! MacroglialCell created_by: He Zhang creation_date: 2013-10-01T23:19:01Z [Term] id: OMIT:0000084 name: OncoGeneratingMiRNA def: "Any cell that covers the nerve fibers in the peripheral nervous system and forms the myelin sheath" [] comment: "A miRNA that, when active, encourages the creation of a tumor, most likely by inhibiting the expression of a tumor suppressor gene."\n"deprecated" is_a: SO:0000276 ! miRNA created_by: He Zhang creation_date: 2013-10-01T23:22:48Z [Term] id: OMIT:0000085 name: OtherMiRNA comment: "deprecated" is_a: SO:0000276 ! miRNA created_by: He Zhang creation_date: 2013-10-01T23:22:48Z [Term] id: OMIT:0000086 name: TumorSuppressingMiRNA comment: "A miRNA that, when active, discourages the creation of a tumor, most likely by inhibiting the expression of an oncogene."\n"deprecated" is_a: SO:0000276 ! miRNA created_by: He Zhang creation_date: 2013-10-01T23:22:48Z [Term] id: OMIT:0000091 name: Virus def: "Small infectious agent that replicates only inside the living cells of other organisms" [] is_a: OMIT:0000052 ! Organism created_by: He Zhang creation_date: 2013-10-01T23:27:46Z [Term] id: OMIT:0000097 name: Tissue def: "An ensemble of similar cells from the same origin that together carry out a specific function" [] comment: "A collection of cells organized by a common function" is_a: snap:ObjectAggregate ! object_aggregate created_by: He Zhang creation_date: 2013-10-01T23:30:47Z [Term] id: OMIT:0000098 name: AdultTissue is_a: OMIT:0000097 ! Tissue created_by: He Zhang creation_date: 2013-10-01T23:32:05Z [Term] id: OMIT:0000099 name: EmbryonicTissue def: "Tissue in an embryo" [] comment: "Tissues existing in the early embryonic stages of development" is_a: OMIT:0000097 ! Tissue created_by: He Zhang creation_date: 2013-10-01T23:32:05Z [Term] id: OMIT:0000100 name: ConnectiveTissue def: "Tissue that connects, supports, binds, or separates other tissues or organs, typically having relatively few cells embedded in an amorphous matrix, often with collagen or other fibers, and including cartilaginous, fatty, and elastic tissues." [] comment: "Tissues originating from mesoderm and performing a structural or connective function between other tissues" is_a: OMIT:0000098 ! AdultTissue created_by: He Zhang creation_date: 2013-10-01T23:33:33Z [Term] id: OMIT:0000101 name: EpithelialTissue def: "Membranous tissue covering internal organs and other internal surfaces of the body." [] comment: "Tissue lining body structures and forming glands" is_a: OMIT:0000098 ! AdultTissue created_by: He Zhang creation_date: 2013-10-01T23:33:33Z [Term] id: OMIT:0000102 name: MuscleTissue def: "Muscle tissue is one of four basic biological tissues present in animals. It is a soft tissue that composes muscles. It is formed during embryo development in a process known as myogenesis." [] comment: "Tissue forming muscles - capable of generating movement of body structures" is_a: OMIT:0000098 ! AdultTissue created_by: He Zhang creation_date: 2013-10-01T23:33:33Z [Term] id: OMIT:0000103 name: NerveTissue def: "Tissue composed of neurons." [] comment: "Tissue forming nerves and neural structures like the brain and spinal cord, used for coordinating bodily functions." is_a: OMIT:0000098 ! AdultTissue created_by: He Zhang creation_date: 2013-10-01T23:33:33Z [Term] id: OMIT:0000104 name: AdiposeTissue def: "A kind of body tissue containing stored fat that serves as a source of energy; it also cushions and insulates vital organs." [] comment: "Fat tissue" is_a: OMIT:0000100 ! ConnectiveTissue created_by: He Zhang creation_date: 2013-10-01T23:34:55Z [Term] id: OMIT:0000105 name: Blood def: "Bodily fluid in animals that delivers necessary substances such as nutrients and oxygen to the cells and transports metabolic waste products away." [] comment: "Blood tissue, including red and white blood cells" is_a: OMIT:0000100 ! ConnectiveTissue created_by: He Zhang creation_date: 2013-10-01T23:34:55Z [Term] id: OMIT:0000106 name: Bone def: "Rigid organs that constitute part of the endoskeleton of vertebrates." [] comment: "Bone tissue - provides structural framework for body with high compressive strength" is_a: OMIT:0000100 ! ConnectiveTissue created_by: He Zhang creation_date: 2013-10-01T23:34:55Z [Term] id: OMIT:0000107 name: Cartilage def: "A tough, elastic, fibrous connective tissue found in various parts of the body, such as the joints, outer ear, and larynx." [] comment: "Tough tissue that connects bones and gives form to many of the soft structures of the body" is_a: OMIT:0000100 ! ConnectiveTissue created_by: He Zhang creation_date: 2013-10-01T23:34:55Z [Term] id: OMIT:0000108 name: CardiacMuscle def: "Type of involuntary striated muscle found in the walls and histological foundation of the heart." [] comment: "Muscle cells of the heart" is_a: OMIT:0000102 ! MuscleTissue created_by: He Zhang creation_date: 2013-10-01T23:36:04Z [Term] id: OMIT:0000109 name: SkeletalMuscle def: "Form of striated muscle tissue which is under the control of the somatic nervous system." [] comment: "Muscle cells of skeletal muscle - those that execute voluntary movement of the skeleton" is_a: OMIT:0000102 ! MuscleTissue created_by: He Zhang creation_date: 2013-10-01T23:36:04Z [Term] id: OMIT:0000110 name: SmoothMuscle def: "Responsible for the contractility of hollow organs, such as blood vessels, the gastrointestinal tract, the bladder, or the uterus." [] comment: "Muscle cells of smooth muscle - found in digestive tract and blood vessels, execute involuntary movement" is_a: OMIT:0000102 ! MuscleTissue created_by: He Zhang creation_date: 2013-10-01T23:36:04Z [Term] id: OMIT:0000111 name: Ectoderm def: "Outermost of the three primary germ layers of an embryo, from which the epidermis, nervous tissue, and, in vertebrates, sense organs develop." [] comment: "The outer layer of cells in the early embryo" is_a: OMIT:0000099 ! EmbryonicTissue created_by: He Zhang creation_date: 2013-10-03T23:21:30Z [Term] id: OMIT:0000112 name: Endoderm def: "Innermost of the three primary germ layers of an animal embryo, developing into the gastrointestinal tract, the lungs, and associated structures." [] comment: "The inner layer of cells in the early embryo" is_a: OMIT:0000099 ! EmbryonicTissue created_by: He Zhang creation_date: 2013-10-03T23:21:30Z [Term] id: OMIT:0000113 name: Mesoderm def: "Middle embryonic germ layer, lying between the ectoderm and the endoderm, from which connective tissue, muscle, bone, and the urogenital and circulatory systems develop." [] comment: "The middle layer of cells in the early embryo" is_a: OMIT:0000099 ! EmbryonicTissue created_by: He Zhang creation_date: 2013-10-03T23:21:30Z [Term] id: OMIT:0000114 name: ExperimentalValidation is_a: GO:0008150 ! biological_process relationship: OMIT:experimentContainsMiRNA SO:0000276 ! miRNA relationship: OMIT:experimentContainsTarget SO:0000704 ! gene created_by: He Zhang creation_date: 2013-10-03T23:31:23Z [Term] id: OMIT:0000115 name: MiRNABinding is_a: GO:0008150 ! biological_process relationship: OMIT:hasMiRNA SO:0000276 ! miRNA relationship: OMIT:hasPrediction SO:0000704 ! gene relationship: OMIT:hasTarget SO:0000704 ! gene relationship: OMIT:hasValidation OMIT:0000114 ! ExperimentalValidation relationship: OMIT:involvedInEvent span:ProcessualEntity ! processual_entity created_by: He Zhang creation_date: 2013-10-03T23:31:23Z [Term] id: OMIT:0000116 name: PathologicalEvent is_a: GO:0008150 ! biological_process created_by: He Zhang creation_date: 2013-10-03T23:31:23Z [Term] id: OMIT:0000117 name: RadiationExposure def: "In health physics, the quantity used to indicate the amount of ionization in air produced by X-ray or gamma radiation while conducting radiologic procedures." [] is_a: GO:0008150 ! biological_process created_by: He Zhang creation_date: 2013-10-03T23:31:23Z [Term] id: OMIT:0000118 name: SignOrSymptom is_a: GO:0008150 ! biological_process created_by: He Zhang creation_date: 2013-10-03T23:31:23Z [Term] id: OMIT:0000119 name: TumorCellDeath is_a: OMIT:0000116 ! PathologicalEvent created_by: He Zhang creation_date: 2013-10-03T23:33:42Z [Term] id: OMIT:0000120 name: TumorCellProliferation is_a: OMIT:0000116 ! PathologicalEvent created_by: He Zhang creation_date: 2013-10-03T23:33:42Z [Term] id: OMIT:0000121 name: TumorMetastasis def: "Metastatic disease, is the spread of a cancer from one organ or part to another non-adjacent organ or par." [] is_a: OMIT:0000116 ! PathologicalEvent created_by: He Zhang creation_date: 2013-10-03T23:33:42Z [Term] id: OMIT:0000122 name: DOIDTerms def: "Pathological condition of a part, organ, or system of an organism resulting from various causes, such as infection, genetic defect, or environmental stress, and characterized by an identifiable group of signs or symptoms." [] is_a: span:ProcessAggregate ! process_aggregate relationship: OMIT:causedBy OMIT:0000040 ! HarmfulRole relationship: OMIT:treatedBy OMIT:0000123 ! Treatment created_by: He Zhang creation_date: 2013-10-03T23:37:16Z [Term] id: OMIT:0000123 name: Treatment is_a: span:ProcessAggregate ! process_aggregate created_by: He Zhang creation_date: 2013-10-03T23:37:16Z [Term] id: OMIT:0000225 name: PharmaceuticalTreatment is_a: OMIT:0000123 ! Treatment creation_date: 2013-10-04T20:10:02Z [Term] id: OMIT:0000226 name: PhysicalTherapy def: "A health care profession primarily concerned with the remediation of impairments and disabilities and the promotion of mobility, functional ability, quality of life and movement potential through examination, evaluation, diagnosis and physical intervention." [] is_a: OMIT:0000123 ! Treatment creation_date: 2013-10-04T20:10:02Z [Term] id: OMIT:0000227 name: PsychologicalTreatment is_a: OMIT:0000123 ! Treatment creation_date: 2013-10-04T20:10:02Z [Term] id: OMIT:0000228 name: Surgery def: "Branch of medicine that deals with the diagnosis and treatment of injury, deformity, and disease by manual and instrumental means." [] is_a: OMIT:0000123 ! Treatment creation_date: 2013-10-04T20:10:02Z [Term] id: OMIT:0000229 name: AnalgesicTreatment is_a: OMIT:0000225 ! PharmaceuticalTreatment creation_date: 2013-10-04T20:19:18Z [Term] id: OMIT:0000230 name: AntibioticTreatment is_a: OMIT:0000225 ! PharmaceuticalTreatment creation_date: 2013-10-04T20:19:18Z [Term] id: OMIT:0000231 name: AntihyperlipidemicTreatment is_a: OMIT:0000225 ! PharmaceuticalTreatment creation_date: 2013-10-04T20:19:18Z [Term] id: OMIT:0000232 name: AntihypertensiveTreatment is_a: OMIT:0000225 ! PharmaceuticalTreatment creation_date: 2013-10-04T20:19:18Z [Term] id: OMIT:0000233 name: Chemotherapy def: "Treatment of cancer with one or more cytotoxic antineoplastic drugs." [] is_a: OMIT:0000225 ! PharmaceuticalTreatment creation_date: 2013-10-04T20:19:18Z [Term] id: OMIT:0000234 name: ImmunosuppressiveTherapy def: "Immunosuppression involves an act that reduces the activation or efficacy of the immune system." [] is_a: OMIT:0000225 ! PharmaceuticalTreatment creation_date: 2013-10-04T20:19:18Z [Term] id: OMIT:0000235 name: RadiationRelease def: "The treatment of disease, esp. cancer, using X-rays or similar forms of radiation." [] is_a: span:ProcessualContext ! processual_context creation_date: 2013-10-04T20:24:14Z [Term] id: OMIT:0000244 name: FMATerms comment: "deprecated"\n"An anatomic location; a named physical feature of the body" is_a: snap:Object ! object created_by: He Zhang creation_date: 2013-10-04T20:48:15Z [Term] id: OMIT:0000481 name: CellularOrganism def: "An organism of microscopic or submicroscopic size, especially a bacterium or protozoan" [] is_a: OMIT:0000052 ! Organism creation_date: 2013-10-07T00:19:58Z [Term] id: OMIT:0000482 name: Archaea def: "microorganisms that are similar to bacteria in size and simplicity of structure but radically different in molecular organization. They are now believed to constitute an ancient intermediate group between the bacteria and eukaryotes" [] is_a: OMIT:0000481 ! CellularOrganism created_by: He Zhang creation_date: 2013-10-07T00:31:14Z [Term] id: OMIT:0000483 name: Bacteria def: "a member of a large group of unicellular microorganisms that have cell walls but lack organelles and an organized nucleus, including some that can cause diseas" [] is_a: OMIT:0000481 ! CellularOrganism created_by: He Zhang creation_date: 2013-10-07T00:31:14Z [Term] id: OMIT:0000800 name: Regulation is_a: GO:0008150 ! biological_process created_by: He Zhang creation_date: 2013-10-25T16:06:10Z [Term] id: OMIT:0000801 name: TEJuxtaposition is_a: SO:0001411 ! biological_region relationship: OMIT:resultedFrom OMIT:0000803 ! TEInsertion created_by: He Zhang creation_date: 2013-10-25T16:05:06Z [Term] id: OMIT:0000803 name: TEInsertion is_a: SO:0000667 ! insertion creation_date: 2013-10-25T16:03:19Z [Term] id: OMIT:0000806 name: AdvantageousRegulation is_a: OMIT:0000800 ! Regulation relationship: OMIT:resultedFrom OMIT:0000803 ! TEInsertion creation_date: 2013-10-25T16:14:58Z [Term] id: OMIT:0000807 name: PositiveStrandInsertion is_a: OMIT:0000803 ! TEInsertion created_by: He Zhang creation_date: 2013-10-25T16:17:26Z [Term] id: OMIT:0000809 name: NegativeStrandInsertion is_a: OMIT:0000803 ! TEInsertion created_by: He Zhang creation_date: 2013-10-25T16:17:26Z [Term] id: PR:000000001 name: protein namespace: protein def: "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA." [PRO:DAN, PRO:WCB] comment: Proteins descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. is_a: PR:000018263 ! amino acid chain relationship: OMIT:regulateProtein SO:0000276 ! miRNA [Term] id: PR:000002968 name: post-translationally modified amino-acid residue namespace: protein def: "A modified amino-acid residue that was modified after its incorporation into an amino acid chain." [PRO:DAN] comment: This includes any residue modification that occurs once translation has begun, and thus includes what are usually considered co-translational modifications. synonym: "post-translationally modified amino acid chain residue" EXACT [PRO:DAN] synonym: "post-translationally modified protein residue" NARROW [PRO:DAN] is_a: PR:000025513 ! modified amino-acid residue [Term] id: PR:000002970 name: pre-translationally modified amino-acid residue namespace: protein alt_id: PR:000018261 def: "A modified amino-acid residue that was modified before its incorporation into an amino acid chain." [PRO:DAN] comment: PRO needs to refer to such residues as distinct from the standard set of amino acids. These are produced exclusively by modification of amino acids acylated to special tRNA before incorporation by ribosomes into proteins. [PSI-MOD]. synonym: "natural, non-standard encoded residue" RELATED [MOD:00868] synonym: "non-standard encoded protein residue" EXACT [] synonym: "pre-translationally modified amino acid chain residue" EXACT [PRO:DAN] synonym: "pre-translationally modified protein residue" NARROW [PRO:DAN] is_a: PR:000025513 ! modified amino-acid residue [Term] id: PR:000018263 name: amino acid chain namespace: protein def: "A molecular entity that is a polymer of amino acids linked by peptide bonds." [PRO:DAN] synonym: "peptide" NARROW [] synonym: "polypeptide" NARROW [] is_a: CHEBI:23367 ! molecular entity [Term] id: PR:000018264 name: proteolytic cleavage product namespace: protein def: "An amino acid chain produced as the result of peptide bond cleavage of a longer amino acid chain." [PRO:DAN] synonym: "peptide" NARROW [] synonym: "polypeptide" NARROW [] is_a: PR:000018263 ! amino acid chain [Term] id: PR:000021935 name: immature protein part namespace: protein def: "A part of a protein that is removed during the protein maturation process." [PRO:DAN] synonym: "cleaved_peptide_region" EXACT [SO:0100011] is_a: BFO:0000024 ! fiat object [Term] id: PR:000021937 name: initiator methionine namespace: protein def: "An immature protein part that is the N-terminal most residue." [PRO:DAN] comment: The initiator methionine is cleaved co-translationally. For this reason, we do not use the derives_from relation when defining protein forms lacking the initiator (because the precursor form does not yet exist at the time of removal). is_a: PR:000021935 ! immature protein part [Term] id: PR:000025513 name: modified amino-acid residue namespace: protein def: "An amino-acid residue that is covalently modified by chemical alteration to the side chain or backbone atoms." [PRO:DAN] synonym: "modified amino acid chain residue" EXACT [PRO:DAN] synonym: "modified protein residue" NARROW [PRO:DAN] is_a: CHEBI:33708 ! amino-acid residue [Term] id: snap:Continuant name: continuant namespace: def: "An entity [bfo:Entity] that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] comment: Definition: An entity [bfo:Entity] that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. synonym: "endurant" RELATED [] is_a: bfo:Entity ! entity union_of: snap:DependentContinuant ! dependent_continuant union_of: snap:IndependentContinuant ! independent_continuant union_of: snap:SpatialRegion ! spatial_region disjoint_from: span:Occurrent ! occurrent relationship: OMIT:fromTaxon OMIT:0000052 ! Organism property_value: has_example "a heart" xsd:string property_value: has_example "a person" xsd:string property_value: has_example "a symphony orchestra" xsd:string property_value: has_example "the color of a tomato" xsd:string property_value: has_example "the disposition of blood to coagulate" xsd:string property_value: has_example "the lawn and atmosphere in front of our building" xsd:string property_value: has_example "the mass of a cloud" xsd:string created_by: He Zhang creation_date: 2013-09-27T11:53:19Z [Term] id: snap:DependentContinuant name: dependent_continuant namespace: def: "A continuant [snap:Continuant] that is either dependent on one or other independent continuant [snap:IndependentContinuant] bearers or inheres in or is borne by other entities." [] comment: Definition: A continuant [snap:Continuant] that is either dependent on one or other independent continuant [snap:IndependentContinuant] bearers or inheres in or is borne by other entities. is_a: snap:Continuant ! continuant union_of: snap:GenericallyDependentContinuant ! generically_dependent_continuant union_of: snap:SpecificallyDependentContinuant ! specifically_dependent_continuant disjoint_from: snap:IndependentContinuant ! independent_continuant disjoint_from: snap:SpatialRegion ! spatial_region created_by: He Zhang creation_date: 2013-09-27T11:55:25Z [Term] id: snap:Disposition name: disposition namespace: def: "A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C." [] comment: Definition: A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C. is_a: snap:RealizableEntity ! realizable_entity disjoint_from: snap:Function ! function disjoint_from: snap:Role ! role property_value: has_example "the disposition of a patient with a weakened immune system to contract disease" xsd:string property_value: has_example "the disposition of a vase to brake if dropped" xsd:string property_value: has_example "the disposition of blood to coagulate" xsd:string property_value: has_example "the disposition of metal to conduct electricity." xsd:string property_value: has_example "the disposition of vegetables to decay when not refrigerated" xsd:string created_by: He Zhang creation_date: 2013-09-29T18:17:53Z [Term] id: snap:FiatObjectPart name: fiat_object_part namespace: def: "A material entity [snap:MaterialEntity] that is part of an object [snap:Object] but is not demarcated by any physical discontinuities." [] comment: Definition: A material entity [snap:MaterialEntity] that is part of an object [snap:Object] but is not demarcated by any physical discontinuities. synonym: "fiat substance part" RELATED [] is_a: snap:MaterialEntity ! material_entity disjoint_from: snap:Object ! object disjoint_from: snap:ObjectAggregate ! object_aggregate property_value: has_example "the dorsal and ventral surfaces of the body" xsd:string property_value: has_example "the east side of Saarbruecken" xsd:string property_value: has_example "the lower right portion of a human torso" xsd:string property_value: has_example "upper and lower lobes of the left lung" xsd:string created_by: He Zhang creation_date: 2013-09-29T18:32:17Z [Term] id: snap:Function name: function namespace: def: "A realizable entity [snap:RealizableEntity] the manifestation of which is an essentially end-directed activity of a continuant [snap:Continuant] entity in virtue of that continuant [snap:Continuant] entity being a specific kind of entity in the kind or kinds of contexts that it is made for." [] comment: Definition: A realizable entity [snap:RealizableEntity] the manifestation of which is an essentially end-directed activity of a continuant [snap:Continuant] entity in virtue of that continuant [snap:Continuant] entity being a specific kind of entity in the kind or kinds of contexts that it is made for. is_a: snap:RealizableEntity ! realizable_entity disjoint_from: snap:Disposition ! disposition disjoint_from: snap:Role ! role property_value: has_example "etc." xsd:string property_value: has_example "the digestive function of the stomach to nutriate the body" xsd:string property_value: has_example "the function of a birth canal to enable transport" xsd:string property_value: has_example "the function of a computer program to compute mathematical equations" xsd:string property_value: has_example "the function of a hammer to drive in nails" xsd:string property_value: has_example "the function of a judge in a court of law" xsd:string property_value: has_example "the function of an automobile to provide transportation" xsd:string property_value: has_example "the function of reproduction in the transmission of genetic material" xsd:string property_value: has_example "the function of the heart in the body: to pump blood" xsd:string property_value: has_example "to receive de-oxygenated and oxygenated blood" xsd:string created_by: He Zhang creation_date: 2013-09-29T18:17:53Z [Term] id: snap:GenericallyDependentContinuant name: generically_dependent_continuant namespace: def: "A continuant [snap:Continuant] that is dependent on one or other independent continuant [snap:IndependentContinuant] bearers. For every instance of A requires some instance of (an independent continuant [snap:IndependentContinuant] type) B but which instance of B serves can change from time to time." [] comment: Definition: A continuant [snap:Continuant] that is dependent on one or other independent continuant [snap:IndependentContinuant] bearers. For every instance of A requires some instance of (an independent continuant [snap:IndependentContinuant] type) B but which instance of B serves can change from time to time. is_a: snap:DependentContinuant ! dependent_continuant disjoint_from: snap:SpecificallyDependentContinuant ! specifically_dependent_continuant property_value: has_example "a certain PDF file that exists in different and in several hard drives" xsd:string created_by: He Zhang creation_date: 2013-09-27T11:56:41Z [Term] id: snap:IndependentContinuant name: independent_continuant namespace: def: "A continuant [snap:Continuant] that is a bearer of quality [snap:Quality] and realizable entity [snap:RealizableEntity] entities, in which other entities inhere and which itself cannot inhere in anything." [] comment: Definition: A continuant [snap:Continuant] that is a bearer of quality [snap:Quality] and realizable entity [snap:RealizableEntity] entities, in which other entities inhere and which itself cannot inhere in anything. synonym: "substantial entity" RELATED [] is_a: snap:Continuant ! continuant union_of: snap:MaterialEntity ! material_entity union_of: snap:ObjectBoundary ! object_boundary union_of: snap:Site ! site disjoint_from: snap:DependentContinuant ! dependent_continuant disjoint_from: snap:SpatialRegion ! spatial_region property_value: has_example "a chair" xsd:string property_value: has_example "a heart" xsd:string property_value: has_example "a leg" xsd:string property_value: has_example "a person" xsd:string property_value: has_example "a symphony orchestra" xsd:string property_value: has_example "an organism" xsd:string property_value: has_example "the bottom right portion of a human torso" xsd:string property_value: has_example "the lawn and atmosphere in front of our building" xsd:string created_by: He Zhang creation_date: 2013-09-27T11:55:25Z [Term] id: snap:MaterialEntity name: material_entity namespace: def: "An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology." [] comment: Definition: An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology. is_a: snap:IndependentContinuant ! independent_continuant union_of: snap:FiatObjectPart ! fiat_object_part union_of: snap:Object ! object union_of: snap:ObjectAggregate ! object_aggregate disjoint_from: snap:ObjectBoundary ! object_boundary disjoint_from: snap:Site ! site property_value: has_example "a chair" xsd:string property_value: has_example "collection of random bacteria" xsd:string property_value: has_example "dorsal surface of the body" xsd:string created_by: He Zhang creation_date: 2013-09-27T11:57:56Z [Term] id: snap:Object name: object namespace: def: "A material entity [snap:MaterialEntity] that is spatially extended, maximally self-connected and self-contained (the parts of a substance are not separated from each other by spatial gaps) and possesses an internal unity. The identity of substantial object [snap:Object] entities is independent of that of other entities and can be maintained through time." [] comment: Definition: A material entity [snap:MaterialEntity] that is spatially extended, maximally self-connected and self-contained (the parts of a substance are not separated from each other by spatial gaps) and possesses an internal unity. The identity of substantial object [snap:Object] entities is independent of that of other entities and can be maintained through time. synonym: "substance" RELATED [] is_a: snap:MaterialEntity ! material_entity disjoint_from: snap:FiatObjectPart ! fiat_object_part disjoint_from: snap:ObjectAggregate ! object_aggregate property_value: has_example "a chair" xsd:string property_value: has_example "a heart" xsd:string property_value: has_example "a lung" xsd:string property_value: has_example "an apple" xsd:string property_value: has_example "an organism" xsd:string created_by: He Zhang creation_date: 2013-09-29T18:32:17Z [Term] id: snap:ObjectAggregate name: object_aggregate namespace: def: "A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries." [] comment: Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries. synonym: "substance aggregate" RELATED [] is_a: snap:MaterialEntity ! material_entity disjoint_from: snap:FiatObjectPart ! fiat_object_part disjoint_from: snap:Object ! object property_value: has_example "a collection of random bacteria" xsd:string property_value: has_example "a flock of geese" xsd:string property_value: has_example "a group of commuters on the subway" xsd:string property_value: has_example "a heap of stones" xsd:string property_value: has_example "the patients in a hospital" xsd:string created_by: He Zhang creation_date: 2013-09-29T18:32:17Z [Term] id: snap:ObjectBoundary name: object_boundary namespace: def: "An independent continuant [snap:IndependentContinuant] that is a lower dimensional part of a spatial entity, normally a closed two-dimensional surface. Boundaries are those privileged parts of object [snap:Object] entities that exist at exactly the point where the object [snap:Object] is separated off from the rest of the existing entities in the world." [] comment: Comment: Boundaries are theoretically difficult entities to account for, however the intuitive notion of a physical boundary as a surface of some sort (whether inside or outside of a thing) will generally serve as a good guide for the use of this universal. synonym: "substance boundary" RELATED [] is_a: snap:IndependentContinuant ! independent_continuant disjoint_from: snap:FiatObjectPart ! fiat_object_part disjoint_from: snap:Object ! object disjoint_from: snap:ObjectAggregate ! object_aggregate disjoint_from: snap:Site ! site property_value: has_example "the outer surface of a cell or cell wall" xsd:string property_value: has_example "the surface of the earth" xsd:string property_value: has_example "the surface of the interior of the stomach" xsd:string property_value: has_example "the surface of the skin" xsd:string created_by: He Zhang creation_date: 2013-09-27T11:57:56Z [Term] id: snap:OneDimensionalRegion name: one_dimensional_region namespace: def: "A spatial region [snap:SpatialRegion] with one dimension." [] comment: Definition: A spatial region [snap:SpatialRegion] with one dimension. is_a: snap:SpatialRegion ! spatial_region disjoint_from: snap:ThreeDimensionalRegion ! three_dimensional_region disjoint_from: snap:TwoDimensionalRegion ! two_dimensional_region disjoint_from: snap:ZeroDimensionalRegion ! zero_dimensional_region property_value: has_example "an edge of a cube-shaped part of space" xsd:string property_value: has_example "the part of space that is a line stretching from one end of absolute space to the other" xsd:string created_by: He Zhang creation_date: 2013-09-27T11:59:24Z [Term] id: snap:Quality name: quality namespace: def: "A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property)." [] comment: Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property). is_a: snap:SpecificallyDependentContinuant ! specifically_dependent_continuant disjoint_from: snap:RealizableEntity ! realizable_entity property_value: has_example "the ambient temperature of air" xsd:string property_value: has_example "the circumference of a waist" xsd:string property_value: has_example "the color of a tomato" xsd:string property_value: has_example "the mass of a piece of gold" xsd:string property_value: has_example "the shape of a nose" xsd:string property_value: has_example "the weight of a chimpanzee" xsd:string created_by: He Zhang creation_date: 2013-09-28T19:10:37Z [Term] id: snap:RealizableEntity name: realizable_entity namespace: def: "A specifically dependent continuant [snap:SpecificallyDependentContinuant] that inheres in continuant [snap:Continuant] entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." [] comment: Comment: If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized. is_a: snap:SpecificallyDependentContinuant ! specifically_dependent_continuant disjoint_from: snap:Quality ! quality property_value: has_example "the disposition of blood to coagulate" xsd:string property_value: has_example "the disposition of metal to conduct electricity" xsd:string property_value: has_example "the function of the reproductive organs" xsd:string property_value: has_example "the role of being a doctor" xsd:string created_by: He Zhang creation_date: 2013-09-28T19:10:37Z [Term] id: snap:Role name: role namespace: def: "A realizable entity [snap:RealizableEntity] the manifestation of which brings about some result or end that is not essential to a continuant [snap:Continuant] in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant [snap:Continuant] in some kinds of natural, social or institutional contexts." [] comment: Definition: A realizable entity [snap:RealizableEntity] the manifestation of which brings about some result or end that is not essential to a continuant [snap:Continuant] in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant [snap:Continuant] in some kinds of natural, social or institutional contexts. is_a: snap:RealizableEntity ! realizable_entity disjoint_from: snap:Disposition ! disposition disjoint_from: snap:Function ! function property_value: has_example "the role of a biological grandfather as legal guardian in the context of a system of laws" xsd:string property_value: has_example "the role of a chemical compound in an experiment" xsd:string property_value: has_example "the role of a patient relative as defined by a hospital administrative form" xsd:string property_value: has_example "the role of a person as a surgeon" xsd:string property_value: has_example "the role of a student in a university" xsd:string property_value: has_example "the role of a woman as a legal mother in the context of system of laws" xsd:string property_value: has_example "the role of ingested matter in digestion" xsd:string created_by: He Zhang creation_date: 2013-09-29T18:17:53Z [Term] id: snap:Site name: site namespace: def: "An independent continuant [snap:IndependentContinuant] consisting of a characteristic spatial shape in relation to some arrangement of other continuant [snap:Continuant] entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site [snap:Site] entities are entities that can be occupied by other continuant [snap:Continuant] entities." [] comment: Comment: An instance of Site [snap:Site] is a mixture of independent continuant [snap:IndependentContinuant] entities which act as surrounding environments for other independent continuant [snap:IndependentContinuant] entities, most importantly for instances of object [snap:Object]. A site [snap:Site] is typically made of object [snap:Object] or fiat object part [snap:FiatObjectPart] entities and a surrounding medium in which is found an object [snap:Object] occupying the site [snap:Site]. Independent continuant [snap:IndependentContinuant] entities may be associated with others (which, then, are site [snap:Site] entities) through a relation of "occupation". That relation is connected to, but distinct from, the relation of spatial location. Site [snap:Site] entities are not to be confused with spatial region [snap:SpatialRegion] entities. In BFO, site [snap:Site] allows for a so-called relational view of space which is different from the view corresponding to the class spatial region [snap:SpatialRegion] (see the comment on this class). is_a: snap:IndependentContinuant ! independent_continuant disjoint_from: snap:FiatObjectPart ! fiat_object_part disjoint_from: snap:Object ! object disjoint_from: snap:ObjectAggregate ! object_aggregate disjoint_from: snap:ObjectBoundary ! object_boundary property_value: has_example "Maria's nostril or her intestines for a variety of bacteria." xsd:string property_value: has_example "a particular room in a particular hospital" xsd:string created_by: He Zhang creation_date: 2013-09-27T11:57:56Z [Term] id: snap:SpatialRegion name: spatial_region namespace: def: "A continuant [snap:Continuant] that is neither bearer of quality [snap:Quality] entities nor inheres in any other entities." [] comment: Comment: All instances of continuant [snap:Continuant] are spatial entities, that is, they enter in the relation of (spatial) location with spatial region [snap:SpatialRegion] entities. As a particular case, the exact spatial location of a spatial region [snap:SpatialRegion] is this region itself. is_a: snap:Continuant ! continuant union_of: snap:OneDimensionalRegion ! one_dimensional_region union_of: snap:ThreeDimensionalRegion ! three_dimensional_region union_of: snap:TwoDimensionalRegion ! two_dimensional_region union_of: snap:ZeroDimensionalRegion ! zero_dimensional_region disjoint_from: snap:DependentContinuant ! dependent_continuant disjoint_from: snap:IndependentContinuant ! independent_continuant property_value: has_example "parts of the sum total of all space in the universe" xsd:string property_value: has_example "the sum total of all space in the universe" xsd:string created_by: He Zhang creation_date: 2013-09-27T11:55:25Z [Term] id: snap:SpecificallyDependentContinuant name: specifically_dependent_continuant namespace: def: "A continuant [snap:Continuant] that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] comment: Definition: A continuant [snap:Continuant] that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. synonym: "mode" RELATED [] synonym: "property" RELATED [] synonym: "trope" RELATED [] is_a: snap:DependentContinuant ! dependent_continuant union_of: snap:Quality ! quality union_of: snap:RealizableEntity ! realizable_entity disjoint_from: snap:GenericallyDependentContinuant ! generically_dependent_continuant property_value: has_example "etc." xsd:string property_value: has_example "the color of a tomato" xsd:string property_value: has_example "the disposition of fish to decay" xsd:string property_value: has_example "the function of the heart in the body: to pump blood" xsd:string property_value: has_example "the liquidity of blood" xsd:string property_value: has_example "the mass of a cloud" xsd:string property_value: has_example "the role of being a doctor" xsd:string property_value: has_example "the smell of mozzarella" xsd:string property_value: has_example "to receive de-oxygenated and oxygenated blood" xsd:string created_by: He Zhang creation_date: 2013-09-27T11:56:41Z [Term] id: snap:ThreeDimensionalRegion name: three_dimensional_region namespace: def: "A spatial region [snap:SpatialRegion] with three dimensions." [] comment: Definition: A spatial region [snap:SpatialRegion] with three dimensions. is_a: snap:SpatialRegion ! spatial_region disjoint_from: snap:OneDimensionalRegion ! one_dimensional_region disjoint_from: snap:TwoDimensionalRegion ! two_dimensional_region disjoint_from: snap:ZeroDimensionalRegion ! zero_dimensional_region property_value: has_example "a cube-shaped part of space" xsd:string property_value: has_example "a sphere-shaped part of space" xsd:string created_by: He Zhang creation_date: 2013-09-27T11:59:24Z [Term] id: snap:TwoDimensionalRegion name: two_dimensional_region namespace: def: "A spatial region [snap:SpatialRegion] with two dimensions." [] comment: Definition: A spatial region [snap:SpatialRegion] with two dimensions. is_a: snap:SpatialRegion ! spatial_region disjoint_from: snap:OneDimensionalRegion ! one_dimensional_region disjoint_from: snap:ThreeDimensionalRegion ! three_dimensional_region disjoint_from: snap:ZeroDimensionalRegion ! zero_dimensional_region property_value: has_example "the surface of a cube-shaped part of space" xsd:string property_value: has_example "the surface of a rectilinear planar figure-shaped part of space" xsd:string property_value: has_example "the surface of a sphere-shaped part of space" xsd:string created_by: He Zhang creation_date: 2013-09-27T11:59:24Z [Term] id: snap:ZeroDimensionalRegion name: zero_dimensional_region namespace: def: "A spatial region [snap:SpatialRegion] with no dimensions." [] comment: Definition: A spatial region [snap:SpatialRegion] with no dimensions. is_a: snap:SpatialRegion ! spatial_region disjoint_from: snap:OneDimensionalRegion ! one_dimensional_region disjoint_from: snap:ThreeDimensionalRegion ! three_dimensional_region disjoint_from: snap:TwoDimensionalRegion ! two_dimensional_region property_value: has_example "a point" xsd:string created_by: He Zhang creation_date: 2013-09-27T11:59:24Z [Term] id: SO:0000001 name: region namespace: sequence def: "A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke] synonym: "sequence" EXACT [] is_a: SO:0000110 ! sequence_feature created_by: He Zhang creation_date: 2013-10-14T14:54:03Z [Term] id: SO:0000002 name: sequence_secondary_structure namespace: sequence def: "A folded sequence." [SO:ke] synonym: "sequence secondary structure" EXACT [] is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000018 name: linkage_group namespace: sequence def: "A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned." [ISBN:038752046] synonym: "linkage group" EXACT [] xref: http://en.wikipedia.org/wiki/Linkage_group "wiki" is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000087 name: nuclear_gene namespace: sequence def: "A gene from nuclear sequence." [SO:xp] synonym: "nuclear gene" EXACT [] xref: http://en.wikipedia.org/wiki/Nuclear_gene "wiki" is_a: SO:0000704 ! gene [Term] id: SO:0000088 name: mt_gene namespace: sequence def: "A gene located in mitochondrial sequence." [SO:xp] synonym: "mitochondrial gene" EXACT [] synonym: "mt gene" EXACT [] xref: http://en.wikipedia.org/wiki/Mitochondrial_gene "wiki" is_a: SO:0000704 ! gene [Term] id: SO:0000089 name: kinetoplast_gene namespace: sequence def: "A gene located in kinetoplast sequence." [SO:xp] synonym: "kinetoplast gene" EXACT [] is_a: SO:0000088 ! mt_gene [Term] id: SO:0000090 name: plastid_gene namespace: sequence def: "A gene from plastid sequence." [SO:xp] synonym: "plastid gene" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0000091 name: apicoplast_gene namespace: sequence def: "A gene from apicoplast sequence." [SO:xp] synonym: "apicoplast gene" EXACT [] is_a: SO:0000090 ! plastid_gene [Term] id: SO:0000092 name: ct_gene namespace: sequence def: "A gene from chloroplast sequence." [SO:xp] synonym: "chloroplast gene" EXACT [] synonym: "ct gene" EXACT [] is_a: SO:0000090 ! plastid_gene [Term] id: SO:0000093 name: chromoplast_gene namespace: sequence def: "A gene from chromoplast_sequence." [SO:xp] synonym: "chromoplast gene" EXACT [] is_a: SO:0000090 ! plastid_gene [Term] id: SO:0000094 name: cyanelle_gene namespace: sequence def: "A gene from cyanelle sequence." [SO:xp] synonym: "cyanelle gene" EXACT [] is_a: SO:0000090 ! plastid_gene [Term] id: SO:0000095 name: leucoplast_gene namespace: sequence def: "A plastid gene from leucoplast sequence." [SO:xp] synonym: "leucoplast gene" EXACT [] is_a: SO:0000090 ! plastid_gene [Term] id: SO:0000096 name: proplastid_gene namespace: sequence def: "A gene from proplastid sequence." [SO:ke] synonym: "proplastid gene" EXACT [] is_a: SO:0000090 ! plastid_gene [Term] id: SO:0000097 name: nucleomorph_gene namespace: sequence def: "A gene from nucleomorph sequence." [SO:xp] synonym: "nucleomorph gene" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0000098 name: plasmid_gene namespace: sequence def: "A gene from plasmid sequence." [SO:xp] synonym: "plasmid gene" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0000099 name: proviral_gene namespace: sequence def: "A gene from proviral sequence." [SO:xp] synonym: "proviral gene" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0000100 name: endogenous_retroviral_gene namespace: sequence def: "A proviral gene with origin endogenous retrovirus." [SO:xp] synonym: "endogenous retroviral gene" EXACT [] is_a: SO:0000099 ! proviral_gene [Term] id: SO:0000104 name: polypeptide namespace: sequence def: "A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma] comment: "This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequence_attribute and therefore meant to describe the quality rather than an actual feature, it was being used erroneously. It is replaced by 'peptidyl' as the polymer attribute." synonym: "protein" EXACT [] xref: http://en.wikipedia.org/wiki/Polypeptide "wiki" is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000108 name: mRNA_with_frameshift namespace: sequence def: "An mRNA with a frameshift." [SO:xp] synonym: "frameshifted mRNA" EXACT [] synonym: "mRNA with frameshift" EXACT [] is_a: SO:0000234 ! mRNA [Term] id: SO:0000110 name: sequence_feature namespace: sequence def: "An extent of biological sequence." [SO:ke] synonym: "located sequence feature" RELATED [] synonym: "located_sequence_feature" EXACT [] synonym: "sequence feature" EXACT [] is_a: snap:Object ! object creation_date: 2013-10-14T14:42:37Z [Term] id: SO:0000111 name: transposable_element_gene namespace: sequence def: "A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast." [SO:ke] synonym: "transposable element gene" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0000127 name: silenced_gene namespace: sequence def: "A gene that is silenced." [SO:xp] synonym: "silenced gene" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0000128 name: gene_silenced_by_DNA_modification namespace: sequence def: "A gene that is silenced by DNA modification." [SO:xp] synonym: "gene silenced by DNA modification" EXACT [] is_a: SO:0000127 ! silenced_gene [Term] id: SO:0000129 name: gene_silenced_by_DNA_methylation namespace: sequence def: "A gene that is silenced by DNA methylation." [SO:xp] synonym: "gene silenced by DNA methylation" EXACT [] synonym: "methylation-silenced gene" EXACT [] is_a: SO:0000128 ! gene_silenced_by_DNA_modification [Term] id: SO:0000138 name: gene_rearranged_at_DNA_level namespace: sequence def: "An epigenetically modified gene, rearranged at the DNA level." [SO:xp] synonym: "gene rearranged at DNA level" EXACT [] is_a: SO:0000898 ! epigenetically_modified_gene [Term] id: SO:0000159 name: deletion namespace: sequence def: "The point at which one or more contiguous nucleotides were excised." [SO:ke] synonym: "deleted_sequence" EXACT [] synonym: "nucleotide deletion" EXACT [] synonym: "nucleotide_deletion" EXACT [] xref: http://en.wikipedia.org/wiki/Nucleotide_deletion "wiki" xref: loinc:LA6692-3 "Deletion" is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000167 name: promoter namespace: sequence def: "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription. subset: SOFA synonym: "promoter sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Promoter "wiki" is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0000169 name: RNApol_I_promoter namespace: sequence def: "A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke] synonym: "pol I promoter" EXACT [] synonym: "polymerase I promoter" EXACT [] synonym: "RNA polymerase A promoter" EXACT [] synonym: "RNApol I promoter" EXACT [] is_a: SO:0001203 ! RNA_polymerase_promoter [Term] id: SO:0000170 name: RNApol_II_promoter namespace: sequence def: "A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke] synonym: "pol II promoter" RELATED [] synonym: "polymerase II promoter" EXACT [] synonym: "RNA polymerase B promoter" EXACT [] synonym: "RNApol II promoter" EXACT [] is_a: SO:0001203 ! RNA_polymerase_promoter [Term] id: SO:0000171 name: RNApol_III_promoter namespace: sequence def: "A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke] synonym: "pol III promoter" EXACT [] synonym: "polymerase III promoter" EXACT [] synonym: "RNA polymerase C promoter" EXACT [] synonym: "RNApol III promoter" EXACT [] is_a: SO:0001203 ! RNA_polymerase_promoter [Term] id: SO:0000185 name: primary_transcript namespace: sequence def: "A transcript that in its initial state requires modification to be functional." [SO:ma] subset: SOFA synonym: "precursor RNA" EXACT [] synonym: "primary transcript" EXACT [] xref: http://en.wikipedia.org/wiki/Primary_transcript "wiki" is_a: SO:0000673 ! transcript [Term] id: SO:0000233 name: mature_transcript namespace: sequence def: "A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke] comment: A processed transcript cannot contain introns. subset: SOFA synonym: "mature transcript" EXACT [] xref: http://en.wikipedia.org/wiki/Mature_transcript "wiki" is_a: SO:0000673 ! transcript relationship: derives_from SO:0000185 ! primary_transcript [Term] id: SO:0000234 name: mRNA namespace: sequence def: "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma] comment: An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "messenger RNA" EXACT [] xref: http://en.wikipedia.org/wiki/MRNA "wiki" is_a: SO:0000233 ! mature_transcript [Term] id: SO:0000276 name: miRNA namespace: sequence def: "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [PMID:12592000] subset: SOFA synonym: "micro RNA" EXACT [] synonym: "microRNA" EXACT [] xref: http://en.wikipedia.org/wiki/MiRNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA relationship: derives_from SO:0000647 ! miRNA_primary_transcript relationship: OMIT:downRegulateEvent span:ProcessualEntity ! processual_entity relationship: OMIT:downRegulateTarget SO:0000704 ! gene relationship: OMIT:hasBinding OMIT:0000115 ! MiRNABinding relationship: OMIT:inOrganism OMIT:0000052 ! Organism relationship: OMIT:miRNAExpressedln span:Process ! process relationship: OMIT:regulateEvent span:ProcessualEntity ! processual_entity relationship: OMIT:regulatemRNATranslation SO:0000234 ! mRNA relationship: OMIT:regulatencRNAFunction SO:0000655 ! ncRNA relationship: OMIT:regulateTarget SO:0000704 ! gene relationship: OMIT:upRegulateEvent span:ProcessualEntity ! processual_entity relationship: OMIT:upRegulateTarget SO:0000704 ! gene [Term] id: SO:0000280 name: engineered_gene namespace: sequence def: "A gene that is engineered." [SO:xp] synonym: "engineered gene" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0000281 name: engineered_foreign_gene namespace: sequence def: "A gene that is engineered and foreign." [SO:xp] synonym: "engineered foreign gene" EXACT [] is_a: SO:0000280 ! engineered_gene is_a: SO:0000285 ! foreign_gene creation_date: 2013-10-11T08:35:27Z [Term] id: SO:0000282 name: mRNA_with_minus_1_frameshift namespace: sequence def: "An mRNA with a minus 1 frameshift." [SO:xp] synonym: "mRNA with minus 1 frameshift" EXACT [] is_a: SO:0000108 ! mRNA_with_frameshift [Term] id: SO:0000283 name: engineered_foreign_transposable_element_gene namespace: sequence def: "A transposable_element that is engineered and foreign." [SO:xp] synonym: "engineered foreign transposable element gene" EXACT [] is_a: SO:0000111 ! transposable_element_gene is_a: SO:0000281 ! engineered_foreign_gene [Term] id: SO:0000285 name: foreign_gene namespace: sequence def: "A gene that is foreign." [SO:xp] synonym: "foreign gene" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0000287 name: fusion_gene namespace: sequence def: "A gene that is a fusion." [SO:xp] synonym: "fusion gene" EXACT [] xref: http://en.wikipedia.org/wiki/Fusion_gene "wiki" is_a: SO:0000704 ! gene [Term] id: SO:0000288 name: engineered_fusion_gene namespace: sequence def: "A fusion gene that is engineered." [SO:xp] synonym: "engineered fusion gene" EXACT [] is_a: SO:0000280 ! engineered_gene is_a: SO:0000287 ! fusion_gene [Term] id: SO:0000296 name: origin_of_replication namespace: sequence def: "The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] synonym: "ori" EXACT [] synonym: "origin of replication" EXACT [] xref: http://en.wikipedia.org/wiki/Origin_of_replication "wiki" is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000298 name: recombination_feature namespace: sequence synonym: "recombination feature" EXACT [] is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000307 name: CpG_island namespace: sequence def: "Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes." [SO:rd] synonym: "CG island" EXACT [] synonym: "CpG island" EXACT [] xref: http://en.wikipedia.org/wiki/CpG_island "wiki" is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000321 name: mRNA_with_plus_1_frameshift namespace: sequence def: "An mRNA with a plus 1 frameshift." [SO:ke] synonym: "mRNA with plus 1 frameshift" EXACT [] is_a: SO:0000108 ! mRNA_with_frameshift [Term] id: SO:0000329 name: mRNA_with_plus_2_frameshift namespace: sequence def: "An mRNA with a plus 2 frameshift." [SO:xp] synonym: "mRNA with plus 2 frameshift" EXACT [] is_a: SO:0000108 ! mRNA_with_frameshift [Term] id: SO:0000335 name: mRNA_with_minus_2_frameshift namespace: sequence def: "A mRNA with a minus 2 frameshift." [SO:ke] synonym: "mRNA with minus 2 frameshift" EXACT [] is_a: SO:0000108 ! mRNA_with_frameshift [Term] id: SO:0000336 name: pseudogene namespace: sequence def: "A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \"normal\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \"normal\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html] xref: http://en.wikipedia.org/wiki/Pseudogene "wiki" is_a: SO:0001411 ! biological_region relationship: non_functional_homolog_of SO:0000704 ! gene created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000363 name: floxed_gene namespace: sequence def: "A transgene that is floxed." [SO:xp] synonym: "floxed gene" EXACT [] is_a: SO:0000902 ! transgene [Term] id: SO:0000370 name: small_regulatory_ncRNA namespace: sequence def: "A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma] subset: SOFA synonym: "small regulatory ncRNA" EXACT [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000373 name: recombinationally_inverted_gene namespace: sequence def: "A recombinationally rearranged gene by inversion." [SO:xp] synonym: "recombinationally inverted gene" EXACT [] is_a: SO:0000456 ! recombinationally_rearranged_gene [Term] id: SO:0000376 name: RNA_6S namespace: sequence def: "A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013] synonym: "6S RNA" EXACT [] synonym: "RNA 6S" EXACT [] xref: http://en.wikipedia.org/wiki/6S_RNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000377 name: CsrB_RsmB_RNA namespace: sequence def: "An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018] synonym: "CsrB RsmB RNA" EXACT [] synonym: "CsrB-RsmB RNA" EXACT [] is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000378 name: DsrA_RNA namespace: sequence def: "DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014] synonym: "DsrA RNA" EXACT [] xref: http://en.wikipedia.org/wiki/DsrA_RNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000384 name: OxyS_RNA namespace: sequence def: "A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035] synonym: "OxyS RNA" EXACT [] xref: http://en.wikipedia.org/wiki/OxyS_RNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000387 name: RprA_RNA namespace: sequence def: "Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034] synonym: "RprA RNA" EXACT [] xref: http://en.wikipedia.org/wiki/RprA_RNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000388 name: RRE_RNA namespace: sequence def: "The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036] synonym: "RRE RNA" EXACT [] is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000389 name: spot_42_RNA namespace: sequence def: "A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021] synonym: "spot-42 RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Spot_42_RNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000409 name: binding_site namespace: sequence def: "A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke] comment: See GO:0005488 : binding. synonym: "binding_or_interaction_site" EXACT [] synonym: "site" RELATED [] xref: http://en.wikipedia.org/wiki/Binding_site "wiki" is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000418 name: signal_peptide namespace: SO comment: The signal peptide can be cleaved either co- or post-translationally. For this reason, we do not use the derives_from relation when defining protein forms lacking the signal peptide (because the precursor form might not yet exist at the time of removal). synonym: "signal" RELATED [uniprot:feature_type] synonym: "signal peptide" EXACT [] is_a: PR:000021935 ! immature protein part [Term] id: SO:0000451 name: gene_with_polyadenylated_mRNA namespace: sequence def: "A gene that encodes a polyadenylated mRNA." [SO:xp] synonym: "gene with polyadenylated mRNA" EXACT [] is_a: SO:0001217 ! protein_coding_gene [Term] id: SO:0000455 name: gene_with_mRNA_with_frameshift namespace: sequence def: "A gene that encodes an mRNA with a frameshift." [SO:xp] synonym: "gene with mRNA with frameshift" EXACT [] is_a: SO:0001217 ! protein_coding_gene [Term] id: SO:0000456 name: recombinationally_rearranged_gene namespace: sequence def: "A gene that is recombinationally rearranged." [SO:ke] synonym: "recombinationally rearranged gene" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0000459 name: gene_with_trans_spliced_transcript namespace: sequence def: "A gene with a transcript that is trans-spliced." [SO:xp] synonym: "gene with trans spliced transcript" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0000462 name: pseudogenic_region namespace: sequence def: "A non-functional descendent of a functional entity." [SO:cjm] synonym: "pseudogenic region" EXACT [] is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000483 name: nc_primary_transcript namespace: sequence def: "A primary transcript that is never translated into a protein." [SO:ke] subset: SOFA synonym: "nc primary transcript" EXACT [] synonym: "noncoding primary transcript" EXACT [] is_a: SO:0000185 ! primary_transcript [Term] id: SO:0000548 name: gene_with_edited_transcript namespace: sequence def: "A gene that encodes a transcript that is edited." [SO:xp] synonym: "gene with edited transcript" EXACT [] is_a: SO:0001217 ! protein_coding_gene [Term] id: SO:0000568 name: bidirectional_promoter namespace: sequence synonym: "bidirectional promoter" EXACT [] is_a: SO:0000167 ! promoter [Term] id: SO:0000581 name: cap namespace: sequence def: "A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html] xref: http://en.wikipedia.org/wiki/5%27_cap "wiki" is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000584 name: tmRNA namespace: sequence def: "A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023] synonym: "10Sa RNA" RELATED [] synonym: "ssrA" RELATED [] xref: http://en.wikipedia.org/wiki/TmRNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000605 name: intergenic_region namespace: sequence def: "A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome." [SO:cjm] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "intergenic region" EXACT [] xref: http://en.wikipedia.org/wiki/Intergenic_region "wiki" is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000609 name: oligo_U_tail namespace: sequence def: "The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602)." [http://www.rna.ucla.edu/] synonym: "oligo U tail" EXACT [] is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000610 name: polyA_sequence namespace: sequence def: "Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke] synonym: "polyA sequence" EXACT [] is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000613 name: bacterial_RNApol_promoter namespace: sequence def: "A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke] synonym: "bacterial RNApol promoter" EXACT [] is_a: SO:0001203 ! RNA_polymerase_promoter [Term] id: SO:0000617 name: RNApol_III_promoter_type_1 namespace: sequence synonym: "RNApol III promoter type 1" EXACT [] is_a: SO:0000171 ! RNApol_III_promoter [Term] id: SO:0000618 name: RNApol_III_promoter_type_2 namespace: sequence synonym: "RNApol III promoter type 2" EXACT [] synonym: "tRNA promoter" RELATED [] is_a: SO:0000171 ! RNApol_III_promoter [Term] id: SO:0000621 name: RNApol_III_promoter_type_3 namespace: sequence synonym: "RNApol III promoter type 3" EXACT [] is_a: SO:0000171 ! RNApol_III_promoter [Term] id: SO:0000627 name: insulator namespace: sequence def: "A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression." [SO:regcreative] subset: SOFA synonym: "insulator element" EXACT [] xref: http://en.wikipedia.org/wiki/Insulator_(genetics) "wiki" is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0000633 name: monocistronic_mRNA namespace: sequence def: "An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd] synonym: "monocistronic mRNA" EXACT [] synonym: "monocistronic processed transcript" EXACT [] xref: http://en.wikipedia.org/wiki/Monocistronic_mRNA "wiki" is_a: SO:0000234 ! mRNA [Term] id: SO:0000634 name: polycistronic_mRNA namespace: sequence def: "An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd] synonym: "polycistronic mRNA" EXACT [] synonym: "polycistronic processed transcript" RELATED [] xref: http://en.wikipedia.org/wiki/Polycistronic_mRNA "wiki" is_a: SO:0000234 ! mRNA [Term] id: SO:0000647 name: miRNA_primary_transcript namespace: sequence def: "A primary transcript encoding a micro RNA." [SO:ke] synonym: "micro RNA primary transcript" EXACT [] synonym: "miRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000654 name: maxicircle_gene namespace: sequence def: "A mitochondrial gene located in a maxicircle." [SO:xp] synonym: "maxi-circle gene" EXACT [] synonym: "maxicircle gene" EXACT [] is_a: SO:0000089 ! kinetoplast_gene [Term] id: SO:0000655 name: ncRNA namespace: sequence def: "An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke] comment: A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript. subset: SOFA synonym: "noncoding RNA" EXACT [] xref: http://en.wikipedia.org/wiki/NcRNA "wiki" is_a: SO:0000233 ! mature_transcript [Term] id: SO:0000657 name: repeat_region namespace: sequence def: "A region of sequence containing one or more repeat units." [SO:ke] synonym: "repeat region" EXACT [] is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000667 name: insertion namespace: sequence def: "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke] synonym: "insertion" EXACT [http://www.ncbi.nlm.nih.gov/dbvar/] synonym: "nucleotide insertion" EXACT [] synonym: "nucleotide_insertion" EXACT [] xref: loinc:LA6687-3 "Insertion" is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000673 name: transcript namespace: sequence def: "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma] subset: SOFA xref: http://en.wikipedia.org/wiki/RNA "wiki" is_a: SO:0000831 ! gene_member_region [Term] id: SO:0000690 name: gene_with_polycistronic_transcript namespace: sequence def: "A gene that encodes a polycistronic transcript." [SO:xp] synonym: "gene with polycistronic transcript" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0000692 name: gene_with_dicistronic_transcript namespace: sequence def: "A gene that encodes a dicistronic transcript." [SO:xp] synonym: "gene with dicistronic transcript" EXACT [] is_a: SO:0000690 ! gene_with_polycistronic_transcript [Term] id: SO:0000693 name: gene_with_recoded_mRNA namespace: sequence def: "A gene that encodes an mRNA that is recoded." [SO:xp] synonym: "gene with recoded mRNA" EXACT [] is_a: SO:0001217 ! protein_coding_gene [Term] id: SO:0000697 name: gene_with_stop_codon_read_through namespace: sequence def: "A gene that encodes a transcript with stop codon readthrough." [SO:xp] synonym: "gene with stop codon read through" EXACT [] is_a: SO:0000693 ! gene_with_recoded_mRNA [Term] id: SO:0000698 name: gene_with_stop_codon_redefined_as_pyrrolysine namespace: sequence def: "A gene encoding an mRNA that has the stop codon redefined as pyrrolysine." [SO:xp] synonym: "gene with stop codon redefined as pyrrolysine" EXACT [] is_a: SO:0000697 ! gene_with_stop_codon_read_through [Term] id: SO:0000704 name: gene namespace: sequence def: "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop] comment: "This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance." xref: http://en.wikipedia.org/wiki/Gene "wiki" is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-09-28T19:09:24Z [Term] id: SO:0000710 name: gene_with_stop_codon_redefined_as_selenocysteine namespace: sequence def: "A gene encoding an mRNA that has the stop codon redefined as selenocysteine." [SO:xp] synonym: "gene with stop codon redefined as selenocysteine" EXACT [] is_a: SO:0000697 ! gene_with_stop_codon_read_through [Term] id: SO:0000711 name: gene_with_mRNA_recoded_by_translational_bypass namespace: sequence def: "A gene with mRNA recoded by translational bypass." [SO:xp] synonym: "gene with mRNA recoded by translational bypass" EXACT [] is_a: SO:0000693 ! gene_with_recoded_mRNA [Term] id: SO:0000712 name: gene_with_transcript_with_translational_frameshift namespace: sequence def: "A gene encoding a transcript that has a translational frameshift." [SO:xp] synonym: "gene with transcript with translational frameshift" EXACT [] is_a: SO:0000693 ! gene_with_recoded_mRNA [Term] id: SO:0000716 name: dicistronic_mRNA namespace: sequence def: "An mRNA that has the quality dicistronic." [SO:ke] synonym: "dicistronic mRNA" EXACT [] synonym: "dicistronic processed transcript" RELATED [] is_a: SO:0000634 ! polycistronic_mRNA [Term] id: SO:0000721 name: gene_with_dicistronic_primary_transcript namespace: sequence def: "A gene that encodes a dicistronic primary transcript." [SO:xp] comment: Requested by Michael, 19 nov 2004. synonym: "gene with dicistronic primary transcript" EXACT [] is_a: SO:0000692 ! gene_with_dicistronic_transcript [Term] id: SO:0000722 name: gene_with_dicistronic_mRNA namespace: sequence def: "A gene that encodes a polycistronic mRNA." [SO:xp] comment: Requested by MA nov 19 2004. synonym: "gene with dicistronic mRNA" EXACT [] synonym: "gene with dicistronic processed transcript" EXACT [] is_a: SO:0000692 ! gene_with_dicistronic_transcript [Term] id: SO:0000725 name: transit_peptide namespace: SO synonym: "transit" RELATED [uniprot:feature_type] synonym: "transit peptide" EXACT [] is_a: PR:000021935 ! immature protein part [Term] id: SO:0000726 name: repeat_unit namespace: sequence def: "The simplest repeated component of a repeat region. A single repeat." [SO:ke] comment: Added to comply with the feature table. A single repeat. synonym: "repeat unit" EXACT [] xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000727 name: CRM namespace: sequence def: "A regulatory_region where more than 1 TF_binding_site together are regulatorily active." [SO:SG] comment: Requested by Stepen Grossmann Dec 2004. subset: SOFA synonym: "cis regulatory module" EXACT [] synonym: "TF module" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0000734 name: exemplar_mRNA namespace: sequence def: "An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group." [http://mged.sourceforge.net/ontologies/MGEDontology.php] comment: Added for the MO people. synonym: "exemplar mRNA" EXACT [] is_a: SO:0000234 ! mRNA [Term] id: SO:0000771 name: QTL namespace: sequence def: "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." [http://rgd.mcw.edu/tu/qtls/] comment: Added in respose to request by Simon Twigger November 14th 2005. synonym: "quantitative trait locus" EXACT [] is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000816 name: rescue_gene namespace: sequence def: "A gene that rescues." [SO:xp] synonym: "rescue gene" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0000818 name: wild_type_rescue_gene namespace: sequence def: "A gene that rescues." [SO:xp] synonym: "wild type rescue gene" EXACT [] is_a: SO:0000816 ! rescue_gene [Term] id: SO:0000830 name: chromosome_part namespace: sequence def: "A region of a chromosome." [SO:ke] comment: This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root. synonym: "chromosome part" EXACT [] is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000831 name: gene_member_region namespace: sequence def: "A region of a gene." [SO:ke] comment: A manufactured term used to allow the parts of a gene to have an is_a path to the root. synonym: "gene member region" EXACT [] is_a: SO:0001411 ! biological_region relationship: member_of SO:0000704 ! gene created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000833 name: transcript_region namespace: sequence def: "A region of a transcript." [SO:ke] comment: This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root. synonym: "transcript region" EXACT [] is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000839 name: polypeptide_region namespace: sequence alt_id: BS:00124 alt_id: BS:00331 def: "Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke] comment: "Added to allow the polypeptide regions to have is_a paths back to the root." synonym: "positional" RELATED [] synonym: "positional polypeptide feature" RELATED [uniprot:feature_type] synonym: "region" NARROW [] synonym: "region or site annotation" RELATED [] synonym: "site" NARROW [uniprot:feature_type] is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000842 name: gene_component_region namespace: sequence synonym: "gene component region" EXACT [] is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0000862 name: capped_mRNA namespace: sequence def: "An mRNA that is capped." [SO:xp] synonym: "capped mRNA" EXACT [] is_a: SO:0000234 ! mRNA [Term] id: SO:0000871 name: polyadenylated_mRNA namespace: sequence def: "An mRNA that is polyadenylated." [SO:xp] synonym: "polyadenylated mRNA" EXACT [] is_a: SO:0000234 ! mRNA [Term] id: SO:0000872 name: trans_spliced_mRNA namespace: sequence def: "An mRNA that is trans-spliced." [SO:xp] synonym: "trans-spliced mRNA" EXACT [] is_a: SO:0000234 ! mRNA [Term] id: SO:0000888 name: maternally_imprinted_gene namespace: sequence def: "A gene that is maternally_imprinted." [SO:xp] synonym: "maternally imprinted gene" EXACT [] is_a: SO:0000898 ! epigenetically_modified_gene [Term] id: SO:0000889 name: paternally_imprinted_gene namespace: sequence def: "A gene that is paternally imprinted." [SO:xp] synonym: "paternally imprinted gene" EXACT [] is_a: SO:0000898 ! epigenetically_modified_gene [Term] id: SO:0000890 name: post_translationally_regulated_gene namespace: sequence def: "A gene that is post translationally regulated." [SO:xp] synonym: "post translationally regulated gene" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0000891 name: negatively_autoregulated_gene namespace: sequence def: "A gene that is negatively autoreguated." [SO:xp] synonym: "negatively autoregulated gene" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0000892 name: positively_autoregulated_gene namespace: sequence def: "A gene that is positively autoregulated." [SO:xp] synonym: "positively autoregulated gene" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0000896 name: translationally_regulated_gene namespace: sequence def: "A gene that is translationally regulated." [SO:xp] synonym: "translationally regulated gene" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0000897 name: allelically_excluded_gene namespace: sequence def: "A gene that is allelically_excluded." [SO:xp] synonym: "allelically excluded gene" EXACT [] is_a: SO:0000898 ! epigenetically_modified_gene [Term] id: SO:0000898 name: epigenetically_modified_gene namespace: sequence def: "A gene that is epigenetically modified." [SO:ke] synonym: "epigenetically modified gene" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0000902 name: transgene namespace: sequence def: "A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another." [SO:xp] xref: http://en.wikipedia.org/wiki/Transgene "wiki" is_a: SO:0000704 ! gene [Term] id: SO:0000929 name: edited_mRNA namespace: sequence def: "An mRNA that is edited." [SO:xp] synonym: "edited mRNA" EXACT [] is_a: SO:0000234 ! mRNA [Term] id: SO:0000941 name: recombinationally_rearranged_vertebrate_immune_system_gene namespace: sequence def: "A recombinationally rearranged gene of the vertebrate immune system." [SO:xp] synonym: "recombinationally rearranged vertebrate immune system gene" EXACT [] is_a: SO:0000456 ! recombinationally_rearranged_gene [Term] id: SO:0000975 name: minicircle_gene namespace: sequence synonym: "minicircle gene" EXACT [] is_a: SO:0000089 ! kinetoplast_gene [Term] id: SO:0000995 name: consensus_mRNA namespace: sequence comment: DO not obsolete without considering MGED mapping. synonym: "consensus mRNA" EXACT [] is_a: SO:0000234 ! mRNA [Term] id: SO:0000996 name: predicted_gene namespace: sequence comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "predicted gene" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0001037 name: mobile_genetic_element namespace: sequence def: "A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMOMIT:14681355] synonym: "MGE" EXACT [] synonym: "mobile genetic element" EXACT [] xref: http://en.wikipedia.org/wiki/Mobile_genetic_element "wiki" is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0001055 name: transcriptional_cis_regulatory_region namespace: sequence def: "A regulatory_region that modulates the transcription of a gene or genes." [SO:regcreative] subset: SOFA synonym: "transcriptional cis regulatory region" EXACT [] is_a: SO:0001679 ! transcription_regulatory_region [Term] id: SO:0001058 name: promoter_targeting_sequence namespace: sequence def: "A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter." [SO:regcreative] synonym: "promoter targeting sequence" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0001062 name: propeptide namespace: SO is_a: PR:000021935 ! immature protein part [Term] id: SO:0001203 name: RNA_polymerase_promoter namespace: sequence def: "A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb] synonym: "RNA polymerase promoter" EXACT [] is_a: SO:0000167 ! promoter [Term] id: SO:0001204 name: Phage_RNA_Polymerase_Promoter namespace: sequence def: "A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb] synonym: "Phage RNA Polymerase Promoter" EXACT [] is_a: SO:0001203 ! RNA_polymerase_promoter [Term] id: SO:0001205 name: SP6_RNA_Polymerase_Promoter namespace: sequence def: "A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb] synonym: "SP6 RNA Polymerase Promoter" EXACT [] is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter [Term] id: SO:0001206 name: T3_RNA_Polymerase_Promoter namespace: sequence def: "A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb] synonym: "T3 RNA Polymerase Promoter" EXACT [] is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter [Term] id: SO:0001207 name: T7_RNA_Polymerase_Promoter namespace: sequence def: "A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb] synonym: "T7 RNA Polymerase Promoter" EXACT [] is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter [Term] id: SO:0001217 name: protein_coding_gene namespace: sequence synonym: "protein coding gene" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0001219 name: retrogene namespace: sequence is_a: SO:0000704 ! gene [Term] id: SO:0001224 name: gene_silenced_by_RNA_interference namespace: sequence def: "A gene that is silenced by RNA interference." [SO:xp] synonym: "gene silenced by RNA interference" EXACT [] synonym: "RNA interference silenced gene" EXACT [] synonym: "RNAi silenced gene" EXACT [] is_a: SO:0000127 ! silenced_gene [Term] id: SO:0001225 name: gene_silenced_by_histone_modification namespace: sequence def: "A gene that is silenced by histone modification." [SO:xp] synonym: "gene silenced by histone modification" EXACT [] is_a: SO:0000127 ! silenced_gene [Term] id: SO:0001226 name: gene_silenced_by_histone_methylation namespace: sequence def: "A gene that is silenced by histone methylation." [SO:xp] synonym: "gene silenced by histone methylation" EXACT [] is_a: SO:0001225 ! gene_silenced_by_histone_modification [Term] id: SO:0001227 name: gene_silenced_by_histone_deacetylation namespace: sequence def: "A gene that is silenced by histone deacetylation." [SO:xp] synonym: "gene silenced by histone deacetylation" EXACT [] is_a: SO:0001225 ! gene_silenced_by_histone_modification [Term] id: SO:0001235 name: replicon namespace: sequence def: "A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207] xref: http://en.wikipedia.org/wiki/Replicon_(genetics) "wiki" is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0001236 name: base namespace: sequence def: "A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke] xref: http://en.wikipedia.org/wiki/Nucleobase "wiki" is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0001237 name: amino_acid namespace: sequence def: "A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb] comment: Probably in the future this will cross reference to Chebi. synonym: "amino acid" EXACT [] xref: http://en.wikipedia.org/wiki/Amino_acid "wiki" is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0001263 name: ncRNA_gene namespace: sequence synonym: "ncRNA gen" EXACT [] synonym: "ncRNA gene" EXACT [] synonym: "non-coding RNA gene" RELATED [] is_a: SO:0000704 ! gene [Term] id: SO:0001264 name: gRNA_gene namespace: sequence synonym: "gRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene [Term] id: SO:0001265 name: miRNA_gene namespace: sequence synonym: "miRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene [Term] id: SO:0001266 name: scRNA_gene namespace: sequence synonym: "scRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene [Term] id: SO:0001267 name: snoRNA_gene namespace: sequence synonym: "snoRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene [Term] id: SO:0001268 name: snRNA_gene namespace: sequence synonym: "snRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene [Term] id: SO:0001269 name: SRP_RNA_gene namespace: sequence synonym: "SRP RNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene [Term] id: SO:0001270 name: stRNA_gene namespace: sequence synonym: "stRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene [Term] id: SO:0001271 name: tmRNA_gene namespace: sequence synonym: "tmRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene [Term] id: SO:0001272 name: tRNA_gene namespace: sequence synonym: "tRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene [Term] id: SO:0001411 name: biological_region namespace: sequence def: "A region defined by its disposition to be involved in a biological process." [SO:cb] synonym: "biological region" EXACT [] is_a: SO:0000001 ! region created_by: He Zhang creation_date: 2013-10-14T14:55:49Z [Term] id: SO:0001431 name: cryptic_gene namespace: sequence def: "A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning." [SO:ke] synonym: "cryptic gene" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0001637 name: rRNA_gene namespace: sequence def: "A gene that encodes for ribosomal RNA." [SO:ke] synonym: "rRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene created_by: kareneilbeck creation_date: 2010-04-21T10:10:32Z [Term] id: SO:0001638 name: piRNA_gene namespace: sequence def: "A gene that encodes for an piwi associated RNA." [SO:ke] synonym: "piRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene created_by: kareneilbeck creation_date: 2010-04-21T10:11:36Z [Term] id: SO:0001639 name: RNase_P_RNA_gene namespace: sequence def: "A gene that encodes an RNase P RNA." [SO:ke] synonym: "RNase P RNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene created_by: kareneilbeck creation_date: 2010-04-21T10:13:23Z [Term] id: SO:0001640 name: RNase_MRP_RNA_gene namespace: sequence def: "A gene that encodes a RNase_MRP_RNA." [SO:ke] synonym: "RNase MRP RNA gene" RELATED [] is_a: SO:0001263 ! ncRNA_gene created_by: kareneilbeck creation_date: 2010-04-21T10:13:58Z [Term] id: SO:0001641 name: lincRNA_gene namespace: sequence def: "A gene that encodes large intervening non-coding RNA." [SO:ke] synonym: "lincRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene created_by: kareneilbeck creation_date: 2010-04-21T10:14:24Z [Term] id: SO:0001643 name: telomerase_RNA_gene namespace: sequence def: "A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase." [SO:ke] synonym: "Telomerase RNA component" EXACT [] synonym: "telomerase RNA gene" EXACT [] synonym: "TERC" EXACT [] xref: http:http\://en.wikipedia.org/wiki/Telomerase_RNA_component "wikipedia" is_a: SO:0001263 ! ncRNA_gene created_by: kareneilbeck creation_date: 2010-05-18T05:26:38Z [Term] id: SO:0001645 name: genetic_marker namespace: sequence def: "A measurable sequence feature that varies within a population." [SO:db] synonym: "genetic marker" RELATED [] is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0001669 name: RNApol_II_core_promoter namespace: sequence def: "The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867] synonym: "RNApol II core promoter" EXACT [] is_a: SO:0000170 ! RNApol_II_promoter created_by: kareneilbeck creation_date: 2010-10-01T03:13:41Z [Term] id: SO:0001671 name: bacterial_RNApol_promoter_sigma_70 namespace: sequence synonym: "bacterial RNA polymerase promoter sigma 70" EXACT [] is_a: SO:0000613 ! bacterial_RNApol_promoter created_by: kareneilbeck creation_date: 2010-10-06T01:41:34Z [Term] id: SO:0001672 name: bacterial_RNApol_promoter_sigma54 namespace: sequence synonym: "bacterial RNA polymerase promoter sigma54" EXACT [] is_a: SO:0000613 ! bacterial_RNApol_promoter created_by: kareneilbeck creation_date: 2010-10-06T01:42:37Z [Term] id: SO:0001679 name: transcription_regulatory_region namespace: sequence def: "A regulatory region that is involved in the control of the process of transcription." [SO:ke] subset: SOFA synonym: "transcription regulatory region" EXACT [] is_a: SO:0005836 ! regulatory_region created_by: kareneilbeck creation_date: 2010-10-12T03:49:35Z [Term] id: SO:0001683 name: sequence_motif namespace: sequence def: "A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif] synonym: "sequence motif" RELATED [] xref: http://en.wikipedia.org/wiki/Sequence_motif "wikipedia" is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0001687 name: restriction_enzyme_recognition_site namespace: sequence def: "The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke] synonym: "restriction endonuclease recognition site" EXACT [] synonym: "restriction enzyme recognition site" EXACT [] is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0001695 name: restriction_enzyme_single_strand_overhang namespace: sequence def: "A terminal region of DNA sequence where the end of the region is not blunt ended." [SO:ke] synonym: "single strand overhang" EXACT [] synonym: "sticky end" RELATED [] is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0001715 name: ISRE namespace: sequence def: "An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding." [http://genesdev.cshlp.org/content/2/4/383.abstrac] comment: Term requested via tracker (2981725) by Alan Ruttenberg, April 2010. It has been described as both an enhancer and a promoter, so the parent is the more general term. synonym: "interferon stimulated response element" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region created_by: kareneilbeck creation_date: 2010-04-05T11:15:08Z [Term] id: SO:0001720 name: epigenetically_modified_region namespace: sequence def: "A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke] synonym: "epigenetically modified region" RELATED [] is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0001739 name: gene_with_non_canonical_start_codon namespace: sequence def: "A gene with a start codon other than AUG." [SO:xp] comment: Requested by flybase, Dec 2010. synonym: "gene with non canonical start codon" EXACT [] is_a: SO:0000704 ! gene created_by: kareneilbeck creation_date: 2011-01-10T01:30:31Z [Term] id: SO:0001740 name: gene_with_start_codon_CUG namespace: sequence def: "A gene with a translational start codon of CUG." [SO:mc] comment: Requested by flybase, Dec 2010. synonym: "gene with start codon CUG" EXACT [] is_a: SO:0001739 ! gene_with_non_canonical_start_codon created_by: kareneilbeck creation_date: 2011-01-10T01:32:35Z [Term] id: SO:0001747 name: open_chromatin_region namespace: sequence def: "A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA." [SO:cb] comment: Requested by John Calley 3125900. synonym: "open chromatin region" EXACT [] is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0001867 name: candidate_gene namespace: sequence def: "A gene suspected of being involved in the expression of a trait." [GMOD:ea] comment: Requested by Bayer Cropscience December, 2011. synonym: "candidate gene" EXACT [] synonym: "target gene" EXACT [] is_a: SO:0000704 ! gene created_by: kareneilbeck creation_date: 2012-01-17T02:53:03Z [Term] id: SO:0001868 name: positional_candidate_gene namespace: sequence def: "A candidate gene whose association with a trait is based on the gene's location on a chromosome." [GMOD:ea] comment: Requested by Bayer Cropscience December, 2011. synonym: "positional candidate gene" EXACT [] synonym: "positional target gene" RELATED [] is_a: SO:0001867 ! candidate_gene created_by: kareneilbeck creation_date: 2012-01-17T02:54:42Z [Term] id: SO:0001869 name: functional_candidate_gene namespace: sequence def: "A candidate gene whose function has something in common biologically with the trait under investigation." [GMOD:ea] comment: Requested by Bayer Cropscience December, 2011. synonym: "functional candidate gene" EXACT [] synonym: "functional target gene" EXACT [] is_a: SO:0001867 ! candidate_gene created_by: kareneilbeck creation_date: 2012-01-17T02:57:30Z [Term] id: SO:0001872 name: rearrangement_breakpoint namespace: sequence def: "A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome." [NCBI:th, PMOMIT:18564416] comment: NCBI definition: An orphan rearrangement between chromosomal location observed in isolation. synonym: "rearrangement breakpoint" EXACT [] is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:0001913 name: bacterial_RNApol_promoter_sigma_ecf namespace: sequence def: "A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." [Invitrogen:kc] comment: Requested by Kevin Clancy - invitrogen -May 2012. synonym: "bacterial RNApol promoter sigma ecf " EXACT [] is_a: SO:0000613 ! bacterial_RNApol_promoter created_by: kareneilbeck creation_date: 2012-06-11T02:41:33Z [Term] id: SO:0005836 name: regulatory_region namespace: sequence def: "A region of sequence that is involved in the control of a biological process." [SO:ke] subset: SOFA synonym: "regulatory region" EXACT [] xref: http://en.wikipedia.org/wiki/Regulatory_region "wiki" is_a: SO:0000831 ! gene_member_region [Term] id: SO:0005853 name: gene_cassette namespace: sequence def: "A gene that can be substituted for a related gene at a different site in the genome." [SGD:se] comment: This would include, for example, the mating type gene cassettes of S. cerevisiae. Gene cassettes usually exist as linear sequences as part of a larger DNA molecule, such as a chromosome or plasmid. synonym: "gene cassette" EXACT [] xref: http://en.wikipedia.org/wiki/Gene_cassette "wiki" is_a: SO:0000704 ! gene [Term] id: SO:0005855 name: gene_group namespace: sequence def: "A collection of related genes." [SO:ma] synonym: "gene group" EXACT [] is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:1000002 name: substitution namespace: sequence def: "A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke] xref: loinc:LA6690-7 "Substitution" is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:1000036 name: inversion namespace: sequence def: "A continuous nucleotide sequence is inverted in the same position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] synonym: "inversion" EXACT [http://www.ncbi.nlm.nih.gov/dbvar/] xref: loinc:LA6689-9 "Inversion" is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: SO:1001196 name: cryptogene namespace: sequence def: "A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma] is_a: SO:0000654 ! maxicircle_gene is_a: SO:0001431 ! cryptic_gene [Term] id: SO:1001261 name: recoded_mRNA namespace: sequence def: "The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract] synonym: "recoded mRNA" EXACT [] is_a: SO:0000234 ! mRNA [Term] id: SO:1001264 name: mRNA_recoded_by_translational_bypass namespace: sequence def: "A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract] synonym: "mRNA recoded by translational bypass" EXACT [] is_a: SO:1001261 ! recoded_mRNA [Term] id: SO:1001265 name: mRNA_recoded_by_codon_redefinition namespace: sequence def: "A recoded_mRNA that was modified by an alteration of codon meaning." [SO:ma] synonym: "mRNA recoded by codon redefinition" EXACT [] is_a: SO:1001261 ! recoded_mRNA [Term] id: SO:1001275 name: retron namespace: sequence def: "Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes." [SO:ma] is_a: SO:0001411 ! biological_region created_by: He Zhang creation_date: 2013-10-14T15:16:46Z [Term] id: span:ConnectedSpatiotemporalRegion name: connected_spatiotemporal_region namespace: def: "A spatiotemporal region [span:SpatiotemporalRegion] that has temporal and spatial dimensions such that all points within the spatiotemporal region are mediately or immediately connected to all other points within the same spatiotemporal region [span:SpatiotemporalRegion]." [] comment: Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has temporal and spatial dimensions such that all points within the spatiotemporal region are mediately or immediately connected to all other points within the same spatiotemporal region [span:SpatiotemporalRegion]. is_a: span:SpatiotemporalRegion ! spatiotemporal_region union_of: span:SpatiotemporalInstant ! spatiotemporal_instant union_of: span:SpatiotemporalInterval ! spatiotemporal_interval disjoint_from: span:ScatteredSpatiotemporalRegion ! scattered_spatiotemporal_region property_value: has_example "the spatial and temporal location of an individual organism's life" xsd:string property_value: has_example "the spatial and temporal location of the development of a fetus" xsd:string created_by: He Zhang creation_date: 2013-10-04T20:27:34Z [Term] id: span:ConnectedTemporalRegion name: connected_temporal_region namespace: def: "A temporal region [span:TemporalRegion] every point of which is mediately or immediately connected with every other point of which." [] comment: Definition: A temporal region [span:TemporalRegion] every point of which is mediately or immediately connected with every other point of which. is_a: span:TemporalRegion ! temporal_region union_of: span:TemporalInstant ! temporal_instant union_of: span:TemporalInterval ! temporal_interval disjoint_from: span:ScatteredTemporalRegion ! scattered_temporal_region property_value: has_example "the 1970s years" xsd:string property_value: has_example "the time from the beginning to the end of a heart attack" xsd:string property_value: has_example "the time taken up by cellular meiosis" xsd:string created_by: He Zhang creation_date: 2013-10-04T20:37:58Z [Term] id: span:FiatProcessPart name: fiat_process_part namespace: def: "A processual entity [span:ProcessualEntity] that is part of a process but that does not have bona fide beginnings and endings corresponding to real discontinuities." [] comment: Definition: A processual entity [span:ProcessualEntity] that is part of a process but that does not have bona fide beginnings and endings corresponding to real discontinuities. is_a: span:ProcessualEntity ! processual_entity disjoint_from: span:Process ! process disjoint_from: span:ProcessBoundary ! process_boundary disjoint_from: span:ProcessualContext ! processual_context property_value: has_example "chewing during a meal" xsd:string property_value: has_example "the middle part of a rainstorm" xsd:string property_value: has_example "the most interesting part of Van Gogh's life" xsd:string property_value: has_example "the worst part of a heart-attack" xsd:string created_by: He Zhang creation_date: 2013-09-28T19:01:24Z [Term] id: span:Occurrent name: occurrent namespace: def: "An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants." [] comment: Definition: An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants. synonym: "perdurant" RELATED [] is_a: bfo:Entity ! entity union_of: span:ProcessualEntity ! processual_entity union_of: span:SpatiotemporalRegion ! spatiotemporal_region union_of: span:TemporalRegion ! temporal_region disjoint_from: snap:Continuant ! continuant property_value: has_example "a surgical operation as processual context for a nosocomical infection" xsd:string property_value: has_example "the life of an organism" xsd:string property_value: has_example "the most interesting part of Van Gogh's life" xsd:string property_value: has_example "the spatiotemporal context occupied by a process of cellular meiosis" xsd:string property_value: has_example "the spatiotemporal region occupied by the development of a cancer tumor" xsd:string created_by: He Zhang creation_date: 2013-09-27T11:53:19Z [Term] id: span:Process name: process namespace: def: "A processual entity [span:ProcessualEntity] that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities." [] comment: Definition: A processual entity [span:ProcessualEntity] that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities. is_a: span:ProcessualEntity ! processual_entity disjoint_from: span:FiatProcessPart ! fiat_process_part disjoint_from: span:ProcessBoundary ! process_boundary disjoint_from: span:ProcessualContext ! processual_context property_value: has_example "the life of an organism" xsd:string property_value: has_example "the process of cell-division" xsd:string property_value: has_example "the process of sleeping" xsd:string created_by: He Zhang creation_date: 2013-09-28T19:01:24Z [Term] id: span:ProcessAggregate name: process_aggregate namespace: def: "A processual entity [span:ProcessualEntity] that is a mereological sum of process [span:Process] entities and possesses non-connected boundaries." [] comment: Definition: A processual entity [span:ProcessualEntity] that is a mereological sum of process [span:Process] entities and possesses non-connected boundaries. is_a: span:ProcessualEntity ! processual_entity disjoint_from: span:FiatProcessPart ! fiat_process_part disjoint_from: span:Process ! process disjoint_from: span:ProcessBoundary ! process_boundary disjoint_from: span:ProcessualContext ! processual_context property_value: has_example "a process of digestion and a process of thinking taken together" xsd:string property_value: has_example "the beating of the hearts of each of seven individuals in the room" xsd:string property_value: has_example "the playing of each of the members of an orchestra" xsd:string created_by: He Zhang creation_date: 2013-09-28T19:01:24Z [Term] id: span:ProcessBoundary name: process_boundary namespace: def: "A processual entity [span:ProcessualEntity] that is the fiat or bona fide instantaneous temporal process boundary." [] comment: Definition: A processual entity [span:ProcessualEntity] that is the fiat or bona fide instantaneous temporal process boundary. is_a: span:ProcessualEntity ! processual_entity disjoint_from: span:FiatProcessPart ! fiat_process_part disjoint_from: span:Process ! process disjoint_from: span:ProcessualContext ! processual_context property_value: has_example "birth" xsd:string property_value: has_example "death" xsd:string property_value: has_example "the detaching of a finger in an industrial accident" xsd:string property_value: has_example "the final separation of two cells at the end of cell-division" xsd:string property_value: has_example "the forming of a synapse" xsd:string property_value: has_example "the incision at the beginning of a surgery" xsd:string property_value: has_example "the onset of REM sleep" xsd:string created_by: He Zhang creation_date: 2013-09-28T19:01:24Z [Term] id: span:ProcessualContext name: processual_context namespace: def: "An occurrent [span:Occurrent] consisting of a characteristic spatial shape inhering in some arrangement of other occurrent [span:Occurrent] entities. Processual context [span:ProcessualContext] entities are characteristically entities at or in which other occurrent [span:Occurrent] entities can be located or occur." [] comment: Comment: An instance of a processual context [span:ProcessualContext] is a mixture of processual entity [span:ProcessualEntity] which stand as surrounding environments for other processual entity [span:ProcessualEntity] entities. The class processual context [span:ProcessualContext] is the analogous among occurrent [span:Occurrent] entities to the class site [snap:Site] among continuant [snap:Continuant] entities. is_a: span:ProcessualEntity ! processual_entity disjoint_from: span:FiatProcessPart ! fiat_process_part disjoint_from: span:Process ! process disjoint_from: span:ProcessBoundary ! process_boundary property_value: has_example "The processual context for a given manipulation occurring as part of an experiment is made of processual entities which occur in parallel" xsd:string property_value: has_example "are not necessarily all parts of the experiment themselves and may involve continuant [snap:Continuant] entities which are in the spatial vicinity of the participants in the experiment." xsd:string created_by: He Zhang creation_date: 2013-09-28T19:01:24Z [Term] id: span:ProcessualEntity name: processual_entity namespace: def: "An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity." [] comment: Definition: An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. is_a: span:Occurrent ! occurrent union_of: span:FiatProcessPart ! fiat_process_part union_of: span:Process ! process union_of: span:ProcessAggregate ! process_aggregate union_of: span:ProcessBoundary ! process_boundary union_of: span:ProcessualContext ! processual_context disjoint_from: span:SpatiotemporalRegion ! spatiotemporal_region disjoint_from: span:TemporalRegion ! temporal_region property_value: has_example "the course of a disease" xsd:string property_value: has_example "the flight of a bird" xsd:string property_value: has_example "the life of an organism" xsd:string property_value: has_example "the process of meiosis" xsd:string creation_date: 2013-09-28T18:35:33Z [Term] id: span:ScatteredSpatiotemporalRegion name: scattered_spatiotemporal_region namespace: def: "A spatiotemporal region [span:SpatiotemporalRegion] that has spatial and temporal dimensions and every spatial and temporal point of which is not connected with every other spatial and temporal point of which." [] comment: Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has spatial and temporal dimensions and every spatial and temporal point of which is not connected with every other spatial and temporal point of which. is_a: span:SpatiotemporalRegion ! spatiotemporal_region disjoint_from: span:ConnectedSpatiotemporalRegion ! connected_spatiotemporal_region property_value: has_example "the space and time occupied by the individual games of the World Cup" xsd:string property_value: has_example "the space and time occupied by the individual liaisons in a romantic affair" xsd:string created_by: He Zhang creation_date: 2013-10-04T20:27:34Z [Term] id: span:ScatteredTemporalRegion name: scattered_temporal_region namespace: def: "A temporal region [span:TemporalRegion] every point of which is not mediately or immediately connected with every other point of which." [] comment: Definition: A temporal region [span:TemporalRegion] every point of which is not mediately or immediately connected with every other point of which. is_a: span:TemporalRegion ! temporal_region disjoint_from: span:ConnectedTemporalRegion ! connected_temporal_region property_value: has_example "the time occupied by the individual games of the World Cup" xsd:string property_value: has_example "the time occupied by the individual liaisons in a romantic affair" xsd:string created_by: He Zhang creation_date: 2013-10-04T20:37:58Z [Term] id: span:SpatiotemporalInstant name: spatiotemporal_instant namespace: def: "A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] at a specific moment." [] comment: Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] at a specific moment. is_a: span:ConnectedSpatiotemporalRegion ! connected_spatiotemporal_region disjoint_from: span:SpatiotemporalInterval ! spatiotemporal_interval property_value: has_example "the spatiotemporal region occupied by a single instantaneous temporal slice (part) of a process" xsd:string created_by: He Zhang creation_date: 2013-10-04T20:31:55Z [Term] id: span:SpatiotemporalInterval name: spatiotemporal_interval namespace: def: "A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] that endures for more than a single moment of time." [] comment: Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] that endures for more than a single moment of time. is_a: span:ConnectedSpatiotemporalRegion ! connected_spatiotemporal_region disjoint_from: span:SpatiotemporalInstant ! spatiotemporal_instant property_value: has_example "the spatiotemporal region occupied by a process or by a fiat processual part" xsd:string created_by: He Zhang creation_date: 2013-10-04T20:31:55Z [Term] id: span:SpatiotemporalRegion name: spatiotemporal_region namespace: def: "An occurrent [span:Occurrent] at or in which processual entity [span:ProcessualEntity] entities can be located." [] comment: Comment: All instances of occurrent [span:Occurrent] are spatiotemporal entities, that is, they enter in the relation of (spatiotemporal) location with spatiotemporal region [span:SpatiotemporalRegion] entities. As a particular case, the exact spatiotemporal location of a spatiotemporal region [span:SpatiotemporalRegion] is this region itself. is_a: span:Occurrent ! occurrent union_of: span:ConnectedSpatiotemporalRegion ! connected_spatiotemporal_region union_of: span:ScatteredSpatiotemporalRegion ! scattered_spatiotemporal_region disjoint_from: span:ProcessualEntity ! processual_entity disjoint_from: span:TemporalRegion ! temporal_region property_value: has_example "the spatiotemporal context occupied by a process of cellular meiosis" xsd:string property_value: has_example "the spatiotemporal region occupied by a human life" xsd:string property_value: has_example "the spatiotemporal region occupied by the development of a cancer tumor" xsd:string creation_date: 2013-09-28T18:35:33Z [Term] id: span:TemporalInstant name: temporal_instant namespace: def: "A connected temporal region [span:ConnectedTemporalRegion] comprising a single moment of time." [] comment: Definition: A connected temporal region [span:ConnectedTemporalRegion] comprising a single moment of time. is_a: span:ConnectedTemporalRegion ! connected_temporal_region disjoint_from: span:TemporalInterval ! temporal_interval property_value: has_example "right now" xsd:string property_value: has_example "the moment at which a child is born" xsd:string property_value: has_example "the moment at which a finger is detached in an industrial accident" xsd:string property_value: has_example "the moment of death" xsd:string created_by: He Zhang creation_date: 2013-10-04T20:41:51Z [Term] id: span:TemporalInterval name: temporal_interval namespace: def: "A connected temporal region [span:ConnectedTemporalRegion] lasting for more than a single moment of time." [] comment: Definition: A connected temporal region [span:ConnectedTemporalRegion] lasting for more than a single moment of time. is_a: span:ConnectedTemporalRegion ! connected_temporal_region disjoint_from: span:TemporalInstant ! temporal_instant property_value: has_example "any continuous temporal duration during which a process occurs" xsd:string created_by: He Zhang creation_date: 2013-10-04T20:41:51Z [Term] id: span:TemporalRegion name: temporal_region namespace: def: "An occurrent [span:Occurrent] that is part of time." [] comment: Comment: All instances of occurrent [span:Occurrent] are temporal entities, that is, they enter in the relation of (temporal) location with temporal region [span:TemporalRegion] entities. As a particular case, the exact spatiotemporal location of a temporal region [span:TemporalRegion] is this region itself. Continuant [snap:Continuant] entities are not temporal entities in the technical sense just explained; they are related to time in a different way, not through temporal location but through a relation of existence at a time or during a period of time (see continuant [snap:Continuant]. is_a: span:Occurrent ! occurrent union_of: span:ConnectedTemporalRegion ! connected_temporal_region union_of: span:ScatteredTemporalRegion ! scattered_temporal_region disjoint_from: span:ProcessualEntity ! processual_entity disjoint_from: span:SpatiotemporalRegion ! spatiotemporal_region property_value: has_example "the duration of a surgical procedure" xsd:string property_value: has_example "the moment of death" xsd:string property_value: has_example "the time it takes to run a marathon" xsd:string creation_date: 2013-09-28T18:35:33Z [Typedef] id: complicated_by name: complicated_by namespace: disease_ontology [Typedef] id: composed_of name: composed_of namespace: disease_ontology def: "Component parts of anatomy of tissue made up of certain cells or other body area/system or tissue types." [DO:lh] [Typedef] id: derives_from name: derives_from namespace: sequence subset: SOFA is_transitive: true [Typedef] id: ends_during name: ends_during namespace: gene_ontology comment: This relation will be used after 2013-05-21. xref: RO:0002093 [Typedef] id: happens_during name: happens_during namespace: gene_ontology comment: This relation will be used after 2013-05-21. xref: RO:0002092 is_transitive: true is_a: ends_during ! ends_during [Typedef] id: has_integral_part name: has_integral_part namespace: sequence def: "X has_integral_part Y if and only if: X has_part Y and Y part_of X." [http://precedings.nature.com/documents/3495/version/1] comment: Example: mRNA has_integral_part CDS. is_a: has_part ! has_part created_by: kareneilbeck creation_date: 2009-08-19T12:01:46Z [Typedef] id: has_material_basis_in name: has_material_basis_in namespace: disease_ontology [Typedef] id: has_part name: has_part namespace: gene_ontology xref: BFO:0000051 xref: OBO_REL:has_part is_transitive: true [Typedef] id: has_symptom name: has_symptom namespace: disease_ontology [Typedef] id: homologous_to name: homologous_to namespace: sequence subset: SOFA is_symmetric: true is_a: similar_to ! similar_to [Typedef] id: inheres_in name: inheres_in namespace: disease_ontology [Typedef] id: integral_part_of name: integral_part_of namespace: sequence def: "X integral_part_of Y if and only if: X part_of Y and Y has_part X." [http://precedings.nature.com/documents/3495/version/1] comment: Example: exon integral_part_of transcript. is_a: part_of ! part_of created_by: kareneilbeck creation_date: 2009-08-19T12:03:28Z [Typedef] id: is_a name: is_a namespace: disease_ontology [Typedef] id: located_in name: located_in namespace: disease_ontology def: "Anatomical location." [DO:lh] [Typedef] id: member_of name: member_of namespace: sequence is_a: part_of ! part_of creation_date: 2013-10-14T17:05:04Z [Typedef] id: negatively_regulates name: negatively_regulates namespace: gene_ontology xref: RO:0002212 holds_over_chain: results_in negatively_regulates is_a: regulates ! regulates [Typedef] id: non_functional_homolog_of name: non_functional_homolog_of namespace: sequence is_a: homologous_to ! homologous_to creation_date: 2013-10-14T17:18:10Z [Typedef] id: OBO_REL:adjacent_to name: adjacent_to namespace: relationship alt_id: OBO_REL:0000012 def: "C adjacent to C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c and c' are in spatial proximity" [PMID:15892874] comment: Note that adjacent_to as thus defined is not a symmetric relation, in contrast to its instance-level counterpart. For it can be the case that Cs are in general such as to be adjacent to instances of C1 while no analogous statement holds for C1s in general in relation to instances of C. Examples are: nuclear membrane adjacent_to cytoplasm; seminal vesicle adjacent_to urinary bladder; ovary adjacent_to parietal pelvic peritoneum instance_level_is_transitive: true [Typedef] id: OBO_REL:agent_in name: agent_in namespace: relationship alt_id: OBO_REL:0000022 is_a: OBO_REL:participates_in ! participates_in inverse_of_on_instance_level: OBO_REL:has_agent [Typedef] id: OBO_REL:contained_in name: contained_in namespace: relationship alt_id: OBO_REL:0000010 def: "C contained_in C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c located_in c' at t, and it is not the case that c *overlaps* c' at t. (c' is a conduit or cavity.)" [PMID:15892874] comment: Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): inverse_of_on_instance_level: OBO_REL:contains [Typedef] id: OBO_REL:contains name: contains namespace: relationship alt_id: OBO_REL:0000011 inverse_of_on_instance_level: OBO_REL:contained_in [Typedef] id: OBO_REL:derived_into name: derived_into namespace: relationship alt_id: OBO_REL:0000016 is_transitive: true inverse_of_on_instance_level: OBO_REL:derives_from [Typedef] id: OBO_REL:has_agent name: has_agent namespace: relationship alt_id: OBO_REL:0000021 def: "As for has_participant, but with the additional condition that the component instance is causally active in the relevant process" [PMID:15892874] is_a: OBO_REL:has_participant ! has_participant inverse_of_on_instance_level: OBO_REL:agent_in [Typedef] id: OBO_REL:has_improper_part name: has_improper_part namespace: relationship alt_id: OBO_REL:0000024 comment: See reasons for obsoletion of improper_part_of is_reflexive: true is_transitive: true is_a: OBO_REL:has_part ! has_part is_obsolete: true inverse_of_on_instance_level: OBO_REL:improper_part_of [Typedef] id: OBO_REL:has_integral_part name: has_integral_part namespace: relationship alt_id: OBO_REL:0000005 is_reflexive: true is_transitive: true is_a: OBO_REL:has_part ! has_part inverse_of: OBO_REL:integral_part_of ! integral_part_of is_anti_symmetric: true [Typedef] id: OBO_REL:has_part name: has_part namespace: relationship alt_id: OBO_REL:0000003 is_reflexive: true is_transitive: true inverse_of_on_instance_level: OBO_REL:part_of is_anti_symmetric: true [Typedef] id: OBO_REL:has_participant name: has_participant namespace: relationship alt_id: OBO_REL:0000019 def: "P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t" [PMID:15892874] comment: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. inverse_of_on_instance_level: OBO_REL:participates_in [Typedef] id: OBO_REL:has_proper_part name: has_proper_part namespace: relationship alt_id: OBO_REL:0000007 is_transitive: true is_a: OBO_REL:has_part ! has_part inverse_of_on_instance_level: OBO_REL:proper_part_of [Typedef] id: OBO_REL:improper_part_of name: improper_part_of namespace: relationship alt_id: OBO_REL:0000025 def: "As for part_of, with the additional constraint that subject and object may be identical" [PMID:15892874] comment: OBSOLETE. The definition is "As for part_of, with the additional constraint that subject and object may be identical". However, part_of is already reflexive, therefore improper_part_of is identical to part_of. If read differently, as "improper_part_of is part_of but not proper_part_of",improper_part_of becomes identity. So, improper_part_of is either identical to part_of or to identity, and not an intuitive synonym for either of them. [Robert Hoehndorf] is_reflexive: true is_transitive: true is_a: OBO_REL:part_of ! part_of is_obsolete: true inverse_of_on_instance_level: OBO_REL:has_improper_part [Typedef] id: OBO_REL:instance_of name: instance_of namespace: relationship alt_id: OBO_REL:0000023 def: "A relation between an instance and a class. For components: a primitive relation between a component instance and a class which it instantiates at a specific time. For processes: a primitive relation, between a process instance and a class which it instantiates, holding independently of time" [PMID:15892874] comment: The instance_of relationship is considered axiomatic by the obo file format specification; ie it is taken for granted. The is_a relation is still included in this ontology for completeness builtin: true [Typedef] id: OBO_REL:integral_part_of name: integral_part_of namespace: relationship alt_id: OBO_REL:0000004 def: "C integral_part_of C' if and only if: C part_of C' AND C' has_part C" [PMID:15892874] is_reflexive: true is_transitive: true is_a: OBO_REL:part_of ! part_of inverse_of: OBO_REL:has_integral_part ! has_integral_part is_anti_symmetric: true [Typedef] id: OBO_REL:located_in name: located_in namespace: relationship alt_id: OBO_REL:0000008 def: "C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.)" [PMID:15892874] comment: Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus is_reflexive: true is_transitive: true inverse_of_on_instance_level: OBO_REL:location_of [Typedef] id: OBO_REL:location_of name: location_of namespace: relationship alt_id: OBO_REL:0000009 is_reflexive: true is_transitive: true inverse_of_on_instance_level: OBO_REL:located_in [Typedef] id: OBO_REL:part_of name: part_of namespace: relationship alt_id: OBO_REL:0000002 def: "For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)" [PMID:15892874] comment: Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell. is_reflexive: true is_transitive: true inverse_of_on_instance_level: OBO_REL:has_part is_anti_symmetric: true [Typedef] id: OBO_REL:participates_in name: participates_in namespace: relationship alt_id: OBO_REL:0000020 inverse_of_on_instance_level: OBO_REL:has_participant [Typedef] id: OBO_REL:preceded_by name: preceded_by namespace: relationship alt_id: OBO_REL:0000017 def: "P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t. " [PMID:15892874] comment: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is_transitive: true inverse_of_on_instance_level: OBO_REL:precedes [Typedef] id: OBO_REL:precedes name: precedes namespace: relationship alt_id: OBO_REL:0000018 is_transitive: true inverse_of_on_instance_level: OBO_REL:preceded_by [Typedef] id: OBO_REL:proper_part_of name: proper_part_of namespace: relationship alt_id: OBO_REL:0000006 def: "As for part_of, with the additional constraint that subject and object are distinct" [PMID:15892874] is_transitive: true is_a: OBO_REL:part_of ! part_of inverse_of_on_instance_level: OBO_REL:has_proper_part [Typedef] id: OBO_REL:transformation_of name: transformation_of namespace: relationship alt_id: OBO_REL:0000013 def: "Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2." [PMID:15892874] comment: When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes. is_transitive: true [Typedef] id: occurs_in name: occurs in namespace: gene_ontology xref: BFO:0000066 transitive_over: part_of ! part_of [Typedef] id: occurs_with name: occurs_with namespace: disease_ontology [Typedef] id: OMIT:affects name: affects domain: OMIT:0000122 ! DOIDTerms range: OMIT:0000244 ! FMATerms created_by: He Zhang creation_date: 2013-10-01T23:40:05Z [Typedef] id: OMIT:affectsTumor name: affectsTumor domain: SO:0000276 ! miRNA created_by: He Zhang creation_date: 2013-10-01T23:40:55Z [Typedef] id: OMIT:age name: age range: xsd:integer ! xsd:integer created_by: haowu creation_date: 2013-10-02T21:40:43Z [Typedef] id: OMIT:annotationInPicTar name: annotationInPicTar domain: OMIT:0000115 ! MiRNABinding range: xsd:string ! xsd:string created_by: haowu creation_date: 2013-10-02T22:04:53Z [Typedef] id: OMIT:causedBy name: causedBy domain: OMIT:0000122 ! DOIDTerms range: OMIT:0000040 ! HarmfulRole created_by: He Zhang creation_date: 2013-10-01T23:41:50Z [Typedef] id: OMIT:causes name: causes domain: OMIT:0000040 ! HarmfulRole range: OMIT:0000122 ! DOIDTerms created_by: He Zhang creation_date: 2013-10-01T23:42:19Z [Typedef] id: OMIT:cellLines name: cellLines domain: OMIT:0000114 ! ExperimentalValidation range: xsd:string ! xsd:string created_by: haowu creation_date: 2013-10-02T21:41:56Z [Typedef] id: OMIT:chromosomeLocation name: chromosomeLocation domain: SO:0000704 ! gene range: xsd:string ! xsd:string created_by: haowu creation_date: 2013-10-02T21:42:14Z [Typedef] id: OMIT:directSupport name: directSupport domain: OMIT:0000114 ! ExperimentalValidation range: xsd:string ! xsd:string created_by: haowu creation_date: 2013-10-02T21:42:34Z [Typedef] id: OMIT:downRegulateEvent name: downRegulateEvent domain: SO:0000276 ! miRNA range: span:ProcessualEntity ! processual_entity is_a: OMIT:regulateEvent ! regulateEvent created_by: He Zhang [Typedef] id: OMIT:downRegulateTarget name: downRegulateTarget domain: SO:0000276 ! miRNA range: SO:0000704 ! gene is_a: OMIT:regulateTarget ! regulateTarget created_by: He Zhang creation_date: 2013-10-05T12:27:05Z [Typedef] id: OMIT:experimentContainsMiRNA name: experimentContainsMiRNA domain: OMIT:0000114 ! ExperimentalValidation range: SO:0000276 ! miRNA created_by: He Zhang creation_date: 2013-10-01T23:43:02Z [Typedef] id: OMIT:experimentContainsTarget name: experimentContainsTarget domain: OMIT:0000114 ! ExperimentalValidation range: SO:0000704 ! gene creation_date: 2013-10-02T21:23:25Z [Typedef] id: OMIT:exprerimentSummary name: exprerimentSummary domain: OMIT:0000114 ! ExperimentalValidation range: xsd:string ! xsd:string created_by: haowu creation_date: 2013-10-02T21:48:45Z [Typedef] id: OMIT:fromTaxon name: fromTaxon domain: snap:Continuant ! continuant range: OMIT:0000052 ! Organism created_by: haowu creation_date: 2013-10-02T21:24:04Z [Typedef] id: OMIT:geneExpressedln name: geneExpressedln domain: SO:0000704 ! gene range: GO:0005623 ! cell created_by: haowu creation_date: 2013-10-02T21:24:23Z [Typedef] id: OMIT:hasBinding name: hasBinding domain: SO:0000276 ! miRNA range: OMIT:0000115 ! MiRNABinding created_by: haowu creation_date: 2013-10-02T21:24:39Z [Typedef] id: OMIT:hasMiRNA name: hasMiRNA domain: OMIT:0000115 ! MiRNABinding range: SO:0000276 ! miRNA created_by: haowu creation_date: 2013-10-02T21:25:23Z [Typedef] id: OMIT:hasPrediction name: hasPrediction domain: OMIT:0000115 ! MiRNABinding range: SO:0000704 ! gene is_a: OMIT:hasTarget ! hasTarget created_by: He Zhang creation_date: 2013-10-05T12:09:43Z [Typedef] id: OMIT:hasTarget name: hasTarget domain: OMIT:0000115 ! MiRNABinding range: SO:0000704 ! gene created_by: He Zhang creation_date: 2013-10-02T21:25:52Z [Typedef] id: OMIT:hasValidation name: hasValidation domain: OMIT:0000115 ! MiRNABinding range: OMIT:0000114 ! ExperimentalValidation created_by: He Zhang creation_date: 2013-10-02T21:27:46Z [Typedef] id: OMIT:id name: id domain: bfo:Entity ! entity range: xsd:string ! xsd:string created_by: He Zhang creation_date: 2013-10-02T21:41:21Z [Typedef] id: OMIT:indirecSupport name: indirecSupport domain: OMIT:0000114 ! ExperimentalValidation range: xsd:string ! xsd:string created_by: He Zhang creation_date: 2013-10-02T21:49:22Z [Typedef] id: OMIT:inOrgan name: inOrgan domain: SO:0000276 ! miRNA range: OMIT:0000244 ! FMATerms created_by: haowu creation_date: 2013-10-02T21:28:05Z [Typedef] id: OMIT:inOrganism name: inOrganism domain: SO:0000276 ! miRNA range: OMIT:0000052 ! Organism created_by: He Zhang creation_date: 2013-10-02T21:28:31Z [Typedef] id: OMIT:involvedInEvent name: involvedInEvent domain: OMIT:0000115 ! MiRNABinding range: span:ProcessualEntity ! processual_entity created_by: He Zhang creation_date: 2013-10-02T22:06:21Z [Typedef] id: OMIT:involvedInTumor name: involvedInTumor domain: SO:0000704 ! gene created_by: He Zhang creation_date: 2013-10-02T22:06:43Z [Typedef] id: OMIT:miRNACompleteName name: miRNACompleteName domain: SO:0000276 ! miRNA range: xsd:string ! xsd:string created_by: He Zhang creation_date: 2013-10-02T21:49:57Z [Typedef] id: OMIT:miRNADescription name: miRNADescription domain: SO:0000276 ! miRNA range: xsd:string ! xsd:string created_by: He Zhang creation_date: 2013-10-02T21:50:28Z [Typedef] id: OMIT:miRNAExpressedln name: miRNAExpressedln domain: SO:0000276 ! miRNA range: span:Process ! process created_by: He Zhang creation_date: 2013-10-02T21:30:06Z [Typedef] id: OMIT:miRNAFunction name: miRNAFunction domain: OMIT:0000115 ! MiRNABinding range: xsd:string ! xsd:string created_by: He Zhang creation_date: 2013-10-02T21:50:47Z [Typedef] id: OMIT:miRNAName name: miRNAName domain: SO:0000276 ! miRNA range: xsd:string ! xsd:string created_by: He Zhang creation_date: 2013-10-02T21:51:08Z [Typedef] id: OMIT:miRNARgulationElement name: miRNARgulationElement domain: OMIT:0000115 ! MiRNABinding range: xsd:string ! xsd:string created_by: He Zhang creation_date: 2013-10-02T21:51:31Z [Typedef] id: OMIT:miRNASeedLocation name: miRNASeedLocation domain: OMIT:0000115 ! MiRNABinding range: xsd:string ! xsd:string created_by: He Zhang creation_date: 2013-10-02T21:51:52Z [Typedef] id: OMIT:miRNASequence name: miRNASequence domain: SO:0000276 ! miRNA range: xsd:string ! xsd:string is_a: OMIT:miRNASequenceLocation ! miRNASequenceLocation created_by: He Zhang creation_date: 2013-10-05T12:29:25Z [Typedef] id: OMIT:miRNASequenceLocation name: miRNASequenceLocation domain: SO:0000276 ! miRNA range: xsd:string ! xsd:string created_by: He Zhang creation_date: 2013-10-02T21:52:19Z [Typedef] id: OMIT:miRNATargetSequence name: miRNATargetSequence domain: OMIT:0000115 ! MiRNABinding range: xsd:string ! xsd:string created_by: He Zhang creation_date: 2013-10-02T21:52:45Z [Typedef] id: OMIT:predictedMRE name: predictedMRE domain: OMIT:0000114 ! ExperimentalValidation range: xsd:string ! xsd:string created_by: He Zhang creation_date: 2013-10-02T21:53:18Z [Typedef] id: OMIT:proteinType name: proteinType domain: snap:Continuant ! continuant range: xsd:string ! xsd:string created_by: He Zhang creation_date: 2013-10-02T21:53:41Z [Typedef] id: OMIT:regulateEvent name: regulateEvent domain: SO:0000276 ! miRNA range: span:ProcessualEntity ! processual_entity is_a: regulates ! regulates created_by: He Zhang creation_date: 2013-10-02T21:30:32Z [Typedef] id: OMIT:regulatemRNATranslation name: regulatemRNATranslation is_a: OMIT:regulateEvent ! regulateEvent created_by: He Zhang [Typedef] id: OMIT:regulatencRNAFunction name: regulatencRNAFunction is_a: OMIT:regulateEvent ! regulateEvent created_by: He Zhang [Typedef] id: OMIT:regulateProtein name: regulateProtein domain: SO:0000276 ! miRNA range: PR:000000001 ! protein is_a: regulates ! regulates created_by: He Zhang creation_date: 2013-10-02T21:34:24Z [Typedef] id: OMIT:regulateTarget name: regulateTarget domain: SO:0000276 ! miRNA range: SO:0000704 ! gene is_a: regulates ! regulates created_by: He Zhang creation_date: 2013-10-02T21:34:42Z [Typedef] id: OMIT:resultedFrom name: resultedFrom creation_date: 2013-10-25T16:23:00Z [Typedef] id: OMIT:sex name: sex range: xsd:string ! xsd:string created_by: He Zhang creation_date: 2013-10-02T21:53:50Z [Typedef] id: OMIT:targetCompleteName name: targetCompleteName domain: SO:0000704 ! gene range: xsd:string ! xsd:string created_by: haowu creation_date: 2013-10-02T21:54:12Z [Typedef] id: OMIT:targetGeneSymbol name: targetGeneSymbol domain: SO:0000704 ! gene range: xsd:string ! xsd:string created_by: haowu creation_date: 2013-10-02T21:55:09Z [Typedef] id: OMIT:targetPrimaryPeptideSequence name: targetPrimaryPeptideSequence domain: SO:0000704 ! gene range: xsd:string ! xsd:string created_by: haowu creation_date: 2013-10-02T21:56:51Z [Typedef] id: OMIT:targetRankInmiRDB name: targetRankInmiRDB domain: OMIT:0000115 ! MiRNABinding range: xsd:string ! xsd:string created_by: haowu creation_date: 2013-10-02T22:04:16Z [Typedef] id: OMIT:targetRankInPictar name: targetRankInPictar domain: OMIT:0000115 ! MiRNABinding range: xsd:string ! xsd:string created_by: He Zhang creation_date: 2013-10-02T22:03:53Z [Typedef] id: OMIT:targetRegulateType name: targetRegulateType domain: OMIT:0000115 ! MiRNABinding range: xsd:string ! xsd:string created_by: He Zhang creation_date: 2013-10-02T22:00:25Z [Typedef] id: OMIT:targetScoreInmiRDB name: targetScoreInmiRDB domain: OMIT:0000115 ! MiRNABinding range: xsd:string ! xsd:string created_by: He Zhang creation_date: 2013-10-02T22:07:43Z [Typedef] id: OMIT:targetScoreInPicTar name: targetScoreInPicTar domain: OMIT:0000115 ! MiRNABinding range: xsd:string ! xsd:string created_by: He Zhang creation_date: 2013-10-02T22:07:26Z [Typedef] id: OMIT:targetScoreInPITA name: targetScoreInPITA domain: OMIT:0000115 ! MiRNABinding range: xsd:string ! xsd:string created_by: He Zhang creation_date: 2013-10-02T22:01:07Z [Typedef] id: OMIT:targetSynonyms name: targetSynonyms domain: SO:0000704 ! gene range: xsd:string ! xsd:string created_by: He Zhang creation_date: 2013-10-02T22:08:09Z [Typedef] id: OMIT:targetTaxon name: targetTaxon domain: SO:0000704 ! gene range: xsd:string ! xsd:string created_by: He Zhang creation_date: 2013-10-02T22:08:21Z [Typedef] id: OMIT:targetTermAsscociations name: targetTermAsscociations domain: SO:0000704 ! gene range: xsd:string ! xsd:string created_by: He Zhang creation_date: 2013-10-02T22:08:39Z [Typedef] id: OMIT:targetType name: targetType domain: SO:0000704 ! gene range: xsd:string ! xsd:string created_by: He Zhang creation_date: 2013-10-02T22:08:52Z [Typedef] id: OMIT:treatedBy name: treatedBy domain: OMIT:0000122 ! DOIDTerms range: OMIT:0000123 ! Treatment created_by: He Zhang creation_date: 2013-10-02T21:35:10Z [Typedef] id: OMIT:treats name: treats domain: OMIT:0000123 ! Treatment range: OMIT:0000122 ! DOIDTerms created_by: He Zhang creation_date: 2013-10-02T21:38:28Z [Typedef] id: OMIT:upRegulateEvent name: upRegulateEvent domain: SO:0000276 ! miRNA range: span:ProcessualEntity ! processual_entity is_a: OMIT:regulateEvent ! regulateEvent [Typedef] id: OMIT:upRegulateTarget name: upRegulateTarget domain: SO:0000276 ! miRNA range: SO:0000704 ! gene is_a: OMIT:regulateTarget ! regulateTarget created_by: He Zhang creation_date: 2013-10-05T12:26:20Z [Typedef] id: part_of name: part_of namespace: sequence def: "X part_of Y if X is a subregion of Y." [http://precedings.nature.com/documents/3495/version/1] comment: Example: amino_acid part_of polypeptide. subset: SOFA is_transitive: true [Typedef] id: positively_regulates name: positively_regulates namespace: gene_ontology xref: RO:0002213 holds_over_chain: results_in positively_regulates is_a: regulates ! regulates [Typedef] id: realized_by name: realized_by namespace: disease_ontology [Typedef] id: realized_by_supression_with name: realized_by_supression_with namespace: disease_ontology [Typedef] id: regulates name: regulates namespace: gene_ontology xref: RO:0002211 holds_over_chain: results_in regulates transitive_over: part_of ! part_of [Typedef] id: results_in name: results_in namespace: gene_ontology comment: This relation is currently used to connect two regulation processes p1 and p2, such that if r1 regulates p1 and r2 regulates p2, and r1 results_in r2 then the regulation of p1 is required for the regulation of p2. For an example of use, see GO:0035958 'regulation of glyoxylate cycle by regulation of transcription from RNA polymerase II promoter'. Note that a precise definition of this relation is under discussion. After it has been formalized it will be added to RO, where it will have a RO ID. Note that the existing identifier and label are subject to change. created_by: cjm creation_date: 2012-03-14T10:35:44Z [Typedef] id: results_in_formation_of name: results_in_formation_of namespace: disease_ontology def: "Formation of structure,cancer,etc./cause and effect." [DO:lh] [Typedef] id: similar_to name: similar_to namespace: sequence subset: SOFA is_symmetric: true [Typedef] id: starts_during name: starts_during namespace: gene_ontology comment: This relations will be used after 2013-05-21. xref: RO:0002091 [Typedef] id: transmitted_by name: transmitted_by namespace: disease_ontology def: "Pathogen is transmitted." [DO:lh]