format-version: 1.2 date: 14:12:2012 13:08 saved-by: VPetri auto-generated-by: OBO-Edit 2.2 synonymtypedef: KEGG "KEGG" RELATED synonymtypedef: NEWSYNTYPE "" RELATED synonymtypedef: PID "PID" RELATED default-namespace: pathway [Term] id: bb:0000000 name: The Erk5 MAP kinase signalng pathway is_obsolete: true [Term] id: ID:0000000 name: is_obsolete: true created_by: VPetri creation_date: 2009-08-27T09:02:34Z [Term] id: PW:0000000 name: term zero is_obsolete: true [Term] id: PW:0000001 name: Pathway Ontology [Term] id: PW:0000002 name: classic metabolic pathway def: "The various, enzyme controlled, series of reactions allowing for the conversion of materials, energy availability and biodegradation of xenobiotics." [OneLook:http\://www.onelook.com/] comment: The definition was compiled based on a number of available defintions in various dictionaries. is_a: PW:0000001 ! Pathway Ontology [Term] id: PW:0000003 name: signaling pathway def: "The pathways where a signal - hormone, neurotransmitter, growth factor, peptide, any molecule - triggers one or multiple cascades of events. This involves a number of molecules, including receptors, proteins, ligands, messengers, any participating molecule. A signaling pathway may be upstream or downstream of other signaling pathways. Signaling pathways control a very broad spectrum of processes as well as pathways." [OneLook:www.onelook.com] comment: The definition was compiled based on a number of definitions available in various dictionaries. is_a: PW:0000001 ! Pathway Ontology [Term] id: PW:0000004 name: regulatory pathway def: "The pathways that control the processes by which a cell or organism develops, adjusts, behaves, responds to conditions or changes in these conditions, or in any manner helps promote and maintain its efficient functioning." [OneLook:www.onelook.com] comment: The definition was complied based on a number of definitions available in several dictionaries is_a: PW:0000001 ! Pathway Ontology [Term] id: PW:0000005 name: carbohydrate metabolic pathway def: "Those metabolic reactions and pathways involved in the oxidation, breakdown and synthesis of carbohydrates in the tissue. The breakdown can be utilized by the body for energy production." [OneLook:www.onelook.com] comment: The definition was compiled using the Online Medical dictionary and the Stedman's medical dictionary available at OneLook is_a: PW:0000002 ! classic metabolic pathway [Term] id: PW:0000006 name: Ras superfamily mediated signaling pathway def: "The Ras superfamily consists of a diverse group of small, monomeric G proteins that function as molecular switches alternating between the GDP-inactive and the GTP-active bound state. The GTP-bound form can interact with many downstream effectors. Ras superfamily controls a broad spectrum of processes; deregulation of Ras cascades has been linked to several forms of cancer. The superfamily is structurally classified in five families." [Gene Ontology:GO\:0007265, PubMed :PMID\: 11027944; 1152757] comment: Numerous articles contributed to this definition, too many to cite independently. synonym: "monomeric G protein mediated signaling pathway" RELATED [] is_a: PW:0000003 ! signaling pathway [Term] id: PW:0000007 name: mitogen activated protein kinase signaling pathway def: "The mitogen -activated protein kinase pathway groups several serine/threonine protein kinases mediated cascades in response to a number of extracellular stimuli. A characteristic feature of these cascades is the presence of at least three kinases in series leading to the activation of a multifunctional MAP kinase." [Gene Ontology:GO\:0000165, KEGG:map04010, PubMed:PMID\: 14570565; PMID\: 14976517; PMID\: 17229475; PMID\: 17306385, Reactome:REACT_634.5] synonym: "KEGG:04010" RELATED [] synonym: "MAPK signaling pathway" EXACT [] is_a: PW:0000003 ! signaling pathway [Term] id: PW:0000008 name: Wnt signaling pathway def: "The secreted glycoproteins of the Wnt family regulate a wide spectrum of developmental processes and they are also playing important roles in the adult organism. Deregulation of Wnt cascades has oncogenic effects and is responsible for tumorigenesis in adults." [PubMed:PMIDs\: 12573432\, 15041171\, 15001769] synonym: "KEGG:04310" RELATED [] is_a: PW:0000650 ! signaling pathway pertinent to development is_a: PW:0000656 ! glycoprotein signaling pathway [Term] id: PW:0000009 name: apoptotic cell death pathway def: "Apoptosis is a programmed cell death pathway that is characterized by particular morphological features such as membrane blebbing and DNA fragmentation. It can be intrinsic or extrinsic and involves the activation of caspases." [Gene Ontology:GO\:0006915, KEGG:map04210, OneLook\, PubMed:PMID\: 18414491; 12196263] synonym: "KEGG:04210" RELATED [] synonym: "programmed cell death pathway" RELATED [] is_a: PW:0000275 ! cell death pathway [Term] id: PW:0000010 name: lipid metabolic pathway def: "The metabolic reactions involved in the oxidation, utilization and/or synthesis of lipids in the tissues." [OneLook:www.onelook.com] is_a: PW:0000002 ! classic metabolic pathway [Term] id: PW:0000011 name: amino acid metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of the primary or standard 20 amino acids found in proteins. Amino acids are described as non-essential or essential depending on whether humans can or can not synthesize them, respectively. Chemically, they are classified as hydrophobic, hydrophilic and special. Amino acid metabolic pathways are also listed with their KEGG entries." [KEGG:http\://www.genome.jp/kegg/, MCW library:Handbooks of Biochemistry] is_a: PW:0000002 ! classic metabolic pathway [Term] id: PW:0000012 name: nucleotide metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of nucleotides. Nucleotides, which are the units of DNA and RNA, can also play important roles in cellular energy, enzyme regulation as well as serve as signaling molecules." [InHouse:PW directory, PubMed:PMID\:21222015; 20561600] is_a: PW:0000002 ! classic metabolic pathway [Term] id: PW:0000013 name: disease pathway def: "Complex human diseases encompass a spectrum of genetic and environmental attributes that together affect the normal functioning of several molecular and cellular pathways. Their combined and accumulated effect is manifested in the anomalous phenotype of the complex condition." [InHouse:InHouse PW dictionary] synonym: "complex human diseases" RELATED [] is_a: PW:0000001 ! Pathway Ontology [Term] id: PW:0000014 name: neurodegenerative disease pathway def: "Neurodegenerative diseases group together a number of conditions of various and many times poorly understood origins that are characterized by the progressive loss of particular neurons, the formation of particular structures such as plaques and fibrils, and protein aggregates. Proteosomal degradation, programmed cell death, oxidative stress, are among a number of pathways thought to be disrupted." [inHouse:InHouse PW dictionary] is_a: PW:0000013 ! disease pathway [Term] id: PW:0000015 name: Alzheimer disease pathway def: "A mostly sporadic, late-onset condition affecting the central nervous system, is the most prevalent neurodegenerative disease and the most common form of dementia. It is characterized by the presence of amyloid plaques and fibril tangles. Possible pathways affected range from protein misfolding and aggregation, to oxidative stress and impaired metal homeostasis." [InHouse:InHouse PW dictionary, KEGG:map05010] synonym: "KEGG:05010" RELATED [] is_a: PW:0000014 ! neurodegenerative disease pathway [Term] id: PW:0000016 name: amyotrophic lateral sclerosis disease pathway def: "A late onset, mostly sporadic neurodegenerative disease characterized by the loss of motor neurons in the brain stem and spinal cord. Various pathways are thought to be deregulated and contribute to the condition; among them calcium and/or zinc homeostasis, apoptosis, Cdk5 and calcineurin dependent processes, and in the case of the more rare, genetically inherited form of the disease, mutations in the cytosolic Cu, Zn superoxide dismutase (SOD1) and the subsequent changes in the processes that involve SOD1." [InHouse:In House PW dictionary, KEGG:map05014] synonym: "ALS pathway" EXACT [] synonym: "KEGG:05014" RELATED [] is_a: PW:0000014 ! neurodegenerative disease pathway [Term] id: PW:0000017 name: Huntington disease pathway def: "An inherited form of a neurodegenerative disease caused by an expanded polyQ (polyglutamine) tract. It mostly affects the striatum and cortex, but extends to other regions later in its development. It manifests itself in movement disorders, psychiatric abnormalities, cognitive defects, and manifold pathways are disrupted." [KEGG:map05016, PubMed:2004\, v.20 (3)\, 146-154.] synonym: "KEGG:05016" RELATED [] is_a: PW:0000171 ! disease pathways related to polyQ repeats [Term] id: PW:0000018 name: Parkinson disease pathway def: "One of the most common neurodegenerative diseases that is characterized by the loss of dopaminergic neurons in the substantia nigra and the presence of cytoplasmic inclusions called Lewy bodies in surrounding neurons. Several pathways are thought to be deregulated; for instance, imbalance of iron homeostasis is believed to contribute to the pathogenesis of the condition." [KEGG:map05012, PubMed:2004\, v.101 (15)\, 5500-5505.] synonym: "KEGG:05012" RELATED [] is_a: PW:0000014 ! neurodegenerative disease pathway [Term] id: PW:0000019 name: prion diseases pathway def: "Prion disease - any of a group of fatal, transmissible neurodegenerative diseases caused by abnormalities of prion protein metabolism, which may result from mutations in the prion protein gene or from infection with pathogenic isoforms of the protein. Characteristics include neuronal loss, gliosis, and extensive vacuolization of the cerebral cortex. Prion diseases may be sporadic, inherited as an autosomal dominant trait, or acquired. Human diseases include Creutzfeldt-Jakob disease, Gerstmann-Strussler syndrome, fatal familial insomnia, and kuru" [KEGG:map05020, OnerLook:www.onelook.com] synonym: "KEGG:05020" RELATED [] is_a: PW:0000014 ! neurodegenerative disease pathway [Term] id: PW:0000020 name: cardiovascular disease pathway def: "Cardiovascular diseases represent a very broad spectrum of conditions that can also combine with diabetes and renal failure." [InHouse:InHouse PW dictionary] is_a: PW:0000013 ! disease pathway [Term] id: PW:0000021 name: hypertension pathway def: "Hypertension, high arterial blood pressure: various criteria for its threshold have been suggested, ranging from 140 mm Hg systolic and 90 mm Hg diastolic to as high as 200 mm Hg systolic and 110 mm Hg diastolic. Hypertension may have no known cause (essential or idiopathic h.) or be associated with other primary diseases (secondary h.)." [OneLook:www.onelook.com] is_a: PW:0000020 ! cardiovascular disease pathway [Term] id: PW:0000022 name: cardiomyopathy pathway def: "Cardiomyopathy - a general diagnostic term designating primary noninflammatory disease of the heart muscle, often of obscure or unknown etiology and not the result of ischemic, hypertensive, congenital, valvular, or pericardial disease. It is usually subdivided into dilated, hypertrophic, and restrictive cardiomyopathy (1). Cardiomyopathy is the deterioration of the cardiac muscle of the heart wall." [OneLook:www.onelook.com] is_a: PW:0000020 ! cardiovascular disease pathway [Term] id: PW:0000023 name: immune response pathway def: "The Immune response pathways mediate the defense of host cells against infection and injury. The first line of defense is provided by the phylogenetically older innate immune response. The later, more versatile response is provided by the pathways of adaptive immunity: the B cell mediated humoral and the T cell mediated cellular or cell-mediated responses." [Gene Ontology:GO\:0006955, MCW library:Handbook of cellular and molecular immunology, OneLook:www.onelook.com] is_a: PW:0000004 ! regulatory pathway [Term] id: PW:0000024 name: inflammatory response pathway def: "Inflammation is the cellular response of the innate immune system to infection or injury. Sensing of infection by pattern recognition receptors triggers signaling cascades leading to the expression of mediator genes such as the pro-inflammatory cytokines." [Gene Ontology:GO\:0006954, MCW library:Cellular and molecular immunology\, by Abbas\, Abul K, OneLook:www.onelook.com, PubMed:PMID\: 20303867\, 20303872\, 15364056\, 16281932\, 16226680] synonym: "CLR signaling pathway" RELATED [] relationship: part_of PW:0000234 ! innate immune response pathway [Term] id: PW:0000025 name: glycolysis/gluconeogenesis pathway def: "Those metabolic reactions involved in the energy-yielding conversion of glucose to pyruvate or in the formation of glucose from non-carbohydrate precursors such as pyruvate, lactate, citric acid cycle intermediates, the carbon skeleton of many amino acids. While many enzymes are shared by the two pathways, a few steps are carried out by pathway-specific enzymes. The two pathways are independently regulated." [KEGG:map00010, OneLook\, MCW libraries:www.onelook.com; Voet & Voet \"Fundamentals of Biochemistry\" 3rd edition] synonym: "KEGG:00010" RELATED [] is_a: PW:0000005 ! carbohydrate metabolic pathway [Term] id: PW:0000026 name: citric acid cycle pathway def: "The series of chemical reactions that are central to all aerobic cells and constitute the citric acid cycle. Also known as the tricarboxylic acid cycle (TCA) or Krebs cycle, it is the center of convergence for all molecular fuels." [Gene Ontology:GO\:0006099, KEGG:map00020, OneLook:www.onelook.com, Reactome:REACT_1046.3] synonym: "KEGG:00020" RELATED [] synonym: "Krebs cycle pathway" RELATED [] synonym: "TCA cycle pathway" RELATED [] synonym: "tricarboxylic cycle pathway" RELATED [] is_a: PW:0000033 ! energy metabolic pathway relationship: part_of PW:0000357 ! energy homeostasis pathway [Term] id: PW:0000027 name: glutamic acid/glutamate metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation glutamic acid/glutamate. Glutamate is the major excitatory neurotransmitter." [OneLook:www.onelook.com] comment: Definition compiled based on the information available for glutamate at OneLook is_a: PW:0000445 ! excitatory neurotransmitter metabolic pathway is_a: PW:0001075 ! hydrophilic amino acid metabolism [Term] id: PW:0000028 name: alanine, aspartate and glutamate metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of alanine, aspartate and glutamate." [OneLook:www.onelook.com] comment: The definition was compiled based on the information on alanine and aspartate available at OneLook. synonym: "KEGG:00250" RELATED [] is_a: PW:0001077 ! amino acid metabolic pathway (KEGG) [Term] id: PW:0000029 name: fatty acid biosynthetic pathway alt_id: PW:0000030 def: "Acetyl-CoA, the starting material for fatty acid biosynthesis, can be derived from amino acid and lipid degradation or the oxidative decarboxylation of pyruvate. Fatty acid biosynthesis involves the condensation of C2 units; it requires seven enzymatic reactions which are carried out by the multifunctional enzyme fatty acid synthase." [Gene Ontology:GO\:0006633, KEGG:map00061, MCW Library:Biochemistry Handbook] synonym: "KEGG:00061" RELATED [] is_a: PW:0000058 ! fatty acid metabolic pathway [Term] id: PW:0000031 name: purine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of purines. Purines consist of a pyrimidine ring fused to an imidazole ring. The nucleobases adenine and guanine in DNA are purines." [OneLook:www.onelook.com] synonym: "KEGG:00230" RELATED [] is_a: PW:0000012 ! nucleotide metabolic pathway [Term] id: PW:0000032 name: pyrimidine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of pyrimidines. Cytosine, thymine and uracil - the nucleobases found in nucleic acids, are pyrimidine derivatives." [OneLook:www.onelook.com] synonym: "KEGG:00240" RELATED [] is_a: PW:0000012 ! nucleotide metabolic pathway [Term] id: PW:0000033 name: energy metabolic pathway def: "Those metabolic reactions and pathways whose role is to release or provide energy." [OneLook:www.onelook.com] is_a: PW:0000002 ! classic metabolic pathway [Term] id: PW:0000034 name: electron transport chain pathway def: "Those metabolic reactions thereby the electrons derived from the oxidation of glucose and lipids or the degradation of amino acids, are passed to oxygen via a series of series of spatially separated complexes. The energy derived generates an electrochemical gradient that drives the synthesis of ATP. The coupling between the electron transport chain, also known as the respiratory chain and the ATP biosynthetic pathway is known as oxidative phosphorylation. Under certain circumstances the two may be uncoupled." [Gene Ontology:GO\:0022904, OneLook:www.onelook.com, PubMed:PMID\: 21625217\, 19760284] synonym: "ETC pathway" RELATED [] synonym: "respiratory chain pathway" RELATED [] relationship: part_of PW:0000357 ! energy homeostasis pathway relationship: part_of PW:0001059 ! oxidative phosphorylation pathway [Term] id: PW:0000035 name: ATP biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of adenosine triphosphate (ATP). ATP synthesis is coupled to the electron transfer or respiratory chain pathway which generates an electrochemical gradient that drives the phosphorylation of ADP. The coupling of the two pathways is called oxidative phosphorylation. Under certain circumstances however, the two may be uncoupled." [Gene Ontology:GO\:0006754, OneLook:www.onelook.com, PubMed:PMID\: 21625217\, 19760284] relationship: part_of PW:0000357 ! energy homeostasis pathway relationship: part_of PW:0001059 ! oxidative phosphorylation pathway [Term] id: PW:0000036 name: nitrogen metabolic pathway def: "Those metabolic reactions in the nitrogen cycle carried out by various microorganisms." [KEGG:map00910] is_a: PW:0000033 ! energy metabolic pathway [Term] id: PW:0000037 name: sulfur metabolic pathway def: "Those metabolic reactions involving sulfur as carried out by various bacteria as well as archea, fungi and plants." [KEGG:map00920, PW InHouse dictionary:PW InHouse dictionary] synonym: "KEGG:00920" RELATED [] is_a: PW:0000033 ! energy metabolic pathway [Term] id: PW:0000038 name: Sterol, vitamin K, vitamine E and cartenoids biosynthesis def: "OBSOLETE. Originally found at KEGG, the term has since been deleted." [PW dictionary:InHouse dictionary] is_obsolete: true [Term] id: PW:0000039 name: bile acid biosynthetic pathway def: "Those metabolic reactions involved in the biosynthesis of bile acid - any of the steroid carboxylic acids derived from cholesterol. Cholic and chenodeoxycholic acids are the primary bile acids and are formed in the liver. Secondary bile acids - deoxycholic and lithocholic - are formed from the primary bile acids through the action of intestinal bacteria. Bile acid also acts as a signal molecule via several nuclear receptors." [OneLook:www.onelook.com, PubMed:PMID\: 22414897] synonym: "KEGG:00120" RELATED [] is_a: PW:0000248 ! isoprenoid metabolic pathway [Term] id: PW:0000040 name: steroid hormone biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of steroid hormones. All steroid hormones are derived from cholesterol. Steroid hormone metabolism is extremely complex and its molecular details are incompletely understood. De novo steroid biosynthesis is confined to very few tissues, primarily the adrenals, the gonads and the placenta." [KEGG:map00140, OneLook:www.onelook.com, PubMed:PMID\: 17926129] synonym: "KEGG:00140" RELATED [] is_a: PW:0001152 ! steroid biosynthetic pathway [Term] id: PW:0000041 name: fructose and mannose metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of fructose and mannose, as depicted in the KEGG diagram." [KEGG:map00051, OneLook:www.onelook.com] synonym: "KEGG:00051" RELATED [] is_a: PW:0000005 ! carbohydrate metabolic pathway [Term] id: PW:0000042 name: galactose metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of galactose - an aldohexose epimeric with glucose at the 4 carbon. Galactose is a component of lactose and other oligosaccharides, cerebrosides and gangliosides, and of various glycolipids and glycoproteins." [Gene Ontology:GO\:0006012, KEGG:map00052, OneLook:www.onelook.com] synonym: "KEGG:00052" RELATED [] is_a: PW:0000005 ! carbohydrate metabolic pathway [Term] id: PW:0000043 name: pyruvate metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of pyruvate - a salt, ester, or anionic form of pyruvic acid. Pyruvate, which is the end-product of glycolysis can be converted to lactate under anaerobic conditions, can be further oxidized via the Krebs or citrate cycle or can be converted back to glucose via gluconeogenesis." [Gene Ontology:GO\:0006090, KEGG:00620, OneLook:www.onelook.com, Reactome:REACT_2071.3] synonym: "KEGG:00620" RELATED [] is_a: PW:0000005 ! carbohydrate metabolic pathway is_a: PW:0000556 ! glucose oxidation pathway [Term] id: PW:0000044 name: Duplicated Glutamate Metabolism term def: "OBSOLETE. Duplicated term. Use PW:0000027." [PW dictionary:InHouse dictionary] is_obsolete: true [Term] id: PW:0000045 name: pentose phosphate pathway def: "Those metabolic reactions involved in the generation of reducing equivalents and five carbon (pentose) sugars. The oxidative phase is irreversible; the non-oxidative is reversible." [Gene Ontology:GO\:0006098, KEGG:map00030, OneLook\, PubMed:www.oneloook.com; http\://www.ncbi.nlm.nih.gov/sites/entrez, Reactome:REACT_1859.1] synonym: "hexose monophosphate pathway (shunt)" RELATED [] synonym: "KEGG:00030" RELATED [] synonym: "pentose phosphate shunt" RELATED [] synonym: "phosphogluconate pathway" RELATED [] is_a: PW:0000005 ! carbohydrate metabolic pathway [Term] id: PW:0000046 name: inositol metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of inositol, a cyclic sugar alcohol occurring in a number of stereoisomers of which the myo-inositol is the most prominent form. myo-inositol provides a structural basis for compounds such as inositol phosphates and phosphatidylinositols which are secondary messengers in several signaling pathways." [Gene Ontology:GO\:0006020, OneLook:www.onelook.com] is_a: PW:0000005 ! carbohydrate metabolic pathway [Term] id: PW:0000047 name: glycine, serine and threonine metabolic pathway def: "Those metabolic reactions involved in the synthesis of glycine, serine and threonine and which are intimately connected with serine being synthesized from glycine and threonine." [OneLook:www.onelook.com] comment: Definition compiled based on the information available at oneLook synonym: "KEGG:00260" RELATED [] is_a: PW:0001077 ! amino acid metabolic pathway (KEGG) [Term] id: PW:0000048 name: methionine cycle/metabolic pathway def: "Those metabolic reactions involved in the synthesis (remethylation), utilization and/or degradation of methionine - an essential amino acid that can provide the methyl group and sulfur necessary for normal metabolism. Humans do not synthesize methionine; it is derived from diet. Through a number of steps, utilization of methionine produces homocysteine (Hcy) which either regenerates the methionine cycle via remethylation pathway or leads to the synthesis of cysteine and derivatives via transsulfuration pathway." [MCW library book:Homocysteine in Health and Disease] is_a: PW:0001074 ! hydrophobic amino acid metabolic pathway [Term] id: PW:0000049 name: cysteine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of cysteine, a non-essential amino acid that could be essential in certain cases." [OneLook:www.onelook.com] comment: Reference compiled based on the information available at OneLook for cysteine. is_a: PW:0001076 ! special amino acid metabolic pathway [Term] id: PW:0000050 name: arginine and proline metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of arginine - an essential amino acid - and proline - an amino acid that can play important roles in protein secondary structure." [OneLook:www.onelook.com] comment: Definition compiled based on the information on arginine and proline available at OneLook synonym: "KEGG:00330" RELATED [] is_a: PW:0001077 ! amino acid metabolic pathway (KEGG) [Term] id: PW:0000051 name: histidine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of histidine, an essential amino acid which can act as either a proton donor or a proton acceptor." [OneLook:www.onelook.com] synonym: "KEGG:00340" RELATED [] is_a: PW:0001075 ! hydrophilic amino acid metabolism is_a: PW:0001077 ! amino acid metabolic pathway (KEGG) [Term] id: PW:0000052 name: tyrosine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of tyrosine - a nonessential amino acid produced from phenylalanine and precursor of thyroid hormones, catecholamines and melanin." [OneLook:www.onelook.com] synonym: "KEGG:00350" RELATED [] is_a: PW:0001074 ! hydrophobic amino acid metabolic pathway is_a: PW:0001077 ! amino acid metabolic pathway (KEGG) [Term] id: PW:0000053 name: phenylalanine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of phenylalanine, an essential amino acid." [OneLook:www.onelook.com] synonym: "KEGG:00360" RELATED [] is_a: PW:0001074 ! hydrophobic amino acid metabolic pathway is_a: PW:0001077 ! amino acid metabolic pathway (KEGG) [Term] id: PW:0000054 name: tryptophan metabolic pathway def: "Those metabolic reactions that are involved in the synthesis, utilization and/or degradation of tryptophan - a dietary essential amino acid and precursor of nicotinamide." [OneLook:www.onelook.com] synonym: "KEGG:00380" RELATED [] is_a: PW:0001074 ! hydrophobic amino acid metabolic pathway is_a: PW:0001077 ! amino acid metabolic pathway (KEGG) [Term] id: PW:0000055 name: nucleotide sugar metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of nucleotide sugars. Nucleotide sugars are glycosyl donors usually classified depending on the type of the nucleoside forming them. Several are used in animals and many others can be found in plants and bacteria." [InHouse:PW dictionary, KEGG:map00520] synonym: "KEGG:00520" RELATED [] is_a: PW:0000005 ! carbohydrate metabolic pathway [Term] id: PW:0000056 name: photosynthesis pathway def: "A chemical combination caused by the action of light; specifically the formation of carbohydrates (with release of molecular oxygen) from carbon dioxide and water in the chlorophyll tissue of plants and blue-green algae under the influence of light. In bacteria, photosynthesis employs hydrogen sulfide, molecular hydrogen, and other reduced compounds in place of water, so that molecular oxygen is not released." [Gene Ontology:GO\:0015979, OneLook:www.onelook.com] is_a: PW:0000033 ! energy metabolic pathway [Term] id: PW:0000057 name: carbon fixation pathway def: "The pathway thereby photosynthetic organisms such as plants and cyanobacteria convert inorganic carbon (usually carbon dioxide) into organic compounds (usually carbohydrates)." [OneLook:www.onelook.com] is_a: PW:0000033 ! energy metabolic pathway [Term] id: PW:0000058 name: fatty acid metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of fatty acids - any long-chain monobasic organic acid." [Gene Ontology:GO\:0006631, KEGG:map00071] synonym: "KEGG:00071" RELATED [] is_a: PW:0000010 ! lipid metabolic pathway [Term] id: PW:0000059 name: signaling pathway pertinent to the brain is_a: PW:0000003 ! signaling pathway [Term] id: PW:0000060 name: long term potentiation def: "Long-term potentiation (LTP) is a strengthening of the synapse that can last from hours to days and months. It is thought to underlie information storage and constitute the cellular basis of learning and memory. LTP engages numerous cascades of events on either side of the synapse and is accompanied by changes in gene expression." [Dorland's:www.onelook.com, Gene Ontology:GO\:0060291, KEGG:map04720] synonym: "KEGG:04720" RELATED [] synonym: "LTP" EXACT [] relationship: part_of PW:0000455 ! excitatory synaptic transmission pathway [Term] id: PW:0000061 name: long term depression def: "Long term depression is a weakening of a synapse that lasts hours to days. It results from either strong synaptic stimulation (as in the cerebellum) or to weak synaptic stimulation (as in the hippocampus), and engages several cascades." [Gene ontology:GO\:0060292, KEGG:map04730, OneLook:www.onelook.com] comment: Adapted from Wikipedia at OneLook synonym: "KEGG:04730" RELATED [] synonym: "LTD" EXACT [] relationship: part_of PW:0000455 ! excitatory synaptic transmission pathway [Term] id: PW:0000062 name: ascorbate and aldarate metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of ascorbate and aldarate, as depicted in the KEGG diagram." [KEGG:map00053, OneLook:www\,onelook.com] synonym: "KEGG:00053" RELATED [] is_a: PW:0000005 ! carbohydrate metabolic pathway [Term] id: PW:0000063 name: glyoxylate and dicarboxylate metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glyoxylate and dicarboxylate, as depicted in the KEGG diagram." [KEGG:map00630, OneLook:http\://www.onelook.com] synonym: "KEGG:00630" RELATED [] is_a: PW:0000005 ! carbohydrate metabolic pathway [Term] id: PW:0000064 name: propanoate metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of propanoate - any salt or ester of propanoic or propionic acid. Several propanoates are used in the food industry." [KEGG:map00640, OneLook\, Online:www.onelook.com; http\://dl.clackamas.cc.or.us/ch106-04/nomencla1.htm] synonym: "KEGG:00640" RELATED [] is_a: PW:0000005 ! carbohydrate metabolic pathway [Term] id: PW:0000065 name: butanoate metabolic pathway def: "Those reactions involved in the synthesis, utilization and/or degradation of butanoate - an ester or salt of n-Butyric acid. Various butanoates are used as ingredients in flavoring and perfumery." [KEGG:map00650, OneLook:www.onelook.com] synonym: "KEGG:00650" RELATED [] is_a: PW:0000005 ! carbohydrate metabolic pathway [Term] id: PW:0000066 name: C5-branched dibasic acid metabolic pathway is_a: PW:0000005 ! carbohydrate metabolic pathway [Term] id: PW:0000067 name: reductive carboxylate cycle - CO2 fixation pathway def: "Those reactions involved in carbon dioxide fixation - the reductive carboxylate cycle (CO2 fixation) - the conversion of atmospheric carbon dioxide to organic carbon compounds, as in photosynthesis." [=OneLook:www.onelook.com, KEGG:map00720] is_a: PW:0000033 ! energy metabolic pathway [Term] id: PW:0000068 name: methane metabolic pathway def: "Those pathways used by methanotrophs and the methanogens that metabolize methane as the sole carbon source or as byproduct." [Gene Ontology:GO\:0015947, KEGG:map00680, OneLook:www.onelook.com] is_a: PW:0000033 ! energy metabolic pathway [Term] id: PW:0000069 name: ketone bodies metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization or degradation of ketone bodies. The chemicals acetoacetate, acetone and beta-hydroxybutyrate are collectively known as ketone bodies, although only the first two are ketones. They provide fuel for heart and skeletal muscle and for the brain during starvation. Excessive accumulation of these acidic chemicals leads to dangerous diabetic conditions known as ketoacidosis." [Gene Ontology:GO\:0046950, KEGG:map00072, MCW Libraries:QU4 V876f 2008, OneLook:www.onelook.com, Reactome:REACT_1861.3] comment: The definition was compiled using the information from a number of biological/medical dictionaries available at OneLook synonym: "KEGG:00072" RELATED [] is_a: PW:0000058 ! fatty acid metabolic pathway [Term] id: PW:0000070 name: C21-steroid hormone biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of C21-steroid hormones. Pregnenolone, the first C21 steroid derived from cholesterol, and progesterone, to which pregnenolone can be converted, provide the starting material for the biosynthesis of C21, C19 and C18 steroid hormones. The C21 class includes glucocorticoids such as cortisol and mineralocorticoids such as aldosterone. Glucocorticoids and mineralocorticoids are collectively referred to as corticosteroids." [KEGG:map00140, PubMed:PMID\: 17926129] synonym: "corticosteroid biosynthetic pathway" RELATED [] is_a: PW:0000040 ! steroid hormone biosynthetic pathway [Term] id: PW:0000071 name: valine, leucine and isoleucine degradation pathway def: "Those metabolic reactions involved in the degradation of valine, leucine and isoleucine - the three, dietary essential, branched amino acids." [OneLook:www.onelook.com] synonym: "KEGG:00280" RELATED [] is_a: PW:0001077 ! amino acid metabolic pathway (KEGG) [Term] id: PW:0000072 name: valine, leucine and isoleucine biosynthetic pathway def: "Those metabolic pathways involved in the synthesis of valine, leucine and isoleucine - the three, dietary essential, branched amino acids." [OneLook:www.onelook.com] synonym: "KEGG:00290" RELATED [] is_a: PW:0001077 ! amino acid metabolic pathway (KEGG) [Term] id: PW:0000073 name: lysine degradation pathway def: "Those metabolic reactions involved in the degradation of lysine." [OneLook:www.onelook.com] synonym: "KEGG:00310" RELATED [] is_a: PW:0001077 ! amino acid metabolic pathway (KEGG) [Term] id: PW:0000074 name: lysine biosynthetic pathway def: "Those metabolic reactions involved in the biosynthesis of lysine - an essential amino acid." [OneLook:www.onelook.comOnline collection of dictionaries] synonym: "KEGG:00300" RELATED [] is_a: PW:0001077 ! amino acid metabolic pathway (KEGG) [Term] id: PW:0000075 name: phenylalanine, tyrosine and tryptophan biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of phenylalanine, tyrosine and tryptophan and which are intimately related. Although the body can not manufacture phenylalanine on its own, phenylalanine is the precursor of tyrosine. Phenylalanine together with tryptophan governs the release of an intestinal hormone - cholecystokinin." [OneLook:www.onelook.com] synonym: "KEGG:00400" RELATED [] is_a: PW:0001077 ! amino acid metabolic pathway (KEGG) [Term] id: PW:0000076 name: urea cycle pathway def: "The series of metabolic reactions, occurring in the liver, by which the ammonia derived from the breakdown of amino acids combines with carbon dioxide to form urea." [OneLook:www.onelook.com] is_a: PW:0000011 ! amino acid metabolic pathway [Term] id: PW:0000077 name: beta-alanine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of beta-alanine. Beta-alanine is an amino acid formed in vivo by the degradation of dihydrouracil and carnosine. Beta-alanine is not used in the syntthesis of proteins but is a component of natural peptides, vitamins sich as vitamin B5 and of conezyme. A rare genetic disorder, hyper-beta-alaninemia, has been reported." [Gene Ontology:GO\:0019482, KEGG:map00410, Onelook:www.onelook.com] synonym: "KEGG:00410" RELATED [] is_a: PW:0000132 ! metabolic pathway of other amino acids [Term] id: PW:0000078 name: cyanoamino acid metabolic pathway def: "Those metabolic reactions involving cyanoamino acid, amino acid derivatives that contain a cyanide group." [Gene Ontology:GO\:0033052, KEGG:map00460] synonym: "KEGG:00460" RELATED [] is_a: PW:0000132 ! metabolic pathway of other amino acids [Term] id: PW:0000079 name: Duplicated Selenoamino acid metabolism term def: "OBSOLETE. Duplicated term. Use PW:0000133" [PW dictionary:InHouse dictionary] is_obsolete: true [Term] id: PW:0000080 name: Duplicated term - Selenoamino acid metabolism def: "OBSOLETE. Duplicated term. Use PW:0000133" [PW dictionary:InHouse dictionary] is_obsolete: true [Term] id: PW:0000081 name: D-glutamine and D-glutamate metabolic pathway def: "Those metabolic reactions involving D-glutamine and D-glutamate as depicted in the KEGG diagram. D-glutamic acid is naturally found primarily in the cell wall of certain bacteria." [Human Metabolome Database:HMDB03339, KEGG:map00471] synonym: "KEGG:00471" RELATED [] is_a: PW:0000132 ! metabolic pathway of other amino acids [Term] id: PW:0000082 name: D-arginine and D-ornithine metabolic pathway def: "Those metabolic reactions involving D-arginine and D-ornithine as depicted in the KEGG diagram." [KEGG:map00472] synonym: "KEGG:00472" RELATED [] is_a: PW:0000132 ! metabolic pathway of other amino acids [Term] id: PW:0000083 name: D-alanine metabolic pathway def: "Those metabolic reactions involving D-alanine, the D-enantiomer of alanine. D-alanine can be found in bacterial cell wall and in some peptide antibiotics." [OneLook:http\://www.onelook.com] is_a: PW:0000132 ! metabolic pathway of other amino acids [Term] id: PW:0000084 name: Duplicated glutathione metabolism term def: "OBSOLETE. Duplicated term. Use PW:0000134" [PW dictionary:InHouse dictionary] is_obsolete: true [Term] id: PW:0000085 name: pathways of replication, repair, gene expression, protein biosynthesis def: "Those pathways involved in and/or controlling DNA duplication and genomic replication, DNA repair, RNA and protein biosynthesis." [InHouse:InHouse PW dictionary] is_a: PW:0000004 ! regulatory pathway xref_unknown: XX: "" [Term] id: PW:0000086 name: cell cycle pathway, mitotic def: "The series of events, collectively known as the cell cycle, that underlie the replication of the genome and the segregation of chromosomes into daughter cells." [Gene Ontology:GO\:0000278, KEGG:map04110, Reactome:REACT_152.3, reactomee:www.reactome.org] comment: Adapted from O'Connell and Walwarth, Genome KnowledgeBase synonym: "KEGG:04110" RELATED [] is_a: PW:0000085 ! pathways of replication, repair, gene expression, protein biosynthesis [Term] id: PW:0000087 name: G1 phase pathway def: "The series of events underlying the progression of early cell cycle into the G phase and under the control of D-type cyclins together with Cdk4 and Cdk6. The formation of the pre-initiation replication complex takes place during this phase." [Reactome:REACT_1590.1, Reactomee:www.reactome.org] relationship: part_of PW:0000086 ! cell cycle pathway, mitotic [Term] id: PW:0000088 name: G1/S transition pathway def: "The series of events underlying the transition from G1 into S phase and under the control of Cyclin E - Cdk2 complexes." [Reactome:REACT_1783.2, reactome:www.reactome.org] relationship: part_of PW:0000086 ! cell cycle pathway, mitotic [Term] id: PW:0000089 name: S phase pathway def: "The series of events underlying duplication of the hereditary material of the cell, formation of two copies of the chromosome." [Reactome:REACT_899.3, Reactome:www.reactome.org] relationship: part_of PW:0000086 ! cell cycle pathway, mitotic [Term] id: PW:0000090 name: G2 phase pathway def: "The series of events underlying the second 'gap' phase of the mitotic cell cycle - an interval between the completion of DNA synthesis and the beginning of mitosis and during which protein synthesis occurs." [Reactome:REACT_1915.2, Reactome:www.reactome.org] relationship: part_of PW:0000086 ! cell cycle pathway, mitotic [Term] id: PW:0000091 name: G2/M transition pathway def: "The series of events underlying the transition from the G2 phase into mitosis." [Reactome:REACT_2203.2, Reactome:www.reactome.org] relationship: part_of PW:0000086 ! cell cycle pathway, mitotic [Term] id: PW:0000092 name: M phase pathway def: "The series of events underlying mitosis (M-phase), in turn comprised of several phases, involving nuclear division and cytokinesis and resulting in the formation of two daughter cells." [Reactome:REACT_910.1, Reactome:www.reactome.org] relationship: part_of PW:0000086 ! cell cycle pathway, mitotic [Term] id: PW:0000093 name: M/G1 transition pathway def: "The series of events underlying progression out of mitosis and division into two daughter cells. It requires the inactivation of cyclinB-cdc2 by the ubiquitin-dependent proteolysis." [Reactome:REACT_1725.1, Reactome:www.reactome.org] relationship: part_of PW:0000086 ! cell cycle pathway, mitotic [Term] id: PW:0000094 name: cell cycle checkpoint pathway def: "Those pathways involved in the control of cell cycle progression as well as its precision and fidelity." [Gene Ontology:GO\:0000075, InHouse:InHouse PW dictionary, Reactome:REACT_1538.1] is_a: PW:0000085 ! pathways of replication, repair, gene expression, protein biosynthesis [Term] id: PW:0000095 name: G1/S DNA damage checkpoint pathway def: "Those pathways of DNA damage response that occur during the G1 phase." [InHouse:PW dictionary, Reactome:REACT_1538.1] is_a: PW:0000094 ! cell cycle checkpoint pathway [Term] id: PW:0000096 name: G2/M checkpoint pathway def: "Those pathways that assure the genome is replicated only once per cell cycle. The checkpoints control for damaged and un-replicated DNA." [InHouse :PW dictionary, Reactome:REACT_828.2] is_a: PW:0000094 ! cell cycle checkpoint pathway [Term] id: PW:0000097 name: mitotic spindle checkpoint pathway def: "The pathway prevents cells with misaligned chromosomes from dividing. Defects of kinetochore function activate checkpoint proteins to initiate a cascade of events that eventually prevent separation of sister chromatid." [InHouse:PW dictionary, Reactome:REACT_2137.2] is_a: PW:0000094 ! cell cycle checkpoint pathway [Term] id: PW:0000098 name: DNA replication pathway def: "DNA replication takes place in the context of the cell cycle during the S-phase. The fast and accurate replication of DNA requires the presence and the coordinated function of a complex of proteins known as the replisome. The exact composition of the replisome in higher organisms still has to be fully determined." [OneLook:http\://www.onelook.com, PubMed:PMID\: 19665592] synonym: "KEGG:03030" RELATED [] relationship: part_of PW:0000086 ! cell cycle pathway, mitotic [Term] id: PW:0000099 name: DNA repair pathway def: "Those pathways involved in the repair of damaged DNA. The damage can involve bases or it can involve breaks in the DNA strand(s)." [Gene Ontology:GO\:0006281, PW InHouse:Cell\, 2004\, v. 117\, p171-184., Reactome:REACT_216.1] is_a: PW:0000085 ! pathways of replication, repair, gene expression, protein biosynthesis [Term] id: PW:0000100 name: transcription pathway def: "The pathways governing and/or regulating DNA transcription and gene expression. DNA transcription into coding and non-coding RNA is accomplished by one prokaryotic and several eukaryotic polymerases. Signaling pathways mediated by various transcription factor are involved in the regulation of gene expression." [InHouse:In House PW dictionary] is_a: PW:0000085 ! pathways of replication, repair, gene expression, protein biosynthesis [Term] id: PW:0000101 name: translation pathway def: "The series of events governing the processes thereby mRNA is translated into a polypeptide chain. Post-translational modifications often accompany the formation of the final, mature protein." [Gene Ontology:GO\:0006412, InHouse:InHouse PW dictionary] is_a: PW:0000085 ! pathways of replication, repair, gene expression, protein biosynthesis [Term] id: PW:0000102 name: the extracellular signal-regulated Raf/Mek/Erk signaling pathway def: "The Raf/Mek/Erk signaling pathway - a Ras activated protein kinase cascade - regulates diverse processes such as cell growth, proliferation and differentiation, in response to cytokines, hormones, growth factors." [Gene Ontology:GO\:0070371, KEGG:map04010, PubMed:PMID\: 15035987; 17229475; 17306385; 17112607, Reactome:REACT_962.4; REACT_1482.4] is_a: PW:0000007 ! mitogen activated protein kinase signaling pathway is_a: PW:0000525 ! Ras mediated signaling pathway [Term] id: PW:0000103 name: transport pathway def: "A pathway that mediates or facilitates the movement of materials, including biochemical substances and/or drugs across the cell membrane." [OneLook\, PubMed\, Online:http\://www.ncbi.nlm.nih.gov/; www.google.com] is_a: PW:0000004 ! regulatory pathway [Term] id: PW:0000104 name: intrinsic apoptotic pathway def: "The apoptotic pathway involving organelles, primarily the mitochondrion and endoplasmic reticulum (ER), and involving the pro and anti-apoptotic members of the Bcl family of proteins, cytochrome c, formation of the apoptosome and activation of caspases." [KEGG:map04210, PubNed:PMID\: 14744432, Reactome:REACT_964.1] comment: The reference was compiled based on the information available in the cited article. is_a: PW:0000009 ! apoptotic cell death pathway [Term] id: PW:0000105 name: Rho/Rac/Cdc42 mediated signaling pathway def: "Members of the Ras related Rho family of proteins control diverse processes such as actin cytoskeletal rearrangements, morphogenesis of dendritic spines, gene expression. Of note is the fact that cytoskeletal rearrangements, primarily actin remodelling have a role to play in vesicular trafficking, a process regulated by Rab proteins." [PubMed:PMID\: 11075828; 8973630; 11152757; 18171430] is_a: PW:0000006 ! Ras superfamily mediated signaling pathway [Term] id: PW:0000106 name: extrinsic apoptotic pathway def: "The apoptotic pathway involving the death receptors mediated route of caspase activation. Members of tumor necrosis superfamily such as the better known Tnf-alph (Tnf), Fas ligand or Trail elicit apoptosis via receptor associated adapters." [KEGG:map04210, PubMed:PMID\: 14744432, Reactome:REACT_1059.1] synonym: "death receptor mediated apoptotic pathway" RELATED [] is_a: PW:0000009 ! apoptotic cell death pathway [Term] id: PW:0000107 name: xenobiotics biodegradation pathway def: "Those reactions involved in the uptake, transformation and disposal of chemical substances and compounds that are foreign to the biological system." [InHouse:InHouse PW dictionary] is_a: PW:0000002 ! classic metabolic pathway [Term] id: PW:0000108 name: caprolactam degradation pathway def: "Those enzymatic reactions involved in the degradation of caprolactam - a cyclic amide of caproic acid used to produce a type of nylon." [Gene Ontology:GO\:0019384, KEGG:map00930, OneLook:www.onelook.com] is_a: PW:0000107 ! xenobiotics biodegradation pathway [Term] id: PW:0000109 name: bisphenol A degradation pathway def: "Those enzymatic reactions involved in the degradation of bisphenol A, known as BPA, an important compound in the production of plastics. However, it is believed to be hazardous to humans and reports have linked several health effects to levels of BPA exposure." [Gene Ontology:GO\:0043636, KEGG:map00363, OneLook:www.onelook.com] is_a: PW:0000107 ! xenobiotics biodegradation pathway [Term] id: PW:0000110 name: toluene and xylene degradation pathway def: "Those enzymatic reactions involved in the degradation of toluene and xylene. Toluene is used as organic solvent in rubber, paint, cement. Xylene represents any of three benzene derivatives used as solvent in printing, rubber, also as a cleaning agent." [KEGG:map00622, Onelook:www.onelook.com] is_a: PW:0000107 ! xenobiotics biodegradation pathway [Term] id: PW:0000111 name: gamma-hexachlorocyclohexane degradation pathway def: "Those enzymatic reactions involved in the degradation of gamma-hexachlorocyclohexane, also known as lindane, used as an insecticide and suspected to be carcinogenic." [KEGG:map00361, OneLook:www.onelook.com] is_a: PW:0000107 ! xenobiotics biodegradation pathway [Term] id: PW:0000112 name: 3-chloroacrylic acid degradation pathway def: "Those enzymatic reactions involved in the degradation of 3-chloroacrylic acid." [KEGG:map00641, Online:Various sources] is_a: PW:0000107 ! xenobiotics biodegradation pathway [Term] id: PW:0000113 name: atrazine degradation pathway def: "Those enzymatic reactions involved in the degradation of atrazine - a herbicide used to kill weeds." [Gene Ontology:GO\:0019381, KEGG:map00791, OneLook:www.onelook.com] is_a: PW:0000107 ! xenobiotics biodegradation pathway [Term] id: PW:0000114 name: benzoate degradation pathway via hydroxylation def: "Those enzymatic reactions involved in the aerobic pathway of benzoate degradation." [Gene Ontology:GO\:0043640, KEGG:map00362, Online :Appl. Env. Microbiology\, 2004\, v.70(9)\, p4861-70.] is_a: PW:0000282 ! benzoate degradation pathway [Term] id: PW:0000115 name: benzoate degradation pathway via CoA ligation def: "Those enzymatic reactions involved in the anaerobic pathway of benzoate degradation." [Gene Ontology:GO\:0010128, KEGG:map00632, Online:http\://umbbd.ahc.umn.edu/benz/benz_map.html] is_a: PW:0000282 ! benzoate degradation pathway [Term] id: PW:0000116 name: carbazole degradation pathway def: "Those enzymatic reactions involved in the degradation of carbazole - a crystalline, slightly basic cyclic compound found in anthracene. It reacts with carbohydrates and is used for assay and analysis of carbohydrates and in making dyes." [Gene Ontology:GO\:0046232, KEGG:map00629, OneLook:www.onelook.com] is_a: PW:0000107 ! xenobiotics biodegradation pathway [Term] id: PW:0000117 name: fluorene degradation pathway def: "Those enzymatic reactions involved in the degradation of fluorene - a colorless, crystalline hydrocarbon. It is obtained from coal tar and used in making dyes." [Gene Ontology:GO\:0019429, KEGG:, KEGG:map00628, OneLook:www.onelook.com] is_a: PW:0000107 ! xenobiotics biodegradation pathway [Term] id: PW:0000118 name: ethylbenzene degradation pathway def: "Those enzymatic reactions involved in the degradation of ethylbenzene - a liquid hydrocarbon used in the manufacture of styrene and as a solvent and diluent for dyes and paints." [KEGG:map00642, OneLook:www.onelook.com] is_a: PW:0000107 ! xenobiotics biodegradation pathway [Term] id: PW:0000119 name: nitrobenzene degradation pathway def: "Those enzymatic reactions involved in the degradation of nitrobenzene - an organic compound that occurs either as yellow crystals or yellow liquid used in the manufacture of aniline. It is a poisonous derivative of benzene." [OneLook:www.onelook.com] is_a: PW:0000107 ! xenobiotics biodegradation pathway [Term] id: PW:0000120 name: styrene degradation pathway def: "Those enzymatic reactions involved in the degradation of styrene - an aromatic hydrocarbon that is colorless and oily. It is used in the manufacture of rubber, resins, plastics. It is a toxic, possibly carcinogenic substance." [Gene Ontology:GO\:0042207, KEGG:map00643, OneLook:www.onelook.com] is_a: PW:0000107 ! xenobiotics biodegradation pathway [Term] id: PW:0000121 name: tetrachloroethene degradation pathway def: "Those enzymatic reactions involved in the degradation of tetrachloroethene - (acetylene tetrachloride) used as solvent for fats, waxes, resins and intermediate in the synthesis of chlorinated hydrocarbons." [KEGG:map00625, OneLook:www.onelook.com] is_a: PW:0000107 ! xenobiotics biodegradation pathway [Term] id: PW:0000122 name: Hedgehog signaling pathway def: "The Hedgehog signaling pathway (Hh) plays important roles in vertebrate embryogenesis, particularly in the differentiation of the neural tube, in vasculogenesis and angiogenesis. Post-embryonically it is believed to play a homeostatic role in the maintenance of stem cells. Alteration of the pathway has been implicated in a number of human cancers." [Gene Ontology:GO\:0007224, KEGG:map04340, PubMed:PMID\: 15205520 \, PMID\: 15596107\, PMID\: 12495844] synonym: "KEGG:04340" RELATED [] synonym: "PID:200168" RELATED [] synonym: "PID:200172" RELATED [] is_a: PW:0000650 ! signaling pathway pertinent to development relationship: part_of PW:0000660 ! hematopoiesis pathway [Term] id: PW:0000123 name: synaptic vesicle endocytosis and recycling pathway def: "The pathway of synaptic vesicle endocytosis and neurotransmitter refill following exocytosis." [PubMed:PMID\: 15217342] is_a: PW:0001072 ! synaptic vesicle cycle pathway [Term] id: PW:0000124 name: cellular detoxification pathway def: "A pathway triggered by exposure to endogenous or exogenous substances. It involves the phase I (oxidative) and phase II (conjugative) metabolizing enzymes and the phase III transport systems. While these system also account for the system's responses to drugs, drug pathways are considered separately." [PharmGKB:http\://www.pharmgkb.org/, PubMed:PMID\:15252150; 17482904, Reactome:REACT_13433.1] is_a: PW:0000004 ! regulatory pathway [Term] id: PW:0000125 name: G protein mediated signaling pathway def: "G-proteins act as signal transducers between effectors and receptors; they function as molecular switches alternating between the GDP-inactive and GTP-active bound state. Many types of signals are received by the members of a large superfamily of receptors that then activate distinct G-proteins which route the signal to many and distinct intracellular signaling pathways." [Gene Ontology:GO\:0007186, PubMed:Science\, 2002\, v296\, p1636-39, Reactome:REACT_14797.1] synonym: "heterotrimeric G protein mediated signaling pathway" RELATED [] is_a: PW:0000003 ! signaling pathway [Term] id: PW:0000126 name: RNA Polymerase I transcription pathway def: "The series of events governing the synthesis of ribosomal RNA (rRNA)." [Gene Ontology:GO\:0006360, InHouse:PW dictionary, Reactome:REACT_1309.1] is_a: PW:0000100 ! transcription pathway [Term] id: PW:0000127 name: RNA Polymerase II transcription pathway def: "The series of events governing the synthesis of messenger RNA (mRNA)." [Gene Ontology:GO\:0006366, InHouse:PW dictionary, Reactome:REACT_1366.1] is_a: PW:0000100 ! transcription pathway [Term] id: PW:0000128 name: RNA Polymerase III transcription pathway def: "The series of events governing the synthesis of transport/transfer RNA (tRNA)." [Gene Ontology:GO\:0006383, InHouse:PW dictionary, Reactome:REACT_1371.1] is_a: PW:0000100 ! transcription pathway [Term] id: PW:0000129 name: base excision repair pathway def: "Base excision repair pathway involves the identification and removal of the damaged base followed by its replacement with the correct nucleotide and ligation of the break in the strand." [Gene Ontology:GO\:0006284, KEGG:map03410, OneLook:www.onelook.com, Reactome:REACT_1104.1] synonym: "BER pathway" EXACT [] synonym: "KEGG:03410" RELATED [] is_a: PW:0000661 ! DNA base repair pathway [Term] id: PW:0000130 name: nucleotide excision repair pathway def: "Nucleotide excision repair pathway is an important mechanism for the detection of helix distoring base alterations such as thymine dimers. Unlike the base excision repair pathway that only removes the damaged bases, the NER pathway removes an entire lesion containing segment. The single-strand gap thus introduced is filled in by DNA polymerase using the undamaged strand as a template." [Gene Ontology:GO\:0006289, KEGG:map03420, OneLook:www.onelook.com, Reactome:REACT_1826.2] synonym: "KEGG:03420" RELATED [] synonym: "NER pathway" EXACT [] is_a: PW:0000661 ! DNA base repair pathway [Term] id: PW:0000132 name: metabolic pathway of other amino acids def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of amino acids other than the common 20 amino acids found in protein. Some of these amino acids like carnitine or homocysteine derive from primary amino acids." [InHouse:PW InHouse dictionary] is_a: PW:0000002 ! classic metabolic pathway [Term] id: PW:0000133 name: selenoamino acid metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of selenoamino acid - an amino acid in which a selenium atom replaces a sulfur atom. Examples include selenocysteine, selenohomocysteine and selenomethionine." [KEGG:map00450, SMPDB:http\://pathman.smpdb.ca/pathways/SMP00029/pathway, Technical glossary:http\://morelife.org/glossary/] synonym: "KEGG:00450" RELATED [] synonym: "selenocompound metabolic pathway" RELATED [] is_a: PW:0000132 ! metabolic pathway of other amino acids [Term] id: PW:0000134 name: glutathione metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glutathione - a tripeptide that acts as an antioxidant and provides protection against reactive oxygen species to the cell." [Gene Ontology:GO\:0006749, KEGG:map00480, OneLook:www.onelook.com] synonym: "KEGG:00480" RELATED [] is_a: PW:0000132 ! metabolic pathway of other amino acids is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins [Term] id: PW:0000135 name: metabolic pathway of cofactors and vitamins def: "Those reactions involved in the synthesis, utilization and/or degradation of cofactors and vitamins. Cofactors are necessary for the proper function of certain proteins and enzymes; they can be inorganic such as the metals ions or the iron-sulfur cluster or organic. Organic compounds that are tightly bound to proteins are also referred to as prosthetic groups. Often, they are or are made from vitamins, compounds that are vital but in small amounts and which are insufficiently synthesized by the organism. Some of these molecules can also perform signaling functions." [OneLook:http\://www.onelook.com] is_a: PW:0000002 ! classic metabolic pathway [Term] id: PW:0000136 name: thiamine metabolic pathway def: "Those metabolic reactions involving thiamine, a water-soluble vitamin of the B complex. It is synthesized in bacteria, fungi and plants while animals obtain thiamine from food. Thiamine insufficiency results in a condition called beriberi." [Gene Ontology:GO\:0006772, KEGG:map00730, OneLook:www.onelook.com] synonym: "KEGG:00730" RELATED [] synonym: "vitamin B1 metabolic pathway" EXACT [] is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins [Term] id: PW:0000137 name: riboflavin metabolic pathway def: "Those metabolic reactions involving riboflavin, also known as vitamin B2 - a water-soluble vitamin. B12 occurs in several products and is a precursor for flavin coenzymes." [Gene Ontology:GO\:0006771, KEGG:map00740, OneLook:www.onelook.com] synonym: "KEGG:00740" RELATED [] synonym: "vitamin B2 metabolic pathway" EXACT [] is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins [Term] id: PW:0000138 name: vitamin B6 metabolic pathway def: "Those metabolic reactions involving vitamin B6 - a water-soluble vitamin that exists in several forms. Vitamin B6 is required for many enzymatic reactions and plays important roles in monoamine and protein synthesis. A number of organisms can carry out de novo synthesis of vitamin B6; humans derive it from diet." [Gene Ontology:GO\:0042816, KEGG:map00750, OneLook\, NIH :www.onelook.com and linkss] synonym: "KEGG:00750" RELATED [] synonym: "pyridoxine metabolic pathway" RELATED [] is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins [Term] id: PW:0000139 name: biotin metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of biotin, also known as vitamin B7 or H, a water-soluble vitamin. Biotin assists in various metabolic reactions and processes." [Gene Ontology:GO\:0006768, KEGG:map00780, OneLook:www.onelook.com>, Reactome:REACT_11153.3] synonym: "KEGG:00780" RELATED [] synonym: "vitamin B7 metabolic pathway" EXACT [] is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins [Term] id: PW:0000140 name: pathway of folate cycle/metabolism def: "The folate cycle/metabolism represents the various reactions involving absorption, transport, conversion and utilization of folate compounds. Folate is the generic term for a number of chemically related molecules of the water-soluble vitamin B family that transfer one-carbon units for a number of important biosynthetic pathways. Folic acid is also known as vitamin B9." [PubMed:PMID\: 15298442; 11001804; PMID\: 15166809] synonym: "KEGG:00790" RELATED [] synonym: "vitamin B9 metabolic pathway" RELATED [] is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins [Term] id: PW:0000141 name: retinol metabolic pathway def: "Those reactions involving retinol, a fat-soluble vitamin that is the dietary form of vitamin A and is important for bone growth and in vision. Precursors of retinol such as carotenoid or retinyl esters are derived from diet and are converted to retinal and retinol, respectively." [Gene Ontology:GO\:0042572, KEGG:map00830, OneLook:www.onelook.com, PubMed:PMID\: 21718801\, 21586336] synonym: "KEGG:00830" RELATED [] is_a: PW:0001003 ! retinoid metabolic pathway [Term] id: PW:0000142 name: ubiquinone biosynthetic pathway def: "Those metabolic reactions involved in the biosynthesis of ubiquinone, also known as coenzyme Q. Ubiquinone is a member of the mitochondrial respiratory chain and plays important roles in cellular metabolism." [Gene Ontology:GO\:0006744, KEGG:map00130, Onelook\, PubMed:PMID\: 14757233] synonym: "KEGG:00130" RELATED [] is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins [Term] id: PW:0000143 name: insulin signaling pathway def: "Processes regulated by insulin and insulin-like growth factor signaling systems include growth and survival of many tissues; for example, neuron and retina, bone, pancreatic beta-cells. Insulin is best known for its role in the regulation of blood glucose. Disregulation of the systems is implicated in a number of metabolic disorders." [Gene Ontology:GO\:0008286, KEGG:map4910, PubMed:PMID\: 12169433, Reactome:REACT_498.5] synonym: "KEGG:04910" RELATED [] synonym: "PID:200014" RELATED [] is_a: PW:0000467 ! peptide and protein hormone signaling pathway relationship: part_of PW:0000357 ! energy homeostasis pathway relationship: part_of PW:0000553 ! glucose homeostasis pathway [Term] id: PW:0000144 name: ubiquitin/proteasome degradation pathway def: "The pathway for the ATP-dependent non-lysosomal proteolysis catalyzed by the 26S proteasome and for which ubiquitylation, the post-translational covalent conjugation of ubiquitin to target proteins is a key signal." [Gene Ontology:GO\:0006511, KEGG:ko04120, PubMed:2001\, v.27\, 171-179.] synonym: "KEGG:03050" RELATED [] synonym: "KEGG:04120" RELATED [] is_a: PW:0000417 ! ubiquitin, ubiquitin-like/proteasome degradation pathway [Term] id: PW:0000145 name: Metabolism of complex carbohydrates def: "OBSOLETE. Originally found at KEGG, the term has since been deleted" [PW dictionary:InHouse dictionary] is_obsolete: true [Term] id: PW:0000146 name: glycan metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glycans. Glycans are a class of compounds that include oligo- and polysaccharides, simple sugars or polymeric structures of mono- or di-saccharides, respectively. The term also refers to the carbohydrate moiety of glycoproteins, proteoglycans and glycolipids." [OneLook:www.onelook.com] is_a: PW:0000002 ! classic metabolic pathway [Term] id: PW:0000147 name: metabolic pathway of secondary metabolites def: "Those reactions involved in the synthesis, utilization and/or degradation of secondary metabolites - products of cellular metabolism that are not essential for, or not directly involved in the normal growth, development or reproduction of an organism. Many of the chemicals that plants or microorganisms produce are secondary metabolites." [OneLook:www.onelook.com] is_a: PW:0000002 ! classic metabolic pathway [Term] id: PW:0000148 name: alkaloid biosynthetic pathway I is_a: PW:0000147 ! metabolic pathway of secondary metabolites [Term] id: PW:0000149 name: alkaloid biosynthetic pathway II is_a: PW:0000147 ! metabolic pathway of secondary metabolites [Term] id: PW:0000150 name: stilbene, coumarine and lignin biosynthetic pathway is_a: PW:0000147 ! metabolic pathway of secondary metabolites [Term] id: PW:0000151 name: starch and sucrose metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of starch and sucrose, as depicted in the KEGG diagram. Starch is a polysaccharide produced by all green plants and is an important carbohydrate in the human diet. Sucrose, or the table sugar is a disaccharide of glucose and fructose that is produced by plants and cyanobacteria." [KEGG:map00500, OneLook:http\://www.onelook.com] synonym: "KEGG:00500" RELATED [] is_a: PW:0000005 ! carbohydrate metabolic pathway [Term] id: PW:0000152 name: amino sugar metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of amino sugars. An amino sugar has an amino group substituent in place of a hydroxyl group. Amino sugars are important constituents of a variety of polysaccharides and glycoproteins." [Gene Ontology:GO\:0006040, KEGG:map00520, OneLook:www.onelook.com] comment: Based on Dorland's Medical dictionary synonym: "KEGG:00520" RELATED [] is_a: PW:0000005 ! carbohydrate metabolic pathway [Term] id: PW:0000153 name: triacylglycerol metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of triacylglycerols - esters of glycerols with three fatty acid molecules. Triglycerides are the common form of transport and storage of fatty acids. Esters with one or two fatty acid molecules are metabolic intermediates present in small amounts." [Gene Ontology:GO\:0006641, KEGG:map00561, MCW library:QU4 M235b 2009, OneLook:www.onelook.com] synonym: "triglyceride metabolic pathway" RELATED [] is_a: PW:0001156 ! glycerolipid metabolic pathway [Term] id: PW:0000154 name: inositol phosphate metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of inositol phosphate which represents all of the possible phosphorylated states of inositol. Inositol phosphates have many important cellular functions." [Gene Ontology:GO\:0043647, KEGG:map00562, OneLook:www.onelook.com] synonym: "KEGG:00562" RELATED [] is_a: PW:0000005 ! carbohydrate metabolic pathway [Term] id: PW:0000155 name: phospholipid metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of phospholipids - lipids containing phosphorus, including those with a glycerol backbone or a backbone of sphingosine or related substances. Phospholipids are the major form of lipid in the cell membrane." [OneLook:www.onelook.com] is_obsolete: true [Term] id: PW:0000156 name: prostaglandin metabolic pathway def: "Those metabolic reactions involving prostaglandins - a family of eicosanoids with many regulatory functions." [MCW library:QU4 M235b 2009] is_a: PW:0000461 ! cyclooxygenase mediated pathway of arachidonic acid metabolism is_a: PW:0000485 ! eicosanoid metabolic pathway [Term] id: PW:0000157 name: glycosaminoglycan metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glycosaminoglycans - any of several high molecular weight linear polysaccharides of repeating disaccharide units. They are important components of connective tissue. When aggregating with proteins, they form proteoglycans." [Gene Ontology:GO\:0030203, MCW Libraries:QU4 V876f 2008, OneLook:www.onelook.com] is_a: PW:0000146 ! glycan metabolic pathway [Term] id: PW:0000158 name: Ras family mediated signaling pathway def: "The Ras family mediated signaling pathways are primarily involved in the regulation of gene expression." [PubMed:PMID\: 11467446; PMID\: 11152757] is_a: PW:0000006 ! Ras superfamily mediated signaling pathway [Term] id: PW:0000159 name: Rab family mediated signaling pathway def: "Rab family mediated signaling pathways are involved in the regulation of intracellular vesicle trafficking. More than 60 Rab members bind to specific effectors to regulate all aspects of vesicular trafficking - from formation and transport of vesicles, to tethering and fusion with target membranes. Of note is that cytoskeletal rearrangements such as actin remodelling, a process regulated by Rho family, have a role to play in vesicular trafficking." [Gene Ontology:GO\:0032482, PubMed:PMID\:16882731; 11152757; 18171430] is_a: PW:0000006 ! Ras superfamily mediated signaling pathway [Term] id: PW:0000160 name: Ran family mediated signaling pathway def: "Ran family mediated signaling pathways are involved in nucleocytoplasmic trafficking." [Gene Ontology:GO\:0031291, PubMed:PMID\:11152757] is_a: PW:0000006 ! Ras superfamily mediated signaling pathway [Term] id: PW:0000161 name: glycosylphosphatidylinositol anchor biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of glycosylphosphatidylinositol (GPI) anchor. The GPI anchor allows for the attachment of cell surface proteins to the cell membrane." [Gene Ontology:GO\:0006506, InHouse:InHouse PW dictionary, KEGG:map00563] synonym: "GPI anchor biosynthesis" RELATED [] synonym: "KEGG:00563" RELATED [] is_a: PW:0000146 ! glycan metabolic pathway [Term] id: PW:0000162 name: sphingolipid biosynthetic pathway is_a: PW:0000197 ! sphingolipid metabolic pathway [Term] id: PW:0000163 name: sphingolipid degradation pathway is_a: PW:0000197 ! sphingolipid metabolic pathway [Term] id: PW:0000164 name: ganglioside metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of ganglioside - any of a group of glycosphingolipids in which the polar head group on ceramide is a sialic acid. Their names include letters and numbers where the letters M, D and T indicate the number of sialic acid residues in the molecule - one, two or three, respectively." [Gene Ontology:GO\:0001573, OneLook:www.onelook.com] synonym: "KEGG:00604" RELATED [] is_a: PW:0000733 ! glycosphingolipid metabolic pathway [Term] id: PW:0000165 name: taurine and hypotaurine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of taurine and hypotaurine." [InHouse:PW InHouse dictionary, KEGG:map00430] synonym: "KEGG:00430" RELATED [] is_a: PW:0000132 ! metabolic pathway of other amino acids [Term] id: PW:0000166 name: monoterpenoid biosynthetic pathway synonym: "KEGG:00760" RELATED [] is_a: PW:0000184 ! terpenoid biosynthetic pathway [Term] id: PW:0000167 name: pantothenic acid metabolic pathway def: "Those metabolic reactions involving pantothenic acid or panthotenate, also known as vitamin B5 - a water-soluble vitamin. Vitamin B5 is the precursor to coenzyme A (CoA) which in turn, plays an essential role in fatty acids and pyruvate metabolism." [KEGG:map00770, OneLook:www.onelook.com] synonym: "KEGG:00770" RELATED [] synonym: "vitamin B5 metabolic pathway" EXACT [] is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins [Term] id: PW:0000168 name: growth factor signaling pathway def: "Those pathways that are triggered through the binding of a growth factor to its particular receptor. Growth factors carry out mitogenic signaling via their largely tyrosine kinase receptors." [InHouse\, OneLook\, Pubmed:PW dictionary\, www.onelook.com; PMID\: 16632420] is_a: PW:0000003 ! signaling pathway [Term] id: PW:0000169 name: nerve growth factor signaling pathway def: "Nerve growth factor (NGF) signaling pathways control a variety of processes such as neuronal cell differentiation, axon growth. Members of the NGF family are best known for their anti-apoptotic role as mediators of neuronal cell survival." [Gene Ontology:GO\:0048011, PubMed:Neuron\, 2004\, v42\, p897-912; Cellular Signaling\, 2004\, v16\, p127-36., Reactome:REACT_11061.4] synonym: "NGF signaling pathway" EXACT [] is_a: PW:0000571 ! neurotrophic factor signaling pathway [Term] id: PW:0000170 name: epidermal growth factor/neuregulin signaling pathway def: "Members of the EGF/neuregulin superfamily are important regulators of tissue development and repair. A characteristic feature is the presence of the EGF module, a 36-40 amino acid sequence with a disulfide-bonded three loop structure necessary for receptor binding." [Gene Ontology:GO\:0007173, KEGG:map04012, MCW e-journal:J. Mol. Evolo.2000\, v50\, p397-412, PubMed:12814936, Reactome:REACT_9417.3] synonym: "EGF/neuregulin signaling pathway" EXACT [] synonym: "KEGG:04012" RELATED [] synonym: "PID:200101" RELATED [] synonym: "PID:200159" RELATED [] is_a: PW:0000168 ! growth factor signaling pathway [Term] id: PW:0000171 name: disease pathways related to polyQ repeats def: "A family of neurodegenerative and other inherited diseases that are caused by the expansion of a polyglutamine tract (polyQ) in the associated disease proteins. The diseases are manifested as distinct neuropathies and multiple pathways are perturbed." [PubMed:2004\, v.20(3)\, 146-154] comment: Definition adapted from an article in Trends in Genetics is_a: PW:0000014 ! neurodegenerative disease pathway [Term] id: PW:0000172 name: spinobulbar muscular atrophy def: "An inherited neurodegenerative disease caused by an expanded polyQ tract. Various pathways are disrupted and contribute to the manifestation of the condition." [PubMed:2004\, v. 20(3)\, 146-154.] synonym: "SBMA" RELATED [] is_a: PW:0000173 ! spinocerebellar ataxia [Term] id: PW:0000173 name: spinocerebellar ataxia def: "An inherited form of neurodegenerative disease caused by an expanded polyQ tract. Several types are grouped under SCA, types 1-3, 6, 7 and 17.Various pathways are disrupted and contribute to the manifestation of the condition." [PubMed:2004\, v.20(3)\, 146-154.] synonym: "SCA" RELATED [] is_a: PW:0000171 ! disease pathways related to polyQ repeats [Term] id: PW:0000174 name: metabolic syndrome pathway def: "The metabolic syndrome is a multiphenotypic condition with concurrent features of several diseases and metabolic abnormalities. Insulin resistance, obesity and hypertension are considered risk factors. Alterations in lipid, glucose and cholesterol metabolic pathways among others, can contribute to the multifactorial metabolic syndrome and the conditions associated with it." [PubMed:2004\, v. 17\, 38047; PMID\: 16932765] is_a: PW:0000020 ! cardiovascular disease pathway [Term] id: PW:0000175 name: familial combined hyperlipidemia pathway def: "A possible subset of the metabolic syndrome, characterized by features such as hypertriglyceridemia, age-dependent changes in plasma total cholesterol, overproduction of triglyceride-rich lipoproteins. Several metabolic and possibly other pathways deviate from their normal functioning." [PubMed :2004\, v.17\, 38-47.] synonym: "FCHL" RELATED [] relationship: part_of PW:0000174 ! metabolic syndrome pathway [Term] id: PW:0000176 name: diabetes pathway def: "A broad condition with various manifestations that is associated with disruptions of several pathways, primarily those involving insulin signaling. High glucose-mediated oxidative stress on VEGF over-expression and VEGF-mediated signaling are thought to play a role in diabetic retinopathy." [InHouse:PW dictionary, Reactome:REACT_15380.1] is_a: PW:0000013 ! disease pathway [Term] id: PW:0000177 name: diabetic nephropathy pathway def: "A common complication of diabetes and a leading cause of end stage renal diseases affecting a number of pathways, particularly the thiol and anti-oxidant pathways." [InPress:Manuscript] is_a: PW:0000176 ! diabetes pathway is_a: PW:0000300 ! renal disease, renal disorder pathway [Term] id: PW:0000178 name: neurological disorder disease pathway def: "Neurological disorders are a group of disorders that involve the central nervous system (brain, brainstem and cerebellum), the peripheral nervous system (including cranial nerves), and the autonomic nervous system (parts of which are located in both central and peripheral nervous system). Major branches are headache, stupor and coma, dementia, seizure, sleep disorders, trauma, infections, neoplasms, neuro-ophthalmology, movement disorders, demyelinating diseases, spinal cord disorders, and disorders of peripheral nerves, muscle and neuromuscular junctions. Many mental illnesses are believed to be neurological disorders of the central nervous system, but they are classified separately. They are not traditionally listed as neurological diseases because their causes are not definitely determined as biological, although there are good reasons to suspect that bipolar disorder and schizophrenia have neuro-chemical causes." [OneLook:www.onelook.com] is_a: PW:0000013 ! disease pathway [Term] id: PW:0000179 name: tuberous sclerosis complex disease pathway def: "An autosomal dominant condition that often leads to seizure and other neurological symptoms and that may be linked to deregulations in the mTOR signaling pathway." [PubMed:2004\, v.29(1)\, 32-38.] synonym: "TSC" RELATED [] is_a: PW:0000178 ! neurological disorder disease pathway [Term] id: PW:0000180 name: mTOR signaling pathway def: "mTOR signaling pathway regulates cellular processes such as translation, ribosome biogenesis, cell growth and autophagy and is regulated or responds to growth factors, energy metabolites and/or levels of nutrients." [KEGG:map04150, PubMed:TIBS\, 2004\, v. 29(1)\, 32-38., Reactome:REACT_6838.1] synonym: "KEGG:04150" RELATED [] synonym: "PID:200096" RELATED [] is_a: PW:0000003 ! signaling pathway is_a: PW:0000085 ! pathways of replication, repair, gene expression, protein biosynthesis relationship: part_of PW:0000357 ! energy homeostasis pathway [Term] id: PW:0000181 name: pathways of protein folding, sorting, modification, translocation and degradation def: "The pathways thereby proteins fold or are maintained in a particular folding state, are sorted for translocation or degradation, are modified to regulate their function or to target them for degradation and finally, are degraded." [InHouse:InHouse PW dictionary] is_a: PW:0000004 ! regulatory pathway [Term] id: PW:0000182 name: lysosomes based pathway of protein degradation def: "A protein degradation pathway that involves proteases residing in lysosomes and exhibiting optimal activity at an acidic pH (e.g., cathepsins)." [PubMed:2003\, v. 285\, f1-f8.] is_a: PW:0000325 ! protein degradation pathway [Term] id: PW:0000183 name: the proteolytic pathway involving calcium-dependent proteases def: "A protein degradation pathway that involves calcium-dependent proteases (e.g., calpains) ," [PubMed:2003\, v. 285\, f1-f8.] is_a: PW:0000325 ! protein degradation pathway [Term] id: PW:0000184 name: terpenoid biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of terpenoids. The terpenoids, sometimes referred to as isoprenoids, are a class of naturally occurring chemicals. Terpenoids are derived from five-carbon isoprene units and are assembled and modified in manifold ways. They are classified according to the number of isoprene units. The mevalonate pathway and the non-mevalonate MEP/DOXP pathway are the two biosynthetic routes. The first can branch into non-sterol and sterol-producing compounds. The second is only found in plants." [Gene Ontology:GO\:0016114, KEGG:map00900, OneLook:www.onelook.com] synonym: "" RELATED [] synonym: "KEGG:00900" RELATED [] is_a: PW:0000147 ! metabolic pathway of secondary metabolites [Term] id: PW:0000185 name: limonene and pinene degradation pathway def: "Those metabolic reactions involved in the degradation of limonene - an essential oil, a monocyclic terpene, found in the peel of oranges and lemons, and pinene - a terpene found in turpentine and many essential oils, used as a solvent and in the manufacture of camphor, insecticides, and synthetic pine oil." [KEGG:map00903, OneLook:www.onelook.com] is_a: PW:0000147 ! metabolic pathway of secondary metabolites [Term] id: PW:0000186 name: streptomycin biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of streptomycin - the first of the aminoglycoside antibiotics to be isolated, derived from Streptomyces griseus; it is effective against a wide variety of aerobic gram-negative bacilli and some gram-positive bacteria, including mycobacteria. Its use is now limited because of the emergence of resistant strains." [Gene Ontology:GO\:0019872, KEGG:map00521, OneLook:www.onelook.com] is_a: PW:0000147 ! metabolic pathway of secondary metabolites [Term] id: PW:0000187 name: erythromycin biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of erythromycin - an intermediate spectrum macrolide (a chemical compound characterized by a large lactone ring containing multiple keto and hydroxyl groups) antibiotic, produced by Streptomyces erythreus, effective against most gram-positive and certain gram-negative bacteria, such as Neisseria species and Haemophilus influenzae, and against spirochetes, some rickettsias, and Entamoeba; it is also highly effective against Mycoplasma pneumoniae. It is used especially in patients allergic to penicillin and in those with penicillin-resistant infections and legionnaires' disease; administered orally or topically." [OneLook:www.onelook.com] is_a: PW:0000147 ! metabolic pathway of secondary metabolites [Term] id: PW:0000188 name: pentose and glucuronate interconversion pathway def: "The series or metabolic reactions involved in the interconversions of the monosaccharide pentose and glucuronate, the salts or esters of glucuronic acid, as depicted in the KEGG diagram." [KEGG:http\://www.genome.ad.jp/kegg/pathway/map/map00040.html, KEGG:map00040] synonym: "KEGG:00040" RELATED [] is_a: PW:0000005 ! carbohydrate metabolic pathway [Term] id: PW:0000189 name: folate mediated one-carbon metabolic pathway def: "Folate mediated one-carbon metabolism refers to the various metabolic reactions/pathways that use folate compounds to transfer one-carbon units for the biosynthesis of a number of biomolecules in the cytoplasm and mitochondrion." [PubMed:PMID\: 15166809 ; PMID\: 11001804; PMID\: 15298442] synonym: "KEGG:00670" RELATED [] is_a: PW:0000140 ! pathway of folate cycle/metabolism [Term] id: PW:0000190 name: porphyrin and chlorophyll metabolic pathway def: "Those reactions involved in the synthesis, utilization and/or degradation of porphyrin - any of a group of compounds containing the porphyrin structure, four pyrrole rings connected by methine bridges in a cyclic configuration, to which a variety of side chains may be attached - and chlorophyll - any of a group of green magnesium-containing porphyrin derivatives occurring in all photosynthetic organisms." [KEGG:map00860, OneLook:www.onelook.com] synonym: "KEGG:00860" RELATED [] is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins [Term] id: PW:0000191 name: keratan sulfate biosynthetic pathway def: "Those metabolic reactions involved in the biosynthesis of keratan sulfate - a glycosaminoglycan found in the cornea, in cartilage, and in the nucleus pulposus and also as the accumulation product in Morquio's syndrome. It consists of repeating disaccharide units in specific linkage, each composed of a sulfated N-acetylglucosamine residue linked to one of galactose, which is usually sulfated. There are two forms, keratan sulfate I and keratan sulfate II, which differ in carbohydrate content and localization; the former occurs in the cornea and the latter in skeletal tissues." [Gene Ontology:GO\:0018146, KEGG:map00533, OneLook:www.onelook.com] synonym: "KEGG:00533" RELATED [] is_a: PW:0000157 ! glycosaminoglycan metabolic pathway [Term] id: PW:0000192 name: N-linked glycan biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of N-linked glycans. A 14 residue sugar is first built on a dolichol carrier and then attached to the amide group of an asparagine of a nascent polypeptide chain. The asparagine is in a specific amino acid sequence. Subsequent processing involves removal as well as addition of various sugars and produces a wide range of N-glycan structures." [KEGG:map00510, MCW Libraries:QU4 V876f 2008] synonym: "KEGG:00510" RELATED [] is_a: PW:0000146 ! glycan metabolic pathway [Term] id: PW:0000193 name: N-Glycan degradation pathway def: "Those metabolic reactions involved in the degradation of N-Glycans. N-Glycans are found attached to the R-group nitrogen of asparagine." [XPW InHouse Dictionary:InHouse Dictionary] is_obsolete: true [Term] id: PW:0000194 name: O-linked glycan biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of O-linked glycans. Sugars are serially added to a fully synthesized polypeptide chain. The initial step involves the transfer of N-acetylgalactosamine to the carboxy group of a serine or threonine. The location of the residue appears to be dictated by structure rather than amino acid signature." [KEGG:map00512, MCW Libraries:QU4 V876f] synonym: "KEGG:00512" RELATED [] synonym: "KEGG:00514" RELATED [] is_a: PW:0000146 ! glycan metabolic pathway [Term] id: PW:0000195 name: chondroitin sulfate biosynthetic pathway def: "Those metabolic reactions involved in the biosynthesis of chondroitin. Chondroitin is a mucopolysaccharide occurring in sulfated form in various animal tissues (as cartilage)." [Gene Ontology:GO\:0030206, KEGG:map00532, OneLook:www.onelook.com] synonym: "KEGG:00532" RELATED [] is_a: PW:0000157 ! glycosaminoglycan metabolic pathway [Term] id: PW:0000196 name: globoside metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of globoside - a glycosphingolipid containing acetylated amino sugars and simple hexoses." [Gene Ontology:GO\:0001575, OneLook:www.onelook.com] synonym: "KEGG:00603" RELATED [] is_a: PW:0000733 ! glycosphingolipid metabolic pathway [Term] id: PW:0000197 name: sphingolipid metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of sphingolipids - important components of animal and plant membranes. They contain a long chain amino alcohol and a ceramide core. Ceramides are also the precursors of glycolipids, also referred to as glycosphingolipids, which have attached sugar(s)." [Gene Ontology:GO\:0006665, MCW library:QU4 M235b 2009, OneLook:www.onelook.com, PubMed:PMID\: 17976918] synonym: "KEGG:00600" RELATED [] is_a: PW:0000010 ! lipid metabolic pathway [Term] id: PW:0000198 name: p38 MAPK signaling pathway def: "A SAPK MAPK pathway that plays an important role in inflammation and may be involved in several forms of cancer." [Gene Ontology:GO\:0051403, KEGG:map04010, PubMed:PMID\: 14570565 ; 15102355 ., Reactome:REACT_12065.1] synonym: "PID:200018" RELATED [] is_a: PW:0000312 ! stress-regulated MAPK signaling pathway [Term] id: PW:0000199 name: the Wnt/calcium signaling pathway def: "A Wnt mediated pathway that is involved in the regulation of cell-cell adhesion and motility." [Gene Ontology:fGO\:0007223, KEGG:map04310, PubMed:PMID\:12573432\, 10858654] synonym: "the Wnt/Ca(II) pathway" RELATED [] is_a: PW:0000597 ! non-canonical Wnt signaling pathway [Term] id: PW:0000200 name: the planar cell polarity Wnt signaling pathway def: "The planar cell polarity (PCP) Wnt signaling pathway plays an essential in morphogenesis through the regulation of tissues patterning." [Gene Ontology:GO\:006071, KEGG:map04310, PubMed:PMID\: 12573432; 16765615] synonym: "PCP Wnt signaling pathway" RELATED [] is_a: PW:0000597 ! non-canonical Wnt signaling pathway [Term] id: PW:0000201 name: canonical Wnt signaling pathway def: "Wnt signaling pathway is involved in many developmental processes. In the conventional or canonical Wnt pathway, beta-catenin is a central component required for the transcriptional control of Wnt signaling target genes." [Gene Ontology:GO\:0060070, KEGG:map04310, PubMed:PMID\: 12573432; 15001769; 18432252, Reactome:REACT_11045.1] synonym: "beta-catenin dependent Wnt signaling pathway" RELATED [] synonym: "PID:200077" RELATED [] is_a: PW:0000008 ! Wnt signaling pathway [Term] id: PW:0000202 name: homologous recombination pathway of double-strand break repair def: "A specific pathway for repair of double-strand breaks. It is thought to be involved in repair of breaks generated in meiotic prophase, or during cell cycle specific phases such as the S and G2 phases." [Gene Ontology:GO\:0000724, KEGG:map03440, PubMed:Cell\, 2004\, v. 117\, p 171-184, Reactome:REACT_1874.1] synonym: "KEGG:03440" RELATED [] is_a: PW:0000663 ! DNA break and strand repair pathway [Term] id: PW:0000203 name: non-homologous end joining pathway of double-strand break repair def: "A specific pathway for repair of double-strand breaks. Possibly constitutive, it is the most important pathways in mammalian cells and plays an important role in mitotically replicating cells." [Gene Ontology:GO\:0006303, KEGG:map03450, PubMed:Cell\, 2004\, v. 117\, 171-184., PubMed:PMID\: 12947387, Reactome:REACT_1022.1] synonym: "KEGG:03450" RELATED [] synonym: "NHEJ pathway of double-strand break repair" EXACT [] is_a: PW:0000663 ! DNA break and strand repair pathway [Term] id: PW:0000204 name: Notch signaling pathway def: "Notch signaling pathway regulates processes involved in early embryonic development. It plays an important role in cell fate determination. Target genes of Notch have been implicated in angiogenesis, somitogenesis, gliogenesis. Deregulation of the Notch signaling pathway underlies a broad spectrum of diseases and clinical conditions." [Gene Ontology:GO\:0007219, KEGG:map04330, PubMed:Several articles in PubMed, Reactome:REACT_299.2] synonym: "KEGG:04330" RELATED [] synonym: "PID:200015" RELATED [] is_a: PW:0000332 ! cell-cell signaling pathway is_a: PW:0000650 ! signaling pathway pertinent to development is_a: PW:0000656 ! glycoprotein signaling pathway [Term] id: PW:0000205 name: dentatorubral-pallidoluysian atrophy disease pathway def: "Dentatorubral-pallidoluysian atrophy (DRPLA) is caused by an expanded trinucleotide repeat in the DRPLA gene. A very rare condition, it can be sporadic or autosomal dominant inherited. Three forms of DRPLA have been clinically classified: the ataxo-choreoathetoid form, the pseudo-Huntington form, and the myoclonic epilepsy form. " [NCBI:OMIM database] synonym: "DRPLA" RELATED [] is_a: PW:0000171 ! disease pathways related to polyQ repeats [Term] id: PW:0000206 name: transforming growth factor-beta signaling pathway def: "Transforming growth factor-beta (TGF-beta) signaling pathway regulates numerous cellular processes such as proliferation, differentiation, migration and cell death. The SMAD dependent pathway represents the core signaling cascade mediated by the TGF-beta superfamily. Mutations in TGF - beta family are responsible for a number of human diseases." [Gene Ontology:GO\:0007179, PubMed:TIBS\, 2004\, v29 (5)\, p265-273. (PMID\: 15130563 )l PMID\:16678165, Reactome:REACT_6844.5] synonym: "TGF- beta signaling pathway - SMAD dependent" EXACT [] is_a: PW:0000329 ! transforming growth factor-beta superfamily mediated signaling pathway [Term] id: PW:0000207 name: central obesity with hypertension pathway relationship: part_of PW:0000174 ! metabolic syndrome pathway [Term] id: PW:0000208 name: type 2 diabetes mellitus pathway def: "Diabetes mellitus is characterized by abnormally high levels of glucose in the blood. Hereditary and environmental factors are likely contributors but the exact mechanisms are not well understood. Type 2 diabetes mellitus, characterized by insulin resistance, involves alterations in insulin secretion and signaling and impaired glucose homeostasis pathways." [KEGG:map04930, OneLook:www.onelook.com] synonym: "KEGG:04930" RELATED [] synonym: "T2D pathway" EXACT [] synonym: "type II diabetes mellitus pathway" EXACT [] is_a: PW:0000176 ! diabetes pathway relationship: part_of PW:0000174 ! metabolic syndrome pathway [Term] id: PW:0000209 name: Jak-Stat signaling pathway def: "The Jak-Stat pathway is a main intracellular cascade initiated primarily in response to cytokine and also other ligand signaling. Four Janus kinases (Jak) and seven signal transducers and activators of transcription (Stat) families of proteins mediate the action of almost 40 cytokine receptors, including the receptor for leptin. Combinations between four Jak(s) and seven Stat(s) shape the outcome of ligand triggered signaling through the various receptors." [Gene Ontology:GO\:0007259, KEGG:map04630, MCW library:Handbook of cellular and molecular immunology, PubMed:14737178; 14668806; 12039028; 17312100] synonym: "KEGG:04630" RELATED [] is_a: PW:0000003 ! signaling pathway is_a: PW:0000818 ! signaling pathway pertinent to immunity [Term] id: PW:0000210 name: SMAD dependent signaling pathways def: "The core intracellular signaling cascade mediated by the TGF-beta superfamily. SMAD proteins function by carrying signals from the cell surface to the nucleus. There are eight vertebrate SMAD proteins and they are activated by two types of TGF-beta receptors in response to TGF cytokines binding.There are two known SMAD-dependent TGF-beta signaling pathways. SMAP pathways can also be activated via NGF signalign pathways" [PubMed:Science\, 2002\, v296\, p1564-7; PMID\: 14534577.PMID\: 15009204] is_obsolete: true [Term] id: PW:0000211 name: amines and polyamines metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of amines and polyamines. Amines are organic compounds where the nitrogen atom of the amino functional group is attached via single bonds to one, two or three alkyl or aryl groups. Polyamines contain one or more amine groups." [Gene Ontology:GO\:0006595, OneLook:www.onelook.com, Reactome:REACT_14820.1] is_a: PW:0000002 ! classic metabolic pathway [Term] id: PW:0000212 name: betaine biosynthetic pathway I is_a: PW:0000211 ! amines and polyamines metabolic pathway [Term] id: PW:0000213 name: betaine biosynthetic pathway II is_a: PW:0000211 ! amines and polyamines metabolic pathway [Term] id: PW:0000214 name: polyamine biosynthetic pathway I is_a: PW:0000211 ! amines and polyamines metabolic pathway [Term] id: PW:0000215 name: polyamine biosynthetic pathway II is_a: PW:0000211 ! amines and polyamines metabolic pathway [Term] id: PW:0000216 name: spermine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of spermine - s polyamine involved in cellular metabolism." [Gene Ontology:GO\:0008215, OneLook:www.onelook.com, XX:] is_a: PW:0000211 ! amines and polyamines metabolic pathway [Term] id: PW:0000217 name: tetrahydrobiopterin metabolic pathway def: "Tetrahydrobiopterin is a cofactor for amino acid hydroxylases involved in the synthesis of several neurotransmitters. It can be synthesized de novo from guanosine triphosphate (GTP) or recycled via a regeneration pathway." [OneLook:http\://www.onelook.com] synonym: "BH4 metabolic pathway" EXACT [] is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins [Term] id: PW:0000218 name: heme biosynthetic pathway def: "Those metabolic reactions involved in the biosynthesis of heme - an iron-containing compound where the iron is complexed within a porphyrin heterocyclic ring. There are several kinds of heme depending on the composition of their side chain. Heme serves as a prosthetic group for a number of proteins." [OneLook:www.onelook.com] is_a: PW:0000221 ! heme metabolic pathway [Term] id: PW:0000219 name: NAD biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of NAD - nicotinamide adenine dinucleotide. NAD can be synthesized de novo from tryptophan or from 'salvageable precursors' such as niacin or nicotinamide. NAD can be phosphorylated to NADP. NAD is used extensively in glycolysis and the citric acid cycle of cellular respiration." [OneLook:www.onelook.com, PubMed:PMID\: 18429699] is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins [Term] id: PW:0000220 name: pyridine nucleotide biosynthetic pathway is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins [Term] id: PW:0000221 name: heme metabolic pathway is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins [Term] id: PW:0000222 name: UDP-N-acetylgalactosamine biosynthetic pathway is_obsolete: true [Term] id: PW:0000223 name: UDP-N-acetylglucosamine biosynthetic pathway is_obsolete: true [Term] id: PW:0000224 name: N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminic acid dissimilation pathway def: "Those metabolic reactions leading to the decomposition of N-acetylglucosamine - an acetylated amino sugar that is an important moiety of glycoproteins, N-acetylmannosamine - the acetylated derivative of mannosamine, and N-acetylneuraminic acid - the most common form of sialic acid in mammals." [OneLook:www.onelook.com] is_a: PW:0000152 ! amino sugar metabolic pathway [Term] id: PW:0000225 name: citrulline degradation pathway def: "Those metabolic reactions involving citrulline. Citrulline, not a DNA coded amino acid, is a product in the urea cycle." [Gene Ontology:GO\:0019241, OneLook:www.onelook.com] is_a: PW:0000132 ! metabolic pathway of other amino acids [Term] id: PW:0000226 name: putrescine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of putrescine - chemical name: tetra-methylene-diamine. A polyamine first found in decaying animal tissues but now known to occur in almost all tissues and in cultures of certain bacteria." [Gene Ontology:GO\:0009445, OneLook:www.onelook.com] is_a: PW:0000211 ! amines and polyamines metabolic pathway [Term] id: PW:0000227 name: G protein mediated signaling pathway via Galphas family def: "Based on sequence similarity, the Galpha genes have been grouped into four classes. Exchange of GDP to GTP promoted through binding to receptors dissociates the heterotrimeric Galpa/beta/gamma complex. GTP-bound Galpha can then interact with downstream effectors. Lipid modification of Galpha regulates membrane localization and interactions with specific effectors." [PubMed:PMID\: 12040175; PMID\: 15747061] is_a: PW:0000125 ! G protein mediated signaling pathway relationship: part_of PW:0000528 ! angiotensin II signaling pathway via AT2 receptor relationship: part_of PW:0000676 ! glucagon signaling pathway relationship: part_of PW:0000713 ! vasopressin signaling pathway via receptor type 2 relationship: part_of PW:0000794 ! epinephrine signaling pathway via adrenergic receptor beta relationship: part_of PW:0000797 ! norepinephrine signaling pathway via adrenergic receptor beta relationship: part_of PW:0000851 ! dopamine signaling pathway via D1 family of receptors relationship: part_of PW:0001091 ! serotonin signaling pathway via receptors engaging G alphas protein family [Term] id: PW:0000228 name: G protein mediated signaling pathway via Galphai family def: "Based on sequence similarity, the Galpha genes have been grouped into four classes. Exchange of GDP to GTP promoted through binding to receptors dissociates the heterotrimeric Galpha/beta/gamma complex. GTP-bound Galpha can then interact with downstream effectors. Lipid modification of Galpha regulates membrane localization and interactions with specific effectors." [PubMed:PMID\: 12040175; PMID\: 15747061] is_a: PW:0000125 ! G protein mediated signaling pathway relationship: part_of PW:0000494 ! oxytocin signaling pathway relationship: part_of PW:0000527 ! angiotensin II signaling pathway via AT1 receptor relationship: part_of PW:0000528 ! angiotensin II signaling pathway via AT2 receptor relationship: part_of PW:0000586 ! orexin/hypocretin signaling pathway via orexin/hypocretin receptor 2 relationship: part_of PW:0000793 ! epinephrine signaling pathway via adrenergic receptor alpha 2 relationship: part_of PW:0000796 ! norepinephrine signaling pathway via adrenergic receptor alpha 2 relationship: part_of PW:0000850 ! glutamate signaling pathway via group II or III glutamate receptor relationship: part_of PW:0000852 ! dopamine signaling pathway via D2 family of receptors relationship: part_of PW:0000856 ! acetylcholine signaling pathway via muscarinic acetylcholine receptors engaging G alphai protein family relationship: part_of PW:0001089 ! serotonin signaling pathway via receptors engaging G alphai protein family [Term] id: PW:0000229 name: G protein mediated signaling pathway via Galphaq family def: "Based on sequence similarity, the Galpha genes have been grouped into four classes. Exchange of GDP to GTP promoted through binding to receptors dissociates the heterotrimeric Galpha/beta/gamma complex. GTP-bound Galpha can then interact with downstream effectors. Lipid modification of Galpha regulates membrane localization and interactions with specific effectors." [PubMed:PMID\: 12040175; PMID\: 15747061] is_a: PW:0000125 ! G protein mediated signaling pathway relationship: part_of PW:0000494 ! oxytocin signaling pathway relationship: part_of PW:0000527 ! angiotensin II signaling pathway via AT1 receptor relationship: part_of PW:0000585 ! orexin/hypocretin signaling pathway via orexin/hypocretin receptor 1 relationship: part_of PW:0000586 ! orexin/hypocretin signaling pathway via orexin/hypocretin receptor 2 relationship: part_of PW:0000712 ! vasopressin signaling pathway via receptor type 1 relationship: part_of PW:0000792 ! epinephrine signaling pathway via adrenergic receptor alpha 1 relationship: part_of PW:0000795 ! norepinephrine signaling pathway via adrenergic receptor alpha 1 relationship: part_of PW:0000849 ! glutamate signaling pathway via group I metabotropic glutamate receptor relationship: part_of PW:0000855 ! acetylcholine signaling pathway via muscarinic acetylcholine receptors engaging G alphaq protein family relationship: part_of PW:0001090 ! serotonin signaling pathway via receptors engaging G alphaq protein family [Term] id: PW:0000230 name: G protein mediated signaling pathway via Galpha12/Galpha13 family def: "Based on sequence similarity, the Galpha genes have been grouped into four classes. Exchange of GDP to GTP promoted through binding to receptors dissociates the heterotrimeric Galpa/beta/gamma complex. GTP-bound Galpha can then interact with downstream effectors. Lipid modification of Galpha regulates membrane localization and interactions with specific effectors." [PubMed:PMID\: 12040175; PMID\: 15747061] is_a: PW:0000125 ! G protein mediated signaling pathway relationship: part_of PW:0000527 ! angiotensin II signaling pathway via AT1 receptor [Term] id: PW:0000231 name: Rap1 pathways def: "A very close relative of Ras, Rap1 mediated pathway appears to control diverse processes such as modulation of growth and differentiation, secretion, integrin linked cell adhesion, morphogenesis." [PubMed:Nature Reviews\, Mol. Cell Biology\, 2001\, v2\, p369-77.] is_obsolete: true [Term] id: PW:0000232 name: phosphatidylinositol 3-kinase-Akt signaling pathway def: "Phosphatidylinositol 3-kinase-Akt signaling pathway involving PI3K class I enzymes, particularly class IA, controls various processes such as cell growth, proliferation and survival. Class IA enzymes couples to receptor tyrosine kinases or their adaptors; class IB couples to G-protein coupled receptor mainly via Galphai. The Akt family of protein kinases are activated downstream of class I PI3Ks and collectively (Akt1, 2, and 3) phosphorylate more than 70 cytoplasmic and nuclear substrates. Deregulation of the pathway has been linked to various forms of cancer." [PubMed:15143962 \, 15023437\, 14737178] synonym: "KEGG:04151" RELATED [] synonym: "phosphoinositide 3-kinase-Akt signaling pathway" EXACT [] synonym: "PI3K-Akt signaling pathway" EXACT [] synonym: "PID:200197" RELATED [] is_a: PW:0000963 ! phosphatidylinositol 3-kinase class I signaling pathway [Term] id: PW:0000233 name: tumor necrosis factor mediated signaling pathway def: "Tumor necrosis factor (Tnf) signaling plays pivotal roles in immunity, cell proliferation, differentiation and apoptosis by activating several pathways. NF-kB is a major pathway activated by Tnf; others include JNK and P38 MAPK. Through receptor associated adapters Tnf elicits apoptosis via the extrinsic pathway. Deregulation of Tnf signaling has been implicated in a great number of human diseases - cerebral malaria, cancer, multiple sclerosis, are a few examples." [Gene Ontology:GO\:0033209, PubMed:PMID\:12040173\, 12655295; 20303867, Reactome:REACT_1432.1] synonym: "PID:200102" RELATED [] synonym: "TNF signaling pathway" RELATED [] synonym: "TNFalpha signaling pathway" RELATED [] is_a: PW:0000106 ! extrinsic apoptotic pathway is_a: PW:0000236 ! tumor necrosis factor superfamily mediated signaling pathway is_a: PW:0000926 ! pro-inflammatory cytokine mediated pathway [Term] id: PW:0000234 name: innate immune response pathway def: "The innate immune response - a universal and ancient form of host defense against infection - is a first line of response to various pathogens and also to damaged cells. It plays a role in stimulating adaptive immunity; molecules generated during innate responses act as second signals that can impact on both the magnitude and the nature of the adaptive response." [Gene Ontology:GO\:0045087, PubMed:PMID\: 11861602; 20303867] is_a: PW:0000023 ! immune response pathway [Term] id: PW:0000235 name: adaptive immune response pathway def: "The adaptive immune response is an evolutionarily newer mechanism that provides great specificity and diversity of antigen recognition, immunological memory and specialized responses. The two types of adaptive immune response pathways are humoral and cellular or cell-mediated." [Gene Ontology:GO\:0002250, MCW library:Handbook on cellular and molecular immunology, PubMed:PMID\: 11861602] is_a: PW:0000023 ! immune response pathway [Term] id: PW:0000236 name: tumor necrosis factor superfamily mediated signaling pathway def: "Members of TNF superfamily mediate autoimmunity and inflammation, cell proliferation, survival and/or apoptosis through a number of signaling mechanisms that involve activation of nuclear factor-kappaB, of caspases and/or of mitogen-activated protein kinases (MAPK). TNF superfamily has been implicated in a wide range of human diseases including tumorigenesis, septic shock, rheumatoid arthritis and other conditions." [PubMed:PMID\: 14555214\, 11796220\, 11239407] synonym: "TNF superfamily signaling pathways" RELATED [] is_a: PW:0000828 ! cytokine mediated signaling pathway [Term] id: PW:0000237 name: stress response pathway is_a: PW:0000004 ! regulatory pathway [Term] id: PW:0000238 name: insulin-like growth factor signaling pathway def: "Processes regulated by insulin and insulin-like growth factor signaling systems include growth and survival of many tissues; for example, neuron and retina, bone, pancreatic beta-cells. Insulin is best known for its role in the regulation of blood glucose. Deregulation of the systems is implicated in a number of metabolic disorders." [Gene Ontology:GO\:0048009, PubMed:PMID\: 12169433] synonym: "PID:200100" RELATED [] is_a: PW:0000168 ! growth factor signaling pathway is_a: PW:0000467 ! peptide and protein hormone signaling pathway [Term] id: PW:0000239 name: type 1 diabetes mellitus pathway def: "Diabetes mellitus is characterized by abnormally high levels of glucose in the blood. Hereditary and environmental factors are likely contributors but the exact mechanisms are not well understood. Type 1 diabetes mellitus pathway involves alterations in immune response pathways resulting in destruction of the insulin-producing beta cells." [KEGG:map04940, OneLook:www.onelook.com] synonym: "KEGG:04940" RELATED [] synonym: "type I diabetes mellitus pathway" EXACT [] is_a: PW:0000176 ! diabetes pathway [Term] id: PW:0000240 name: neuropsychiatric disease pathway is_a: PW:0000013 ! disease pathway [Term] id: PW:0000241 name: schizophrenia pathway def: "Schizophrenia is a psychiatric diagnosis denoting a persistent, often chronic, mental illness variously affecting behavior, thinking, and emotion. The term schizophrenia comes from the Greek words schizo, (split or divide) and phrenos, (mind) and is best translated as \"shattered mind\"." [OneLook:www.onelook.com] is_a: PW:0000240 ! neuropsychiatric disease pathway [Term] id: PW:0000242 name: bipolar disorder pathway def: "As categorized by the DSM-IV, bipolar disorder is a form of mood disorder characterized by a variation of mood between a phase of manic or hypomanic elation, hyperactivity and hyper imagination, and a depressive phase of inhibition, slowness to conceive ideas and move, and anxiety or sadness. Together these form what is commonly known as manic depression. Manic depression, with its two principal sub-types, bipolar disorder and major depression, was first clinically described near the end of the 19th century by psychiatrist Emil Kraepelin, who published his account of the disease in his Textbook of Psychiatry. DSM-IV is the Diagnostic and Statistical Manual of Mental Disorders, published by the American Psychiatric Association, is the handbook used most often in diagnosing mental disorders in the United States and other countries." [OneLook:www.onelook.com] is_a: PW:0000240 ! neuropsychiatric disease pathway [Term] id: PW:0000243 name: vascular endothelial growth factor signaling pathway def: "The VEGF family plays key roles in angiogenesis and lymphangiogenesis. Through their receptors, VEGFs can initiate a diverse and complex network of signaling cascades. Deregulation of VEGFs mediated pathways, mostly through upregulation of VEGFs expression, has been implicated in a number of conditions, primarily cancer." [Gene Ontology:GO\:0048010, KEGG:map04370, OneLook\, PubMed:PMID\: 15563310; PMID\: 15544039, Reactome:REACT_12529.1] synonym: "KEGG:04370" RELATED [] synonym: "PID:200109" RELATED [] synonym: "PID:200188" RELATED [] synonym: "VEGF signaling pathways" EXACT [] is_a: PW:0000168 ! growth factor signaling pathway [Term] id: PW:0000244 name: angiotensin II signaling pathway def: "Angiotensin II signaling pathways play a critical role in the control of cardiovascular and renal homeostasis. Angiotensin II pathway can also contribute to cardiovascular diseases such as hypertension, atherosclerosis and heart failure." [PubMed:PMID\: 15638741\, PMID\: 15883759] is_a: PW:0000245 ! angiotensin signaling pathway [Term] id: PW:0000245 name: angiotensin signaling pathway def: "Angiotensin peptides Ang II, Ang III, Ang IV and Ang (1-7) generated from a single precursor protein - angiotensinogen - regulate an array of physiological and pathophysiological processes." [PubMed:PMID\: 12676163; PMID\: 12676165\, 15638741] is_a: PW:0000467 ! peptide and protein hormone signaling pathway relationship: part_of PW:0000492 ! renin-angiotensin cascade pathway [Term] id: PW:0000246 name: Rheb mediated signaling pathway def: "The Rheb family of proteins plays an essential role in the regulation of cell growth and cell cycle. Rheb could be a mediator of the mTOR signaling pathway. The results have been shown for Drosophila but remained to be established for mammals." [PubMed:PMID\: 15240005] is_a: PW:0000158 ! Ras family mediated signaling pathway [Term] id: PW:0000247 name: transforming growth factor-beta Smad independent signaling pathway def: "TGF-beta can activate signaling cascades others than the Smad mediated ones, including MAPK pathways such as Erk, p38 and JNK. The mechanisms of MAPK pathways activation by TGF-beta are not well understood." [PubMed:PMID\: 14534577] synonym: "TGF-beta Smad independent signaling pathway" RELATED [] is_a: PW:0000206 ! transforming growth factor-beta signaling pathway [Term] id: PW:0000248 name: isoprenoid metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of isoprenoids - a large class of biomolecules characterized by the presence of repeating structural isoprene units. Isoprenoids are precursors of sterols such as cholesterol and its derivative and also of non-sterols molecules many of which are used in the post-translational modification of proteins." [MCW library:QU4 M235b 2009] is_a: PW:0000010 ! lipid metabolic pathway [Term] id: PW:0000249 name: lipopolysaccharide biosynthetic pathway def: "Those metabolic reactions involved in the biosynthesis of lipopolysaccharides, also known as lipoglycans, found in the outer membrane of Gram-negative bacteria. They are large molecules consisting of a lipid and a polysaccharide joined by a covalent bond. In host cells they act as endotoxins which are recognized by members of the Toll-like receptors to elicit strong immune responses." [Gene Ontology:GO\:0009103, KEGG:map00540, OneLook:www.onelook.com] synonym: "" RELATED [] synonym: "lipoglycan biosynthetic pathway" RELATED [] synonym: "LPS biosynthetic pathway" RELATED [] is_a: PW:0000876 ! bacterial polysaccharide metabolic pathway [Term] id: PW:0000250 name: peptidoglycan biosynthetic pathway def: "Those metabolic reactions involved in the biosynthesis of peptidoglycan - a high molecular weight polymer that forms the tough, rigid structure of bacterial cell walls. It is made up of three parts: (1) a backbone, composed of alternating N-acetylglucosamine and N-acetylmuramic acid; (2) a set of identical tetrapeptide side-chains attached to N-acetylmuramic acid; and (3) a set of identical peptide cross-bridges. The backbone is the same in all bacterial species; however, the tetrapeptide side-chains and the peptide cross-bridges vary from species to species." [Gene Ontology:GO\:0009252, KEGG:map00550, OneLook:www.onelook.com] synonym: "murein biosynthetic pathway" RELATED [] is_a: PW:0000876 ! bacterial polysaccharide metabolic pathway [Term] id: PW:0000251 name: diterpenoid biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of diterpenoid. Terpenoids are a large class of naturally-occurring organic chemicals. They are derived from five-carbon units and are modifed in manifold ways." [Gene Ontology:GO\:0016102, KEGG:map00904, OneLook:www.onelook.com] synonym: "KEGG:00904" RELATED [] is_a: PW:0000184 ! terpenoid biosynthetic pathway [Term] id: PW:0000252 name: monoterpenoid biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of monoterpenoid. Terpenoids are a large class of naturally-occurring organic chemicals. They are derived from five-carbon units and are modifed in manifold ways." [Gene Ontology:GO\:0016099, KEGG:map00902, OneLook:www.onelook.com] is_a: PW:0000147 ! metabolic pathway of secondary metabolites [Term] id: PW:0000253 name: indole and ipecac alkaloid biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of indole and ipecac. Indole is a heterocyclic compound, obtained from coal tar, and produced by the decomposition of tryptophan in the intestine, being partly responsible for the peculiar odor of the feces. It is also found in cultures of Vibrio cholerae and other bacteria; a color test for its production is used in classifying enteric bacteria. Ipecac is derived from the dried rhizome and roots of Cephaelis ipecacuanha or of C. acuminata. It is a mixture of alkaloids, primarily emetine and cephaelin." [OneLook:www.onelook.com] is_a: PW:0000147 ! metabolic pathway of secondary metabolites [Term] id: PW:0000254 name: penicillins and cephalosporins biosynthetic pathway def: "Those metabolic reactions involved in the biosynthesis of penicillin and cephalosporins. The former is the best known antibiotic which blocks the cross linking reaction in peptidoglycan synthesis, thus destroying the bacterial cell wall. The latter represents a broad class of antibiotics similar to penicillin, both chemically and in mode of action." [KEGG:map00311, OneLook:www.onelook.com] is_a: PW:0000147 ! metabolic pathway of secondary metabolites [Term] id: PW:0000255 name: beta-Lactam resistance pathway def: "Those pathways that confer to an organism resistance to the action of beta-lactams - a class of broad spectrum antibiotics that are structurally and pharmacologically related to penicillins and cephalosporins." [KEGG:map00312, OneLook:www.onelook.com] is_a: PW:0000147 ! metabolic pathway of secondary metabolites [Term] id: PW:0000256 name: polyketides biosynthetic pathway def: "Those metabolic reactions involved in the biosynthesis of polyketides. Polyketides are a group of secondary metabolites made by microorganisms that possess a broad range of pharmacologically important activities such as antimicrobial, antifungal, antiparasitic and antitumor." [Internet:http\://linux1.nii.res.in/~pksdb/polyketide.html] is_a: PW:0000147 ! metabolic pathway of secondary metabolites [Term] id: PW:0000257 name: polyketide sugar biosynthetic pathway is_a: PW:0000147 ! metabolic pathway of secondary metabolites [Term] id: PW:0000258 name: tetracycline biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of tetracycline - any of a group of biosynthetic antibiotics. Some are isolated from certain species of Streptomyces and others are produced semisynthetically." [Gene Ontology:GO\:0043644, KEGG:map00253, OneLook:www.onelook.com] is_a: PW:0000147 ! metabolic pathway of secondary metabolites [Term] id: PW:0000259 name: clavulanic acid biosynthetic pathway def: "Those metabolic reactions involved in the biosynthesis of clavulanic acid. Clavulanic acid is a beta-lactam antibiotic produced by a bacterium of the genus Streptomyces (S. clavuligerus) that is a beta-lactamase inhibitor and is usually used in the form of its clavulanate salt of potassium especially in combination with amoxicillin" [Gene Ontology:GO\:0033050, Internet:Google, KEGG:map00331] is_a: PW:0000147 ! metabolic pathway of secondary metabolites [Term] id: PW:0000260 name: puromycin biosynthetic pathway def: "Those metabolic reactions involved in the biosynthesis of puromycin - an antibiotic produced by Streptomyces alboniger, which has been used experimentally as an antineoplastic because of its ability to inhibit protein synthesis; it also has trypanosomicidal and amebicidal activity and was formerly used in the treatment of African trypanosomiasis and amebic dysentery." [Gene Ontology:GO\:0043638, KEGG:map00231, OneLook:www.onelook.com] is_a: PW:0000147 ! metabolic pathway of secondary metabolites [Term] id: PW:0000261 name: neuronal secretory pathway def: "The unique morphology of the neuron defies the classical organization of secretory pathways. The neuronal secretory pathway represents the intracellular trafficking route for proteins involved in synaptic transmission and plasticity as well as for lipids necessary for outgrowth and remodeling of the somatodendritic compartment. Neurons possess both somatic and dendritic Golgi compartments." [PubMed:PMID\: 15232591] relationship: part_of PW:0000059 ! signaling pathway pertinent to the brain [Term] id: PW:0000262 name: altered metabolic pathway def: "Those metabolic pathways that deviate from what their normal course should be. Aberrant metabolic pathways, alone or in combination with other pathways, underlie many conditions, disorders and/or diseases." [PW Dictionary:InHouse dictionary] is_a: PW:0000002 ! classic metabolic pathway [Term] id: PW:0000263 name: altered regulatory pathway def: "Those regulatory pathways that deviate from what their normal course should be. Aberrant regulatory pathways, alone or in combination with other pathways underlie many conditions, disorders and/or diseases." [PW Dictionary:InHouse Dictionary] is_a: PW:0000004 ! regulatory pathway [Term] id: PW:0000264 name: altered signaling pathway def: "Those signaling pathways that deviate from what their normal course should be. Aberrant signaling pathways, alone or in combination with other pathways underlie many conditions, disorders and/or diseases." [PW Dictionary:InHouse Dictionary] is_a: PW:0000003 ! signaling pathway [Term] id: PW:0000265 name: Creutzfeldt-Jakob disease pathway def: "Creutzfeldt-Jakob disease - a rare prion disease, associated with a number of different mutations of the prion protein gene, existing in sporadic, familial (as an autosomal dominant), and infectious forms, with onset usually in middle life, and having a wide variety of clinical and pathological features. The most commonly seen are varying degrees of spongiform degeneration of neurons, neuronal loss, gliosis, and amyloid plaque formation, accompanied by rapidly progressive dementia, myoclonus, motor disturbances." [OneLook:www.onelook.com] synonym: "CJD" RELATED [] is_a: PW:0000019 ! prion diseases pathway [Term] id: PW:0000266 name: Gerstmann-Strussler syndrome, Gerstmann-Strussler-Scheinker syndrome pathway def: "Gerstmann-Strussler syndrome, Gerstmann-Strussler-Scheinker syndrome - a group of rare prion diseases, of autosomal dominant inheritance but linked to different mutations of the prion protein gene. Common characteristics include cognitive and motor disturbances, the presence of multicentric amyloid plaques in the brain. Its manifestations include cerebellar ataxia and dementia, rigidity, tremor, memory loss and others, depending on the form of the condition." [OneLook:www.onelook.com] is_a: PW:0000019 ! prion diseases pathway [Term] id: PW:0000267 name: fatal familial insomnia pathway def: "Fatal familial insomnia - an inherited prion disease, transmitted as an autosomal dominant trait, affecting primarily the ventral and dorsomedial nuclei of the thalamus and characterized by progressive insomnia, hallucinations, stupor, and coma ending in death within 6 months to 3 years of onset; autonomic and motor disturbances are also present." [OneLook:www.onelook.com] is_a: PW:0000019 ! prion diseases pathway [Term] id: PW:0000268 name: kuru def: "Kuru - an infectious form of prion disease with a long incubation period, found only among the Fore and neighboring peoples of New Guinea. It is thought to be associated with ritual cannibalism. Its manifestations include truncal and limb ataxia, tremor, others; ends invariably in death. Amyloid plaques are present in about two thirds of affected individuals." [OneLook:www.onelook.com] is_a: PW:0000019 ! prion diseases pathway [Term] id: PW:0000269 name: protein folding pathway def: "Those reactions and molecular interactions underlying the folding of a protein into its functional three-dimensional structure. Folding takes place in the cytoplasm and, in the case of secreted proteins, in the endoplasmic reticulum. Proteins are checked (quality control) for proper folding and misfolded proteins are targeted for degradation." [Gene Ontology:GO\:0006457, MCW e-journals:Current Opinions in Cell Biology] is_a: PW:0000181 ! pathways of protein folding, sorting, modification, translocation and degradation relationship: part_of PW:0000280 ! secretory pathway [Term] id: PW:0000270 name: presynaptic differentiation is_a: PW:0000261 ! neuronal secretory pathway [Term] id: PW:0000271 name: postsynaptic differentiation is_a: PW:0000261 ! neuronal secretory pathway [Term] id: PW:0000272 name: neuron-to-neuron signaling pathways is_a: PW:0000059 ! signaling pathway pertinent to the brain [Term] id: PW:0000273 name: neuron-to-neuron signaling pathway via the electrical synapse def: "A simpler pathway of neuron-to-neuron signaling involving the direct flow of ionic currents. It is a reciprocal pathway involving membrane-to-membrane apposition known as gap junction." [PubMed:Annu. Rev. Neurosci. 2004\, v27\, p393-418., Reactome:REACT_16881.2] is_a: PW:0000272 ! neuron-to-neuron signaling pathways [Term] id: PW:0000274 name: neuron-to-neuron signaling pathway via the chemical synapse def: "A neurotransmitter-releasing pathway of neuron-to-neuron communication. It involves fusion of neurotransmitter-filled synaptic vesicles with the plasma membrane, activation of postsynaptic receptors. It also involves recycling and re-release of synaptic vesicles." [PubMed :Annu. Rev. Neursci. 2003\, v26\, 701-28., Reactome:REACT_13477.2] synonym: "Neurotransmission pathway" RELATED [] is_a: PW:0000272 ! neuron-to-neuron signaling pathways [Term] id: PW:0000275 name: cell death pathway def: "A cell death pathway represents the particular series of events leading to the demise of a whole cell or parts of its contents. It plays an essential role in cellular and tissues homeostasis. Deregulation of cell death can contribute to the development of cancer and neurodegeneration." [PubMed:PMID\: 18414491; 12196263; 20211164] is_a: PW:0000004 ! regulatory pathway [Term] id: PW:0000276 name: non-apoptotic cell death pathway def: "Non-apoptotic cell death pathway refers collectively to those types of cell death whose functional and/or morphological features are different from the apoptotic cell death." [PubMed:PMID\: 18414491; 12196263] is_a: PW:0000275 ! cell death pathway [Term] id: PW:0000277 name: senescence pathway is_a: PW:0000276 ! non-apoptotic cell death pathway [Term] id: PW:0000278 name: autophagy pathway def: "Autophagic pathway involves the sequestration of misfolded or long-lived proteins and of defective organelles within double membrane vesicles, delivery of the cargo to lysosomes for degradation and recycling." [Onelook:www.onelook.com, PubMed:PMID\:20211164\, 20034776\, 20089931] synonym: "KEGG:04140" RELATED [] is_a: PW:0000276 ! non-apoptotic cell death pathway [Term] id: PW:0000279 name: necrosis pathway def: "Necrosis represents the sum of the morphological changes indicative of cell death and caused by the progressive degradative action of enzymes; it may affect groups of cells or part of a structure or an organ. There are many causes of necrosis including injury, infection, cancer, infarction, inflammation, others. There are several distinctive morphologic patterns of necrosis." [Onelook:www.onelook.com] is_a: PW:0000276 ! non-apoptotic cell death pathway [Term] id: PW:0000280 name: secretory pathway def: "The secretory pathway is the route by which secreted proteins travel from their biosynthesis and folding to their final destination. It involves ER insertion where folding and quality control of folding take place, move to Golgi and trans-Golgi Network (TGN) where sorting and final modifications take place, exit from Golgi and vesicular transport via exocytosis to final destinations." [PubMed:PMID\:18354421; 17686625; 18216874] is_a: PW:0000181 ! pathways of protein folding, sorting, modification, translocation and degradation [Term] id: PW:0000281 name: endocytosis pathway def: "The endocytic pathway allows for recycling of cargo delivered via the exocytic route, uptake of nutrients, internalization of receptors but also the engulfing of dying cells or of material foreign to the cell. Endocytosis can be subdivided into four pathways: Four pathways Endocytosis can take place via the clathrin-mediated endocytosis, caveolae-mediated endocytosis, micropinocytosis and phagocytosis." [Gene Ontology:GO\:0006897, PubMed:PubMed\:PMID\:18354421\, 16882731\, 16985500] synonym: "" RELATED [] synonym: "KEGG:04144" RELATED [] is_a: PW:0000004 ! regulatory pathway [Term] id: PW:0000282 name: benzoate degradation pathway def: "Those enzymatic reactions involved in the degradation of benzoate - a salt of benzoic acid or benzene carboxylic acid, a fungistatic compound widely used as a food preservative." [Gene Ontology:GO\:0043639, InHouse:PW dictionary] is_a: PW:0000107 ! xenobiotics biodegradation pathway [Term] id: PW:0000283 name: altered glycan metabolic pathway def: "Those metabolic pathways involving glycan that deviate from what their normal course should be. Aberrant glycan metabolic pathways, alone or in combination with other pathways, underlie various diseases." [PubMed:PMID\: 15459677] is_a: PW:0000146 ! glycan metabolic pathway is_a: PW:0000262 ! altered metabolic pathway [Term] id: PW:0000284 name: altered glycosaminoglycan pathway def: "Those metabolic pathways involving glycosaminoglycans that deviate from what their normal course should be. Aberrant glycosaminoglycan pathways, alone or in combination with other pathways underlie various diseases." [PubMed:PMID\: 15459677] is_a: PW:0000157 ! glycosaminoglycan metabolic pathway is_a: PW:0000283 ! altered glycan metabolic pathway [Term] id: PW:0000285 name: altered heparan sulfate pathway def: "Those metabolic pathways involving heparan sulfate (HS) that deviate from what their normal course should be. Aberrant HS pathways, alone or in combination with other pathways may be involved in diseases. An example is the potential role of HS in Alzheimer's disease." [PubMed:PMID\: 14530380] is_a: PW:0000284 ! altered glycosaminoglycan pathway is_a: PW:0000524 ! heparan sulfate biosynthetic pathway [Term] id: PW:0000286 name: integrin mediated signaling pathway def: "Integrins signal bi-directionally across the plasma membrane. Inside-out signaling modulates their interaction with ligands to regulate cell adhesion and ECM organization. Ligand binding initiates and shapes many signaling events and links to the cytoskeleton. Via protein clustering and ECM organization integrins synergize with and/or modulate various growth factor pathways. Integrin signaling regulates multiple processes including gene expression, cell proliferation, differentiation and survival." [Gene Ontology:GO\:0007229, KEGG:map04510, PubMed:PMID\: 15009204 \, PMID\: 14570568; 15276463, Reactome:REACT_13552.1] is_a: PW:0000648 ! cell adhesion signaling pathway [Term] id: PW:0000287 name: altered apoptotic cell death def: "Those apoptotic pathways that deviate from what their normal course should be. Aberrant pathways of programmed cell death, alone or in combination with other pathways underlie various diseases." [PW:InHouse] is_a: PW:0000009 ! apoptotic cell death pathway is_a: PW:0000289 ! altered cell death pathway [Term] id: PW:0000288 name: altered intrinsic apoptotic pathway def: "An intrinsic apoptotic pathway that deviates from what its normal course should be. Aberrant intrinsic apoptotic pathway, alone or in combination with other pathways underlies various diseases." [PW:InHouse] is_a: PW:0000104 ! intrinsic apoptotic pathway is_a: PW:0000287 ! altered apoptotic cell death [Term] id: PW:0000289 name: altered cell death pathway def: "Those pathways of cell death that deviate from what their normal course should be. Aberrant pathways of cell death, alone or in combination with other pathways underlie various diseases." [PW:Inhouse] is_a: PW:0000263 ! altered regulatory pathway is_a: PW:0000275 ! cell death pathway [Term] id: PW:0000290 name: altered pathway of replication, repair, gene expression and protein biosynthesis def: "Those pathways of replication, gene expression and protein biosynthesis that deviate from what their normal course should be. Aberrant pathways of replication, gene expression and protein biosynthesis, alone or in combination with other pathways underlie various diseases." [PW:Inhouse] is_a: PW:0000085 ! pathways of replication, repair, gene expression, protein biosynthesis is_a: PW:0000263 ! altered regulatory pathway [Term] id: PW:0000292 name: altered DNA repair pathway def: "Those pathways of DNA repair that deviate from what their normal course should be. Aberrant pathways of DNA repair, alone or in combination with other pathways underlie various diseases." [PW:InHouse] is_a: PW:0000099 ! DNA repair pathway is_a: PW:0000290 ! altered pathway of replication, repair, gene expression and protein biosynthesis [Term] id: PW:0000293 name: altered pathway of protein folding, sorting, modification, translocation and degradation def: "Those pathways of protein folding, sorting, modification, translocation and degradation that deviate from what their normal course should be. Aberrant protein pathways, alone or in combination with other pathways underlie various diseases." [PW:InHouse] is_a: PW:0000181 ! pathways of protein folding, sorting, modification, translocation and degradation is_a: PW:0000263 ! altered regulatory pathway [Term] id: PW:0000294 name: altered ubiquitin/proteasome degradation pathway def: "An ubiquitin/proteasome degradation pathway that deviates from what its normal course should be. Aberrations in the pathway have been implicated in a number of diseases. Examples include certain malignancies, disorders of the immune and inflammatory responses and neurodegeneration." [PubMed:PMID\: 14556719] is_a: PW:0000144 ! ubiquitin/proteasome degradation pathway is_a: PW:0000418 ! altered ubiquitin, ubiquitin-like degradation pathway [Term] id: PW:0000295 name: altered integrin mediated signaling pathway def: "An integrin signaling pathway that deviates from what its normal course should be. Aberrant integrin signaling pathway, alone or in combination with other pathways underlies various diseases. An example is hypertrophic cardiomyopathy that involves integrins and the synergy between integrins and growth factors. Aberrant integrin signaling has also been correlated with tumor progression in several cancers." [PubMed:PMID\: 15276463] is_a: PW:0000286 ! integrin mediated signaling pathway is_a: PW:0000671 ! altered cell adhesion signaling pathway [Term] id: PW:0000296 name: hypertrophic cardimyopathy pathway def: "Hypertrophic cardiomyopathy, or HCM, is a disease of the myocardium (the muscle of the heart) in which a portion of the myocardium is thickened. Many physiological and pathological conditions as well as many pathways underlie the hypertrophic response." [KEGG:map05410, OneLook\, PubMed:www.onelook.org\, PMID\: 15276462] synonym: "HCM pathway" EXACT [] synonym: "KEGG:05410" RELATED [] is_a: PW:0000022 ! cardiomyopathy pathway [Term] id: PW:0000297 name: platelet-derived growth factor signaling pathway def: "PDGF signaling pathway plays an important role in the regulation of cell growth and survival." [Gene Ontology:GO\:0048008, PubMed:PMID\: 14515146, Reactome:REACT_16888.1] synonym: "PDGF signaling pathway" RELATED [] synonym: "PID:200149" RELATED [] synonym: "PID:200162" RELATED [] synonym: "PID:200201" RELATED [] is_a: PW:0000168 ! growth factor signaling pathway [Term] id: PW:0000298 name: altered growth factor signaling pathway def: "Those growth factor mediated signaling pathways that deviate from what their normal course should be. Aberrant growth factor mediated pathways, alone or in combination with other pathways underlie various diseases." [PW:InHouse3] is_a: PW:0000168 ! growth factor signaling pathway is_a: PW:0000264 ! altered signaling pathway [Term] id: PW:0000299 name: myocardial infarction pathway def: "Myocardial infarction, commonly known as heart attack, is a serious, sudden heart condition characterized by varying degrees of chest pain, weakness, sweating, nausea, and vomiting, sometimes causing loss of consciousness. It occurs when parts of the heart muscle die because they are not supplied with enough blood." [OneLook:www.onelook.org] is_a: PW:0000020 ! cardiovascular disease pathway [Term] id: PW:0000300 name: renal disease, renal disorder pathway def: "The congenital and acquired diseases affecting the kidney." [PW:InHouse] is_a: PW:0000013 ! disease pathway [Term] id: PW:0000301 name: renal failure pathway def: "Renal failure implies the loss of kidney function. It can be acute and rapidly progressing, or chronic with slow progression. Chronic renal failure may involve a number of kidney diseases and end-stage renal failure is the ultimate consequence." [Onelook:www.onelook.com] is_a: PW:0000300 ! renal disease, renal disorder pathway [Term] id: PW:0000302 name: glomerulonephritis pathway def: "Glomerulonephritis is accompanied by inflammation of the capillary loops in the glomeruli of the kidney. It occurs in acute, subacute, and chronic forms and may be secondary to hemolytic streptococcal infection. Evidence also supports possible immune or autoimmune mechanisms." [Onelook:www.onelook.org] is_a: PW:0000300 ! renal disease, renal disorder pathway [Term] id: PW:0000303 name: p53-dependent G1/S DNA damage checkpoint pathway def: "The p53-dependent pathway of G1 arrest in response to damaged DNA." [InHouse:PW dictionary, Reactome:REACT_85.1] synonym: "ATM pathway" RELATED PID [] is_a: PW:0000095 ! G1/S DNA damage checkpoint pathway [Term] id: PW:0000304 name: p53-independent G1/S DNA damage checkpoint pathway def: "The p53-independent pathway of G1/S arrest in response to damaged DNA." [InHouse:PW dictionary, Reactome:REACT_1208.1] is_a: PW:0000095 ! G1/S DNA damage checkpoint pathway [Term] id: PW:0000305 name: altered carbohydrate metabolic pathway def: "Those pathways of carbohydrate metabolism that deviate from what their normal course should be. Aberrant carbohydrate metabolic pathways, alone or in combination with other pathways, underlie various diseases." [InHouse:PW dictionary] is_a: PW:0000005 ! carbohydrate metabolic pathway is_a: PW:0000262 ! altered metabolic pathway [Term] id: PW:0000306 name: altered galactose metabolic pathway def: "Those pathways of galactose metabolism that deviate from what their normal course should be. An aberrant galactose metabolic pathways, alone or in combination with other pathways underlies various diseases. One example is the involvement of aberrant galactose catabolism in cancer." [InHouse :PW dictionary] is_a: PW:0000042 ! galactose metabolic pathway is_a: PW:0000305 ! altered carbohydrate metabolic pathway [Term] id: PW:0000307 name: coagulative necrosis pathway def: "Coagulative necrosis is typically seen in hypoxic environments. Cell outlines remain after cell death and can be observed by light microscopy (e.g. myocardial infarction, infarct of the spleen)." [Onelook:www.onelook.com] is_a: PW:0000279 ! necrosis pathway [Term] id: PW:0000308 name: liquefactive necrosis pathway def: "Liquefactive necrosis is associated with cellular destruction and pus formation (e.g. pneumonia)." [onelook:www.onelook.com] is_a: PW:0000279 ! necrosis pathway [Term] id: PW:0000309 name: caseous necrosis pathway def: "Caseous necrosis is a mix of coagulative necrosis and liquefactive necrosis (e.g. tuberculosis)." [OneLook:www.onelook.com] is_a: PW:0000279 ! necrosis pathway [Term] id: PW:0000310 name: fatty necrosis pathway def: "Fatty necrosis results from the action of lipases on fatty tissues (e.g. acute pancreatitis)." [Onelook:www.onelook.com] is_a: PW:0000279 ! necrosis pathway [Term] id: PW:0000311 name: fibrinoid necrosis pathway def: "Fibrinoid necrosis involves the deposition of fibrin and other plasma proteins in the walls of afferent renal arterioles in malignant hypertension, often accompanied by an inflammatory infiltrate within the walls and thrombosis of the vessel lumen. " [Onelook:www.onelook.com] is_a: PW:0000279 ! necrosis pathway [Term] id: PW:0000312 name: stress-regulated MAPK signaling pathway def: "MAPK signaling pathways that are responding to stress or injury as well as inflammatory cytokines" [PubMed :PMID\: 10209154 ; PMID\: 14570565; PMID\: 17306385; PMID\: 17229475] synonym: "SAPK signaling pathway" RELATED [] is_a: PW:0000007 ! mitogen activated protein kinase signaling pathway [Term] id: PW:0000313 name: c-Jun N-terminal kinases MAPK signaling pathway def: "A stress induced MAPK pathway that regulates an array of processes such as gene expression, cell migration, cytoskeletal organization, apoptosis." [Gene Ontology:GO\:0007254, KEGG:map04010, PubMed :PMID\: 15102441] synonym: "JNK signaling pathway" RELATED [] is_a: PW:0000312 ! stress-regulated MAPK signaling pathway [Term] id: PW:0000314 name: calcium/calmodulin dependent signaling pathway def: "Those signaling pathways that are mediated through the binding of calmodulin - a multifunctional calcium transducer - to its target effectors." [PubMed:PMID\: 10884684 \, PMID\: 14671000] synonym: "Ca/CaM dependent signaling pathways" RELATED [] is_a: PW:0001140 ! calcium/calcium-mediated signaling pathway [Term] id: PW:0000315 name: calcineurin signaling pathway def: "Calcineurin - a calcium/calmodulin dependent serine/threonine phosphatase - plays important regulatory roles in cardiac muscle growth and differentiation, memory processes and apoptosis." [PuvMed:PMID\: 15232210 \,] is_a: PW:0000314 ! calcium/calmodulin dependent signaling pathway is_a: PW:0000653 ! serine/threonine-specific phophatase mediated signaling pathway [Term] id: PW:0000316 name: calcium/calmodulin dependent kinase signaling pathway def: "Calcium/calmodulin dependent kinases - a family of multifunctional serine/threonine kinases - play important regulatory roles in cell proliferation." [PubMed:PMID\: 14671000] synonym: "Ca/CaM dependent CaMKs pathway" RELATED [] is_a: PW:0000314 ! calcium/calmodulin dependent signaling pathway [Term] id: PW:0000317 name: nuclear factor of activated T-cells signaling pathway def: "Members of the NFAT family of transcription factors, once de-phosphorylated by calcineurin translocate from the cytoplasm to the nucleus where they induce the transcription of genes involved in the immune response, cell-cell interactions. NFAT signaling is believed to play important roles in the development and function of the cardiovascular system." [Gene Ontology:GO\:0033173, pUBmED:PMID\: 11983154 \,PMID\: 12975316] synonym: "NFAT signaling pathway" RELATED [] is_a: PW:0000716 ! transcription factor mediated signaling pathway [Term] id: PW:0000318 name: altered calcium/calmodulin dependent pathway def: "Those calcium/CaM dependent pathways that deviate from what their normal course should be. Aberrant calcium/CaM dependent pathways, alone or in combination with other pathways underlie many diseases. One example is the potential role disruptions within these pathways play in cardiac hypertrophy." [PW dictionary:InHouse PW] synonym: "altered Ca/CaM dependent pathway" RELATED [] is_a: PW:0000264 ! altered signaling pathway is_a: PW:0000314 ! calcium/calmodulin dependent signaling pathway [Term] id: PW:0000319 name: altered calcineurin signaling pathway def: "A calcineurin signaling pathway that deviates from what its normal course should be. Aberrant calcineurin pathway, alone or in combination with other pathways underlie various diseases. One example is the role a constitutively active calcineurin plays in cardiac hypertrophy, via the NFAT pathway." [PubMed:PMID\: 15276472] is_a: PW:0000315 ! calcineurin signaling pathway is_a: PW:0000318 ! altered calcium/calmodulin dependent pathway [Term] id: PW:0000320 name: novobiocin biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of novobiocin, an aminocoumarin antibiotic. It is also known as albamycin or cathomycin and is produced by an actinomycete of the order Actinobacteria." [Gene Ontology:GO\:0043642, KEGG:map00401, OneLook:www.onelook.com] is_a: PW:0000147 ! metabolic pathway of secondary metabolites [Term] id: PW:0000321 name: altered Hedgehog signaling pathway def: "A Hedgehog signaling pathway that deviates from what its normal course should be. Aberrant Hedgehog signaling pathway has been involved in a number of human cancers." [PubMed:PMID\: 12495844\, PMID\: 15205520.] is_a: PW:0000122 ! Hedgehog signaling pathway is_a: PW:0000673 ! altered signaling pathway pertinent to development [Term] id: PW:0000322 name: ephrin - ephrin receptor bidirectional signaling axis def: "Ephrins and their receptors constitute a bidirectional signaling pathway transducing forward signals through the receptors and reverse signals through the ephrins that influence the behavior of both interacting cells. The Eph/ephrin axis plays important roles in cell morphology, adhesion and migration. Its disruption has been implicated in several human cancers." [Gene Ontology:GO\:0048013, PubMed:PMID\: 15093606] synonym: "eph/ephrin receptor bidirectional signaling axis" EXACT [] synonym: "PID:200052" RELATED [] synonym: "PID:200059" RELATED [] synonym: "PID:200142" RELATED [] synonym: "PID:200204" RELATED [] synonym: "PID:200216" RELATED [] is_a: PW:0000332 ! cell-cell signaling pathway [Term] id: PW:0000323 name: altered ephrin - ephrin receptor bidirectional signaling pathway def: "An Eph/ephrin bidirectional axis that deviates from what its normal course should be. Aberrant Eph/ephrins axis has been implicated in a number of human cancers." [PubMed:PMID\: 15561600] is_a: PW:0000322 ! ephrin - ephrin receptor bidirectional signaling axis is_a: PW:0000336 ! altered cell-cell signaling pathway [Term] id: PW:0000324 name: altered Notch signaling pathway def: "A Notch signaling pathway that deviates from what its normal course should be. Aberrant Notch signaling pathway has been implicated in a number of human cancers." [PubMed:PMID\: 14988924\, 15288257\,PMID\: 11549580.] is_a: PW:0000204 ! Notch signaling pathway is_a: PW:0000336 ! altered cell-cell signaling pathway is_a: PW:0000669 ! altered glycoprotein signaling pathway is_a: PW:0000673 ! altered signaling pathway pertinent to development [Term] id: PW:0000325 name: protein degradation pathway def: "Those pathways involved in the degradation of proteins." [Gene Ontology:GO\:0030163, InHouse:InHouse PW dictionary] is_a: PW:0000181 ! pathways of protein folding, sorting, modification, translocation and degradation [Term] id: PW:0000326 name: altered protein degradation pathway is_a: PW:0000293 ! altered pathway of protein folding, sorting, modification, translocation and degradation is_a: PW:0000325 ! protein degradation pathway [Term] id: PW:0000327 name: protein disulphide bond pathway def: "The pathways involved in the formation, reduction and isomerization of disulphide bonds in proteins. Disulphide bonds are essential for the stability of proteins that are secreted or are localized to organelles of the secretory pathway." [PubMed:PMID\: 10754564] is_a: PW:0000269 ! protein folding pathway [Term] id: PW:0000328 name: fibroblast growth factor signaling pathway def: "The family of fibroblast growth factors comprises 22 ligands that bind several receptors. The pathway plays important roles during embryonic and postnatal development. Disregulation of the pathway has been associated with several types of cancer." [Gene Ontology:GO\:0007173, PubMed:PMID\:19601767; 19379279, Reactome:REACT_9470.2] synonym: "FGF signaling pathway" RELATED [] synonym: "PID:200220" RELATED [] is_a: PW:0000168 ! growth factor signaling pathway [Term] id: PW:0000329 name: transforming growth factor-beta superfamily mediated signaling pathway def: "The TGF-beta superfamily of growth factors regulates a broad spectrum of processes such as angiogenesis, embryonic development, cell differentiation, proliferation, wound healing. Binding to two types of serine/threonine receptors and activation of Smad proteins is a common theme. However, ligand-receptor interaction and the identity of the activated Smad protein(s) appear to be member specific." [KEGG:map04350, PubMed:PMID\: 15473857] synonym: "KEGG:04350" RELATED [] synonym: "TGF-beta superfamily mediated signaling pathway" EXACT [] is_a: PW:0000168 ! growth factor signaling pathway [Term] id: PW:0000330 name: Bone morphogenetic proteins signaling pathway def: "The bone morphogenetic proteins (BMP) are related to TGF-beta and activins and are members of the TGF-beta superfamily. The BMP signaling pathway plays important roles in induction and patterning of the mesoderm. BMP pathway cross-talks to other pathways such as TGF-beta, Wnt, MAPK, Notch, JAK-STAT and others." [Gene Ontology:GO\:0030509, PubMed:PMID\: 15368350, Reactome:REACT_12034.1] synonym: "BMP signaling pathway " EXACT [] synonym: "PID:200144" RELATED [] is_a: PW:0000329 ! transforming growth factor-beta superfamily mediated signaling pathway [Term] id: PW:0000331 name: activin signaling pathway def: "Activins are members of the TGF-beta superfamily of growth factors. The pathway plays important roles in embryonic development, inflammation, reproductive biology. Deregulation of activin signaling contributes to a number of pathological conditions." [Gene Ontology:GO\:0032924, PubMed:PMID\:19273500; 16997617; 16885529] synonym: "PID:200029" RELATED [] is_a: PW:0000329 ! transforming growth factor-beta superfamily mediated signaling pathway [Term] id: PW:0000332 name: cell-cell signaling pathway def: "Cell-cell signaling pathway conveys information between cells using cell adhesion molecules." [RGD:InHouse dictionary] is_a: PW:0000648 ! cell adhesion signaling pathway [Term] id: PW:0000333 name: cadherin mediated signaling pathway def: "Cadherins represent a large protein superfamily with many and important roles in cell adhesion and signaling. Cadherins are characterized by the presence of the extracellular cadherin, calcium-binding repeat. The number and structural similarities of repeats across families vary." [PubMed:PMID\: 18848899; 11171368] is_a: PW:0000332 ! cell-cell signaling pathway [Term] id: PW:0000334 name: connexin signaling pathway is_a: PW:0000332 ! cell-cell signaling pathway [Term] id: PW:0000335 name: altered transforming growth factor-beta superfamily mediated signaling pathway def: "Those TGF-beta superfamily mediated signaling pathways that deviate from what their normal course should be. Alone or in combination with other pathways they underlie many conditions such as pulmonary hypertension and various types of cancer." [PubMed:PMID\:18313409] synonym: "altered TGF-beta superfamily mediated signaling pathway" RELATED [] is_a: PW:0000298 ! altered growth factor signaling pathway is_a: PW:0000329 ! transforming growth factor-beta superfamily mediated signaling pathway [Term] id: PW:0000336 name: altered cell-cell signaling pathway def: "Those cell-cell signaling pathways that deviate from what their normal course should be." [PW dictionary:InHouse PW dictionary] is_a: PW:0000332 ! cell-cell signaling pathway is_a: PW:0000671 ! altered cell adhesion signaling pathway [Term] id: PW:0000337 name: selectin signaling pathway def: "Selectins represent a small family of lectin-like adhesion receptors that mediate cell-cell interactions via calcium-dependent recognition of sialylated glycans. The exact role of this signaling pathway is not well known." [PubMed:PMID\:] is_a: PW:0000332 ! cell-cell signaling pathway [Term] id: PW:0000338 name: altered cadherins mediated signaling pathway is_a: PW:0000333 ! cadherin mediated signaling pathway [Term] id: PW:0000339 name: altered connexins mediated signaling pathway is_a: PW:0000334 ! connexin signaling pathway [Term] id: PW:0000340 name: altered Notch signaling pathway involving the main players def: "An altered Notch signaling pathway due to mutation(s) in the main players. They include receptor(s), ligand(s), and members of the CSL complex." [InHouse:PW dictionary] is_a: PW:0000324 ! altered Notch signaling pathway [Term] id: PW:0000341 name: altered Notch signaling pathway involving the macromolecules modifying the main players def: "An altered Notch signaling pathway due to mutation(s) in the enzymes, macromolecules that act upon the main players. They include proteases, elements of the proteo- and glucosaminoglycan metabolic pathways, ubiquitin ligases, other proteins that modulate availability, sensitivity, endocytosis of ligands/receptors." [InHouse:PW dictionary] is_a: PW:0000324 ! altered Notch signaling pathway [Term] id: PW:0000342 name: altered Notch signaling pathway involving target gene(s) def: "An altered Notch signaling pathway due to mutation(s) in the target gene(s). They may include members of the HES and HERP families of basic helix-loop-helix (bHLH) transcriptional repressors." [InHouse:PW dictionary] is_a: PW:0000324 ! altered Notch signaling pathway [Term] id: PW:0000343 name: altered Notch signaling pathway involving promoters def: "An altered Notch signaling pathway due to mutation(s) in the promoters of target gene(s)." [InHouse:PW dictionary] is_a: PW:0000324 ! altered Notch signaling pathway [Term] id: PW:0000344 name: cerebrovascular disease pathway is_a: PW:0000013 ! disease pathway [Term] id: PW:0000345 name: cerebral arterial diseases pathway is_a: PW:0000344 ! cerebrovascular disease pathway [Term] id: PW:0000346 name: CADASIL pathway def: "CADASIL - cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy - a disease of the small cerebral arteries characterized by subcortical stroke and vascular dementia. It is associated with mutations in the Notch3 gene. More than fifty mutations are clustered within the first EGF repeats and involve the gain or loss of a cysteine." [PubMed:PMID\: 14667809; PMID\: 14986825] is_a: PW:0000345 ! cerebral arterial diseases pathway [Term] id: PW:0000347 name: cardiovascular abnormalities pathway is_a: PW:0000020 ! cardiovascular disease pathway [Term] id: PW:0000348 name: congenital heart defects pathway is_a: PW:0000347 ! cardiovascular abnormalities pathway [Term] id: PW:0000349 name: Alagille syndrome pathway def: "Alagille syndrome is a developmental disease characterized by defects in heart, as well as liver, skeleton and eye. Abnormalities of the central nervous system are also found. The disease is associated with mutations across the entire Jag1 gene." [PubMed:PMID\: 14986825] is_a: PW:0000348 ! congenital heart defects pathway [Term] id: PW:0000350 name: altered vascular endothelial growth factor signaling pathway def: "A VEGF mediated pathway that deviates from what its normal course should be. Aberrant VEGF mediated pathways have been implicated in a number of human cancers. Upregulation of VEGF expression is associated with cancer and tumor growth." [PubMed:PMID\: 15563310] synonym: "altered VEGF signaling pathways" RELATED [] is_a: PW:0000243 ! vascular endothelial growth factor signaling pathway is_a: PW:0000298 ! altered growth factor signaling pathway [Term] id: PW:0000351 name: altered vascular endothelial growth factor signaling pathway involving the main players def: "An altered VEGF signaling pathway due to mutation(s) in the main players. They include the various VEGF molecules and VEGF receptors." [InHouse:InHouse PW dictionary] synonym: "altered VEGF signaling pathway involving the main players" RELATED [] is_a: PW:0000350 ! altered vascular endothelial growth factor signaling pathway [Term] id: PW:0000352 name: altered vascular endothelial growth factor signaling pathway involving the macromolecules modifying the main players def: "An altered VEGF signaling pathway due to mutation(s) in the enzymes that process VEGF, such as the plasmin and furin-like proteases." [InHouse:In House PW dictionary] synonym: "altered VEGF signaling pathway involving the macromolecules modifying the main players" RELATED [] is_a: PW:0000350 ! altered vascular endothelial growth factor signaling pathway [Term] id: PW:0000353 name: altered vascular endothelial growth factor signaling pathway involving proteins affecting its expression def: "An altered VEGF signaling pathway due to mutation(s), any activity change in the proteins that regulate VEGF expression. They include transcription factors such as the hypoxia-inducible factor and the many proteins impacting on the stability and/or activity of these factors." [InHouse :InHouse PW dictionary] synonym: "altered VEGF signaling pathway involving proteins affecting its expression" RELATED [] is_a: PW:0000350 ! altered vascular endothelial growth factor signaling pathway [Term] id: PW:0000354 name: glycerophospholipid metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glycerophospholipids, also known as phospholipids. They are key components of membranes and some are also involved in signaling." [Gene Ontology:GO\:0006650, KEGG:map00564, MCW library:QU4 M235b 2009] synonym: "KEGG:00564" RELATED [] synonym: "phospholipid metabolic pathway" RELATED [] is_a: PW:0000010 ! lipid metabolic pathway [Term] id: PW:0000355 name: homeostasis pathway def: "Those pathways involved in the maintenance of the internal environment of an organism, the adequate levels of substances and nutrients, the stability of normal body states and the feedback regulatory mechanisms that control them." [OneLook:www.onelook.com] is_a: PW:0000004 ! regulatory pathway [Term] id: PW:0000356 name: oxygen homeostasis pathway def: "The pathways involved in responding to changes in and maintenance of adequate oxygen levels." [Gene Ontology:GO\:0032364, PubMed:PMID\: 11181957; 11181957; 12603312; 14597660; 15031665] is_a: PW:0000355 ! homeostasis pathway [Term] id: PW:0000357 name: energy homeostasis pathway def: "Those pathways involved in the balance between energy uptake and energy expenditure. Disturbance of this equilibrium has been linked to various conditions including obesity." [PubMed:PMID\: 15703762 \, PMID\: 11239410] is_a: PW:0000355 ! homeostasis pathway [Term] id: PW:0000358 name: altered homeostasis pathway def: "Those homeostatic pathways that deviate from what their normal course should be. Aberrant homeostatic pathways, alone or in combination with other pathways, underlie many conditions, disorders and/or diseases." [PW dictionary:PW InHouse dictionary] is_a: PW:0000263 ! altered regulatory pathway is_a: PW:0000355 ! homeostasis pathway [Term] id: PW:0000359 name: altered energy homeostasis pathway def: "Those pathways of energy homeostasis that deviate from what their normal course should be. Obesity in particular has been associated with disturbances in the control of energy balance." [PubMed :PMID\: 15703762 \,PMID\: 11239410] is_a: PW:0000357 ! energy homeostasis pathway is_a: PW:0000358 ! altered homeostasis pathway [Term] id: PW:0000360 name: hypoxia inducible factor pathway def: "The hypoxia inducible transcription factor is activated in response to hypoxic conditions to promote the expression of many genes that play important roles in glucose and energy metabolism, angiogenesis and erythropoiesis." [PubMed:PMID\: 11181957 PMID\: 12603312 \, PMID\: 14597660\, PMID\: 15031665 .] synonym: "HIF pathway" EXACT [] synonym: "PID:200036" RELATED [] synonym: "PID:200202" RELATED [] is_a: PW:0000100 ! transcription pathway relationship: part_of PW:0000356 ! oxygen homeostasis pathway [Term] id: PW:0000361 name: altered oxygen homeostasis pathway is_a: PW:0000356 ! oxygen homeostasis pathway is_a: PW:0000358 ! altered homeostasis pathway [Term] id: PW:0000362 name: the ion channels pathway def: "The acute hypoxic response is mediated through the activity of excitable cells via oxygen-sensing ion channels." [PubMed:PMID\: 11181957] relationship: part_of PW:0000356 ! oxygen homeostasis pathway [Term] id: PW:0000363 name: leptin system pathway def: "Leptin acts on two populations of hypothalamic neurons that express orexigenic (feeding inducing) and anorexigenic genes, respectively. Leptin reduces the expression of genes from the former and enhances the expression of genes from the latter neurons. Leptin mediated response acts primarily via Jak-dependent activation of STAT." [Gene Ontology:GO\:0033210, PubMed:PMID\: 12079865\, PMID\: 11239410 .] is_a: PW:0000467 ! peptide and protein hormone signaling pathway relationship: part_of PW:0000357 ! energy homeostasis pathway [Term] id: PW:0000364 name: altered leptin system pathway is_a: PW:0000359 ! altered energy homeostasis pathway is_a: PW:0000363 ! leptin system pathway is_a: PW:0000511 ! altered peptide and protein hormone signaling pathway [Term] id: PW:0000365 name: melanocortin system pathway def: "The melanocortin dependent system is involved in a diverse number of pathways such as pigmentation, steroidogenesis, sexual function, energy homeostasis. Its implication in energy homeostasis is of particular interest as alterations of this system have been associated with obesity." [PubMed:PMID\: 12556347 \,PMID\: 15189116 \,PMID\: 11874690] is_a: PW:0000467 ! peptide and protein hormone signaling pathway relationship: part_of PW:0000357 ! energy homeostasis pathway [Term] id: PW:0000366 name: altered melanocortin system pathway def: "A melanocortin dependent system pathway that deviates from what its normal course should be. Mutations in the prohormone gene PMOC and the modifying enzyme PC1 are linked to obesity. Mutations in MC2R receptor and its accessory protein MRAP have been associated with type 1 and 2 familial glucocorticoid deficiency, respectively." [PubMed :PMID\: 11874690\, 19028547] is_a: PW:0000359 ! altered energy homeostasis pathway is_a: PW:0000365 ! melanocortin system pathway is_a: PW:0000511 ! altered peptide and protein hormone signaling pathway [Term] id: PW:0000367 name: altered Jak-Stat signaling pathway def: "Jak-Stat signaling pathways that deviate from what their normal course should be." [InHouse:PW InHouse dictionary] is_a: PW:0000209 ! Jak-Stat signaling pathway is_a: PW:0000264 ! altered signaling pathway [Term] id: PW:0000368 name: Non-Stat, Jak dependent pathway def: "Those pathways dependent on activation by JAK kinases but independent of Stat proteins." [PubMed:PMID\: 12884916] is_a: PW:0000003 ! signaling pathway [Term] id: PW:0000369 name: nuclear factor, erythroid derived 2, like 2 signaling pathway def: "The nuclear factor, erythroid derived 2, like (Nfe2l2) also known as Nrf2 is a redox sensitive transcription factor that regulates the expression of phase II drug metabolizing enzymes and of other antioxidant as well as anti-inflammatory genes." [PubMed:PMID\: 15252150\, 22874821\, 20815789\, 20486759] synonym: "Nrf2 signaling pathway" EXACT [] is_a: PW:0000124 ! cellular detoxification pathway is_a: PW:0000378 ! oxidative stress response pathways is_a: PW:0000716 ! transcription factor mediated signaling pathway [Term] id: PW:0000370 name: aryl hydrocarbon receptor signaling pathway def: "The aryl hydrocarbon receptor (AhR) is a transcription factor whose ligands include a variety of aromatic hydrocarbons and which regulates the expression of phase I and phase II drug-metabolizing enzymes. Phase I enzymes convert otherwise inactive hydrocarbons into active metabolites with potential carcinogenic effects, thus rendering AhR a player in tumor initiation." [PubMed:PMID\: 15627472 \, 15451023\, 20868221\, 20106901] synonym: "AhR signaling pathway" EXACT [] is_a: PW:0000124 ! cellular detoxification pathway is_a: PW:0000716 ! transcription factor mediated signaling pathway [Term] id: PW:0000371 name: calcium homeostasis pathway def: "The maintenance of adequate intracellular calcium levels are crucial in order to assure the availability of this important ion and, at the same time prevent against the damage its high concentration can cause. Pumps and exchangers move the calcium ions into organelles or outside the cell, channels of many types allow for its transient flow inside the cell. Calcium transport, which maintains and controls the calcium gradient, and calcium signaling, which the gradient promotes, are inextricably connected in the fabric of calcium homeostasis." [PubMed:PMID\:17574670\, 18083096] is_a: PW:0000589 ! metal homeostasis pathway [Term] id: PW:0000372 name: altered calcium homeostasis pathway is_a: PW:0000358 ! altered homeostasis pathway is_a: PW:0000371 ! calcium homeostasis pathway [Term] id: PW:0000373 name: glutathione conjugation pathway def: "The glutathione conjugation of endogenous and exogenous electrophilic compounds represents a major pathway phase II biotransformation. The glutathione conjugates may either be excreted or undergo further processing." [MCW - book:QV 600 C335t 2001; PMID\:17482904, Reactome:REACT_6959.3] synonym: "phase II biotransformation" RELATED [] is_a: PW:0000378 ! oxidative stress response pathways is_a: PW:0000858 ! phase II biotransformation pathway [Term] id: PW:0000374 name: alternate pathways of glutathione conjugates processing def: "Pathways of glutathione conjugates processing other than the mercapturic acid pathway." [InHouse dictionary:PW InHouse dictionary] is_a: PW:0000373 ! glutathione conjugation pathway [Term] id: PW:0000375 name: phase I biotransformation pathway via cytochrome P450 def: "The major phase I biotransformation pathway for the activation of endogenous and exogenous substances carried out by members of the cytochrome P450 superfamily." [Book: QV 600 C335t 2001; PMID\:17482904\, 19835560, Reactome:REACT_13705.1] synonym: "KEGG:00980" RELATED [] synonym: "KEGG:00982 " RELATED [] is_a: PW:0000857 ! phase I biotransformation pathway [Term] id: PW:0000376 name: cytochrome P450-independent phase I biotransformation pathway def: "A minor phase I biotransformation pathway for the activation of endogenous and exogenous substances carried by flavin-containing monooxygenases." [PubMed:PMID\: 19835560] is_a: PW:0000857 ! phase I biotransformation pathway [Term] id: PW:0000377 name: glutathione conjugates processing - the mercapturic acid pathway def: "The mercapturic acid pathway of glutathione conjugates processing involves the sequential cleavage of glutamyl and glycine residues of glutathione followed by cysteine N-acetylation." [MCW book:QV 600 C335t 2001] is_a: PW:0000373 ! glutathione conjugation pathway [Term] id: PW:0000378 name: oxidative stress response pathways def: "Oxidative stress occurs when the redox balance between pro- and anti-oxidants is upset due to an increase in endogenous or exogenous pro-oxidant stimuli. The response triggers the upregulation of antioxidant and detoxification systems. Oxidants can also act as second messengers to trigger a variety of cellular signaling pathways." [Gene Ontology:GO\:0006979, InHouse:PW InHouse dictionary] is_a: PW:0000237 ! stress response pathway [Term] id: PW:0000379 name: endoplasmic reticulum stress - the unfolded protein response pathway def: "Inhibition of protein folding or its disruption by mutant proteins in the endoplasmic reticulum triggers a signal transduction response known as the unfolded protein response (UPR). UPR increases the biosynthetic capacity while decreasing the biosynthetic burden of the secretory pathway through up- and downregulation of gene expression." [Gene Ontology:GO\:0030968, PubMed:PMID\: 15603751; PMID\: 15952902] synonym: "ER stress - UPR pathway" RELATED [] is_a: PW:0000237 ! stress response pathway [Term] id: PW:0000380 name: transport pathway for the elimination of drugs, endogenous or exogenous compounds and metabolites def: "Drugs, endogenous and exogenous compounds processed through the phase I and II of bioactivation pathways (biotransformation) pathways are eliminated via phase III transport pathway carried out by several transporter families." [Gene Ontology:GO\:0015893, PubMed:PMID\: 17220560] is_a: PW:0000103 ! transport pathway is_a: PW:0000378 ! oxidative stress response pathways relationship: part_of PW:0000124 ! cellular detoxification pathway [Term] id: PW:0000381 name: multidrug resistance-associated protein mediated transport pathway synonym: "MRP mediated pathway" RELATED [] is_a: PW:0000380 ! transport pathway for the elimination of drugs, endogenous or exogenous compounds and metabolites [Term] id: PW:0000382 name: multidrug resistance protein mediated transport pathway synonym: "MDR mediated pathway" RELATED [] is_a: PW:0000380 ! transport pathway for the elimination of drugs, endogenous or exogenous compounds and metabolites [Term] id: PW:0000383 name: multispecific organic anion transporter mediated transport pathway synonym: "OAT mediated pathway" RELATED [] is_a: PW:0000380 ! transport pathway for the elimination of drugs, endogenous or exogenous compounds and metabolites [Term] id: PW:0000384 name: G2/M DNA damage checkpoint pathway def: "The G2M checkpoint pathways assure the genome is replicated only once per cell cycle. The checkpoints control for damaged and un-replicated DNA. Various DNA damage checkpoints lead to inhibition of the cyclin- dependent kinases that regulate the next cell cycle point." [InHouse:PW dictionary, Reactome:REACT_897.2] is_a: PW:0000096 ! G2/M checkpoint pathway [Term] id: PW:0000385 name: G2/M DNA replication checkpoint pathway def: "Those pathways that assure the genome is replicated only once per cell cycle. The checkpoints control for damaged and un-replicated DNA. Un-replicated DNA signals to block the cell cycle from proceeding. The mechanism by which the cell detects un-replicated DNA is not known." [InHouse:PW dictionary, Reactome:REACT_1846.2] is_a: PW:0000096 ! G2/M checkpoint pathway [Term] id: PW:0000386 name: Rap1 mediated signaling pathway def: "A very close relative of Ras, Rap1 mediated pathway appears to control diverse processes such as modulation of growth and differentiation, secretion, integrin linked cell adhesion, morphogenesis." [PubMed :PMID\: 11331911] is_a: PW:0000158 ! Ras family mediated signaling pathway [Term] id: PW:0000387 name: Arf family mediated signaling pathway def: "Arf family mediated signaling pathways are involved in the regulation of intracellular vesicle trafficking. In paritcular they appear to control early events such as vesicle budding." [Gene Ontology:GO\:0032011, PubMed:PMID\: 11152757; PMID\: 11152757] synonym: "PID:200195" RELATED [] is_a: PW:0000006 ! Ras superfamily mediated signaling pathway [Term] id: PW:0000388 name: Reelin signaling pathway def: "Reelin signaling pathway regulates neuronal positioning and may also play a role in synaptic plasticity. The reelin gene appears to be downregulated in the schizophrenic brains but the link between the reelin pathway and the disease remains to be established." [PubMed:PMID\: 14993361; PMID\: 12764038;PMID\: 14715136] synonym: "PID:200062" RELATED [] is_a: PW:0000059 ! signaling pathway pertinent to the brain is_a: PW:0000656 ! glycoprotein signaling pathway [Term] id: PW:0000389 name: altered pathway pertinent to signaling in the brain is_a: PW:0000059 ! signaling pathway pertinent to the brain is_a: PW:0000264 ! altered signaling pathway [Term] id: PW:0000390 name: altered Reelin signaling pathway is_a: PW:0000388 ! Reelin signaling pathway is_a: PW:0000389 ! altered pathway pertinent to signaling in the brain is_a: PW:0000669 ! altered glycoprotein signaling pathway [Term] id: PW:0000391 name: altered Ras superfamily mediated signaling pathway synonym: "altered monomeric G protein mediated signaling pathway" RELATED [] is_a: PW:0000006 ! Ras superfamily mediated signaling pathway is_a: PW:0000264 ! altered signaling pathway [Term] id: PW:0000392 name: altered Ras mediated signaling pathway def: "A Ras mediated signaling pathway that deviates from what its normal course should be. Aberrant Ras mediated signaling pathways have been implicated in a number of human cancers and deregulation of Ras has been reported even in the absence of mutations." [PubMed:PMID\: 11027944] is_a: PW:0000391 ! altered Ras superfamily mediated signaling pathway is_a: PW:0000525 ! Ras mediated signaling pathway [Term] id: PW:0000393 name: altered mTOR signaling pathway is_a: PW:0000180 ! mTOR signaling pathway is_a: PW:0000290 ! altered pathway of replication, repair, gene expression and protein biosynthesis is_a: PW:0000359 ! altered energy homeostasis pathway [Term] id: PW:0000394 name: dopamine signaling pathway def: "Dopamine signaling plays important roles in processes such as motivation, learning and movement. It also plays several roles in the periphery as a modulator of renal and cardiovascular and the endocrine systems. Dopamine signals to a family of at least 5 receptors that are classified into two subfamilies that couple to distinct G proteins to elicit diverse downstream events. Deregulation of the pathway has been implicated in several neuropsychiatric and neurological disorders." [Gene Ontology:GO\:0007212, PubMed:PMID\:18353279; 17408758] synonym: "dopaminergic pathway" RELATED [] synonym: "KEGG:04728" RELATED [] is_a: PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse is_a: PW:0000798 ! catecholamine signaling pathway [Term] id: PW:0000395 name: altered dopamine signaling pathway synonym: "altered dopaminergic pathway" RELATED [] is_a: PW:0000389 ! altered pathway pertinent to signaling in the brain is_a: PW:0000394 ! dopamine signaling pathway [Term] id: PW:0000396 name: spermidine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of spermidine - a polyamine involved in cellular metabolism." [Gene Ontology:GO\:0008216, OneLook:www.onelook.com] is_a: PW:0000211 ! amines and polyamines metabolic pathway [Term] id: PW:0000397 name: cobalamin metabolic pathway def: "Those metabolic reactions involving cobalamin, known as vitamin B12 - a water-soluble vitamin. Cobalamin which important roles in a number of metabolic pathways. There are several related compounds whose synthesis occurs in bacteria but whose conversion can be carried out in higher organisms." [OneLook:http\://www.onelook.com] synonym: "Vitamin B12 metabolic pathway" RELATED [] is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins [Term] id: PW:0000398 name: homocysteine metabolic pathway def: "Homocysteine (Hcy) metabolism is at the interesection of two pathways: the remethylation pathway that regenerates the methionine cycle and the transsulfuration pathway that gives rise to cysteine and derivatives. Hcy pathway also engages choline, folate, vitamin(s) metabolism and links to the metabolism of other amino acids and compounds." [MCW library book :Homocysteine in Health and Disease - edited by Ralph Carmel and Donald W Jacobsen] synonym: "Hcy metabolism" RELATED [] is_a: PW:0000132 ! metabolic pathway of other amino acids [Term] id: PW:0000399 name: remethylation pathway of homocysteine metabolism - cobalamin dependent relationship: part_of PW:0000398 ! homocysteine metabolic pathway [Term] id: PW:0000400 name: transsulfuration pathway of homocysteine metabolism def: "The transulfuration pathway is one of the two routes of homocysteine metabolism. It allows for the transfer of sulfur from methionine to cysteine. 70% of cysteine is then converted to glutathione and the remainder ends up as either taurine or pyruvate and sulfate." [MCW library book:Homocysteine in Health and Disease - edited by Ralph Carmel and Donald W Jacobsen] relationship: part_of PW:0000398 ! homocysteine metabolic pathway [Term] id: PW:0000401 name: remethylation pathway of homocysteine metabolism - cobalamin independent, betaine dependent relationship: part_of PW:0000398 ! homocysteine metabolic pathway [Term] id: PW:0000402 name: altered metabolic pathway of other amino acids def: "Those metabolic pathways of amino acids other than the common amino acids that deviate from what their normal course should be. Aberrant metabolic pathways of other amino acids, alone or in combination with other pathways, underlie various diseases." [InHouse :PW InHouse dictionary] is_a: PW:0000132 ! metabolic pathway of other amino acids is_a: PW:0000262 ! altered metabolic pathway [Term] id: PW:0000403 name: altered amino acid metabolic pathway def: "Those pathways of amino acid metabolism that deviate from what their normal course should be. Aberrant amino acid metabolic pathways, alone or in combination with other pathways, underlie various diseases." [InHouse :PW InHouse dictionary] is_a: PW:0000011 ! amino acid metabolic pathway is_a: PW:0000262 ! altered metabolic pathway [Term] id: PW:0000404 name: creatine metabolic pathway def: "Those metabolic reactions involving creatine. Officially methyl guanidino-acetic acid formed from arginine and glycine and the methyl group of methionine, creatine supplies energy to muscle cells." [Gene Ontology:GO\:0006600, PubMed; Onelook:PMID\: 10893433; www.onelook.com, Reactome:REACT_813.2] is_a: PW:0000033 ! energy metabolic pathway is_a: PW:0000132 ! metabolic pathway of other amino acids [Term] id: PW:0000405 name: synaptic vesicle exocytosis - neurotransmitter release pathway def: "Release of neurotransmitters is mediated through the exocytosis of neurotransmitter-filled synaptic vesicles. Synaptic vesicle trafficking cycle is composed of a number of steps that culminate in calcium-triggered fusion and release." [PubMed:PMID\: 10488439; PMID\: 15217342] is_a: PW:0001072 ! synaptic vesicle cycle pathway [Term] id: PW:0000406 name: metabolic pathway pertinent to the brain is_a: PW:0000002 ! classic metabolic pathway [Term] id: PW:0000407 name: neurotransmitter metabolic pathway is_a: PW:0000406 ! metabolic pathway pertinent to the brain [Term] id: PW:0000408 name: acetylcholine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of acetylcholine - an ester of choline and acetic acid that acts as a neurotransmitter in both the peripheral nervous system and the central nervous system." [OneLook:www.onelook.com] is_a: PW:0000436 ! amine neurotransmitter metabolic pathway [Term] id: PW:0000409 name: dopamine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of dopamine that acts as a neurotransmitter and a neurohormone. Dopamine has multiple functions in the brain." [OneLook:www.onelook.com, PubMed:PMID\: 19342614] is_a: PW:0000443 ! catecholamine metabolic pathway [Term] id: PW:0000410 name: serotonin metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of serotonin - an amine neurotransmitter that is believed to play important roles in a number of conditions such as depression, bipolar disorder, anxiety." [OneLook:www.onelook.com] is_a: PW:0000444 ! indoleamine and related compounds metabolic pathway [Term] id: PW:0000411 name: histamine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of histamine - a biogenic amine that acts as a neurotransmitter and is also involved in the local immune responses." [OneLook:www.onelook.com] is_a: PW:0000444 ! indoleamine and related compounds metabolic pathway [Term] id: PW:0000412 name: gamma-aminobutyric acid metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of gamma-aminobutyric acid (GABA)." [OneLook:http\://www.onelook.com] synonym: "GABA metabolism" RELATED [] is_a: PW:0000446 ! inhibitory neurotransmitter metabolic pathway [Term] id: PW:0000413 name: heme catabolic pathway def: "Those metabolic reactions involved in the degradation of heme - an iron-containing compound where the iron is complexed within a porphyrin heterocyclic ring, There are several kinds of hemes depending on the composition of their side chain. Heme serves as a prosthetic group for a number of proteins." [OneLook:www.onelook.com] is_a: PW:0000221 ! heme metabolic pathway [Term] id: PW:0000414 name: protein degradation pathway via the 'core' 20S proteasome pathway def: "The 'core' 20S proteasome degrades oxidized and/or unfolded proteins in an ATP and ubiquitin independent manner. The association with the 19S regulatory cap yields the 26S proteasome which has substrate selectivity and ATP and ubiquitin-dependent activity." [PubMed:PMID\: 9212076;] is_a: PW:0000325 ! protein degradation pathway [Term] id: PW:0000415 name: proteasome degradation pathway involving cullin-dependent ubiquitin ligases def: "A proteasome degradation pathway mediated by cullins. Cullins are components of E3 ligase complexes and substrates for Nedd8 - a ubiquitin-like molecule. Neddylation is thought to modulate the activity of cullins." [PubMed:PMID\: 10806345; PMID\: 15021886] is_a: PW:0000144 ! ubiquitin/proteasome degradation pathway [Term] id: PW:0000416 name: sentrinization pathway def: "A pathway of protein modification via conjugation with sentrin - a family of ubiquitin-like protein. Sentrinization does not target proteins to the proteasome, rather it targets proteins to particular cellular compartments." [PubMed:PMID\: 10806345; 15808504] synonym: "SUMO modification pathway" RELATED [] synonym: "sumoylation pathway" RELATED [] is_a: PW:0000433 ! protein modification pathway via conjugation with ubiquitin and ubiqutin-like molecules [Term] id: PW:0000417 name: ubiquitin, ubiquitin-like/proteasome degradation pathway def: "The pathway for the ATP-dependent non-lysosomal proteolysis catalyzed by the 26S proteasome and for which ubiquitylation, the post-translational covalent conjugation of ubiquitin, or ubiquitin-like, to target proteins is a key signal." [PubMed:PMID\: 10993052] is_a: PW:0000325 ! protein degradation pathway [Term] id: PW:0000418 name: altered ubiquitin, ubiquitin-like degradation pathway is_a: PW:0000326 ! altered protein degradation pathway is_a: PW:0000417 ! ubiquitin, ubiquitin-like/proteasome degradation pathway [Term] id: PW:0000419 name: water transport pathway def: "The pathways by which water flows into and out of the cell and into and out of sub-cellular compartments for multi-cellular organisms and mediated by members of the aquaporin family of water channels (WCP). The 13 members identified in mammals are grouped into three subfamilies: aquaporins, selective for water; aquaglyceroporins, permeable to both water and small molecules; superaquaporins, the sub-cellular aquaporins. WCPs belong to the superfamily of major intrinsic proteins (MIPs)." [Gene Ontology:GO\:0006833, PubMed:PMID\: 19165894] is_a: PW:0000103 ! transport pathway [Term] id: PW:0000420 name: altered c-Jun N-terminal kinase MAPK signaling pathway synonym: "altered JNK signaling pathway" RELATED [] is_a: PW:0000313 ! c-Jun N-terminal kinases MAPK signaling pathway is_a: PW:0000422 ! altered stress-regulated MAPK signaling pathway [Term] id: PW:0000421 name: altered mitogen activated protein kinase pathway def: "A mitogen activated protein kinase pathway that deviates from what its normal course should be. Altered MAPK pathways have been linked to a spectrum of conditions." [PW InHouse dictionary:InHouse] synonym: "altered MAPK signaling pathway" RELATED [] is_a: PW:0000007 ! mitogen activated protein kinase signaling pathway is_a: PW:0000264 ! altered signaling pathway [Term] id: PW:0000422 name: altered stress-regulated MAPK signaling pathway synonym: "altered SAPK pathways" RELATED [] is_a: PW:0000312 ! stress-regulated MAPK signaling pathway is_a: PW:0000421 ! altered mitogen activated protein kinase pathway [Term] id: PW:0000423 name: surfactant homeostasis pathway is_a: PW:0000355 ! homeostasis pathway [Term] id: PW:0000424 name: altered surfactant homeostasis pathway def: "A surfactant homeostatic pathway that deviates from what its normal course should be. Mutations in surfactant proteins and in ABCA3 - a member of the ABC transporters have been implicated in the altered pathway and associated with conditions such as Respiratory Distress Syndrome (RDS) in newborns and lung diseases in infants." [PubMed:15985750] is_a: PW:0000358 ! altered homeostasis pathway is_a: PW:0000423 ! surfactant homeostasis pathway [Term] id: PW:0000425 name: diabetic retinopathy pathway def: "High glucose-mediated oxidative stress effects on the expression of vascular endothelial growth factor are thought to play a role in diabetic retinopathy" [PubMed:PMID\: 16026270] is_a: PW:0000176 ! diabetes pathway [Term] id: PW:0000426 name: protein sorting pathway def: "In the secretory pathway, protein sorting, mainly in trans-Golgi Network (TGN), but also in other compartments, underlies cargo recognition by various carriers to assure the specificity of final localization." [PubMed:PMID\:18354421; 17686625; 18216874] is_a: PW:0000181 ! pathways of protein folding, sorting, modification, translocation and degradation relationship: part_of PW:0000280 ! secretory pathway [Term] id: PW:0000427 name: molybdenum cofactor biosynthetic pathway def: "Molybdenum cofactor is a complex between molybdopterin and an oxide of molybdenum and is required for the activity of several enzymes." [OneLook:http\://www.onelook.com] is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins [Term] id: PW:0000428 name: altered molybdenum cofactor biosynthetic pathway is_a: PW:0000427 ! molybdenum cofactor biosynthetic pathway is_a: PW:0000429 ! altered metabolic pathway of cofactors and vitamins [Term] id: PW:0000429 name: altered metabolic pathway of cofactors and vitamins is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins is_a: PW:0000262 ! altered metabolic pathway [Term] id: PW:0000430 name: killed term is_obsolete: true [Term] id: PW:0000431 name: another killed term is_obsolete: true [Term] id: PW:0000432 name: protein modification pathway def: "Protein modification pathway exerts a central role in the regulation of protein function and the pathways these function impinge upon. It is also used to target protein for degradation. In the more special aspect of protein modification in the secretory pathway, it involves the final modification of glycoproteins and glycosaminoglycans as well as processing of proteins to their mature forms." [InHouse:InHouse PW dictionary] is_a: PW:0000181 ! pathways of protein folding, sorting, modification, translocation and degradation [Term] id: PW:0000433 name: protein modification pathway via conjugation with ubiquitin and ubiqutin-like molecules def: "Conjugation of proteins with ubiquitin and ubiquitin-like molecules proceeds via a similar cascade-like, enzyme-driven mechanism but of diverse functionality." [PubMed:PMID\: 10806345] is_a: PW:0000432 ! protein modification pathway [Term] id: PW:0000434 name: ubiquitination pathway def: "A pathway of protein modification via conjugation with ubiquitin. Ubiquitination is primarily involved in targeting protein to the proteasome for degradation. It is also involved in membrane protein trafficking." [PubMed:PMID\: 10806345] is_a: PW:0000433 ! protein modification pathway via conjugation with ubiquitin and ubiqutin-like molecules [Term] id: PW:0000435 name: neddylation pathway def: "A pathway of protein modification via conjugation with Nedd8 - a ubiquitin-like protein. All Nedd8 targets appear to be members of the cullin family. Cullins participate in the assembly of various E3 ligase complexes. Neddylation pathway is important for embryogenesis and cell cycle control in metazoa, embryonic development in animals." [PubMed:10806345; 15021886] is_a: PW:0000433 ! protein modification pathway via conjugation with ubiquitin and ubiqutin-like molecules [Term] id: PW:0000436 name: amine neurotransmitter metabolic pathway is_a: PW:0000407 ! neurotransmitter metabolic pathway [Term] id: PW:0000437 name: amino acid neurotransmitter metabolic pathway is_a: PW:0000407 ! neurotransmitter metabolic pathway [Term] id: PW:0000438 name: alanine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of alanine. Alanine is a non-essential amino acid with roles in glucose and protein metabolism." [OneLook:www.onelook.com] is_a: PW:0001074 ! hydrophobic amino acid metabolic pathway [Term] id: PW:0000439 name: aspartic acid/aspartate metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of aspartic acid/aspartate. Aspartic acid is a non-essential amino acid with roles in glucose, protein and nucleotide metabolism. In the brain, it can act as a neurotransmitter." [OneLook:www.onelook.com] is_a: PW:0000445 ! excitatory neurotransmitter metabolic pathway is_a: PW:0001075 ! hydrophilic amino acid metabolism [Term] id: PW:0000440 name: glycine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glycine, a non-essential amino acid. Glycine is major inhibitory neurotransmitter." [OneLook:http\://www.onelook.com] is_a: PW:0000446 ! inhibitory neurotransmitter metabolic pathway is_a: PW:0001076 ! special amino acid metabolic pathway [Term] id: PW:0000441 name: epinephrine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of epinephrine - a catecholamine derived from the amino acids phenylalanine and tyrosine. It acts as a hormone and a neurotransmitter." [OneLook:www.onelook.com, PubMed:PMID\: 19342614] synonym: "adrenaline metabolism" RELATED [] is_a: PW:0000443 ! catecholamine metabolic pathway [Term] id: PW:0000442 name: norepinephrine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of norepinephrine - a catecholamine derived from the amino acid tyrosine. It acts as a hormone and a neurotransmitter." [OneLook:www.onelook.com, PubMed:PMID\: 19342614] synonym: "noradrenaline metabolism" RELATED [] is_a: PW:0000443 ! catecholamine metabolic pathway [Term] id: PW:0000443 name: catecholamine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of catecholamines - chemical compounds derived from tyrosine. Epinephrine, norepinephrine and dopamine are among the most abundant and are produced primarily from the adrenal medulla and the postganglionic fibers of the sympathetic nervous system." [OneLook:www\,onelook.com, PubMed:PMID\: 19342614] is_a: PW:0000211 ! amines and polyamines metabolic pathway is_a: PW:0000436 ! amine neurotransmitter metabolic pathway [Term] id: PW:0000444 name: indoleamine and related compounds metabolic pathway def: "Any of a number of indole derivatives containing an amine group." [OneLook:www.onelook.com] is_a: PW:0000436 ! amine neurotransmitter metabolic pathway [Term] id: PW:0000445 name: excitatory neurotransmitter metabolic pathway is_a: PW:0000437 ! amino acid neurotransmitter metabolic pathway [Term] id: PW:0000446 name: inhibitory neurotransmitter metabolic pathway is_a: PW:0000437 ! amino acid neurotransmitter metabolic pathway [Term] id: PW:0000447 name: peptide neurotransmitter metabolic pathway is_a: PW:0000407 ! neurotransmitter metabolic pathway [Term] id: PW:0000448 name: neuropeptide Y metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of neuropeptide Y." [OneLook:www.onelook.com] is_a: PW:0000447 ! peptide neurotransmitter metabolic pathway [Term] id: PW:0000449 name: enkephalin metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of enkephalin, a pentapeptide involved in the regulation of nociception." [OneLook:www.onelook.com] is_a: PW:0000447 ! peptide neurotransmitter metabolic pathway [Term] id: PW:0000450 name: neurotensin metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of neurotensin." [OneLook:www.onelook.com] is_a: PW:0000447 ! peptide neurotransmitter metabolic pathway [Term] id: PW:0000451 name: beta-endorphin metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of beta-endorphine - a peptide neurotransmitter that may play a role in depression." [OneLook:www.onelook.com] is_a: PW:0000447 ! peptide neurotransmitter metabolic pathway [Term] id: PW:0000452 name: substance P metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of substance P - a short-chain polypeptide that acts as a neurotransmitter and a neuromodulator." [OneLook:www\,onelook.com] is_a: PW:0000447 ! peptide neurotransmitter metabolic pathway [Term] id: PW:0000453 name: isoprenoid biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of an isoprenoid. Isoprenoids are precursors of both sterols and non-sterol derivatives." [MCW library:QU4 M235b 2009] synonym: "steroid alcohol" RELATED [] is_a: PW:0000248 ! isoprenoid metabolic pathway [Term] id: PW:0000454 name: cholesterol biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of cholesterol, an essential sterol component of mammalian cell membrane." [Gene Ontology:GO\:0006695, OneLook:www.onelook.com, Reactome:REACT_9405.2] is_a: PW:0001152 ! steroid biosynthetic pathway [Term] id: PW:0000455 name: excitatory synaptic transmission pathway def: "Synaptic transmission, or neurotransmission is the pathway of neuron-to-neuron signaling via the chemical synapse and mediated by neurotransmitters. Their effect can be excitatory or inhibitory and many neurotransmitters can exert either effect. The major excitatory neurotransmitter is the amino acid glutamate." [OneLook:www.onelook.com] synonym: "excitatory neurotransmission pathway" RELATED [] is_a: PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse [Term] id: PW:0000456 name: Inhibitory synaptic transmission pathway def: "Synaptic transmission, or neurotransmission is the pathway of neuron-to-neuron signaling via the chemical synapse and mediated by neurotransmitters. Their effect can be excitatory or inhibitory and many neurotransmitters can exert either effect. The major inhibitory neurotransmitter is gamma-aminobutyric acid (GABA)." [OneLook:www.onelook.com] synonym: "Inhibitory neurotransmission pathway" RELATED [] is_a: PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse [Term] id: PW:0000457 name: angiotensin III signaling pathway def: "Angiotensin III is derived from angiotensin II through the action of aminopeptidase A and in turn is cleaved by aminopeptidase N to generate angiotensin IV. Angiotensin III appears to function in a manner similar to angiotensin II. It plays a role in vasoconstriction and the control of arterial blood pressure. Angiotensin III may be the effective angiotensin peptide in the central nervous system." [PubMed: 10961935\, PMID\: 11295571] is_a: PW:0000245 ! angiotensin signaling pathway [Term] id: PW:0000458 name: angiotensin IV signaling pathway def: "Angiotensin IV is derived from angiotensin III through the action of aminopeptidase N. The receptor for angiotensin IV has been shown to be the insulin-regulated membrane aminopeptidase. Studies suggest that angiotensin IV signaling activates a number of intracellular second messenger systems and plays a role in vascular remodeling and memory." [PubMed:PMID\: 15549174 \, PMID 12591177] is_a: PW:0000245 ! angiotensin signaling pathway [Term] id: PW:0000459 name: apelin signaling pathway def: "Apelin signaling pathway plays a role in the vascular, cardiac, bone and digestive systems as well as the brain." [Gene Ontology:GO\:0060183, PubMed:PMID\: 15601620; PMID\: 15907343] is_a: PW:0000467 ! peptide and protein hormone signaling pathway [Term] id: PW:0000460 name: arachidonic acid metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of arachidonic acid - a polyunsaturated fatty acid." [Gene Ontology:GO\:0019369, KEGG:map00590, OneLook:www.onelook.com] synonym: "KEGG:00590" RELATED [] is_a: PW:0000058 ! fatty acid metabolic pathway [Term] id: PW:0000461 name: cyclooxygenase mediated pathway of arachidonic acid metabolism def: "The cyclooxygase pathway is one of the three major routes of arachidonic acid oxygenation." [PubMed:PMID\: 15896353] is_a: PW:0000460 ! arachidonic acid metabolic pathway [Term] id: PW:0000462 name: lipoxygenase mediated pathway of arachidonic acid metabolism def: "lipoxygenase pathway is one of three major routes of arachidonic acid oxygenation" [PubMed :PMID\: 15896353] is_a: PW:0000460 ! arachidonic acid metabolic pathway [Term] id: PW:0000463 name: cytochrome P450 monooxygenase mediated pathway of arachidonic acid metabolism def: "Cytochrome P450 monooxygenase pathway is one the three major routes of arachidonic acid oxygenation." [PubMed:PMID\: 15896353] is_a: PW:0000460 ! arachidonic acid metabolic pathway [Term] id: PW:0000464 name: leukotriene metabolic pathway def: "Those metabolic reactions involving leukotrienes - a family of eicosanoids whose effects include vasoconstriction and bronchoconstriction." [MCW library:QU4 M235b 2009] is_a: PW:0000462 ! lipoxygenase mediated pathway of arachidonic acid metabolism is_a: PW:0000485 ! eicosanoid metabolic pathway [Term] id: PW:0000465 name: hormone signaling pathway def: "Hormones are a class of molecules that are used as messengers between cells and serve as signals to the target cell. Vertebrate hormones belong to three classes: amine and amino acid derived, peptide and protein hormones, and lipid and phospholipid derived hormones." [OneLook:www.onelook.com] is_a: PW:0000003 ! signaling pathway [Term] id: PW:0000466 name: amine and amino acid-derived hormone signaling pathway is_a: PW:0000465 ! hormone signaling pathway [Term] id: PW:0000467 name: peptide and protein hormone signaling pathway is_a: PW:0000465 ! hormone signaling pathway [Term] id: PW:0000468 name: steroid hormone signaling pathway def: "steroid hormones - steroids that act as hormones - can be grouped into several categories depending on the receptor to which they bind." [OneLook:www.onelook.com] is_a: PW:0000469 ! lipid hormone signaling pathway [Term] id: PW:0000469 name: lipid hormone signaling pathway def: "The main categories of lipid hormones are the eicosanoids derived from arachidonic acid metabolism and the cholesterol derived steroid hormones." [OneLook:www.onelook.com] is_a: PW:0000465 ! hormone signaling pathway [Term] id: PW:0000470 name: natriuretic peptide signaling pathway def: "The natriuretic peptide family consists of three peptide hormones of diverse roles in cardiovascular as well as neuroendocrine and renal functions." [PubMed:PMID\: 15911062 PMID\: 15758553; PMID\: 15246247;] is_a: PW:0000467 ! peptide and protein hormone signaling pathway [Term] id: PW:0000471 name: atrial natriuretic peptide signaling pathway def: "Atrial natriuretic peptide hormone pathway plays important roles in the regulation of body fluid volume and blood pressure. " [PubMed:PMID\: 15911062 PMID\: 15758553; PMID\: 15246247] synonym: "ANP signaling pathway" RELATED [] is_a: PW:0000470 ! natriuretic peptide signaling pathway [Term] id: PW:0000472 name: brain natriuretic peptide signaling pathway def: "brain natriuretic peptide signaling pathway appears to elicit cardiovascular, renal and endocrine functions similar to those elicited by the atrial natriuretic peptide." [PubMed:PMID\: 15911062 PMID\: 15758553; PMID\: 1524624] synonym: "BNP signaling pathway" RELATED [] is_a: PW:0000470 ! natriuretic peptide signaling pathway [Term] id: PW:0000473 name: C-type natriuretic peptide signaling pathway def: "The role of the C-type signaling pathway is not well established. The receptor for the C-type natriuretic peptide, unlike the receptors for the other two types of peptides, is non-guanylyl cyclase receptor that appears to couple to adenylyl cyclase inhibition/phospholipase C activation via Gi family of G-protein. " [PubMed:PMID\: 15911062 PMID\: 15758553; PMID\: 15246247; PMID\: 15911072] synonym: "C-type brain natriuretic peptide signaling pathway" RELATED [] synonym: "CNP signaling pathway" RELATED [] is_a: PW:0000470 ! natriuretic peptide signaling pathway [Term] id: PW:0000474 name: coagulation cascade pathway def: "The coagulation cascade is the series of events proceeding via either the tissue factor or the contact activation pathway and leading to the formation of fibrin clots. Coagulation and inflammatory pathways are connected in a cross talk. Impaired anticoagulation pathways affect this balanced dialog and lead to various conditions and infections." [Gene Ontology:GO\:0050817, OneLook:www.onelook.com] synonym: "KEGG:04610" RELATED [] synonym: "secondary hemostasis" RELATED [] relationship: part_of PW:0000475 ! hemostasis pathway [Term] id: PW:0000475 name: hemostasis pathway def: "Hemostasis is the response to blood vessel injury to prevent blood loss via platelet mediated primary homeostasis and the secondary homeostasis of coagulation. The latter is a complex cascade which is triggered by the innate immune response and inflammation." [Gene Ontology:GO\:0007599, Reactome:REACT_604.2, Various:PubMed\, Wikipedia\, Reactome] synonym: "haemostasis pathway" RELATED [] is_a: PW:0000476 ! cardiovascular system homeostasis pathway [Term] id: PW:0000476 name: cardiovascular system homeostasis pathway is_a: PW:0000355 ! homeostasis pathway [Term] id: PW:0000477 name: natural anticoagulant pathway is_a: PW:0000476 ! cardiovascular system homeostasis pathway [Term] id: PW:0000478 name: tissue factor pathway inhibitor synonym: "TFPI" RELATED [] is_a: PW:0000477 ! natural anticoagulant pathway [Term] id: PW:0000479 name: heparin-antithrombin pathway is_a: PW:0000477 ! natural anticoagulant pathway [Term] id: PW:0000480 name: protein C anticoagulant pathway is_a: PW:0000477 ! natural anticoagulant pathway [Term] id: PW:0000481 name: fibrinolytic cascade pathway def: "The steps leading to the activation of plasminogen and the subsequent breaking down of a fibrin clot - the product of coagulation cascade." [Gene Ontology:GO\:0042730, PubMed\, OneLook:www.onelook.com] is_a: PW:0000476 ! cardiovascular system homeostasis pathway [Term] id: PW:0000482 name: lipoprotein metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of lipoproteins - any of the protein-lipid complexes. In the blood lipoproteins carry fats essential for the cell. Genetic variability and environmental (nongenetic) factors contribute to alterations in the homeostasis of lipid metabolic pathways and constitute cardiovascular disease risk." [Gene Ontology:GO\:0042157, PubMed:PMID\: 16011471, Reactome:REACT_6823.1] is_a: PW:0000010 ! lipid metabolic pathway [Term] id: PW:0000483 name: altered lipid metabolic pathway def: "Those lipid metabolic pathways that deviate from what their normal course should be. Aberrant lipid metabolic pathways, alone or in combination with other pathways underlie a number of diseases." [InHouse:PW InHouse dictionary] is_a: PW:0000010 ! lipid metabolic pathway is_a: PW:0000262 ! altered metabolic pathway [Term] id: PW:0000484 name: altered lipoprotein metabolic pathway def: "Those lipoprotein metabolic pathways that deviate from what their normal course should be. Aberrant lipoprotein metabolic pathways, alone or in combination with other pathways underlie several diseases." [In House:PW In House dictionary] is_a: PW:0000482 ! lipoprotein metabolic pathway is_a: PW:0000483 ! altered lipid metabolic pathway [Term] id: PW:0000485 name: eicosanoid metabolic pathway def: "Eicosanoids are molecules derived from arachidonic acid or omega-3 fatty acid derivatives that can act as hormones. Examples include the prostaglandin, the leukotrienes and the thromboxane families." [MCW library:QU4 M235b 2009, OneLook:www.onelook.com] is_a: PW:0000010 ! lipid metabolic pathway [Term] id: PW:0000486 name: class I major histocompatibility complex pathway def: "Peptides generated from proteolytic degradation of cytosolic proteins are translocated to the ER where they associate with class I MHC molecules. Peptide-class I MHC complexes move through the Golgi and are transported to the cell surface to be recognized by CD8+ T cells." [MCW:Handbook on cellular nad molecular immunology, PubMed:16181325] synonym: "class I MHC pathway" RELATED [] synonym: "MHC class I antigen presentation pathway" RELATED [] is_a: PW:0000825 ! antigen processing and presentation pathway [Term] id: PW:0000487 name: class II major histocompatibility complex pathway def: "Peptides generated from enzymatic degradation of proteins internalized in late endosomes or lysosomes bind to class II MHC molecules. Peptide-class II MHC complexes are delivered to the cell surface to be recognized by CD4+ T cells." [MCW:Handbook on cellular and molecular immunology, PubMed:16181322] synonym: "class II MHC pathway" RELATED [] is_a: PW:0000825 ! antigen processing and presentation pathway [Term] id: PW:0000488 name: antigen processing pathway def: "Antigen processing pathway engages the proteosomal machinery in the cytosol, ER specific proteases as well as chaperones for loading the HMC class I molecules with the 8-10 amino acid peptides" [PubMed:16181325] is_obsolete: true [Term] id: PW:0000489 name: angiopoietin signaling pathway def: "Angiopoietin signaling pathway is involved in the regulation of angiogenic remodeling. Recent studies suggest that the pathway may also be involved in lymphangiogenesis and possibly in the development of hematopoietic system." [PubMed:PMID\: 16225862] is_a: PW:0000168 ! growth factor signaling pathway [Term] id: PW:0000490 name: transforming growth factor-beta Smad dependent signaling pathway def: "Transforming growth factor-beta (TGF-beta) signaling is one of the best characterized module of the Tgf-b superfamily pathways. Binding to the type II receptor leads to activation of the type I receptor and subsequent activation of Smad pathway. Nuclear translocation of Smad(s) and interaction with transcription factors rleads to activation or repression of many genes." [PubMed:PMID\: 16678165] synonym: "PID:200227" RELATED [] synonym: "TGF-beta Smad dependent signaling pathway" EXACT [] is_a: PW:0000206 ! transforming growth factor-beta signaling pathway [Term] id: PW:0000491 name: vasopressin signaling pathway def: "The hormone vasopressin plays central roles in cardiovascular and water homeostasis by signaling via two receptor types, G-protein coupled receptors coupling to particular G alpha subunits of heterotrimeric G proteins." [PubMed:PMID\: 14624682; 18431594] synonym: "arginine-vasopressin signaling pathway" RELATED [] synonym: "Avp signaling pathway" RELATED [] is_a: PW:0000467 ! peptide and protein hormone signaling pathway [Term] id: PW:0000492 name: renin-angiotensin cascade pathway def: "The renin-angiotensin cascade (RAS) generates a number of bioactive peptides with diverse physiological and pathophysiological functions. RAS exerts vasoconstriction, vasodilation or vascular remodeling, cell proliferation or anti-proliferation effects, depending on which angiotensin peptide generates the signaling. Some of these features are also shared by the kallikrein-kinin system (KKS); the two systems can interact and cross-talk." [KEGG:ko04614, PubMed:PMID\: 15883759 PMID\: 15638741 \, PMID\: 12676165 \, PMID\: 12793984 \, PMID\: 16816138] synonym: "KEGG:04614" RELATED [] synonym: "RAS system signaling pathway" RELATED [] is_a: PW:0000003 ! signaling pathway [Term] id: PW:0000493 name: corticotropin-releasing hormone signaling pathway def: "Corticotropin-releasing hormone is secreted by the hypothalamus in response to stress or fear and signaling through its receptors stimulates secretion of corticotropic (adrenocorticotropic, ACTH) hormone by the anterior pituitary. ACTH is one of the cleavage products of pro-opiomelanocortin (POMC)." [PubMed:PMID\: 20132811] synonym: "CRH" RELATED [] is_a: PW:0000467 ! peptide and protein hormone signaling pathway [Term] id: PW:0000494 name: oxytocin signaling pathway def: "The peptide hormone oxytocin plays a central role in parturition, lactation and sexual behavior." [PubMed:PMID\: 14624682] is_a: PW:0000467 ! peptide and protein hormone signaling pathway [Term] id: PW:0000495 name: Gas6 - Axl signaling axis def: "Gas6, a vitamin K-dependent growth factor signals through the Axl subfamily of tyrosine kinase receptors. The Gas6-Axl axis appears to be involved in growth and survival of various cell types as well as in tissue remodeling and regeneration. Deregulation of the axis is involved in a number of conditions, particularly renal." [Pubmed:PMID\: 16285961 PMID\: 11290560 ; PMID\: 16362042] synonym: "Gas6-Axl signaling system" RELATED [] is_a: PW:0000168 ! growth factor signaling pathway [Term] id: PW:0000496 name: exogenous pathway relationship: part_of PW:0000482 ! lipoprotein metabolic pathway [Term] id: PW:0000497 name: endogenous pathway relationship: part_of PW:0000482 ! lipoprotein metabolic pathway [Term] id: PW:0000498 name: reverse cholesterol transport pathway def: "Reverse cholesterol transport (RCT) is the pathway by which cholesterol from extrahepatic cells/tissue is transported to the liver for excretion. The pathway may prevent the development of atherosclerosis by reducing the accumulation of cholesterol in the wall of arteries." [Gene Ontology:GO\:0043691, PubMed:PMID\: 16258026] synonym: "RCT pathway" RELATED [] synonym: "selective cholesterol uptake pathway" RELATED [] is_a: PW:0000103 ! transport pathway relationship: part_of PW:0000482 ! lipoprotein metabolic pathway [Term] id: PW:0000499 name: nuclear factor kappa B signaling pathway def: "NF-kB signaling plays an essential role in the mammalian immune system. The classical/canonical pathway, downstream but not exclusively of tumor necrosis factor/receptor 1 signaling, is regarded as a paradigm of NF-kB signaling. The classical and the non-classical pathway downstream of a subset of Tnf receptor superfamily, share similar sets of core components, albeit in distinct ways. Collectively they regulate the expression of a vast array of genes." [PubMed:PMID\: 15371334\, 18267068\, 17072321] synonym: "KEGG:04064" RELATED [] synonym: "NF-kappaB signaling pathway" EXACT [] synonym: "NF-kB signaling pathway" RELATED [] synonym: "PID:200021" RELATED [] synonym: "PID:200031" RELATED [] synonym: "PID:200048" RELATED [] is_a: PW:0000100 ! transcription pathway is_a: PW:0000716 ! transcription factor mediated signaling pathway is_a: PW:0000818 ! signaling pathway pertinent to immunity [Term] id: PW:0000500 name: tyrosine-based hormone signaling pathway is_a: PW:0000466 ! amine and amino acid-derived hormone signaling pathway [Term] id: PW:0000501 name: thyroid hormone signaling pathway def: "Thyroid hormone signaling pathway plays important roles in glucose and lipid metabolism. The thyroid hormone receptors are nuclear receptors that once activated act as transcription factors." [PubMed:PMID\: 20015660\, 20872316] is_a: PW:0000500 ! tyrosine-based hormone signaling pathway [Term] id: PW:0000502 name: complement system pathway def: "The complement system is an important effector of innate and also of humoral adaptive immunity. It consists of three biochemical cascades that are differently initiated but share similar late steps and effector functions. The complement pathway and the coagulation cascade are connected in a cross talk. Impaired anticoagulation pathways affect this balanced dialog and lead to various conditions and infections." [KEGG:map04610, MCW library:Handbook on cellular and molecular immunology, PubMed:PMID\: 11287977] synonym: "KEGG:04610" RELATED [] relationship: part_of PW:0000234 ! innate immune response pathway relationship: part_of PW:0000823 ! humoral immunity pathway [Term] id: PW:0000503 name: classical complement pathway def: "The classical complement pathway is one of the three biochemical pathways of the complement system. It is activated by antigen-bound antibodies." [KEGG:map04610, PubMed:PMID\:11287977] synonym: "classical pathway" RELATED [] is_a: PW:0000502 ! complement system pathway [Term] id: PW:0000504 name: lectin complement pathway def: "The lectin pathway is one of the three biochemical pathways of the complement system. It is activated by microbial polysaccharides binding to circulating lectins." [Gene Ontology:GO\:0001867, KEGG :map04610, PubMed:PMID\:11287977] synonym: "lectin pathway" RELATED [] synonym: "mannose-binding lectin pathway" RELATED [] is_a: PW:0000502 ! complement system pathway [Term] id: PW:0000505 name: alternative complement pathway def: "The alternative pathway is one of the three biochemical pathways of the complement system. Stable activation of the alternative pathway occurs on microbial cell surfaces." [Gene Ontology :GO\:0006957, KEGG:map04610, PubMed:PMID\:11287977] synonym: "alternative pathway" RELATED [] is_a: PW:0000502 ! complement system pathway [Term] id: PW:0000506 name: endothelin signaling pathway def: "Endothelins represent a family of three vasoconstrictor peptides that play a role in several intracellular signaling pathways and have been associated with hypertension, heart failure and myocardial infarction." [PubMed:PMID\: 16269952\, PMID\: 15124920] synonym: "PID:200005" RELATED [] is_a: PW:0000467 ! peptide and protein hormone signaling pathway [Term] id: PW:0000507 name: estrogen signaling pathway def: "Estrogens are C18 steroid hormones that constitutes the females sex hormones. Estrogen signals via the estrogen receptor which ones activated drive the expression of target genes." [OneLook:www.onelook.com, PubMed:PMID\: 14993442\, 19996532] is_a: PW:0000100 ! transcription pathway is_a: PW:0000567 ! sex steroids signaling pathway is_a: PW:0000716 ! transcription factor mediated signaling pathway [Term] id: PW:0000508 name: platelet aggregation pathway def: "The pathway involving the attachment of platelets to one another and leading to the formation of a thrombus. Platelets attachment can be induced by a variety of agents." [Gene Ontology:GO\:0070527, PubMed\, OneLook:www.onelook.com] synonym: "primary hemostasis" RELATED [] relationship: part_of PW:0000475 ! hemostasis pathway [Term] id: PW:0000509 name: altered hormone signaling pathway is_a: PW:0000264 ! altered signaling pathway is_a: PW:0000465 ! hormone signaling pathway [Term] id: PW:0000510 name: altered insulin-like growth factor signaling pathway is_a: PW:0000238 ! insulin-like growth factor signaling pathway is_a: PW:0000511 ! altered peptide and protein hormone signaling pathway [Term] id: PW:0000511 name: altered peptide and protein hormone signaling pathway is_a: PW:0000467 ! peptide and protein hormone signaling pathway is_a: PW:0000509 ! altered hormone signaling pathway [Term] id: PW:0000512 name: Interleukin mediated signaling pathway is_a: PW:0000828 ! cytokine mediated signaling pathway [Term] id: PW:0000513 name: interleukin-10 family mediated signaling pathway def: "The interleukin-10 family comprises several interleukins, including members of the interferon type III also known as interferon lambda or interferon-like type, that carry out various immunomodulatory functions." [PubMed:PMID\: 11929132\, 21112807\, 20454917] synonym: "Il-10 family mediated signaling pathway" RELATED [] is_a: PW:0000512 ! Interleukin mediated signaling pathway [Term] id: PW:0000514 name: interleukin-6 family mediated signaling pathway def: "Interleukin-6 family includes several members involved in a wide range of biological processes such as immune regulation, inflammation, hematopoiesis and oncogenesis. All members share a common signal transducer, gp130 which activates Jak-Stat and Raf/Mek/Erk signaling pathways." [PubMed:PMID\: 21715184; 20410258] synonym: "Il-6 family mediated signaling pathway" EXACT [] is_a: PW:0000512 ! Interleukin mediated signaling pathway [Term] id: PW:0000515 name: Interleukin-10 signaling pathway def: "Interleukin-10 signaling is involved in various immunomodulatory functions. It promotes the release of immune mediators and antigen presentation exerting important anti-inflammatory effects that may primarily characterize this family member. Signaling by Il-10 and the other members of the family activate the intracellular Jak-Stat cascade." [PubMed:PMID\: 20454917; 21115385] synonym: "Il-10 signaling pathway" RELATED [] is_a: PW:0000513 ! interleukin-10 family mediated signaling pathway [Term] id: PW:0000516 name: interleukin-6 signaling pathway def: "Interleukin-6 signaling is involved in a wide range of biological processes such as immune regulation, inflammation, hematopoiesis and oncogenesis. A signal transducer common to all family members, gp130 activates Jak-Stat and Raf/Mek/Erk signaling pathways." [PubMed:PMID\: 21715184; 20410258; 20303867] synonym: "Il-6 signaling pathway" EXACT [] synonym: "PID:200146" RELATED [] is_a: PW:0000514 ! interleukin-6 family mediated signaling pathway is_a: PW:0000926 ! pro-inflammatory cytokine mediated pathway [Term] id: PW:0000517 name: arterial occlusive disease pathway def: "A pathway leading to a general or specific artery occlusion." [MeSH:Medical Subject Headings] is_a: PW:0000020 ! cardiovascular disease pathway [Term] id: PW:0000518 name: atherosclerosis pathway def: "A pathway leading to the thickening of medium and large arteries. While lipoprotein related pathways are of interest, monogenic conditions such as those linked to mutations in the laminin gene may also provide clues regarding atherosclerosis pathways." [PubMed:PMID\: 15205220] is_a: PW:0000517 ! arterial occlusive disease pathway [Term] id: PW:0000519 name: 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane degradation pathway def: "Those enzymatic reactions involved in the degradation of DDT - a chlorinated organic insecticide and environmental pollutant. Although it is banned in the United States, it is still widely used in developing countries." [Gene Ontology:GO\:0046701, KEGG:http\://umbbd.msi.umn.edu/ddt/ddt_map.html, KEGG:map00351] synonym: "DDT degradation pathway" RELATED [] is_a: PW:0000107 ! xenobiotics biodegradation pathway [Term] id: PW:0000520 name: 2,4-dichlorobenzoate degradation pathway def: "Those enzymatic reactions involved in the degradation of 2,4-dichlorobenzoate - a key intermediate in the aerobic degradation of over 200 polychlorinated biphenyls." [:, Gene Ontology:GO\:0046298, KEGG:http\://umbbd.msi.umn.edu/dcb/dcb_map.html, KEGG:map00623] is_a: PW:0000107 ! xenobiotics biodegradation pathway [Term] id: PW:0000521 name: 1,2-dichloroethane degradation pathway def: "Those enzymatic reactions involved in the degradation of 1,2-dichloroethane - a moderately reactive alkylating compound." [KEGG:http\://umbbd.msi.umn.edu/dce/dce_map.html, KEGG:map00631] is_a: PW:0000107 ! xenobiotics biodegradation pathway [Term] id: PW:0000522 name: flavonoid biosynthetic pathway def: "Those enzymatic reactions involved in the biosynthesis of flavonoids - a class of plant secondary metabolites generally known for their antioxidant activity." [Gene Ontology:GO\:0009813, KEGG:map00941, OneLook:www.onelook.com] is_a: PW:0000147 ! metabolic pathway of secondary metabolites [Term] id: PW:0000523 name: linoleic acid metabolic pathway def: "Those enzymatic reactions involved in the synthesis, utilization or degradation of linoleic acid - an unsaturated omega-6 fatty acid. Linoleic acid is an essential fatty acid that humans and other animals cannot synthesize and must obtain from diet." [Gene Ontology:GO\:0043651, KEGG:map00591, OneLook:http\://www.onelook.com] synonym: "KEGG:00591" RELATED [] is_a: PW:0000058 ! fatty acid metabolic pathway [Term] id: PW:0000524 name: heparan sulfate biosynthetic pathway def: "Those metabolic reactions involved in the biosynthesis of heparan sulfate. Heparan sulfate is a glycosaminoglycan occurring in the cell membrane of most cells. It consists of repeating disaccharide units in specific linkage, each composed of a glucosamine residue linked to an uronic acid, either glucuronic acid or L-iduronic acid, which may be sulfated." [Gene Ontology:GO\:0030210, KEGG:map00534, OneLook:www.onelook.com] synonym: "KEGG:00534" RELATED [] is_a: PW:0000157 ! glycosaminoglycan metabolic pathway [Term] id: PW:0000525 name: Ras mediated signaling pathway is_a: PW:0000158 ! Ras family mediated signaling pathway [Term] id: PW:0000526 name: kallikrein-kinin system signaling pathway def: "The kallikrein-kinin system (KKA) generates a number of bioactive peptides with diverse physiological and pathophysiological functions. These features are also shared by the renin-angiotensin system (RAS); the two systems can interact and cross-talk." [Gene ontology:GO\:0002255, XX:PMID\: 12558525\, PMID\: 12793984 PMID\: 16177542\, PMID\: 12676165] synonym: "KKS system signaling pathway" RELATED [] is_a: PW:0000003 ! signaling pathway [Term] id: PW:0000527 name: angiotensin II signaling pathway via AT1 receptor def: "Angiotensin II signaling through the angiotensin type 1 receptor (AT1) activates downstream signaling pathways and elicits a broad range of physiological responses. It is involved in the regulation of blood pressure and volume, water and electrolyte balance and exerts a potent vasoconstrictive effect." [PubMed:16141358\, 10977869\, 12676164] is_a: PW:0000244 ! angiotensin II signaling pathway [Term] id: PW:0000528 name: angiotensin II signaling pathway via AT2 receptor def: "Angiotensin II signaling through the angiotensin type 2 receptor (AT2) is less well understood and rather controversial. It appears to counteract AT1 receptor function and promote apoptosis. Alternatively, it may complement the effects of AT1 receptor with deleterious consequences in cardiac pathologies. AT2 receptor appears to function in a G-protein dependent as well as independent manner." [PubMed : 10977869\, 15158138\, 16286568 \, 12734384] is_a: PW:0000244 ! angiotensin II signaling pathway [Term] id: PW:0000529 name: angiotensin (1-7) signaling pathway def: "Angiotensin (1-7) is derived from angiotensin II through the action of angiotensin converting enzyme 2 (ACE2) or from angiotensin I through the action of neutral endopeptidase (NEP). Angiotensin (1-7) signaling appears to have a vasodilatory effect but the exact action of this peptide in humans remains to be established." [PubMed:PMID\: 15687842\, PMID\: 16520407\, PMID\: 15962175] is_a: PW:0000245 ! angiotensin signaling pathway [Term] id: PW:0000530 name: angiotensin III signaling pathway via AT1 receptor def: "Angiotensin III, like angiotensin II, binds to the type 1 and 2 receptors and triggers downstream signaling pathways. In rats, angiotensin III signaling through the receptor type 1 (AT1) can modulate noradrenergic transmission via phospholipase C activation." [PubMed:PubMed 11100981\,] is_a: PW:0000457 ! angiotensin III signaling pathway [Term] id: PW:0000531 name: angiotensin III signaling pathway via AT2 receptor def: "The role of angiotensin type 2 receptor is less well understood. In rats, angiotensin III can mediate natriuresis through the activation of receptor type 2." [PubMed: 16380540] is_a: PW:0000457 ! angiotensin III signaling pathway [Term] id: PW:0000532 name: glycogen biosynthetic pathway def: "Those metabolic reactions leading to the biosynthesis of glycogen, a highly branched polysaccharide. Glycogen is the storage form of glucose in the cell; it represents an energy reserve that can be mobilized when and where there is a need for glucose." [Gene Ontology:GO\:00005978, PubMed\, OneLook:www.onelook.com, Reactome:REACT_1736.2] synonym: "glycogenesis" RELATED [] is_a: PW:0000533 ! glycogen metabolic pathway is_a: PW:0000557 ! glucose storage pathway [Term] id: PW:0000533 name: glycogen metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glycogen, a highly branched polysaccharide that constitutes the major form of glucose storage in the cell." [InHouse:www.rgd.mcw] is_a: PW:0000005 ! carbohydrate metabolic pathway [Term] id: PW:0000534 name: glycogen degradation pathway def: "Those metabolic reactions involved in the breakdown of glycogen to glucose-6-phosphate. Glucose-6-phosphate can then be dephosphorylated to glucose or it can be utilized via glycolysis for energy production; an alternative pathways of G6P utilization is the oxidative phase of the pentose phosphate shunt. A small percentage of glucose-6-phosphate can be converted to hexosamines." [Gene Ontology:GO\:0005980, OneLook:www.onelook.com, Reactome:REACT_1008.1] synonym: "glycogenolysis " RELATED [] is_a: PW:0000533 ! glycogen metabolic pathway is_a: PW:0000685 ! glucose biosynthesis pathway [Term] id: PW:0000535 name: protein transport pathway is_a: PW:0000103 ! transport pathway [Term] id: PW:0000536 name: constitutive secretory pathway def: "In the constitutive secretory pathway, secreted proteins are sorted into transport vesicles and targeted to their destination in the absence of a signal." [Gene Ontology:GO\:0045054, InHouse:InHouse PW dictionary] is_a: PW:0000280 ! secretory pathway [Term] id: PW:0000537 name: regulated secretory pathway def: "In the regulated secretory pathway, secreted proteins are sorted into secretory vesicles which are stored intracellularly and move to the final destination upon receiving a signal." [Gene Ontology:GO\:0045055, InHouse:InHouse PW dictionary] is_a: PW:0000280 ! secretory pathway [Term] id: PW:0000538 name: nuclear protein import pathway is_a: PW:0000535 ! protein transport pathway [Term] id: PW:0000539 name: ghrelin system pathway def: "Ghrelin is an appetite-stimulating hormone secreted primarily from the stomach in response to fasting that can downregulate energy expenditure and lead to weight increase." [PubMef:PMID\: 17202582; PMID\: 16550252] is_a: PW:0000467 ! peptide and protein hormone signaling pathway relationship: part_of PW:0000357 ! energy homeostasis pathway [Term] id: PW:0000540 name: obesity disease pathway def: "Obesity, usually defined as 20% or more excess body weight, constitutes a major public health problem and an independent risk factor for a number of conditions such as hypertension and diabetes. Deregulation of energy homeostasis, of various metabolic and signaling pathways, genetic and environmental aspects, all can contribute to the development of an obese state." [OneLook:www.onelook.com] is_a: PW:0000013 ! disease pathway [Term] id: PW:0000541 name: signaling pathway involving second messengers is_a: PW:0000003 ! signaling pathway [Term] id: PW:0000542 name: adenosine monophosphate-activated protein kinase (AMPK) signaling pathway def: "AMPK senses changes in cellular energy as ATP/AMP ratio. AMP binding allosterically activates AMPK; subsequent phosphorylation events lead to repression of energy consuming pathways. One target of AMPK is mTOR signaling pathway. AMPK activates the inhibitory Tsc2 while inhibiting mTorc1 complex." [PubMed:PMID\: 16885148; PMID\: 15509864] synonym: "5'AMP-activated protein kinase" RELATED [] synonym: "AMPK signaling pathway" RELATED [] is_a: PW:0000541 ! signaling pathway involving second messengers relationship: part_of PW:0000357 ! energy homeostasis pathway [Term] id: PW:0000543 name: protein kinase A (PKA) signaling pathway def: "Protein kinase A (PKA) signaling is a widely used intracellular pathway and the major route for channeling the cAMP signal. cAMP is regulated by adenylyl cyclases that produce it and phosphodiesterases that hydrolyze it. Compartmentalization of PKA signaling is mediated by the AKAP family of scaffold proteins that bring together the kinase, cAMP modulators and sometimes the targets." [Gene Ontology:GO\:0010737, PubMed:PMID\:14715913; 16214430, Reactome:REACT_15530.1] synonym: "cAMP-dependent protein kinase A signaling pathway" RELATED [] synonym: "cAMP/PKA signaling pathway" RELATED [] is_a: PW:0000541 ! signaling pathway involving second messengers [Term] id: PW:0000544 name: altered reverse cholesterol transport pathway def: "An impaired pathway of reverse cholesterol transport and efflux can pose a risk for the development of cardiovascular disease. This varies in severity and manifestation depending on which gene in the pathway is affected." [PubMed:PMID\: 16258026] synonym: "altered RCT pathway" RELATED [] is_a: PW:0000484 ! altered lipoprotein metabolic pathway is_a: PW:0000498 ! reverse cholesterol transport pathway is_a: PW:0000545 ! altered transport pathway [Term] id: PW:0000545 name: altered transport pathway is_a: PW:0000103 ! transport pathway is_a: PW:0000263 ! altered regulatory pathway [Term] id: PW:0000546 name: mRNA decay pathway def: "The pathways of mRNA quality control thereby erroneous mRNA is degraded in the nucleus or cytoplasm, or normal mRNA accumulated in the nucleus is degraded." [Gene Ontology:GO\:0006402, KEGG:map03018, PubMed:PMID\: 15933735] synonym: "KEGG:03015" RELATED [] synonym: "mRNA quality control pathway" EXACT [] synonym: "mRNA surveillance pathway" EXACT [] is_a: PW:0001161 ! RNA degradation pathway [Term] id: PW:0000547 name: exosome mediated mRNA decay pathway def: "The nuclear exosome pathway degrades erroneous mRNA as well as normal mRNA that has accumulated in the nucleus. The exosome is required for processing of other RNA molecules as well." [PubMed:PMID\: 15933735\, 18786828] synonym: "exosome mediated mRNA degradation pathway" EXACT [] is_a: PW:0000546 ! mRNA decay pathway [Term] id: PW:0000548 name: nonsense-mediated mRNA decay pathway def: "The nonsense-mediated decay pathway (NMD) degrades mRNA that contains a premature translation termination codon (PTC) and is one of the best characterized systems in eukaryotes." [Gene Ontology:GO\:0000184, PubMed:PMID\: 15933735; PMID\: 17010613] synonym: "NMD pathway" EXACT [] is_a: PW:0000546 ! mRNA decay pathway [Term] id: PW:0000549 name: nonstop mRNA decay pathway def: "The nonstop mRNA decay pathway degrades mRNA that lacks a translation termination codon." [Gene Ontology:GO\:0070481, PubMed:PMID\: 15933735] synonym: "NSD pathway" EXACT [] is_a: PW:0000546 ! mRNA decay pathway [Term] id: PW:0000550 name: Staufen-mediated mRNA decay pathway def: "Staufen-mediated mRNA decay pathway (SMD) is a rather novel pathway identified in mammals. Staufen (Stau1) is thought to be involved in mRNA localization and it has recently been shown to be involved in mRNA decay. It shares some of the features of the nonsense-mediated mRNA decay pathway (NMD) but does not require components essential for NMD." [PubMed:PMID\: 15933735; PMID\: 15809649; PMID\: 15680326] synonym: "SMD pathway" RELATED [] is_a: PW:0000546 ! mRNA decay pathway [Term] id: PW:0000551 name: altered mRNA decay pathway def: "An mRNA decay pathway that deviates from what its normal course should be. An aberrant mRNA decay pathway would lead to the translation of erroneous mRNA with potentially serious consequences." [InHouse PW:InHouse PW] is_a: PW:0000290 ! altered pathway of replication, repair, gene expression and protein biosynthesis is_a: PW:0000546 ! mRNA decay pathway [Term] id: PW:0000552 name: brassinosteroid biosynthetic pathway def: "Those metabolic reactions involved in the biosynthesis of brassinosteroids or brassins, a group of plant hormones released in response to low oxygen and sugar, or to root stresses." [Gene Ontology:GO\:0016132, KEGG:map00905, KEGG\, OneLook:http\://www.onelook.com] is_a: PW:0000147 ! metabolic pathway of secondary metabolites [Term] id: PW:0000553 name: glucose homeostasis pathway def: "Those pathways involved in the balanced maintenance of glucose levels, transport and processing as demanded by the needs of the cells, tissues and organs. Glucose is an important and the most efficient fuel source. Disruption of glucose homeostasis underlies many complex disorders." [Gene Ontology:GO\:0042593, PubMed:PMID\: 15466941] is_a: PW:0000355 ! homeostasis pathway [Term] id: PW:0000554 name: glucose transport pathway def: "Glucose diffusion into cells requires specific transporter proteins. Two families of hexose transporters facilitate glucose transport down its concentration gradient." [Gene Ontology:GO\:0015758, PubMed:PMID\: 15466941 ; PMID\: 15449578, Reactome:REACT_212.3] is_a: PW:0000575 ! sugar transport pathway relationship: part_of PW:0000553 ! glucose homeostasis pathway [Term] id: PW:0000555 name: glucose utilization pathway def: "The various pathways thereby glucose is oxidized to produce energy, is converted to other molecules or is stored for further use." [PubMed:PMID\: 15466941] relationship: part_of PW:0000553 ! glucose homeostasis pathway [Term] id: PW:0000556 name: glucose oxidation pathway def: "The various pathways thereby glucose is converted to other compounds to yield primarily ATP. The final oxidation of glucose to carbon dioxide and water produces a net of 38 molecules of ATP per molecule of glucose." [PubMed:PMID\: 15466941] is_a: PW:0000555 ! glucose utilization pathway [Term] id: PW:0000557 name: glucose storage pathway def: "Glycogen is the major form of glucose storage. Excess glucose is converted into glycogen - a highly branched polysaccharide. When glucose is rapidly needed, glycogen can be broken down via glycogenolysis." [PubMed:PMID\: 15466941] is_a: PW:0000555 ! glucose utilization pathway [Term] id: PW:0000558 name: glucose conversion pathway is_a: PW:0000555 ! glucose utilization pathway [Term] id: PW:0000559 name: hexosamine biosynthetic pathway def: "The formation of nucleotide hexosamines, primarily UDP-N-acetylglucosamine, constitutes the final step in the hexosamine biosynthetic pathway which provides substrates for the O-linked glycosylation of proteins. Glycoproteins that are either secreted from the cell or inserted into the plasma membrane undergo N-linked glycosylation. The O-linked glycosylation of nuclear and/or cytosolic proteins confers a signaling dimension to the hexosamine biosynthetic pathway." [PubMed:PMID\: 15466941; PMID\: 16885148] is_a: PW:0000558 ! glucose conversion pathway is_a: PW:0000570 ! hexosamine metabolic pathway [Term] id: PW:0000560 name: facilitative sugar transporter mediated glucose transport pathway def: "The GLUT family contains 14 members in mammals which can be grouped into 3 classes based on sequence similarities. The members of group I (best characterized) and of group III transporters facilitate glucose transport." [PubMed:PMID\: 15466941; 15449578; 18171430; 17717074; 18570632] synonym: "GLUT mediated glucose transport pathway" RELATED [] is_a: PW:0000554 ! glucose transport pathway [Term] id: PW:0000561 name: sodium-glucose cotransporter mediated glucose transport pathway def: "The sodium-glucose or the sodium-dependent glucose cotransporters are characterized by the presence of 14 transmembrane alpha-helices. The N- and C-termini are responsible for permeating sodium and sugar, respectively." [PubMed:PMID\: 15466941 ; PMID\: 15449578] synonym: "SGLT mediated glucose transport pathway" RELATED [] is_a: PW:0000554 ! glucose transport pathway [Term] id: PW:0000562 name: growth hormone signaling pathway def: "The growth hormone signaling pathway is an important regulator of postnatal development. However, despite many years of research, the molecular mechanism underlying its many actions are incompletely understood. It is believed that its actions involve direct and indirect routes. An example of the latter is the role the pathway plays in stimulating the production of insulin-like growth factor." [Gene Ontology:GO\:0060396, PubMed:PMID\:19407495; 8853443] is_a: PW:0000467 ! peptide and protein hormone signaling pathway [Term] id: PW:0000563 name: adiponectin signaling pathway def: "Adiponectin signaling, a hormone secreted by the adipose tissue, impacts on metabolic pathways such as glucose and lipid metabolism, possibly via activation of AMPK pathway. Its deregulation has been linked to obesity, cardiovascular diseases, diabetes and metabolic syndrome." [Gene Ontology:GO\:0033211, PubMed:PMID\: 16823476; PMID\: 16634986; PMID\: 17140553] is_a: PW:0000467 ! peptide and protein hormone signaling pathway [Term] id: PW:0000564 name: androgen signaling pathway def: "Androgens are C19 steroids that constitutes the male sex hormones. They are also the precursors of female sex hormones, the estrogens. Testosterone and its more potent metabolite, dihydrotestosterone bind to androgen receptors to then translocate to the nucleus and activate the transcription of target genes. Many regulators , both activators and repressors, have been identified. Upregulation of receptor activity has been implicated in prostate cancer." [PubMed:PMID\: 17163421 \, 18657355] synonym: "PID:200105" RELATED [] is_a: PW:0000100 ! transcription pathway is_a: PW:0000567 ! sex steroids signaling pathway is_a: PW:0000716 ! transcription factor mediated signaling pathway [Term] id: PW:0000565 name: eicosanoid signaling pathway def: "Eicosanoids are molecules derived from omega-3 or omega-6 fats that can act as hormones. The receptors are G protein coupled (GPCR0 or the nuclear peroxisome proliferator-activated receptor gamma." [OneLook:www.onelook.com] synonym: "PID:200082" RELATED [] is_a: PW:0000469 ! lipid hormone signaling pathway [Term] id: PW:0000566 name: corticosteroid signaling pathway def: "Corticosteroids group together glucocorticoids and mineralocorticoids, C21-steroid hormones derived from cholesterol. They control a wide range of physiological and cellular responses. Synthetic drugs mimicking their effects are used in the treatment of many conditions. Side effects, long-term use and/or natural deficiencies have been associated with various disorders." [OneLook:www.onelook.com] is_a: PW:0000468 ! steroid hormone signaling pathway [Term] id: PW:0000567 name: sex steroids signaling pathway def: "Sex steroid mediated signaling pathways have important roles in the development and/or maintenance of sex-specific characteristics or attributes." [OneLook:www.onelook.com] is_a: PW:0000468 ! steroid hormone signaling pathway [Term] id: PW:0000568 name: aldosterone signaling pathway def: "Aldosterone signaling through the mineralocorticoid receptor plays an important role in the balance of fluids and electrolytes in the body. Its biosynthesis is primarily regulated by the renin-angiotensin system and potassium ions concentration." [PubMed:PMID\: 16002531 PMID\: 17293689 ;] synonym: "KEGG:04960" RELATED [] is_a: PW:0000100 ! transcription pathway is_a: PW:0000783 ! mineralocorticoid signaling pathway [Term] id: PW:0000569 name: cortisol signaling pathway def: "Cortisol, also known as hydrocortison, is the most important glucocorticoid. Cortisol signaling, via binding to the glucocorticoid receptor present in almost every animal cell, is essential for many cellular and physiological functions." [OneLook:www.onelook.com] synonym: "PID:200030" RELATED [] is_a: PW:0000100 ! transcription pathway is_a: PW:0000782 ! glucocorticoid signaling pathway [Term] id: PW:0000570 name: hexosamine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of hexosamines, amino sugars created by adding an amino group to a hexose. Hexosamines, particularly N-acetylglucosamine, are used to modify proteins." [PubMed\, Onelook:NCBI\, www.onelook.com] is_a: PW:0000152 ! amino sugar metabolic pathway [Term] id: PW:0000571 name: neurotrophic factor signaling pathway def: "Signaling pathways activated by members of the neurotrophic family of growth factors are involved in differentiation of progenitor cells, survival and differentiation of neural cells." [OneLook:www.onelook.com] synonym: "KEGG:04722" RELATED [] is_a: PW:0000059 ! signaling pathway pertinent to the brain is_a: PW:0000168 ! growth factor signaling pathway [Term] id: PW:0000572 name: brain-derived neurotrophic factor signaling pathway def: "Brain-derived neurotrophic factor signaling pathway plays important roles in the growth, differentiation and survival of neurons." [Gene Ontology:GO\:0031547, OneLook:www.onelook.com] synonym: "BDNF signaling pathway" EXACT [] is_a: PW:0000571 ! neurotrophic factor signaling pathway [Term] id: PW:0000573 name: pentose phosphate pathway - oxidative phase def: "The oxidative (linear) phase of the pentose phosphate pathway involves the oxidation and decarboxylation of glucose-6-phosphate to produce the 5 carbon sugar ribulose-5-phosphate and the generation of NADPH." [Gene Ontology:GO\:0009051, OneLook\, PubMed:www.oneloook.com; http\://www.ncbi.nlm.nih.gov/sites/entrez] is_a: PW:0000556 ! glucose oxidation pathway relationship: part_of PW:0000045 ! pentose phosphate pathway [Term] id: PW:0000574 name: pentose phosphate pathway - non-oxidative phase def: "The non-oxidative (circular) phase of the pentose phosphate pathway involves conversion of ribulose-5-phosphate to ribose-5-phosphate, important in the synthesis of nucleotides and nucleic acid, or to 3 or 6 carbon sugars." [Gene Ontology:GO\:0009052, OneLookc\, PubMed:www.oneloook.com; http\://www.ncbi.nlm.nih.gov/sites/entrez] relationship: part_of PW:0000045 ! pentose phosphate pathway [Term] id: PW:0000575 name: sugar transport pathway def: "Those pathways that mediate the transport of sugars across the cell membrane. Transport of glucose, one of the major energy sources in the cell, is an important aspect of sugar transport pathway." [Online\, Pubmed:http\://www.yahoo.com; http\://www.ncbi.nlm.nih.gov/] synonym: "carbohydrate transport pathway" RELATED [] is_a: PW:0000103 ! transport pathway [Term] id: PW:0000576 name: facilitative sugar transporter mediated sugar transport pathway def: "The GLUT family contains 14 members in mammals which can be grouped into 3 classes based on sequence similarities. These transporters are characterized by the presence of 12 transmembrane alpha helices. Of the 14 members of the GLUT family, 11 have been shown to be involved in sugar transport pathway." [PubMed:PMID\: 15466941 ; PMID\: 15449578] synonym: "GLUT mediated sugar transport pathway" RELATED [] is_a: PW:0000575 ! sugar transport pathway [Term] id: PW:0000577 name: cytokine and chemokine mediated signaling pathway def: "Cytokines are small proteins released by the cell and acting as intercellular mediators. Chemokines are a subset of cytokine that can attract and activate leukocytes. They are characterized by a small size and the presence of four cysteines whose location is important for their structural folding. Cytokines or chemokines binding to cognate receptors triggers numerous downstream signaling cascades." [MCW library:Handbook on molecular and cellular immunology] is_a: PW:0000003 ! signaling pathway [Term] id: PW:0000578 name: scatter factor/hepatocyte growth factor signaling pathway def: "Scatter factor/hepatocyte signaling impacts on various biological processes such as proliferation and survival, morphogenesis and motility. SF/HGF and its receptor c-Met have also been implicated in tumor growth and angiogenesis." [Gene Ontology:GO\:0048012, PubMed:PMID\:16212809\, 16778093\, 18175071] synonym: "HGF/SF signaling pathway" RELATED [] synonym: "SF/HGF signaling pathway" RELATED [] is_a: PW:0000168 ! growth factor signaling pathway [Term] id: PW:0000579 name: somatostatin signaling pathway def: "Somatostatin signaling through its receptors regulates processes such as proliferation, secretion and motility via inhibition of growth hormone and factor. The potential anti-tumor activity of somatostatin has led to the development and clinical use of its analogs." [OubMed:PMID\: 16625838; PMID\: 15153426; PMID\: 15078190; PMID\: 15853632] synonym: "somatotropin release inhibitory factor" RELATED [] synonym: "SRIF" RELATED [] is_a: PW:0000467 ! peptide and protein hormone signaling pathway [Term] id: PW:0000580 name: translation initiation pathway def: "Translation initiation is the first of the three stages of translation pathway in eukaryotes." [Gene Ontology:GO\:0006413, PubMed:PMID\: 17680008] relationship: part_of PW:0000101 ! translation pathway [Term] id: PW:0000581 name: translation elongation pathway def: "Translation elongation is the second of the three stages of translation pathway in eukaryotes." [Gene Ontology:GO\:0006414, PubMed:PMID\: 17680008] relationship: part_of PW:0000101 ! translation pathway [Term] id: PW:0000582 name: translation termination pathway def: "Translation termination is the third of the three stages of translation pathway in eukaryotes." [Gene Ontology:GO\:0006415, PubMed:PMID\: 17680008] relationship: part_of PW:0000101 ! translation pathway [Term] id: PW:0000583 name: orexin/hypocretin signaling pathway def: "The orexin/hypocretin signaling appears to play a role in the stimulation of food intake. Alterations of the system are associated with the narcolepsy sleep disorder." [OneLook\, PubMed:www.onelook.com; PMID\: 17299454] is_a: PW:0000467 ! peptide and protein hormone signaling pathway [Term] id: PW:0000584 name: altered orexin/hypocretin signaling pathway def: "An orexin/hypocretin signaling pathway that deviates from what its normal course should be. Alterations in orexin/hypocretin signaling pathway have been linked to narcolepsy. It may also play a role in obesity." [PubMed:PMID\: 17299454] is_a: PW:0000511 ! altered peptide and protein hormone signaling pathway is_a: PW:0000583 ! orexin/hypocretin signaling pathway [Term] id: PW:0000585 name: orexin/hypocretin signaling pathway via orexin/hypocretin receptor 1 def: "Orexin/hypocretin signaling through receptor 1 couples to Galphaq class of G proteins. Orexin/hypocretin receptor 1 primarily binds orexin A. Orexin A and B are derived from prepro-orexin precursor." [PubMed:PMID\: 17299454] is_a: PW:0000583 ! orexin/hypocretin signaling pathway [Term] id: PW:0000586 name: orexin/hypocretin signaling pathway via orexin/hypocretin receptor 2 def: "Orexin/hypocretin signaling through receptor 2 couples to Galphaq and the inhibitory Galphai classes of G proteins. Orexin/hypocretin receptor 2 binds both orexin A and B derived from the prepro-orexin precursor." [PubMed:PMID\: 17299454] is_a: PW:0000583 ! orexin/hypocretin signaling pathway [Term] id: PW:0000587 name: narcolepsy disease pathway def: "Narcolepsy is a neurological condition characterized by excessive day sleep, an inability to maintain awake states. Dysfunction of the orexin/hypocretin signaling pathway has been linked to this condition." [PubMed:PMID\: 17299454] is_a: PW:0000178 ! neurological disorder disease pathway [Term] id: PW:0000588 name: altered adiponectin signaling pathway def: "An adiponectin signaling pathway that deviates from what its normal course should be. Deregulation of adiponectin signaling have been linked to obesity, cardiovascular diseases, diabetes and metabolic syndrome." [PubMed:PMID\: 16823476; PMID\: 16634986; PMID\: 17140553] is_a: PW:0000511 ! altered peptide and protein hormone signaling pathway is_a: PW:0000563 ! adiponectin signaling pathway [Term] id: PW:0000589 name: metal homeostasis pathway def: "Those pathways involved in the proper balance of metal ion levels, uptake and transport, utilization and storage as demanded by the needs of cells, tissues and organs. Disruption of metal ion homeostasis can have toxic and harmful consequences." [InHouse:PW-InHouse] is_a: PW:0000355 ! homeostasis pathway [Term] id: PW:0000590 name: iron homeostasis pathway def: "Those pathways involved in the proper balance of iron levels, uptake and transport, utilization and storage as needed by cells, tissues and organs. Iron is essential for many life processes but its reactivity makes it potentially dangerous." [Gene Ontology:GO\:0055072, PubMed:PMID\: 17194590; PMID\: 17014365; PMID\: 17367269] is_a: PW:0000589 ! metal homeostasis pathway [Term] id: PW:0000591 name: iron transport pathway is_a: PW:0000593 ! metal ion transport pathway relationship: part_of PW:0000590 ! iron homeostasis pathway [Term] id: PW:0000592 name: iron storage pathway relationship: part_of PW:0000590 ! iron homeostasis pathway [Term] id: PW:0000593 name: metal ion transport pathway def: "Those pathways that mediate the uptake and transport of metal ions. Metal ion transport pathways are important aspects of metal ion homeostasis." [InHouse:PW-InHouse] is_a: PW:0000103 ! transport pathway [Term] id: PW:0000594 name: altered glucose homeostasis pathway def: "The pathways involved in the balanced maintenance of glucose levels, transport and processing as demanded by the needs of the cells, tissues and organs assure the maintenance of glucose homeostasis. Disruption in these pathways alter glucose homeostasis and underlie many complex disorders - type 2 diabetes and its associated complications is one example." [PubMed:PMID\:15466941] is_a: PW:0000358 ! altered homeostasis pathway is_a: PW:0000553 ! glucose homeostasis pathway [Term] id: PW:0000595 name: phosphatidylinositol 3-kinase signaling pathway def: "Phosphatidylinositol kinases represent a family of lipid kinases that phosphorylate the 3' position of the inositol ring in target substrates. They are grouped into three classes: class I further subdivided into subclass A and B, class II and class III. By far the best known and characterized is class I, particularly IA that signals downstream of receptor tyrosine kinases and engages the Akt family of kinases." [PubMed:PMID\: 17052169\, 17641274\, 16847462] synonym: "KEGG:04070" RELATED [] synonym: "phosphoinositide 3-kinase signaling pathway" RELATED [] synonym: "PI3K signaling pathway" RELATED [] is_a: PW:0000541 ! signaling pathway involving second messengers [Term] id: PW:0000596 name: altered insulin signaling pathway def: "An insulin signaling pathway that deviates from what its normal course should be. Deregulation of insulin signaling can have profound health consequences due to its potential to alter glucose and energy homeostasis." [InHouse:PW dictionary] is_a: PW:0000143 ! insulin signaling pathway is_a: PW:0000359 ! altered energy homeostasis pathway is_a: PW:0000511 ! altered peptide and protein hormone signaling pathway is_a: PW:0000594 ! altered glucose homeostasis pathway [Term] id: PW:0000597 name: non-canonical Wnt signaling pathway def: "The non-canonical Wnt signaling pathway groups the various Wnt signaling routes that are beta-catenin independent." [PubMed:PMID\: 16019432; 18432252] synonym: "beta-catenin independent Wnt signaling pathway" RELATED [] synonym: "PID:200020" RELATED [] is_a: PW:0000008 ! Wnt signaling pathway [Term] id: PW:0000598 name: altered Wnt signaling pathway def: "A Wnt signaling pathway that deviates from what its normal course should be. Deregulation of Wnt signaling has been implicated in several cancers as well as diseases other than cancer." [PubMed:PMID\: 18188179; 18432252] is_a: PW:0000008 ! Wnt signaling pathway is_a: PW:0000669 ! altered glycoprotein signaling pathway is_a: PW:0000673 ! altered signaling pathway pertinent to development [Term] id: PW:0000599 name: altered canonical Wnt signaling pathway def: "A canonical Wnt signaling pathway that deviates from what its normal course should be. Mutations in core components of the canonical pathway have been implicated in several types of cancer as well as diseases other than cancer." [PubMed:PMID\: 18188179; 18432252] is_a: PW:0000201 ! canonical Wnt signaling pathway is_a: PW:0000598 ! altered Wnt signaling pathway [Term] id: PW:0000600 name: altered non-canonical Wnt signaling pathway def: "A non-canonical Wnt signaling pathway that deviates from what its normal course should be. Deregulation of the beta-catenin independent pathway appears to play a role in the biology of tumors." [PubMed:PMID\: 18271916] is_a: PW:0000597 ! non-canonical Wnt signaling pathway is_a: PW:0000598 ! altered Wnt signaling pathway [Term] id: PW:0000601 name: altered p38 MAPK signaling pathway is_a: PW:0000198 ! p38 MAPK signaling pathway is_a: PW:0000422 ! altered stress-regulated MAPK signaling pathway [Term] id: PW:0000602 name: altered extracellular signal-regulated Raf/Mek/Erk signaling pathway def: "A Raf/Mek/Erk signaling pathway that deviates from what its normal course should be. Aberrant Raf/Mek/Erk signaling has been implicated in many types of cancer." [PubMed:PMID\: 17126425; 17229475] is_a: PW:0000102 ! the extracellular signal-regulated Raf/Mek/Erk signaling pathway is_a: PW:0000421 ! altered mitogen activated protein kinase pathway [Term] id: PW:0000603 name: Erk5 MAPK signaling pathway def: "Erk5 pathway, also known as the big MAP kinase, is activated by various stresses but not by inflammatory cytokines. In HeLa and PC12 cells, the pathway can be activated by growth factors." [Gene Ontology:GO\:0070375, KEGG:map04010, PubMed:PMID\: 17229475 ; PMID\: 17306385, Reactome:REACT_12020.1] synonym: "Bmk1 MAPK signaling pathway" RELATED [] is_a: PW:0000007 ! mitogen activated protein kinase signaling pathway [Term] id: PW:0000604 name: altered Erk5 MAPK signaling pathway is_a: PW:0000421 ! altered mitogen activated protein kinase pathway is_a: PW:0000603 ! Erk5 MAPK signaling pathway [Term] id: PW:0000605 name: cancer pathway def: "Cancer, or malignant neoplasm, represents a category of diseases characterized by uncontrolled cell growth and avoidance of apoptosis, invasion and metastasis. Deregulation of many pathways - signaling, regulatory, metabolic and combination of them, have been implicated in susceptibility to or development of these conditions. Generally, cancer is classified according to the tissue or organ affected." [PubMed:PMID\: 10647931] synonym: "neoplasm pathway" RELATED [] is_a: PW:0000013 ! disease pathway [Term] id: PW:0000606 name: urogenital cancer pathway def: "Urogenital cancer groups those malignancies that affect the urinary system and reproductive organs. Deregulation of several pathways along with genetic damage accumulated over time can lead to the development of these conditions." [InHouse:InHouse PW dictionary] synonym: "genitourinary cancer pathway" RELATED [] synonym: "urinogenital cancer pathway" RELATED [] is_a: PW:0000605 ! cancer pathway [Term] id: PW:0000607 name: ovarian cancer pathway def: "Ovarian cancer is a leading cause of cancer deaths in women. Several susceptibility genes have been identified and they have a role to play in pathways involved in or regulating proliferation, DNA repair and apoptosis." [PubMed:PMID\:12413930; PMID\:12886939; PMID\:15111296] synonym: "ovarian neoplasm pathway" RELATED [] is_a: PW:0000606 ! urogenital cancer pathway [Term] id: PW:0000608 name: cervical cancer pathway def: "Cervical cancer affects the cervical area and human papilloma virus (HPV) infection plays a major role in the pathogenesis of the condition. A number of HPV proteins interact with and affect the function of several host proteins that play a role in apoptoptic pathway and/or those involved in cell proliferation." [PubMed:PMID\:10471054; PMID\:11486705] synonym: "cervical neoplasm pathway" RELATED [] is_a: PW:0000606 ! urogenital cancer pathway [Term] id: PW:0000609 name: prostate cancer pathway def: "Prostate cancer is a frequent form of cancer in men over the age of fifty. It is usually asymptomatic but when in an advanced stage, it may spread to other parts of the body causing symptoms others than those sometimes observed. Several susceptibility as well as defective genes have been identified." [KEGG:map05215, PubMed:PMID\: 15149739; PMID\: 12878745; PMID\: 14752525] synonym: "KEGG:05215" RELATED [] synonym: "prostate neoplasm pathway" EXACT [] is_a: PW:0000606 ! urogenital cancer pathway [Term] id: PW:0000610 name: bladder cancer pathway def: "Bladder cancer groups several types of malignant tumors of the urinary bladder. It is more prevalent in men than in women and combines both risk factors such as tobacco and exposure to certain carcinogens and genetic factors. Mutations in genes involved in a number of signaling pathways have been implicated in the development of these conditions." [KEGG:map05219, PubMed:PMID\:17158541; PMID\:16474624] synonym: "bladder neoplasm pathway" EXACT [] synonym: "KEGG:05219" RELATED [] is_a: PW:0000606 ! urogenital cancer pathway [Term] id: PW:0000611 name: endometrial cancer pathway def: "Endometrial cancer affects the lining of the uterus, or endometrium. Hormonal and genetic alterations play a role in the development of this carcinoma type. Mutations in genes acting in several pathways have been associated with the condition and its types." [KEGG:map05213, PubMed:PMID\:12583434; PMID\:15947972; PMID\:16508724] synonym: "endometrial neoplasm pathway" EXACT [] synonym: "KEGG:05213" RELATED [] is_a: PW:0000606 ! urogenital cancer pathway [Term] id: PW:0000612 name: colorectal cancer pathway def: "Colorectal cancer are malignant tumors of the colon and rectum. Both risk factors usually relating to life style such as physical exercise or use of tobacco and genetics contribute to the development of the condition. Mutations in the components of canonical Wnt and Smad-dependent TGF-beta signaling and of DNA mismatch repair pathways have been associated with the pathogenesis of colorectal cancer pathway." [KEGG:map05210, OneLook:www.onelook.com] synonym: "colorectal neoplasm pathway" EXACT [] synonym: "KEGG:05210" RELATED [] is_a: PW:0000627 ! gastrointestinal cancer pathway [Term] id: PW:0000613 name: altered transforming growth factor-beta signaling pathway def: "A trasforming growth factor-beta (TGF-beta) signaling pathway that deviates from what its normal course should be. Altered Tgf-b signaling, primarily the well characterized SMAD dependent pathway, has been implicated in numerous conditions." [PubMed:PMID\: 16678165; 18313409] synonym: "altered TGF-beta signaling pathway" RELATED [] is_a: PW:0000206 ! transforming growth factor-beta signaling pathway is_a: PW:0000335 ! altered transforming growth factor-beta superfamily mediated signaling pathway [Term] id: PW:0000614 name: altered transforming growth factor-beta Smad dependent signaling pathway def: "A transfoming growth factor-beta Smad dependent signaling pathway that deviates from what its normal course should be. Altered TGF-beta Smad dependent signaling has been implicated in vascular conditions and tumorigenesis." [PubMed:PMID\:18313409] synonym: "altered TGF-beta Smad dependent signaling pathway" RELATED [] is_a: PW:0000490 ! transforming growth factor-beta Smad dependent signaling pathway is_a: PW:0000613 ! altered transforming growth factor-beta signaling pathway [Term] id: PW:0000615 name: altered bone morphogenetic protein signaling pathway def: "A bone morphogenetic protein (BMP) signaling pathway that deviates from what its normal course should be. Altered BMP signaling has been implicated in cardiovascular condition, pulmonary hypertension, the juvenile polyposis syndrome (JPS)." [PubMed:PMID\:18313409] synonym: "altered BMP signaling pathway" RELATED [] is_a: PW:0000330 ! Bone morphogenetic proteins signaling pathway is_a: PW:0000335 ! altered transforming growth factor-beta superfamily mediated signaling pathway [Term] id: PW:0000616 name: altered tumor necrosis factor superfamily mediated signaling pathway def: "Those tumor necrosis factor superfamily mediated pathways that deviate from what their normal course should be. Altered tumor necrosis factor superfamily pathways have been implicated in a spectrum of conditions ranging from septic shock and tumorigenesis to diabetes, rheumatoid arthritis and various inflammatory diseases." [PubMed:PMID\: 14555214\, 11796220\, 11239407] synonym: "altered TNF superfamily signaling pathay" RELATED [] is_a: PW:0000236 ! tumor necrosis factor superfamily mediated signaling pathway is_a: PW:0000617 ! altered cytokine mediated signaling pathway [Term] id: PW:0000617 name: altered cytokine mediated signaling pathway def: "A cytokine mediated signaling pathway that deviates from what its normal course should be. Aberrant cytokine signaling pathway, alone or in combination with other pathways underlie various diseases." [InHouse:PW dictionary] is_a: PW:0000264 ! altered signaling pathway is_a: PW:0000828 ! cytokine mediated signaling pathway [Term] id: PW:0000618 name: altered tumor necrosis factor mediated signaling pathway def: "A tumor necrosis factor (Tnf) signaling pathway that deviates from what its normal course should be. Altered Tnf signaling has been implicated in many human diseases - cerebral malaria, cancer, multiple sclerosis - are a few examples." [PubMed:PMID\:12040173\, 12655295\, 14504472] synonym: "altered TNF signaling pathway" RELATED [] synonym: "altered TNF-alpha signaling pathway" RELATED [] is_a: PW:0000233 ! tumor necrosis factor mediated signaling pathway is_a: PW:0000616 ! altered tumor necrosis factor superfamily mediated signaling pathway is_a: PW:0000680 ! altered extrinsic apoptotic pathway [Term] id: PW:0000619 name: altered nuclear factor kappa B signaling pathway def: "A nuclear factor kappa B (NF-kB) signaling pathway that deviates from what its normal course should be. Altered NF-kB signaling has been implicated in a number of conditions including immunodeficiency, inflammation and several forms of cancer." [PubMed:PMID\: 17072330\, 17072331] synonym: "altered NF-kappaB signaling pathway" RELATED [] synonym: "altered NF-kB signaling pathway" RELATED [] is_a: PW:0000499 ! nuclear factor kappa B signaling pathway is_a: PW:0000719 ! altered transcription factor mediated signaling pathway is_a: PW:0000807 ! altered transcription pathway [Term] id: PW:0000620 name: altered signaling pathways involving second messengers def: "Those signaling pathways involving second messengers that deviate from what their normal course should be. Deregulation of these pathways can have far reaching consequences." [InHouse:PW dictionary] is_a: PW:0000264 ! altered signaling pathway is_a: PW:0000541 ! signaling pathway involving second messengers [Term] id: PW:0000621 name: altered phosphatidylinositol 3-kinase signaling pathway is_a: PW:0000595 ! phosphatidylinositol 3-kinase signaling pathway is_a: PW:0000620 ! altered signaling pathways involving second messengers [Term] id: PW:0000622 name: altered phosphatidylinositol 3-kinase-Akt signaling pathway def: "A phosphatidylinositol 3-kinase-Akt signaling pathway that deviates from what its normal course should be. Altered phosphatidylinositol 3-kinase-Akt signaling pathway has been implicated in several forms of cancer. The components of the pathway are attractive targets for the development of therapeutics." [PubMed:PMID\:18473732\, 18288941\, 18288939\, 17952368] is_a: PW:0000232 ! phosphatidylinositol 3-kinase-Akt signaling pathway is_a: PW:0000964 ! altered phosphatidylinositol 3-kinase class I signaling pathway [Term] id: PW:0000623 name: altered scatter factor/hepatocyte growth factor signaling pathway def: "A scatter factor/hepatocyte growth factor signaling pathway that deviates from what its normal course should be. Aberrant Hgf signaling via Met receptor has been implicated in numerous forms of cancer." [PubMed:PMID\:18175071] synonym: "altered HGF/SF signaling pathway" RELATED [] synonym: "altered SF/HGF signaling pathway" RELATED [] is_a: PW:0000298 ! altered growth factor signaling pathway is_a: PW:0000578 ! scatter factor/hepatocyte growth factor signaling pathway [Term] id: PW:0000624 name: breast cancer pathway def: "Breast cancer or neoplasm is the most common cancer among women and the second worldwide after lung cancer. Deregulated pathways such estrogen or PI3K-Akt signaling have been implicated in breast cancer. In many cases, the disease is estrogen-dependent and it is possible that dysregulation of miRNA may correlate with the expression of estrogen receptor. Mutations in a number of other genes such as Brca1, 2 and 3 or p53 have also been associated with breast cancer." [OMIM:OMIM\:114480, PubMed:PMID\: 17275086\, 20739888] synonym: "breast neoplasm" RELATED [] is_a: PW:0000605 ! cancer pathway [Term] id: PW:0000625 name: digestive system cancer pathway def: "A general term grouping neoplastic pathways of the biliary tract, liver, pancreas and the gastrointestinal system." [MeSH\, OMIM:] synonym: "digestive system neoplasm pathway" RELATED [] synonym: "gastrointestinal neoplasm pathway" RELATED [] is_a: PW:0000605 ! cancer pathway [Term] id: PW:0000626 name: pancreatic cancer pathway def: "Pancreatic cancer, a malignant tumor of the pancreas, has both genetic and predisposing factors. Deregulated pathways, such as TGF-B, PI3K-Akt or RAF/MEK/ERK, have been implicated in the development of pancreatic cancer." [KEGG:map05212, PubMed:PMID\: 17898532\, 18662538] synonym: "KEGG:05212" RELATED [] synonym: "pancreatic neoplasm pathway" EXACT [] is_a: PW:0000625 ! digestive system cancer pathway is_a: PW:0000700 ! endocrine gland cancer pathway [Term] id: PW:0000627 name: gastrointestinal cancer pathway def: "A general term grouping neoplastic pathways of the esophagus, gastric or stomach and intestinal system." [OMIM\, MeSH:] synonym: "gastrointestinal neoplasm pathway" RELATED [] is_a: PW:0000625 ! digestive system cancer pathway [Term] id: PW:0000628 name: intestinal cancer pathway synonym: "intestinal neoplasm pathway" RELATED [] is_a: PW:0000627 ! gastrointestinal cancer pathway [Term] id: PW:0000629 name: gastric cancer pathway def: "Gastric cancer is the forth most common form of cancer worldwide and has a high death rate. Deregulated pathways, such as Wnt, PI3K-Akt or RAF/MEK/ERK, have been implicated in the development of gastric cancer." [PubMeD:PMID\: 17203201] synonym: "gastric neoplasm pathway" RELATED [] synonym: "stomach cancer pathway" RELATED [] synonym: "stomach neoplam pathway" RELATED [] is_a: PW:0000627 ! gastrointestinal cancer pathway [Term] id: PW:0000630 name: liver cancer pathway synonym: "" RELATED [] synonym: "hepatic cancer pathway" RELATED [] synonym: "hepatic neoplasm pathway" RELATED [] synonym: "liver neoplasm pathway" RELATED [] is_a: PW:0000625 ! digestive system cancer pathway [Term] id: PW:0000631 name: head and neck cancer pathway def: "A general term grouping neoplastic pathways of the upper aerodigestive system. Deregulated pathways, such as TGF-B, PI3K-Akt or epidermal growth factor (EGF) signaling, have been implicated in the of head and neck cancer." [OMIM\, MeSH\, PUbMed:PMID\: 18662538] synonym: "head and neck neoplasm pathway" RELATED [] is_a: PW:0000605 ! cancer pathway [Term] id: PW:0000632 name: bone cancer pathway synonym: "bone neoplasm pathway" RELATED [] is_a: PW:0000605 ! cancer pathway [Term] id: PW:0000633 name: skin cancer pathway synonym: "" RELATED [] synonym: "skin neoplasm pathway" RELATED [] is_a: PW:0000605 ! cancer pathway [Term] id: PW:0000634 name: altered planar cell polarity Wnt signaling pathway def: "A planar cell polarity Wnt signaling pathway that deviates from what its normal course should be. Altered planar cell polarity Wnt signaling has been implicated in a number of conditions including gastric and pancreatic cancer." [PubMed:PMID\: 17203201] synonym: "altered PCP signaling pathway" RELATED [] is_a: PW:0000200 ! the planar cell polarity Wnt signaling pathway is_a: PW:0000600 ! altered non-canonical Wnt signaling pathway [Term] id: PW:0000635 name: altered Wnt/calcium signaling pathway synonym: "altered Wnt/Ca(II) signaling pathway" RELATED [] is_a: PW:0000199 ! the Wnt/calcium signaling pathway is_a: PW:0000600 ! altered non-canonical Wnt signaling pathway [Term] id: PW:0000636 name: exocytic pathway def: "Exocytic pathway involves trafficking of secretory vesicles to their final destination. It consists of several steps: budding, transport mediated by microtubule and actin associated molecular motors, tethering/docking and fusion with target membrane. Members of the Arf and Rab family of Ras superfamily are involved in the control of exit from Golgi and exocytic route, respectively." [PubMed:PMID\:18354421; 16882731] relationship: part_of PW:0000280 ! secretory pathway [Term] id: PW:0000637 name: protein modification pathway in the secretory pathway def: "In the secretory pathway, the protein modification pathway involves the appropriate modification of glycoproteins and proteoglycans. It also provides for processing of the pro-forms of proteins into their mature form." [PubMed:PMID\:18354421] is_a: PW:0000432 ! protein modification pathway relationship: part_of PW:0000280 ! secretory pathway [Term] id: PW:0000638 name: Endoplasmic Reticulum-associated degradation pathway def: "In the endoplasmic reticulum correctly folded proteins are targeted for further export whereas misfolded proteins are retained and targeted for degradation." [Gene Ontology:GO\:0030433, PubMed:PMID\:18216874; 18075753] synonym: "ERAD pathway" RELATED [] synonym: "KEGG:04141" RELATED [] is_a: PW:0000325 ! protein degradation pathway [Term] id: PW:0000639 name: insulin responsive facilitative sugar transporter mediated glucose transport pathway def: "The GLUT family contains 14 members in mammals which can be grouped into 3 classes based on sequence similarities. The members of group I (best characterized) and of group III transporters facilitate glucose transport. Of the three members of group I, Slc2a4 (Glut4), is involved in insulin-mediated uptake of glucose in the heart, skeletal muscle and adipose tissue. The response - central to glucose homeostasis - brings together several signaling and trafficking events." [PubMed:PMID\: 15466941; 15449578; 18171430; 17717074; 18570632] synonym: "PID:200196" RELATED [] is_a: PW:0000560 ! facilitative sugar transporter mediated glucose transport pathway [Term] id: PW:0000640 name: glycolysis pathway def: "The glycolytic pathway converts the six-carbon glucose to two three-carbon pyruvate molecules. The ten reactions of glycolysis can be subdivided into an energy consuming 'stage I' and an energy generating 'stage II'. The net energy yield is two molecules of ATP. Pyruvate can further be oxidized via the citrate cycle, converted to lactose under anaerobic conditions or back to glucose via gluconeogenesis." [Gene Ontology:GO\:0006096, KEGG:map00010, MCW Libraries:Voet & Voet \"Fundamentals od Biochemistry\" 3rd edition, Reactome :REACT_1383.5] synonym: "Embden-Meyerhof-Parnas pathway" RELATED [] synonym: "KEGG:00010" RELATED [] is_a: PW:0000025 ! glycolysis/gluconeogenesis pathway is_a: PW:0000556 ! glucose oxidation pathway [Term] id: PW:0000641 name: gluconeogenesis pathway def: "The gluconegenic pathway involves the synthesis of glucose from noncarbohydrate precursors. They include the glycolysis products pyruvate and lactate, citric acid cycle intermediates and the carbon skeletons of many amino acids." [Gene Ontology:GO\:0006094, KEGG:map00010, MCW Libraries:Voet & Voet \"Fundamentals of Biochemistry\" 3rd edition, Reactome:REACT_1520.3] synonym: "KEGG:00010" RELATED [] is_a: PW:0000025 ! glycolysis/gluconeogenesis pathway is_a: PW:0000685 ! glucose biosynthesis pathway [Term] id: PW:0000642 name: fatty acid degradation pathway def: "Fatty acid degradation occurs primarily via beta oxidation in the mitochondrion and for very long chain fatty acids, in peroxisomes. Other pathways include the degradation of branched-chain, unsaturated and odd-chain fatty acids." [MCW libraries:Biochemistry Handbook, MCW libraries:QU4 M235b 2009] is_a: PW:0000058 ! fatty acid metabolic pathway [Term] id: PW:0000643 name: altered glycogen metabolic pathway def: "A glycogen metabolic pathway that deviates from what its normal course should be. Aberrant glycogen metabolism has been associated with several glycogen storage diseases." [MCW libraries:Biochemistry Handbook] is_a: PW:0000305 ! altered carbohydrate metabolic pathway is_a: PW:0000533 ! glycogen metabolic pathway [Term] id: PW:0000644 name: altered glycogen biosynthetic pathway def: "A glycogen biosynthetic pathway that deviates from what its normal coursse should be. Aberrant glycogen metabolism has been associated with several glycogen storage diseases." [MCW libraries:Biochemistry Handbook] is_a: PW:0000532 ! glycogen biosynthetic pathway is_a: PW:0000643 ! altered glycogen metabolic pathway [Term] id: PW:0000645 name: altered glycogen degradation pathway def: "A glycogen degradation pathway that deviates from what its normal course should be. Aberrant glycogen metabolism has been associated with several glycogen storage diseases." [MCW libraries:Biochemistry Handbook] is_a: PW:0000534 ! glycogen degradation pathway is_a: PW:0000643 ! altered glycogen metabolic pathway [Term] id: PW:0000646 name: cell-extracellular matrix signaling pathway def: "Cell-extracellular matrix signaling pathway conveys information between cells and components of the extracellular matrix using cell adhesion molecules." [RGD:<, RGD:InHouse, RGD:InHouse dictionary] synonym: "cell-ECM signaling pathway" EXACT [] synonym: "KEGG:04512" RELATED [] is_a: PW:0000648 ! cell adhesion signaling pathway [Term] id: PW:0000647 name: forkhead signaling pathway def: "Forkhead proteins represent a large family of transcription factors that regulate the expression of genes involved in cell growth, proliferation and survival as well as organ development and speech acquisition." [PubMed:PMID\: 12801727; 18174472; 15492844; 15516968; 19274050; 17275054] is_a: PW:0000100 ! transcription pathway is_a: PW:0000716 ! transcription factor mediated signaling pathway [Term] id: PW:0000648 name: cell adhesion signaling pathway def: "Cell adhesion signaling pathway conveys information between cells or between cells and the extracellular matrix (ECM) using cell adhesion molecules (CAMs). While many CAMs appear to be specialized for either cell-cell or cell-ECM communication, integrin family of receptors mediates both types of signaling." [OneLook:www.onelook.com] is_a: PW:0000003 ! signaling pathway [Term] id: PW:0000649 name: is_obsolete: true [Term] id: PW:0000650 name: signaling pathway pertinent to development is_a: PW:0000003 ! signaling pathway [Term] id: PW:0000651 name: aging pathway is_a: PW:0000004 ! regulatory pathway [Term] id: PW:0000652 name: phosphatase mediated signaling pathway def: "Phosphatases are essential components of biological pathways. Phosphorylaton by protein kinases and dephosphorylation by protein phosphatases exert major regulatory roles. In addition, they can also initiate signaling cascades." [PubMed:PMID\: 19099538] is_a: PW:0000003 ! signaling pathway [Term] id: PW:0000653 name: serine/threonine-specific phophatase mediated signaling pathway def: "Serine/threonine-specific phosphatase mediated signaling presents an interesting case. If the number of tyrosine kinases and of tyrosine phosphatases is similar (~100 in mammals), serine/threonine kinases have diversified to some 400 members in the course of evolution while the serine/threonine phosphatases count to about 25. The functional versatility is confered through the diversity of regulatory subunits with which they interact. The holoenzyme dictates the role the protein complex plays in signaling pathways." [PubMed:PMID\: 15780597; 17079133; 19099538] is_a: PW:0000652 ! phosphatase mediated signaling pathway [Term] id: PW:0000654 name: tyrosine-specific phosphatase mediated signaling pathway def: "The protein tyrosine phosphatase superfamily exerts essential roles in signaling pathways. The coordinated interplay of tyrosine kinase mediated phosphorylation and tyrosine phosphatase mediated dephosphorylation of substrates shape the functional topology of signaling networks. The PTP superfamily is composed of four families." [PubMed:PMID\: 17057753; 15817824; 15186772; 19099538] is_a: PW:0000652 ! phosphatase mediated signaling pathway [Term] id: PW:0000655 name: glycoconjugated protein signaling pathway def: "Those signaling pathways mediated or intiated by oligosaccharide or polysaccharide linked proteins." [OneLook:www\,onelook.com] is_a: PW:0000003 ! signaling pathway [Term] id: PW:0000656 name: glycoprotein signaling pathway def: "Those pathways initiated or mediated by glycoproteins. Glycoproteins have oligosaccharides attached to their amino acid side chains via N- or O-glycosylation. Glycoproteins represent a large category of proteins encompassing a wide range of functionalities." [OneLook:www.onelook.com] is_a: PW:0000655 ! glycoconjugated protein signaling pathway [Term] id: PW:0000657 name: proteoglycan signaling pathway def: "Those pathways initiated or mediated by proteoglycans - heavily glycosylated proteins that have glycosaminoglycan (GAG) chain(s) linked to their protein cores. GAGs are long unbranched polysaccharides of repeating disaccharide units. Proteoglycans are categorized by the nature of the GAG chain or by their size." [OneLook:www.onelook.com] is_a: PW:0000655 ! glycoconjugated protein signaling pathway [Term] id: PW:0000658 name: glypican signaling pathway def: "Glypicans are heparan sulfate proteoglycans represented by six families in mammals. They impact on a number of signaling pathways; the effect on signaling can be either inhibitory or stimulatory, depending on the context. They also appear to integrate directional cues important for neuronal migration, axon guidance and synapse formation." [PubMed:PMID\: 18505598; 16937008] synonym: "PID:200026" RELATED [] synonym: "PID:200126" RELATED [] synonym: "PID:200225" RELATED [] is_a: PW:0000657 ! proteoglycan signaling pathway [Term] id: PW:0000659 name: syndecan signaling pathway def: "Syndecan family of proteoglycans appears to be involved in cell-adhesion, paricularly cell-extracellular matrix (ECM) signaling and to integrate with the integrin pathway. They also appear to integrate directional cues important for neuronal migration, axon guidance and synapse formation." [PubMed:PMID\:16937008; 17971838] synonym: "PID:200134" RELATED [] synonym: "PID:200156" RELATED [] synonym: "PID:200192" RELATED [] synonym: "PID:200198" RELATED [] is_a: PW:0000646 ! cell-extracellular matrix signaling pathway is_a: PW:0000657 ! proteoglycan signaling pathway [Term] id: PW:0000660 name: hematopoiesis pathway def: "Hematopoiesis refers to the formation of blood cellular components. All components are derived from the hematopoietic stem cells residing in the marrow. A great amount of new blood cells needs to be produced daily to maintain steady state levels of circulation." [www.onelook.com:OneLook] is_a: PW:0000476 ! cardiovascular system homeostasis pathway [Term] id: PW:0000661 name: DNA base repair pathway def: "The pathways rresponsible for removing one or several damaged nucleotides or of nucleotides mismatched during DNA replication." [OneLook:www.onelook.com] is_a: PW:0000099 ! DNA repair pathway [Term] id: PW:0000662 name: mismatch repair pathway def: "Mismatch repair pathway assures the maintenance of normal Watson-Crick base pairing. Bases incorrectly matched during DNA replication are removed and replaced with the correct ones." [Gene Ontology:GO\:0006298, KEGG:map03430, OneLook:www.onelook.com] synonym: "KEGG:03430" RELATED [] synonym: "MMR pathway" EXACT [] is_a: PW:0000661 ! DNA base repair pathway [Term] id: PW:0000663 name: DNA break and strand repair pathway alt_id: PW:0000131 alt_id: PW:0000291 alt_id: PW:0000664 alt_id: PW:0000665 def: "The pathway dealing with repair of single- or double-strand breaks of the DNA or of strand damage such interstrand cross links." [OneLook:www.onelook.com] is_a: PW:0000099 ! DNA repair pathway [Term] id: PW:0000666 name: altered DNA base repair pathway def: "A base repair pathway that deviates from what its normal course should be. Aberrant base repair pathways have been linked to several diseases." [OneLook:www.onelook.com] is_a: PW:0000292 ! altered DNA repair pathway is_a: PW:0000661 ! DNA base repair pathway [Term] id: PW:0000667 name: altered DNA break repair pathway is_a: PW:0000292 ! altered DNA repair pathway is_a: PW:0000663 ! DNA break and strand repair pathway [Term] id: PW:0000668 name: altered mismatch repair pathway def: "A mismatch repair pathway that deviates from what its normal course should be. Mutations in several genes in the pathway have been implicated in cases of colorectal cancer, primarily the inherited forms. To a lesser extent they are found in other types of cancer, such as for instance type 1 endometrial." [PubMed:Several articles] synonym: "altered MMR pathway" RELATED [] is_a: PW:0000662 ! mismatch repair pathway is_a: PW:0000666 ! altered DNA base repair pathway [Term] id: PW:0000669 name: altered glycoprotein signaling pathway def: "A glycoprotein signaling pathway that deviates from what its normal course should be." [OneLook:www.onelook.com] is_a: PW:0000656 ! glycoprotein signaling pathway is_a: PW:0000670 ! altered glycoconjugated protein signaling pathway [Term] id: PW:0000670 name: altered glycoconjugated protein signaling pathway def: "A glycoconjugated protein signaling pathway that deviates from what its normal course should be." [OneLook:www.onelook.com] is_a: PW:0000264 ! altered signaling pathway is_a: PW:0000655 ! glycoconjugated protein signaling pathway [Term] id: PW:0000671 name: altered cell adhesion signaling pathway is_a: PW:0000264 ! altered signaling pathway is_a: PW:0000648 ! cell adhesion signaling pathway [Term] id: PW:0000672 name: altered cell-extracellular matrix signaling pathway is_a: PW:0000671 ! altered cell adhesion signaling pathway [Term] id: PW:0000673 name: altered signaling pathway pertinent to development is_a: PW:0000264 ! altered signaling pathway is_a: PW:0000650 ! signaling pathway pertinent to development [Term] id: PW:0000674 name: insulin secretion pathway def: "Insulin secretion by pancreatic beta-cells is an important aspect of glucose homeostasis. A major component of glucose stimulated insulin secretion is represented by the route dependent on the ATP sensitive potassium channels. However, other contributions are also likely to promote insulin secretion." [Gene Ontology:GO\:0030073, PubMed:PMID\: 18774732; 18728221, Reactome:REACT_18325.2] relationship: part_of PW:0000553 ! glucose homeostasis pathway [Term] id: PW:0000675 name: glucagon secretion pathway def: "Glucagon is secreted by pancreatic alpha cell; the mechanisms of its release in response to low glucose levels are poorly understood." [PubMed:PMID\: 18647881; 18600596; 18522828] relationship: part_of PW:0000553 ! glucose homeostasis pathway [Term] id: PW:0000676 name: glucagon signaling pathway def: "Glucagon signaling responds to low levels of circulating glucose to stimulate its release. The action of glucagon signaling is counter-regulatory to the action of insulin and it plays an essential role in glucose homeostasis." [PubMwd:PMID\: 12626323] is_a: PW:0000467 ! peptide and protein hormone signaling pathway relationship: part_of PW:0000553 ! glucose homeostasis pathway [Term] id: PW:0000677 name: altered insulin secretion pathway def: "An insulin secretion pathway that deviates from what its normal course should be. Altered insulin secretion has been associated with type 2 diabetes mellitus. Multiple defects are thought to underle malfunctions of insulin secretion; the exact molecular mechanisms are only partially understood." [PubMed:PMID\:18640585] is_a: PW:0000594 ! altered glucose homeostasis pathway is_a: PW:0000674 ! insulin secretion pathway [Term] id: PW:0000678 name: altered glucagon secretion pathway def: "A glucagon secretion pathway that deviates from what its normal course should be. Elevated serum glucagon has been observed in patients with type 2 diabetes. The pathway of glucagon secretion is not well understood and this complicates the understanding of how the pathway may falter." [PubMed:PMID\: 17623014] is_a: PW:0000594 ! altered glucose homeostasis pathway is_a: PW:0000675 ! glucagon secretion pathway [Term] id: PW:0000679 name: altered glucagon signaling pathway def: "A glucagon signaling pathway that deviates from what its normal course should be. Glucagon signaling counteracts the signaling of insulin and the potential exists that an alteration of glucagon signaling has a role to play in diabetes type 2. Serum glucagon is elevated in patients with the disease; the mechanisms leading to and the consequences of elevated glucagon remain to be established." [PubMed:PMID\: 17623014] is_a: PW:0000511 ! altered peptide and protein hormone signaling pathway is_a: PW:0000594 ! altered glucose homeostasis pathway is_a: PW:0000676 ! glucagon signaling pathway [Term] id: PW:0000680 name: altered extrinsic apoptotic pathway is_a: PW:0000106 ! extrinsic apoptotic pathway is_a: PW:0000287 ! altered apoptotic cell death [Term] id: PW:0000681 name: FasL mediated signaling pathway def: "Fas ligand binding to its receptor triggers a conformational change that allows the receptor to assemble a signaling complex known as DISC, followed by recruitment of pro-caspase-8 and activation of caspase-3 and -7. It is believed that Fas mediated signaling to elicit apoptosis follows two routes." [PubMed:14744432, Reactome:REACT_900.1] synonym: "PID:200080" RELATED [] is_a: PW:0000106 ! extrinsic apoptotic pathway is_a: PW:0000236 ! tumor necrosis factor superfamily mediated signaling pathway [Term] id: PW:0000682 name: Trail mediated signaling pathway def: "Trail mediated signaling leads to apoptosis via assembly of the DISC complex (Death-Inducing Signaling Complex) downstream of its receptors." [PubMed:PMID\:14744432, Reactome:REACT_402.1] synonym: "PID:200068" RELATED [] is_a: PW:0000106 ! extrinsic apoptotic pathway is_a: PW:0000236 ! tumor necrosis factor superfamily mediated signaling pathway [Term] id: PW:0000683 name: integrin mediated cell-cell signaling pathway def: "A cell-cell signaling pathway mediated by integrins, a family of receptors that convey both 'outside-in' and 'inside-out' signals." [RGD:InHouse dictionary] is_a: PW:0000286 ! integrin mediated signaling pathway is_a: PW:0000332 ! cell-cell signaling pathway created_by: VPetri creation_date: 2009-08-03T02:43:27Z [Term] id: PW:0000684 name: integrin mediated cell-extracellular matrix signaling pathway def: "A cell-extracellular matrix signaling pathway mediated by integrins, a family of receptors that convey both 'outside-in' and 'inside-out' signals." [RGD:InHouse] synonym: "integrin mediated cell-ECM signaling pathway" RELATED [] is_a: PW:0000286 ! integrin mediated signaling pathway is_a: PW:0000646 ! cell-extracellular matrix signaling pathway created_by: VPetri creation_date: 2009-08-03T02:45:17Z [Term] id: PW:0000685 name: glucose biosynthesis pathway def: "The metabolic pathways for generating glucose to meet the body's glucose needs. Gluconeogenesis in the liver and to some extent in kidney is the major pathway of glucose production; glycogenolysis is another route for generating glucose in these tissues." [:, MCW Libraries:ISBN-13 978-0470-12930-2] relationship: part_of PW:0000553 ! glucose homeostasis pathway created_by: VPetri creation_date: 2009-08-05T08:54:36Z [Term] id: PW:0000686 name: altered vasopressin signaling pathway def: "A vasopressin signaling pathway that deviates from what its normal course should be. Altered vasopressin signaling manifests clinically as problems associated with water and sodium balance." [PubMed:PMID\: 18431594\, 17761027] is_a: PW:0000491 ! vasopressin signaling pathway is_a: PW:0000511 ! altered peptide and protein hormone signaling pathway created_by: VPetri creation_date: 2009-08-27T09:07:02Z [Term] id: PW:0000687 name: altered sugar transport pathway def: "A sugar transport pathway that deviates from what its normal course should be. Alterations in sugar transport, particularly glucose, can potentially have very harmful consequences." [InHouse:PW dictionary] is_a: PW:0000545 ! altered transport pathway is_a: PW:0000575 ! sugar transport pathway created_by: VPetri creation_date: 2009-10-07T11:59:25Z [Term] id: PW:0000688 name: altered facilitative sugar transporter mediated sugar transport pathway def: "A facilitative sugar transporter mediated sugar transport pathway that deviates from what its normal course should be. Alterations in sugar transport, particularly glucose, can potentially have very harmful consequences." [InHouse:PW dictionary] is_a: PW:0000576 ! facilitative sugar transporter mediated sugar transport pathway is_a: PW:0000687 ! altered sugar transport pathway created_by: VPetri creation_date: 2009-10-07T12:05:27Z [Term] id: PW:0000689 name: altered glucose transport pathway def: "A glucose transport pathway that deviates from what its normal course should be. Alterations in glucose transport can potentially have very harmful consequences." [InHouse:PW dictionary] is_a: PW:0000554 ! glucose transport pathway is_a: PW:0000594 ! altered glucose homeostasis pathway is_a: PW:0000687 ! altered sugar transport pathway created_by: VPetri creation_date: 2009-10-07T12:08:39Z [Term] id: PW:0000690 name: altered facilitative sugar transporter mediated glucose transport pathway def: "A faclitative sugar transporter mediated glucose transport pathway that deviates from what its normal course should be. Alterations in glucose transport can potentially have very harmful consequences." [InHouse:PW dictionary] is_a: PW:0000560 ! facilitative sugar transporter mediated glucose transport pathway is_a: PW:0000689 ! altered glucose transport pathway created_by: VPetri creation_date: 2009-10-07T12:12:44Z [Term] id: PW:0000691 name: altered sodium-glucose contransporter mediated glucose transport pathway def: "A sodium-glucose contransporter mediated glucose transport pathway that deviates from what its normal course should be. Alterations in glucose transport can potentially have very harmful consequences." [InHouse:PW] is_a: PW:0000561 ! sodium-glucose cotransporter mediated glucose transport pathway is_a: PW:0000689 ! altered glucose transport pathway created_by: VPetri creation_date: 2009-10-07T12:21:13Z [Term] id: PW:0000692 name: altered insulin responsive facilitative sugar transporter mediated glucose transport pathway def: "An insulin responsive facilitative sugar transporter mediated glucose transport pathway that deviates from what its normal course should be. Alterations in the pathway can manifest in insulin resistance, a hallmark of type 2 diabetes." [PubMed:PMID\: 17629673] is_a: PW:0000639 ! insulin responsive facilitative sugar transporter mediated glucose transport pathway is_a: PW:0000690 ! altered facilitative sugar transporter mediated glucose transport pathway created_by: VPetri creation_date: 2009-10-07T12:24:18Z [Term] id: PW:0000693 name: biphenyl degradation pathway def: "Those enzymatic reactions involved in the degradation of biphenyl, an aromatic hydrocarbon used as a starting material for the production of polychlorinated biphenyls or as an intermediate for the production of a variety of organic compounds." [KEGG:map00621, OneLook:www.onelook.com] is_a: PW:0000107 ! xenobiotics biodegradation pathway created_by: VPetri creation_date: 2009-10-20T08:59:23Z [Term] id: PW:0000694 name: geraniol degradation pathway def: "Those enzymatic reactions involved in the degradation of geraniol, a monoterpenoid and an alcohol, used in perfumes and in flavors." [KEGG:map00281, OneLook:www.onelook.com] is_a: PW:0000107 ! xenobiotics biodegradation pathway created_by: VPetri creation_date: 2009-10-20T09:30:32Z [Term] id: PW:0000695 name: is_obsolete: true created_by: VPetri creation_date: 2009-10-20T10:20:07Z [Term] id: PW:0000696 name: zeatin biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of zeatin - a plant hormone derived from adenine. It induces plant growth and has been reported to have anti-aging effects on human skin fibroblasts." [Gene Ontology:GO\:0033398, KEGG:map00908, OneLook:www.onelook.com] is_a: PW:0000147 ! metabolic pathway of secondary metabolites created_by: VPetri creation_date: 2009-10-20T10:23:22Z [Term] id: PW:0000697 name: carotenoid biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of carotenoids, organic pigments found in plants and other photosynthetic organisms. Some can act as antioxidants." [Gene Ontology:GO\:0016120, KEGG:map00906, OneLook:www.onelook.com] is_a: PW:0000147 ! metabolic pathway of secondary metabolites created_by: VPetri creation_date: 2009-10-20T10:29:04Z [Term] id: PW:0000698 name: thyroid cancer pathway def: "Thyroid cancer refers to one of several types of malignant tumors of the thyroid gland of which the papillary thyroid cancer is the most frequent accounting for almost 80% of all cases. The other types include follicular, medullary and anaplastic." [KEGG:map05216, OneLook:www.onelook.com] synonym: "KEGG:05216" RELATED [] synonym: "thyroid neoplasm pathway" EXACT [] is_a: PW:0000631 ! head and neck cancer pathway is_a: PW:0000700 ! endocrine gland cancer pathway created_by: vpetri creation_date: 2009-10-28T01:33:42Z [Term] id: PW:0000699 name: parathyroid cancer pathway def: "Parathyroid cancer is a rare type of cancer whose causes are unknown. There are four parathyroid glands, each of the two lobes of the thyroid gland houses two." [OneLook:www.onelook.com] is_a: PW:0000631 ! head and neck cancer pathway created_by: vpetri creation_date: 2009-10-28T01:39:16Z [Term] id: PW:0000700 name: endocrine gland cancer pathway synonym: "" RELATED [] synonym: "endocrine gland neoplasm pathway" RELATED [] is_a: PW:0000605 ! cancer pathway created_by: vpetri creation_date: 2009-10-28T01:48:29Z [Term] id: PW:0000701 name: thoracic cancer pathway synonym: "thoracic neoplasm pathway" RELATED [] is_a: PW:0000605 ! cancer pathway created_by: vpetri creation_date: 2009-10-28T01:55:10Z [Term] id: PW:0000702 name: respiratory tract cancer pathway synonym: "respiratory tract neoplasm pathway" RELATED [] is_a: PW:0000701 ! thoracic cancer pathway created_by: vpetri creation_date: 2009-10-28T01:57:08Z [Term] id: PW:0000703 name: lung cancer pathway def: "Lung cancer is one of the most common cause of cancer-related death in men but also very common in women. The main types are represented by small cell and non-small cell lung carcinomas. The former tends to respond better to chemotherapy; the latter is at times treated surgically." [OneLook:www.onelook.com] synonym: "lung neoplasm pathway" RELATED [] is_a: PW:0000702 ! respiratory tract cancer pathway created_by: vpetri creation_date: 2009-10-28T02:00:27Z [Term] id: PW:0000704 name: small cell lung cancer pathway def: "Small cell lung cancer is an aggressive type of lung cancer. Several pathways appear to be deregulated and they include the intrinsic apoptotic pathway, PI3K-Akt signaling and changes in oncogene transcription factors such as Myc and p53." [KEGG:map05222, OneLook\, KEGG:www.onelook.com] synonym: "KEGG:05222" RELATED [] synonym: "SCLC pathway" EXACT [] synonym: "small cell lung neoplasm pathway" EXACT [] is_a: PW:0000703 ! lung cancer pathway created_by: vpetri creation_date: 2009-10-28T02:00:59Z [Term] id: PW:0000705 name: non-small cell lung cancer pathway def: "Non-small cell lung cancer groups together several non-small cell lung carcinomas. The main types are represented by squamous cell, adeno- and large-cell carcinoma. Alterations in Ras and epidermal growth factors signaling, among others, have been implicated in the condition." [KEGG:map05223, OneLook\, KEGG:www.onelook.com] synonym: "KEGG:05223" RELATED [] synonym: "non-small cell lung neoplasm pathway" EXACT [] synonym: "NSCLC pathway" EXACT [] is_a: PW:0000703 ! lung cancer pathway created_by: vpetri creation_date: 2009-10-28T02:45:27Z [Term] id: PW:0000706 name: leukemia pathway def: "Leukemia is a cancer of the blood or bone marrow. The term covers a broad spectrum of conditions subdivided by proliferation type - acute and chronic, and by cell type - myeloid and lymphocytic leukemia." [OneLook:www.onelook..com] is_a: PW:0000605 ! cancer pathway created_by: vpetri creation_date: 2009-10-28T03:34:16Z [Term] id: PW:0000707 name: myeloid leukemia pathway def: "Myeloid leukemia affects cells of the myeloid lineage and their precursors and in turn is subdivided by proliferation type." [OneLook:www.onelook.com] is_a: PW:0000706 ! leukemia pathway created_by: vpetri creation_date: 2009-10-28T03:55:53Z [Term] id: PW:0000708 name: lymphoid leukemia pathway def: "Lymphoid leukemia affects lymphoid tissues and there are increase numbers of circulating lymphoblasts and lymphocytes." [OneLook:www.onelook.com] synonym: "lymphocytic leukemia pathway" RELATED [] is_a: PW:0000706 ! leukemia pathway created_by: vpetri creation_date: 2009-10-28T04:33:38Z [Term] id: PW:0000709 name: acute myeloid leukemia pathway def: "Acute myeloid leukemia is a common type of leukemia among adults. Abnormal cells are present inside the bone marrow that grow very vast and replace healthy blood cells. Several signaling pathways are disrupted and/or constitutively activated." [KEGG:map05221, OneLook :www.onelook.com] synonym: "KEGG:05221" RELATED [] is_a: PW:0000707 ! myeloid leukemia pathway created_by: vpetri creation_date: 2009-10-28T04:39:13Z [Term] id: PW:0000710 name: chronic myeloid leukemia pathway def: "Chronic myeloid leukemia, a slowly progressing condition, is a type of leukemia where too many white blood cells are made in the bone marrow." [KEGG:map05220, OneLook:www.onelook.com, XX:] synonym: "KEGG:05220" RELATED [] is_a: PW:0000707 ! myeloid leukemia pathway created_by: vpetri creation_date: 2009-10-28T04:39:38Z [Term] id: PW:0000711 name: glioma pathway def: "Gliomas are tumors of the brain categorized by the type of cell they are associated with, their location and grade. Several pathways appear to be deregulated via amplifications, overexpression, mutations or loss." [OneLook:www.onelook.com] synonym: "KEGG:05214" RELATED [] is_a: PW:0000605 ! cancer pathway created_by: vpetri creation_date: 2009-10-29T04:24:22Z [Term] id: PW:0000712 name: vasopressin signaling pathway via receptor type 1 def: "Vasopressin signaling via receptor type 1 couples to Gq alpha subunit leading to stimulation of phospholipase C beta, subsequent generation of second messengers and increase in intracellular calcium resulting in vasoconstriction." [PubMed:PMID\: 14624682; 11091117] is_a: PW:0000491 ! vasopressin signaling pathway created_by: vpetri creation_date: 2009-11-03T08:25:33Z [Term] id: PW:0000713 name: vasopressin signaling pathway via receptor type 2 def: "Vasopressin signaling via receptor type 2 plays a central role in water homeostasis by regulating the translocation of Aqp2 channel. The receptor couples to Gs alpha subunit leading to activation of adenylyl cyclase, production of cyclic AMP and triggering of protein kinase A (PKA) signaling pathway. PKA regulates both the translocation and the expression of the channel." [PubMed:PMID\: 14624682; 11091117; 18431594; 17761027] synonym: "KEGG:04962" RELATED [] is_a: PW:0000491 ! vasopressin signaling pathway created_by: vpetri creation_date: 2009-11-03T08:39:15Z [Term] id: PW:0000714 name: altered vasopressin signaling pathway via receptor type 1 def: "A vasopressin, receptor type 1 mediated signaling pathway, that deviates from what its normal course should be. Alterations in this pathway might relate to septic shock." [PubMed:PMID\: 17133186] is_a: PW:0000686 ! altered vasopressin signaling pathway is_a: PW:0000712 ! vasopressin signaling pathway via receptor type 1 created_by: vpetri creation_date: 2009-11-03T08:51:23Z [Term] id: PW:0000715 name: altered vasopressin signaling pathway via receptor type 2 def: "A vasopressin, receptor type 2 mediated signaling pathway, that deviates from what its normal course should be. Alterations in the pathway have been associated with Nephrogenic Diabetes Insipidus (NDI) caused by mutations in the receptor or, more rarely, in aquaporin channel 2." [PubMed:PMID\: 17761027] is_a: PW:0000686 ! altered vasopressin signaling pathway is_a: PW:0000713 ! vasopressin signaling pathway via receptor type 2 created_by: vpetri creation_date: 2009-11-03T09:09:09Z [Term] id: PW:0000716 name: transcription factor mediated signaling pathway def: "Transcription factors mediated signaling, by impacting on the expression and function of target genes, regulate a wide range of processes." [InHouse:PW dictionary] is_a: PW:0000003 ! signaling pathway created_by: VPetri creation_date: 2009-11-30T01:34:55Z [Term] id: PW:0000717 name: forkhead class O signaling pathway def: "The signaling pathway mediated by the FoxO subgroup of forkhead family of transcription factors regulates cell cycle and survival via the expression of its target genes. FoxO pathway is negatively regulated by PI3K-Akt pathway downstream of insulin signaling. It is positively regulated by the Jnk pathway of stress activated MAPK cascade." [PubMed:PMID\: 17275054; 19274050] synonym: "FoxO signaling pathway" RELATED [] is_a: PW:0000647 ! forkhead signaling pathway created_by: VPetri creation_date: 2009-11-30T01:42:57Z [Term] id: PW:0000718 name: p53 signaling pathway def: "p53 transcription factor is a tumor suppressor frequently mutated in cancer. p53 is at the hub of many signaling and regulatory pathways. In response to various stresses, it promotes apoptosis, cell cycle arrest and other defense pathways via transcription dependent as well as independent routes. A key regulator of p53 is Mdm2; Mdm2 is a transcriptional target of p53 thus providing a negative feedback loop." [PubMed:PMID\: 18927276; 18783169; 19776744; 19007744; 19407794] synonym: "" RELATED [] synonym: "KEGG:04115" RELATED [] synonym: "PID:200206" RELATED [] is_a: PW:0000100 ! transcription pathway is_a: PW:0000237 ! stress response pathway is_a: PW:0000303 ! p53-dependent G1/S DNA damage checkpoint pathway is_a: PW:0000716 ! transcription factor mediated signaling pathway created_by: VPetri creation_date: 2009-11-30T03:01:53Z [Term] id: PW:0000719 name: altered transcription factor mediated signaling pathway def: "A transcription factor mediated signaling pathway that deviates from what its normal course should be. Deregulation of such pathways has been linked to cancer and various other diseases." [InHouse:PW dictionary] is_a: PW:0000264 ! altered signaling pathway is_a: PW:0000716 ! transcription factor mediated signaling pathway created_by: VPetri creation_date: 2009-11-30T03:40:53Z [Term] id: PW:0000720 name: altered p53 signaling pathway def: "A p53 signaling pathway that deviates from what its normal course should be. Due to its central role at the intersection of many cellular pathways, disturbance of p53 network can have far-reaching negative consequences. The tumor suppressor Tp53 gene is frequently mutated in cancer." [PubMed:PMID\: 19776744] is_a: PW:0000718 ! p53 signaling pathway is_a: PW:0000719 ! altered transcription factor mediated signaling pathway is_a: PW:0000807 ! altered transcription pathway created_by: VPetri creation_date: 2009-11-30T03:43:14Z [Term] id: PW:0000721 name: nicotine pathway is_a: PW:0000923 ! nervous system drug pathway created_by: VPetri creation_date: 2010-01-18T03:34:19Z [Term] id: PW:0000722 name: warfarin drug pathway def: "The pharmacokinetics and pharmacodynamics pathway of warfarin. Warfarin is used as anticoagulant that antagonizes the vitamin K dependent clotting pathway. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/] is_a: PW:0000922 ! blood and blood forming organs drug pathway created_by: VPetri creation_date: 2010-01-18T03:34:31Z [Term] id: PW:0000723 name: anti-diabetic drug pathway def: "The pharmacokinetics and pharmacodynamics of anti-diabetic drugs such as repaglinide, nateglinide and sulfonylurea - inhibitors of ATP-dependent potassium channel. By blocking the channel they stimulate insulin secretion to lower blood glucose level. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/, PubMed:PMID\: PMID\:11259325; 12919179] is_a: PW:0000921 ! alimentary tract and metabolism drug pathway created_by: VPetri creation_date: 2010-01-18T03:43:49Z [Term] id: PW:0000724 name: statin drug pathway def: "The pharmacokinetics and pharmacodynamics pathway of statin. Statins are a class of drugs used to lower cholesterol. They act as inhibitors of HMG-CoA reductase, the enzyme that catalyzes an early rate-limiting step in cholesterol biosynthesis. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/] is_a: PW:0000920 ! cardiovascular system drug pathway created_by: VPetri creation_date: 2010-01-19T10:48:44Z [Term] id: PW:0000725 name: potassium channel inhibitors pharmacodynamics pathway def: "The pathway of anti-diabetic drugs-target interaction and of the biochemical or physiological responses to them. Repaglinide, nateglinide and sulfonylurea are used as inhibitors of ATP-dependent potassium channel. By blocking the channel they stimulate insulin secretion to lower blood glucose level. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/] is_a: PW:0000723 ! anti-diabetic drug pathway created_by: VPetri creation_date: 2010-01-20T12:12:30Z [Term] id: PW:0000726 name: repaglinide pharmacokinetics pathway def: "The pathway of processing - absorption, distribution, metabolism or elimination - of repaglinide. The drug is used as an inhibitor of ATP-dependent potassium channel. By blocking the channel it stimulates insulin secretion to lower blood glucose level. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/, PubMed:PMID\:12919179] is_a: PW:0000723 ! anti-diabetic drug pathway created_by: VPetri creation_date: 2010-01-20T12:14:07Z [Term] id: PW:0000727 name: nateglinide pharmacokinetics pathway def: "The pathway of processing - absorption, distribution, metabolism or elimination - of nateglinide. The drug is used as an inhibitor of ATP-dependent potassium channel. By blocking the channel it stimulates insulin secretion to lower blood glucose level. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/, PubMed:PMID\:11259325] is_a: PW:0000723 ! anti-diabetic drug pathway created_by: VPetri creation_date: 2010-01-20T12:15:46Z [Term] id: PW:0000728 name: statin pharmacodynamics pathway def: "The pathway of statins-target interaction and of the biochemical or physiological responses to them. Statins are a class of drugs used to lower cholesterol. They act as inhibitors of HMG-CoA reductase, the enzyme that catalyzes an early rate-limiting step in cholesterol biosynthesis. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/] is_a: PW:0000724 ! statin drug pathway created_by: VPetri creation_date: 2010-01-20T12:21:51Z [Term] id: PW:0000729 name: statin pharmacokinetics pathway def: "The pathway of processing - absorption, distribution, metabolism or elimination - of statin. Statins are a class of drugs used to lower cholesterol. They act as inhibitors of HMG-CoA reductase, the enzyme that catalyzes an early rate-limiting step in cholesterol biosynthesis. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/] is_a: PW:0000724 ! statin drug pathway created_by: VPetri creation_date: 2010-01-20T12:22:12Z [Term] id: PW:0000730 name: warfarin pharmacokinetics pathway def: "The pathway of processing - absorption, distribution, metabolism or elimination - of warfarin. Warfarin is used as anticoagulant that antagonizes the vitamin K dependent clotting pathway. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/] is_a: PW:0000722 ! warfarin drug pathway created_by: VPetri creation_date: 2010-01-20T12:42:35Z [Term] id: PW:0000731 name: warfarin pharmacodynamics pathway def: "The pathway of warfarin-target interaction and of the biochemical or physiological responses to drug. Warfarin is used as anticoagulant that antagonizes the vitamin K dependent clotting pathway. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/] is_a: PW:0000722 ! warfarin drug pathway created_by: VPetri creation_date: 2010-01-20T12:42:55Z [Term] id: PW:0000732 name: thromboxane metabolic pathway def: "Those metabolic reactions involving thromboxanes - a family of eicosanoids whose effects include vasoconstriction and platelet aggregation." [MCW library:QU4 M235b 2009] is_a: PW:0000485 ! eicosanoid metabolic pathway created_by: VPetri creation_date: 2010-02-17T11:26:21Z [Term] id: PW:0000733 name: glycosphingolipid metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glycosphingolipids - glycolipids with sugar(s) attached to the ceramide core. Based on the sequences of the core carbohydrate residues, they are classified into a number of series such as lacto- and neolacto-, globo-, ganglio- or muco-series." [Gene Ontology:GO\:0006687, MCW library:QU4 M235b 2009, PubMed:PMID\: 18845618\, 15207828\, 17976918] synonym: "glycolipid metabolic pathway" RELATED [] synonym: "GSL metabolic pathway" RELATED [] is_a: PW:0000197 ! sphingolipid metabolic pathway created_by: VPetri creation_date: 2010-02-17T02:03:36Z [Term] id: PW:0000734 name: cerebroside metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of cerebroside, sphingolipids in which the sugar is a monosaccharide." [MCW library:QU4 M235b 2009] is_a: PW:0000733 ! glycosphingolipid metabolic pathway created_by: VPetri creation_date: 2010-02-17T02:05:26Z [Term] id: PW:0000735 name: altered sphingolipid metabolic pathway def: "A sphingolipid metabolic pathway that deviates from what its normal course should be. Altered sphingolipid metabolism has been associated with several lysosomal storage diseases and most appear to be fatal." [MCW library:QU4 M235b 2009, PW dictionary:InHouse dictionary] is_a: PW:0000197 ! sphingolipid metabolic pathway is_a: PW:0000483 ! altered lipid metabolic pathway created_by: VPetri creation_date: 2010-02-17T02:08:31Z [Term] id: PW:0000736 name: triacylglycerol biosynthetic pathway def: "The de novo synthesis of triacylglycerol, the common form of fatty acid transport and storage. Most triacylglycerols are synthesized in the liver and stored in the adipose tissue." [Gene Ontology:GO\:0019432, MCW library:QU4 M235b 2009] synonym: "lipogenesis pathway" RELATED [] is_a: PW:0000153 ! triacylglycerol metabolic pathway created_by: VPetri creation_date: 2010-02-17T02:15:19Z [Term] id: PW:0000737 name: triacylglycerol degradation pathway def: "The degradation pathway of triacylglycerols when the energy reserves are low such as in the fasting state, during exercise or in response to stress. Triacylglycerols are the common form of fatty acid transport and storage." [Gene Ontology:GO\:0019433, MCW library:QU4 M235b 2009] synonym: "lipolysis pathway" RELATED [] is_a: PW:0000153 ! triacylglycerol metabolic pathway created_by: VPetri creation_date: 2010-02-17T02:19:06Z [Term] id: PW:0000738 name: fatty acid beta degradation pathway def: "Fatty acid degradation via beta oxidation, the most common fatty acid degradation pathway, occurs in four reactions resulting in the formation of acetyl-CoA and a fatty acyl-CoA two carbon shorter than the one that began the cycle. Acetyl-CoA can undergo further oxidation via the Krebs cycle or can be converted to ketone bodies." [MCW library:QU4 M235b 2009] synonym: "fatty acid beta oxidation pathway" RELATED [] is_a: PW:0000642 ! fatty acid degradation pathway created_by: VPetri creation_date: 2010-02-17T02:50:24Z [Term] id: PW:0000739 name: fatty acid alpha degradation pathway def: "The degradation of branched-chain fatty acids is carried out by the alpha oxidation pathway. In humans, this pathway occurs in peroxisomes." [MCW library:QU4 M235b 2009] is_a: PW:0000642 ! fatty acid degradation pathway created_by: VPetri creation_date: 2010-02-17T03:02:55Z [Term] id: PW:0000740 name: unsaturated fatty acid degradation pathway def: "The pathway of unsaturated fatty acids requires additional enzymes." [MCW library:QU4 M235b 2009] is_a: PW:0000642 ! fatty acid degradation pathway created_by: VPetri creation_date: 2010-02-17T03:06:21Z [Term] id: PW:0000741 name: altered ganglioside metabolic pathway def: "A ganglioside metabolic pathway that deviates from what its normal course should be. For instance, Tay-Sachs disease is caused by a deficiency in the enzyme that degrades ganglioside GM2. This and other conditions involving impaired sphingolipid metabolism are collectively known as sphingolipid storage disease." [:, MCW library:QU4 M235b 2009] is_a: PW:0000164 ! ganglioside metabolic pathway is_a: PW:0000742 ! altered glycosphingolipid metabolic pathway created_by: vpetri creation_date: 2010-02-18T12:39:44Z [Term] id: PW:0000742 name: altered glycosphingolipid metabolic pathway def: "A glycoshingolipid metabolic pathway that deviates from what its normal course should be. Altered glycosphingolipid metabolism has been associated with several lysosomal storage diseases and most appear to be fatal." [MCW library:QU4 M235b 2009] is_a: PW:0000733 ! glycosphingolipid metabolic pathway is_a: PW:0000735 ! altered sphingolipid metabolic pathway created_by: vpetri creation_date: 2010-02-18T01:03:56Z [Term] id: PW:0000743 name: galactocerebroside metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of galactocerebroside, a cerebroside in which the monosaccharide is galactose." [MCW library:QU4 M235b 2009] is_a: PW:0000734 ! cerebroside metabolic pathway created_by: vpetri creation_date: 2010-02-18T01:15:17Z [Term] id: PW:0000744 name: glucocerebroside metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glucocerebroside, a cerebroside in which the monosaccharide is glucose." [MCW library:QU4 M235b 2009] is_a: PW:0000734 ! cerebroside metabolic pathway created_by: vpetri creation_date: 2010-02-18T01:15:47Z [Term] id: PW:0000745 name: sphingomyelin metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of sphingomyelin - a sphingolipid found abundantly in the myelin sheath of nerve cells." [Gene Ontology:GO\:0006684, MCW library:QU4 M235b 2009] is_a: PW:0000197 ! sphingolipid metabolic pathway created_by: vpetri creation_date: 2010-02-18T01:28:17Z [Term] id: PW:0000746 name: altered sphingomyelin metabolic pathway def: "A sphingomyelin metabolic pathway that deviates from what its normal course should be. For instance, Niemann-Pick disease is caused by a deficiency in the enzyme that degrades sphingomyelin. This and other conditions involving impaired sphingolipid metabolism are collectively known as sphingolipid storage disease." [MCW library:QU4 M235b 2009] is_a: PW:0000735 ! altered sphingolipid metabolic pathway is_a: PW:0000745 ! sphingomyelin metabolic pathway created_by: vpetri creation_date: 2010-02-18T01:34:19Z [Term] id: PW:0000747 name: altered galactocerebroside metabolic pathway def: "A galactocerebroside metabolic pathway that deviates from what its normal course should be. For instance, Krabbe's disease is caused by a deficiency in the enzyme that degrades galactocerebroside. This and other conditions involving impaired sphingolipid metabolism are collectively known as sphingolipid storage disease." [MCW library:QU4 M235b] is_a: PW:0000743 ! galactocerebroside metabolic pathway is_a: PW:0000748 ! altered cerebroside metabolic pathway created_by: vpetri creation_date: 2010-02-18T01:41:25Z [Term] id: PW:0000748 name: altered cerebroside metabolic pathway def: "A cerebroside metabolic pathway that deviates from what its normal course should be. Altered cerebroside metabolism has been associated with several lysosomal storage diseases and most appear to be fatal." [MCW library:QU4 M235b 2009] is_a: PW:0000734 ! cerebroside metabolic pathway is_a: PW:0000742 ! altered glycosphingolipid metabolic pathway created_by: vpetri creation_date: 2010-02-18T01:45:45Z [Term] id: PW:0000749 name: altered glucocerebroside metabolic pathway def: "A glucocerebroside metabolic pathway that deviates from what its normal course should be. For instance, Gaucher's disease is caused by a deficiency in the enzyme that degrades glucocerebroside. This and other conditions involving impaired sphingolipid metabolism are collectively known as sphingolipid storage disease." [MCW library:QU4 M235b 2009] is_a: PW:0000744 ! glucocerebroside metabolic pathway is_a: PW:0000748 ! altered cerebroside metabolic pathway created_by: vpetri creation_date: 2010-02-18T02:02:09Z [Term] id: PW:0000750 name: altered isoprenoid metabolic pathway def: "An isoprenoid metabolic pathway that deviates from what its normal course should be. Aberrant isoprenoid metabolism, as evidenced in alterations in cholesterol metabolism, has been associated with a variety of conditions." [MCW library:QU85 B615 2008, PubMed:fPMID\: 16876788] is_a: PW:0000248 ! isoprenoid metabolic pathway is_a: PW:0000483 ! altered lipid metabolic pathway created_by: VPetri creation_date: 2010-02-23T03:06:26Z [Term] id: PW:0000751 name: altered isoprenoid biosynthetic pathway def: "An isoprenoid biosynthetic pathway that deviates from what its normal course should be. Aberrant isoprenoid biosynthetic pathway, as evidenced in altered cholesterol biosynthesis has been associated with several conditions." [MCW library:QU85 B615 2008, PubMed:PMID\: 16876788] is_a: PW:0000453 ! isoprenoid biosynthetic pathway is_a: PW:0000750 ! altered isoprenoid metabolic pathway created_by: VPetri creation_date: 2010-02-23T03:12:58Z [Term] id: PW:0000752 name: altered cholesterol biosynthetic pathway def: "A cholesterol biosynthetic pathway that deviates from what its normal course should be. Aberrant cholesterol biosynthesis involves defects in enzymes of both early and later steps leading to several disorders." [MCW library:QU 85 B615 2008, PubMed:PMID\: 16876788] is_a: PW:0000454 ! cholesterol biosynthetic pathway is_a: PW:0000751 ! altered isoprenoid biosynthetic pathway created_by: VPetri creation_date: 2010-02-23T03:18:14Z [Term] id: PW:0000753 name: sterol regulatory element-binding protein signaling pathway def: "The sterol regulatory element-binding protein (SREBP) pathway has important roles in the control of lipid and cholesterol metabolism. SREBPs are sterol regulated transcription factors that belong to the bHLH family." [PubMed:17303406] synonym: "SREBP signaling pathway" RELATED [] is_a: PW:0000100 ! transcription pathway is_a: PW:0000716 ! transcription factor mediated signaling pathway created_by: VPetri creation_date: 2010-02-24T10:47:34Z [Term] id: PW:0000754 name: drug pathway def: "The pharmacokinetics and the pharmacodynamics pathway elicited by the administration of specific drugs. The systems involved in drug processing and responses are also those handling exogenous compounds. The distinction between a random encounter with a foreign compound and the processing of a substance administered for treatment along with the importance of genetic variation for the individual responses to particular drugs warrant their separate consideration." [PharmGKB:http\://www.pharmgkb.org/] is_a: PW:0000001 ! Pathway Ontology created_by: VPetri creation_date: 2010-03-15T11:01:15Z [Term] id: PW:0000755 name: benzodiazepine drug pathway def: "The pharmacokinetics and pharmacodynamics pathway of benzodiazepines, a class of drugs acting upon the central nervous system. The drugs are administered as sedatives. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/] is_a: PW:0000923 ! nervous system drug pathway created_by: VPetri creation_date: 2010-03-15T11:26:01Z [Term] id: PW:0000756 name: benzodiazepine pharmacokinetics pathway def: "The pathway of processing - absorption, distribution, metabolism or elimination - of benzodiazepines. Benzodiazepine represent a class of drugs used as sedatives. They act as ligands for the GABAa receptor to stimulate its inhibitory activity. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/] is_a: PW:0000755 ! benzodiazepine drug pathway created_by: VPetri creation_date: 2010-03-15T11:30:00Z [Term] id: PW:0000757 name: benzodiazepine pharmacodynamics pathway def: "The pathway of benzodiazepine-target interaction and of the biochemical or physiological responses to drug. Benzodiazepines are a class of drugs used as sedatives. They act as ligands for the GABAa receptor to stimulate its inhibitory activity. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/] is_a: PW:0000755 ! benzodiazepine drug pathway created_by: VPetri creation_date: 2010-03-15T11:31:43Z [Term] id: PW:0000758 name: gemcitabine pathway def: "The pharmacokinetics and pharmacodynamics pathway of gemcitabine, a cytidine analogue that is administered as a prodrug for the treatment of certain types of cancer. The diphosphate form is an inhibitor of ribonucleotide reductases, essential enzymes of deoxyribonucleotide synthesis. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [:, PharmGKB:http\://www.pharmgkb.org/] is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway created_by: VPetri creation_date: 2010-03-17T08:04:55Z [Term] id: PW:0000759 name: gemcitabine pharmacokinetics pathway def: "The pathway of processing - absorption, distribution, metabolism or elimination of gemcitabine. Gemcitabine is a cytidine analogue administered as a prodrug for the treatment of certain cancers. The diphosphate form is an inhibitor of ribonucleotide reductases, essential enzymes of deoxyribonucleotide synthesis. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/do/serve?objId=PA2036, SMPDB:http\://pathman.smpdb.ca/pathways/SMP00446/pathway] is_a: PW:0000758 ! gemcitabine pathway created_by: VPetri creation_date: 2010-03-17T08:18:10Z [Term] id: PW:0000760 name: gemcitabine pharmacodynamics pathway def: "The pathway of gemcitabine-target interaction and of the biochemical or physiological responses to drug. Gemcitabine is a cytidine analogue that is administered as a prodrug for the treatment of certain types of cancer. The diphosphate form is an inhibitor of ribonucleotide reductases, essential enzymes of deoxyribonucleotide synthesis. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/do/serve?objId=PA2036, SMPDB:http\://pathman.smpdb.ca/pathways/SMP00446/pathway] is_a: PW:0000758 ! gemcitabine pathway created_by: VPetri creation_date: 2010-03-17T08:27:03Z [Term] id: PW:0000761 name: celecoxib drug pathway def: "The pharmacokinetics and pharmacodynamics pathway of celecoxib, a selective cyclooxygenase 2 inhibitor used for the treatment of osteoarthritis and rheumatoid arthritis. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:www.pharmgkb.org/] synonym: "celebrex pathway" RELATED [] is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway created_by: VPetri creation_date: 2010-03-17T08:51:56Z [Term] id: PW:0000762 name: celecoxib pharmacokinetics pathway def: "The pathway of processing - absorption, distribution, metabolism or elimination of celecoxib - a selective inhibitor of cyclooxygenase 2 used for the treatment of osteoarthritis and rheumatoid arthritis. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/do/serve?objId=PA152241951, SMPDB:http\://pathman.smpdb.ca/pathways/SMP00096/pathway] synonym: "celebrex pharmacokinetics pathway" RELATED [] is_a: PW:0000761 ! celecoxib drug pathway created_by: VPetri creation_date: 2010-03-17T09:03:48Z [Term] id: PW:0000763 name: celecoxib pharmacodynamics pathway def: "The pathway of celecoxib-target interaction and of the biochemical or physiological responses to drug. Celecoxib is a selective inhibitor of cyclooxygenase 2 used for the treatment of osteoarthritis and rheumatoid arthritis. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/do/serve?objId=PA152241951, SMPDB:http\://pathman.smpdb.ca/pathways/SMP00096/pathway, XX:] is_a: PW:0000761 ! celecoxib drug pathway created_by: VPetri creation_date: 2010-03-17T09:14:56Z [Term] id: PW:0000764 name: ifosfamide drug pathway def: "The pharmacokinetics and pharmacodynamics pathway of ifosfamide, am antitumor agent used in the treatment of certain cancers. It is administered as a prodrug that has to be converted to the active form. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/, SMPDB:http\://pathman.smpdb.ca/pathways/SMP00448/pathway] is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway created_by: VPetri creation_date: 2010-03-22T01:04:43Z [Term] id: PW:0000765 name: ifosfamide pharmacokinetics pathway def: "The pathway of processing - absorption, distribution, metabolism or elimination of ifosfamide, a prodrug used against solid tumors. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/do/serve?objId=PA2037, SMPFB:http\://pathman.smpdb.ca/pathways/SMP00448/pathway] is_a: PW:0000764 ! ifosfamide drug pathway created_by: VPetri creation_date: 2010-03-22T01:13:38Z [Term] id: PW:0000766 name: ifosfamide pharmacodynamics pathway def: "The pathway of ifosfamide-target interaction and of the biochemical or physiological responses to drug. Ifosfamide is administered as a prodrug and is widely used as an alkylating agent for the treatment of certain cancers. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/search/pathway/ifos/ifos-pd.jsp, SMPDB:http\://pathman.smpdb.ca/pathways/SMP00448/pathway] is_a: PW:0000764 ! ifosfamide drug pathway created_by: VPetri creation_date: 2010-03-22T01:21:34Z [Term] id: PW:0000767 name: omeprazole drug pathway def: "The pharmacokinetics and pharmacodynamics pathway of omeprazole, a proton pump inhibitor. Omeprazole is the representative compound of a class of such inhibitors that are administered for the treatment of acid-related disorders. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/, SMPDB:http\://pathman.smpdb.ca/pathways/SMP00226/pathway] synonym: "proton pump inhibitor pathway" RELATED [] is_a: PW:0000918 ! proton pump inhibitor drug pathway created_by: VPetri creation_date: 2010-03-22T01:39:19Z [Term] id: PW:0000768 name: omeprazole pharmacokinetics pathway def: "The pathway of processing - absorption, distribution, metabolism or elimination of omeprazole, a representative compound of a class of proton pump inhibitors. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/do/serve?objId=PA152530846, SMPDB:http\://pathman.smpdb.ca/pathways/SMP00226/pathway] synonym: "proton pump inhibitor pharmacokinetics pathway" RELATED [] is_a: PW:0000767 ! omeprazole drug pathway created_by: VPetri creation_date: 2010-03-22T01:44:57Z [Term] id: PW:0000769 name: omeprazole pharmacodynamics pathway def: "The pathway of omeprazole-target interaction and of the biochemical or physiological responses to drug. Omeprazole is a representative compound of a class of proton pump inhibitors used in the treatment of acid-related disorders. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/search/pathway/proton-pump/proton-pump-pd.jsp, SMPDB:http\://pathman.smpdb.ca/pathways/SMP00226/pathway] synonym: "proton pump inhibitor pharmacodynamics pathway" RELATED [] is_a: PW:0000767 ! omeprazole drug pathway created_by: VPetri creation_date: 2010-03-22T01:50:32Z [Term] id: PW:0000770 name: C19-steroid hormone biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of C19-steroid hormones. Pregnenolone, a C21 steroid derived from cholesterol, and progesterone, to which pregnenolone can be converted, provide the starting material for the C21, C19 and C18 steroid hormones. The C19 class is represented by androgens such as testosterone." [PubMed:PMID\: 17926129\, 18720009] synonym: "androgen biosynthetic pathway" RELATED [] is_a: PW:0000040 ! steroid hormone biosynthetic pathway created_by: VPetri creation_date: 2010-04-20T03:43:21Z [Term] id: PW:0000771 name: mineralocorticoid biosynthetic pathway def: "Mineralocorticoids are a group of C21 steroid hormones synthesized by the adrenal cortex and so named because of their effects on the concentration of sodium as well as potassium and chloride. The group is best exemplified by aldosterone." [www.onelook.com:OneLook] is_a: PW:0000070 ! C21-steroid hormone biosynthetic pathway created_by: VPetri creation_date: 2010-04-20T04:01:52Z [Term] id: PW:0000772 name: glucocorticoid biosynthetic pathway def: "Glucocorticoids are a group of C21 steroid hormones synthesized by the adrenal cortex and so named because of their effects on glucose metabolism. They also play a role in developmental processes and the immune system. The group is best exemplified by cortisol." [www.onelook.com:OneLook] is_a: PW:0000070 ! C21-steroid hormone biosynthetic pathway created_by: VPetri creation_date: 2010-04-20T04:31:54Z [Term] id: PW:0000773 name: aldosterone biosynthetic pathway def: "Aldosterone is a C21 mineralocorticoid produced in the outer zone, the zona glomerulosa, of the adrenal cortex from the cholesterol precursor. It plays important roles in the regulation of water and salt balance." [PubMed:PMID\: 17926129] is_a: PW:0000771 ! mineralocorticoid biosynthetic pathway created_by: VPetri creation_date: 2010-04-20T04:49:31Z [Term] id: PW:0000774 name: cortisol biosynthetic pathway def: "Cortisol is a C21 glucocorticoid produced in the middle zone, the zona fasciculata, of the adrenal cortex from the cholesterol precursor. It plays important roles in carbohydrate and other nutrients metabolism." [PubMed:PMID\: 17926129] is_a: PW:0000772 ! glucocorticoid biosynthetic pathway created_by: VPetri creation_date: 2010-04-20T04:49:53Z [Term] id: PW:0000775 name: altered epidermal growth factor/neuregulin signaling pathway def: "An epidermal growth factor/neuregulin signaling pathway that deviates from what its normal course should be. Deregulation of the pathway, mostly as upregulation due to the increased expression or amplification of ligands and/or receptors, or mutations leading to such increases, has been linked to numerous forms of cancer, such as pancreatic, lung, endometrial and breast." [InHouse:PW dictionary] is_a: PW:0000170 ! epidermal growth factor/neuregulin signaling pathway is_a: PW:0000298 ! altered growth factor signaling pathway created_by: VPetri creation_date: 2010-04-26T10:53:15Z [Term] id: PW:0000776 name: ketone bodies biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of acetoacetate and beta-hydroxybutyrate also known as ketone bodies although only acetoacetate is a ketone. Generally, the acetyl-CoA derived from fatty acids oxidation enters the citrate cycle. In the liver, a substantial fraction of acetyl-CoA is converted to ketone bodies which are then released into the blood stream for supply to peripheral tissues." [Gene Ontology:GO\:0042181, KEGG:map00072, MCW Libraries:QU4 V876f 2008, Reactome:REACT_1464.3] is_a: PW:0000069 ! ketone bodies metabolic pathway created_by: VPetri creation_date: 2010-05-20T01:06:48Z [Term] id: PW:0000777 name: ketone bodies degradation pathway def: "Those metabolic reactions that convert acetoacetate and beta-hydroxybutyrate back to acetyl-CoA which then can enter the citrate cycle for energy production. The ketone bodies are synthesized in the liver and released into to blood stream to supply fuel to peripheral tissues, heart and skeletal muscle in particular and during starvation, the brain." [Gene Ontology:GO\:0046952, KEGG:map00072, MCW Libraries:QU4 V876f 2008] is_a: PW:0000069 ! ketone bodies metabolic pathway created_by: VPetri creation_date: 2010-05-20T01:23:02Z [Term] id: PW:0000778 name: testosterone biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of testosterone, a C19-steroid hormone secreted primarily in the testes and ovaries and to a lesser extend by the adrenal glands." [OneLook:www.onelook.com] is_a: PW:0000770 ! C19-steroid hormone biosynthetic pathway created_by: VPetri creation_date: 2010-05-20T02:21:52Z [Term] id: PW:0000779 name: dehydroepiandrosterone biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of dehydroepiandrosterone, a C19 steroid hormone produced in the adrenal cortex and a primary precursor of estrogens." [OneLook:www.onelook.com] synonym: "DHEA biosynthetic pathway" RELATED [] is_a: PW:0000770 ! C19-steroid hormone biosynthetic pathway created_by: VPetri creation_date: 2010-05-20T02:25:04Z [Term] id: PW:0000780 name: C18-steroid hormone biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of C18-steroid hormones. Pregnenolone, a C21 steroid derived from cholesterol, and progesterone, to which pregnenolone can be converted, provide the starting material for the C21, C19 and C18 steroid hormones. The C18 class is represented by estrogens. The major natural estrogens are beta-estradiol - the primary estrogen, the estrone of menopause and the estriol of pregnancy." [OneLook:www.onelook.com, PubMed:PMID\: 17926129] synonym: "estrogen biosynthetic pathway" RELATED [] is_a: PW:0000040 ! steroid hormone biosynthetic pathway created_by: VPetri creation_date: 2010-05-20T02:42:49Z [Term] id: PW:0000781 name: estradiol biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of estradiol, the major C18 steroid hormone. The term generally refers to the 17 beta isomer, the most potent form of estrogen." [OneLook:www.onelook.com] synonym: "17beta-estradiol biosynthetic pathway" RELATED [] is_a: PW:0000780 ! C18-steroid hormone biosynthetic pathway created_by: VPetri creation_date: 2010-05-20T03:08:05Z [Term] id: PW:0000782 name: glucocorticoid signaling pathway def: "Glucocorticoids, C21-steroid hormones, initiate signaling by binding to their specific nuclear receptor to regulate metabolism, development and immune response. The major glucocorticoid is cortisol." [OneLook:www.onelook.com] is_a: PW:0000566 ! corticosteroid signaling pathway created_by: VPetri creation_date: 2010-05-21T01:43:39Z [Term] id: PW:0000783 name: mineralocorticoid signaling pathway def: "Mineralocorticoids, C21 steroid hormones, initiate signaling by binding to their cognate receptor to regulate water and mineral levels. The main endogenous mineralocorticoid is aldosterone." [OneLook:www.onelook.com] is_a: PW:0000566 ! corticosteroid signaling pathway created_by: VPetri creation_date: 2010-05-21T02:05:00Z [Term] id: PW:0000784 name: altered androgen signaling pathway def: "An androgen signaling pathway that deviates from what its normal course should be. Altered androgen signaling, due to upregulation of the androgen receptor , has been implicated in prostate cancer." [PubMed:PMID\: 17163421\, 18657355] is_a: PW:0000564 ! androgen signaling pathway is_a: PW:0000719 ! altered transcription factor mediated signaling pathway is_a: PW:0000787 ! altered sex steroids signaling pathway is_a: PW:0000807 ! altered transcription pathway created_by: VPetri creation_date: 2010-06-01T09:36:38Z [Term] id: PW:0000785 name: altered lipid hormone signaling pathway is_a: PW:0000469 ! lipid hormone signaling pathway is_a: PW:0000509 ! altered hormone signaling pathway created_by: VPetri creation_date: 2010-06-02T09:54:05Z [Term] id: PW:0000786 name: altered steroid hormone signaling pathway is_a: PW:0000468 ! steroid hormone signaling pathway is_a: PW:0000785 ! altered lipid hormone signaling pathway created_by: VPetri creation_date: 2010-06-02T09:54:34Z [Term] id: PW:0000787 name: altered sex steroids signaling pathway is_a: PW:0000567 ! sex steroids signaling pathway is_a: PW:0000786 ! altered steroid hormone signaling pathway created_by: VPetri creation_date: 2010-06-02T09:55:15Z [Term] id: PW:0000788 name: glucose-dependent insulinotropic peptide signaling pathway def: "Glucose-dependent insulinotropic peptide signaling plays an important role in promoting insulin secretion. Gip is secreted from the K intestinal cells in response to nutrient ingestion. It signals via a G-protein coupled receptor to increase calcium and cAMP and activate downstream signaling pathways." [PubMed:PMID\: 19074620] synonym: "GIP signaling pathway" RELATED [] is_a: PW:0000467 ! peptide and protein hormone signaling pathway created_by: VPetri creation_date: 2010-06-18T02:32:43Z [Term] id: PW:0000789 name: glucagon-like peptide-1 signaling pathway def: "Glucagon-like peptide-1 signaling pathway plays an important role in promoting insulin secretion. GLp-1 is secreted from the L intestinal cells in response to nutrient ingestion. It signals via a G-protein coupled receptor to increase calcium and cAMP and activate numerous downstream signaling pathways." [PubMed:PMID\: 19074620] is_a: PW:0000467 ! peptide and protein hormone signaling pathway created_by: VPetri creation_date: 2010-06-18T02:44:07Z [Term] id: PW:0000790 name: epinephrine signaling pathway def: "Epinephrine acts as a hormone and a neurotransmitter. It promotes various actions by signaling via various adrenergic receptors, G-protein coupled receptor type. The alpha receptor 1 and 2 couple to the Galphaq and Galphai subunits of heterotrimeric G proteins, respectively. The three beta receptors couple to the Galphas subunit." [OneLook:www.onelook.com] is_a: PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse is_a: PW:0000798 ! catecholamine signaling pathway created_by: VPetri creation_date: 2010-06-18T03:39:46Z [Term] id: PW:0000791 name: norepinephrine signaling pathway def: "Norepinephrine acts as a hormone and a neurotransmitter. It promotes various actions by signaling via various adrenergic receptors, G-protein coupled receptor type. The alpha receptor 1 and 2 couple to the Galphaq and Galphai subunits of heterotrimeric G proteins, respectively. The three beta receptors couple to the Galphas subunit." [OneLook:www.onelook.com] is_a: PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse is_a: PW:0000798 ! catecholamine signaling pathway created_by: VPetri creation_date: 2010-06-18T03:50:51Z [Term] id: PW:0000792 name: epinephrine signaling pathway via adrenergic receptor alpha 1 def: "Epinephrine acts as a hormone and a neurotransmitter. It promotes various actions by signaling via various adrenergic receptors, G-protein coupled receptor type. The alpha 1 receptors couple to the Galphaq subunit." [OneLook:www.onelook.com] is_a: PW:0000790 ! epinephrine signaling pathway created_by: VPetri creation_date: 2010-06-18T03:54:56Z [Term] id: PW:0000793 name: epinephrine signaling pathway via adrenergic receptor alpha 2 def: "Epinephrine acts as a hormone and a neurotransmitter. It promotes various actions by signaling via various adrenergic receptors, G-protein coupled receptor type. The alpha 2 receptors couple to the Galphai subunit." [OneLook:www.onelook.com] is_a: PW:0000790 ! epinephrine signaling pathway created_by: VPetri creation_date: 2010-06-18T03:55:32Z [Term] id: PW:0000794 name: epinephrine signaling pathway via adrenergic receptor beta def: "Epinephrine acts as a hormone and a neurotransmitter. It promotes various actions by signaling via various adrenergic receptors, G-protein coupled receptor type. The beta receptors couple to the Galphas subunit. Beta 2 receptor may also couple to Galphai." [OneLook:www.onelook.com] is_a: PW:0000790 ! epinephrine signaling pathway created_by: VPetri creation_date: 2010-06-18T03:56:07Z [Term] id: PW:0000795 name: norepinephrine signaling pathway via adrenergic receptor alpha 1 def: "Norepinephrine acts as a hormone and a neurotransmitter. It promotes various actions by signaling via various adrenergic receptors, G-protein coupled receptor type. The alpha 1 receptors couple to the Galphaq subunit." [OneLook:www.onelook.com] is_a: PW:0000791 ! norepinephrine signaling pathway created_by: VPetri creation_date: 2010-06-18T03:58:19Z [Term] id: PW:0000796 name: norepinephrine signaling pathway via adrenergic receptor alpha 2 def: "Norepinephrine acts as a hormone and a neurotransmitter. It promotes various actions by signaling via various adrenergic receptors, G-protein coupled receptor type. The alpha 2 receptors couple to the Galphai subunit." [OneLook:www.onelook.com] is_a: PW:0000791 ! norepinephrine signaling pathway created_by: VPetri creation_date: 2010-06-18T03:59:08Z [Term] id: PW:0000797 name: norepinephrine signaling pathway via adrenergic receptor beta def: "Norepinephrine acts as a hormone and a neurotransmitter. It promotes various actions by signaling via various adrenergic receptors, G-protein coupled receptor type. The beta receptors couple to the Galphas subunit. Beta 2 receptor may also couple to Galphai." [OneLook:www.onelook.com] is_a: PW:0000791 ! norepinephrine signaling pathway created_by: VPetri creation_date: 2010-06-18T03:59:44Z [Term] id: PW:0000798 name: catecholamine signaling pathway def: "Catecholamines act as hormones and neurotransmitters. The major catecholamines are dopamine, epinephrine and norepinephrine. They are derived from tyrosine and are not to be confused with tyrosine-based hormones." [OneLook:www.onelook.com] is_a: PW:0000466 ! amine and amino acid-derived hormone signaling pathway created_by: VPetri creation_date: 2010-06-18T04:09:20Z [Term] id: PW:0000799 name: adrenergic beta receptor drug pathway - beta-agonist and beta-blocker def: "The pharmacokinetics and pharmacodynamics pathway of adrenergic beta receptors drugs - beta-agonists and blockers. Adrenergic beta receptors, in response to epinephrine or norepinephrine couple to the Gs alpha subunit of heterotrimeric G protein to elicit several responses. Beta-agonists are used to stimulate while beta-blocker antagonists are used to inhibit these responses, as necessary. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PubMed:PMID\: 19874988] is_a: PW:0000920 ! cardiovascular system drug pathway is_a: PW:0000924 ! respiratory system drug pathway created_by: VPetri creation_date: 2010-06-30T10:47:27Z [Term] id: PW:0000800 name: adrenergic beta receptor agonist and beta-blocker pharmacokinetics pathway def: "The pathway of processing - absorption, distribution, metabolism or elimination - of beta adrenergic receptor drugs. The beta-agonists are used to stimulate while the beta-blockers are used to inhibit the action of adrenergic beta receptors, as necessary. Adrenergic beta receptors are G-protein coupled receptors that in response to epinephrine or norepinephrine elicit various sympathetic responses important for proper cardiac function and in the case of beta2 receptor, smooth muscle relaxation and bronchodilation. Genetic variations can result in changes in the availability of the drug." [PubMed:PMID\: 19874988] is_a: PW:0000799 ! adrenergic beta receptor drug pathway - beta-agonist and beta-blocker created_by: VPetri creation_date: 2010-07-01T08:56:44Z [Term] id: PW:0000801 name: adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway def: "The pathway of beta adrenergic drug-target interactions and of the biochemical or physiological responses to them. The beta-agonists are used to stimulate while the beta-blockers are used to inhibit the action of adrenergic beta receptors, as necessary. Adrenergic beta receptors are G-protein coupled receptors that in response to epinephrine or norepinephrine elicit various sympathetic responses important for proper cardiac function and in the case of beta2 receptor, smooth muscle relaxation and bronchodilation. Genetic variations can cause differences in the response of the organism to the drug." [PubMed:PMID\: 19874988] is_a: PW:0000799 ! adrenergic beta receptor drug pathway - beta-agonist and beta-blocker created_by: VPetri creation_date: 2010-07-01T09:12:37Z [Term] id: PW:0000802 name: dopamine biosynthetic pathway is_a: PW:0000409 ! dopamine metabolic pathway created_by: VPetri creation_date: 2010-08-13T02:17:38Z [Term] id: PW:0000803 name: epinephrine biosynthetic pathway def: "Those metabolic reactions involved in the biosynthesis of epinephrine. Epinephrine is primarily synthesised in adrenal chromaffin cells in response to specific stresses that activate the sympatho-adreno-medullary system." [PubMed:PMID\: 19342614] is_a: PW:0000441 ! epinephrine metabolic pathway created_by: VPetri creation_date: 2010-08-13T02:18:06Z [Term] id: PW:0000804 name: norepinephrine biosynthetic pathway def: "Those metabolic reactions involved in the biosynthesis of norepinephrine. Norepinephrine is primarily synthesised in sympathetic neurons in response to stresses such as cold or pain." [PubMed:PMID\: 19342614] is_a: PW:0000442 ! norepinephrine metabolic pathway created_by: VPetri creation_date: 2010-08-13T02:18:28Z [Term] id: PW:0000805 name: altered Trail mediated signaling pathway def: "A Trail mediated signaling pathway that deviates from what its normal course should be. Mutations with the death domain of the receptors or deletions within the region containing the receptor genes have been reported for certain types of lymphomas." [PubMed:PMID\: 20336667\, 18813321] is_a: PW:0000680 ! altered extrinsic apoptotic pathway is_a: PW:0000682 ! Trail mediated signaling pathway created_by: VPetri creation_date: 2010-09-10T04:41:18Z [Term] id: PW:0000806 name: altered FasL mediated signaling pathway def: "A FasL mediated signaling pathway that deviates from what its normal course should be." [PubMed:PMID\: 10712254] is_a: PW:0000680 ! altered extrinsic apoptotic pathway is_a: PW:0000681 ! FasL mediated signaling pathway created_by: VPetri creation_date: 2010-09-10T05:12:24Z [Term] id: PW:0000807 name: altered transcription pathway def: "A transcription pathway that deviates from what its normal course should be. Aberrant transcription can have devastating consequences. Altered signaling mediated by various transcription factors has been implicated in a spectrum of human diseases." [InHouse:InHouse PW dictionary] is_a: PW:0000100 ! transcription pathway is_a: PW:0000290 ! altered pathway of replication, repair, gene expression and protein biosynthesis created_by: VPetri creation_date: 2010-10-08T11:40:35Z [Term] id: PW:0000808 name: microRNA pathway def: "MicroRNAs (miRNAs) are a large family of small RNAs involved in the post transcriptional regulation of gene expression. The biogenesis and function of miRNA is subject to complex control. Deregulation of miRNA expression has been linked to many diseases including cancer." [PubMed:PMID\: 20661255; 20471939; 20885409] synonym: "miRNA pathway" RELATED [] is_a: PW:0000809 ! small non-coding RNA pathway created_by: VPetri creation_date: 2010-10-08T12:35:16Z [Term] id: PW:0000809 name: small non-coding RNA pathway def: "The small non-coding RNA pathways have emerged as potent regulators of gene expression. Three major classes have been identified of which the microRNA (miRNA) system is the better understood one." [PubMed:PMID\: 19165215\, 20484662] is_a: PW:0000085 ! pathways of replication, repair, gene expression, protein biosynthesis created_by: VPetri creation_date: 2010-10-15T02:16:18Z [Term] id: PW:0000810 name: endogenous small interfering RNA pathway synonym: "endo-siRNA" RELATED [] is_a: PW:0000809 ! small non-coding RNA pathway created_by: VPetri creation_date: 2010-10-15T03:37:08Z [Term] id: PW:0000811 name: Piwi-interacting RNA pathway def: "Piwi-RNA (piRNAs) are believed to play a role in gene silencing, particularly the silencing of transposons as many" [Cell:new article] synonym: "piRNA pathway" RELATED [] is_a: PW:0000809 ! small non-coding RNA pathway created_by: VPetri creation_date: 2010-10-15T03:48:40Z [Term] id: PW:0000812 name: altered small non-coding RNA pathway def: "A small non-coding RNA pathway that deviates from what its normal course should. For instance, alterations in miRNA pathway have been associated with many diseases including various types of cancer." [PubMed:PMID\: 19882673\, 20885409] is_a: PW:0000290 ! altered pathway of replication, repair, gene expression and protein biosynthesis is_a: PW:0000809 ! small non-coding RNA pathway created_by: VPetri creation_date: 2010-10-15T03:53:29Z [Term] id: PW:0000813 name: altered microRNA pathway def: "A microRNA pathway that deviates from what its normal course should be. An altered miRNA pathway has been implicated in many diseases including various forms of cancer." [PubMed:PMID\: 20885409] synonym: "altered miRNA pathway" RELATED [] is_a: PW:0000808 ! microRNA pathway is_a: PW:0000812 ! altered small non-coding RNA pathway created_by: VPetri creation_date: 2010-10-15T04:05:12Z [Term] id: PW:0000814 name: Toll-like receptor signaling pathway def: "Toll-like receptors represent a large and the better understood family of pattern recognition receptors that sense an array of exogenous structures and recent evidence shows they can also recognize defective endogenous molecules. The intracellular signaling cascades they set in motion lead to the expression of inflammatory mediators." [PubMed:PMID\: 20303867\, 20303872] synonym: "KEGG:04620" RELATED [] synonym: "TLR signaling pathway" EXACT [] is_a: PW:0000925 ! pattern recognition receptor mediated pathway created_by: VPetri creation_date: 2010-10-27T11:29:27Z [Term] id: PW:0000815 name: C-type lectin receptor signaling pathway def: "C-type lectin receptors represent one of four classes of pattern recognition receptors. The intracellular signaling cascades they set in motion lead to the expression of inflammatory mediators." [PubMed:PMID\: 20303867\, 20303872] is_a: PW:0000925 ! pattern recognition receptor mediated pathway created_by: VPetri creation_date: 2010-10-27T11:38:01Z [Term] id: PW:0000816 name: Retinoic acid-inducible gene (RIG) I-like receptor signaling pathway def: "This family of pattern recognition receptors are cytoplasmic proteins that recognize exogenous cytoplasmic DNA. The signaling cascades they set in motion lead to the expression of inflammatory mediators." [PubMed:PMID\: 20303867\, 20303872] synonym: "KEGG:04622" RELATED [] synonym: "RLR signaling pathway" EXACT [] is_a: PW:0000925 ! pattern recognition receptor mediated pathway created_by: VPetri creation_date: 2010-10-27T11:43:26Z [Term] id: PW:0000817 name: NOD-like receptor signaling pathway def: "NOD-like receptors are cytosolic proteins that recognize components of bacterial peptidoglycans. The signaling cascades they set in motion lead to the expression of inflammatory mediators." [PubMed:PMID\: 20303867\, 20303872] synonym: "KEGG:04621" RELATED [] synonym: "NLR signaling pathway" EXACT [] is_a: PW:0000925 ! pattern recognition receptor mediated pathway created_by: VPetri creation_date: 2010-10-27T11:45:03Z [Term] id: PW:0000818 name: signaling pathway pertinent to immunity def: "Those signaling pathways that mediate or are involved in the various aspects of immune responses." [MCW library:Cellular and molecular immunity\, by Abbas\, Abul K] is_a: PW:0000003 ! signaling pathway created_by: VPetri creation_date: 2010-10-27T03:08:21Z [Term] id: PW:0000819 name: signaling pathway in the innate immune response is_a: PW:0000818 ! signaling pathway pertinent to immunity created_by: VPetri creation_date: 2010-10-27T03:09:00Z [Term] id: PW:0000820 name: signaling pathway in the adaptive immune response is_a: PW:0000818 ! signaling pathway pertinent to immunity created_by: VPetri creation_date: 2010-10-27T03:09:29Z [Term] id: PW:0000821 name: T cell receptor signaling pathway def: "T cell receptor (TCR) signaling in developing thymocytes is important for the establishment of CD4 and CD8 lineages. Mature T cells express either CD4 or CD8 co-receptors which are essential for the interaction with peptide-bound class II or class I MHC complexes to elicit CD4 T helper (Th) or CD8 cytotoxic T lymphocyte responses, respectively. In either case, T cells initiated signaling activates the expression of genes whose products mediate these responses." [MCW library:Handbook of cellular and molecular immunology, PubMed:PMID\: 16448548\, 20537906] synonym: "KEGG:04660" RELATED [] synonym: "TCR signaling pathway" EXACT [] is_a: PW:0000820 ! signaling pathway in the adaptive immune response relationship: part_of PW:0000824 ! cell-mediated immunity pathway created_by: VPetri creation_date: 2010-10-27T03:28:43Z [Term] id: PW:0000822 name: B cell receptor signaling pathway def: "Antigen recognition by B cell receptors initiates signaling cascades that activate the expression of genes whose products are important for\nB cell functional responses." [MCW library:Handbook on cellular and molecular immunology, PubMed:PMID\: 20591989\, 19827951] synonym: "BCR signaling pathway" EXACT [] synonym: "KEGG:04662" RELATED [] is_a: PW:0000820 ! signaling pathway in the adaptive immune response relationship: part_of PW:0000823 ! humoral immunity pathway created_by: VPetri creation_date: 2010-10-27T04:44:51Z [Term] id: PW:0000823 name: humoral immunity pathway def: "Humoral immunity is mediated by antibodies secreted by the B cell lymphocytes. Antibodies recognize antigens of extracellular microbes and act to neutralize and eliminate them. Activation of B cells can occur in a T cell dependent or independent manner." [MCW library:Textbook on cellular and molecular immunology] is_a: PW:0000235 ! adaptive immune response pathway created_by: VPetri creation_date: 2010-11-01T01:49:11Z [Term] id: PW:0000824 name: cell-mediated immunity pathway def: "Cell-mediated immune response pathways are carried out by T cell lymphocytes. T cells receptors recognize peptides bound to a major histocompability complex (MHC) on the antigen presenting cell. Depending on whether the co-receptor is CD4 or CD8, the receptors will interact with MHC class II or class I to elicit distinct responses against intracellular pathogens." [MCW library:Handbook of cellular and molecular immunology] is_a: PW:0000235 ! adaptive immune response pathway created_by: VPetri creation_date: 2010-11-01T01:49:42Z [Term] id: PW:0000825 name: antigen processing and presentation pathway def: "The pathways of antigen processing and presentation assure the generation of peptides that have the structural attributes necessary for the association with and their placement near major histocompatibility complex (MHC) molecules. Protein antigen present in vesicular compartments generate class II peptides, those in cytosol class I." [MCW library:Handbook on cellular and molecular immunology] synonym: "KEGG:04612" RELATED [] relationship: part_of PW:0000824 ! cell-mediated immunity pathway created_by: VPetri creation_date: 2010-11-01T05:17:15Z [Term] id: PW:0000826 name: T cell receptor signaling pathway in CD4+ T cells def: "T cells that express the CD4 co-receptor, also called T helper cells, recognize class II MHC presented antigens derived from internalized microbes to initiate a signaling cascade that results in enhanced microbicidal capacity of phagocytes. T helper cells can be further subdivided into subsets of CD4+ T cells based on the distinct cytokines they produce and effector functions they perform." [MCW:Handbook on cellular and molecular immunology] is_a: PW:0000821 ! T cell receptor signaling pathway created_by: VPetri creation_date: 2010-11-03T10:24:41Z [Term] id: PW:0000827 name: T cell receptor signaling pathway in CD8+ T cells def: "T cells that express the CD8 co-receptor, also called cytotoxic or cytolytic T cells, recognize class I MHC presented antigens derived from cytosolic proteins to initiate a signaling cascade that results in killing of the target cell." [MCW:Handbook on cellular and molecular immunology] is_a: PW:0000821 ! T cell receptor signaling pathway created_by: VPetri creation_date: 2010-11-03T10:44:22Z [Term] id: PW:0000828 name: cytokine mediated signaling pathway def: "Cytokine initiated signaling pathways play important roles in innate and adaptive immunity, as well as cell proliferation and apoptosis." [MCW library:Handbook on molecular and cellular immunology] synonym: "KEGG:04060" RELATED [] is_a: PW:0000577 ! cytokine and chemokine mediated signaling pathway is_a: PW:0000818 ! signaling pathway pertinent to immunity created_by: VPetri creation_date: 2010-11-03T03:48:57Z [Term] id: PW:0000829 name: chemokine mediated signaling pathway def: "Chemokine initiated pathways play important roles in the innate and adaptive immunity. They are also involved in development and tissue maintenance. The presence and localization of four cysteines is important for structural folding and is also the basis for chemokine classification. The spacing between the first two cysteine residues divides the family members into four groups. Most mammalian chemokines belong to the CC and CXC families. Chemokines signal via G-protein coupled receptors to engage distinct G protein signaling and downstream cascades." [MCW library:Handbook on molecular and cellular immunology, PubMed:PMID\: 15062643] synonym: "KEGG:04062" RELATED [] is_a: PW:0000577 ! cytokine and chemokine mediated signaling pathway is_a: PW:0000818 ! signaling pathway pertinent to immunity created_by: VPetri creation_date: 2010-11-03T04:27:00Z [Term] id: PW:0000830 name: CXC chemokine mediated signaling pathway def: "The CXC family members are characterized by the presence of two cysteine resides separated by one amino acid. CXC and CC are the two most prominent families. This family of chemokines is also subdivided into two subgroups: the one with the ELR motif - ELR (+) and the one without - ELR(-), respectively. Generally, ELR(+) and ELR(-) members bind to distinct chemokine, G-coupled protein, receptors. The effects of their signaling is for the most part angiogenic or angiostatic, respectively." [MCW:Handbook on cellular and molecular immunology, PubMed:PMID\: 15062643; 18579287] is_a: PW:0000829 ! chemokine mediated signaling pathway created_by: VPetri creation_date: 2010-11-04T11:30:26Z [Term] id: PW:0000831 name: CC chemokine mediated signaling pathway def: "The CC family members are characterized by the presence of two adjacent cysteine residues. The CC and the CXC family are the two most prominent families. Chemokines signal via G-protein coupled receptors to engage distinct G protein signaling and downstream cascades." [MCW:Handbook on cellular and molecular biology] is_a: PW:0000829 ! chemokine mediated signaling pathway created_by: VPetri creation_date: 2010-11-04T11:30:33Z [Term] id: PW:0000832 name: C chemokine mediated signaling pathway def: "The C family of chemokine is small and its members have two rather than four cysteines residues. Chemokines signal via G-protein coupled receptors to engage distinct G protein signaling and downstream cascades." [MCW:Handbook on cellular and molecular immunology, PubMed:PMID\: 15062643] is_a: PW:0000829 ! chemokine mediated signaling pathway created_by: VPetri creation_date: 2010-11-04T11:32:38Z [Term] id: PW:0000833 name: CX3C chemokine mediated signaling pathway def: "The CX3X family of chemokine is small and characterized by the presence of three residues separating the first two cysteines. Currently, only one member is known in mammals. Chemokines signal via G-protein coupled receptors to engage distinct G protein signaling and downstream cascades." [MCW:Handbook on cellular and molecular immunology, PubMed:PMID\: 15062643] is_a: PW:0000829 ! chemokine mediated signaling pathway created_by: VPetri creation_date: 2010-11-12T05:03:05Z [Term] id: PW:0000834 name: bile acid transport pathway def: "Bile acid absorption by the intestinal epithelium and hepatic recycling collectively group the transport pathway of the important molecules of cholesterol catabolism." [PubMed:PMID\: 18837078\, 17404808] synonym: "KEGG:04976" RELATED [] is_a: PW:0000103 ! transport pathway created_by: VPetri creation_date: 2010-12-22T02:05:33Z [Term] id: PW:0000835 name: anti-estrogen drug pathway def: "Breast cancer is a major cause of death among Western women and many breast tumors are estrogen-dependent. Pharmacologically two major therapies have been developed: one targets the estrogen receptors via antagonists and selective modulators (SERM) and the second targets estrogen synthesis via aromatase inhibitors." [PubMed:PMID\: 20644568] is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway created_by: VPetri creation_date: 2011-01-06T02:11:32Z [Term] id: PW:0000836 name: aromatase inhibitor pathway def: "Aromatase inhibitors block the last step of estrogen biosynthesis. They can be classified into first-, second- and third-generation drugs. Depending on whether they inactivate the aromatase complex irreversibly or reversibly, they can be further subdivided into type I and II, respectively. Currently, third generation drugs are being used." [PubMed:PMID\: 12402060\, 14513434] is_a: PW:0000835 ! anti-estrogen drug pathway created_by: VPetri creation_date: 2011-01-07T05:07:46Z [Term] id: PW:0000837 name: tamoxifen drug pathway def: "The pharmacokinetics and pharmacodynamics pathway of tamoxifen - one of the most widely used anti-estrogen drug that targets the estrogen receptor. The drug is a modulator than acts as an antagonist in breast cancer cells but can be an agonist in bone and the cardiovascular system. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PubMed:PMID\: 19629072] is_a: PW:0000835 ! anti-estrogen drug pathway created_by: VPetri creation_date: 2011-01-17T01:05:40Z [Term] id: PW:0000838 name: tamoxifen pharmacokinetics pathway def: "The pathway of processing - absorption, distribution, metabolism or elimination - of tamoxifen - a SERM anti-estrogen drug. Genetic variations can result in changes in the availability of the drug. For instance, variation in CYP2D6, an important enzyme for the production of a primary drug metabolite, impacts on the available concentration of the drug." [PubMed:PMID\: PMID\: 19629072] is_a: PW:0000837 ! tamoxifen drug pathway created_by: VPetri creation_date: 2011-01-17T01:06:28Z [Term] id: PW:0000839 name: tamoxifen pharmacodynamics pathway def: "The pathway of tamoxifen-target interaction and of the biochemical or physiological responses to it. In breast cancer cells, tamoxifen binding antagonizes estrogen binding and the subsequent conformational changes necessary for co-activators recruitment. It may also prompt the recruitment of co-repressor. Genetic variations can cause differences in the response of the organism to the drug." [PubMed:PMID\: 19629072] is_a: PW:0000837 ! tamoxifen drug pathway created_by: VPetri creation_date: 2011-01-17T01:06:59Z [Term] id: PW:0000840 name: protein kinase C (PKC) signaling pathway def: "Protein kinase C constitutes a family of serine/threonine kinases activated by diacylglycerol (DAG) and calcium whose signal transduction plays important roles in many cellular processes. Ligand activated G protein-coupled receptors, via Galphaq pathway, stimulate phospholipase C which cleaves PIP2 into DAG and IP3. IP3 promotes calcium release." [Gene Ontology:GO\:0070528, PubMed:PMID\: 19934406] is_a: PW:0000541 ! signaling pathway involving second messengers created_by: VPetri creation_date: 2011-03-09T10:02:32Z [Term] id: PW:0000841 name: acetylcholine signaling pathway def: "Acetylcholine signaling plays important roles in the central and peripheral nervous system and exerts both excitatory and inhibitory effects." [OneLook:www.onelook.com] synonym: "ACh signaling pathway" EXACT [] synonym: "KEGG:04725" RELATED [] is_a: PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse created_by: VPetri creation_date: 2011-03-09T11:08:00Z [Term] id: PW:0000842 name: acetylcholine signaling pathway via nicotinic acetylcholine receptor def: "Activation of ionotropic nicotinic acetylcholine receptor leads to membrane depolarization and subsequent excitatory postsynaptic potential and to activation of voltage-gated ion channels. In humans, 17 subunits have been identified that can form various pentameric receptors." [OneLook:www.onelook.com] is_a: PW:0000841 ! acetylcholine signaling pathway created_by: VPetri creation_date: 2011-03-09T11:18:32Z [Term] id: PW:0000843 name: acetylcholine signaling pathway via muscarinic acetylcholine receptor def: "Acetylcholine signaling via the metabotropic muscarinic receptors exerts important roles in the parasympathetic nervous system. The five G protein-coupled receptors can be classified according to the G proteins they engage. Receptors M1, M3 and M5 predominantly couple to Galphaq whereas receptors M2 and M4 predominantly coupled to Galphai pathways." [GO:GO\:0007213, OneLook:www.onelook.com, PubMed:PMID\: 18082893] is_a: PW:0000841 ! acetylcholine signaling pathway created_by: VPetri creation_date: 2011-03-09T11:29:22Z [Term] id: PW:0000844 name: glutamate signaling pathway def: "Glutamate signaling via the ionotropic AMPA or NMDA and several metabotropic receptors plays important roles in the modulation of synaptic plasticity, long term depression or potentiation, and in learning and memory." [GO:GO\:0007215, OneLook:www.onelook.com] synonym: "KEGG:04724" RELATED [] is_a: PW:0000455 ! excitatory synaptic transmission pathway created_by: VPetri creation_date: 2011-03-09T11:57:08Z [Term] id: PW:0000845 name: glutamate signaling pathway via NMDA receptor def: "Glutamate signaling via the ionotropic NMDA glutamate receptor plays important roles in synaptic plasticity and in learning and memory. The receptor is ligand-gated and voltage-dependent and requires glycine as a co-agonist." [GO:GO\:0035235, OneLook:www.onelook.com] is_a: PW:0000844 ! glutamate signaling pathway created_by: VPetri creation_date: 2011-03-09T12:10:19Z [Term] id: PW:0000846 name: glutamate signaling pathway via AMPA receptor def: "Glutamate signaling via the ionotropic AMPA receptor plays important roles in long-term potentiation (LTP). The AMPA receptors are both receptors and cation channels." [GO:GO\:0035235, OneLook:www.onelook.com] is_a: PW:0000844 ! glutamate signaling pathway created_by: VPetri creation_date: 2011-03-09T12:24:02Z [Term] id: PW:0000847 name: glutamate signaling pathway via metabotropic glutamate receptor def: "Glutamate signaling via the various metabotropic, G protein-coupled receptors plays important roles in both the central and peripheral nervous systems. Based on their structure and physiological function, the receptors have been classified into three groups. Group I receptors couple to Galphaq, group II and III couple to Galphai" [GO:GO\:0007216, OneLook:www.onelook.com, XX:] is_a: PW:0000844 ! glutamate signaling pathway created_by: VPetri creation_date: 2011-03-09T01:06:26Z [Term] id: PW:0000848 name: gamma-aminobutyric acid signaling pathway def: "Gamma-aminobutyric acid signals at inhibitory synapses via the type A receptor, which is part of a ligand-gated ion channel and the type B receptors which are metabotropic, G protein-coupled receptors." [GO:GO\:0007214, OneLook:www.onelook.com] synonym: "KEGG:04727" RELATED [] is_a: PW:0000456 ! Inhibitory synaptic transmission pathway created_by: VPetri creation_date: 2011-03-09T02:10:16Z [Term] id: PW:0000849 name: glutamate signaling pathway via group I metabotropic glutamate receptor is_a: PW:0000847 ! glutamate signaling pathway via metabotropic glutamate receptor created_by: VPetri creation_date: 2011-03-09T03:02:04Z [Term] id: PW:0000850 name: glutamate signaling pathway via group II or III glutamate receptor is_a: PW:0000847 ! glutamate signaling pathway via metabotropic glutamate receptor created_by: VPetri creation_date: 2011-03-09T03:03:07Z [Term] id: PW:0000851 name: dopamine signaling pathway via D1 family of receptors def: "Dopamine signaling via D1-like receptors engages the Galphas family of G proteins leading to activation of adenylyl cyclases and increase in intracellular cAMP. Dopamine receptors 1 and 5 belong to this family." [GO:GO\:0007212, OneLook:www.onelook.com, PubMed:PMID\: 17413183, XX:] is_a: PW:0000394 ! dopamine signaling pathway created_by: VPetri creation_date: 2011-03-09T03:15:01Z [Term] id: PW:0000852 name: dopamine signaling pathway via D2 family of receptors def: "Dopamine signaling via D2-like family of receptors engages the Galphai family of G proteins leading to inhibition of adenylyl cyclases and reduction of intracellular cAMP. Dopamine receptors 2, 3 and 4 belong to this family." [GO:GO\:0007212, OneLook:www.onelook.com, PubMed:PMID\: 17413183] is_a: PW:0000394 ! dopamine signaling pathway created_by: VPetri creation_date: 2011-03-09T03:22:26Z [Term] id: PW:0000853 name: histamine signaling pathway def: "Histamine signaling is important for the central and to some extent the peripheral nervous systems and is also involved in the immune responses. Histamine signaling in the brain involves receptors 1 and 3 that couple to Galphaq and Galphai, respectively." [OneLook:www.onelook.com] is_a: PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse created_by: VPetri creation_date: 2011-03-09T03:53:00Z [Term] id: PW:0000854 name: serotonin signaling pathway def: "Serotonin signaling exerts many roles, from regulation of appetite, mood and sleep to involvement in learning and memory and in muscle contraction. Serotonin signals via several receptors known as 5-hydroxytryptamine or 5-HT receptors. With one exception, 5-HT receptors are G protein-coupled receptors engaging distinct G protein signaling to elicit distinct, both inhibitory and excitatory responses." [OneLook:www.onelook.com, PubMed:PMID\:20925600\, 18571247\, 18676031] synonym: "KEGG:04726" RELATED [] is_a: PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse created_by: VPetri creation_date: 2011-03-09T04:11:20Z [Term] id: PW:0000855 name: acetylcholine signaling pathway via muscarinic acetylcholine receptors engaging G alphaq protein family def: "Acetylcholine signaling via receptor type M1, M3 and M5 primarily engages G alphaq protein family resulting in activation of phospholipase C and mobilization of intracellular calcium. The receptors are expressed in various areas of the brain such as the cerebral cortex and hippocampus. Receptor M3 is also found in smooth muscle; receptor M5 is found in the substantia nigra." [PubMed:PMID\: 18082893] is_a: PW:0000843 ! acetylcholine signaling pathway via muscarinic acetylcholine receptor created_by: VPetri creation_date: 2011-04-01T10:31:48Z [Term] id: PW:0000856 name: acetylcholine signaling pathway via muscarinic acetylcholine receptors engaging G alphai protein family def: "Acetylcholine signaling via receptor type M2 and M4 primarily engages G alphai protein family resulting in inhibition of adenylate cyclases and reduction of intracellular cAMP. The receptors are expressed in various areas of the brain such as the cerebral cortex, hippocampus and the striatum. Receptor M2 is also expressed in smooth muscle, heart and lung." [PubMed:PMID\: 18082893] is_a: PW:0000843 ! acetylcholine signaling pathway via muscarinic acetylcholine receptor created_by: VPetri creation_date: 2011-04-01T11:01:32Z [Term] id: PW:0000857 name: phase I biotransformation pathway def: "Phase I biotransformation pathway involves the conversion of endogenous and exogenous substances to more polar metabolites. Members of the cytochrome P450 superfamily and to a lesser extent, flavin containing monooxygenases mediate the reactions." [PubMed:PMID\: 19835560] relationship: part_of PW:0000124 ! cellular detoxification pathway created_by: VPetri creation_date: 2011-04-04T04:25:01Z [Term] id: PW:0000858 name: phase II biotransformation pathway def: "Phase II biotransformation pathway involves the conjugation of phase I products to various hydrophilic moieties that renders them more suitable for excretion. Various enzyme superfamilies are involved in carrying out the specific conjugation of metabolites." [PubMed:PMID\: 19835560\, 20668491] relationship: part_of PW:0000124 ! cellular detoxification pathway created_by: VPetri creation_date: 2011-04-04T04:37:36Z [Term] id: PW:0000859 name: glucuronidation conjugation pathway def: "Glucuronidation of phase I products by members of the UDP-glucuronosyltranferase superfamily represents the major phase II conjugation pathway." [PubMed:PMID\: 20668491] is_a: PW:0000858 ! phase II biotransformation pathway created_by: VPetri creation_date: 2011-04-04T05:03:51Z [Term] id: PW:0000860 name: sulfonation conjugation pathway def: "The sulfonation of phase I products by members of the sulfotransferase family represents a major route of phase II biotransformation, second to the glucuronidation pathway." [PubMed:PMID\: 20668491] is_a: PW:0000858 ! phase II biotransformation pathway created_by: VPetri creation_date: 2011-04-04T05:12:08Z [Term] id: PW:0000861 name: pyrimidine biosynthetic pathway def: "Those enzymatic reactions involved in the synthesis of pyrimidine nucleotides. A major route for pyrimidine synthesis is the novo pathway. However, an alternate pathway, the salvage pathway, converts nucleosides generated by DNA or RNA breakdown back to nucleotide monophosphates which can then re-enter the biosynthetic pathway." [PubMed:PMID\:16098809\, 15096496] is_a: PW:0000032 ! pyrimidine metabolic pathway created_by: vpetri creation_date: 2011-06-03T03:33:51Z [Term] id: PW:0000862 name: de novo pyrimidine biosynthetic pathway def: "In the de novo biosynthetic pathway, pyrimidines are synthesized from simple precursors. Six reactions carried out by three genes in higher eukaryotes result in the formation of UMP, the precursor of all other pyrimidine nucleotides." [PubMed:PMID\:16098809\, 15096496] is_a: PW:0000861 ! pyrimidine biosynthetic pathway created_by: vpetri creation_date: 2011-06-03T03:58:08Z [Term] id: PW:0000863 name: pyrimidine salvage pathway def: "The salvage pathway of pyrimidine biosynthesis, mostly used in resting and differentiated cells, allows for the synthesis of pyrimidines from intermediates derived from DNA and RNA degradation pathways." [PubMed:PMID\:16098809\, 15096496] is_a: PW:0000861 ! pyrimidine biosynthetic pathway created_by: vpetri creation_date: 2011-06-03T04:12:23Z [Term] id: PW:0000864 name: pyrimidine degradation pathway def: "Those enzymatic reactions involved in the degradation of pyrimidines." [PubMed:PMID\:16098809] is_a: PW:0000032 ! pyrimidine metabolic pathway created_by: vpetri creation_date: 2011-06-03T04:46:14Z [Term] id: PW:0000865 name: purine biosynthetic pathway def: "Those enzymatic reactions involved in the synthesis of purine nucleotides. A major route for purine synthesis is the novo pathway. However, an alternate pathway, the salvage pathway, can also be used." [OneLook:www.onelook.com] is_a: PW:0000031 ! purine metabolic pathway created_by: VPetri creation_date: 2011-06-06T04:49:00Z [Term] id: PW:0000866 name: purine degradation pathway def: "Those enzymatic reactions involved in the degradation pathway of purines. Several enzymes are involved in the breakdown of adenine and guanine to uric acid which is then excreted in the urine in humans and higher primates. In other mammals, uric acid is further oxidized to allantoin." [OneLook:www.onelook.com] is_a: PW:0000031 ! purine metabolic pathway created_by: VPetri creation_date: 2011-06-06T04:49:30Z [Term] id: PW:0000867 name: de novo purine biosynthetic pathway def: "De novo purine biosynthesis requires ten enzymatic reactions to produce inosine monophosphate (IMP). Both adenine and guanine are then derived from IMP via several reactions. Purines are synthesized as nucleosides, i.e., as bases attached to ribose. Purines can also be created synthetically." [PubMed:PMID\:18712276] is_a: PW:0000865 ! purine biosynthetic pathway created_by: VPetri creation_date: 2011-06-06T04:50:02Z [Term] id: PW:0000868 name: purine salvage pathway is_a: PW:0000865 ! purine biosynthetic pathway created_by: VPetri creation_date: 2011-06-06T04:50:32Z [Term] id: PW:0000869 name: gefitinib drug pathway def: "The pharmacokinetics and pharmacodynamics pathway of gefitinib. Gefitinib is the first selective inhibitor of EGFR whose mutations within the tyrosine kinase domain have been associated with hyperactive epidermal growth factor signaling in non-small cell lung cancers. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PubMed:PMID\:21196393; PMID\:19657272] is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway created_by: VPetri creation_date: 2011-06-09T05:30:25Z [Term] id: PW:0000870 name: gefitinib pharmacokinetics pathway def: "The pathway of processing - absorption, distribution, metabolism or elimination - of gefitinib. Gefitinib is the first selective inhibitor of EGFR whose mutations within the tyrosine kinase domain have been associated with hyperactive epidermal growth factor signaling in non-small cell lung cancers. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/do/serve?objId=PA152325160&objCls=Pathway, PubMed:PMID\:15801543] is_a: PW:0000869 ! gefitinib drug pathway created_by: VPetri creation_date: 2011-06-09T05:30:58Z [Term] id: PW:0000871 name: gefitinib pharmacodynamics pathway def: "The pathway of gefitinib-target interactions and of the biochemical or physiological responses to drug. Gefitinib is the first selective inhibitor of EGFR whose mutations within the tyrosine kinase domain have been associated with hyperactive epidermal growth factor signaling in non-small cell lung cancers. Genetic variations can cause differences in the response of the organism to the drug." [PubMed:PMID\:21388312] is_a: PW:0000869 ! gefitinib drug pathway created_by: VPetri creation_date: 2011-06-09T05:31:16Z [Term] id: PW:0000872 name: erlotinib drug pathway def: "The pharmacokinetics and pharmacodynamics pathway of erlotinib. Erlotinib is the second (after gefitinib) selective inhibitor of EGFR whose mutations within the tyrosine kinase domain have been associated with hyperactive epidermal growth factor signaling in non-small cell lung cancers. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PubMed:PMID\:20072828; 19657272] is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway created_by: VPetri creation_date: 2011-06-14T03:33:11Z [Term] id: PW:0000873 name: erlotinib pharmacokinetics pathway def: "The pathway of processing - absorption, distribution, metabolism or elimination - of erlotinib. Erlotinib is the second (after gefitinib) selective inhibitor of EGFR whose mutations within the tyrosine kinase domain have been associated with hyperactive epidermal growth factor signaling in non-small cell lung cancers. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/do/serve?objId=PA154426903&objCls=Pathway, PubMed:PMID\:19657272] is_a: PW:0000872 ! erlotinib drug pathway created_by: VPetri creation_date: 2011-06-14T03:33:51Z [Term] id: PW:0000874 name: erlotinib pharmacodynamics pathway def: "The pathway of erlotinib-target interaction and of the biochemical or physiological responses to drug. Erlotinib is the second (after gefitinib) selective inhibitor of EGFR whose mutations within the tyrosine kinase domain have been associated with hyperactive epidermal growth factor signaling in non-small cell lung cancers. Genetic variations can cause differences in the response of the organism to the drug." [PubMed:PMID\:20072828] is_a: PW:0000872 ! erlotinib drug pathway created_by: VPetri creation_date: 2011-06-14T03:34:08Z [Term] id: PW:0000875 name: deoxyribonucleotide metabolic pathway def: "Deoxyribonucleotide synthesis occurs via the de novo pathway mediated by ribonucleotide reductase or via the salvage pathway. The de novo pathway is responsible for the bulk of dNTP during the S phase of cell cycle whereas the salvage pathway mostly operates in the quiescent state of the cell. Several cytosolic and mitochondrial enzymes are responsible for the initial steps of the salvage pathway in the two compartments and for the reverse reactions that control the size of the dNTP pool." [PubMed:PMID\:16756507; 15158709; 20561600; 17525869] is_a: PW:0000012 ! nucleotide metabolic pathway created_by: VPetri creation_date: 2011-07-01T10:58:55Z [Term] id: PW:0000876 name: bacterial polysaccharide metabolic pathway def: "Those metabolic reaction involved in the synthesis, utilization and/or degradation of polysaccharides that are components of bacterial cell wall. They may also act as virulence factors." [OneLook:www.onelook.com] is_a: PW:0000146 ! glycan metabolic pathway created_by: VPetri creation_date: 2011-07-11T09:36:18Z [Term] id: PW:0000877 name: nucleotide sugar biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of nucleotide sugars that provide donors for the glycosylation of proteins or lipids. UTP is the primary nucleotide used in the reaction." [OneLook:www.onelook.com] is_a: PW:0000055 ! nucleotide sugar metabolic pathway created_by: VPetri creation_date: 2011-07-11T10:29:49Z [Term] id: PW:0000878 name: phosphatidylcholine biosynthetic pathway def: "Phosphatidylcholine is the predominant phospholipid of eukaryotic membranes. Of the three known biosynthetic pathways, two are found in eukaryotes and one, the CDP-choline, is the best characterized." [PubMed:PMID\:15749057] is_a: PW:0000354 ! glycerophospholipid metabolic pathway created_by: VPetri creation_date: 2011-07-11T10:44:15Z [Term] id: PW:0000879 name: altered cortisol signaling pathway def: "A cortisol signaling pathway that deviates from what its normal course should be. Mutations in the glucocorticoid receptor have been associated with rare, sporadic or familial, glucocorticoid resistance." [PubMed:PMID\: 21448414] is_a: PW:0000569 ! cortisol signaling pathway is_a: PW:0000881 ! altered glucocorticoid signaling pathway created_by: VPetri creation_date: 2011-08-23T09:15:01Z [Term] id: PW:0000880 name: altered corticosteroid signaling pathway is_a: PW:0000566 ! corticosteroid signaling pathway created_by: VPetri creation_date: 2011-08-23T09:19:49Z [Term] id: PW:0000881 name: altered glucocorticoid signaling pathway is_a: PW:0000782 ! glucocorticoid signaling pathway is_a: PW:0000880 ! altered corticosteroid signaling pathway created_by: VPetri creation_date: 2011-08-23T09:20:35Z [Term] id: PW:0000882 name: interleukin-1 family mediated signaling pathway def: "The interleukin-1 family mediated signaling plays important roles in innate and adaptive immune responses. The best characterized member of the family is interleukin-1 followed by interleukin-18 and the more recently identified interleukin-33. Other family members are less well characterized." [PubMed:PMID\:20081871] synonym: "Il-1 family mediated signaling pathway" RELATED [] is_a: PW:0000512 ! Interleukin mediated signaling pathway created_by: VPetri creation_date: 2011-08-29T11:08:06Z [Term] id: PW:0000883 name: interleukin-1 signaling pathway def: "Interleukin-1 signaling, primarily via interleukin-1beta, plays important roles in innate and adaptive immune responses. Binding of the processed cytokine to its receptor, allows for the recruitment of several accessory and adaptor proteins leading to the activation of NF-kappaB and MAPK signaling cascades. A natural receptor antagonist and a decoy receptor act as regulators of interleukin 1alpha and beta." [PubMed:PMID\:20081871\, 21219179; 20303867] synonym: "Il-1 signaling pathway" EXACT [] synonym: "PID:200089" RELATED [] is_a: PW:0000882 ! interleukin-1 family mediated signaling pathway is_a: PW:0000926 ! pro-inflammatory cytokine mediated pathway created_by: VPetri creation_date: 2011-08-29T11:15:28Z [Term] id: PW:0000884 name: interleukin-18 signaling pathway def: "Interleukin-18 signaling plays important roles in innate and adaptive immunity. In the central nervous system (CNS), Il-18 and its receptors have been shown to play a role in neuroinflammatory and neurodegenerative processes as well as behavior and homeostasis. In addition, Il-18 may be a mediator of inflammation in rheumatoid arthritis." [PubMed :PMID\:20081871; 20113500; 21864160] synonym: "Il-18 signaling pathway" RELATED [] is_a: PW:0000882 ! interleukin-1 family mediated signaling pathway created_by: VPetri creation_date: 2011-08-29T11:16:18Z [Term] id: PW:0000885 name: interleukin-33 signaling pathway def: "Interleukin-33 is the most recently discovered member of the interleukin-1 family. Like with the other members of the family, signaling by interleukin-33 plays important roles in inflammation and immunity and may be critical for the development of inflammatory and immune diseases." [PubMed:PMID\:20081871; 21934731] synonym: "Il-33 signaling pathway" RELATED [] is_a: PW:0000882 ! interleukin-1 family mediated signaling pathway created_by: VPetri creation_date: 2011-08-29T11:16:46Z [Term] id: PW:0000886 name: interleukin-19 signaling pathway is_a: PW:0000513 ! interleukin-10 family mediated signaling pathway created_by: VPetri creation_date: 2011-12-06T09:28:03Z [Term] id: PW:0000887 name: interleukin-20 signaling pathway is_a: PW:0000513 ! interleukin-10 family mediated signaling pathway created_by: VPetri creation_date: 2011-12-06T09:37:36Z [Term] id: PW:0000888 name: interleukin-22 signaling pathway def: "Interleukin-22 signaling triggers the Jak-Stat intracellular cascade resulting in the activation of various T helper (Th) cells." [PubMed:PMID\: 11929132; 20127093] synonym: "Il-22 signaling pathway" RELATED [] is_a: PW:0000513 ! interleukin-10 family mediated signaling pathway created_by: VPetri creation_date: 2011-12-06T09:38:18Z [Term] id: PW:0000889 name: interleukin-24 signaling pathway is_a: PW:0000513 ! interleukin-10 family mediated signaling pathway created_by: VPetri creation_date: 2011-12-06T09:39:50Z [Term] id: PW:0000890 name: interleukin-26 signaling pathway is_a: PW:0000513 ! interleukin-10 family mediated signaling pathway created_by: VPetri creation_date: 2011-12-06T09:40:28Z [Term] id: PW:0000891 name: interleukin-28A signaling pathway synonym: "interferon lambda2 signaling pathway" RELATED [] is_a: PW:0000513 ! interleukin-10 family mediated signaling pathway created_by: VPetri creation_date: 2011-12-06T10:26:15Z [Term] id: PW:0000892 name: interleukin-28B signaling pathway synonym: "interferon lambda3 signaling pathway" RELATED [] is_a: PW:0000513 ! interleukin-10 family mediated signaling pathway created_by: VPetri creation_date: 2011-12-06T10:29:31Z [Term] id: PW:0000893 name: interleukin-29 signaling pathway synonym: "interferon lambda1 signaling pathway" RELATED [] is_a: PW:0000513 ! interleukin-10 family mediated signaling pathway created_by: VPetri creation_date: 2011-12-06T10:30:34Z [Term] id: PW:0000894 name: interferon mediated signaling pathway def: "The interferons represent a subset of cytokines whose signaling is involved in various aspects of innate and adaptive immunity. Based on the type of receptors they employ, interferons have been classified into type I and II. A third type, the lambda interferons, are members of the interleukin 10 family." [PubMed:PMID\: 17502369\, 20712454] is_a: PW:0000828 ! cytokine mediated signaling pathway created_by: VPetri creation_date: 2011-12-06T10:46:23Z [Term] id: PW:0000895 name: type I interferon signaling pathway def: "Type I interferon, which includes all but one of the seven known human genes, binds to distinct receptors that activate the Jak-Stat signaling pathway." [PubMed:PMID\:17502369] is_a: PW:0000894 ! interferon mediated signaling pathway created_by: VPetri creation_date: 2011-12-06T10:58:32Z [Term] id: PW:0000896 name: type II interferon signaling pathway def: "Type II interferon, of which there is only one in humans, binds to distinct receptors that activate Jak-Stat signaling pathway. It is known as the interferon gamma signaling." [PubMed:PMID\: 17502369] synonym: "interferon gamma signaling" RELATED [] synonym: "PID:200129" RELATED [] is_a: PW:0000894 ! interferon mediated signaling pathway created_by: VPetri creation_date: 2011-12-06T11:07:25Z [Term] id: PW:0000897 name: interleukin-17 family mediated signaling pathway def: "The interleukin-17 family mediated signaling plays important roles in inflammation and the development of autoimmunity as well as in the host defense against fungal and bacterial infections." [PubMed:PMID\: 21349428] synonym: "Il-17 family mediated signaling pathway" RELATED [] is_a: PW:0000512 ! Interleukin mediated signaling pathway created_by: VPetri creation_date: 2011-12-06T11:23:23Z [Term] id: PW:0000898 name: interleukin-17E signaling pathway def: "Interleukin-17E signaling, also known as interleukin-25, induces the production of Th2 cell cytokine leading to enhancement of Th2 cell responses." [PubMed:PMID\: 21349428] synonym: "Il-17E signaling pathway" RELATED [] synonym: "Il-25 signaling pathway" RELATED [] is_a: PW:0000897 ! interleukin-17 family mediated signaling pathway created_by: VPetri creation_date: 2011-12-06T02:31:33Z [Term] id: PW:0000899 name: interleukin-17A signaling pathway def: "Of the six family members of interleukin-17 family, interleukin-17A is the founding member and the better characterized system. While interleukin-17A binds the same receptor as interleukin-17F and can also heterodimerize with it, its signaling elicits distinct and broader responses." [PubMed:PMID\: 21349428] synonym: "Il-17A signaling pathway" RELATED [] is_a: PW:0000897 ! interleukin-17 family mediated signaling pathway created_by: VPetri creation_date: 2011-12-06T02:31:40Z [Term] id: PW:0000900 name: interleukin-17F signaling pathway def: "Interleukin-17F binds the same receptor as interleukin-17A and can also heterodimerize with it. However, its signaling while sharing features of interleukin-17A pathway also elicits distinct responses." [PubMed:PMID\: 21349428] is_a: PW:0000897 ! interleukin-17 family mediated signaling pathway created_by: VPetri creation_date: 2011-12-06T02:41:48Z [Term] id: PW:0000901 name: altered interleukin mediated signaling pathway def: "An interleukin mediated signaling pathway that deviates from what its normal course should be. Aberrant interleukin signaling pathway, alone or in combination with other pathways underlie various diseases." [InHouse:PW dictionary] is_a: PW:0000512 ! Interleukin mediated signaling pathway is_a: PW:0000617 ! altered cytokine mediated signaling pathway created_by: VPetri creation_date: 2011-12-06T03:18:18Z [Term] id: PW:0000902 name: interleukin-11 signaling pathway is_a: PW:0000514 ! interleukin-6 family mediated signaling pathway created_by: vpetri creation_date: 2012-01-23T04:17:23Z [Term] id: PW:0000903 name: leukemia inhibitory factor signaling pathway synonym: "LIF signaling pathway" RELATED [] is_a: PW:0000514 ! interleukin-6 family mediated signaling pathway created_by: vpetri creation_date: 2012-01-23T04:19:00Z [Term] id: PW:0000904 name: ciliary neurotrophic factor signaling pathway synonym: "C" RELATED [] synonym: "CNTF signaling pathway" RELATED [] is_a: PW:0000514 ! interleukin-6 family mediated signaling pathway created_by: vpetri creation_date: 2012-01-23T04:21:01Z [Term] id: PW:0000905 name: oncostatin M signaling pathway synonym: "OSM signaling pathway" RELATED [] is_a: PW:0000514 ! interleukin-6 family mediated signaling pathway created_by: vpetri creation_date: 2012-01-23T04:22:25Z [Term] id: PW:0000906 name: interleukin-2 family mediated signaling pathway def: "Interleukin-2 family of cytokines, also known as gamma(c) family because of the shared gamma(c) receptor, plays crucial roles in the regulation of T cells." [PubMed:PMID\: 21889323; 19543225] synonym: "Il-2 family mediated signaling pathway" RELATED [] is_a: PW:0000512 ! Interleukin mediated signaling pathway created_by: VPetri creation_date: 2012-03-23T12:26:10Z [Term] id: PW:0000907 name: interleukin-2 signaling pathway def: "Interleukin-2 is the prototypical member of the interleukin-2 family of cytokines. The signaling pathway initiated by Il-2 and the other family members activates the Jak-Stat intracellular cascade to regulate T cell, innate and adaptive immune responses." [PubMed:PMID\: 21889323; 19543225] synonym: "Il-2 signaling pathway" EXACT [] synonym: "PID:200098" RELATED [] is_a: PW:0000906 ! interleukin-2 family mediated signaling pathway created_by: VPetri creation_date: 2012-03-23T12:33:40Z [Term] id: PW:0000908 name: interleukin-7 signaling pathway is_a: PW:0000906 ! interleukin-2 family mediated signaling pathway created_by: VPetri creation_date: 2012-03-23T12:38:11Z [Term] id: PW:0000909 name: interleukin-9 signaling pathway is_a: PW:0000906 ! interleukin-2 family mediated signaling pathway created_by: VPetri creation_date: 2012-03-23T12:39:11Z [Term] id: PW:0000910 name: interleukin-15 signaling pathway is_a: PW:0000906 ! interleukin-2 family mediated signaling pathway created_by: VPetri creation_date: 2012-03-23T12:39:32Z [Term] id: PW:0000911 name: interleukin-21 signaling pathway is_a: PW:0000906 ! interleukin-2 family mediated signaling pathway created_by: VPetri creation_date: 2012-03-23T12:39:52Z [Term] id: PW:0000912 name: interleukin-4 signaling pathway def: "Interleukin-4 is a member of interleukin 2 family of cytokine whose signaling is important for the differentiation of naive T helper cells." [PubMed:PMID\: 21889323] synonym: "Il-4 signaling pathway" EXACT [] synonym: "PID:200022" RELATED [] is_a: PW:0000906 ! interleukin-2 family mediated signaling pathway created_by: VPetri creation_date: 2012-03-23T12:48:51Z [Term] id: PW:0000913 name: interleukin-12 family mediated signaling pathway def: "Interleukin-12 family members of heterodimeric cytokines are produced by antigen presenting cells. The signaling they initiate triggers the Jak-Stat intracellular cascade and plays important roles in the regulation of T helper (Th) cell differentiation." [PubMed:PMID\: 20885915] synonym: "Il-12 family mediated signaling pathway" RELATED [] is_a: PW:0000512 ! Interleukin mediated signaling pathway created_by: VPetri creation_date: 2012-03-23T03:39:11Z [Term] id: PW:0000914 name: interleukin-12 signaling pathway def: "Interleukin-12 signaling activates the Jak-Stat intracellular cascade and promotes the differentiation and proliferation of Th1 cells and the production of interferon-gamma." [PubMed:PMID\: 20885915; 21553332] synonym: "Il-12 signaling pathway" EXACT [] synonym: "PID:200045" RELATED [] is_a: PW:0000913 ! interleukin-12 family mediated signaling pathway created_by: VPetri creation_date: 2012-03-23T03:43:43Z [Term] id: PW:0000915 name: interleukin-23 signaling pathway synonym: "Il-23 signaling pathway" EXACT [] synonym: "PID:200154" RELATED [] is_a: PW:0000913 ! interleukin-12 family mediated signaling pathway created_by: VPetri creation_date: 2012-03-23T03:49:27Z [Term] id: PW:0000916 name: interleukin-27 signaling pathway synonym: "Il-27 signaling pathway" EXACT [] synonym: "PID:200028" RELATED [] is_a: PW:0000913 ! interleukin-12 family mediated signaling pathway created_by: VPetri creation_date: 2012-03-23T03:49:45Z [Term] id: PW:0000917 name: interleukin-35 signaling pathway is_a: PW:0000913 ! interleukin-12 family mediated signaling pathway created_by: VPetri creation_date: 2012-03-23T03:50:45Z [Term] id: PW:0000918 name: proton pump inhibitor drug pathway def: "The pharmacokinetics and pharmacodynamics of proton pump inhibitor (PPI), a class of compounds that block the acid secretion from parietal cells in the stomach. A representative PPI compound is omeprazole. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/] is_a: PW:0000921 ! alimentary tract and metabolism drug pathway created_by: VPetri creation_date: 2012-03-28T02:13:39Z [Term] id: PW:0000919 name: antineoplastic and immunomodulatory drug pathway def: "The pharmacokinetics and pharmacodynamics of compounds used as antineoplastic or as immunomodulatory agents. It is to be noted here that genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/] is_a: PW:0000754 ! drug pathway created_by: VPetri creation_date: 2012-03-28T02:35:45Z [Term] id: PW:0000920 name: cardiovascular system drug pathway def: "The pharmacokinetics and pharmacodynamics of compounds used for the treatment of various cardiovascular conditions. It has to be noted here that genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/index.jsp] is_a: PW:0000754 ! drug pathway created_by: VPetri creation_date: 2012-03-28T02:45:12Z [Term] id: PW:0000921 name: alimentary tract and metabolism drug pathway def: "The pharmacokinetics and pharmacodynamics of compounds used for the treatment of alimentary tract and metabolism-related conditions. It has to be noted here that genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/index.jsp] is_a: PW:0000754 ! drug pathway created_by: VPetri creation_date: 2012-03-28T02:49:20Z [Term] id: PW:0000922 name: blood and blood forming organs drug pathway def: "The pharmacokinetics and pharmacodynamics of compounds used for the treatment of conditions associated with blood and blood forming organs. It has to be noted here that genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/index.jsp] is_a: PW:0000754 ! drug pathway created_by: VPetri creation_date: 2012-03-28T02:55:34Z [Term] id: PW:0000923 name: nervous system drug pathway def: "The pharmacokinetics and pharmacodynamics of compounds used for the treatment of conditions associated with the nervous system. It has to be noted here that genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/index.jsp] is_a: PW:0000754 ! drug pathway created_by: VPetri creation_date: 2012-03-28T02:58:10Z [Term] id: PW:0000924 name: respiratory system drug pathway def: "The pharmacokinetics and pharmacodynamics of compounds used for the treatment of conditions associated with the respiratory system. It has to be noted here that genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/index.jsp] is_a: PW:0000754 ! drug pathway created_by: VPetri creation_date: 2012-04-05T03:45:08Z [Term] id: PW:0000925 name: pattern recognition receptor mediated pathway def: "Pattern recognition receptors (PRR) respond to a diverse array of exogenous molecules and also several endogenous ones. PRR's 'sensing' of pathogen-associated molecular patterns (PAMP) or damage-associated (DAMP) prompts signaling cascades leading to the expression of pro-inflammatory genes." [MCW library:Cellular and molecular immunology\, by Abbas\, Abul K, PubMed:PMID\:20303867; 20303872] is_a: PW:0000024 ! inflammatory response pathway is_a: PW:0000819 ! signaling pathway in the innate immune response created_by: VPetri creation_date: 2012-04-24T11:34:22Z [Term] id: PW:0000926 name: pro-inflammatory cytokine mediated pathway def: "An early response of the innate immunity is the secretion of cytokines critical for the acute inflammatory response. The major pro-inflammatory cytokines are tumor necrosis factor alpha and the interleukins 1 and 6." [MCW library:cellular and molecular immunology\, by Abbas\, Abul K, PubMed:PMID\:20303867, XX:] is_a: PW:0000024 ! inflammatory response pathway created_by: VPetri creation_date: 2012-04-24T11:43:45Z [Term] id: PW:0000927 name: anti-tumor necrosis factor drug pathway def: "Tumor necrosis factor (TNF) inhibitors are used in the treatment of rheumatoid arthritis. The inhibitors are recombinant proteins that bind the soluble and membrane-associated TNF and inhibit the effects of this pro-inflammatory cytokine." [PubMed:PMID\:21039421] synonym: "anti-TNF drug pathway" RELATED [] is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway created_by: VPetri creation_date: 2012-04-26T02:36:43Z [Term] id: PW:0000928 name: tocilizumab drug pathway def: "Tocilizumab is a humanized anti-interleukin 6 (Il-6) receptor antibody used in the treatment of patients with rheumatoid arthritis, Castleman's disease or juvenile idiopathic arthritis. Tocilizumab binds to the soluble and membrane associated interleukin-6 receptor and competitively blocks binding of Il-6 to its receptor(s) and inhibits the effects of this potent cytokine." [PubMed:PMID\: 21419125] synonym: "Actemra drug pathway" RELATED [] is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway created_by: VPetri creation_date: 2012-04-26T03:00:42Z [Term] id: PW:0000929 name: anakinra drug pathway def: "Anakinra is a recombinant, non-glycosylated version of the human interleukin-1 (Il-1) receptor antagonist used for the treatment of inflammation associated with rheumatoid arthritis. Like the natural antagonist, anakinra competitively inhibits binding of interleukin-1 to its receptor and the subsequent effects of this potent pro-inflammatory cytokine." [wikipedia:anakinra entry] synonym: "kineret drug pathway" RELATED [] is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway created_by: VPetri creation_date: 2012-04-26T03:26:25Z [Term] id: PW:0000930 name: methotrexate drug pathway def: "The pharmacokinetics and pharmacodynamics of methotrexate (MTX), a folate analogue used in the treatment of cancers and autoimmune diseases. The impact of MTX on cancer and rheumatoid arthritis is thought to arise through distinct mechanisms and pharmacodynamic pathways. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/pathway/PA2039] is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway created_by: VPetri creation_date: 2012-04-27T01:27:25Z [Term] id: PW:0000931 name: methotrexate pharmacokinetics pathway def: "The pathway of processing - absorption, distribution, metabolism or elimination - of methotrexate (MTX), a folate analogue used in the treatment of cancers and autoimmune diseases. Genetic variations can result in changes in the availability of the drug and It is believed that variability in MTX pharmacokinetics is linked to genetic variations in transporter proteins." [PharmGKB:http\://www.pharmgkb.org/pathway/PA165816349] synonym: "MTX pharmacokinetics pathway" RELATED [] is_a: PW:0000930 ! methotrexate drug pathway created_by: VPetri creation_date: 2012-04-27T01:46:47Z [Term] id: PW:0000932 name: methotrexate pharmacodynamics pathway def: "The pathway of methotrexate-target interaction and of the biochemical or physiological responses to drug. The impact of MTX on cancer and rheumatoid arthritis is thought to arise through distinct mechanisms and pharmacodynamic pathways. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/pathway/PA2039] synonym: "MTX pharmacodynamics pathway" RELATED [] is_a: PW:0000930 ! methotrexate drug pathway created_by: VPetri creation_date: 2012-04-27T02:16:39Z [Term] id: PW:0000933 name: tumor necrosis factor member 14 signaling pathway def: "Tumor necrosis factor member 14, also known as Light, binds the lymphotoxin beta receptor and the tumor necrosis receptor member 14 known as Hvem of the tumor necrosis receptor superfamily to elicit important responses for the dendritic (DC) and T cells of the immune system." [PubMed:PMID\: 2169337\, 11239407\, 12787557] synonym: "Tnfsf14 (Light) signaling pathway" RELATED [] synonym: "Tnfsf14 signaling pathway" RELATED [] is_a: PW:0000236 ! tumor necrosis factor superfamily mediated signaling pathway created_by: VPetri creation_date: 2012-05-01T10:26:22Z [Term] id: PW:0000934 name: tumor necrosis factor member 13 signaling pathway def: "Tumor necrosis factor member 13 also known as April, binds the tumor necrosis factor receptor member 13B known as Taci and receptor member 17 known as Bcma of the tumor necrosis factor receptor superfamily to elicit important responses for the B cells of the immune system." [PubMed:PMID\: 2169337\, 11239407\, 12787557] synonym: "Tnfsf13 (April) signaling pathway" RELATED [] synonym: "Tnfsf13 signaling pathway" RELATED [] is_a: PW:0000236 ! tumor necrosis factor superfamily mediated signaling pathway created_by: VPetri creation_date: 2012-05-01T11:00:20Z [Term] id: PW:0000935 name: tumor necrosis factor member 13b signaling pathway def: "The tumor necrosis factor member 13b known as Baff binds to three receptor of the tumor necrosis factor receptor superfamily - the receptor member 13B known as Taci and member 17 known as Bcma to which member 13 of the ligand superfamily also binds, and additionally to member 13C of the receptor superfamily to elicit important responses for the B cells of the immune system." [PubMed:PMID\: 2169337\, 11239407\, 12787557] synonym: "Tnfsf13b (Baff) signaling pathway" RELATED [] synonym: "Tnfsf13b signaling pathway" RELATED [] is_a: PW:0000236 ! tumor necrosis factor superfamily mediated signaling pathway created_by: VPetri creation_date: 2012-05-01T11:11:44Z [Term] id: PW:0000936 name: chemokine (C-C motif) ligand 1 signaling pathway def: "Chemokine ligand 1 signaling engages the chemokine (C-C motif) receptor 8 (Ccr8) and together with other CC chemokines is classified as a member of the allergenic subgroup." [PubMed:PMID\: 15062643] synonym: "Ccl1 signaling pathway" EXACT [] is_a: PW:0000831 ! CC chemokine mediated signaling pathway created_by: vpetri creation_date: 2012-05-01T02:12:50Z [Term] id: PW:0000937 name: chemokine (C-C motif) ligand 2 signaling pathway def: "Chemokine ligand 1 signaling engages the chemokine (C-C motif) receptor 2 (Ccr2) and together with other CC chemokines is classified as a member of the allergenic subgroup." [PubMed:PMID\: 15062643] synonym: "Ccl2 signaling pathway" EXACT [] is_a: PW:0000831 ! CC chemokine mediated signaling pathway created_by: vpetri creation_date: 2012-05-01T02:20:28Z [Term] id: PW:0000938 name: chemokine (C-C motif) ligand 3 signaling pathway def: "Chemokine ligand 3 signaling pathway engages chemokine (C-C motif) receptors 2 and 5 (Ccr2 and Ccr5) and together with other chemokines is classified as a member of the pro-inflammatory subgroup." [PubMed:PMID\: 15062643] synonym: "Ccl3 signaling pathway" EXACT [] is_a: PW:0000831 ! CC chemokine mediated signaling pathway created_by: vpetri creation_date: 2012-05-01T02:30:19Z [Term] id: PW:0000939 name: chemokine (C-C motif) ligand 4 signaling pathway def: "Chemokine ligand 4 signaling engages the chemokine (C-C motif) receptor 5 (Ccr5) and together with other chemokines is classified as a member of the pro-inflammatory subgroup." [PubMed:PMID\: 15062643] synonym: "Ccl4 signaling pathway" EXACT [] is_a: PW:0000831 ! CC chemokine mediated signaling pathway created_by: vpetri creation_date: 2012-05-01T02:34:32Z [Term] id: PW:0000940 name: chemokine (C-C motif) ligand 5 signaling pathway def: "Chemokine ligand 5 signaling engages chemokine (C-C motif) receptors 1, 3 and 5 (Ccr1, Ccr3 and Ccr5) and together with other chemokines is classified as a member of the pro-inflammatory subgroup." [PubMed:PMID\: 15062643] synonym: "Ccl5 signaling pathway" EXACT [] is_a: PW:0000831 ! CC chemokine mediated signaling pathway created_by: vpetri creation_date: 2012-05-01T02:39:00Z [Term] id: PW:0000941 name: chemokine (C-C motif) ligand 6 signaling pathway def: "Chemokine ligand 6 signaling is known to act in rodents and does not appear to have a human equivalent. Ccl6, together with other chemokines is classified as a member of the pro-inflammatory subgroup." [PubMed:PMID\: 15062643] synonym: "Ccl6 signaling pathway" EXACT [] is_a: PW:0000831 ! CC chemokine mediated signaling pathway created_by: vpetri creation_date: 2012-05-01T02:43:25Z [Term] id: PW:0000942 name: chemokine (C-C motif) ligand 7 signaling pathway def: "Chemokine ligand 7 signaling engages chemokine (C-C) motif receptors 1, 2, and 3 (Ccr1, Ccr2, Ccr3) and together with other chemokines is classified as a member of the allergenic subgroup." [PubMed:PMID\: 15062643] synonym: "Ccl7 signaling pathway" EXACT [] is_a: PW:0000831 ! CC chemokine mediated signaling pathway created_by: vpetri creation_date: 2012-05-01T02:51:25Z [Term] id: PW:0000943 name: chemokine (C-C motif) ligand 8 signaling pathway def: "Chemokine ligand 8 signaling engages chemokine (C-C motif) receptors 3 and 5 (Ccr3 and Ccr5) and together with other chemokines is classified as a member of the allergenic subgroup." [PubMed:PMID\: 15062643] synonym: "Ccl8 signaling pathway" EXACT [] is_a: PW:0000831 ! CC chemokine mediated signaling pathway created_by: vpetri creation_date: 2012-05-01T02:54:39Z [Term] id: PW:0000944 name: chemokine (C-C motif) ligand 11 signaling pathway def: "Chemokine ligand 11 signaling engages the chemokine (C-C motif) receptor 3 (Ccr3) and together with other chemokines is classified as a member of the allergenic subgroup." [PubMed:PMID\: 15062643] synonym: "Ccl11 signaling pathway" EXACT [] synonym: "eotaxin signaling pathway" RELATED [] is_a: PW:0000831 ! CC chemokine mediated signaling pathway created_by: vpetri creation_date: 2012-05-01T03:09:44Z [Term] id: PW:0000945 name: chemokine (C-C motif) ligand 12 signaling pathway def: "Chemokine ligand 12 signaling is known to act in rodents and does not appear to have a human equivalent. Ccl12, together with other chemokines is classified as a member of the allergenic subgroup." [PubMed:PMID\: 15062643] synonym: "Ccl12 signaling pathway" EXACT [] is_a: PW:0000831 ! CC chemokine mediated signaling pathway created_by: vpetri creation_date: 2012-05-01T03:16:03Z [Term] id: PW:0000946 name: chemokine (C-C motif) ligand 13 signaling pathway def: "Chemokine ligand 13 signaling engages chemokine (C-C motif) receptors 2 and 3 (Ccr2 and Ccr3) and together with other chemokines is classified as a member of the allergenic subgroup." [PubMed:PMID\: 15062643] synonym: "Ccl13 signaling pathway" EXACT [] is_a: PW:0000831 ! CC chemokine mediated signaling pathway created_by: vpetri creation_date: 2012-05-01T03:17:54Z [Term] id: PW:0000947 name: chemokine (C-C motif) ligand 17 signaling pathway def: "Chemokine ligand 17 signaling engages the chemokine (C-C motif) receptor 4 (Ccr4) and together with other chemokines is classified as a member of the developmental subgroup." [PubMed:PMID\: 15062643] synonym: "Ccl17 signaling pathway" EXACT [] is_a: PW:0000831 ! CC chemokine mediated signaling pathway created_by: vpetri creation_date: 2012-05-01T03:23:46Z [Term] id: PW:0000948 name: chemokine (C-C motif) ligand 22 signaling pathway def: "Chemokine ligand 22 signaling engages the chemokine (C-C motif) receptor 4 (Ccr4) and together with other chemokines is classified as member of the developmental subgroup." [PubMed:PMID\: 15062643, XX:] synonym: "Ccl22 signaling pathway" EXACT [] is_a: PW:0000831 ! CC chemokine mediated signaling pathway created_by: vpetri creation_date: 2012-05-01T03:26:56Z [Term] id: PW:0000949 name: chemokine (C-C motif) ligand 25 signaling pathway def: "Chemokine ligand 25 signaling engages the chemokine (C-C motif) receptor 9 (Ccr9) and together with other chemokines is classified as a member oft he developmental subgroup." [PubMed:PMID\: 15062643] synonym: "Ccl25 signaling pathway" EXACT [] is_a: PW:0000831 ! CC chemokine mediated signaling pathway created_by: vpetri creation_date: 2012-05-01T03:31:08Z [Term] id: PW:0000950 name: chemokine (C-C motif) ligand 24 signaling pathway def: "Chemokine ligand 24 signaling engages the chemokine (C-C motif) receptor 3 (Ccr3) and together with other chemokines is classified as member of the allergenic subgroup." [Pubmed:PMID\: 15062643] synonym: "Ccl24 signaling pathway" EXACT [] synonym: "eotaxin-2 signaling pathway" RELATED [] is_a: PW:0000831 ! CC chemokine mediated signaling pathway created_by: vpetri creation_date: 2012-05-01T03:37:14Z [Term] id: PW:0000951 name: chemokine (C-C motif) ligand 26 signaling pathway def: "Chemokine ligand 26 signaling engages the chemokine (C-C motif) receptor 3 (Ccr3) and together with other chemokines is classified as member of the allergenic subgroup." [PubMed:PMID\: 15062643] synonym: "Ccl26 signaling pathway" EXACT [] synonym: "eotaxin-3 signaling pathway" RELATED [] is_a: PW:0000831 ! CC chemokine mediated signaling pathway created_by: vpetri creation_date: 2012-05-01T03:39:19Z [Term] id: PW:0000952 name: chemokine (C-C motif) ligand 14 signaling pathway def: "Chemokine ligand 14 signaling engages chemokine (C-C motif) receptors 1 and 5 (Ccr1 and Ccr5) and together with other chemokines is classified as a member of the HCC (hemofiltrate CC chemokine) subgroup." [PubMed:PMID\: 15062643] synonym: "Ccl14 signaling pathway" EXACT [] is_a: PW:0000831 ! CC chemokine mediated signaling pathway created_by: vpetri creation_date: 2012-05-02T03:16:19Z [Term] id: PW:0000953 name: chemokine (C-C motif) ligand 15 signaling pathway def: "Chemokine ligand 15 signaling engages chemokine (C-C motif) receptors 1 and 3 (Ccr1 and Ccr3) and together with other chemokines is classified as a member of the HCC (hemofiltrate CC chemokine) subgroup." [PubMed:PMID\: 15062643] synonym: " Ccl15 signaling pathway" EXACT [] is_a: PW:0000831 ! CC chemokine mediated signaling pathway created_by: vpetri creation_date: 2012-05-02T03:32:48Z [Term] id: PW:0000954 name: chemokine (C-C motif) ligand 16 signaling pathway def: "Chemokine ligand 16 signaling engages chemokine (C-C motif) receptors 1 and 2 (Ccr1 and Ccr2) and together with other chemokines is classified as a member of the HCC (hemofiltrate CC chemokine) subgroup." [PubMed:PMID\: 15062643] synonym: "Ccl16 signaling pathway" EXACT [] is_a: PW:0000831 ! CC chemokine mediated signaling pathway created_by: vpetri creation_date: 2012-05-02T03:34:53Z [Term] id: PW:0000955 name: chemokine (C-C motif) ligand 23 signaling pathway def: "Chemokine ligand 23 signaling engages the chemokine (C-C motif) receptor 1 (Ccr1) and together with other chemokines is classified as a member of the HCC (hemofiltrate CC chemokine) subgroup." [PubMed:PMID\: 15062643] synonym: "Ccl23 signaling pathway" EXACT [] is_a: PW:0000831 ! CC chemokine mediated signaling pathway created_by: vpetri creation_date: 2012-05-02T03:37:10Z [Term] id: PW:0000956 name: chemokine (C-C motif) ligand 27 signaling pathway def: "Chemokine ligand 27 signaling engages chemokine (C-C motif) receptor 10 (Ccr10) and does not appear to be a member of any of the chemokines subgroups." [PubMed:PMID\: 15062643] synonym: "Ccl27 signaling pathway" EXACT [] is_a: PW:0000831 ! CC chemokine mediated signaling pathway created_by: VPetri creation_date: 2012-05-15T01:08:34Z [Term] id: PW:0000957 name: chemokine (C-X-C motif) ligand 1 signaling pathway def: "Chemokine (C-X-C) ligand 1belongs to the growth-related oncogene (GRO) subgroup whose signaling engages receptor 2 and promotes chemotaxis of neutrophils." [PubMed:PMID\: 18579287] synonym: "Cxcl1 signaling pathway" EXACT [] synonym: "Gro alpha signaling pathway" RELATED [] is_a: PW:0000971 ! CXC chemokine ELR(+) subgroup mediated signaling pathway created_by: VPetri creation_date: 2012-05-15T01:23:49Z [Term] id: PW:0000958 name: forkhead class A signaling pathway def: "The signaling pathway mediated by the FoxA subgroup of forkhead family of transcription factors plays important roles in development and in modulating steroid hormone signaling. Three FoxA genes carry out overlapping yet distinct functions. FOXA1 appears to modulate steroid receptor activity in breast and prostate cancer." [PubMed:PMID\: 21934649; 19274050; 20591647; 21934649] synonym: "FoxA signaling pathway" RELATED [] synonym: "PID:200087" RELATED [] synonym: "PID:200226" RELATED [] is_a: PW:0000647 ! forkhead signaling pathway created_by: VPetri creation_date: 2012-05-17T11:10:35Z [Term] id: PW:0000959 name: lipid signaling pathway is_a: PW:0000003 ! signaling pathway created_by: VPetri creation_date: 2012-05-17T01:09:58Z [Term] id: PW:0000960 name: sphingosine 1-phosphate signaling pathway def: "Sphingosine 1-phosphate (S1P), a sphingolipid metabolite, can signal intracellularly as a second messenger or extracellularly as a ligand for five G protein coupled receptors. S1P pathway plays important roles in processes such as cell migration, proliferation and survival. The five receptors engage similar G proteins but their expression varies." [PubMed:PMID\: 18552276; 22159476] synonym: "PID:200046" RELATED [] synonym: "PID:200054" RELATED [] synonym: "PID:200076" RELATED [] synonym: "PID:200085" RELATED [] synonym: "PID:200123" RELATED [] synonym: "PID:200211" RELATED [] synonym: "S1P signaling pathway" RELATED [] is_a: PW:0000541 ! signaling pathway involving second messengers is_a: PW:0000959 ! lipid signaling pathway created_by: VPetri creation_date: 2012-05-17T01:10:40Z [Term] id: PW:0000961 name: ceramide signaling pathway def: "Ceramide signaling can act as a lipid second messenger or as a mediator of various cellular signaling pathways by promoting receptor clustering. The pathway plays important roles in apoptosis." [PubMed:PMID\: 20607622] synonym: "KEGG:05212" RELATED [] synonym: "PID:200119" RELATED [] is_a: PW:0000541 ! signaling pathway involving second messengers is_a: PW:0000959 ! lipid signaling pathway created_by: VPetri creation_date: 2012-05-17T01:43:41Z [Term] id: PW:0000962 name: visual phototransduction pathway def: "The signaling pathway initiated by light induced isomerization of 11-cis retinal and subsequent activation of its photoreceptors in rods and cones." [PubMed:PMID\: 22074921\, 18514002] synonym: "KEGG:04744" RELATED [] is_a: PW:0001008 ! photosignal transduction pathway is_a: PW:0001116 ! vitamin A and metabolites signaling pathway relationship: part_of PW:0001007 ! vitamin A homeostasis created_by: VPetri creation_date: 2012-05-17T05:16:34Z [Term] id: PW:0000963 name: phosphatidylinositol 3-kinase class I signaling pathway def: "Phosphatidylinositol kinases represent a family of lipid kinases that phosphorylate the 3' position of the inositol ring in target substrates. They are grouped into three classes: class I further subdivided into subclass A and B, class II and class III. By far the best known and characterized is class I, particularly IA that signals downstream of receptor tyrosine kinases and engages the Akt family of kinases." [PubMed:PMID\: 17052169\, 17641274\, 16847462] synonym: "PID:200116" RELATED [] is_a: PW:0000595 ! phosphatidylinositol 3-kinase signaling pathway created_by: VPetri creation_date: 2012-05-18T10:40:25Z [Term] id: PW:0000964 name: altered phosphatidylinositol 3-kinase class I signaling pathway is_a: PW:0000621 ! altered phosphatidylinositol 3-kinase signaling pathway created_by: VPetri creation_date: 2012-05-18T10:41:53Z [Term] id: PW:0000965 name: phosphatidylinositol 3-kinase class II signaling pathway def: "Phosphatidylinositol kinases represent a family of lipid kinases that phosphorylate the 3' position of the inositol ring in target substrates. They are grouped into three classes: class I further subdivided into subclass A and B, class II and class III. By far the best known and characterized is class I, particularly IA that signals downstream of receptor tyrosine kinases and engages the Akt family of kinases." [PubMed:PMID\: 17052169\, 17641274\, 16847462] is_a: PW:0000595 ! phosphatidylinositol 3-kinase signaling pathway created_by: VPetri creation_date: 2012-05-18T10:50:58Z [Term] id: PW:0000966 name: phosphatidylinositol 3-kinase class III signaling pathway def: "Phosphatidylinositol kinases represent a family of lipid kinases that phosphorylate the 3' position of the inositol ring in target substrates. They are grouped into three classes: class I further subdivided into subclass A and B, class II and class III. By far the best known and characterized is class I, particularly IA that signals downstream of receptor tyrosine kinases and engages the Akt family of kinases." [PubMed:PMID\: 17052169\, 17641274\, 16847462] is_a: PW:0000595 ! phosphatidylinositol 3-kinase signaling pathway created_by: VPetri creation_date: 2012-05-18T10:53:38Z [Term] id: PW:0000967 name: interleukin-3/interleukin-5/GM-CSF mediated signaling pathway def: "Interleukin-3, interleukin 5 and granulocyte-macrophage colony-stimulating factors family of hemopoietic cytokine mediate overlapping and distinct signals. Collectively they regulate the production and activation of hemopoietic cells." [PubMed:PMID\: 19436055] synonym: "hemopoietic cytokine family mediated signaling pathway" RELATED [] synonym: "Il-3/Il-5/GM-CSF family mediated signaling pathway" EXACT [] is_a: PW:0000512 ! Interleukin mediated signaling pathway created_by: VPetri creation_date: 2012-05-22T11:30:25Z [Term] id: PW:0000968 name: interleukin-3 signaling pathway def: "Interleukin-3 signaling plays important roles in the function of hematopoietic cells." [PubMed:PMID\: 11312115] synonym: "Il-3 signaling pathway" EXACT [] synonym: "PID:200145" RELATED [] is_a: PW:0000967 ! interleukin-3/interleukin-5/GM-CSF mediated signaling pathway created_by: VPetri creation_date: 2012-05-22T11:43:49Z [Term] id: PW:0000969 name: interleukin-5 signaling pathway def: "Interleukin-5 signaling plays important roles in the function of hematopoietic cells." [PubMed:PMID\: 11312115] synonym: "Il-5 signaling pathway" EXACT [] synonym: "PID:200107" RELATED [] is_a: PW:0000967 ! interleukin-3/interleukin-5/GM-CSF mediated signaling pathway created_by: VPetri creation_date: 2012-05-22T11:44:14Z [Term] id: PW:0000970 name: granulocyte-macrophage colony-stimulating factor signaling pathway def: "GM-CSF signaling, like the other hemopoietic cytokines, is involved in the production and activation of hemopoietic cells. The GM-CSF pathway acts on monocytes, macrophages and granulocytes and is also involved in the regulation of T and dendritic cells functions." [PubMed:PMID\: 19436055] synonym: "GM-CSF signaling pathway" EXACT [] synonym: "PID:200019" RELATED [] is_a: PW:0000967 ! interleukin-3/interleukin-5/GM-CSF mediated signaling pathway created_by: VPetri creation_date: 2012-05-22T11:44:40Z [Term] id: PW:0000971 name: CXC chemokine ELR(+) subgroup mediated signaling pathway def: "The CXC chemokine ELR(+) subgroup mediated signaling primarily engages receptor 2 to promote angiogenic effects." [PubMed:PMID\: 18579287] is_a: PW:0000830 ! CXC chemokine mediated signaling pathway created_by: VPetri creation_date: 2012-05-22T02:49:53Z [Term] id: PW:0000972 name: CXC chemokine ELR(-) subgroup mediated signaling pathway def: "CXC chemokine (ELR-) subgroup mediated signaling primarily engages receptor 3 to promote angiostatic effects." [PubMed:PMID\:18579287] is_a: PW:0000830 ! CXC chemokine mediated signaling pathway created_by: VPetri creation_date: 2012-05-22T02:49:59Z [Term] id: PW:0000973 name: chemokine (C-X-C motif) ligand 2 signaling pathway def: "Chemokine (C-X-C) ligand 2 belongs to the growth-related oncogene (GRO) subgroup whose signaling engages receptor 2 to promote chemotaxis of neutrophils." [PubMed:PMID\: 18579287] synonym: "Cxcl2 signaling pathway" EXACT [] synonym: "Gro beta signaling pathway" RELATED [] is_a: PW:0000971 ! CXC chemokine ELR(+) subgroup mediated signaling pathway created_by: VPetri creation_date: 2012-05-22T03:26:21Z [Term] id: PW:0000974 name: chemokine (C-X-C motif) ligand 3 signaling pathway def: "Chemokine (C-X-C) ligand 3 belongs to the growth-related oncogene (GRO) subgroup whose signaling engages receptor 2 to promote chemotaxis of neutrophils." [PubMed:PMID\: 18579287] synonym: "Cxcl3 signaling pathway" EXACT [] synonym: "Gro gamma signaling pathway" RELATED [] is_a: PW:0000971 ! CXC chemokine ELR(+) subgroup mediated signaling pathway created_by: VPetri creation_date: 2012-05-22T03:29:34Z [Term] id: PW:0000975 name: chemokine (C-X-C motif) ligand 5 signaling pathway def: "Chemokine (C-X-C) ligand 5 signaling engages receptor 2 to exert potent chemotactic functions in neutrophil activation." [PubMed:PMID\: 18579287] synonym: "Cxcl5 signaling pathway" EXACT [] synonym: "Ena-78 signaling pathway" RELATED [] is_a: PW:0000971 ! CXC chemokine ELR(+) subgroup mediated signaling pathway created_by: VPetri creation_date: 2012-05-22T03:37:57Z [Term] id: PW:0000976 name: chemokine (C-X-C motif) ligand 6 signaling pathway def: "Chemokine (C-X-C0) ligand 6 engages receptors 1 and 2 to promote chemoattraction of neutrophils and angiogenic effects, respectively." [PubMed:PMID\: 18579287] synonym: "Cxcl6 signaling pathway" EXACT [] is_a: PW:0000971 ! CXC chemokine ELR(+) subgroup mediated signaling pathway created_by: VPetri creation_date: 2012-05-22T03:42:45Z [Term] id: PW:0000977 name: chemokine (C-X-C motif) ligand 7 signaling pathway is_a: PW:0000971 ! CXC chemokine ELR(+) subgroup mediated signaling pathway created_by: VPetri creation_date: 2012-05-22T03:48:29Z [Term] id: PW:0000978 name: chemokine (C-X-C motif) ligand 8 signaling pathway def: "Chemokine (C-X-C) ligand 8, also known as interleukin-8 (Il-8), although a chemokine, engages receptor 1 and 2 to promote angiogenic effects." [PubMed:PMID\: 18579287] synonym: "Cxcl8 signaling pathway" EXACT [] synonym: "Il-8 signaling pathway" RELATED [] synonym: "PID:200136" RELATED [] is_a: PW:0000971 ! CXC chemokine ELR(+) subgroup mediated signaling pathway created_by: VPetri creation_date: 2012-05-22T03:49:12Z [Term] id: PW:0000979 name: chemokine (C-X-C motif) ligand 4 signaling pathway def: "Chemokine (C-X-C) ligand 4 signaling engages receptor 3 to promote angiostatic effects." [PubMed:PMID\: 18579287] synonym: "Cxcl4 signaling pathway" EXACT [] is_a: PW:0000972 ! CXC chemokine ELR(-) subgroup mediated signaling pathway created_by: VPetri creation_date: 2012-05-22T03:55:01Z [Term] id: PW:0000980 name: chemokine (C-X-C motif) ligand 9 signaling pathway def: "Chemokine (C-X-C) ligand 9 engages receptor 3 to promote angiostatic effects." [PubMed:PMID\: 18579287] synonym: "Cxcl9 signaling pathway" EXACT [] synonym: "Mig signaling pathway" RELATED [] is_a: PW:0000972 ! CXC chemokine ELR(-) subgroup mediated signaling pathway created_by: VPetri creation_date: 2012-05-22T03:57:41Z [Term] id: PW:0000981 name: chemokine (C-X-C motif) ligand 10 signaling pathway def: "Chemokine (C-X-C) ligand 10 signaling engages receptor 3 to promote angiostatic effects." [PubMed:PMID\: 18579287] synonym: "Cxcl10 signaling pathway" EXACT [] is_a: PW:0000972 ! CXC chemokine ELR(-) subgroup mediated signaling pathway created_by: VPetri creation_date: 2012-05-22T04:00:20Z [Term] id: PW:0000982 name: chemokine (C-X-C motif) ligand 11 signaling pathway def: "Chemokine (C-X-C) ligand 11 signaling engages receptor 3 to promote angiostatic effects." [PubMed:PMID\: 18579287] synonym: "Cxcl11 signaling pathway" EXACT [] is_a: PW:0000972 ! CXC chemokine ELR(-) subgroup mediated signaling pathway created_by: VPetri creation_date: 2012-05-22T04:10:07Z [Term] id: PW:0000983 name: chemokine (C-X-C motif) ligand 12 signaling pathway is_a: PW:0000972 ! CXC chemokine ELR(-) subgroup mediated signaling pathway created_by: VPetri creation_date: 2012-05-22T05:01:33Z [Term] id: PW:0000984 name: chemokine (C-X-C motif) ligand 13 signaling pathway is_a: PW:0000972 ! CXC chemokine ELR(-) subgroup mediated signaling pathway created_by: VPetri creation_date: 2012-05-22T05:02:28Z [Term] id: PW:0000985 name: chemokine (C-X-C motif) ligand 14 signaling pathway is_a: PW:0000972 ! CXC chemokine ELR(-) subgroup mediated signaling pathway created_by: VPetri creation_date: 2012-05-22T05:03:13Z [Term] id: PW:0000986 name: chemokine (C-X-C motif) ligand 16 signaling pathway is_a: PW:0000972 ! CXC chemokine ELR(-) subgroup mediated signaling pathway created_by: VPetri creation_date: 2012-05-22T05:04:00Z [Term] id: PW:0000987 name: erythropoietin signaling pathway def: "Erythropoietin (EPO) signaling is crucial for the production of blood cell or erythropoiesis and also plays important roles in wound healing and responses to neural injury. EPO is a glycoprotein hormone and also a cytokine whose receptor belongs to type I cytokine receptor. The pathway engages the Jak-Stat intracellular cascade." [OneLook:www.onelook.com, PubMed:PMID\: 21307776] synonym: "EPO signaling pathway" EXACT [] synonym: "PID:200183" RELATED [] is_a: PW:0000467 ! peptide and protein hormone signaling pathway is_a: PW:0000828 ! cytokine mediated signaling pathway created_by: VPetri creation_date: 2012-05-24T02:57:05Z [Term] id: PW:0000988 name: classical cadherin signaling pathway def: "Classical cadherins, such as E- or N-cadherin are single-span transmembrane proteins with five extracellular cadherin repeats and a conserved cytoplasmic tail. Their interaction with many cytoskeletal and signaling molecules underlies the calcium-dependent cell-cell adhesion and signaling. While E- and N-cadherin share some of the interacting partners, they have different localization and impact on distinct cellular events." [PubMed:PMID\: 11171368\, 21444749] is_a: PW:0000333 ! cadherin mediated signaling pathway created_by: VPetri creation_date: 2012-05-25T10:07:46Z [Term] id: PW:0000989 name: desmosomal cadherin signaling pathway def: "Desmosomal cadherins, which can be further subdivided into two subgroups, possess the five cadherin repeats but have distinct cytoplasmic tails." [PubMed:PMID\: 11171368] is_a: PW:0000333 ! cadherin mediated signaling pathway created_by: VPetri creation_date: 2012-05-25T10:37:23Z [Term] id: PW:0000990 name: protocadherin signaling pathway def: "Protocadherin represent a very large family which can be further subdivided into two groups. The protocadherin are predominantly expressed in the nervous system. They have up to seven cadherin repeats but distict and even divergent cytoplasmic regions." [PubMed:PMID\: 11171368\, 17936607] is_a: PW:0000333 ! cadherin mediated signaling pathway created_by: VPetri creation_date: 2012-05-25T10:37:53Z [Term] id: PW:0000991 name: atypical cadherin signaling pathway def: "The atypical, or uncoventional group includes the seven transmembrane (7TM), GPCR-like cadherins with up to nine cadherin repeats along with EGF-like and laminin motifs, the large FAT and the t-Cadherin proteins." [PubMed:PMID\: 11171368] is_a: PW:0000333 ! cadherin mediated signaling pathway created_by: VPetri creation_date: 2012-05-25T10:38:11Z [Term] id: PW:0000992 name: E-cadherin signaling pathway def: "E-cadherin or the epithelial cadherin encoded by the Cdh1 gene, is a member of the classical cadherin family and among the best studied cadherin pathway. Deregulation of the pathway has been associated with several forms of cancer." [PubMed:PMID\: 11171368\, 21444749] synonym: "Cdh1 signaling pathway" RELATED [] synonym: "PID:200124" RELATED [] synonym: "PID:200147" RELATED [] synonym: "PID:200182" RELATED [] is_a: PW:0000988 ! classical cadherin signaling pathway created_by: VPetri creation_date: 2012-05-25T10:51:52Z [Term] id: PW:0000993 name: N-cadherin signaling pathway def: "N-cadherin, or neuronal cadherin, is predominantly expressed in the brain. The pathway plays important roles in learning and memory." [PubMed:PMID\: 11171368\, 21444749] synonym: "Cdh2 signaling pathway" RELATED [] synonym: "PID:200209" RELATED [] is_a: PW:0000988 ! classical cadherin signaling pathway created_by: VPetri creation_date: 2012-05-25T10:52:18Z [Term] id: PW:0000994 name: altered classical cadherin signaling pathway is_a: PW:0000338 ! altered cadherins mediated signaling pathway is_a: PW:0000988 ! classical cadherin signaling pathway created_by: VPetri creation_date: 2012-05-25T11:18:01Z [Term] id: PW:0000995 name: altered E-cadherin signaling pathway is_a: PW:0000992 ! E-cadherin signaling pathway is_a: PW:0000994 ! altered classical cadherin signaling pathway created_by: VPetri creation_date: 2012-05-25T11:18:51Z [Term] id: PW:0000996 name: antiinfective drug pathway def: "The pharmacokinetics and pharmacodynamics of compounds used as antiinfective agents. It is to be noted here that genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org] synonym: "anti-infective drug pathway" EXACT [] is_a: PW:0000754 ! drug pathway created_by: VPetri creation_date: 2012-05-25T11:37:29Z [Term] id: PW:0000997 name: nucleoside and nucleotide mediated signaling pathway is_a: PW:0000003 ! signaling pathway created_by: VPetri creation_date: 2012-05-25T11:48:24Z [Term] id: PW:0000998 name: adenosine signaling pathway def: "Adenosine signaling is involved in the regulation of several physiological processes. It uses four receptors of the GPCR family that activate the Gaphas and Galphai types of G proteins to increase or decrease the levels of cAMP. The adenosine receptors are a class of purinergic or purinoreceptors." [PubMed:PMID\: 21622100\, 21185259] is_a: PW:0000997 ! nucleoside and nucleotide mediated signaling pathway created_by: VPetri creation_date: 2012-05-25T11:53:37Z [Term] id: PW:0000999 name: adenosine triphosphate signaling pathway def: "Adenosine triphosphate (ATP) extracellular signaling activates the P2X ligand-gated ion channels that are permeable to sodium, potassium and calcium ions. There are several P2X subtypes that are involved in a range of physiological processes. ATP along with other nucleotide also engages a class of metabotropic purinergic receptors known as P2Y that couple to either the Galphaq or to G alphai subunit of heterotrimeric G proteins. ATP is the sole ligand of P2Y 11 receptor." [PubMed:PMID\: 22535247\, 21586365] synonym: "ATP signaling pathway" EXACT [] is_a: PW:0000997 ! nucleoside and nucleotide mediated signaling pathway created_by: VPetri creation_date: 2012-05-25T12:03:02Z [Term] id: PW:0001000 name: nucleotide signaling via the purinergic P2Y receptors. def: "The P2Y receptors are a class of purinergic or purinoreceptors, Gprotein-coupled receptors that respond to ADP, ATP, UDP, UTP and UDP-glucose to activate either the Galphaq or the Galphai mediated signal transduction pathways." [PubMed:PMID\: 16968944\, 20594935] is_a: PW:0000997 ! nucleoside and nucleotide mediated signaling pathway created_by: VPetri creation_date: 2012-05-25T12:11:33Z [Term] id: PW:0001001 name: adenosine triphosphate signaling via the P2X ligand-gated ion channel synonym: "ATP signaling via the P2X ligand-gated ion channel" EXACT [] is_a: PW:0000999 ! adenosine triphosphate signaling pathway created_by: VPetri creation_date: 2012-05-30T02:32:59Z [Term] id: PW:0001002 name: copper homeostasis pathway is_a: PW:0000589 ! metal homeostasis pathway created_by: VPetri creation_date: 2012-05-31T04:20:42Z [Term] id: PW:0001003 name: retinoid metabolic pathway def: "Those metabolic reactions involving the fat-soluble vitamin A and its metabolites. Vitamin A, retinol and vitamin A activities of metabolites such as retinal and retinoic acids are essential for visual transduction as well as for neuro and immune system functions and epithelial differentiation. Plants and microorganisms can synthesize vitamin A de novo while higher organisms derive it from diet as precursors carotenoids or retinyl esters." [PubMed:PMID\: 21554983] synonym: "vitamin A metabolic pathway" RELATED [] is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins relationship: part_of PW:0001007 ! vitamin A homeostasis created_by: VPetri creation_date: 2012-06-04T10:52:32Z [Term] id: PW:0001004 name: retinoic acid metabolic pathway def: "The reactions involved in deriving retinoic acid (RA) from retinal and its further processing to more polar derivatives. Retinoic acid engages several retinoic acid receptors; its actions are important for the neuro and immune system functions and energy balance. Deregulation of proper RA activity has been associated with obesity and cancer." [PubMed:PMID\: 21621639] synonym: "RA metabolic pathway" EXACT [] is_a: PW:0001003 ! retinoid metabolic pathway created_by: VPetri creation_date: 2012-06-04T11:05:02Z [Term] id: PW:0001005 name: retinoid cycle metabolic pathway def: "The series of reactions involved in the regeneration of the visual chromophore 11-cis retinal from the all-trans retinal released from the light -activated rhodopsin." [PubMed:PMID\: 21447403] synonym: "visual cycle metabolic pathway" EXACT [] is_a: PW:0001003 ! retinoid metabolic pathway created_by: VPetri creation_date: 2012-06-04T11:19:05Z [Term] id: PW:0001006 name: vitamin homeostasis is_a: PW:0000355 ! homeostasis pathway created_by: VPetri creation_date: 2012-06-04T01:28:58Z [Term] id: PW:0001007 name: vitamin A homeostasis def: "The pathways involved in the balanced maintenance of vitamin A and vitamin A metabolites uptake and transport, utilization and storage, as demanded by the needs of cells, tissues and organs. 11-cis retinal is the visual chromophore while retinoic acid signaling through its nuclear receptors transcription factors exerts the rest and manifold functions of vitamin A." [PubMed:PMID\: 21554983\, 21586336\, 21621639] synonym: "vitamin A homeostasis" EXACT [] is_a: PW:0001006 ! vitamin homeostasis created_by: VPetri creation_date: 2012-06-04T01:30:04Z [Term] id: PW:0001008 name: photosignal transduction pathway is_a: PW:0000003 ! signaling pathway created_by: VPetri creation_date: 2012-06-05T10:44:24Z [Term] id: PW:0001009 name: ascorbic acid metabolic pathway def: "Those metabolic reactions involving ascorbic acid, known as vitamin C, a water-soluble vitamin. Vitamin C is an essential antioxidant that is derived from glucose. Unlike many animals, humans do not have the ability to produce it. Vitamin C acts as an antioxidant." [OneLook:http\://www.onelook.com] synonym: "vitamin C metabolic pathway" RELATED [] is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins created_by: VPetri creation_date: 2012-06-05T11:40:08Z [Term] id: PW:0001010 name: niacin metabolic pathway def: "Those metabolic reactions involving niacin, also known as vitamin B3 or vitamin PP - a water-soluble vitamin. Niacin represents an essential nutrient and is also a precursor of NAD through a salvage pathway. Niacin is among the few vitamins humans can synthesize." [OneLoook:http\://www.onelook.com] synonym: "KEGG:00760" RELATED [] synonym: "vitamin B3 metabolic pathway" RELATED [] is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins created_by: VPetri creation_date: 2012-06-05T11:44:25Z [Term] id: PW:0001011 name: vitamin D metabolic pathway def: "Those metabolic reactions involving vitamin D - a fat-soluble vitamin. Vitamin D represents a group of fat-soluble compounds that can be synthesized from cholesterol and exposure to sunlight. In view of the latter source, it is not considered a true vitamin. One of its metabolites, calcitriol acts in a hormone-like manner as a signaling molecule." [OneLook:http\://www.onelook.com] is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins created_by: VPetri creation_date: 2012-06-05T12:01:10Z [Term] id: PW:0001012 name: vitamin and vitamin metabolites signaling pathway def: "Vitamin and metabolites of vitamin in addition to representing important nutrients and aid in cellular metabolism can also, in a hormone-like manner, acts as signaling molecules." [PubMed:PMID\: 22614789\, 22318625\, 22020178] is_a: PW:0000003 ! signaling pathway created_by: VPetri creation_date: 2012-06-05T12:07:26Z [Term] id: PW:0001013 name: vitamin D signaling pathway def: "The active vitamin D metabolite plays important roles in cell growth and differentiation and in immunity. Its receptor is a transcription factor nuclear receptor." [PubMed:PMID\: 22213316] is_a: PW:0000100 ! transcription pathway is_a: PW:0000716 ! transcription factor mediated signaling pathway is_a: PW:0001012 ! vitamin and vitamin metabolites signaling pathway created_by: VPetri creation_date: 2012-06-05T12:13:52Z [Term] id: PW:0001014 name: retinoic acid signaling pathway def: "Retinoic acid, a vitamin A-derived metabolite plays important roles in development and cell differentiation. all-trans retinoic acid (RA) binds to nuclear RA (RARs) and X (RXRs) receptor subtypes that once activated act as transcription factors." [PubMed:PMID\: 22318625\, 22020178] synonym: "RA signaling pathway" EXACT [] is_a: PW:0000100 ! transcription pathway is_a: PW:0000716 ! transcription factor mediated signaling pathway is_a: PW:0001116 ! vitamin A and metabolites signaling pathway relationship: part_of PW:0001007 ! vitamin A homeostasis created_by: VPetri creation_date: 2012-06-05T12:22:48Z [Term] id: PW:0001015 name: vitamin E metabolic pathway def: "Those metabolic reactions involving vitamin E - a fat-soluble vitamin which represents a class of chemical compounds known as tocopherols. The alpha- and gamma-tocopherols appear to be the main dietary forms. Vitamin E is best known for its antioxidant properties." [PubMed:PMID\: 15256801] synonym: "tocopherol metabolic pathway" RELATED [] is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins created_by: VPetri creation_date: 2012-06-11T01:34:39Z [Term] id: PW:0001016 name: vitamin K metabolic pathway def: "Those metabolic reactions involving vitamin K - a fat-soluble vitamin which represents a group of related compounds. K1 and K2 are the main naturally-occurring forms. Vitamin K is an essential cofactor for many vitamin K-dependent proteins such as several coagulation factors or the anticoagulant proteins C and S." [PubMed:PMID\: 22407747\, 21968919] is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins created_by: VPetri creation_date: 2012-06-11T01:46:25Z [Term] id: PW:0001017 name: renal cell cancer pathway def: "Renal cell cancer, although representing a small percentage of human neoplasms, has one of the highest rate of mortality amongst genitourinary cancers. Several mutated genes and associated altered pathways have been implicated in the condition but many more remain to be elucidated." [PubMed:PMID\: 22112490] synonym: "KEGG:05211" RELATED [] is_a: PW:0000606 ! urogenital cancer pathway created_by: VPetri creation_date: 2012-07-03T01:03:23Z [Term] id: PW:0001018 name: immune disease pathway is_a: PW:0000013 ! disease pathway created_by: VPetri creation_date: 2012-07-03T01:17:41Z [Term] id: PW:0001019 name: rheumatoid arthritis pathway def: "The rheumatoid arthritis is an autoimmune condition characterized by persistent inflammation. Several pro-inflammatory cytokine and chemokines are overactivated." [PubMed:PMID\: 22357455] synonym: "KEGG:05323" RELATED [] is_a: PW:0001018 ! immune disease pathway created_by: VPetri creation_date: 2012-07-03T01:18:10Z [Term] id: PW:0001020 name: basal cell carcinoma pathway def: "Basal cell carcinoma is the most common form of skin cancer that is mostly sporadic. Hedgehog signaling pathway via sonic hedgehog appears to be constitutively active. Mutations in Tp53 are also frequent." [OneLook:www.onelook.com] synonym: "KEGG:05217" RELATED [] is_a: PW:0000633 ! skin cancer pathway created_by: VPetri creation_date: 2012-07-10T12:40:11Z [Term] id: PW:0001021 name: melanoma pathway def: "Melanoma is a form of skin cancer which, despite being less common than other form of skin malignancies, it can be dangerous if not detected earlier and it accounts for the highest percentage if skin cancer related deaths. Oncogenic Nras and other mutations in downstream pathways appear to be associated with it." [OneLook:www.onelook.com] synonym: "KEGG:05218" RELATED [] is_a: PW:0000633 ! skin cancer pathway created_by: VPetri creation_date: 2012-07-10T12:47:47Z [Term] id: PW:0001022 name: asthma disease pathway def: "Asthma, a complex condition with many phenotypic manifestations, is primarily characterized by inflammation of the airways. Environmental and genetic factors contribute to it through complex and incompletely understood interactions." [OneLook:http\://www.onelook.com] synonym: "KEGG:05310" RELATED [] is_a: PW:0001018 ! immune disease pathway created_by: VPetri creation_date: 2012-07-10T01:39:57Z [Term] id: PW:0001023 name: systemic lupus erythematosus pathway def: "Systemic lupus erythematosus (SLE) is an autoimmune condition that can affect many parts of the body and which, although treatable, does not have a cure. Activation of complement and deregulations of immune regulatory and signaling pathways contribute in ways that are incompletely understood." [OneLook:http\://www.onelook.com] synonym: "KEGG:05322" RELATED [] synonym: "SLE pathway" EXACT [] is_a: PW:0001018 ! immune disease pathway created_by: VPetri creation_date: 2012-07-10T01:48:28Z [Term] id: PW:0001024 name: autoimmune thyroid disease pathway def: "Autoimmune thyroid disease (AITD) groups several conditions generally relatively mild but that can progress to serious symptoms." [localhealth:http\://www.localhealth.com] synonym: "AITD pathway" EXACT [] synonym: "KEGG:05320" RELATED [] is_a: PW:0001018 ! immune disease pathway created_by: VPetri creation_date: 2012-07-10T01:56:40Z [Term] id: PW:0001025 name: allograft rejection pathway def: "Allograft, or transplant rejection, results from the recipient's autoimmune response to the nonself antigens." [OneLook:www.onelook.com] synonym: "KEGG:05330" RELATED [] is_a: PW:0001018 ! immune disease pathway created_by: VPetri creation_date: 2012-07-11T10:38:17Z [Term] id: PW:0001026 name: graft-versus-host disease pathway def: "Graft-versus-host disease (GVHD) is a complication following transplantation of cells, tissues or organs from a genetically non-identical donor in which the donor T cells attack the host cells. Several pro-inflammatory pathways are activated as a result of damage in the host tissue induced by the procedure. GVHD is commonly associated with stem cell or bone marrow transplant." [OneLook:http\://www.onelook.com] synonym: "GVHD pathway" EXACT [] synonym: "KEGG:05332" RELATED [] is_a: PW:0001018 ! immune disease pathway created_by: VPetri creation_date: 2012-07-11T10:43:26Z [Term] id: PW:0001027 name: primary immunodeficiency disease pathway def: "Primary immunodeficiency groups disorders that result from the immune system malfunctioning that affect both cell-mediated and humoral immunity pathways." [OneLook:http\://www.onelook.com] synonym: "KEGG:05340" RELATED [] is_a: PW:0001018 ! immune disease pathway created_by: VPetri creation_date: 2012-07-11T10:56:46Z [Term] id: PW:0001028 name: infectious disease pathway def: "Infectious diseases are caused by pathogens that have gained access to the host organism and have managed to avoid the host defence mechanisms while taking over some of the host pathways." [OneLook:http\://www.onelook.com] synonym: "communicable disease pathway" RELATED [] synonym: "transmissible disease pathway" RELATED [] is_a: PW:0000013 ! disease pathway created_by: VPetri creation_date: 2012-07-11T11:07:42Z [Term] id: PW:0001029 name: substance dependence disease pathway is_a: PW:0000013 ! disease pathway created_by: VPetri creation_date: 2012-07-11T11:08:32Z [Term] id: PW:0001030 name: cocaine addiction pathway def: "Prolonged use of cocaine results in cardivascular and brain damage. Cocaine is thought to bind to the dopamine reuptake transporter thus blocking the reuptake of dopamine into nerve terminals. The resulting higher concentration of dopamine in synapses leads to overactivation of dopamine receptors such as D1 and of signaling pathways downstream of it overall believed to be critical in mediating the behavioral responses to cocaine." [KEGG:map05030, OneLook:http\://www.onelook.com] synonym: "KEGG:05030" RELATED [] is_a: PW:0001029 ! substance dependence disease pathway created_by: VPetri creation_date: 2012-07-11T11:18:43Z [Term] id: PW:0001031 name: amphetamine addiction pathway def: "Amphetamine is believed to promote an elevation in extracellular dopamine. Higher and high levels of the drug lead to overactivation of transcription factors and cofactors." [KEGG:map\:05031, OneLook:http\://www.onelook.com] synonym: "KEGG:05031" RELATED [] is_a: PW:0001029 ! substance dependence disease pathway created_by: VPetri creation_date: 2012-07-11T11:31:37Z [Term] id: PW:0001032 name: morphine addiction pathway def: "Morphine, an effective pain killer drug, can also be extremely addictive. Activation of dopamine neurons and reduction of inhibitory synaptic transmission might be associated with the effects or morphine. Changes in neuronal responses and communication may underlie the addictive behavior." [KEGG:map05032, OneLook:http\://www.onelook.com] synonym: "KEGG:05032" RELATED [] is_a: PW:0001029 ! substance dependence disease pathway created_by: VPetri creation_date: 2012-07-11T11:41:36Z [Term] id: PW:0001033 name: nicotine addiction pathway def: "Nicotine, like the other addictive substances, impacts on the dopaminergic and mesolimbic reward circuitries. Nicotine is also a ligand for the nicotinic acetylcholine receptors which are ligand-gated ion channels." [KEGG:map05033, OneLook:http\://www.onelook.com] synonym: "KEGG:05033" RELATED [] is_a: PW:0001029 ! substance dependence disease pathway created_by: VPetri creation_date: 2012-07-11T11:46:55Z [Term] id: PW:0001034 name: alcoholism pathway def: "The mechanisms of alcohol dependence, or alcoholism, are not well understood. Like in the case of other substances of abuse, alcohol may lead to stimulation of dopamine release and overactivation of dopamine-related circuitries." [KEGG:map05034, OneLook:http\://www.onelook.com] synonym: "alcohol dependence pathway" EXACT [] synonym: "KEGG:05034" RELATED [] is_a: PW:0001029 ! substance dependence disease pathway created_by: VPetri creation_date: 2012-07-11T11:57:05Z [Term] id: PW:0001035 name: arrhythmogenic right ventricular cardiomyopathy pathway def: "Arrhythmogenic right ventricular cardiomyopathy (ARVC) represents an inherited heart muscle condition leading to arrhythmia and heart failure that could results in death. Mutations in several genes and disruption of associated pathways have been implicated in the condition." [KEGG:map05412, OneLook:http\://www.onelook.com] synonym: "ARVC pathway" EXACT [] synonym: "KEGG:05412" RELATED [] is_a: PW:0000022 ! cardiomyopathy pathway created_by: VPetri creation_date: 2012-07-11T12:12:10Z [Term] id: PW:0001036 name: dilated cardiomyopathy pathway def: "Dilated cardiomyopathy (DCM) is a condition in which the heart is weakened and enlarged resulting in inefficient blood pumping. Although mostly occurring in adults, it can also affect children." [KEGG:map05414, OneLook:http\://www.onelook.com] synonym: "KEGG:05414" RELATED [] synonym: "DCM pathway" EXACT [] is_a: PW:0000022 ! cardiomyopathy pathway created_by: VPetri creation_date: 2012-07-11T12:20:46Z [Term] id: PW:0001037 name: myocarditis pathway def: "Myocarditis, a condition associated with inflammation of the heart muscle that can have both infections and non-infectious etiologies with the former being the primary cause. Viral proteins, once inside the host cells interfere with the function of host gene and they can either avoid or appropriate host pathways." [KEGG:map05416, OneLook:http\://www.onelook.com] synonym: "KEGG:05416" RELATED [] is_a: PW:0000022 ! cardiomyopathy pathway created_by: VPetri creation_date: 2012-07-11T12:29:11Z [Term] id: PW:0001038 name: maturity onset diabetes of the young pathway def: "Maturity onset diabetes of the young (MODY) represents any of a number of hereditary, monogenic forms of diabetes caused by mutations in several genes." [KEGG:map04950, OneLoook:http\://www.onelook.com] synonym: "KEGG:04950" RELATED [] synonym: "MODY pathway" EXACT [] is_a: PW:0000176 ! diabetes pathway created_by: VPetri creation_date: 2012-07-11T12:37:25Z [Term] id: PW:0001039 name: Vibrio cholerae infection pathway def: "Vibrio cholerae disease is an infection of the small intestine resulting in dehydration and electrolyte imbalance which in some cases can cause death. Cholera toxin, is one the main virulence factors of the Gram-negative Vibrio cholerae bacterium which, together with other virulence factors can invade the host." [KEGG:map05110, OneLook:http\://www.onelook.com] synonym: "KEGG:05110" RELATED [] is_a: PW:0001028 ! infectious disease pathway created_by: VPetri creation_date: 2012-07-11T12:46:22Z [Term] id: PW:0001040 name: Salmonella infection pathway def: "Salmonella, a Gram-negative bacterium of which many species exist, in humans can cause gastroenteritis or the more severe typhoid fever. Salmonella enters the host via the digestive tract; bacteria that escape the host defense machinery can survive and replicate in Salmonella-containing vacuole (SCV) whose maturation they control." [KEGG:map05132, OneLook:http\://www.onelook.com] synonym: "KEGG:05132" RELATED [] is_a: PW:0001028 ! infectious disease pathway created_by: VPetri creation_date: 2012-07-11T12:59:20Z [Term] id: PW:0001041 name: pathogenic Escherichia coli infection pathway def: "The pathogenic Escherichia coli strains EPEC and EHEC (enteropathogenic and enterohemorrhagic E. coli, respectively) can cause sever food poisoning in humans. The non-pathogenic strains are part of the gut normal flora with beneficial contributions for the host." [KEGG:map05130, OneLook:http\://www.onelook.com] synonym: "KEGG:05130" RELATED [] synonym: "pathogenic E. coli infection pathway" EXACT [] is_a: PW:0001028 ! infectious disease pathway created_by: VPetri creation_date: 2012-07-11T01:23:38Z [Term] id: PW:0001042 name: Shigella infection pathway def: "Shigella, a Gram-negative bacterium that is related to Salmonella and to Escherichia coli, is a disease causing agent in humans and primates. Shigellosis, also known as bacillary dysentery or Marlow syndrome is due to colonization of the intestinal epithelium and the subsequent evasion of the host defense machinery and use of host intracellular pathways by the bacteria." [KEGG:map05131, OneLook:http\://www.onelook.com] synonym: "bacillary dysentery pathway" RELATED [] synonym: "KEGG:05131" RELATED [] synonym: "Marlow syndrome pathway" RELATED [] synonym: "Shigellosis pathway" RELATED [] is_a: PW:0001028 ! infectious disease pathway created_by: VPetri creation_date: 2012-07-11T01:44:11Z [Term] id: PW:0001043 name: Bordetella pertussis infection pathway def: "The Gram-negative Bordetella pertusis Gram-negative is the causative agent of pertussis or whooping cough. One of its main virulence factors, pertussis toxin blocks the interaction of Galphai subunit of heterotrimeric G protein with its partner receptors. This results in unrestrained adenylyl cyclase activity and subsequent increased concentration of cAMP which affects normal intracellular signaling." [KEGG:map05133, OneLook:http\://www.onelook.com] synonym: "KEGG:05133" RELATED [] synonym: "pertussis pathway" RELATED [] is_a: PW:0001028 ! infectious disease pathway created_by: VPetri creation_date: 2012-07-11T03:37:54Z [Term] id: PW:0001044 name: Legionella infection pathway def: "Legionella, a pathogenic Gram-negative bacterium that includes species such as legionella pneumophila, causes several respiratory infections of which Legionnaires' disease is potentially fatal. L. pneumophila can grow within lung macrophages and is known to subvert several host pathways." [KEGG:map05134, OneLook:http\://www.onelook.com] synonym: "KEGG:05134" RELATED [] is_a: PW:0001028 ! infectious disease pathway created_by: VPetri creation_date: 2012-07-11T04:04:16Z [Term] id: PW:0001045 name: Staphylococcus aureus infection pathway def: "Staphylococcus aureus, a Gram-positive bacteria of which there are many species, usually colonizes the skin and mucous membranes of humans and other organisms and are mostly harmless. However, they can also cause a range of infections of which some can be extremely severe." [KEGG:map05150, OneLook:http\://www.onelook.com] synonym: "KEGG:05150" RELATED [] is_a: PW:0001028 ! infectious disease pathway created_by: VPetri creation_date: 2012-07-11T04:18:10Z [Term] id: PW:0001046 name: Mycobacterium tuberculosis infection pathway def: "Mycobacterium tuberculosis is the causative agent of most forms of tuberculosis. Once in the lung, they interfere with a number of intracellular pathways and processes." [KEGG:map05152, OneLook:http\://www.onelook.com] synonym: "KEGG:05152" RELATED [] is_a: PW:0001028 ! infectious disease pathway created_by: VPetri creation_date: 2012-07-11T04:31:42Z [Term] id: PW:0001047 name: Leishmania infection pathway def: "Leishmania is a protozoan parasite and a number of its species can infect mammals including humans. While the cutaneous leishmanianis is the most common form, others such as visceral or mucosal have also been reported. The infection results in alterations in a number of host signaling pathways." [KEGG:map5140, OneLook:http\://www.onelook.com] synonym: "KEGG:05140" RELATED [] is_a: PW:0001028 ! infectious disease pathway created_by: VPetri creation_date: 2012-07-13T11:53:50Z [Term] id: PW:0001048 name: Trypanosoma infection pathway def: "Trypanosoma is a protozoan parasite of which T brucei and cruzi are responsible for causing the sleeping sickness and Chagas disease, respectively. Several host signaling and regulatory pathways are altered in the infection." [KEGG:map5142, OneLook:http\://www.onelook.com] synonym: "" RELATED [] synonym: "KEGG:5142" RELATED [] is_a: PW:0001028 ! infectious disease pathway created_by: VPetri creation_date: 2012-07-13T12:03:02Z [Term] id: PW:0001049 name: Trypanosoma brucei infection pathway def: "Trypanosoma brucei, a protozoan parasite of the trypanosoma genus is the causative agent of sleeping sickness, also known as the African trypanosomias as its vector is the tsetse fly common to the sub-Saharan Africa. Several pro-inflammatory cytokines are overactivated. The neurological damage the infection causes is irreversible and the disease is fatal." [KEGG:map5143, OneLook:http\://www.onelook.com] synonym: "African trypanosomiasis" EXACT [] synonym: "KEGG:05143" RELATED [] is_a: PW:0001048 ! Trypanosoma infection pathway created_by: VPetri creation_date: 2012-07-13T12:14:00Z [Term] id: PW:0001050 name: Trypanosoma cruzi infection pathway def: "Trypanosoma cruzi of the genus Trypanosoma is the causative agent of the Chagas disease, also known as the American trypanosomiasis as it occurs primarily in poor areas of the Americas, mostly Central and South America. Infection interferes with a number of intracellular pathways and it appears to activate calcium signaling." [KEGG:map05142, OneLook:http\://www.onelook.com] synonym: "American trypanosomiasis" EXACT [] synonym: "Chagas disease pathway" EXACT [] synonym: "KEGG:05142" RELATED [] is_a: PW:0001048 ! Trypanosoma infection pathway created_by: VPetri creation_date: 2012-07-13T12:26:45Z [Term] id: PW:0001051 name: Plasmodium infection pathway def: "Plasmodium is a parasite of which several species can infect humans and cause malaria. Severe malaria, which is primarily caused by Plasmodium falciparum, can lead to death and the fatalities are mostly children. Deregulated induction of cytokines appears to play a role in the infection." [KEGG:map05144] synonym: "KEGG:05144" RELATED [] synonym: "malaria infection pathway" EXACT [] is_a: PW:0001028 ! infectious disease pathway created_by: VPetri creation_date: 2012-07-13T12:36:12Z [Term] id: PW:0001052 name: Toxoplasma gondii infection pathway def: "Toxoplasma gondii whose host includes various warm-blooded species including humans, is the causative agent of toxoplasmosis. The infection interferes with a number of host pathways; in its most severe manifestations it can be fatal." [KEGG:map05145, OneLook:http\://www.onelook.com] synonym: "KEGG:05145" RELATED [] is_a: PW:0001028 ! infectious disease pathway created_by: VPetri creation_date: 2012-07-13T01:00:51Z [Term] id: PW:0001053 name: Entamoeba histolyca infection pathway def: "Entamoeba histolyca is a prozoan parasite that is the causative agent of amoebiasis which affects the intestinal tissue leading to severe dysentery and ulcerations. It can also infect other tissues such as the liver to a lesser extent the brain, lungs and spleen." [KEGG:map5146, OneLook:http\://www.onelook.com] synonym: "amoebiasis infection pathway" EXACT [] synonym: "KEGG:05146" RELATED [] is_a: PW:0001028 ! infectious disease pathway created_by: VPetri creation_date: 2012-07-13T01:13:24Z [Term] id: PW:0001054 name: influenza A virus infection pathway def: "Influenza A virus is the causative agent of seasonal epidemics and occasional pandemics of influenza which affects the respiratory system." [KEGG:map05164] synonym: "KEGG:05164" RELATED [] is_a: PW:0001028 ! infectious disease pathway created_by: VPetri creation_date: 2012-07-13T01:21:37Z [Term] id: PW:0001055 name: hepatitis C virus infection pathway def: "Hepatitis C virus is the causative agent of hepatitis C, a chronic liver disease in humans. The virus interferes with several signaling and regulatory pathways in the host cells." [KEGG:map05160, OneLook:http\://www.onelook.com] synonym: "KEGG:05160" RELATED [] is_a: PW:0001028 ! infectious disease pathway created_by: VPetri creation_date: 2012-07-13T01:22:51Z [Term] id: PW:0001056 name: Herpes simplex virus infection pathway synonym: "KEGG:05168" RELATED [] is_a: PW:0001028 ! infectious disease pathway created_by: VPetri creation_date: 2012-07-16T01:24:16Z [Term] id: PW:0001057 name: Epstein-Barr virus infection pathway synonym: "KEGG:05169" RELATED [] is_a: PW:0001028 ! infectious disease pathway created_by: VPetri creation_date: 2012-07-16T01:26:38Z [Term] id: PW:0001058 name: measles infection pathway def: "Measles virus (MV) of the genus Morbilivirus is the causative agent of the condition that bears its name. The condition causes immunosuppression and several MV proteins are thought to interfere with the normal host immune responses." [KEGG:map05162, OneLook:http\://wwwonelook.com] synonym: "KEGG:05162" RELATED [] is_a: PW:0001028 ! infectious disease pathway created_by: VPetri creation_date: 2012-07-16T01:37:38Z [Term] id: PW:0001059 name: oxidative phosphorylation pathway def: "Oxidative phosphorylation is the coupling of the electron transport chain and the ATP biosynthetic pathways. The electron transfer chain generates an electrochemical gradient that drives the phosphorylation of ADP. Under certain circumstances the two may be uncoupled." [Gene Ontology:GO\:0006119, KEGG:map00190, PubMed:PMID\: 21625217\, 19760284] synonym: "KEGG:00190" RELATED [] is_a: PW:0000033 ! energy metabolic pathway created_by: VPetri creation_date: 2012-07-18T09:38:02Z [Term] id: PW:0001060 name: primary bile acid biosynthetic pathway def: "Primary bile acids, cholic and chenodeoxycholic acids, are derived from cholesterol in the liver. Upon conjugation with glycine or taurine they can be secreted into the intestine." [KEGG:map00120, OneLook:http\://www.onelook.com] synonym: "KEGG:00120" RELATED [] is_a: PW:0000039 ! bile acid biosynthetic pathway created_by: VPetri creation_date: 2012-07-18T10:47:50Z [Term] id: PW:0001061 name: secondary bile acid biosynthetic pathway def: "Secondary bile acids, deoxycholic and lithocholic acids, are synthesized from the primary ones by intestinal bacteria. like the primary bile acids, they need to be conjugated to glycine or taurine prior to secretion." [KEGG:map00121, OneLook:http\://www.onelook.com] is_a: PW:0000039 ! bile acid biosynthetic pathway created_by: VPetri creation_date: 2012-07-18T10:54:59Z [Term] id: PW:0001062 name: lacto-series glycosphingolipid metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of lacto-series type of glycosphingolipids." [PubMed:PMID\:1 7976918] synonym: "KEGG:00601" RELATED [] is_a: PW:0000733 ! glycosphingolipid metabolic pathway created_by: VPetri creation_date: 2012-07-19T01:18:59Z [Term] id: PW:0001063 name: lipoic acid metabolic pathway def: "The metabolic reactions involving lipoic acid, a compound derived from octanoic acid that contains two sulfur centers. Lipoic acid is a co-factor for the pyruvate dehydrogenase complex responsible for the irreversible decarboxylation of pyruvate to acetyl-CoA." [KEGG:map00785, OneLook:http\://www.onelook.com, PubMed:PMID\: 17052205] synonym: "KEGG:00785" RELATED [] is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins created_by: VPetri creation_date: 2012-07-19T01:37:53Z [Term] id: PW:0001064 name: phosphonate and phosphinate metabolic pathway def: "Those metabolic reactions involving phosphonate and phosphinate, organic compounds that contain carbon-phosphorus bonds and which can be synthesized by bacteria and protists." [KEGG:mapp00440] is_a: PW:0000132 ! metabolic pathway of other amino acids created_by: VPetri creation_date: 2012-07-23T03:43:37Z [Term] id: PW:0001065 name: interstrand cross link repair pathway def: "Interstrand cross links (ICL) of DNA can be induced by both endogenous and exogenous ligands. ICL if not repaired will lead to cell death. ICL repair pathway, also known as Fanconi anemia pathway is the cellular response to this type of DNA damage." [PubMed:PMID\: 20713514\, 21605559\, 19061902] synonym: "Fanconi anemia pathway" EXACT [] synonym: "ICL repair pathway" EXACT [] synonym: "KEGG:03460" RELATED [] is_a: PW:0000663 ! DNA break and strand repair pathway created_by: VPetri creation_date: 2012-07-24T09:31:12Z [Term] id: PW:0001066 name: ribosome biogenesis pathway def: "The pathway of ribosome biogenesis underlies the production of ribosomal RNAs, of core ribosomal and associated proteins and of small nucleolar RNAs along with their accurate assembly into the mature ribosome. It starts in the nucleolus with the final assembly and maturation steps in the cytoplasm. Alterations in the pathway result in specific phenotypes collectively known as ribosomopathies." [PubMed:PMID\: 20875629\, 20194897] synonym: "KEGG:03008" RELATED [] relationship: part_of PW:0000101 ! translation pathway created_by: VPetri creation_date: 2012-07-25T03:15:38Z [Term] id: PW:0001067 name: altered ribosome biogenesis pathway def: "Alterations in the pathway result in specific phenotypes collectively known as ribosomopathies." [PubMed:PMID\: 20194897] is_a: PW:0001066 ! ribosome biogenesis pathway is_a: PW:0001068 ! altered translation pathway created_by: VPetri creation_date: 2012-07-25T04:19:34Z [Term] id: PW:0001068 name: altered translation pathway is_a: PW:0000101 ! translation pathway is_a: PW:0000290 ! altered pathway of replication, repair, gene expression and protein biosynthesis created_by: VPetri creation_date: 2012-07-25T04:21:04Z [Term] id: PW:0001069 name: gonadotropin-releasing hormone signaling pathway def: "Gonadotropin-releasing hormone signaling pathway induces the synthesis and secretion of luteinizing and follicle-stimulating hormones from the pituitary." [PUbMed:PMID\: 22024993] synonym: "GnRH signaling pathway" EXACT [] synonym: "KEGG:04912" RELATED [] synonym: "luteinizing hormone-releasing hormone signaling pathway" RELATED [] is_a: PW:0000467 ! peptide and protein hormone signaling pathway created_by: VPetri creation_date: 2012-07-30T11:02:37Z [Term] id: PW:0001070 name: luteinizing hormone signaling pathway is_a: PW:0000467 ! peptide and protein hormone signaling pathway created_by: VPetri creation_date: 2012-07-30T11:12:02Z [Term] id: PW:0001071 name: follicle-stimulating hormone signaling pathway def: "Follicle-stimulating hormone signaling is important for the normal development and function of the ovaries and testes." [PubMed:PMID\: 21372710] synonym: "FSH signaling pathway" EXACT [] is_a: PW:0000467 ! peptide and protein hormone signaling pathway created_by: VPetri creation_date: 2012-07-30T11:13:34Z [Term] id: PW:0001072 name: synaptic vesicle cycle pathway def: "The cycle of synaptic vesicle exocytosis and neurotransmitter release and the subsequent endocytosis and recycling of synaptic vesicles at nerve terminals." [PubMed:PMID\: 15217342] synonym: "KEGG:04721" RELATED [] relationship: part_of PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse created_by: VPetri creation_date: 2012-07-30T03:31:02Z [Term] id: PW:0001073 name: spliceosome pathway def: "The spliceosome is a multimegadalton ribonucleoprotein complex that removes the exons to produce the mature mRNA, including several mature mRNAs from a single RNA transcript via alternative splicing. Its structural complexity is paralleled by an equally complex assembly pathway with many and sometimes reversible steps." [PubMed:PMID\: 22480731\, 21441581\, 22010274] synonym: "KEGG:03040" RELATED [] is_a: PW:0000085 ! pathways of replication, repair, gene expression, protein biosynthesis created_by: VPetri creation_date: 2012-07-31T09:43:57Z [Term] id: PW:0001074 name: hydrophobic amino acid metabolic pathway def: "Those metabolic reactions involving hydrophobic, uncharged amino acids. Hydrophobic amino acids include alanine, valine, isoleucine, leucine and methionine with hydrocarbon side chains and the phenylalanine, tyrosine and tryptophan with bulky, aromatic side chains." [MCE library:Handbooks of biochemistry] is_a: PW:0000011 ! amino acid metabolic pathway created_by: VPetri creation_date: 2012-07-31T10:30:19Z [Term] id: PW:0001075 name: hydrophilic amino acid metabolism def: "Those metabolic reactions involving hydrophilic, polar amino acids. The hydrophilic amino acids include the charged acidic aspartic acid and glutamic acid whose salts are glutamate and aspartate, respectively, the charged basic lysine and arginine and the uncharged polar asparagine, glutamine, serine and threonine. Histidine, whose side chain contains an imidazole can shift from positively charged to neutral." [MCW library:Handbooks of biochemistry] is_a: PW:0000011 ! amino acid metabolic pathway created_by: VPetri creation_date: 2012-07-31T10:39:29Z [Term] id: PW:0001076 name: special amino acid metabolic pathway def: "Those metabolic reactions involving special amino acids. The special amino acids include cysteine whose side chain contains a sulfhydryl group, glycine whose side chain is a hydrogen atom and proline whose side chain bends to form a ring and hose rigidity limits the folding abilities of proteins around proline residues." [MCW library:Nahdbooks of biochemistry] is_a: PW:0000011 ! amino acid metabolic pathway created_by: VPetri creation_date: 2012-07-31T10:47:08Z [Term] id: PW:0001077 name: amino acid metabolic pathway (KEGG) def: "Those metabolic reactions involving amino acids as listed in the Kyoto Encyclopedia of Genes and Genomes (KEGG)." [KEGG:http\://www.genome.jp/kegg/] is_a: PW:0000011 ! amino acid metabolic pathway created_by: VPetri creation_date: 2012-07-31T10:56:10Z [Term] id: PW:0001078 name: cysteine and methionine metabolic pathway synonym: "KEGG:00270" RELATED [] is_a: PW:0001077 ! amino acid metabolic pathway (KEGG) created_by: VPetri creation_date: 2012-07-31T11:04:19Z [Term] id: PW:0001079 name: proline metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of proline, a non-essential amino acid that could be essential in certain cases." [OneLook:http\://www.onelook.com] is_a: PW:0001076 ! special amino acid metabolic pathway created_by: VPetri creation_date: 2012-07-31T11:05:36Z [Term] id: PW:0001080 name: valine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of valine, an essential amino acid." [OneLook:http\://www.onelook.com] is_a: PW:0001074 ! hydrophobic amino acid metabolic pathway created_by: VPetri creation_date: 2012-07-31T11:06:01Z [Term] id: PW:0001081 name: lysine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of lysine, an essential amino acid." [OneLook:http\://www.onelook.com] is_a: PW:0001075 ! hydrophilic amino acid metabolism created_by: VPetri creation_date: 2012-07-31T11:07:54Z [Term] id: PW:0001082 name: arginine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of arginine, a non-essential amino acid that could be essential in certain cases." [OneLook:http\://www.onelook.com] is_a: PW:0001075 ! hydrophilic amino acid metabolism created_by: VPetri creation_date: 2012-07-31T11:08:11Z [Term] id: PW:0001083 name: asparagine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of asparagine, a non-essential amino acid." [OneLook:http\://www.onelook.com] is_a: PW:0001075 ! hydrophilic amino acid metabolism created_by: VPetri creation_date: 2012-07-31T11:08:57Z [Term] id: PW:0001084 name: serine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of serine, a non-essential amino acid that could be essential in certain cases." [OneLook:http\://www.onelook.com] is_a: PW:0001075 ! hydrophilic amino acid metabolism created_by: VPetri creation_date: 2012-07-31T11:10:13Z [Term] id: PW:0001085 name: threonine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of threonine, an essential amino acid." [OneLook:http\://www.onelook.com] is_a: PW:0001075 ! hydrophilic amino acid metabolism created_by: VPetri creation_date: 2012-07-31T11:11:19Z [Term] id: PW:0001086 name: glutamine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glutamine, a non-essential amino acid that could be essential in certain cases." [OneLook:http\://www.onelook.com] is_a: PW:0001075 ! hydrophilic amino acid metabolism created_by: VPetri creation_date: 2012-07-31T11:12:05Z [Term] id: PW:0001087 name: isoleucine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of isoleucine, an essential amino acid." [OneLook:http\://www.onelook.com] is_a: PW:0001074 ! hydrophobic amino acid metabolic pathway created_by: VPetri creation_date: 2012-07-31T11:18:29Z [Term] id: PW:0001088 name: leucine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of leucine, an essential amino acid." [OneLook:http\://www.onelook.com] is_a: PW:0001074 ! hydrophobic amino acid metabolic pathway created_by: VPetri creation_date: 2012-07-31T11:18:56Z [Term] id: PW:0001089 name: serotonin signaling pathway via receptors engaging G alphai protein family def: "Serotonin signaling via receptor family 1 and 5 primarily engages G alphai protein family resulting in inhibition of adenylate cyclases and reduction of intracellular cAMP. There are five receptors subtypes in family 1 and one in the human family 5." [PubMed:PMID\: 20945968] is_a: PW:0000854 ! serotonin signaling pathway created_by: VPetri creation_date: 2012-08-01T03:14:20Z [Term] id: PW:0001090 name: serotonin signaling pathway via receptors engaging G alphaq protein family def: "Serotonin signaling via receptor family 2 engages G alphaq protein family resulting in activation of phospholipase C, mobilization of calcium ions and production of inositol 1,4,5-triphosphate (IP3) and diacylglycerol (DAG). There are three receptors subtypes in family 2." [PubMed:PMID\: 20945968] is_a: PW:0000854 ! serotonin signaling pathway created_by: VPetri creation_date: 2012-08-01T03:20:07Z [Term] id: PW:0001091 name: serotonin signaling pathway via receptors engaging G alphas protein family def: "Serotonin signaling via receptor family 4, 6, and 7 engages G alphas protein family resulting in activation of adenylyl cyclases and increased concentration of cAMP. There are seven receptor subtypes in family 4 and only one in families 6 and 7." [PubMed:PMID\: 20945968] is_a: PW:0000854 ! serotonin signaling pathway created_by: VPetri creation_date: 2012-08-01T03:28:58Z [Term] id: PW:0001092 name: serotonin signaling via receptor family 3 def: "Serotonin family 3 receptor is a ligand-gated Na+/K+ channel with two receptor subtypes and their heterodimerization is believed to be necessary for their function. Serotonin signaling results in depolarization of plasma membrane." [PubMed:PMID\: 20945968] is_a: PW:0000854 ! serotonin signaling pathway created_by: VPetri creation_date: 2012-08-01T03:33:01Z [Term] id: PW:0001093 name: bile acid signaling pathway def: "Bile acid binds to and activates several nuclear receptors such as the farnesoid X and liver X receptors." [PubMed:PMID\: 22414897] is_a: PW:0000716 ! transcription factor mediated signaling pathway is_a: PW:0000959 ! lipid signaling pathway created_by: VPetri creation_date: 2012-08-03T10:23:51Z [Term] id: PW:0001094 name: altered estrogen signaling pathway def: "Disregulated estrogen signaling is associated with the growth and development of breast cancers; estrogen mediated transcription is constitutively active in more than 50% of cases." [PubMed:PMID\:9608332] is_a: PW:0000507 ! estrogen signaling pathway is_a: PW:0000787 ! altered sex steroids signaling pathway created_by: VPetri creation_date: 2012-08-03T10:51:00Z [Term] id: PW:0001095 name: zidovudine drug pathway def: "The pharmacokinetics and pharmacodynamics pathway of zidovudine, an anti-viral drug used for the treatment of HIV infection. It belongs to the family of nucleoside analog reverse transcriptase inhibitors." [PharmGKB:http\://www.pharmgkb.org] synonym: "ZDV drug pathway" RELATED [] is_a: PW:0000996 ! antiinfective drug pathway created_by: VPetri creation_date: 2012-08-03T11:18:59Z [Term] id: PW:0001096 name: zidovudine pharmacokinetics pathway def: "The pathway of processing - absorption, distribution, metabolism or elimination - of zidovudin, a drug used for the treatment of HIV. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org] is_a: PW:0001095 ! zidovudine drug pathway created_by: VPetri creation_date: 2012-08-03T11:23:05Z [Term] id: PW:0001097 name: zidovudine pharmacodynamics pathway def: "The pathway of zidovudin-target interaction and of the biochemical or physiological responses to them. Zidovuding is a drug used for the treatment of HIV infection. Zidovudin, in its active triphoshate form, inhibits HIV-1 reverse transcriptase activity. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:www.pharmgkb.org] is_a: PW:0001095 ! zidovudine drug pathway created_by: VPetri creation_date: 2012-08-03T11:25:55Z [Term] id: PW:0001098 name: tramadol drug pathway def: "The pharmacokinetics and pharmacodynamics pathway of tramadol, an analgesic used for the treatment of moderate to moderately severe pain. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [OneLook:http\://www.onelook.com, PharmGKB:http\://www.pharmgkb.org] is_a: PW:0000923 ! nervous system drug pathway created_by: VPetri creation_date: 2012-08-03T11:37:59Z [Term] id: PW:0001099 name: tramadol pharmacokinetics pathway def: "The pathway of processing - absorption, distribution, metabolism or elimination - of tramadol, an analgesic used in the treatment of pain. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.onelook.com] is_a: PW:0001098 ! tramadol drug pathway created_by: VPetri creation_date: 2012-08-03T11:41:01Z [Term] id: PW:0001100 name: tramadol pharmacodynamics pathway def: "The pathway of tramadol-target interaction and of the biochemical or physiological responses to drug. Tramadol is an analgesic used for the treatment of pain. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org] is_a: PW:0001098 ! tramadol drug pathway created_by: VPetri creation_date: 2012-08-03T11:41:20Z [Term] id: PW:0001101 name: viral carcinogenesis pathway def: "A number of human viruses have been shown to be associated/contribute to approximately 10 to 15% of cancers. The viral particles encode oncogenes whose escape from the host defense system impacts on many cellular pathways and promotes tumor development." [OneLook:http\://www.onelook.com, PubMed :PMID\: 21102637\, 21445966\, 20971551] synonym: "KEGG:05203" RELATED [] is_a: PW:0000605 ! cancer pathway created_by: VPetri creation_date: 2012-09-06T16:03:33Z [Term] id: PW:0001102 name: altered hypoxia inducible factor pathway def: "A hypoxia inducible pathway that deviates from what its normal course should be. Mutations in the von Hippel-Lindau (Vhl), the E3 ubiquitin ligase which targets Hif alpha for degradation under normoxic conditions, lead to a constitutively active pathway regardless the levels of oxygen. Mutations in Vhl and a number of other genes have been implicated in renal cancers." [PubMed:PMID\: 22406000] is_a: PW:0000360 ! hypoxia inducible factor pathway is_a: PW:0000361 ! altered oxygen homeostasis pathway created_by: VPetri creation_date: 2012-10-04T11:04:37Z [Term] id: PW:0001103 name: acid-base homeostasis pathway def: "The pathways that respond to and control the levels of protons, bicarbonate and carbon dioxide and of ammonia the cells. Several sensing pathways , i.e., prompting intracellular signaling cascade, and transport have been identified as critical players. The kidneys play a major role along with the respiratory system." [PubMed:PMID\: 22362904] is_a: PW:0000355 ! homeostasis pathway created_by: VPetri creation_date: 2012-10-04T12:58:08Z [Term] id: PW:0001104 name: pH sensing signaling pathway def: "The pathway that respond to increases or decreases in protons, or pH levels and whose signaling aim at restoring systemic acid-base balance. Several G-protein coupled receptor (GPCRs) and ion channel mediated signaling have been reported in the literature." [PubMed:PMID\:20683624] synonym: "proton-activated signaling pathway" RELATED [] is_a: PW:0001105 ! acid and base sensing signaling pathway relationship: part_of PW:0001103 ! acid-base homeostasis pathway created_by: VPetri creation_date: 2012-10-04T13:14:56Z [Term] id: PW:0001105 name: acid and base sensing signaling pathway def: "The signaling pathway elicited by changes in pH and bicarbonate levels." [PubMed:PMID\: 20683624] is_a: PW:0000003 ! signaling pathway created_by: VPetri creation_date: 2012-10-04T13:39:02Z [Term] id: PW:0001106 name: bicarbonate sensing signaling pathway def: "The signaling pathway elicited by increased levels of bicarbonate. Bicarbonate results from the instantaneous dissociation of carbonic acid, the end product of carbonic anhydrase hydration of exogenous or metabolically produced carbon dioxide." [PubMed:PMID\: 20683624] is_a: PW:0001105 ! acid and base sensing signaling pathway relationship: part_of PW:0001103 ! acid-base homeostasis pathway created_by: VPetri creation_date: 2012-10-04T13:43:43Z [Term] id: PW:0001107 name: sorafenib drug pathway def: "The pharmacokinetics and pharmacodynamics pathway of sorafenib, a multikinase inhibitor used in the treatment of cancer, in particular for advanced renal cell carcinoma. The drug binds to the intracytoplasmic domain of tyrosine kinase receptors blocking the downstream signaling cascade. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PubMed:PMID\: 22263843\, 21419641] is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway created_by: VPetri creation_date: 2012-10-04T15:24:58Z [Term] id: PW:0001108 name: sorafenib pharmacokinetics pathway def: "The pathway of processing - absorption, distribution, metabolism or elimination - of sorafenib. The drug was the first oral multikinase inhibitor approved for the treatment of renal cell carcinoma. Genetic variations can result in changes in the availability of the drug." [PharmGKB:http\://www.pharmgkb.org/pathway/PA165959537, PubMed:PMID\: 21419641] is_a: PW:0001107 ! sorafenib drug pathway created_by: VPetri creation_date: 2012-10-04T15:30:52Z [Term] id: PW:0001109 name: sorafenib pharmacodynamics pathway def: "The pathway of sorafenib-target interaction and of the biochemical or physiological responses to drug. Sorafenib is the first multikinase inhibitor approved for the treatment of renal cell carcinoma. The drug binds to the intracytoplasmic domain of tyrosine kinase receptors blocking the downstream signaling cascade. Genetic variations can cause differences in the response of the organism to the drug." [PharmGKB:http\://www.pharmgkb.org/pathway/PA165959584, PubMed:PMID\: 21419641] is_a: PW:0001107 ! sorafenib drug pathway created_by: VPetri creation_date: 2012-10-04T15:31:17Z [Term] id: PW:0001110 name: sunitinib drug pathway def: "The pharmacokinetics and pharmacodynamics pathway of sunitinib, a multikinase inhibitor used in the treatment of cancer, in particular for advanced renal cell carcinoma. The drug binds to the intracytoplasmic domain of tyrosine kinase receptors blocking the downstream signaling cascade. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PubMed:PMID\: 22328304] is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway created_by: VPetri creation_date: 2012-10-04T15:54:48Z [Term] id: PW:0001111 name: tocilizumab pharmacokinetics pathway is_a: PW:0000928 ! tocilizumab drug pathway created_by: VPetri creation_date: 2012-10-04T15:57:07Z [Term] id: PW:0001112 name: tocilizumab pharmacodynamics pathway is_a: PW:0000928 ! tocilizumab drug pathway created_by: VPetri creation_date: 2012-10-04T15:57:36Z [Term] id: PW:0001113 name: sunitinib pharmacokinetics pathway def: "The pathway of processing - absorption, distribution, metabolism or elimination - of sunitinib. The drug is a multikinase inhibitor approved for the treatment of renal cell carcinoma. Genetic variations can result in changes in the availability of the drug." [PubMed:PMID\: 22328304] is_a: PW:0001110 ! sunitinib drug pathway created_by: VPetri creation_date: 2012-10-04T15:58:20Z [Term] id: PW:0001114 name: sunitinib pharmacodynamics pathway def: "The pathway of sunitinib-target interaction and of the biochemical or physiological responses to drug. Sunitinib is a multikinase inhibitor approved for the treatment of renal cell carcinoma. The drug binds to the intracytoplasmic domain of tyrosine kinase receptors blocking the downstream signaling cascade. Genetic variations can cause differences in the response of the organism to the drug." [PubMed:PMID\: 2232830] is_a: PW:0001110 ! sunitinib drug pathway created_by: VPetri creation_date: 2012-10-04T15:58:42Z [Term] id: PW:0001115 name: non-visual phototransduction pathway def: "A signaling cascade triggered by light in the visible and red spectrum whose sensor appears to be cytochrome c oxidase, the terminal enzyme of the electron transfer chain, and which relies on a retrograde mitochondrion-to-nucleus pathway that translates in the upregulation of various genes. Unlike the visual phototransduction, this pathway does not require vitamin A metabolites." [PubMed:PMID\: 20681024] is_a: PW:0001008 ! photosignal transduction pathway created_by: VPetri creation_date: 2012-10-11T09:27:12Z [Term] id: PW:0001116 name: vitamin A and metabolites signaling pathway is_a: PW:0001012 ! vitamin and vitamin metabolites signaling pathway created_by: VPetri creation_date: 2012-10-11T10:05:25Z [Term] id: PW:0001117 name: retinol mediated signaling pathway def: "A signaling pathway mediated by a signaling complex for which retinol or vitamin A appears to be an essential docking molecule and redox sensor. The pathway may play an important role in regulating the tricarboxylic acid cycle through the pyruvate dehydrogenase complex by mechanisms that are still to be elucidated." [PubMed:PMID\: 21763457] is_a: PW:0001116 ! vitamin A and metabolites signaling pathway created_by: VPetri creation_date: 2012-10-11T10:06:06Z [Term] id: PW:0001118 name: altered energy metabolic pathway is_a: PW:0000262 ! altered metabolic pathway created_by: VPetri creation_date: 2012-10-12T16:31:32Z [Term] id: PW:0001119 name: altered citric acid cycle pathway def: "Defects in components of the citrate cycle have been shown to relate to several types of cancer. For instance, mutations in fumarate hydratase are associated with renal cancer, in succinate dehydrogenase in renal as well as paragangliomas and pheochromocytomas. Mutations in isocitrate dehydrogenase have also been implicated in several types of cancer. Defects in this central metabolic network result in unwanted activation of hypoxia inducible factor whose target genes are involved in angiogenesis, erythropoiesis, glycolysis, among others." [PubMed:PMID\: 21764377\, 23001348] is_a: PW:0000026 ! citric acid cycle pathway is_a: PW:0000359 ! altered energy homeostasis pathway is_a: PW:0001118 ! altered energy metabolic pathway created_by: VPetri creation_date: 2012-10-12T16:32:05Z [Term] id: PW:0001120 name: bevacizumab drug pathway def: "The pharmacokinetics and pharmacodynamics pathway of bevacizumab, a humanized monoclonal antibody that inhibits VEGF activity. It is used for the treatment of several types of advanced cancers. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PubMed:PMID\: 22594892] is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway created_by: VPetri creation_date: 2012-10-15T08:49:28Z [Term] id: PW:0001121 name: bevacizumab pharmacokinetics pathway def: "The pathway of processing - absorption, distribution, metabolism or elimination - of bevacizumab, a VEGF inhibitor used in the treatment of several types of tumors. Genetic variations can result in changes in the availability of the drug." [PubMed:PMID\: 22594892\:] is_a: PW:0001120 ! bevacizumab drug pathway created_by: VPetri creation_date: 2012-10-15T08:56:41Z [Term] id: PW:0001122 name: bevacizumab pharmacodynamics pathway def: "The pathway of bevacizumab-target interaction and of the biochemical or physiological responses to drug. The drug is an inhibitor of VEGF and is used in the treatment of several types of cancers such as for instance renal cell carcinoma. VEGF is a target of hypoxia inducible factor pathway, which is constitutively active in the condition. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PubMed:PMID\: 22594892] is_a: PW:0001120 ! bevacizumab drug pathway created_by: VPetri creation_date: 2012-10-15T08:57:45Z [Term] id: PW:0001123 name: axitinib drug pathway def: "The pharmacokinetics and pharmacodynamics pathway of axitinib, a receptor tyrosine kinase inhibitor used in the treatment of renal cell carcinoma as well as other tumors. Angiogenic factors such as vascular endothelial or platelet derived growth factors are direct and indirect targets of hypoxia inducible factor pathway, constitutively active in renal cell carcinoma. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PubMed:PMID\: 22170007] is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway created_by: VPetri creation_date: 2012-10-19T11:46:54Z [Term] id: PW:0001124 name: axitinib pharmacokinetics pathway def: "The pathway of processing - absorption, distribution, metabolism or elimination - of axitinib, a receptor tyrosine kinase inhibitor used in the treatment of renal cell carcinoma and other tumors. Axitinib is a selective second generation inhibitor of vascular endothelial growth factor receptors 1, 2 and 3. Genetic variations can result in changes in the availability of the drug." [PubMed:PMID\: 22170007] is_a: PW:0001123 ! axitinib drug pathway created_by: VPetri creation_date: 2012-10-19T11:49:57Z [Term] id: PW:0001125 name: axitinib pharmacodynamics pathway def: "The pathway of axitinib-target interaction and of the biochemical or physiological responses to drug. Axitinib is a receptor tyrosine kinase inhibitor used in the treatment of renal cell carcinoma as well as other tumors. Axitinib is a selective second generation inhibitor of vascular endothelial growth factor receptors 1, 2 and 3. Genetic variations can cause differences in the response of the organism to the drug." [PubMed:PMID\: 22170007] is_a: PW:0001123 ! axitinib drug pathway created_by: VPetri creation_date: 2012-10-19T11:50:16Z [Term] id: PW:0001126 name: everolimus drug pathway def: "The pharmacokinetics and pharmacodynamics pathway of everolimus, an inhibitor of mTOR pathway used in the treatment of several types of tumors, including renal cell carcinoma. Hypoxia inducible factor (HIF) pathway is constitutively active in the disease; mTOR regulates the translation of HIF-alpha gene. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PubMed:PMID\: 20456985] is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway created_by: VPetri creation_date: 2012-10-19T13:54:12Z [Term] id: PW:0001127 name: everolimus pharmacokinetics pathway def: "The pathway of processing - absorption, distribution, metabolism or elimination - of everolimus, an inhibitor of mTOR pathway used in the treatment of renal cell carcinoma and other tumors. Genetic variations can result in changes in the availability of the drug." [PubMed:PMID\: 20456985\, 22624503] is_a: PW:0001126 ! everolimus drug pathway created_by: VPetri creation_date: 2012-10-19T15:41:34Z [Term] id: PW:0001128 name: everolimus pharmacodynamics pathway def: "The pathway of everolimus-target interaction and of the biochemical or physiological responses to drug. The drug is an inhibitor of mTOR pathway and is used in the treatment of renal cell carcinoma and other types of tumors. Genetic variations can cause differences in the response of the organism to the drug." [PubMed:PMID\: 20456985] is_a: PW:0001126 ! everolimus drug pathway created_by: VPetri creation_date: 2012-10-19T15:45:06Z [Term] id: PW:0001129 name: temsirolimus drug pathway def: "The pharmacokinetics and pharmacodynamics pathway of temsirolimus, an inhibitor of mTOR pathway used in the treatment of renal cell carcinoma and other types of tumors. Hypoxia inducible factor (HIF) pathway is constitutively active in renal cell carcinoma; HIF-alpha translation is under the control of mTOR pathway. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PubMed:PMID\: 20456985] is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway created_by: VPetri creation_date: 2012-10-19T16:04:14Z [Term] id: PW:0001130 name: temsirolimus pharmacokinetics pathway def: "The pathway of processing - absorption, distribution, metabolism or elimination - of temsirolimus, an inhibitor of mTOR pathway used in the treatment of renal cell carcinoma and other tumors. Genetic variations can result in changes in the availability of the drug." [PubMed:PMID\: 20456985] is_a: PW:0001129 ! temsirolimus drug pathway created_by: VPetri creation_date: 2012-10-19T16:12:25Z [Term] id: PW:0001131 name: temsirolimus pharmacodynamics pathway def: "The pathway of temsirolimus-target interaction and of the biochemical or physiological responses to drug. The drug is an inhibitor of mTOR pathway and is used in the treatment of renal cell carcinoma and other types of tumors. Genetic variations can cause differences in the response of the organism to the drug." [PubMed:PMID\: 20456985] is_a: PW:0001129 ! temsirolimus drug pathway created_by: VPetri creation_date: 2012-10-19T16:12:49Z [Term] id: PW:0001132 name: pazopanib drug pathway def: "The pharmacokinetics and pharmacodynamics pathway of pazopanib, a receptor tyrosine kinase inhibitor used in the treatment of renal cell carcinoma as well as other tumors. Angiogenic factors such as vascular endothelial or platelet derived growth factors are direct and indirect targets of hypoxia inducible factor pathway, constitutively active in renal cell carcinoma. Genetic variations can result in changes in drug availability and can cause differences in the response of the organism to the drug." [PubMed:PMID\: 20456985] is_a: PW:0000919 ! antineoplastic and immunomodulatory drug pathway created_by: VPetri creation_date: 2012-10-19T16:13:35Z [Term] id: PW:0001133 name: pazopanib pharmacokinetics pathway def: "he pathway of processing - absorption, distribution, metabolism or elimination - of pazopanib. The drug is a multikinase inhibitor approved for the treatment of renal cell carcinoma. Genetic variations can result in changes in the availability of the drug." [PubMed:PMID\: 20456985] is_a: PW:0001132 ! pazopanib drug pathway created_by: VPetri creation_date: 2012-10-19T16:13:55Z [Term] id: PW:0001134 name: pazopanib pharmacodynamics pathway def: "The pathway of pazopanib-target interaction and of the biochemical or physiological responses to drug. Pazopanib is a selective multikinase inhibitor approved for the treatment or renal cell carcinoma. The drug binds to the intracytoplasmic domain of tyrosine kinase receptors blocking the downstream signaling cascade. Genetic variations can cause differences in the response of the organism to the drug." [PubMed:PMID\: 20456985] is_a: PW:0001132 ! pazopanib drug pathway created_by: VPetri creation_date: 2012-10-19T16:14:15Z [Term] id: PW:0001135 name: parathyroid hormone signaling pathway def: "Parathyroid hormone (PTH) signaling acts to increase the concentration of calcium in the blood. Receptor type 1 is abundantly expressed in kidney and bone and is the bona fide receptor through which PTH accomplishes its function. Receptor type 2 was until recently considered an orphan receptor but it signals through a PTH-related hormone. Both receptor types are G-protein coupled (GPCR) receptors." [PubMed:PMID\: 21777186\, 19857544\, 23060860] synonym: "PTH signaling pathway" RELATED [] is_a: PW:0000467 ! peptide and protein hormone signaling pathway relationship: part_of PW:0000371 ! calcium homeostasis pathway created_by: VPetri creation_date: 2012-11-01T09:32:46Z [Term] id: PW:0001136 name: fatty acid elongation pathway def: "The C16 palmitate product of fatty acid biosynthetic pathway can be esterifed to triacylglycerol or converted to longer chain saturated and unsaturated fatty acid molecules by elongases and desaturases, depending on the needs of the cell. The elongation pathway takes place in the endoplasmic reticulum or in the mitochondrion. Longer chain fatty acids are present in certain specialized tissues; for instance, myelin contains large amounts of C22 and C24 molecules." [KEGG:map00062] synonym: "KEGG:00062" RELATED [] is_a: PW:0000058 ! fatty acid metabolic pathway created_by: VPetri creation_date: 2012-11-02T15:26:41Z [Term] id: PW:0001137 name: unsaturated fatty acid biosynthetic pathway def: "The C16 palmitate product of fatty acid biosynthetic pathway can be esterifed to triacylglycerol or converted to longer chain saturated and unsaturated fatty acid molecules by elongases and desaturases, depending on the needs of the cell. Unsaturated fatty acids are essential membrane components." [KEGG:map01040] synonym: "KEGG:01040" RELATED [] is_a: PW:0000058 ! fatty acid metabolic pathway created_by: VPetri creation_date: 2012-11-02T15:40:42Z [Term] id: PW:0001138 name: ether lipid metabolic pathway def: "Those metabolic reactions involving ether lipids, lipid molecules in which one or several of the carbons on glycerol has an ether linkage to an alkyl chain. Ether lipids are constituents of cell membrane; some metabolites could act as signaling second messengers or carry out antioxidant functions." [KEGG:map00565, OneLook:http\://www.onelook.com] synonym: "KEGG:00565" RELATED [] is_a: PW:0001137 ! unsaturated fatty acid biosynthetic pathway created_by: VPetri creation_date: 2012-11-02T16:17:56Z [Term] id: PW:0001139 name: calcium transport pathway def: "Calcium is pumped into organelles or outside the cell by pumps and exchangers to maintain the low calcium concentration necessary for cell viability. Many type of channels, some calcium-selective, others of lower selectivity or calcium-permeant, allow for the flow of calcium from external sources or internal stores into the cell to initiate many signaling events. The movement of calcium ions, which controls and maintains the calcium gradient, and calcium signaling, which the gradient promotes, are inextricably connected in the fabric of calcium homeostasis." [PubMed:PMID\: 18083096\, 12838335] is_a: PW:0000593 ! metal ion transport pathway relationship: part_of PW:0000371 ! calcium homeostasis pathway created_by: VPetri creation_date: 2012-11-05T09:59:28Z [Term] id: PW:0001140 name: calcium/calcium-mediated signaling pathway def: "Calcium signaling impacts on a large and diverse spectrum of cellular processes such as gene expression and cell death, proliferation, muscle contraction and energy metabolism, learning, memory and synaptic plasticity. Calcium acts in signal transduction as a first as well as a second messenger. Calcium transport, which controls and maintains the calcium gradient, and calcium signaling, which the gradient promotes, are inextricably connected in the fabric of calcium homeostasis." [PubMed:PMID\: 19243429\, 18083096\, 17574670\, 12838335] synonym: "KEGG:04020" RELATED [] is_a: PW:0000003 ! signaling pathway relationship: part_of PW:0000371 ! calcium homeostasis pathway created_by: VPetri creation_date: 2012-11-05T10:53:28Z [Term] id: PW:0001141 name: calcium signaling pathway via the calcium-sensing receptor def: "Calcium signaling through the calcium-sensing receptor controls the secretion of parathyroid hormone in the parathyroid glands and calcium reabsorption in the kidneys. Calcium is considered the main physiological agonist but other divalent cations can also activate the receptor. The G protein coupled receptor (GPCR) is believed to engage several types of Galpha proteins and to have many other interacting partners. The pathway leads to activation of MAPK cascades and transactivation of epidermal growth factor/neuregulin signaling but the molecular details are not fully understood." [PubMed:PMID\: 20729338] is_a: PW:0001140 ! calcium/calcium-mediated signaling pathway created_by: VPetri creation_date: 2012-11-07T13:22:52Z [Term] id: PW:0001142 name: clathrin-mediated endocytosis pathway def: "The clathrin-mediated endocytosis pathway involves clathrin-coated vesicles used for the engulfment of material." [PubMed:PMID\:16985500, Wikipedia:http\://en.wikipedia.org/wiki/Endocytosis] is_a: PW:0000281 ! endocytosis pathway created_by: VPetri creation_date: 2012-11-08T15:18:18Z [Term] id: PW:0001143 name: caveolae-mediated endocytosis pathway is_a: PW:0000281 ! endocytosis pathway created_by: VPetri creation_date: 2012-11-08T15:40:59Z [Term] id: PW:0001144 name: micropinocytosis pathway is_a: PW:0000281 ! endocytosis pathway created_by: VPetri creation_date: 2012-11-08T15:41:28Z [Term] id: PW:0001145 name: phagocytosis pathway def: "Phagocytosis pathway is used for the removal of unwanted material such as dying cells and also of foreign material. As such is also part of the immune response. Various receptors on the surface of a phagocytic cell will recognize/bind material and induce signaling cascades." [PubMed:PMID\: 16985500\, 9039775] synonym: "KEGG:04145" RELATED [] is_a: PW:0000281 ! endocytosis pathway created_by: VPetri creation_date: 2012-11-08T15:41:47Z [Term] id: PW:0001146 name: Fc gamma receptor mediated signaling pathway def: "The signaling cascade initiated by an activated Fc gamma receptor. Fc receptors are classified by the type of antibody they recognize; thus, Fc gamma receptors bind IgG, the most common type of antibody. Fc gamma receptors belong to the immunoglobulin superfamily." [PubMed:PMID\: 15466916] synonym: "KEGG:04666" RELATED [] is_a: PW:0001145 ! phagocytosis pathway is_a: PW:0001150 ! Fc receptor mediated signaling pathway created_by: VPetri creation_date: 2012-11-08T16:04:35Z [Term] id: PW:0001147 name: eicosanoid signaling pathway via peroxisome proliferator-activated receptor gamma synonym: "eicosanoid signaling pathway via PPARG" EXACT [] synonym: "KEGG:03320" RELATED [] is_a: PW:0000565 ! eicosanoid signaling pathway created_by: VPetri creation_date: 2012-11-08T16:29:11Z [Term] id: PW:0001148 name: hepatitis B virus infection pathway def: "Hepatitis B virus (HBV) is the causative agent of hepatitis B, an inflammatory condition of the liver affecting people in parts of Asia and Africa. The virus interferes with a number of regulatory and signaling pathways in the host." [Wikipedia:http\://en.wikipedia.org/wiki/Hepatitis_B] synonym: "KEGG:05161" RELATED [] is_a: PW:0001028 ! infectious disease pathway created_by: VPetri creation_date: 2012-11-09T08:47:08Z [Term] id: PW:0001149 name: human T-lymphotropic virus type 1 infection pathway def: "The human T-lymphotropic virus type 1 (HTLV-1) is a pathogenic retrovirus causing a type of cancer known as adult T-cell leukemia and lymphoma and a demyelinating condition referred to as HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP). A viral regulatory protein known as Tax, which is a transcriptional co-factor, interferes with a number of signaling pathways in the host." [wikipedia:http\://en.wikipedia.org/wiki/Human_T-lymphotropic_virus] synonym: "HTLV-1 infection pathway" EXACT [] synonym: "KEGG:05166" RELATED [] is_a: PW:0001028 ! infectious disease pathway created_by: VPetri creation_date: 2012-11-09T09:00:17Z [Term] id: PW:0001150 name: Fc receptor mediated signaling pathway def: "Fc receptors mediated signaling exerts important regulatory and modulatory roles in immunity. Fc receptors are classified by the type of antibody they recognize. They are widely expressed on immune system cells and a number of other cell types. With one exception, they mediate activating signaling cascades." [PubMed:PMID\:17981207] is_a: PW:0000235 ! adaptive immune response pathway is_a: PW:0000820 ! signaling pathway in the adaptive immune response created_by: VPetri creation_date: 2012-11-09T10:50:09Z [Term] id: PW:0001151 name: Fc epsilon receptor mediated signaling pathway def: "The signaling cascade initiated by an activated Fc gamma receptor. Fc receptors are classified by the type of antibody they recognize; thus, Fc epsilon receptors bind IgE antibody." [PubMed:PMID\:17981207] synonym: "KEGG:04664" RELATED [] is_a: PW:0001150 ! Fc receptor mediated signaling pathway created_by: VPetri creation_date: 2012-11-09T11:02:34Z [Term] id: PW:0001152 name: steroid biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of steroids. Notable examples include cholesterol and steroid hormones." [wikipedia:http\://en.wikipedia.org/wiki/Steroid] synonym: "KEGG:00100" RELATED [] is_a: PW:0000453 ! isoprenoid biosynthetic pathway created_by: VPetri creation_date: 2012-11-09T15:05:33Z [Term] id: PW:0001153 name: caffeine metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of caffeine, a xanthine alkaloid found in the seeds, leaves, and fruit of certain plants that humans use as a stimulant." [KEGG:00232, wikipedia:http\://en.wikipedia.org/wiki/Caffeine] synonym: "KEGG:00232" RELATED [] is_a: PW:0000147 ! metabolic pathway of secondary metabolites created_by: VPetri creation_date: 2012-11-09T15:14:24Z [Term] id: PW:0001154 name: glycosaminoglycan degradation pathway def: "Those metabolic reactions involved in the degradation of glycosaminoglycans." [KEGG:00531] synonym: "KEGG:00531" RELATED [] is_a: PW:0000157 ! glycosaminoglycan metabolic pathway created_by: VPetri creation_date: 2012-11-09T15:21:46Z [Term] id: PW:0001155 name: butirosin and neomycin biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of butirosin and neomycin -aminoglycoside antibiotics produced by Bacillus circulans and Streptomyces fradiae, respectively." [OneLook:http\://www.onelook.com] synonym: "KEGG:00524" RELATED [] is_a: PW:0000147 ! metabolic pathway of secondary metabolites created_by: VPetri creation_date: 2012-11-09T15:34:08Z [Term] id: PW:0001156 name: glycerolipid metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glycerolipids which are composed of mono-, di-, and tri-substituted glycerols. Triacylglycerol, or triglyceride, is the best known example." [OneLook:http\://www.onelook.com] synonym: "KEGG:00561" RELATED [] is_a: PW:0000010 ! lipid metabolic pathway created_by: VPetri creation_date: 2012-11-09T15:42:02Z [Term] id: PW:0001157 name: ether lipid metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of ether lipids. On these molecules one or more of the carbon atoms of glycerol is bonded to an alkyl group via an ether linkage." [wikipedia:http\://en.wikipedia.org/wiki/Ether_lipid] synonym: "KEGG:00565" RELATED [] is_a: PW:0000010 ! lipid metabolic pathway created_by: VPetri creation_date: 2012-11-09T15:51:41Z [Term] id: PW:0001158 name: alpha-linoleic acid metabolic pathway def: "Those enzymatic reactions involved in the synthesis, utilization or degradation of alpha-linoleic acid - an unsaturated omega-3 fatty acid. alpha-linoleic acid is an essential fatty acid that humans and other animals cannot synthesize and must obtain from diet." [wikipedia:http\://en.wikipedia.org/wiki/Alpha-Linolenic_acid] synonym: "KEGG:00592" RELATED [] is_a: PW:0000058 ! fatty acid metabolic pathway created_by: VPetri creation_date: 2012-11-09T16:06:00Z [Term] id: PW:0001159 name: aminoacyl-tRNA biosynthetic pathway def: "Aminoacyl-tRNA, or transfer RNA (tRNA) carries amino acids to ribosomes and is part of the translation pathway. tRNAs are specific for the amino acids with which they are associated. Their synthesis involves adenylation of the amino acid followed by its transfer; both steps require ATP." [wikipedia:http\://en.wikipedia.org/wiki/Aminoacyl-tRNA] synonym: "KEGG:00970" RELATED [] relationship: part_of PW:0000101 ! translation pathway created_by: VPetri creation_date: 2012-11-09T16:13:47Z [Term] id: PW:0001160 name: RNA transport pathway def: "The pathway thereby various RNA molecules synthesized in the nucleus are exported to the cytoplasm to be further processed such as the protein-coding mRNA or to fulfill particular functions." [PubMed:PMID\: 21776079\, 15519698] synonym: "KEGG:03013" RELATED [] synonym: "RNA nuclear export pathway" RELATED [] is_a: PW:0000085 ! pathways of replication, repair, gene expression, protein biosynthesis is_a: PW:0000103 ! transport pathway created_by: VPetri creation_date: 2012-11-12T15:25:17Z [Term] id: PW:0001161 name: RNA degradation pathway def: "The turnover pathway of RNA molecules produced by the three eukaryotic polymerases. It includes the degradation of defective molecules by the RNA surveillance or decay pathway." [PubMed:PMID\:19239894] synonym: "KEGG:03018" RELATED [] is_a: PW:0000085 ! pathways of replication, repair, gene expression, protein biosynthesis created_by: VPetri creation_date: 2012-11-12T15:38:14Z [Term] id: PW:0001162 name: chemical compound signaling pathway is_a: PW:0000003 ! signaling pathway created_by: VPetri creation_date: 2012-11-13T09:02:24Z [Term] id: PW:0001163 name: cannabinoid signaling pathway def: "Cannabinoids are a class of rather diverse chemical compounds of which some, like endocannabinoids are naturally produced by the body in humans and other animals, while others are found in plants or are synthesized. Signaling is mediated by the cannabinoid receptors that are G protein coupled (GPCR) receptors. The endogenous cannabinoids are lipids and the signaling route is referred to as retrograde as travel 'backwards' from the postsynaptic to the presynaptic cell." [wikipedia:http\://en.wikipedia.org/wiki/Cannabinoid] is_a: PW:0001162 ! chemical compound signaling pathway created_by: VPetri creation_date: 2012-11-13T09:02:41Z [Term] id: PW:0001164 name: endocannabinoid signaling pathway def: "The signaling pathway initiated by the endogenous cannabinoids that activate the G protein coupled (GPCR) cannabinoid receptors and utilize a retrograde route from the postsynaptic to the presynaptic neuron." [PubMed:PMID\: 21531987] synonym: "KEGG:04723" RELATED [] synonym: "retrograde endocannabinoid signaling pathway" RELATED [] is_a: PW:0000959 ! lipid signaling pathway is_a: PW:0001163 ! cannabinoid signaling pathway created_by: VPetri creation_date: 2012-11-13T09:19:29Z [Term] id: PW:0001165 name: lipid neurotransmitter metabolic pathway is_a: PW:0000407 ! neurotransmitter metabolic pathway created_by: VPetri creation_date: 2012-11-13T09:46:51Z [Term] id: PW:0001166 name: endocannabinoid metabolic pathway is_a: PW:0001165 ! lipid neurotransmitter metabolic pathway created_by: VPetri creation_date: 2012-11-13T09:47:42Z [Typedef] id: part_of name: part_pf