format-version: 1.2 date: 09:06:2011 17:33 saved-by: VPetri auto-generated-by: OBO-Edit 2.1-beta1 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/ "Online collection of dictionaries"] 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 "Online collection of dictionaries"] 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 "Online collection of dictionaries"] 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 involved in the oxidation, breakdown and synthesis of carbohydrates in the tissue. The breakdown can be utilized by the body for energy." [OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Associated GO term", PubMed :PMID\: 11027944; 1152757 "Review article"] 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 "Associated GO term", KEGG:map04010 "Associated KEGG map", PubMed:PMID\: 14570565; PMID\: 14976517; PMID\: 17229475; PMID\: 17306385 "PW review articles on MAPK", Reactome:REACT_634.5 "Associated entry at Reactome"] synonym: "MAPK signaling pathway" RELATED [] 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 an oncogenic effect and is responsible for tumorigenesis in adults." [PubMed:PMIDs\: 12573432\, 15041171\, 15001769 "A series of articles"] 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 "Associated GO term", KEGG:map04210 "Associated KEGG map", OneLook\, PubMed:PMID\: 18414491; 12196263] 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 "Online collection of dictionaries"] 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. Some of these metabolic pathways can give rise to non-standard amino acid - for instance carnitine or homocysteine - and the two pathway categories in these cases are entwined." [In House:In House PW dictionary "Definition supplied by the PW editorial team."] 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 and enzyme regulation." [InHouse:PW directory "Reference compiled by the PW editorial team"] 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 "Definition compiled by the PW editorial team based on the information from a number of sources"] 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 "Definition supplied by the PW editorial team"] 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 "Definition provided by the PW editorial team", KEGG:map05010 "Associated KEGG map"] 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 "Definition supplied by the PW editorial team", KEGG:map05014 "Associated KEGG map"] synonym: "ALS" 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 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 "Associated KEGG map", PubMed:2004\, v.20 (3)\, 146-154. "Article in Trends in Genetics"] 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 "Associated KEGG map", PubMed:2004\, v.101 (15)\, 5500-5505. "Definition compiled from an article in PNAS"] 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 "Associated KEGG map", OnerLook:www.onelook.com "Online collection of dictionaries - Dorland's."] 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 "A term compiled by the PW editorial team."] 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 "Online collection of dictionaries"] 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. Cardiomyopathies can generally be categorized into two groups: ischemic cardiomyopathy and nonischemic cardiomyopathy (2)." [OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Associated GO term", MCW:Handbook of cellular and molecular immunology, OneLook:www.onelook.com "Online collection of dictionaries"] 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." [Gene Ontology:GO\:0006954 "Associated GO term", OneLook:www.onelook.com "Online collection of dictionaries", PubMed:PMID\: 20303867\, 20303872\, 15364056\, 16281932\, 16226680 "Review articles in PubMed"] 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 "Associated KEGG map", OneLook\, MCW libraries:www.onelook.com; Voet & Voet \"Fundamentals of Biochemistry\" 3rd edition "Online collection of dictionaries, textbook"] is_a: PW:0000005 ! carbohydrate metabolic pathway [Term] id: PW:0000026 name: citrate cycle pathway def: "The series of chemical reactions that are central to all aerobic cells and constitute the citrate cycle. Also known as the tricarboxylic acid cycle, the TCA or Krebs cycle, it is the second of three metabolic pathways that are involved in fuel molecule catabolism and ATP production." [Gene Ontology:GO\:0006099 "Associated GO term", KEGG:map00020 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries", Reactome:REACT_1046.3 "Related entry at Reactome"] synonym: "Krebs cycle" RELATED [] synonym: "TCA cycle" RELATED [] is_a: PW:0000005 ! carbohydrate metabolic pathway [Term] id: PW:0000027 name: glutamate metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glutamate - a salt, ester, or nonionic form of glutamic acid. Glutamate is also the major excitatory neurotransmitter." [OneLook:www.onelook.com "Online collection of dictionaries"] comment: Definition compiled based on the information available for glutamate at OneLook is_a: PW:0000011 ! amino acid metabolic pathway is_a: PW:0000445 ! excitatory neurotransmitter metabolic pathway [Term] id: PW:0000028 name: alanine and aspartate metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of alanine and aspartate - two non-essential amino acids required for the breakdown of glucose and proteins as well as for protein biosynthesis." [OneLook:www.onelook.com "Online collection of dictionaries"] comment: The definition was compiled based on the information on alanine and aspartate available at OneLook. is_a: PW:0000011 ! amino acid metabolic pathway [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 biosynthsis involves the condensation of C2 units; it requires seven enzymatic reactions which are carried out by the multifuinctional enzyme fatty acid synthase." [Gene Ontology:GO\:0006633 "Related GO term", KEGG:map00061 "Associated KEGG map", MCW Library:Biochemistry Handbook "Voet & Voet, 3rd edition"] synonym: "fatty acid biosynthesis (path 2)" 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 "Online collection of dictionaries - Wikipedia"] 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 "Online collection of dictionaries - Wikipedia"] is_a: PW:0000012 ! nucleotide metabolic pathway [Term] id: PW:0000033 name: energy metabolic pathway def: "Those metabolic reactions whose role is to release or to provide energy." [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000002 ! classic metabolic pathway [Term] id: PW:0000034 name: oxidative phosphorylation pathway def: "Those metabolic reactions involved in coupling ATP synthesis to the respiratory or electron transport chain. The electrons derived from the oxidation of glucose and lipids or the degradation of amino acids, are passed to oxygen through a number of steps and carriers. The free energy of electron transport drives the synthesis of ATP." [Gene Ontology:GO\:0006119 "Associated GO term", KEGG:map00190 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000033 ! energy metabolic pathway [Term] id: PW:0000035 name: ATP synthetic pathway def: "Those metabolic reactions involved in the synthesis of adenosine triphosphate (ATP) - a molecule present in all living cells which serves as an energy source for many metabolic processes and is required for the synthesis of ribonucleic acid." [Gene Ontology:GO\:0006754 "Related GO term", OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000033 ! energy metabolic pathway [Term] id: PW:0000036 name: nitrogen metabolic pathway def: "Those metabolic reactions involving nitrogen and nitrogenous compounds." [KEGG:map00910 "Associated KEGG map", PW InHouse dictionary:PW InHouse dictionary "Definition compiled by the PW editorial team."] is_a: PW:0000033 ! energy metabolic pathway [Term] id: PW:0000037 name: sulfur metabolic pathway def: "Those metabolic reactions involving sulfur or compounds that contain sulfur such as cysteine, methionine and glutathione." [KEGG:map00920 "Associated KEGG map", PW InHouse dictionary:PW InHouse dictionary "Definition compiled from a number of sources by the PW editorial team."] 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 "Decision of the PW editorial board"] 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, lithocholic, and ursodeoxycholic acids - are formed from the primary bile acids through the action of intestinal bacteria." [OneLook:www.onelook.com "Online collection of dictionaries - Dorland's."] 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 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries", PubMed:PMID\: 17926129] is_a: PW:0000453 ! isoprenoid 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, a ketohexose, and of mannose, an aldohexose." [KEGG:map00051 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Related GO term", KEGG:map00052 "Associated KEGG map", OneLook:www.onelook.com "Adapted from Dorland's Medical Dictionary"] 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 "Related GO term", KEGG:00620 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries", Reactome:REACT_2071.3 "Related entry at Reactome"] 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 "Decision of the PW editorial board."] is_obsolete: true [Term] id: PW:0000045 name: pentose phosphate pathway def: "Those metabolic reactions involved in the generation of reducing equivalents and 5 carbon (pentose) sugars." [Gene Ontology:GO\:0006098 "Associated GO term", KEGG:map00030 "Associated KEGG map", OneLook\, PubMed:www.oneloook.com; http\://www.ncbi.nlm.nih.gov/sites/entrez "Various online resources and articles in PubMed", Reactome:REACT_1859.1 "Associated entry at Reactome"] synonym: "hexose monophosphate pathway (shunt)" 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 stereoisoforms." [Gene Ontology:GO\:0006020 "Related GO term", OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Online collection of dictionaries"] comment: Definition compiled based on the information available at oneLook is_a: PW:0000011 ! amino acid metabolic pathway [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 vya remethylation pathway or leads to the synthesis of cysteine and derivatives via transulfuration pathway." [MCW library book:Homocysteine in Health and Disease "Cambridge Press, 2001"] is_a: PW:0000011 ! 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 thiol group containing amino acid." [OneLook:www.onelook.com "Online collection of dictionaries"] comment: Reference compiled based on the information available at OneLook for cysteine. is_a: PW:0000011 ! 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 "Online collection of dictionaries"] comment: Definition compiled based on the information on arginine and proline available at OneLook is_a: PW:0000011 ! amino acid metabolic pathway [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 proton acceptor." [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000011 ! amino acid metabolic pathway [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 "Online collection of dictionaries"] is_a: PW:0000011 ! amino acid metabolic pathway [Term] id: PW:0000053 name: phenylalanine metabolic pathway def: "Those metabolic reactions that are part of the phenylalanine cycle - an essential amino acid that the body can not manufacture." [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000011 ! amino acid metabolic pathway [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 "Online collection of dictionaries"] is_a: PW:0000011 ! amino acid metabolic pathway [Term] id: PW:0000055 name: nucleotide sugar metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of nucleotide sugars." [InHouse:PW dictionary "Definition compiled by the PW editorial team", KEGG:map00520 "Related KEGG map"] 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 "Related GO term", KEGG:map00195 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries - Dorland's."] is_a: PW:0000033 ! energy metabolic pathway [Term] id: PW:0000057 name: carbon fixation pathway def: "The pathway thereby photosynthetic organisms such as plants convert inorganic carbon (usually carbon dioxide) into organic compounds (usually carbohydrates)." [OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Related GO term", KEGG:map00071 "Associated KEGG map", PW InHouse dictionary:PW In House Dictionary "Definition compiled from a number of dictionaries"] 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 "Online collection of dictionaries - Dorland's", Gene Ontology:GO\:0060291 "Related GO term", KEGG:map04720 "Associated KEGG map"] synonym: "LTP" RELATED [] 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 "Related GO term", KEGG:map04730 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] comment: Adapted from Wikipedia at OneLook synonym: "LTD" RELATED [] 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. Ascorbate is a derivative of ascorbic acid, or vitamin C." [KEGG:map00053 "Associated KEGG map", OneLook:www\,onelook.com "Online collection of dictionaries"] is_a: PW:0000005 ! carbohydrate metabolic pathway [Term] id: PW:0000063 name: glyoxylate and dicarboxylate metabolic pathway 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." [KEGG:map00640 "Associated KEGG map", OneLook\, Online:www.onelook.com; http\://dl.clackamas.cc.or.us/ch106-04/nomencla1.htm "Definition compiled from both OneLook and Google"] 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, perfumery." [KEGG:map00650 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries - Wikipedia - definition"] 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 "Online collection of dictionaries - Dorland's definition", KEGG:map00720 "Associated KEGG map"] is_a: PW:0000033 ! energy metabolic pathway [Term] id: PW:0000068 name: methane metabolic pathway def: "Those pathways involving methane - a colorless, odorless inflammable gas produced by decomposition of organic matter, which may explode when mixed with air or oxygen. Methane is the first member of a homologous series of saturated hydrocarbons, including butane, ethane, hexane, pentane and propane." [Gene Ontology:GO\:0015947 "Related GO term", KEGG:map00680 "Associated KEGG map", OneLook:www.onelook.com "online collection of dictionaries"] 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 "Related GO term", KEGG:map00072 "Related KEGG map", MCW Libraries:QU4 V876f 2008 "Vouet Biocehmistry, third edition", OneLook:www.onelook.com "Online collection of dictionaries", Reactome:REACT_1861.3 "Related entry at Reactome"] comment: The definition was compiled using the information from a number of biological/medical dictionaries available at OneLook 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 "Related KEGG map", 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 "Online collection of dictionaries"] is_a: PW:0000011 ! amino acid metabolic pathway [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 "Online collection of dictionaries"] is_a: PW:0000011 ! amino acid metabolic pathway [Term] id: PW:0000073 name: lysine degradation pathway def: "Those metabolic reactions involved in the degradation of lysine" [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000011 ! amino acid metabolic pathway [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] is_a: PW:0000011 ! amino acid metabolic pathway [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 "Online collection of dictionaries"] is_a: PW:0000011 ! amino acid metabolic pathway [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 "Online collection of dictionaries"] 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. Since neuronal uptake and neuronal receptor sensitivity to beta-alanine have been demonstrated, the compound may be a false transmitter replacing GABA. A rare genetic disorder, hyper-beta-alaninemia, has been reported" [Gene Ontology:GO\:0019482 "Related GO term", KEGG:map00410 "Associated KEGG map", Onelook:www.onelook.com "Online collection of dictionaries - Dorland's medical dictionary"] is_a: PW:0000132 ! metabolic pathway of other amino acids [Term] id: PW:0000078 name: cyanoamino acid metabolic pathway 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 "Decision of the PW editorial board"] is_obsolete: true [Term] id: PW:0000080 name: Duplicated term - Selenoamino acid metabolism def: "OBSOLETE. Duplicated term. Use PW:0000133" [PW dictionary:InHouse dictionary "Decision of the PW editorial board."] is_obsolete: true [Term] id: PW:0000081 name: D-glutamine and D-glutamate metabolic pathway is_a: PW:0000132 ! metabolic pathway of other amino acids [Term] id: PW:0000082 name: D-arginine and D-ornithine metabolic pathway is_a: PW:0000132 ! metabolic pathway of other amino acids [Term] id: PW:0000083 name: D-alanine metabolic pathway 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 "Decision of the PW editorial board"] 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 "Definitions compiled by the PW editorial team based on the information from a number of sources."] 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 "Associated GO term", KEGG:map04110 "Associated KEGG map", Reactome:REACT_152.3 "Associated entry at Reactome", reactomee:www.reactome.org "Reactome offers a number of pathways and related proteins"] comment: Adapted from O'Connell and Walwarth, Genome KnowledgeBase 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 "Associated entry at Reactome", Reactomee:www.reactome.org "Reactpme offers a number of pathways and related proteins"] 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 "Associated entry at Reactome", reactome:www.reactome.org "Definition based on the information provided by Reactome"] 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 "Associated entry at Reactome", Reactome:www.reactome.org "Based on the information available at Reactome."] 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 "Associated entry at Reactome", Reactome:www.reactome.org "Based on the information available at Reactome"] 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 "Associateed entry at Reactome", Reactome:www.reactome.org "Based on the information provided at Reactome"] 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 "Associated entry at Reactome", Reactome:www.reactome.org "Based on the information available at Reactome"] 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 "Associated entry at Reactome", Reactome:www.reactome.org "Definition based on the information available at Reactome"] 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 "Associated GO term", InHouse:InHouse PW dictionary "Definition compiled by the PW editorial team based on the information from a number of sources", Reactome:REACT_1538.1 "Associated entry at Reactome"] 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 "Definition compiled by the PW editorial board based on the information at the Reactome.", Reactome:REACT_1538.1 "Associated entry at Reactome"] 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 "Definition compiled by the PW editorial board based on the information at the Reactome.", Reactome:REACT_828.2 "Associated entry at Reactome"] 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 "Based on the entry atReactome", Reactome:REACT_2137.2 "Associated entry at Reactome"] 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 formation of the pre-initiation replication complex takes place during the preceeding G1 phase. The separation of pre-initiation and activation assures a better control of the pathway." [General:PW board "General definition"] 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 ine the DNA strand(s)." [Gene Ontology:GO\:0006281 "Associated GO term", PW InHouse:Cell\, 2004\, v. 117\, p171-184. "Generalized definition based on an article on specific pathways for double-strand break repair.", Reactome:REACT_216.1 "Associated entry at Reactome"] 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 "Definition compiled by the PW editorial team based on the information from a number of sources"] 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 "Associated GO term", InHouse:InHouse PW dictionary "Definition compiled by the PW editorial team based on the information from a number of sources"] 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 "Related GO term", KEGG:map04010 "Related KEGG map", PubMed:PMID\: 15035987; 17229475; 17306385; 17112607 "Adapted from an article in Cell", Reactome:REACT_962.4; REACT_1482.4 "Realted entries at Reactome"] 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 "Various resources"] 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 "Related KEGG map", PubNed:PMID\: 14744432 "Article in Cell", Reactome:REACT_964.1 "Associated entry at Reactome"] 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 "Related KEGG map", PubMed:PMID\: 14744432 "Article published in Cell", Reactome:REACT_1059.1 "Associated entry at Reactome"] 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 "Definition compiled by the PW editorial team"] 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 "Related GO term", KEGG:map00930 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries."] 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 "Related GO term", KEGG:map00363 "Related KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Associated KEGG map", Onelook:www.onelook.com "Onelook collection of dictionaries."] 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 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries."] 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 "Associated KEGG map", 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 "Related GO term", KEGG:map00791 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries."] 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 "Related GO term", KEGG:map00362 "Associated KEGG map", Online :Appl. Env. Microbiology\, 2004\, v.70(9)\, p4861-70. "Article found online"] 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 "Related GO term", KEGG:map00632 "Associated KEGG map", Online:http\://umbbd.ahc.umn.edu/benz/benz_map.html "Online description"] 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 "Related GO term", KEGG:map00629 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Related GO term", KEGG:, KEGG:map00628 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries."] 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 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries."] 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 "Online collection of dictionaries."] 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 "Related GO term", KEGG:map00643 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries."] 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 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries."] 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 "Related GO term", KEGG:map04340 "Associated KEGG map", PubMed:PMID\: 15205520 \, PMID\: 15596107\, PMID\: 12495844 "Articles dealing with the Hedgehog signaling pathway"] 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 "Review article in PubMed"] relationship: part_of PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse [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 "Review article in PubMed", Reactome:REACT_13433.1 "Related entry at Reactome"] 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 "Related GO term", PubMed:Science\, 2002\, v296\, p1636-39 "Review article", Reactome:REACT_14797.1 "Related entry at Reactome"] 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 "Related GO term", InHouse:PW dictionary "Definition compiled by the PW editorial team", Reactome:REACT_1309.1 "Associated entry at Reactome"] 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 "Related GO term", InHouse:PW dictionary "Definition compiled by the PW editorial team", Reactome:REACT_1366.1 "Associated entry at Reactome"] 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 "Related GO term", InHouse:PW dictionary "Definition compiled by the PW editorial team", Reactome:REACT_1371.1 "Associated entry at Reactome"] 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 "Associated GO term", KEGG:map03410 "Assocciated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries", Reactome:REACT_1104.1 "Associated entry at Reactome"] synonym: "BER pathway" 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 "Associated GO term", KEGG:map03420 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries", Reactome:REACT_1826.2 "Associated entry at Reactome"] synonym: "NER pathway" RELATED [] 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 and the two pathway categories in these cases are entwined." [InHouse:PW InHouse dictionary "Definition compiled bi the PW editorial board"] 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." [KEGG:map00450 "Associated KEGG map", Technical glossary:http\://morelife.org/glossary/ "Online technical glossary"] 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 "Related GO term", KEGG:map00480 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000132 ! metabolic pathway of other amino acids is_a: PW:0000217 ! metabolic pathway of prosthetic groups, electron carriers and reductants [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 - compounds that are essential for the functioning of enzymes and/or are necessary for the normal metabolic functioning of the body." [InHouse:In House PW dictionary "Definition compiled by the PW editorial team", Reactome:REACT_11193.1 "Related entry at Reactome"] 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. Animals obtain thiamine from food. Thiamine insufficiency results in a condition called beriberi." [Gene Ontology:GO\:0006772 "Related GO term", KEGG:map00730 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] 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. It occurs in several products and is an essential nutrient for man." [Gene Ontology:GO\:0006771 "Related GO term", KEGG:map00740 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] 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 participates in many metabolic processes. A number of organisms can carry out de novo synthesis of vitamin B6; humans derive it from diet." [Gene Ontology:GO\:0042816 "Related GO term", KEGG:map00750 "Associated KEGG map", OneLook\, NIH :www.onelook.com and linkss "Wikipedia and links to NIH Office of Dietary Supplements"] 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. Biotin assists in various metabolic reactions and processes." [Gene Ontology:GO\:0006768 "Related GO term", KEGG:map00780 "Associated KEGG map", OneLook:www.onelook.com> "Online collection of dictionaries, Wikipedia", Reactome:REACT_11153.3 "Related entry at Reactome"] 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 f 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." [PubMed:PMID\: 15298442; 11001804; PMID\: 15166809 "Review articles in PubMed"] 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 derived from diet are converted to retinol by tissues." [Gene Ontology:GO\:0042572 "Related GO term", KEGG:map00830 "Associated KEGG map", PneLook:www.onelook.com "Online collection of dictionaries - Wikipedia"] is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins [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 "Related GO term", KEGG:map00130 "Related KEGG map", Onelook\, PubMed:PMID\: 14757233 "Dorland/s and a review article in PubMed"] 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. Deregulation of the systems is implicated in a number of metabolic disorders." [Gene Ontology:GO\:0008286 "Related GO term", KEGG:map4910 "Associated KEGG map", PubMed:PMID\: 12169433 "Review article", Reactome:REACT_498.5 "Related entry at Reactome"] synonym: "" 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 "Related GO term", KEGG:ko04120 "Related KEGG map", PubMed:2001\, v.27\, 171-179. "Definition compiled based on a review article published in Neuropathology and Applied Neurobiology"] 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 "Decision of the PW editorial board"] 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 refers to the carbohydrate moiety of glycoproteins, proteoglycans and glycolipids." [OneLook:www.onelook.com "Online collection of dictionaries"] 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 normal growth, development or reproduction of the plant or organism. Many of the chemicals that plants or microorganisms produce are secondary metabolites, including antibiotics." [OneLook:www.onelook.com "Online collection of dictionaries"] 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 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 "Related GO term", KEGG:map00520 "Related KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] comment: Based on Dorland's Medical dictionary 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 "Related GO term", KEGG:map00561 "Associated KEGG map", MCW library:QU4 M235b 2009 "McKee handbook of biochemistry - fourth edition", OneLook:www.onelook.com "Online collection of dictionaries"] synonym: "triglyceride metabolic pathway" RELATED [] is_a: PW:0000010 ! lipid 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 is a cyclic hexahydric alcohol with six possible isomers." [Gene Ontology:GO\:0043647 "Related GO term", KEGG:map00562 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Online collection of dictionaries"] 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 "McKee Handbook of Biochemistry - fourth edition"] 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 "Related GO term", MCW Libraries:QU4 V876f 2008 "Voet & Voet Biochemistry, third edition", OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Adapted from an article in the Journal of Mammary Gland Biology and Neoplasia"] 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 "Associated GO term", 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 "Associated GO term", 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 anchor." [Gene Ontology:GO\:0006506 "Related GO term", InHouse:InHouse PW dictionary "Definition compiled by the PW editorial board", KEGG:map00563 "Associated KEGG map"] synonym: "GPI anchor biosynthesis" RELATED [] is_a: PW:0000146 ! glycan metabolic pathway [Term] id: PW:0000162 name: glycosphingolipid biosynthetic pathway - lactoseries is_a: PW:0000733 ! glycosphingolipid metabolic pathway [Term] id: PW:0000163 name: glycosphingolipid biosynthetic pathway - neolactoseries is_a: PW:0000733 ! glycosphingolipid 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 "Related GO term", OneLook:www.onelook.com "Online collection of dictionaries - Dorland's."] 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 "Associated KEGG map"] is_a: PW:0000132 ! metabolic pathway of other amino acids [Term] id: PW:0000166 name: nicotinate and nicotinamide metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of nicotinate - the dissociated form of nicotinic acid and of nicotinamide - the amide of niacin or vitamin B3." [KEGG:map00760 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins [Term] id: PW:0000167 name: pantothenate and CoA biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of panthotenic acid, also known as vitamin B5. Vitamin B5 is an essential nutrient, is necessary for the synthesis of coenzyme A (CoA) and is also involved in the metabolism of proteins, lipids and carbohydrates." [KEGG:map00770 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Definition compiled by the PW editorial board; various resources at onelook, review articles"] 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 "Related GO term", PubMed:Neuron\, 2004\, v42\, p897-912; Cellular Signaling\, 2004\, v16\, p127-36. "Articles in PubMed", Reactome:REACT_11061.4 "Associated entry at Reactome"] synonym: "NGF signaling pathway" RELATED [] 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 "related GO term", KEGG:map04012 "Related KEGG map", MCW e-journal:J. Mol. Evolo.2000\, v50\, p397-412 "Review article on EGF receptors and ligands", PubMed:12814936 "Review article", Reactome:REACT_9417.3 "Related entry at Reactome"] synonym: "EGF/neuregulin signaling pathway" 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 "Article in Trends in Genetics"] 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. "From an article in Trends in Genetics"] 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. "From an article in Trends in genetics"] 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 "From an article in Physiological Genomics, review article in PubMed"] 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. "From an article in Physiological Genomics"] synonym: "FCHL" RELATED [] is_a: 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 "Definition compiled by the PW editorial team", Reactome:REACT_15380.1 "Associated entry at Reactome"] 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 "From an article in press - HMGC affiliated authors."] 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 "Online collection of dictionaries - Wikipedia"] 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. "Definition derived from an article in TIBS discussing the mTOR signaling pathway"] 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 "Associated KEGG map", PubMed:TIBS\, 2004\, v. 29(1)\, 32-38., Reactome:REACT_6838.1 "Associated entry at Reactome"] is_a: PW:0000003 ! signaling pathway is_a: PW:0000085 ! pathways of replication, repair, gene expression, protein biosynthesis [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 "Definition compiled by the PW editorial team based on the information from a number of sources"] 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. "American Journal of Physiology, Renal Physiology"] 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. "From a review article published in American Journal of Physiology, Renal Physiology"] 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. They 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." [Gene Ontology:GO\:0016114 "Related GO term", KEGG:map00900 "Related KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] synonym: "" RELATED [] synonym: "ter" RELATED [] synonym: "terpenoid backbone biosynthetic pathway" RELATED [XX:] 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 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Related GO term", KEGG:map00521 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Online collection of dictionaries"] 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 pentose and glucuronate as depicted in the KEGG diagrams." [KEGG:http\://www.genome.ad.jp/kegg/pathway/map/map00040.html "Based on the entry found at KEGG", KEGG:map00040 "Associated KEGG map"] 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 "Review articles in PubMed"] 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 porphin structure, four pyrrole rings connected by methylidyne 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 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Related GO term", KEGG:map00533 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries."] 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 "Associated KEGG map", MCW Libraries:QU4 V876f 2008 "Voet & Voet Biochemistry, third edition"] 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 "PW 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 "Associated KEGG map", MCW Libraries:QU4 V876f "Voet & Voet Biochemistry, third edition"] 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 "Related GO term", KEGG:map00532 "Associated KEGG map", OneLook:www.onelook.com "Online collection if dictionaries."] 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 "Related GO term", OneLook:www.onelook.com "Online collection of dictionaries - Dorland's."] 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 "Related GO term", MCW library:QU4 M235b 2009 "McKee Handbook of Biochemistry - fourth edition", OneLook:www.onelook.com "Online collection of dictionaries - Dorland's."] 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 "Related GO term", KEGG:map04010 "Related KEGG map", PubMed:PMID\: 14570565 ; 15102355 . "Review articles on p38 pathway", Reactome:REACT_12065.1 "Related entry at Reactome"] 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 "Related GO term", KEGG:map04310 "Related KEGG map", 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 "Related GO term", KEGG:map04310 "Related KEGG map", 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 "Related GO term", KEGG:map04310 "Related KEGG map", PubMed:PMID\: 12573432; 15001769; 18432252, Reactome:REACT_11045.1 "Associated entry at Reactome"] synonym: "beta-catenin dependent Wnt signaling pathway" 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 "Related GO term", KEGG:map03440 "Related KEGG map", PubMed:Cell\, 2004\, v. 117\, p 171-184 "Article on double strand repair pathways", Reactome:REACT_1874.1 "Related entry at Reactome"] is_a: PW:0000663 ! DNA break 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 "Related GO term", KEGG:map03450 "Related KEGG map", PubMed:Cell\, 2004\, v. 117\, 171-184. "Article published in Cell on the double-strand specific break repair pathways.", PubMed:PMID\: 12947387 "Review article in Oncogene, 002", Reactome:REACT_1022.1 "Related entry at Reactome"] synonym: "NHEJ pathway of double-strand break repair" RELATED [] is_a: PW:0000663 ! DNA break 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 "Associated GO term", KEGG:map04330 "Associated KEGG map", PubMed:Several articles in PubMed "Based on a number of review articles", Reactome:REACT_299.2 "Associated entry at Reactome"] 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 "Definition compiled based on the information available at OMIM"] 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 "Related GO term", PubMed:TIBS\, 2004\, v29 (5)\, p265-273. (PMID\: 15130563 )l PMID\:16678165, Reactome:REACT_6844.5 "Associated entry at Reactome"] synonym: "TGF- beta signaling pathway - SMAD dependent" RELATED [] is_a: PW:0000329 ! transforming growth factor-beta superfamily mediated signaling pathway [Term] id: PW:0000207 name: central obesity with hypertension pathway is_a: 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 impairment of glucose homeostasis pathways." [KEGG:map04930 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] synonym: "type II diabetes mellitus pathway" RELATED [] is_a: PW:0000174 ! metabolic syndrome pathway is_a: PW:0000176 ! diabetes pathway [Term] id: PW:0000209 name: Jak-Stat signaling pathway def: "The Jak-Stat pathway involves signaling from cytokine or growth factor receptor(s) to the nucleus via Janus kinases (Jak) and the signal transducers and activators of transcription (Stat) families of proteins. Combinations between four Jak(s) and seven Stat(s) shape the outcome of ligand triggered signaling through the various receptors." [Gene Ontology:GO\:0007259 "Related GO term", KEGG:map04630 "Associated KEGG map", PubMed:14737178; 14668806; 12039028; 17312100 "Articles in PubMed"] is_a: PW:0000003 ! signaling pathway [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 "Articles in Science and Nature, Eur. J. Biochem"] 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 "Related GO term", OneLook:www.onelook.com "Online collection of dictionaries - Wikipedia.", Reactome:REACT_14820.1 "Related entry at Reactome"] 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 "Related GO term", OneLook:www.onelook.com "Oneline collection of dictionaries", XX:] is_a: PW:0000211 ! amines and polyamines metabolic pathway [Term] id: PW:0000217 name: metabolic pathway of prosthetic groups, electron carriers and reductants def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of molecules whose role or function is as prosthetic groups, electron carriers or reductants." [InHouse :PW InHouse dictionary "Definition compiled by the PW editorial board."] is_a: PW:0000002 ! classic metabolic pathway [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 "Online collection of dictionaries"] is_a: PW:0000217 ! metabolic pathway of prosthetic groups, electron carriers and reductants [Term] id: PW:0000219 name: NAD biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of NAD - nicotinamide adenine dinucleotide. NAD is used extensively in glycolysis and the citric acid cycle of cellular respiration. " [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000217 ! metabolic pathway of prosthetic groups, electron carriers and reductants [Term] id: PW:0000220 name: pyridine nucleotide biosynthetic pathway is_a: PW:0000217 ! metabolic pathway of prosthetic groups, electron carriers and reductants [Term] id: PW:0000221 name: thioredoxin pathway is_a: PW:0000217 ! metabolic pathway of prosthetic groups, electron carriers and reductants [Term] id: PW:0000222 name: UDP-N-acetylgalactosamine biosynthetic pathway is_a: PW:0000152 ! amino sugar metabolic pathway [Term] id: PW:0000223 name: UDP-N-acetylglucosamine biosynthetic pathway is_a: PW:0000152 ! amino sugar metabolic pathway [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 "Online collection of dictionaries."] is_a: PW:0000152 ! amino sugar metabolic pathway [Term] id: PW:0000225 name: citrulline degradation pathway def: "Those metabolic reactions involved in the degradation of citrulline - alpha-amino delta-carbamido normal valeric acid. Citrulline is made from ornithine in the urea cycle; it also is a by-product of nitric oxide synthase catalyzed reactions." [Gene Ontology:GO\:0019241 "Related GO term", OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Related GO term", OneLook:www.onelook.com "Online collection of dictionaries - Dorland's Medical Dictionary"] 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 "Review articles"] 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 [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 "Review articles"] 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 [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 "Review articles"] 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 [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 "Review articles"] 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. "Review article"] 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: "phosphoinositide 3-kinase-Akt signaling pathway" RELATED [] synonym: "PI3K-Akt signaling pathway" RELATED [] is_a: PW:0000595 ! phosphatidylinositol 3-kinase 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 "Associated GO term", PubMed:PMID\:12040173\, 12655295 "Review article", Reactome:REACT_1432.1 "Associated entry at Reactome"] 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 [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 "Associated GO term", PubMed:PMID\: 11861602 "Review article in Annual Review of Immunology"] 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 "Associated GO term", PubMed:PMID\: 11861602 "Review article"] 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 or apoptosis through a number of signaling mechanisms that involve activation of nuclear factor-kappaB, of caspases or of mitogen-activated protein kinases. TNF superfamily has been implicated in a wide range of human diseases including tumorigenesis, septic shock, diabetes, rheumatoid arthritis, other inflammatory conditions." [PubMed:PMID\: 14555214\, 11796220\, 11239407 "Review article"] 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 "Related GO term", PubMed:PMID\: 12169433 "Review article"] 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 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] synonym: "type I diabetes mellitus pathway" RELATED [] 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 "Online collection of dictionaries - Wikipedia"] 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 "Online collection of dictionaries - Wikipedia"] 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 "Related GO term", KEGG:map04370 "Associated KEGG map", OneLook\, PubMed:PMID\: 15563310; PMID\: 15544039 "Review articles,", Reactome:REACT_12529.1 "Associated entry at Reactome"] synonym: "VEGF signaling pathways" RELATED [] 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 "Review article"] 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 "Several review articles in PubMed"] is_a: PW:0000467 ! peptide and protein hormone signaling pathway relationship: part_of PW:0000492 ! renin-angiotensin system signaling 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 "Review article on Rheb"] 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 "McKee handbook of biochemistry - fourth editio"] 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 - a complex of lipid and polysaccharide." [Gene Ontology:GO\:0009103 "Related GO term", KEGG:map00540 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] synonym: "" RELATED [] synonym: "LPS biosynthetic pathway" RELATED [] is_a: PW:0000146 ! glycan 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 "Related GO term", KEGG:map00550 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries - Dorland's"] synonym: "murein biosynthetic pathway" RELATED [] is_a: PW:0000146 ! glycan 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 "Related GO term", KEGG:map00904 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000147 ! metabolic pathway of secondary metabolites [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 "Related GO term", KEGG:map00902 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Online collection of dictionaries - Dorland's and other Internet resources."] 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 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Online information on polyketides"] 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 "Related GO term", KEGG:map00253 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries - Dorland's Medical Dictionary"] 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 "Related GO term", Internet:Google "Definition compiled from a number of Web sources.", KEGG:map00331 "Associated KEGG map"] 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 "Related GO term", KEGG:map00231 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries - Dorland'sn"] 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 "Review article"] is_a: 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 "Definition compiled from many sources."] 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 "Definition compiled from many sources"] 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 "Definition compiled from many sources."] 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 "Online collection of dictionaries - Dorland's."] 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 "Online collection of dictionaries - adapted from Dorland's."] 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 "Online collection of dictionaries - Dorland's."] 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 "Online collection of dictionaries - adapted from Dorland's."] 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 "Associated GO term", MCW e-journals:Current Opinions in Cell Biology "Review article in v16 (4), p343-349."] 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. "Review article", Reactome:REACT_16881.2 "Related entry at Reactome"] 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 "Related entry at Reactome"] 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 "Online collection of dictionaries - Dorland's", PubMed:PMID\:20211164\, 20034776\, 20089931] 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 "Online collection of dictionaries"] 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 "reviews"] is_a: PW:0000181 ! pathways of protein folding, sorting, modification, translocation and degradation [Term] id: PW:0000281 name: endocytic pathway def: "The endocytic pathway allows for recycling of cargo delivered via the exocytic route, uptake of nutrients, internalization of receptors. Endocytosis can take place via the clathrin dependent or clathrin independent pathway." [Gene Ontology:GO\:0006897 "Related GO term", PubMed:PubMed\:PMID\:18354421; 16882731] is_a: PW:0000181 ! pathways of protein folding, sorting, modification, translocation and degradation [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 "Related GO term", InHouse:PW dictionary "A compiled definition"] 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 "Review article on glycomics and drug development"] 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 "Review article on glycomics and drug development"] 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 "Heparan sulfate interacts with BACE1 and affects the processing of amyloid precursor protein"] 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 "Associated GO term", KEGG:map04510 "Related KEGG map", PubMed:PMID\: 15009204 \, PMID\: 14570568; 15276463 "Review articles , Nature reviews, Annu. Rev. Cell. Dev. Biol.; Cardiovascular Research", Reactome:REACT_13552.1 "Related entry at Reactome"] 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 "Definition compiled by the PW editorial board."] 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 "Definition compiled by the PW editorial board."] 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 "Definition compiled by the PW editorial board."] 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 "Definition compiled by the PW editorial board."] 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 "Definition compiled by the PW editorial board."] 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 "Definition compiled by the PW editorial board."] 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 "Review article in Neuron"] 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 "Review article in Cardiovascular Research, 2004."] 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 could lead to a hypertrophic response." [KEGG:map05410 "Associated KEGG map", OneLook\, PubMed:www.onelook.org\, PMID\: 15276462 "Online collection of dictionaries - Wikipedia, article"] synonym: "HCM" 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 "Related GO term", PubMed:PMID\: 14515146 "Review article", Reactome:REACT_16888.1 "Associated entry at Reactome"] synonym: "PDGF signaling pathway" 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 "Definition compiled by the PW editorial board."] 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 "Online collection of dictionaries - Wikipedia"] 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 "Definition compiled by the PW editorial board"] 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 "Online collection of dictionaries - Wikipedia"] 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 "Online collection of dictionaries - Dorland's."] 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 "Associated entry at Reactome"] 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 "Definition compiled by the PW editorial board based on the information at the Reactome.", Reactome:REACT_1208.1 "Associated entry at Reactome"] 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 "Definition compiled by the PW editorial board."] 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 "Definition compiled by the PW editorial board."] 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 "Online collection of dictionaries"] 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 "Online collection of dictionaries"] 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 "Online collection of dictionaries"] 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 "Online collection of dictionaries"] 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 "Review articles on MAPK"] 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 "Related GO term", KEGG:map04010 "Related KEGG map", PubMed :PMID\: 15102441 "Review article on the JNK MAPK pathway"] 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 "Review articles"] synonym: "Ca/CaM dependent signaling pathways" RELATED [] is_a: PW:0000003 ! 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 \, "Article in PubMed, Molecules and Cells"] 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 kinases pathway def: "Calcium/calmodulin dependent kinases - a family of multifunctional serine/threonine kinases - play important regulatory roles in cell proliferation." [PubMed:PMID\: 14671000 "Review article on PubMed"] 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 "Related GO term", pUBmED:PMID\: 11983154 \,PMID\: 12975316 "Review articles in Cell, Genes and Development"] synonym: "NFAT signaling pathway" RELATED [] is_a: PW:0000315 ! calcineurin 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 "Definition compiled by the PW editorial board"] 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 "Review article in Cardiovascular Research"] 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 "Related GO term", KEGG:map00401 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] 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. "Articles on Hedgehog signaling and human diseases."] 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 "Related GO term", PubMed:PMID\: 15093606 "Review article on ephrins and their receptors"] 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 "A survey article A survey article on the role of eph-ephrin axis in cancer"] 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. "Various articles on Notch signaling pathway and diseases"] 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 "Related GO term", InHouse:InHouse PW dictionary "Definition compiled by the PW editorial board."] 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 "Review article in Trends in Cell Biology"] 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 "Related GO term", PubMed:PMID\:19601767; 19379279, Reactome:REACT_9470.2 "Related entry at Reactome"] synonym: "FGF signaling pathway" 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 "Associated KEGG map", PubMed:PMID\: 15473857 "Review article and references therein"] synonym: "TGF-beta superfamily mediated signaling pathway" RELATED [] 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 "Associated GO term", PubMed:PMID\: 15368350 "Review article in J Cell Biochem", Reactome:REACT_12034.1 "Associated entry at Reactome"] synonym: "BMP signaling pathway " 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 "Related GO term", PubMed:PMID\:19273500; 16997617; 16885529] 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: cadherins signaling pathway is_a: PW:0000332 ! cell-cell signaling pathway [Term] id: PW:0000334 name: connexins 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 "Definition compiled by the PW editorial board."] 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\: "Review article"] is_a: PW:0000332 ! cell-cell signaling pathway [Term] id: PW:0000338 name: altered cadherins mediated signaling pathway is_a: PW:0000333 ! cadherins signaling pathway [Term] id: PW:0000339 name: altered connexins mediated signaling pathway is_a: PW:0000334 ! connexins 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 "Definition compiled by the PW editorial board"] 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 "Definition compiled by the PW editorial board"] 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 "Definition compiled by the PW editorial boardd."] 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 "Definition compiled by the PW editorial board."] 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 "Review article"] 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 "Definition compiled by the PW editorial board"] 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 "Definition compiled by the PW editorial board"] 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 "Definition compiled by the PW editorial board."] 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 "Related GO term", KEGG:map00564 "Associated KEGG map", MCW library:QU4 M235b 2009 "McKee Handbook of Biochemistry - fourth edition"] 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 "Online collection of dictionaries"] 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 "Associated GO term", 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 forms of human obesity." [PubMed:PMID\: 15703762 \, PMID\: 11239410 "Review articles on obesity."] 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 "Definition compiled by the PW editorial board."] 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 "Review articles on obesity"] is_a: PW:0000357 ! energy homeostasis pathway is_a: PW:0000358 ! altered homeostasis pathway [Term] id: PW:0000360 name: the chronic hypoxic response - the hypoxia inducible factor - alpha pathway def: "The chronic hypoxic response is mediated by the hypoxia-inducible transcription factor. It involves changes in the expression of genes that play important roles in angiogenesis and erythropoiesis." [PubMed:PMID\: 11181957 PMID\: 12603312 \, PMID\: 14597660\, PMID\: 15031665 . "Review articles in PubMed."] synonym: "the chronic hypoxic response - the HIF-alpha pathway" RELATED [] 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 acute hypoxic response - 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 "Review article in PubMed"] 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 "Related GO term", PubMed:PMID\: 12079865\, PMID\: 11239410 . "Review article - Ann. N.Y. Acd. Sci."] 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 "Review articles in PubMed"] 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 a modifying enzyme PC1 are linked to obesity." [PubMed :v "review article on PMOC"] 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 "Definition compiled by the PW editorial group"] 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 "Review article regarding non-STAT JAK signaling pathway"] is_a: PW:0000003 ! signaling pathway [Term] id: PW:0000369 name: the ARE-Nrf mediated pathway of drug-metabolizing enzyme expression def: "The ARE-Nrf mediated pathway regulates the expression of phase II drug-metabolizing enzymes." [PubMed:15252150 [ "Review article in PubMed"] is_a: PW:0000124 ! cellular detoxification pathway is_a: PW:0000378 ! oxidative stress response pathways [Term] id: PW:0000370 name: the XRE-AhR mediated pathway of drug-metabolizing enzyme expression def: "The XRE-AhR mediated pathway regulates the expression of phase I and phase II drug-metabolizing enzymes." [PubMed:PMID\: 15627472 \, PMID\: 15451023 "Articles in PubMed"] is_a: PW:0000124 ! cellular detoxification pathway [Term] id: PW:0000371 name: calcium homeostasis pathway 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 "Casarett and Doull's toxicology : the basic science of poisons / editor, Curtis D. Klaassen", Reactome:REACT_6959.3 "Related entry at Reactome"] 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 "Definition compiled by the PW editorial board based on a number of articles"] 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 "of drug-metabolizing enzyme expression", Reactome:REACT_13705.1 "Related entry at Reactome"] synonym: "" 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 "Casarett"] 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 "Related GO term", InHouse:PW InHouse dictionary "Definition compiled by the PW editorial board."] 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 "Related GO term", PubMed:PMID\: 15603751; PMID\: 15952902 "Review articles in PubMed"] 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 "Related GO term", 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 "Based on the entry at Reactome", Reactome:REACT_897.2 "Associated entry at Reactome"] 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 "Based on the entry at Reactome", Reactome:REACT_1846.2 "Associated entry at Reactome"] 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 "Review article"] 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 "Associated GO term", PubMed:PMID\: 11152757; PMID\: 11152757] 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 "Articles on Reelin"] 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 [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 "Related GO term", PubMed:PMID\:18353279; 17408758] synonym: "dopaminergic pathway" 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 "Related GO term", OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000211 ! amines and polyamines metabolic pathway [Term] id: PW:0000397 name: Vitamin B12 (cobalamin) metabolic pathway 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 transulfuration 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 "Cambridge University Press, 2001"] 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: transulfuration 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 "Cambridge University Press, 2001"] 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 "Definition compiled by the PW editorial board"] 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 "Definition compiled by the PW editorial board"] 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 enzymatic reactions involved in the metabolism of 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 "Related GO term", PubMed; Onelook:PMID\: 10893433; www.onelook.com "Review article in PubMed, Wikipedia", Reactome:REACT_813.2 "Related entry at Reactome"] 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 neurotrasmitters is mediated through the exocytosis of neurotrasnmiter-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 "Review articles in PubMed"] relationship: part_of PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse [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 "Online collection of dictionaries - Wikipedia"] 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 "Online collection of dictionaries - Wikipedia", 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 "Online collection of dictionaries"] 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 "Online collection of dictionaries"] is_a: PW:0000444 ! indoleamine and related compounds metabolic pathway [Term] id: PW:0000412 name: gamma-aminobutyric acid metabolic pathway 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 "Online collection of dictionaries"] is_a: PW:0000217 ! metabolic pathway of prosthetic groups, electron carriers and reductants [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; "Review articles"] 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 "Review articles in PubMed"] 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 "Review articles in PubMed"] 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 "Review article in Pubmed"] 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 "Associated GO term", 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 "definition compiled by the PW editorial board"] 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 "Review article in PubMed"] 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 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 "Based on several readings"] 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 "Review article in PubMed"] 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 "Review article in PubMed"] 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 "Review articles in PubMed"] 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 "Online collection of dictionaries"] is_a: PW:0000028 ! alanine and aspartate metabolic pathway [Term] id: PW:0000439 name: aspartate metabolic pathway def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of aspartate/aspartic acid. 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 "Online collection of dictionaries"] is_a: PW:0000028 ! alanine and aspartate metabolic pathway is_a: PW:0000445 ! excitatory neurotransmitter metabolic pathway [Term] id: PW:0000440 name: glycine metabolic pathway is_a: PW:0000047 ! glycine, serine and threonine metabolic pathway is_a: PW:0000446 ! inhibitory neurotransmitter 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 "Online collection of dictionaries - Wikipedia", 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 "Online collection of dictionaries - Wikipedia", 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 "Online collection of dictionaries - Wikipedia", 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 "Online collection of dictionaries"] 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 "Online collection of dictionaries"] 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 enkephalins." [OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Online collection of dictionaries"] 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 "Online collection of articles"] 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 "Online collection of articles - Wikipedia"] 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 "McKee handbook of biochemistry - fourth editio"] 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 "Related GO term", OneLook:www.onelook.com "Online collection of dictionaries", Reactome:REACT_9405.2 "Related entry at Reactome"] is_a: PW:0000453 ! isoprenoid 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 "Review article in PubMed"] 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 "Review articles in PubMed"] 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 "Related GO term", PubMed:PMID\: 15601620; PMID\: 15907343 "review articles"] is_a: PW:0000003 ! 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 "Related GO term", KEGG:map00590 "Associated KEGG map", OneLook:www.onelook.com "Wikipedia at OneLook"] 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 "Review article"] 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 "Review article"] 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 "Review article"] 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 "McKee Handbook of Biochemistry - fourth edition"] 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 "online collection of dictionaries - wikipedia"] 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 "Online collection of dictionaries -wikipedia"] 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 "Online collection of dictionaries - wikipedia"] 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; "Review articles in PubMed"] 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 "Review articles in PubMed"] 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 "Review articles in PubMed"] 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 "Review articles in PubMed"] 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 "Related GO term", OneLook:www.onelook.com "Online collection of dictionaries - Dorland's, Wikipedia"] 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 "Associated GO term", Reactome:REACT_604.2 "Associated entry at Reactome", 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 "Related GO term", 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 "Related GO term", PubMed:PMID\: 16011471 "Review article in PubMed", Reactome:REACT_6823.1 "Related entry at Reactome"] 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 "McKee Handbook of Biochemistry - fourth edition", OneLook:www.onelook.com "Online collection of dictionaries - wikipedia"] 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 "Review article on MHC I pathway"] 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 "Brief review on MHC mediated pathways"] synonym: "class " RELATED [] 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 "Review article on MHC class I complex pathway"] 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 "Review article on angiopoietin pathway in angiogenic remodeling and possibly in lymphangiogenesis"] 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 "one of many reviews used to annotate and graph the pathway"] synonym: "TGF-beta Smad dependent signaling pathway" RELATED [] 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 "Reviews"] 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 system signaling pathway def: "The renin-angiotensin system (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 "Associated KEGG map", PubMed:PMID\: 15883759 PMID\: 15638741 \, PMID\: 12676165 \, PMID\: 12793984 \, PMID\: 16816138 "Several review articles."] 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 "Review"] 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 "Review articles in Pubmed"] 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 "Associated GO term", PubMed:PMID\: 16258026 "Review article"] 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 many genes." [PubMed:PMID\: 15371334\, 18267068\, 17072321 "Review articles"] synonym: "NF-kappaB signaling pathway" RELATED [] synonym: "NF-kB signaling pathway" RELATED [] is_a: PW:0000100 ! transcription pathway is_a: PW:0000716 ! transcription factor mediated signaling pathway [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 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." [KEGG:map04610 "Related KEGG map", MCW:Handbook on cellular and molecular immunology, PubMed:PMID\: 11287977 "Review article"] 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 "Related KEGG map", 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 "Related GO term", KEGG :map04610 "Related KEGG map", 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 "Related GO term", KEGG:map04610 "Related KEGG map", PubMed:PMID\:11287977] synonym: "" RELATED [] 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 "Review articles in PubMed"] 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." [OneLook:www.onelook.com "Online collection of dictionaries - wikipedia"] 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 "Associated GO term", 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 signaling pathway via interleukin-10 family members is_a: PW:0000512 ! Interleukin mediated signaling pathway [Term] id: PW:0000514 name: Interleukin signaling pathway via interleukin-6 family members is_a: PW:0000512 ! Interleukin mediated signaling pathway [Term] id: PW:0000515 name: Interleukin-10 signaling pathway is_a: PW:0000513 ! Interleukin signaling pathway via interleukin-10 family members [Term] id: PW:0000516 name: Interleukin-6 signaling pathway is_a: PW:0000514 ! Interleukin signaling pathway via interleukin-6 family members [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 "Article on laminopathies and atherosclerosis"] 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 "Related GO term", KEGG:http\://umbbd.msi.umn.edu/ddt/ddt_map.html "Adapted from the link at KEGG.", KEGG:map00351 "Associated KEGG map"] 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 "Related GO term", KEGG:http\://umbbd.msi.umn.edu/dcb/dcb_map.html "Adapted from KEGG", KEGG:map00623 "Related KEGG map"] 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 "Adapted from the link at KEGG", KEGG:map00631 "Associated KEGG map"] 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 "Related GO term", KEGG:map00941 "Associated KEGG map", OneLook:www.onelook.com "Online collections of dictionaries - wikipedia"] 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 and degradation of linoleic acid - an unsaturated omega-6 fatty acid." [Gene Ontology:GO\:0043651 "Related GO term", KEGG:map00591 "Associated KEGG map", OneLook:http\://www.onelook.com "Online collection of dictionaries - wikipedia"] 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 "Related GO term", KEGG:map00534 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries - Dorland's"] 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 "Related GO term", 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 "Review article on At1 receptor and its pleiotropic effects, on angiotensin receptors, angiotensin type 2 receptor."] 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 "Articles on the pleiotropic AT1 receptor, all angiotensin receptors"] 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 "Review articles in PubMed"] 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 "Related GO term", PubMed\, OneLook:www.onelook.com, Reactome:REACT_1736.2 "Related entry at Reactome"] 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 "Definition compiled by the PW editorial board."] 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 "Related GO term", OneLook:www.onelook.com "Online collection of dictionaries; wikipedia", Reactome:REACT_1008.1 "Related entry at Reactome"] 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 "Associated GO term", InHouse:InHouse PW dictionary "Based on combined readings"] 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 "Associated GO term", InHouse:InHouse PW dictionary "Based on combined readings"] 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 "Review articles in PubMed, also OneLook - Wikipedia"] 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 "Online collection of dictionaries"] 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 [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 "Related GO term", PubMed:PMID\:14715913; 16214430, Reactome:REACT_15530.1 "Related entry at reactome"] 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 "Review article"] 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 pathways 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 "Related GO term", KEGG:map03018 "Related KEGG map", PubMed:PMID\: 15933735] synonym: "mRNA quality control pathways" RELATED [] synonym: "mRNA surveillance pathways" RELATED [] is_a: PW:0000085 ! pathways of replication, repair, gene expression, protein biosynthesis [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." [PubMed:PMID\: 15933735] synonym: "exosome mediated mRNA degradation pathway" RELATED [] is_a: PW:0000546 ! mRNA decay pathways [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 "Associated GO term", PubMed:PMID\: 15933735; PMID\: 17010613 "Reviews in PubMed"] synonym: "NMD pathway" RELATED [] is_a: PW:0000546 ! mRNA decay pathways [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 "Associated GO term", PubMed:PMID\: 15933735] is_a: PW:0000546 ! mRNA decay pathways [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 "Review articles in PubMed"] synonym: "SMD pathway" RELATED [] is_a: PW:0000546 ! mRNA decay pathways [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 "Definition compiled by the PW editorial team"] is_a: PW:0000290 ! altered pathway of replication, repair, gene expression and protein biosynthesis is_a: PW:0000546 ! mRNA decay pathways [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 "Related GO term", KEGG:map00905 "Associated KEGG map", KEGG\, OneLook:http\://www.onelook.com "Wikipedia"] 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 "Related GO term", PubMed:PMID\: 15466941 "Review article on the cellular fate of glucose"] 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 "Related GO term", PubMed:PMID\: 15466941 ; PMID\: 15449578 "Review articles", Reactome:REACT_212.3 "Related entry at Reactome"] 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 "Review article on the cellular fate of glucose"] 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 "Review article on the cellular fate of glucose."] 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 "Review article on the cellular fate of glucose"] 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 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 "Review articles in PubMed"] 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 "Review articles in PubMed"] 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 "Review articles in PubMed"] 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 "Related GO term", 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 "Related GO term", PubMed:PMID\: 16823476; PMID\: 16634986; PMID\: 17140553 "Review articles on adiponectins"] 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] 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: eicosanoids signaling pathway def: "eicosanoids are molecules derived from omegoa-3 or omega-6 fats that can act as hormones. " [OneLook:www.onelook.com "Online collection of dictionaries - wikipedia"] 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 "Online collection of dictionaries - wikipedia"] 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 "Online collection of dictionaries - wikipedia"] 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-angiotenin system and potassium ions concentration." [PubMed:PMID\: 16002531 PMID\: 17293689 ; "Review articles in PubMed"] 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] 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 "Various sources"] 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 particular cells, neuronal survival." [OneLook:www.onelook.com "Online collection of dictionaries - wikipedia"] 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 "Related GO term", OneLook:www.onelook.com "online collection of dictionaries- wikipedia"] synonym: "BDNF signaling pathway" RELATED [] 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 "Associated GO term", OneLook\, PubMed:www.oneloook.com; http\://www.ncbi.nlm.nih.gov/sites/entrez "Various online resources and PubMed articles"] 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 "Associated GO term", OneLookc\, PubMed:www.oneloook.com; http\://www.ncbi.nlm.nih.gov/sites/entrez "Various online resources and articles in Pubmed"] 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/ "Various resources"] 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 "Review articles in PubMed"] 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:Handbook on molecular and ceullar immunology, Onelook:www.onelook.com] 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 "Related GO term", PubMed:PMID\:16212809\, 16778093\, 18175071 "Review articles"] 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 "Review articles in PubMed"] 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 "Associated GO term", 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 "Associated GO term", 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 "Associated GO term", 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 "Review article"] 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 "Review article"] 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 "Review article"] 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 "Review article"] 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 "Review articles in PubMed"] 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 "definition based on a number of PubMed and other references"] 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 "Associated GO term", 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 "Definition based on PubMed and other references"] 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: "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 [] 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 "Related GO term", KEGG:map04010 "Related KEGG map", PubMed:PMID\: 17229475 ; PMID\: 17306385 "Review articles in PubMed", Reactome:REACT_12020.1 "Related entry at Reactome"] 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 "Review article in PubMed"] 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 "Definition compiled by the PW editorial team"] 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 "References for ovarian cancer at KEGG"] 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 "References for cervical cancer at KEGG"] 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 "Associated KEGG map", PubMed:PMID\: 15149739; PMID\: 12878745; PMID\: 14752525 "References for prostate cancer at KEGG"] synonym: "prostate neoplasm pathway" RELATED [] 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 "Associated KEGG map", PubMed:PMID\:17158541; PMID\:16474624 "References for bladder cancer at KEGG"] synonym: "bladder neoplasm pathway" 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 "Associated KEGG map", PubMed:PMID\:12583434; PMID\:15947972; PMID\:16508724 "References for endometrial cancer at KEGG"] synonym: "endometrial neoplasm pathway" 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 "Associated KEGG map", OneLook:www.onelook.com "online collection of dictionaries"] synonym: "colorectal neoplasm pathway" 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 "Review articles"] 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 "Review articles"] 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 "Review articles"] 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:0000621 ! altered phosphatidylinositol 3-kinase 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 "Associated KEGG map", PubMed:PMID\: 17898532\, 18662538] synonym: "pancreatic neoplasm pathway" RELATED [] 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. Deregulates pathways, such as Wnt, PI3K-Akt or RAF/MEK/ERK, have been implicated in the development of gastric cancer." [PubMeD:PMID\: 17203201 "Review article on Stat3-Wnt5a"] 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: "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 "Review article on Stat3 and Wnt5A"] 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 secretory pathway, misfolded proteins are recognized and targeted for degradation." [Gene Ontology:GO\:0030433 "Related GO term", PubMed:PMID\:18216874; 18075753] synonym: "ERAD pathway" 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 "Review articles"] 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 glycolyssis 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 "Associated GO term", KEGG:map00010 "Related KEGG map", MCW Libraries:Voet & Voet \"Fundamentals od Biochemistry\" 3rd edition "Textbook", Reactome :REACT_1383.5 "Associated entry at Reactome"] synonym: "Embden-Meyerhof-Parnas pathway" 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 "Associated GO term", KEGG:map00010 "Related KEGG map", MCW Libraries:Voet & Voet \"Fundamentals of Biochemistry\" 3rd edition "Textbook", Reactome:REACT_1520.3 "Associated entry at Reactome"] 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 "Voet & Voet, 3rd edition", MCW libraries:QU4 M235b 2009 "McKee Handbook of Biochemistry - fourth edition"] 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 "Voet & Voet, 3rd edition"] 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 "Voet & Voet, 3rd edition"] 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 "Voet & Voet 3rd edition"] 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" 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 "online collection of dictionaries"] 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 "Online collection of dictionaries"] 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 "Online collection of dictionaries"] 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 "Online collection of dictionaries"] 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] 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] 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 "Online collection of dictionaries"] 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 "Online collection ofdictionaries"] 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 "Associated GO term", KEGG:map03430 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] synonym: "MMR pathway" RELATED [] is_a: PW:0000661 ! DNA base repair pathway [Term] id: PW:0000663 name: DNA break repair pathway alt_id: PW:0000131 alt_id: PW:0000291 alt_id: PW:0000664 alt_id: PW:0000665 def: "The pathway dealing with single- or double-strand breaks of the DNA backbone." [OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Online collection of dictionaries"] 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 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 "Online collection of dictionaries"] 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 "Online collection of databases"] 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 "Associated GO term", PubMed:PMID\: 18774732; 18728221, Reactome:REACT_18325.2 "Related entry at Reactome"] 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 "Associated entry at Reactome"] 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 "Associated entry at Reactome"] 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 "Fundamentals of Biochemistry"] 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 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Related GO term", KEGG:map00908 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Related GO term", KEGG:map00906 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] 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 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries"] synonym: "thyroid neoplasm pathway" RELATED [] is_a: PW:0000631 ! head and neck 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 "Online collection of dictionaries"] 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 "Online collection of dictionaries"] 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 "Associated KEGG map", OneLook\, KEGG:www.onelook.com] synonym: "SCLC pathway" RELATED [] synonym: "small cell lung neoplasm pathway" RELATED [] 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 "Associated KEGG map", OneLook\, KEGG:www.onelook.com] synonym: "non-small cell lung neoplasm pathway" RELATED [] synonym: "NSCLC pathway" RELATED [] 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 "Online collection of dictionaries"] 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 "Online collection of dictionaries"] 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 "Online collection of dictionaries"] 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 "Associated KEGG map", OneLook :www.onelook.com "Online collection of dictionaries"] 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 is a type of leukemia where too many white blood cells are made in the bone marrow. The condition progresses slowly." [KEGG:map05220 "Associated KEGG map", OneLook:www.onelook.com "Online collection of dictionaries", XX:] is_a: PW:0000707 ! myeloid leukemia pathway created_by: vpetri creation_date: 2009-10-28T04:39:38Z [Term] id: PW:0000711 name: glioma pathway 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 "review on vasopressin receptors"] 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] 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:17275054] 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] is_a: PW:0000100 ! transcription pathway is_a: PW:0000237 ! stress response 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-fetching 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:0000754 ! 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:0000754 ! 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:0000754 ! 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:0000754 ! 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 "McKee Handbook of Biochemistry - fourth edition"] 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." [Gene Ontology:GO\:0006687 "Related GO term", MCW library:QU4 M235b 2009 "McKee Handbook of Biochemistry - fourth edition"] synonym: "glycolipid 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 "McKee Handbook of Biochemistry - fourth edition"] 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 "McKee Handbook of Biochemistry - fourth edition", 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 "Related GO term", MCW library:QU4 M235b 2009 "McKee Handbook of Biochemistry - fourth edition"] 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 "Related GO term", MCW library:QU4 M235b 2009 "McKee Handbook of Biochemistry - fourth edition"] 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 "McKee Handbook of Biochemistry - fourth edition"] 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 "McKee Handbook of Biochemistry - fourth edition"] 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 "McKee Handbook of Biochemistry - fourth edition"] 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 "McKee Handbook of Biochemistry - fourth edition"] 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 "McKee Handbook of Biochemistry - fourth edition"] 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 "McKee Handbook of Biochemistry - fourth edition"] 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 "McKee Handbook of Biochemistry - fourth edition"] 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 "Related GO term", MCW library:QU4 M235b 2009 "McKee Handbook of Biochemistry - fourth edition"] 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 "McKee Handbook of Biochemistry - fourth edition"] 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 "McKee Handbook of Biochemistry - fourth edition"] 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 "McKee Handbook of Biochemistry - fourth edition"] 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 "Handbook on the biochemistry of lipids", 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 "Handbook on the biochemistry of lipids", 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 "Handbook on the biochemistry of lipids", 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:0000754 ! 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:0000754 ! 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:0000754 ! 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:0000754 ! 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:0000754 ! 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 "Online collection of dictionary"] 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 "Online collection of dictionaries"] 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 "Related GO term", KEGG:map00072 "Related Kegg map", MCW Libraries:QU4 V876f 2008 "Voet Biochemistry, third edition", Reactome:REACT_1464.3 "Related entry at Reactome"] 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 "Related GO term", KEGG:map00072 "Related Kegg map", MCW Libraries:QU4 V876f 2008 "Voet Biochemistry, third edition"] 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:0000754 ! 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 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\, 2030387] synonym: "TLR signaling pathway" RELATED [] is_a: PW:0000024 ! inflammatory response pathway is_a: PW:0000819 ! signaling pathway in the innate immune response 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\, 2030387] is_a: PW:0000024 ! inflammatory response pathway is_a: PW:0000819 ! signaling pathway in the innate immune response 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\, 2030387] synonym: "RLR signaling pathway" RELATED [] is_a: PW:0000024 ! inflammatory response pathway is_a: PW:0000819 ! signaling pathway in the innate immune response 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\, 2030387] synonym: "NLR signaling pathway" RELATED [] is_a: PW:0000024 ! inflammatory response pathway is_a: PW:0000819 ! signaling pathway in the innate immune response 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 immune responses. While signaling mediated by cytokines are chemokines plays important roles in immunity, it also serves functions beyond immunity." [InHouse:PW dictionary] 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:Handbook of cellular and molecular immunology, PubMed:PMID\: 16448548\, 20537906] synonym: "TCR signaling pathway" RELATED [] 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:Handbook on cellular and molecular immunology, PubMed:PMID\: 20591989\, 19827951] synonym: "BCR signaling pathway" 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: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:Handbook on cellular and molecular immunology] 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, cell proliferation and apoptosis." [MCW:Handbook on molecular and cellular immunology] is_a: PW:0000577 ! cytokine and chemokine mediated signaling pathway 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." [MCW:Handbook on molecular and cellular immunology, OneLook:www.onelook.com] is_a: PW:0000577 ! cytokine and chemokine mediated signaling pathway 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. Chemokines signal via G-protein coupled receptors to engage distinct G protein signaling and downstream cascades." [MCW:Handbook on cellular and molecular immunology] 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 resides and along with 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] 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. Chemokines signal via G-protein coupled receptors to engage distinct G protein signaling and downstream cascades." [MCW:Handbook on cellular and molecular immunology] 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] 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:0000754 ! 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 "Related GO term", 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] 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 "Related GO term", 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 "Associated GO term", OneLook:www.onelook.com] 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 "Related GO term", 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 "Related GO term", 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 "Related GO term", 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 "Associated GO term", OneLook:www.onelook.com] 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 "Related GO term", 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 "Related GO term", 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 responses." [OneLook:www.onelook.com, PubMed:PMID\:20925600\, 18571247\, 18676031] 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 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 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 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 is_a: PW:0000754 ! drug pathway created_by: VPetri creation_date: 2011-06-09T05:30:25Z [Term] id: PW:0000870 name: gefitinib pharmacokinetics pathway 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 is_a: PW:0000869 ! gefitinib drug pathway created_by: VPetri creation_date: 2011-06-09T05:31:16Z [Typedef] id: part_of name: part_pf