format-version: 1.0 date: 23:03:2007 13:15 saved-by: VPetri auto-generated-by: DAG-Edit 1.418 default-namespace: pathway [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 [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 [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 [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 [Term] id: PW:0000006 name: small G proteins - the Ras superfamily signaling pathway def: "The Ras superfamily consists of a diverse group of small\, monomeric G proteins that cycle between the GTP/GDP-bound state due\, at least in part to their GTPase activity. In the GTP-bound form they can interact with many downstream effector molecules. Rsa superfamily medaietd pathways control a broad spectrum of processes. Upregulation of Ras cascades has been linked to several forms of cancer. The superfamily is strucutrally classified in five families." [PubMed :PMID\: 11027944 "Review article"] comment: Numerous articles contributed to this definition\, too many to cite independently. is_a: PW:0000003 [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." [PubMed:PMID\: 14570565; PMID\: 14976517 "TPW review articles on MAPK"] synonym: "MAPK signaling pathway" [] is_a: PW:0000003 [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. Misregulation 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:0000003 [Term] id: PW:0000009 name: programmed cell death pathway def: "A form of cell death in which a programmed sequence of events leads to the elimination of cells without releasing harmful substances into the surrounding area. It plays a crucial role in developing and maintaining health by eliminating old cells\, unnecessary cells and/or unhealthy cells. When it does not work right cells that should die may become immortal\, like in cancer and leukemia\, or too many cells are killed\, like in neurodegenerative diseases. Apoptosis is a term that is used interchangeably with programmed cell death but it refers to the structural changes a cell undergoes\, whereas programmed cell death refers to the whole sequence of events" [OneLook:www.onelook.com "Online collection of dictionaries"] synonym: "apoptotic cell death pathway" [] is_a: PW:0000275 [Term] id: PW:0000010 name: lipid metabolic pathway def: "The metabolic reactions involved in the oxidation\, decomposition and synthesis of lipids in the tissues." [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000002 [Term] id: PW:0000011 name: amino acid metabolic pathway def: "Those metabolic reactions involved in the synthesis\, utilization and/or degradation of the common amino acids." [In House:In House PW dictionary "Definition supplied by the PW editorial team."] is_a: PW:0000002 [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 [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 conplex condition." [InHouse:InHouse PW dictionary] synonym: "complex human diseases" [] is_a: PW:0000001 [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 [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"] is_a: PW:0000014 [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"] synonym: "ALS" [] is_a: PW:0000014 [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 nanifold pathways are disrupted." [PubMed:2004\, v.20 (3)\, 146-154. "Article in Trends in Genetics"] is_a: PW:0000171 [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." [PubMed:2004\, v.101 (15)\, 5500-5505. "Definition compiled from an article in PNAS"] is_a: PW:0000014 [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" [OnerLook:www.onelook.com "Online collection of dictionaries - Dorland's."] is_a: PW:0000014 [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 [Term] id: PW:0000021 name: hypertension 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 [Term] id: PW:0000022 name: cardiomyopathy 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 [Term] id: PW:0000023 name: immune response pathway def: "The term groups together the various classes of defense responses and their accompanying pathways the organism uses to handle tissue injury and exposure to antigens\, and to protect itself against pathogens" [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000004 [Term] id: PW:0000024 name: inflammatory response pathway def: "Inflammation is part of the innate immune system response to infection or injury. It triggers coagulation while inhibiting anticoagulation. The inflammatory and coagulation pathways are connected in a cross-talk. Impaired anticoagulation pathways affect this balanced dialog and lead to various conditions and infections." [OneLook:www.onelook.com "Online collection of dictionaries", PubMed:PMID\: 15364056\, PMID\: 16281932\, PMID\: 16226680 "Review articles in PubMed"] relationship: part_of PW:0000234 [Term] id: PW:0000025 name: glycolysis/gluconeogenesis pathway def: "Those metabolic reactions involved in the energy-yielding\, anaerobic conversion of glucose to simpler compounds and in the formation of glucose from non-carbohydrate precursors such as amino acids and fat." [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000005 [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 Kreb cycle is the second of three metabolic pathways that are involved in fuel molecule catabolism and ATP production." [OneLook:www.onelook.com "Online collection of dictionaries"] synonym: "TCA cycle" [] is_a: PW:0000005 [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 is_a: PW:0000445 [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 [Term] id: PW:0000029 name: fatty acid biosynthetic pathway alt_id: PW:0000030 synonym: "fatty acid biosynthesis (path 2)" [] is_a: PW:0000058 [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 [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 [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 [Term] id: PW:0000034 name: oxidative phosphorylation pathway def: "Those metabolic reactions involved in coupling ATP phosphorylation to the respiratory chain." [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000033 [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." [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000033 [Term] id: PW:0000036 name: nitrogen metabolic pathway def: "Those metabolic reactions involving nitrogen and nitrogenous compounds." [PW InHouse dictionary:PW InHouse dictionary "Definition compiled by the PW editorial team."] is_a: PW:0000033 [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." [PW InHouse dictionary:PW InHouse dictionary "Definition compiled from a number of sources by the PW editorial team."] is_a: PW:0000033 [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 he 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 [Term] id: PW:0000040 name: androgen and estrogen metabolic pathway def: "Those metabolic reactions involved in the synthesis\, utilization and/or degradation of androgen - a general term for any male sex hormone - and estrogen - a general term for female sex hormones." [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000248 [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." [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000005 [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. " [OneLook:www.onelook.com "Adapted from Dorland's Medical Dictionary"] is_a: PW:0000005 [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. In biochemistry\, the term is used interchangeably with pyruvic acid\, even though pyruvate technically refers to the negatively charged ion. Pyruvate is the end product of glycolysis\, and in turn may be converted to lactate or acetyl CoA or to ethanol (as in yeasts)." [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000005 [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: "A pathway of hexose oxidation in which glucose-6-phosphate undergoes two successive oxidations by NADP\, the final one being an oxidative decarboxylation to form a pentose phosphate." [OneLook:www.oneloook.com "Online collection of dictionaries"] is_a: PW:0000005 [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." [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000005 [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 [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." [MCW library book:Homocysteine in Health and Disease "Cambridge Press\, 2001"] is_a: PW:0000011 is_a: PW:0000399 is_a: PW:0000401 [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 is_a: PW:0000400 [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 [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 [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 [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 [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 [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"] is_a: PW:0000005 [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. " [OneLook:www.onelook.com "Online collection of dictionaries - Dorland's."] is_a: PW:0000033 [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 [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." [PW InHouse dictionary:PW In House Dictionary "Definition compiled from a number of dictionaries"] is_a: PW:0000010 [Term] id: PW:0000059 name: pathway pertinent to signaling in the brain is_a: PW:0000003 [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"] synonym: "LTP" [] relationship: part_of PW:0000455 [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 of events." [OneLook:www.onelook.com "Online collection of dictionaries"] comment: Adapted from Wikipedia at OneLook synonym: "LTD" [] relationship: part_of PW:0000455 [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." [OneLook:www\,onelook.com "Online collection of dictionaries"] is_a: PW:0000005 [Term] id: PW:0000063 name: glyoxylate and dicarboxylate metabolic pathway is_a: PW:0000005 [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." [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 [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." [OneLook:www.onelook.com "Online collection of dictionaries - Wikipedia - definition"] is_a: PW:0000005 [Term] id: PW:0000066 name: C5-branched dibasic acid metabolic pathway is_a: PW:0000005 [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"] is_a: PW:0000033 [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. " [OneLook:www.onelook.com "online collection of dictionaries"] is_a: PW:0000033 [Term] id: PW:0000069 name: ketone bodies metabolic pathway def: "Those metabolic reactions involved in the degradation and synthesis 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 energy during starvation or when not enough insulin is available to derive energy from the breakdown of glucose. Excessive accumulation of these acidic chemicals leads to dangerous diabetic conditions known as ketoacidosis." [OneLook:www.onelook.com "Online collection of dictionaries"] comment: The definition was compiled using the information from a number of biological/medical dictionaries available at OneLook is_a: PW:0000010 [Term] id: PW:0000070 name: C21-Steroid hormone metabolic pathway is_a: PW:0000248 [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 [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: "" [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." [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 [Term] id: PW:0000087 name: G1 phase 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" [Reactomee:www.reactome.org "Reactpme offers a number of pathways and related proteins"] relationship: part_of PW:0000086 [Term] id: PW:0000088 name: G1/S transition def: "The series of events underlying the transition from G1 into S phase and under the control of Cyclin E - Cdk2 complexes." [reactome:www.reactome.org "Definition based on the information provided by Reactome"] relationship: part_of PW:0000086 [Term] id: PW:0000089 name: S phase def: "The series of events underlying duplication of the hereditary material of the cell\, formation of two copies of the chromosome." [Reactome:www.reactome.org "Based on the information available at Reactome."] relationship: part_of PW:0000086 [Term] id: PW:0000090 name: G2 phase 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:www.reactome.org "Based on the information available at Reactome"] relationship: part_of PW:0000086 [Term] id: PW:0000091 name: G2/M transition def: "The series of events underlying the transition from the G2 phase into mitosis." [Reactome:www.reactome.org "Based on the information provided at Reactome"] relationship: part_of PW:0000086 [Term] id: PW:0000092 name: M phase 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:www.reactome.org "Based on the information available at Reactome"] relationship: part_of PW:0000086 [Term] id: PW:0000093 name: M/G1 transition 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:www.reactome.org "Definition based on the information available at Reactome"] relationship: part_of PW:0000086 [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." [InHouse:PW dictionary "Definition compiled by the PW editorial board based on the information provided by the Reactome."] is_a: PW:0000085 [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."] is_a: PW:0000094 [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 unreplicated DNA." [InHouse :PW dictionary "Definition compiled by the PW editorial board based on the information at the Reactome."] is_a: PW:0000094 [Term] id: PW:0000097 name: mitotic spindle checkpoint pathway is_a: PW:0000094 [Term] id: PW:0000098 name: DNA replication pathway def: "Those pathways involved in the synthesis of DNA. " [General:PW board "General definition"] is_a: PW:0000085 [Term] id: PW:0000099 name: DNA repair pathway def: "Those pathways involved in the repair of damaged DNA." [PW InHouse:Cell\, 2004\, v. 117\, p171-184. "Generalized definition based on an article on specific pathways for double-strand break repair."] is_a: PW:0000085 [Term] id: PW:0000100 name: transcription pathway def: "The series of events governing the processes whereby DNA is transcribed into RNA." [InHouse:In House PW dictionary "Definition provided by the PW editorial team"] is_a: PW:0000085 [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." [InHouse:InHouse PW dictionary "Definition compiled by the PW editorial team"] is_a: PW:0000085 [Term] id: PW:0000102 name: The extracellular signal-regulated RAF/MEK/ERK 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." [PubMed:PMID\: 15035987 "Adapted from an article in Cell"] is_a: PW:0000007 is_a: PW:0000525 [Term] id: PW:0000103 name: transport pathway is_a: PW:0000004 [Term] id: PW:0000104 name: intrinsic apoptotic pathway def: "The apoptotic pathway involving organelles\, primarily the endoplasmic reticulum (ER) and the mitochondrion\, involving the pro and anti-apoptotic members of the Bcl family of proteins\, cytochrome c\, formation of the apoptosome and activation of caspases." [PubNed:PMID\: 14744432 "Article in Cell"] comment: The reference was conpiled based on the information available in the cited article. is_a: PW:0000009 [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." [PubMed:PMID\: 11075828; PMID\: 8973630 ""] is_a: PW:0000006 [Term] id: PW:0000106 name: extrinsic death receptor pathway def: "The apoptotic pathway involving the death receptors mediated route of caspase activation." [PubMed:PMID\: 14744432 "Article published in Cell"] is_a: PW:0000009 [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 [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. " [OneLook:www.onelook.com "Online collection of dictionaries."] is_a: PW:0000107 [Term] id: PW:0000109 name: biphenyl degradation pathway is_a: PW:0000107 [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. " [Onelook:www.onelook.com "Onelook collection of dictionaries."] is_a: PW:0000107 [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. " [OneLook:www.onelook.com "Online collection of dictionaries."] is_a: PW:0000107 [Term] id: PW:0000112 name: 3-chloroacrylic acid degradation pathway is_a: PW:0000107 [Term] id: PW:0000113 name: atrazine degradation pathway def: "Those enzymatic reactions involved in the degradation of atrazine - a herbicide used to kill weeds. " [OneLook:www.onelook.com "Online collection of dictionaries."] is_a: PW:0000107 [Term] id: PW:0000114 name: benzoate degradation pathway via hydroxylation def: "The aerobic pathway of benzoate degradation." [Online :Appl. Env. Microbiology\, 2004\, v.70(9)\, p4861-70. "Article found online"] is_a: PW:0000282 [Term] id: PW:0000115 name: benzoate degradation pathway via CoA ligation def: "The anaerobic pathway of benzoate degradation." [Online:http\://umbbd.ahc.umn.edu/benz/benz_map.html "Online description"] is_a: PW:0000282 [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. " [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000107 [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. Ir fluoresces\, hence its name." [OneLook:www.onelook.com "Online collection of dictionaries."] is_a: PW:0000107 [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." [OneLook:www.onelook.com "Online collection of dictionaries."] is_a: PW:0000107 [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 [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 and irritant substance\, possibly carcinogenic. " [OneLook:www.onelook.com "Online collection of dictionaries."] is_a: PW:0000107 [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. " [OneLook:www.onelook.com "Online collection of dictionaries."] is_a: PW:0000107 [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." [PubMed:PMID\: 15205520 \, PMID\: 15596107\, PMID\: 12495844 "Articles dealing with the Hedgehog signaling pathway"] is_a: PW:0000003 [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 [Term] id: PW:0000124 name: cellular detoxification pathway def: "The detoxification pathway triggered by exposure to chemicals involves the phase I and phase II metabolizing enzymes as well as the phase III transport systems." [PubhMed:15252150\, "Review articel in PubMed"] is_a: PW:0000004 [Term] id: PW:0000125 name: G protein signaling pathway def: "G-proteins act as signal transducer between effectors and receptors. 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." [PubMed:Science\, 2002\, v296\, p1636-39 "Review article"] is_a: PW:0000003 [Term] id: PW:0000126 name: RNA Polymerase I transcription pathway def: "The series of events governing the synthesis of ribosomal RNA (rRNA)." [InHouse:PW dictionary "Definition compiled by the PW editorial team"] is_a: PW:0000100 [Term] id: PW:0000127 name: RNA Polymerase II transcription pathway def: "The series of events governing the synthesis of messenger RNA (mRNA)." [InHouse:PW dictionary "Definition compiled by the PW editorial team"] is_a: PW:0000100 [Term] id: PW:0000128 name: RNA Polymerase III transcription pathway def: "The series of events governing the synthesis of transport/transfer RNA (tRNA)." [InHouse:PW dictionary "Definition compiled by the PW editorial team"] is_a: PW:0000100 [Term] id: PW:0000129 name: base excision repair pathway def: "A major pathway of DNA repair\, it involves a great number of enzymes necessary to recognize and remove bases modified in specific ways. Base excision may take place by either a single-nucleotide or a multiple-nucleotide replacement pathway. " [From Reactome:10583946 - given by Reactome "Definition based on the Reactome's description of the pathway"] is_a: PW:0000099 [Term] id: PW:0000130 name: nucleotide excision repair pathway is_a: PW:0000099 [Term] id: PW:0000131 name: double strand break repair pathway def: "The pathways involved in the control of double-strand break repair. " [PubMed:Cell\, 2004\, v. 117\, p171-184. ""] is_a: PW:0000099 [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 amino acids." [InHouse:PW InHouse dictionary "Definition compiled bi the PW editorial board"] is_a: PW:0000002 [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. " [Technical glossary:http\://morelife.org/glossary/ "Online technical glossary"] is_a: PW:0000132 [Term] id: PW:0000134 name: glutathione metabolic pathway is_a: PW:0000132 is_a: PW:0000217 [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"] is_a: PW:0000002 [Term] id: PW:0000136 name: thiamine metabolic pathway is_a: PW:0000135 [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. " [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000135 [Term] id: PW:0000138 name: Vitamin B6 metabolic pathway def: "Those 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." [OneLook\, NIH :www.onelook.com and linkss "Wikipedia and links to NIH Office of Dietary Supplements"] is_a: PW:0000135 [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 various metabolic reactions and processes." [OneLook:www.onelook.com> "Online collection of dictionaries\, Wikipediaa"] is_a: PW:0000135 [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 is_a: PW:0000398 [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. " [PneLook:www.onelook.com "Online collection of dictionaries - Wikipedia"] is_a: PW:0000135 [Term] id: PW:0000142 name: ubiquinone biosynthetic pathway def: "Those metabolic reactions involved in the biosynthesis of ubiqunone\, also known as coenzyme Q. Ubiquinone is a member of the mitochondrial respiratory chain and plays important roles in cellular metabolism." [Onelook\, PubMed:PMID\: 14757233 "Dorland/s and a review article in PubMed"] is_a: PW:0000135 [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." [PubMed:PMID\: 12169433 "Review article"] is_a: PW:0000467 [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." [PubMed:2001\, v.27\, 171-179. "Definition compiled based on a review article published in Neuropathology and Applied Neurobiology"] is_a: PW:0000417 [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 or polysaccharides. Polysaccharides are polymers usually more than ten monosaccharides residues long forming branched or unbranched chains." [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000002 [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 [Term] id: PW:0000148 name: alkaloid biosynthetic pathway I is_a: PW:0000147 [Term] id: PW:0000149 name: alkaloid biosynthetic pathway II is_a: PW:0000147 [Term] id: PW:0000150 name: stilbene, coumarine and lignin biosynthetic pathway is_a: PW:0000147 [Term] id: PW:0000151 name: starch and sucrose metabolic pathway is_a: PW:0000005 [Term] id: PW:0000152 name: aminosugars metabolic pathway def: "Those metabolic reactions involved in the synthesis\, utilization and/or degradation of aminosugars - sugars in which an amino group substituent has replaced a hydroxyl group. The aminosugars and their acyl derivatives are constituents of a variety of polysaccharides\, glycoproteins\, and glycolipids. " [OneLook:www.onelook.com "Online collection of dictionaries"] comment: Based on Dorland's Medical dictionary is_a: PW:0000005 [Term] id: PW:0000153 name: glycerolipid metabolic pathway def: "Those metabolic reactions involved in the synthesis\, utilization and/or degradation of glycerolipids - acyl esters of glycerol. Glycerolipid is a trihydroxy sugar alcohol that is the backbone of many lipids and an important intermediate in carbohydrate and lipid metabolism. " [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000010 [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." [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000005 [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_a: PW:0000010 [Term] id: PW:0000156 name: prostaglandin metabolic pathway is_a: PW:0000461 is_a: PW:0000485 [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 heteropolysaccharides having disaccharide repeating units containing an N-acetylhexosamine and a hexose or hexuronic acid; either or both residues may be sulfated. " [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000146 [Term] id: PW:0000158 name: Ras family signaling pathway def: "The Ras family mediated signaling pathway 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 [Term] id: PW:0000159 name: Rab family signaling pathway def: "Rab family mediated signaling pathways are involved in intracellular vesicle trafficking. " [XXPubMed:To be added "Articles at home"] is_a: PW:0000006 [Term] id: PW:0000160 name: Ran family signaling pathway def: "Ran family mediated signaling pathways are involved in nucleocytoplasmic trafficking. " [PubMed:to be added] is_a: PW:0000006 [Term] id: PW:0000161 name: glycosylphosphatidylinositol anchor biosynthetic pathway def: "Those metabolic reactions involved in the synthesis of glycosylphosphatidylinositol anchor." [InHouse:InHouse PW dictionary "Definition compiled by the PW editorial board"] synonym: "GPI anchor biosynthesis" [] is_a: PW:0000146 [Term] id: PW:0000162 name: glycosphingolipid biosynthetic pathway - lactoseries is_a: PW:0000197 [Term] id: PW:0000163 name: glycosphingolipid biosynthetic pathway - neolactoseries is_a: PW:0000197 [Term] id: PW:0000164 name: ganglioside biosynthetic pathway def: "Those metabolic reactions involved in the biosynthesis of ganglioside - any of a group of glycosphingolipids in which the polar head group on ceramide is a sialic acid containing oligosaccharide linked via a glucose residue. They occur predominantly in tissues of the central nervous system. The most basic core structure is ceramide-glucose-galactose-N-acetylneuraminic acid." [OneLook:www.onelook.com "Online collection of dictionaries - Dorland's."] is_a: PW:0000197 [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] is_a: PW:0000132 [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 - and nicotinamide - the amide form of nicotinic acid\, or vitamin B3." [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000135 [Term] id: PW:0000167 name: pantothenate and CoA biosynthetic pathway is_a: PW:0000135 [Term] id: PW:0000168 name: cytokine, chemokine, growth factor mediated signaling pathway def: "Those pathways that are triggered through the binding of a cytokine\, chemokine or growth factor to its particular receptor. " [InHouse:PW dictionary "Definition compiled by the PW editorial board."] is_a: PW:0000003 [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." [PubMed:Neuron\, 2004\, v42\, p897-912; Cellular Signaling\, 2004\, v16\, p127-36. "Articles in PubMed"] synonym: "NGF signaling pathway" [] is_a: PW:0000168 [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. " [MCW e-journal:J. Mol. Evolo.2000\, v50\, p397-412 "Review article on EGF receptors and ligands", PubMed:12814936 "Review article"] synonym: "EGF/neuregulin signaling pathway" [] is_a: PW:0000168 [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 [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" [] is_a: PW:0000173 [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" [] is_a: PW:0000171 [Term] id: PW:0000174 name: metabolic syndrome def: "The metabolic syndrome is a rather broad category that may include distinct genetic diseases and which involves the disturbance of several biochemical and metabolic pathways such as lipid\, glucose and cholesterol metabolism\, insulin resistance." [PubMed:2004\, v. 17\, 38047. "From an article in Physiological Genomics"] is_a: PW:0000020 [Term] id: PW:0000175 name: familial combined hyperlipidemia 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" [] is_a: PW:0000174 [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 overexpression and VEGF-mediated signaling are thought to play a role in diabetic retinopathy" [InHouse:PW dictionary "Definition compiled by the PW editorial team"] is_a: PW:0000013 [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 is_a: PW:0000300 [Term] id: PW:0000178 name: neurological disorder 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 [Term] id: PW:0000179 name: tuberous sclerosis complex 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" [] is_a: PW:0000178 [Term] id: PW:0000180 name: mTOR signaling pathway def: "mTOR signaling pathway controls processes such as cell growth or those that determine the size of cells and organs and is regulated or responds to growth factors\, energy metabolites and/ot level of nutrients." [PubMed:2004\, v. 29(1)\, 32-38. "From an article in TIBS"] is_a: PW:0000003 [Term] id: PW:0000181 name: pathways of protein folding, sorting, modification, degradation def: "The pathways thereby proteins fold or are maintained in a particular folding state\, are modified to be sorted for translocation to particular cellular localizations or sorted for degradation and finally\, are degraded." [PW InHouse dictionary:www.onelook.com "Online collection of dictionaries - adapted from Dorland's."] is_a: PW:0000019 [Term] id: PW:0000269 name: protein folding pathway def: "Those reactions and molecular interactions involving chaperones and folding enzymes necessary for the proper folding of proteins in the endoplasmic reticulum. It also includes quality control and ER-associated degradation of misfolded proteins." [MCW e-journals:Current Opinions in Cell Biology "Review article in v16 (4)\, p343-349."] is_a: PW:0000181 [Term] id: PW:0000270 name: presynaptic differentiation is_a: PW:0000261 [Term] id: PW:0000271 name: postsynaptic differentiation is_a: PW:0000261 [Term] id: PW:0000272 name: neuron-to-neuron signaling pathways is_a: PW:0000059 [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"] is_a: PW:0000272 [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. ""] synonym: "Neurotransmission pathway" [] is_a: PW:0000272 [Term] id: PW:0000275 name: cell death pathway def: "All pathways that are involved in cell death. " [PW:InHouse "Definition compiled by the PW editorial board."] is_a: PW:0000004 [Term] id: PW:0000276 name: non-apoptotic cell death pathway is_a: PW:0000275 [Term] id: PW:0000277 name: senescence pathway is_a: PW:0000276 [Term] id: PW:0000278 name: autophagy pathway def: "A form of cell death involving the segregation of part of the cell's own cytoplasmic material within a membrane and its digestion after fusion of the segregated vacuole with a lysosome. " [Onelook:www.onelook.com "Online collection of dictionaries - Dorland's"] is_a: PW:0000276 [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 [Term] id: PW:0000280 name: secretory pathway is_a: PW:0000426 [Term] id: PW:0000281 name: endocytic pathway is_a: PW:0000426 [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." [InHouse:PW dictionary "A compiled definition"] is_a: PW:0000107 [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 is_a: PW:0000262 [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 is_a: PW:0000283 [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 is_a: PW:0000524 [Term] id: PW:0000286 name: integrin signaling pathway def: "Integrins - a large family of transmembrane receptors\, translate positional cues within the extracellular matrix into biochemical signals that couple to many downstream pathways. Alone or through synergy with growth factors\, integrins regulate multiple processes including organogenesis\, gene expression\, cell proliferation\, differentiation\, migration and death. " [PubMed:PMID\: 15009204 \, PMID\: 14570568; 15276463 "Review articles \, Nature reviews\, Annu. Rev. Cell. Dev. Biol.; Cardiovascular Research"] is_a: PW:0000332 [Term] id: PW:0000287 name: altered programmed cell death def: "Those pathways of programmed cell death 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 is_a: PW:0000289 [Term] id: PW:0000288 name: altered intrinsic apoptotic pathway def: "The 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 is_a: PW:0000287 [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 is_a: PW:0000275 [Term] id: PW:0000290 name: altered pathway of replication, 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:Inhouse4 "Definition compiled by the PW editorial board."] is_a: PW:0000085 is_a: PW:0000263 [Term] id: PW:0000291 name: altered double strand break repair pathway def: "Those pathways of double strand break repair that deviate from what their normal course should be. Aberrant double strand repair pathways\, alone or in combination with other pathways\, underlie various diseases. " [PW:InHouse "Definition compiled by the PW editorial board."] is_a: PW:0000131 is_a: PW:0000292 [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 is_a: PW:0000290 [Term] id: PW:0000293 name: altered pathway of protein folding, sorting, modification and degradation def: "Those pathways of protein folding\, sorting and degradation that deviate from what their normal course should be. Aberrant pathways of protein folding\, sorting and degradation\, alone or in combination with other pathways underlie various diseases. " [PW:InHouse "Definition compiled by the PW editorial board."] is_a: PW:0000181 is_a: PW:0000263 [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 is_a: PW:0000418 [Term] id: PW:0000295 name: altered integrin 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. " [PubMed:PMID\: 15276463 "Review articel in Cardiovascular Research\, 2004."] is_a: PW:0000286 is_a: PW:0000336 [Term] id: PW:0000296 name: hypertrophic cardimyopathy def: "Hypertrophic cardiomyopathy\, or HCM\, is a disease of the myocardium (the muscle of the heart) in which a portion of the myocardium is hypertrophied (thickened). Many physiological and pathological conditions as well as many pathways could lead to a hypertrophic response. " [OneLook\, PubMed:www.onelook.org\, PMID\: 15276462 "Online collection of dictionaries - Wikipedia\, article"] is_a: PW:0000022 [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. " [PubMed:PMID\: 14515146 "Review article"] synonym: "PDGF signaling pathway" [] is_a: PW:0000168 [Term] id: PW:0000298 name: altered cytokine, chemokine, growth factor mediated signaling pathway def: "Those chemokie\, cytokine\, growth factor mediated signaling pathways that deviate from what their normal course should be. Aberrant growth factor\, cytokine\, chemokine 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 is_a: PW:0000264 [Term] id: PW:0000299 name: myocardial infarction 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 [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 [Term] id: PW:0000301 name: renal failure 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 [Term] id: PW:0000302 name: glomerulonephritis 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 [Term] id: PW:0000303 name: p53-dependent G1/S DNA damage checkpoint pathway is_a: PW:0000095 [Term] id: PW:0000304 name: p53-independent G1/S DNA damage checkpoint pathway def: "The p53-independent pathway of CDKs inhibition." [InHouse:PW dictionary "Definition compiled by the PW editorial board based on the information at the Reactome."] is_a: PW:0000095 [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 is_a: PW:0000262 [Term] id: PW:0000306 name: altered galactose metabolic pathway def: "Those pathways of galactose metabolism that deviate from what their normal course should be. Aberrant galactose metabolic pathways\, alone or in combination with other pathways underlie 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 is_a: PW:0000305 [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 [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 [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 [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 [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 [Term] id: PW:0000312 name: stress-regulated MAPK signaling pathway def: "A group of MAPK signaling pathways that are responding to stress or injury." [PubMed :PMID\: 10209154 ; PMID\: 14570565 "Two review articles on MAPK"] synonym: "SAPK signaling pathway" [] is_a: PW:0000007 [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." [PubMed :PMID\: 15102441 "Review articel on the JNK MAPK pathway"] synonym: "JNK signaling pathway" [] is_a: PW:0000312 [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" [] is_a: PW:0000003 [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 [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" [] is_a: PW:0000314 [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." [pUBmED:PMID\: 11983154 \,PMID\: 12975316 "Review articles in Cell\, Genes and Development"] synonym: "NFAT signaling pathway" [] is_a: PW:0000315 [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" [] is_a: PW:0000264 is_a: PW:0000314 [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 is_a: PW:0000318 [Term] id: PW:0000320 name: novobiocin biosynthetic pathway is_a: PW:0000147 [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 is_a: PW:0000264 [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." [PubMed:PMID\: 15093606 "Review article on ephrins and their receptors"] is_a: PW:0000332 [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 cancerer"] is_a: PW:0000322 is_a: PW:0000336 [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 is_a: PW:0000336 [Term] id: PW:0000325 name: protein degradation pathway def: "Those pathways involved in the degradation of proteins." [InHouse:InHouse PW dictionary "Definition compiled by the PW editorial board."] is_a: PW:0000181 [Term] id: PW:0000326 name: altered protein degradation pathway is_a: PW:0000293 is_a: PW:0000325 [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 [Term] id: PW:0000328 name: fibroblast growth factor signaling pathway synonym: "FGF signaling pathway" [] is_a: PW:0000168 [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." [PubMed:PMID\: 15473857 "Review article and references therein"] synonym: "TGF-beta superfamily mediated signaling pathways" [] is_a: PW:0000168 [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\, others." [PubMed:PMID\: 15368350 "Review article in J Cell Biochem"] synonym: "BMP signaling pathway - SMAD dependent" [] is_a: PW:0000329 [Term] id: PW:0000331 name: activin signaling pathway is_a: PW:0000329 [Term] id: PW:0000332 name: cell-cell signaling pathway is_a: PW:0000003 [Term] id: PW:0000333 name: cadherins signaling pathway is_a: PW:0000332 [Term] id: PW:0000334 name: connexins signaling pathway is_a: PW:0000332 [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 types of cancer\, renal conditions\, pulmonary hypertension." [PW dictionary:InHouse PW dictionary "Definition compiled by the PW editorial board."] is_a: PW:0000298 is_a: PW:0000329 [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:0000264 is_a: PW:0000332 [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 [Term] id: PW:0000338 name: altered cadherins mediated signaling pathway is_a: PW:0000333 [Term] id: PW:0000339 name: altered connexins mediated signaling pathway is_a: PW:0000334 [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)\, members of the CSL complex." [InHouse:PW dictionary "Definition compiled by the PW editorial board"] is_a: PW:0000324 [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 [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) reanscriptional repressors." [InHouse:PW dictionary "Definition compiled by the PW editorial boardd."] is_a: PW:0000324 [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 [Term] id: PW:0000344 name: cerebrovascular disease pathway is_a: PW:0000013 [Term] id: PW:0000345 name: cerebral arterial diseases is_a: PW:0000344 [Term] id: PW:0000346 name: CADASIL 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 [Term] id: PW:0000347 name: cardiovascular abnormalities is_a: PW:0000020 [Term] id: PW:0000348 name: congenital heart defects is_a: PW:0000347 [Term] id: PW:0000349 name: Alagille syndrome 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 [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" [] is_a: PW:0000243 is_a: PW:0000298 [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" [] is_a: PW:0000350 [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" [] is_a: PW:0000350 [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 dictionaryry "Definition compiled by the PW editorial board."] synonym: "altered VEGF signaling pathway involving proteins affecting its expression" [] is_a: PW:0000350 [Term] id: PW:0000354 name: glycerophospholipid metabolic pathway def: "Those metabolic reactions involved in the synthesis\, utilization and/or degradation pf glycerophospholipids - amphipathic lipids with a glycerol backbone." [InHouse:PW InHouse dictionary "Definition compiled by the PW editorial board."] is_a: PW:0000153 is_a: PW:0000155 [Term] id: PW:0000355 name: homeostasis pathway def: "Those pathways involved in the maintenance of the internal environment of an organism\, the stability of normal body states\, the feedback regulatory mechanisms." [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000004 [Term] id: PW:0000356 name: oxygen homeostasis pathway is_a: PW:0000355 [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 [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 is_a: PW:0000355 [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 is_a: PW:0000358 [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" [] is_a: PW:0000356 [Term] id: PW:0000361 name: altered oxygen homeostasis pathway is_a: PW:0000356 is_a: PW:0000358 [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"] is_a: PW:0000356 [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 via Jak-dependent activation of STAT. " [PubMed:PMID\: 12079865\, PMID\: 11239410 . "Review article - Ann. N.Y. Acd. Sci."] is_a: PW:0000357 is_a: PW:0000467 [Term] id: PW:0000364 name: altered leptin system pathway is_a: PW:0000359 is_a: PW:0000363 is_a: PW:0000511 [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:0000357 is_a: PW:0000467 [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 is_a: PW:0000365 is_a: PW:0000511 [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 is_a: PW:0000264 [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:0000209 [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 is_a: PW:0000378 [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 [Term] id: PW:0000371 name: calcium homeostasis pathway is_a: PW:0000355 [Term] id: PW:0000372 name: altered calcium homeostasis pathway is_a: PW:0000358 is_a: PW:0000371 [Term] id: PW:0000373 name: glutathione conjugation pathway def: "The glutathione conjugation of endogenous and exogenous electrophilic compounds represents a major pathway of cellular defense. The glutathione conjugates may either be excreted or undergo further processing." [MCW - book:QV 600 C335t 2001 "Casarett and Doull's toxicology \: the basic science of poisons / editor\, Curtis D. Klaassen"] is_a: PW:0000124 is_a: PW:0000378 [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 [Term] id: PW:0000375 name: bioactivation pathway via cytochrome P450 def: "The major pathway of xenobiotic activation to produce reactive intermediates." [Book: QV 600 C335t 2001 "of drug-metabolizing enzyme expression"] is_a: PW:0000124 [Term] id: PW:0000376 name: cytochrome P450-independent bioactivation pathway is_a: PW:0000124 [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 [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." [InHouse:PW InHouse dictionary "Definition compiled by the PW editorial board."] is_a: PW:0000237 [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 is 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." [PubMed:PMID\: 15603751; PMID\: 15952902 "Review articles in PubMed"] synonym: "ER stress - UPR pathway" [] is_a: PW:0000237 is_a: PW:0000269 [Term] id: PW:0000380 name: transport pathway for the elimination of drugs, endogenous or exogenous compounds and metabolites is_a: PW:0000103 is_a: PW:0000124 is_a: PW:0000378 [Term] id: PW:0000381 name: multidrug resistance-associated proteins mediated transport pathway synonym: "MRP mediated pathway" [] is_a: PW:0000380 [Term] id: PW:0000382 name: multidrug resistance proteins mediated transport pathway synonym: "MDR mediated pathway" [] is_a: PW:0000380 [Term] id: PW:0000383 name: multispecific organic anion transporter mediated transport pathway synonym: "OAT mediated pathway" [] is_a: PW:0000380 [Term] id: PW:0000384 name: G2/M DNA damage checkpoint pathway is_a: PW:0000096 [Term] id: PW:0000385 name: G2/M DNA replication checkpoint pathway is_a: PW:0000096 [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 [Term] id: PW:0000387 name: Arf family signaling pathway def: "Arf family mediated signaling pathways are involved in intracellular vesicle trafficking. " [PubMed:To be added] is_a: PW:0000006 [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 [Term] id: PW:0000389 name: altered pathway pertinent to signaling in the brain is_a: PW:0000059 is_a: PW:0000264 [Term] id: PW:0000390 name: altered Reelin signaling pathway is_a: PW:0000388 is_a: PW:0000389 [Term] id: PW:0000391 name: altered small G proteins - the Ras superfamily - mediated signaling pathway is_a: PW:0000006 is_a: PW:0000264 [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 is_a: PW:0000525 [Term] id: PW:0000393 name: altered mTOR signaling pathway is_a: PW:0000180 [Term] id: PW:0000394 name: dopamine signaling pathway synonym: "dopaminergic pathway" [] is_a: PW:0000059 [Term] id: PW:0000395 name: altered dopamine signaling pathway synonym: "altered dopaminergic pathway" [] is_a: PW:0000389 is_a: PW:0000394 [Term] id: PW:0000396 name: spermidine metabolic pathway is_a: PW:0000211 [Term] id: PW:0000397 name: Vitamin B12 (cobalamin) metabolic pathway is_a: PW:0000135 [Term] id: PW:0000398 name: homocysteine metabolic pathway def: "Homocysteine metabolism is at the interesection of two pathways\: the remethylation or the methionine cycle pathway and the transulfuration pathway. 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" [] is_a: PW:0000132 [Term] id: PW:0000399 name: remethylation pathway of homocysteine metabolism - cobalamin dependent is_a: PW:0000398 [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"] is_a: PW:0000398 [Term] id: PW:0000401 name: remethylation pathway of homocysteine metabolism - cobalamin independent, betaine dependent is_a: PW:0000398 [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 is_a: PW:0000262 [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 is_a: PW:0000262 [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 methionne\, creatine supplies energy to muscle cells." [PubMed; Onelook:PMID\: 10893433; www.onelook.com "Review article in PubMed\, Wikipedia"] is_a: PW:0000033 is_a: PW:0000132 [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 [Term] id: PW:0000406 name: metabolic pathway pertinent to the brain is_a: PW:0000002 [Term] id: PW:0000407 name: neurotransmitter metabolic pathway is_a: PW:0000406 [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 [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 collectio of dictionaries - Wikipedia"] is_a: PW:0000443 [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 importnat roles in a number of conditions such as depression\, bipolar disorder\, anxiety." [OneLook:www.onelook.com "Online collection of dictionaries"] is_a: PW:0000444 [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 [Term] id: PW:0000412 name: gamma-aminobutyric acid metabolic pathway synonym: "GABA metabolism" [] is_a: PW:0000446 [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 hetercyclic 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 [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 [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 [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" [] synonym: "sumoylation pathway" [] is_a: PW:0000433 [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 protens is a key signal." [PubMed:PMID\: 10993052 "Review article in Pubmed"] is_a: PW:0000325 [Term] id: PW:0000418 name: altered ubiquitin, ubiquitin-like degradation pathway is_a: PW:0000326 is_a: PW:0000417 [Term] id: PW:0000419 name: water transport pathway is_a: PW:0000103 [Term] id: PW:0000420 name: altered c-Jun N-terminal kinase MAPK signaling pathway synonym: "altered JNK signaling pathway" [] is_a: PW:0000313 is_a: PW:0000422 [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 MAAPK 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" [] is_a: PW:0000007 is_a: PW:0000264 [Term] id: PW:0000422 name: altered stress-regulated MAPK pathway synonym: "altered SAPK pathways" [] is_a: PW:0000312 is_a: PW:0000421 [Term] id: PW:0000423 name: surfactant homeostasis pathway is_a: PW:0000355 [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 is_a: PW:0000423 [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 [Term] id: PW:0000426 name: protein sorting pathway is_a: PW:0000181 is_a: PW:0000535 [Term] id: PW:0000427 name: molybdenum cofactor biosynthetic pathway is_a: PW:0000135 [Term] id: PW:0000428 name: altered molybdenum cofactor biosynthetic pathway is_a: PW:0000427 is_a: PW:0000429 [Term] id: PW:0000429 name: altered metabolic pathway of cofactors and vitamins is_a: PW:0000135 is_a: PW:0000262 [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 is_a: PW:0000181 [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 [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 [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 [Term] id: PW:0000436 name: primary amine neurotransmitter metabolic pathway is_a: PW:0000407 [Term] id: PW:0000437 name: amino acid neurotransmitter metabolic pathway is_a: PW:0000407 [Term] id: PW:0000438 name: alanine metabolic pathway is_a: PW:0000028 [Term] id: PW:0000439 name: aspartate metabolic pathway is_a: PW:0000028 is_a: PW:0000445 [Term] id: PW:0000440 name: glycine metabolic pathway is_a: PW:0000047 is_a: PW:0000446 [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 - Wikipediaia"] synonym: "adrenaline metabolism" [] is_a: PW:0000443 [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"] synonym: "noradrenaline metabolism" [] is_a: PW:0000443 [Term] id: PW:0000443 name: catecholamine neurotransmitter metabolic pathway def: "Those enxymatic 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"] is_a: PW:0000436 [Term] id: PW:0000444 name: indoleamine and related compounds neurotransmitter 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 [Term] id: PW:0000445 name: excitatory neurotransmitter metabolic pathway is_a: PW:0000437 [Term] id: PW:0000446 name: inhibitory neurotransmitter metabolic pathway is_a: PW:0000437 [Term] id: PW:0000447 name: peptide neurotransmitter metabolic pathway is_a: PW:0000407 [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 [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 [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 [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 [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 [Term] id: PW:0000453 name: sterol biosynthetic pathway synonym: "steroid alcohol" [] is_a: PW:0000248 [Term] id: PW:0000454 name: cholesterol biosynthetic pathway is_a: PW:0000453 [Term] id: PW:0000455 name: Excitatory synaptic transmission pathway synonym: "Excitatory neurotransmission pathway" [] is_a: PW:0000274 [Term] id: PW:0000456 name: Inhibitory synaptic transmission pathway synonym: "Inhibitory neurotransmismission pathway" [] is_a: PW:0000274 [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. Ir 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 [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. Studes 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 [Term] id: PW:0000459 name: apelin signaling pathway def: "apelin signaling pathway appears to play a role in the regulation of cardiovascular function as well as water and food intake." [PubMed:PMID\: 15601620; PMID\: 15907343 "review articles"] is_a: PW:0000003 [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." [OneLook:www.onelook.com "Wikipedia at OneLook"] is_a: PW:0000058 [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 [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 [Term] id: PW:0000463 name: cytochrome P450 monooxygenase mediated pathway of arachdonic 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 [Term] id: PW:0000464 name: leukotriene metabolic pathway is_a: PW:0000462 is_a: PW:0000485 [Term] id: PW:0000465 name: hormone mediated signaling pathway def: "Hormones are a class of molecules that are used as messengers between cells and serve as signal to the target cell. Vertebrate hormones belong to four classes\: amine-derived. peptide hormones\, steroid hormones and lipid and phospholipid hormones." [OneLook:www.onelook.com "online collection of dictionaries - wikipedia"] is_a: PW:0000003 [Term] id: PW:0000466 name: amine and amino acid-derived hormone signaling pathway is_a: PW:0000465 [Term] id: PW:0000467 name: peptide and protein hormone signaling pathway is_a: PW:0000465 [Term] id: PW:0000468 name: steroid hormone signaling pathway is_a: PW:0000465 [Term] id: PW:0000469 name: lipid hormone signaling pathway is_a: PW:0000465 [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 [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" [] is_a: PW:0000470 [Term] id: PW:0000472 name: brain natriuretic peptide signaling pathway def: "brain natriuretic peptide signaling pathway appear to elicit cardiovascular\, renal and endocrine functions similar to those elicited by the atrial natriueritc peptide." [PubMed:PMID\: 15911062 PMID\: 15758553; PMID\: 1524624 "Review articles in PubMed"] synonym: "BNP signaling pathway" [] is_a: PW:0000470 [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" [] synonym: "CNP signaling pathway" [] is_a: PW:0000470 [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 clot. Coagulation and inflammatory pathways are connected in a cross talk. Impaired anticoagulation pathways affect this balanced dialog and lead to various conditions and infections." [OneLook:www.onelook.com "Online collection of dictionaries - Dorland's\, Wikipedia"] synonym: "secondary hemostasis" [] relationship: part_of PW:0000475 [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." [Various:PubMed\, Wikipedia\, Reactome] synonym: "haemostasis pathway" [] is_a: PW:0000476 [Term] id: PW:0000476 name: cardiovascular system homeostasis pathway is_a: PW:0000355 [Term] id: PW:0000477 name: natural anticoagulant pathway is_a: PW:0000476 [Term] id: PW:0000478 name: tissue factor pathway inhibitor synonym: "TFPI" [] is_a: PW:0000477 [Term] id: PW:0000479 name: heparin-antithrombin pathway is_a: PW:0000477 [Term] id: PW:0000480 name: protein C anticoagulant pathway is_a: PW:0000477 [Term] id: PW:0000481 name: fibrinolytic cascade pathway is_a: PW:0000476 [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." [PubMed:PMID\: 16011471 "Review article in PubMed"] is_a: PW:0000010 [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 is_a: PW:0000262 [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 is_a: PW:0000483 [Term] id: PW:0000485 name: prostaglandin and leukotriene metabolic pathway is_a: PW:0000460 [Term] id: PW:0000486 name: major histocompatibility complex class I antigen presentation pathway def: "Antigen processing and prsentation by MHC class I molecules primarily involves peptides derived from endogenous\, cytosolic proteins. " [PubMed:16181325 "Review article on MHC I pathway"] synonym: "MHC class I antigen presentation pathway" [] is_a: PW:0000235 [Term] id: PW:0000487 name: major histocompatibility complex dlass II antigen presentation pathway def: "Antigen processing and presentation by MHC class II molecules involves peptides derived from exogenous proteins and from endogenous\, lysosomal proteins." [XXPubMed:16181322 "Brief review on MHC mediated pathways"] is_a: PW:0000235 [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 chpaerones for loading the HMC class I molecules with the 8-10 amino acid peptides " [PubMed:16181325 "Review article on MHC class I complex pathway"] relationship: part_of PW:0000486 [Term] id: PW:0000489 name: angiopoietin signaling pathway def: "Angiopoietin signaling pathway is onvolved in the regulation of angiogenic remodelling. Recent studies suggest that the pathway may also be invfolved in lymphangiogenesis and possibly in the development of hematopoietic system." [PubMed:PMID\: 16225862 "Review article on angiopoietin pathway in angiogenic remodelling and possibly in lymphangiogenesis"] is_a: PW:0000168 [Term] id: PW:0000490 name: transforming growth factor-beta signaling pathway - SMAD dependent is_a: PW:0000206 [Term] id: PW:0000491 name: vasopressin signaling pathway def: "The peptide hormone vasopressin plays a central role in osmotic and cardiovascular homeostasis. " [PubMed:PMID\: 14624682 "Review"] is_a: PW:0000467 [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. " [PubMed:PMID\: 15883759 PMID\: 15638741 \, PMID\: 12676165 \, PMID\: 12793984 \, PMID\: 16816138 "Several review articles."] synonym: "RAS system signaling pathway" [] is_a: PW:0000003 [Term] id: PW:0000493 name: corticotropin-releasing hormone signaling pathway synonym: "CRH" [] is_a: PW:0000467 [Term] id: PW:0000494 name: oxytocin signling pathway def: "The peptide hormone oxytocin plays a central role in parturition\, lactation and sexual behavior." [PubMed:PMID\: 14624682 "Review"] is_a: PW:0000467 [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 remodelling 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" [] is_a: PW:0000168 [Term] id: PW:0000496 name: exogenous pathway relationship: part_of PW:0000482 [Term] id: PW:0000497 name: endogenous pathway relationship: part_of PW:0000482 [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 imay prevent the development of atherosclerosis by reducing the accumulation of cholesterol in the wall of arteries." [PubMed:PMID\: 16258026 "review article"] synonym: "RCT pathway" [] synonym: "selective cholesterol uptake pathway " [] is_a: PW:0000103 relationship: part_of PW:0000482 [Term] id: PW:0000499 name: Nuclear Factor Kappa B signaling pathway synonym: "NF-kB signaling pathway" [] synonym: "NF-kappaB signaling pathway" [] is_a: PW:0000236 [Term] id: PW:0000500 name: tyrosine-derived hormone signaling pathway is_a: PW:0000466 [Term] id: PW:0000501 name: thyroid hormone signaling pathway is_a: PW:0000500 [Term] id: PW:0000502 name: complement system pathway def: "The complement system which consists of three pathways that converge in the generation of C3 convertase\, is part of the innate immune response and bridges the innate and adaptive immunity" [PubMed:PMID\: 11287977 "Review article"] relationship: part_of PW:0000234 [Term] id: PW:0000503 name: classical complement pathway is_a: PW:0000502 [Term] id: PW:0000504 name: mannose-binding lectin complement pathway is_a: PW:0000502 [Term] id: PW:0000505 name: alternative complement pathway is_a: PW:0000502 [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 [Term] id: PW:0000507 name: estrogen signaling pathway is_a: PW:0000468 [Term] id: PW:0000508 name: platelet aggregation pathway synonym: "primary hemostasis" [] relationship: part_of PW:0000475 [Term] id: PW:0000509 name: altered hormone mediated signaling pathway is_a: PW:0000264 is_a: PW:0000465 [Term] id: PW:0000510 name: altered insulin-like growth factor signaling pathway is_a: PW:0000238 is_a: PW:0000511 [Term] id: PW:0000511 name: altered peptide and protein hormone signaling pathway is_a: PW:0000467 is_a: PW:0000509 [Term] id: PW:0000512 name: Interleukin mediated signaling pathway is_a: PW:0000168 [Term] id: PW:0000513 name: Interleukin signaling pathway via interleukin-10 family members is_a: PW:0000512 [Term] id: PW:0000514 name: Interleukin signaling pathway via interleukin-6 family members is_a: PW:0000512 [Term] id: PW:0000515 name: Interleukin-10 signaling pathway is_a: PW:0000513 [Term] id: PW:0000516 name: Interleukin-6 signaling pathway is_a: PW:0000514 [Term] id: PW:0000517 name: arterial occlusive disease pathway def: "A pathway leading to a general orspecific artery occlusion." [MeSH:Medical Subject Headings] is_a: PW:0000020 [Term] id: PW:0000518 name: Atherosclerosis pathway def: "A pathway leading to the thickening of medium and large mscular arteries. While lipoprotein related pathways are of interest\, monogenic conditions such as those limked 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 [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\, Altough banned in the U.S.\, it is still widely used in developing countries. " [KEGG:http\://umbbd.msi.umn.edu/ddt/ddt_map.html "Adapted from the link at KEGG."] synonym: "DDT degradation pathway" [] is_a: PW:0000107 [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. " [KEGG:http\://umbbd.msi.umn.edu/dcb/dcb_map.html "Adapted from KEGG"] is_a: PW:0000107 [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. compound." [KEGG:http\://umbbd.msi.umn.edu/dce/dce_map.html "Adapted from the link at KEGG"] is_a: PW:0000107 [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." [OneLook:www.onelook.com "Online collections of dictionaries - wikipedia"] is_a: PW:0000147 [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." [OneLook:http\://www.onelook.com "Online collection of dictionaries - wikipedia"] is_a: PW:0000058 [Term] id: PW:0000524 name: heparan sulfate biosynthetic pathway def: "Those metabolic reactions invbolved 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." [OneLook:www.onelook.com "Online collection of dictionaries - Dorland's"] is_a: PW:0000157 [Term] id: PW:0000525 name: Ras mediated signalign pathway is_a: PW:0000158 [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 featured are also shared by the renin-angiotensin system (RAS); the two systems can interact and cross-talk." [XX:PMID\: 12558525\, PMID\: 12793984 PMID\: 16177542\, PMID\: 12676165] synonym: "KKS system signaling pathway" [] is_a: PW:0000003 [Term] id: PW:0000527 name: Angiotensin II signaling pathway through the 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 plietropic effects\, on anbgiotensin receptors\, angiotensin type 2 receptor."] is_a: PW:0000244 [Term] id: PW:0000528 name: Angiotensin II signaling pathway through the 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 paathologies. 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 [Term] id: PW:0000529 name: angiotensin (1-7) signaling pathway def: "Angiotensin(1-7) is derived from angiotensin II through the action of angiotensin coverting 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 [Term] id: PW:0000530 name: Angiotensin III signaling pathway through the 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." [XX:PubMed 11100981\,] is_a: PW:0000457 [Term] id: PW:0000531 name: Angiotensin III signaling pathway through the 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 [Term] id: PW:0000532 name: glycogen biosynthetic pathway def: "Those metabolic reactions leading to the biosynthesis of glycogen\, a highly branched polysaccharide that consitutes the main storage form of glucose in the cell. This is a three step\, endergonic pathway." [PubMed\, online:www.onelook.com; rgd.mcw.edu "Rat article for which the term was needed and some inspiration from wikipedia"] is_a: PW:0000533 [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 consitutess the major storage form of glucose in the cell." [InHouse:www.rgd.mcw "Definition compiled by the PW editorial board."] is_a: PW:0000005 [Term] id: PW:0000534 name: glycogen degradation pathway def: "Those metabolic reaction involved in the breakdown of glycogen to glucose-6-phosphate. This is a three step\, exergonic pathway" [OneLook:www.onelook.com "Online collection of dictionaries; wikipedia"] synonym: "glycogenolysis " [] is_a: PW:0000533 [Term] id: PW:0000535 name: protein transport pathway is_a: PW:0000103 [Term] id: PW:0000536 name: constitutive secretory pathway is_a: PW:0000280 [Term] id: PW:0000537 name: regulated secretory pathway is_a: PW:0000280 [Term] id: PW:0000538 name: nuclear protein import pathway is_a: PW:0000535 [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:0000357 is_a: PW:0000467 [Term] id: PW:0000540 name: obesity pathway def: "Obesity\, usually defined as 2o% 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 metabolisms\, 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 [Term] id: PW:0000541 name: signaling pathways involving second messengers is_a: PW:0000003 [Term] id: PW:0000542 name: adenosine monophosphate-activated protein kinase (AMPK) signaling pathway def: "AMPK senses changes in cellular energy as ATP\:ADP ratio. ADP binding allosterically activates AMPK; subsequent phosphorylation events and regulation of downstream targets lead to activation/repression of energy pathways." [PubMed:PMID\: 16885148; PMID\: 15509864] synonym: "5'AMP-activated protein kinase" [] synonym: "AMPK signaling pathway" [] is_a: PW:0000003 [Term] id: PW:0000543 name: protein kinase A (PKA) signaling pathway synonym: "cAMP-dependent protein kinase A signaling pathway" [] synonym: "cAMP/PKA signaling pathway" [] is_a: PW:0000541 [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 manifetation depending on which gene in the pathway is affected." [PubMed:PMID\: 16258026 "Review article"] synonym: "altered RCT pathway" [] is_a: PW:0000484 is_a: PW:0000498 is_a: PW:0000545 [Term] id: PW:0000545 name: altered transport pathway is_a: PW:0000103 is_a: PW:0000263 [Typedef] id: part_of name: part_pf