format-version: 1.0
date: 15:05:2008 15:48
saved-by: VPetri
auto-generated-by: OBO-Edit 1.101
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 ! Pathway Ontology

[Term]
id: PW:0000003
name: signaling pathway
def: "The pathways where a signal - hormone, neurotransmitter, growth factor, peptide, any molecule - triggers one or multiple cascades of events. This involves a number of molecules, including receptors, proteins, ligands, messengers, any participating molecule. A signaling pathway may be upstream or downstream of other signaling pathways. Signaling pathways control a very broad spectrum of processes as well as pathways." [OneLook:www.onelook.com "Online collection of dictionaries"]
comment: The definition was compiled based on a number of definitions available in various dictionaries.
is_a: PW:0000001 ! Pathway Ontology

[Term]
id: PW:0000004
name: regulatory pathway
def: "The pathways that control the processes by which a cell or organism develops, adjusts, behaves, responds to conditions or changes in these conditions, or in any manner helps promote and maintain its efficient functioning." [OneLook:www.onelook.com "Online collection of dictionaries"]
comment: The definition was complied based on a number of definitions available in several dictionaries
is_a: PW:0000001 ! Pathway Ontology

[Term]
id: PW:0000005
name: carbohydrate metabolic pathway
def: "Those metabolic reactions involved in the oxidation, breakdown and synthesis of carbohydrates in the tissue. The breakdown can be utilized by the body for energy." [OneLook:www.onelook.com "Online collection of dictionaries"]
comment: The definition  was compiled using the Online Medical dictionary and the Stedman's medical dictionary available at OneLook
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000006
name: 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. Ras superfamily mediated pathways control a broad spectrum of processes. Upregulation of Ras cascades has been linked to several forms of cancer. The superfamily is structurally 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 ! signaling pathway

[Term]
id: PW:0000007
name: mitogen activated protein kinase signaling pathway
def: "The mitogen -activated protein kinase pathway groups several  serine/threonine protein kinases mediated cascades in response to a number of extracellular stimuli.  A characteristic feature of these cascades is the presence of at least three kinases in series leading to the activation of a multifunctional MAP kinase." [PubMed:PMID\: 14570565; PMID\: 14976517 "TPW review articles on MAPK"]
related_synonym: "MAPK signaling pathway" []
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000008
name: Wnt signaling pathway
def: "The secreted glycoproteins of the Wnt family regulate a wide spectrum of developmental processes and they are also playing important roles in the adult organism. Disregulation 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 ! signaling pathway

[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"]
related_synonym: "apoptotic cell death pathway" []
is_a: PW:0000275 ! cell death pathway

[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 ! classic metabolic pathway

[Term]
id: PW:0000011
name: amino acid metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of the primary or standard 20 amino acids found in proteins. Some of these metabolic pathways can give rise to non-standard amino acid - for instance carnitine or homocysteine - and the two pathway categories in these cases are entwined." [In House:In House PW dictionary "Definition supplied by the PW editorial team."]
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000012
name: nucleotide metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of nucleotides. Nucleotides, which are the units of DNA and RNA, can also play important roles in cellular energy and enzyme regulation." [InHouse:PW directory "Reference compiled by the PW editorial team"]
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000013
name: disease pathway
def: "Complex human diseases encompass a spectrum of genetic and environmental attributes that together affect the normal functioning of several molecular and cellular pathways. Their combined and accumulated effect is manifested in the anomalous phenotype of the complex condition." [InHouse:InHouse PW dictionary "Definition compiled by the PW editorial team based on the information from a number of sources"]
related_synonym: "complex human diseases" []
is_a: PW:0000001 ! Pathway Ontology

[Term]
id: PW:0000014
name: neurodegenerative disease pathway
def: "Neurodegenerative diseases group together a number of conditions of various and many times poorly understood origins that are characterized by the progressive loss of particular neurons, the formation of particular structures such as plaques and fibrils, and protein aggregates. Proteosomal degradation, programmed cell death, oxidative stress, are among a number of pathways thought to be disrupted.  " [inHouse:InHouse PW dictionary "Definition supplied by the PW editorial team"]
is_a: PW:0000013 ! disease pathway

[Term]
id: PW:0000015
name: Alzheimer disease pathway
def: "A mostly sporadic, late-onset condition affecting the central nervous system, is the most prevalent neurodegenerative disease and the most common form of dementia. It is characterized by the presence of amyloid plaques and fibril tangles. Possible pathways affected range from protein misfolding and aggregation, to oxidative stress and impaired metal homeostasis." [InHouse:InHouse PW dictionary "Definition provided by the PW editorial team"]
is_a: PW:0000014 ! neurodegenerative disease pathway

[Term]
id: PW:0000016
name: amyotrophic lateral sclerosis disease pathway
def: "A late onset, mostly sporadic neurodegenerative disease characterized by the loss of motor neurons in the brain stem and spinal cord. Various pathways are thought to be deregulated and contribute to the condition; among them calcium and/or zinc homeostasis, apoptosis, Cdk5 and calcineurin dependent processes, and in the case of the more rare, genetically inherited form of the disease, mutations in the cytosolic Cu, Zn superoxide dismutase (SOD1) and the subsequent changes in the processes that involve SOD1." [InHouse:In House PW dictionary "Definition supplied by the PW editorial team"]
related_synonym: "ALS" []
is_a: PW:0000014 ! neurodegenerative disease pathway

[Term]
id: PW:0000017
name: Huntington disease pathway
def: "An inherited form of a neurodegenerative disease caused by an expanded polyQ tract. It mostly affects the striatum and cortex, but extends to other regions later in its development. It manifests itself in movement disorders, psychiatric abnormalities, cognitive defects, and manifold pathways are disrupted." [PubMed:2004\, v.20 (3)\, 146-154. "Article in Trends in Genetics"]
is_a: PW:0000171 ! disease pathways related to polyQ repeats

[Term]
id: PW:0000018
name: Parkinson disease pathway
def: "One of the most common neurodegenerative diseases that is characterized by the loss of dopaminergic neurons  in the substantia nigra and the presence of cytoplasmic inclusions called Lewy bodies in surrounding neurons. Several pathways are thought to be deregulated; for instance, imbalance of iron homeostasis is believed to contribute to the pathogenesis of the condition." [PubMed:2004\, v.101 (15)\, 5500-5505. "Definition compiled from an article in PNAS"]
is_a: PW:0000014 ! neurodegenerative disease pathway

[Term]
id: PW:0000019
name: prion diseases pathway
def: "Prion disease - any of a group of fatal, transmissible neurodegenerative diseases caused by abnormalities of prion protein metabolism, which may result from mutations in the prion protein gene or from infection with pathogenic isoforms of the protein.  Characteristics include neuronal loss, gliosis, and extensive vacuolization of the cerebral cortex. Prion diseases may be sporadic, inherited as an autosomal dominant trait, or acquired. Human diseases include Creutzfeldt-Jakob disease, Gerstmann-Strussler syndrome, fatal familial insomnia, and kuru" [OnerLook:www.onelook.com "Online collection of dictionaries - Dorland's."]
is_a: PW:0000014 ! neurodegenerative disease pathway

[Term]
id: PW:0000020
name: cardiovascular disease pathway
def: "Cardiovascular diseases represent a very broad spectrum of conditions that can also combine with diabetes and renal failure. " [InHouse:InHouse PW dictionary "A term compiled by the PW editorial team."]
is_a: PW:0000013 ! disease pathway

[Term]
id: PW:0000021
name: hypertension
def: "Hypertension, high arterial blood pressure: various criteria for its threshold have been suggested, ranging from 140 mm Hg systolic and 90 mm Hg diastolic to as high as 200 mm Hg systolic and 110 mm Hg diastolic. Hypertension may have no known cause (essential or idiopathic h.) or be associated with other primary diseases (secondary h.)." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000020 ! cardiovascular disease pathway

[Term]
id: PW:0000022
name: cardiomyopathy
def: "Cardiomyopathy - a general diagnostic term designating primary noninflammatory disease of the heart muscle, often of obscure or unknown etiology and not the result of ischemic, hypertensive, congenital, valvular, or pericardial disease. It is usually subdivided into dilated, hypertrophic, and restrictive cardiomyopathy (1). Cardiomyopathy is the deterioration of the cardiac muscle of the heart wall. Cardiomyopathies can generally be categorized into two groups: ischemic cardiomyopathy and nonischemic cardiomyopathy (2)." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000020 ! cardiovascular disease pathway

[Term]
id: PW:0000023
name: immune response pathway
def: "The 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 ! regulatory pathway

[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 ! innate immune response pathway

[Term]
id: PW:0000025
name: glycolysis/gluconeogenesis pathway
def: "Those metabolic reactions involved in the energy-yielding, anaerobic or aerobic 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 ! carbohydrate metabolic pathway
is_a: PW:0000556 ! glucose oxidation pathway

[Term]
id: PW:0000026
name: citrate cycle pathway
def: "The series of chemical reactions that are central to all aerobic cells and constitute the citrate cycle. Also known as the tricarboxylic acid cycle, the TCA or Krebs cycle, it is the second of three metabolic pathways that are involved in fuel molecule catabolism and ATP production." [OneLook:www.onelook.com "Online collection of dictionaries"]
related_synonym: "Krebs cycle" []
related_synonym: "TCA cycle" []
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000027
name: glutamate metabolic pathway
def: "Those metabolic reactions involved in  the synthesis, utilization and/or degradation of glutamate - a salt, ester, or nonionic form of glutamic acid. Glutamate is also the major excitatory neurotransmitter." [OneLook:www.onelook.com "Online collection of dictionaries"]
comment: Definition compiled based on the information available for glutamate at OneLook
is_a: PW:0000011 ! amino acid metabolic pathway
is_a: PW:0000445 ! excitatory neurotransmitter metabolic pathway

[Term]
id: PW:0000028
name: alanine and aspartate metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of alanine and aspartate - two non-essential amino acids required for the breakdown of glucose and proteins as well as for protein biosynthesis." [OneLook:www.onelook.com "Online collection of dictionaries"]
comment: The definition was compiled based on the information on alanine and aspartate available at OneLook
is_a: PW:0000011 ! amino acid metabolic pathway

[Term]
id: PW:0000029
name: fatty acid biosynthetic pathway
alt_id: PW:0000030
related_synonym: "fatty acid biosynthesis (path 2)" []
is_a: PW:0000058 ! fatty acid metabolic pathway

[Term]
id: PW:0000031
name: purine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of purines. Purines consist of a pyrimidine ring fused to an imidazole ring. The nucleobases adenine and guanine in DNA are purines." [OneLook:www.onelook.com "Online collection of dictionaries - Wikipedia"]
is_a: PW:0000012 ! nucleotide metabolic pathway

[Term]
id: PW:0000032
name: pyrimidine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of pyrimidines. Cytosine, thymine and uracil - the nucleobases found in nucleic acids, are pyrimidine derivatives. " [OneLook:www.onelook.com "Online collection of dictionaries - Wikipedia"]
is_a: PW:0000012 ! nucleotide metabolic pathway

[Term]
id: PW:0000033
name: energy metabolic pathway
def: "Those metabolic reactions whose role is to release or to provide energy." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000034
name: oxidative phosphorylation pathway
def: "Those metabolic reactions involved in coupling ATP phosphorylation to the respiratory chain." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000033 ! energy metabolic pathway

[Term]
id: PW:0000035
name: ATP synthetic pathway
def: "Those metabolic reactions involved in  the synthesis of adenosine triphosphate (ATP) - a molecule present in all living cells which serves as an energy source for many metabolic processes and is required for the synthesis of ribonucleic acid." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000033 ! energy metabolic pathway

[Term]
id: PW:0000036
name: nitrogen metabolic pathway
def: "Those metabolic reactions involving nitrogen and nitrogenous compounds." [PW InHouse dictionary:PW InHouse dictionary "Definition compiled by the PW editorial team."]
is_a: PW:0000033 ! energy metabolic pathway

[Term]
id: PW:0000037
name: sulfur metabolic pathway
def: "Those metabolic reactions involving sulfur or compounds that contain sulfur such as cysteine, methionine and glutathione." [PW InHouse dictionary:PW InHouse dictionary "Definition compiled from a number of sources by the PW editorial team."]
is_a: PW:0000033 ! energy metabolic pathway

[Term]
id: PW:0000038
name: Sterol, vitamin K, vitamine E and cartenoids  biosynthesis
def: "OBSOLETE. Originally found at KEGG, the term has since been deleted." [PW dictionary:InHouse dictionary "Decision of the PW editorial board"]
is_obsolete: true

[Term]
id: PW:0000039
name: bile acid biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of bile acid - any of the steroid carboxylic acids derived from cholesterol. Cholic and chenodeoxycholic acids are the primary bile acids and are formed in the liver. Secondary bile acids - deoxycholic, lithocholic, and ursodeoxycholic acids - are formed from the primary bile acids through the action of intestinal bacteria, " [OneLook:www.onelook.com "Online collection of dictionaries - Dorland's."]
is_a: PW:0000248 ! steroid biosynthetic pathway

[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 ! steroid biosynthetic pathway

[Term]
id: PW:0000041
name: fructose and mannose metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of fructose, a ketohexose, and of mannose, an aldohexose." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000042
name: galactose metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of galactose - an aldohexose epimeric with glucose at the 4 carbon. Galactose is a component of lactose and other oligosaccharides, cerebrosides and gangliosides, and of various glycolipids and glycoproteins. " [OneLook:www.onelook.com "Adapted from Dorland's Medical Dictionary"]
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000043
name: pyruvate metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of pyruvate - a salt, ester, or anionic form of pyruvic acid. Pyruvate can be converted to lactate at the end of the anaerobic glycolysis, or can be further oxidized via the Krebs or the citric acid cycle." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000005 ! carbohydrate metabolic pathway
is_a: PW:0000556 ! glucose oxidation pathway

[Term]
id: PW:0000044
name: Duplicated Glutamate Metabolism term
def: "OBSOLETE. Duplicated term. Use PW:0000027." [PW dictionary:InHouse dictionary "Decision of the PW editorial board."]
is_obsolete: true

[Term]
id: PW:0000045
name: pentose phosphate pathway
def: "Those metabolic reactions involved in the generation of reducing equivalents and 5 carbon (pentose) sugars." [OneLook\, PubMed:www.oneloook.com; http\://www.ncbi.nlm.nih.gov/sites/entrez "Various online resources and articles in PubMed"]
related_synonym: "hexose monophosphate pathway (shunt)" []
related_synonym: "pentose phosphate shunt" []
related_synonym: "phosphogluconate pathway" []
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000046
name: inositol metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of inositol, a cyclic sugar alcohol occurring in a number of stereoisoforms." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000047
name: glycine, serine and threonine metabolic pathway
def: "Those metabolic reactions involved in the synthesis of glycine, serine and threonine and which are intimately connected with serine being synthesized from glycine and threonine." [OneLook:www.onelook.com "Online collection of dictionaries"]
comment: Definition compiled based on the information available at oneLook
is_a: PW:0000011 ! amino acid metabolic pathway

[Term]
id: PW:0000048
name: methionine cycle/metabolic pathway
def: "Those metabolic reactions involved in the synthesis (remethylation), utilization and/or degradation of methionine - an essential amino acid that can provide the methyl group and sulfur necessary for normal metabolism." [MCW library book:Homocysteine in Health and Disease "Cambridge Press, 2001"]
is_a: PW:0000011 ! amino acid metabolic pathway
is_a: PW:0000399 ! remethylation pathway of homocysteine metabolism - cobalamin dependent
is_a: PW:0000401 ! remethylation pathway of homocysteine metabolism - cobalamin independent, betaine dependent

[Term]
id: PW:0000049
name: cysteine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of cysteine - a thiol group containing amino acid." [OneLook:www.onelook.com "Online collection of dictionaries"]
comment: Reference compiled based on the information available at OneLook for cysteine.
is_a: PW:0000011 ! amino acid metabolic pathway
is_a: PW:0000400 ! transulfuration pathway of homocysteine metabolism

[Term]
id: PW:0000050
name: arginine and proline metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of arginine - an essential amino acid - and proline - an amino acid that can play important roles in protein secondary structure." [OneLook:www.onelook.com "Online collection of dictionaries"]
comment: Definition compiled based on the information on arginine and proline available at OneLook
is_a: PW:0000011 ! amino acid metabolic pathway

[Term]
id: PW:0000051
name: histidine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of histidine, an essential amino acid which can act as either a proton donor or proton acceptor." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000011 ! amino acid metabolic pathway

[Term]
id: PW:0000052
name: tyrosine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of tyrosine - a nonessential amino acid produced from phenylalanine and precursor of thyroid hormones, catecholamines and melanin." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000011 ! amino acid metabolic pathway

[Term]
id: PW:0000053
name: phenylalanine metabolic pathway
def: "Those metabolic reactions that are part of the phenylalanine cycle - an essential amino acid that the body can not manufacture." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000011 ! amino acid metabolic pathway

[Term]
id: PW:0000054
name: tryptophan metabolic pathway
def: "Those metabolic reactions that are involved in the synthesis, utilization and/or degradation of tryptophan - a dietary essential amino acid and precursor of nicotinamide." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000011 ! amino acid metabolic pathway

[Term]
id: PW:0000055
name: nucleotide sugar metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of nucleotide sugars" [InHouse:PW dictionary "Definition compiled by the PW editorial team"]
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000056
name: photosynthesis pathway
def: "A chemical combination caused by the action of light; specifically the formation of carbohydrates (with release of molecular oxygen) from carbon dioxide and water in the chlorophyll tissue of plants and blue-green algae under the influence of light. In bacteria, photosynthesis employs hydrogen sulfide, molecular hydrogen, and other reduced compounds in place of water, so that molecular oxygen is not released. " [OneLook:www.onelook.com "Online collection of dictionaries - Dorland's."]
is_a: PW:0000033 ! energy metabolic pathway

[Term]
id: PW:0000057
name: carbon fixation pathway
def: "The pathway thereby photosynthetic organisms such as plants convert inorganic carbon (usually carbon dioxide) into organic compounds (usually carbohydrates)." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000033 ! energy metabolic pathway

[Term]
id: PW:0000058
name: fatty acid metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of fatty acids - any long-chain monobasic organic acid." [PW InHouse dictionary:PW In House Dictionary "Definition compiled from a number of dictionaries"]
is_a: PW:0000010 ! lipid metabolic pathway

[Term]
id: PW:0000059
name: pathway pertinent to signaling in the brain
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000060
name: long term potentiation
def: "Long-term potentiation (LTP) is a strengthening of the synapse that can last from hours to days and months.  It is thought to underlie information storage and constitute the cellular basis of learning and memory.  LTP engages numerous cascades of events on either side of the synapse and is accompanied by changes in gene expression." [Dorland's:www.onelook.com "Online collection of dictionaries - Dorland's"]
related_synonym: "LTP" []
relationship: part_of PW:0000455 ! Excitatory synaptic transmission pathway

[Term]
id: PW:0000061
name: long term depression
def: "Long term depression is a weakening of a synapse that lasts hours to days. It results from either strong synaptic stimulation (as in the cerebellum) or to weak synaptic stimulation (as in the hippocampus), and engages several cascades of events." [OneLook:www.onelook.com "Online collection of dictionaries"]
comment: Adapted from Wikipedia at OneLook
related_synonym: "LTD" []
relationship: part_of PW:0000455 ! Excitatory synaptic transmission pathway

[Term]
id: PW:0000062
name: ascorbate and aldarate metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of ascorbate and aldarate. Ascorbate is a derivative of ascorbic acid, or vitamin C." [OneLook:www\,onelook.com "Online collection of dictionaries"]
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000063
name: glyoxylate and dicarboxylate metabolic pathway
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000064
name: propanoate metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of propanoate - any salt or ester of propanoic or propionic acid." [OneLook\, Online:www.onelook.com; http\://dl.clackamas.cc.or.us/ch106-04/nomencla1.htm "Definition compiled from both OneLook and Google"]
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000065
name: butanoate metabolic pathway
def: "Those reactions involved in the synthesis, utilization and/or degradation of butanoate - an ester or salt of  n-Butyric acid. Various butanoates are used as ingredients in flavoring, perfumery." [OneLook:www.onelook.com "Online collection of dictionaries - Wikipedia - definition"]
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000066
name: C5-branched dibasic acid metabolic pathway
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000067
name: reductive carboxylate cycle - CO2 fixation pathway
def: "Those reactions involved in carbon dioxide fixation - the reductive carboxylate cycle (CO2 fixation) - the conversion of atmospheric carbon dioxide to organic carbon compounds, as in photosynthesis." [=OneLook:www.onelook.com "Online collection of dictionaries - Dorland's definition"]
is_a: PW:0000033 ! energy metabolic pathway

[Term]
id: PW:0000068
name: methane metabolic pathway
def: "Those pathways involving methane - a colorless, odorless inflammable gas produced by decomposition of organic matter, which may explode when mixed with air or oxygen. Methane is the first member of a homologous series of saturated hydrocarbons, including butane, ethane, hexane, pentane and propane. " [OneLook:www.onelook.com "online collection of dictionaries"]
is_a: PW:0000033 ! energy metabolic pathway

[Term]
id: PW:0000069
name: ketone bodies metabolic pathway
def: "Those metabolic reactions involved in the 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 ! lipid metabolic pathway

[Term]
id: PW:0000070
name: C21-Steroid hormone metabolic pathway
is_a: PW:0000248 ! steroid biosynthetic pathway

[Term]
id: PW:0000071
name: valine, leucine and isoleucine degradation pathway
def: "Those metabolic reactions involved in the degradation of valine, leucine and isoleucine - the three, dietary essential, branched amino acids." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000011 ! amino acid metabolic pathway

[Term]
id: PW:0000072
name: valine, leucine and isoleucine biosynthetic pathway
def: "Those metabolic pathways involved in the synthesis of valine, leucine and isoleucine - the three, dietary essential, branched amino acids." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000011 ! amino acid metabolic pathway

[Term]
id: PW:0000073
name: lysine degradation pathway
def: "Those metabolic reactions involved in the degradation of lysine" [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000011 ! amino acid metabolic pathway

[Term]
id: PW:0000074
name: lysine biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of lysine - an essential amino acid." [OneLook:www.onelook.comOnline collection of dictionaries]
is_a: PW:0000011 ! amino acid metabolic pathway

[Term]
id: PW:0000075
name: phenylalanine, tyrosine and tryptophan biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of phenylalanine, tyrosine and tryptophan and which are intimately related. Although the body can not manufacture phenylalanine on its own, phenylalanine is the precursor of tyrosine. Phenylalanine together with tryptophan governs the release of an intestinal hormone - cholecystokinin." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000011 ! amino acid metabolic pathway

[Term]
id: PW:0000076
name: pathway of urea cycle and metabolism of amino groups
def: "The series of metabolic reactions, occurring in the liver, by which the ammonia derived from the breakdown of amino acids combines with carbon dioxide to form urea. " [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000011 ! amino acid metabolic pathway

[Term]
id: PW:0000077
name: beta-alanine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of beta-alanine. Beta-alanine is an amino acid formed in vivo by the degradation of dihydrouracil and carnosine. Since neuronal uptake and neuronal receptor sensitivity to beta-alanine have been demonstrated, the compound may be a false transmitter replacing GABA. A rare genetic disorder, hyper-beta-alaninemia, has been reported" [Onelook:www.onelook.com "Online collection of dictionaries - Dorland's medical dictionary"]
is_a: PW:0000132 ! metabolic pathway of other amino acids

[Term]
id: PW:0000078
name: cyanoamino acid metabolic pathway
is_a: PW:0000132 ! metabolic pathway of other amino acids
d: PW:0000080

[Term]
id: PW:0000079
name: Duplicated Selenoamino acid metabolism term
def: "OBSOLETE. Duplicated term. Use PW:0000133" [PW dictionary:InHouse dictionary "Decision of the PW editorial board"]
is_obsolete: true

[Term]
id: PW:0000080
name: Duplicated term - Selenoamino acid metabolism
def: "OBSOLETE. Duplicated term. Use PW:0000133" [PW dictionary:InHouse dictionary "Decision of the PW editorial board."]
is_obsolete: true

[Term]
id: PW:0000081
name: D-glutamine and D-glutamate metabolic pathway
is_a: PW:0000132 ! metabolic pathway of other amino acids

[Term]
id: PW:0000082
name: D-arginine and D-ornithine metabolic pathway
is_a: PW:0000132 ! metabolic pathway of other amino acids

[Term]
id: PW:0000083
name: D-alanine metabolic pathway
is_a: PW:0000132 ! metabolic pathway of other amino acids

[Term]
id: PW:0000084
name: Duplicated glutathione metabolism term
def: "OBSOLETE. Duplicated term. Use PW:0000134" [PW dictionary:InHouse dictionary "Decision of the PW editorial board"]
is_obsolete: true

[Term]
id: PW:0000085
name: pathways of replication, gene expression, protein biosynthesis
def: "Those pathways involved in and/or controlling the series of events allowing for DNA duplication and repair, genomic replication, RNA and protein biosynthesis." [InHouse:InHouse PW dictionary "Definitions compiled by the PW editorial team based on the information from a number of sources."]
is_a: PW:0000004 ! regulatory pathway
xref_unknown: XX:<new dbxref> ""

[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 ! pathways of replication, gene expression, protein biosynthesis

[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 ! cell cycle pathway, mitotic

[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 ! cell cycle pathway, mitotic

[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 ! cell cycle pathway, mitotic

[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 ! cell cycle pathway, mitotic

[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 ! cell cycle pathway, mitotic

[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 ! cell cycle pathway, mitotic

[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 ! cell cycle pathway, mitotic

[Term]
id: PW:0000094
name: cell cycle checkpoint pathway
def: "Those pathways involved in the control of cell cycle progression as well as its precision and fidelity." [InHouse:InHouse PW dictionary "Definition compiled by the PW editorial team based on the information from a number of sources"]
is_a: PW:0000085 ! pathways of replication, gene expression, protein biosynthesis

[Term]
id: PW:0000095
name: G1/S DNA damage checkpoint pathway
def: "Those pathways of DNA damage response that occur during the G1 phase." [InHouse:PW dictionary "Definition compiled by the PW editorial board based on the information at the Reactome."]
is_a: PW:0000094 ! cell cycle checkpoint pathway

[Term]
id: PW:0000096
name: G2/M checkpoint pathway
def: "Those pathways that assure the genome is replicated only once per cell cycle. The checkpoints control for damaged and unreplicated DNA." [InHouse :PW dictionary "Definition compiled by the PW editorial board based on the information at the Reactome."]
is_a: PW:0000094 ! cell cycle checkpoint pathway

[Term]
id: PW:0000097
name: mitotic spindle checkpoint pathway
is_a: PW:0000094 ! cell cycle checkpoint pathway

[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 ! pathways of replication, gene expression, protein biosynthesis

[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 ! pathways of replication, gene expression, protein biosynthesis

[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 compiled by the PW editorial team based on the information from a number of sources"]
is_a: PW:0000085 ! pathways of replication, gene expression, protein biosynthesis

[Term]
id: PW:0000101
name: translation pathway
def: "The series of events governing the processes thereby mRNA is translated into a polypeptide chain. Post-translational modifications often accompany the formation of the final, mature protein." [InHouse:InHouse PW dictionary "Definition compiled by the PW editorial team based on the information from a number of sources"]
is_a: PW:0000085 ! pathways of replication, gene expression, protein biosynthesis

[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 ! mitogen activated protein kinase signaling pathway
is_a: PW:0000525 ! Ras mediated signaling pathway

[Term]
id: PW:0000103
name: transport pathway
def: "A pathway that mediates or facilitates the movement of materials, including biochemical substances and/or drugs across the cell membrane." [OneLook\, PubMed\, Online:http\://www.ncbi.nlm.nih.gov/; www.google.com "Various resources"]
is_a: PW:0000004 ! regulatory pathway

[Term]
id: PW:0000104
name: intrinsic apoptotic pathway
def: "The apoptotic pathway involving organelles, primarily the 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 compiled based on the information available in the cited article.
is_a: PW:0000009 ! programmed cell death pathway

[Term]
id: PW:0000105
name: Rho/Rac/Cdc42 mediated signaling pathway
def: "Members of the Ras related Rho family of proteins control diverse processes such as actin cytoskeletal rearrangements, morphogenesis of dendritic spines." [PubMed:PMID\: 11075828; PMID\: 8973630]
is_a: PW:0000006 ! small G proteins - the Ras superfamily signaling pathway

[Term]
id: PW:0000106
name: extrinsic apoptotic pathway
def: "The apoptotic pathway involving the death receptors mediated route of caspase activation." [PubMed:PMID\: 14744432 "Article published in Cell"]
related_synonym: "death receptor mediated apoptotic pathway" []
is_a: PW:0000009 ! programmed cell death pathway

[Term]
id: PW:0000107
name: xenobiotics biodegradation pathway
def: "Those reactions involved in the uptake, transformation and disposal of chemical substances and compounds that are foreign to the biological system." [InHouse:InHouse PW dictionary "Definition compiled by the PW editorial team"]
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000108
name: caprolactam degradation pathway
def: "Those enzymatic reactions involved in the degradation of caprolactam - a cyclic amide of caproic acid used to produce a type of nylon. " [OneLook:www.onelook.com "Online collection of dictionaries."]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000109
name: biphenyl degradation pathway
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000110
name: toluene and xylene degradation pathway
def: "Those enzymatic reactions involved in the degradation of toluene and xylene. Toluene is used as organic solvent in rubber, paint, cement. Xylene represents any of three benzene derivatives used as solvent in printing, rubber, also as a cleaning agent. " [Onelook:www.onelook.com "Onelook collection of dictionaries."]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000111
name: gamma-hexachlorocyclohexane degradation pathway
def: "Those enzymatic reactions involved in the degradation of gamma-hexachlorocyclohexane,  also known as lindane, used as an insecticide and suspected to be carcinogenic. " [OneLook:www.onelook.com "Online collection of dictionaries."]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000112
name: 3-chloroacrylic acid degradation pathway
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000113
name: atrazine degradation pathway
def: "Those enzymatic reactions involved in the degradation of atrazine - a herbicide used to kill weeds. " [OneLook:www.onelook.com "Online collection of dictionaries."]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000114
name: benzoate degradation pathway via hydroxylation
def: "The aerobic pathway of benzoate degradation." [Online :Appl. Env. Microbiology\, 2004\, v.70(9)\, p4861-70. "Article found online"]
is_a: PW:0000282 ! benzoate degradation pathway

[Term]
id: PW:0000115
name: benzoate degradation pathway via CoA ligation
def: "The anaerobic pathway of benzoate degradation." [Online:http\://umbbd.ahc.umn.edu/benz/benz_map.html "Online description"]
is_a: PW:0000282 ! benzoate degradation pathway

[Term]
id: PW:0000116
name: carbazole degradation pathway
def: "Those enzymatic reactions involved in the degradation of carbazole - a crystalline, slightly basic cyclic compound found in anthracene. It reacts with carbohydrates and is used for assay and analysis of carbohydrates and in making dyes. " [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000117
name: fluorene degradation pathway
def: "Those enzymatic reactions involved in the degradation of fluorene - a colorless, crystalline hydrocarbon. It is obtained from coal tar and used in making dyes. It fluoresces, hence its name." [OneLook:www.onelook.com "Online collection of dictionaries."]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000118
name: ethylbenzene degradation pathway
def: "Those enzymatic reactions involved in the degradation of ethylbenzene - a liquid hydrocarbon used in the manufacture of styrene and as a solvent and diluent for dyes and paints." [OneLook:www.onelook.com "Online collection of dictionaries."]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000119
name: nitrobenzene degradation pathway
def: "Those enzymatic reactions involved in the degradation of nitrobenzene - an organic compound that occurs either as yellow crystals or yellow liquid used in the manufacture of aniline. It is a poisonous derivative of benzene. " [OneLook:www.onelook.com "Online collection of dictionaries."]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000120
name: styrene degradation pathway
def: "Those enzymatic reactions involved in the degradation of styrene - an aromatic hydrocarbon that is colorless and oily. It is used in the manufacture of rubber, resins, plastics. It is a toxic and irritant substance, possibly carcinogenic. " [OneLook:www.onelook.com "Online collection of dictionaries."]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000121
name: tetrachloroethene degradation pathway
def: "Those enzymatic reactions involved in the degradation of tetrachloroethene - (acetylene tetrachloride) used as solvent for fats, waxes, resins and intermediate in the synthesis of chlorinated hydrocarbons. " [OneLook:www.onelook.com "Online collection of dictionaries."]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000122
name: Hedgehog signaling pathway
def: "The Hedgehog signaling pathway (Hh) plays important roles in vertebrate embryogenesis, particularly in the differentiation of the neural tube, in vasculogenesis and angiogenesis. Post-embryonically it is believed to play a homeostatic role in the maintenance of stem cells. Alteration of the pathway has been implicated in a number of human cancers." [PubMed:PMID\: 15205520 \, PMID\: 15596107\,  PMID\: 12495844 "Articles dealing with the Hedgehog signaling pathway"]
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000123
name: synaptic vesicle endocytosis and recycling pathway
def: "The pathway of synaptic vesicle endocytosis and neurotransmitter refill following exocytosis." [PubMed:PMID\: 15217342 "Review article in PubMed"]
relationship: part_of PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse

[Term]
id: PW:0000124
name: cellular detoxification pathway
def: "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:PMID\:15252150 "Review article in PubMed"]
is_a: PW:0000004 ! regulatory pathway

[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 ! signaling pathway

[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 ! transcription pathway

[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 ! transcription pathway

[Term]
id: PW:0000128
name: RNA Polymerase III transcription pathway
def: "The series of events governing the synthesis of transport/transfer RNA (tRNA)." [InHouse:PW dictionary "Definition compiled by the PW editorial team"]
is_a: PW:0000100 ! transcription pathway

[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 ! DNA repair pathway

[Term]
id: PW:0000130
name: nucleotide excision repair pathway
is_a: PW:0000099 ! DNA repair pathway

[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 ! DNA repair pathway

[Term]
id: PW:0000132
name: metabolic pathway of other amino acids
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of amino acids other than the common 20 amino acids found in protein. Some of these amino acids like carnitine or homocysteine derive from primary amino acids and the two pathway categories in these cases are entwined." [InHouse:PW InHouse dictionary "Definition compiled bi the PW editorial board"]
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000133
name: selenoamino acid metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of selenoamino acid - an amino acid in which a selenium atom replaces a sulfur atom. " [Technical glossary:http\://morelife.org/glossary/ "Online technical glossary"]
is_a: PW:0000132 ! metabolic pathway of other amino acids

[Term]
id: PW:0000134
name: glutathione metabolic pathway
is_a: PW:0000132 ! metabolic pathway of other amino acids
is_a: PW:0000217 ! metabolic pathway of prosthetic groups, electron carriers and reductants

[Term]
id: PW:0000135
name: metabolic pathway of cofactors and vitamins
def: "Those reactions involved in the synthesis, utilization and/or degradation of cofactors and vitamins - compounds that are essential for the functioning of enzymes and/or are necessary for the normal metabolic functioning of the body." [InHouse:In House PW dictionary "Definition compiled by the PW editorial team"]
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000136
name: thiamine metabolic pathway
is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins

[Term]
id: PW:0000137
name: riboflavin metabolic pathway
def: "Those metabolic reactions involving riboflavin, also known as vitamin B2. It occurs in several products and is an essential nutrient for man. " [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins

[Term]
id: PW:0000138
name: Vitamin B6 metabolic pathway
def: "Those 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 ! metabolic pathway of cofactors and vitamins

[Term]
id: PW:0000139
name: biotin metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of biotin, also known as vitamin B7 or H. Biotin assists various metabolic reactions and processes." [OneLook:www.onelook.com> "Online collection of dictionaries, Wikipedia"]
is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins

[Term]
id: PW:0000140
name: pathway of folate cycle/metabolism
def: "The folate cycle/metabolism represents the various reactions involving absorption, transport, conversion and utilization of f folate compounds. Folate is the generic term for a number of chemically related molecules of the water-soluble vitamin B family that transfer one-carbon units for a number of important biosynthetic pathways. " [PubMed:PMID\: 15298442; 11001804; PMID\: 15166809 "Review articles in PubMed"]
is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins
is_a: PW:0000398 ! homocysteine metabolic pathway

[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 ! metabolic pathway of cofactors and vitamins

[Term]
id: PW:0000142
name: ubiquinone biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of ubiquinone, also known as coenzyme Q. Ubiquinone is a member of the mitochondrial respiratory chain and plays important roles in cellular metabolism." [Onelook\, PubMed:PMID\: 14757233 "Dorland/s and a review article in PubMed"]
is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins

[Term]
id: PW:0000143
name: insulin signaling pathway
def: "Processes regulated by insulin and insulin-like growth factor signaling systems include growth and survival of many tissues; for example, neuron and retina, bone, pancreatic beta-cells. Insulin is best known for its role in the regulation of blood glucose. Deregulation of the systems is implicated in a number of metabolic disorders." [PubMed:PMID\: 12169433 "Review article"]
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000144
name: ubiquitin/proteasome degradation pathway
def: "The pathway for the ATP-dependent non-lysosomal proteolysis catalyzed by the 26S proteasome and for which ubiquitylation, the post-translational covalent conjugation of ubiquitin to target proteins is a key signal." [PubMed:2001\, v.27\, 171-179. "Definition compiled based on a review article published in Neuropathology and Applied Neurobiology"]
is_a: PW:0000417 ! ubiquitin, ubiquitin-like/proteasome degradation pathway

[Term]
id: PW:0000145
name: Metabolism of complex carbohydrates
def: "OBSOLETE. Originally found at KEGG, the term has since been deleted" [PW dictionary:InHouse dictionary "Decision of the PW editorial board"]
is_obsolete: true

[Term]
id: PW:0000146
name: glycan metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glycans 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 ! classic metabolic pathway

[Term]
id: PW:0000147
name: metabolic pathway of secondary metabolites
def: "Those reactions involved in the synthesis, utilization and/or degradation of secondary metabolites  - products of cellular metabolism that are not essential for normal growth, development or reproduction of the plant or organism.  Many of the chemicals that plants or microorganisms produce are secondary metabolites, including antibiotics." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000148
name: alkaloid biosynthetic pathway I
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000149
name: alkaloid biosynthetic pathway II
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000150
name: stilbene, coumarine and lignin biosynthetic pathway
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000151
name: starch and sucrose metabolic pathway
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000152
name: 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 ! carbohydrate metabolic pathway

[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 ! lipid metabolic pathway

[Term]
id: PW:0000154
name: inositol phosphate metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of inositol phosphate which represents all of the possible phosphorylated states of inositol. Inositol is a cyclic hexahydric alcohol with six possible isomers." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000155
name: phospholipid metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of phospholipids - lipids containing phosphorus, including those with a glycerol backbone or a backbone of sphingosine or related substances. Phospholipids are the major form of lipid in the cell membrane." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000010 ! lipid metabolic pathway

[Term]
id: PW:0000156
name: prostaglandin metabolic pathway
is_a: PW:0000461 ! cyclooxygenase mediated pathway of arachidonic acid metabolism
is_a: PW:0000485 ! eicosanoids metabolic pathway

[Term]
id: PW:0000157
name: glycosaminoglycan metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or  degradation of glycosaminoglycans - any of several high molecular weight linear 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 ! glycan metabolic pathway

[Term]
id: PW:0000158
name: Ras family signaling pathway
def: "The Ras family mediated signaling pathways are primarily involved in the regulation of gene expression." [PubMed:PMID\: 11467446; PMID\: 11152757 "Adapted from an article in the Journal of Mammary Gland Biology and Neoplasia"]
is_a: PW:0000006 ! small G proteins - the Ras superfamily signaling pathway

[Term]
id: PW:0000159
name: Rab family signaling pathway
def: "Rab family mediated signaling pathways are involved in intracellular vesicle trafficking. " [PubMed:To be added]
is_a: PW:0000006 ! small G proteins - the Ras superfamily signaling pathway

[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 ! small G proteins - the Ras superfamily signaling pathway

[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"]
related_synonym: "GPI anchor biosynthesis" []
is_a: PW:0000146 ! glycan metabolic pathway

[Term]
id: PW:0000162
name: glycosphingolipid biosynthetic pathway - lactoseries
is_a: PW:0000197 ! glycosphingolipid metabolic pathway

[Term]
id: PW:0000163
name: glycosphingolipid biosynthetic pathway - neolactoseries
is_a: PW:0000197 ! glycosphingolipid metabolic pathway

[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 ! glycosphingolipid metabolic pathway

[Term]
id: PW:0000165
name: taurine and hypotaurine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of taurine and hypotaurine." [InHouse:PW InHouse dictionary]
is_a: PW:0000132 ! metabolic pathway of other amino acids

[Term]
id: PW:0000166
name: nicotinate and nicotinamide metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of nicotinate - the dissociated form of nicotinic acid and of nicotinamide - the amide of niacin or vitamin B3." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins

[Term]
id: PW:0000167
name: pantothenate and CoA biosynthetic pathway
is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins

[Term]
id: PW:0000168
name: growth factor signaling pathway
def: "Those pathways that are triggered through the binding of a growth factor to its particular receptor. Growth factors carry out mitogenic signaling via their largely tyrosine kinase receptors." [InHouse\, OneLook\, Pubmed:PW dictionary\, www.onelook.com; PMID\: 16632420 "Definition compiled by the PW editorial board; various resources at onelook, review articles"]
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000169
name: nerve growth factor signaling pathway
def: "Nerve growth factor (NGF) signaling pathways control a variety of processes such as neuronal cell differentiation, axon growth. Members of the NGF family are best known for their anti-apoptotic role as mediators of neuronal cell survival." [PubMed:Neuron\, 2004\, v42\, p897-912; Cellular Signaling\, 2004\, v16\, p127-36. "Articles in PubMed"]
related_synonym: "NGF signaling pathway" []
is_a: PW:0000571 ! neurotrophic factor signaling pathway

[Term]
id: PW:0000170
name: epidermal growth factor/neuregulin signaling pathway
def: "Members of the EGF/neuregulin superfamily are important regulators of tissue development and repair. A characteristic feature is the presence of the EGF module, a 36-40 amino acid sequence with a disulfide-bonded three loop structure necessary for receptor binding. " [MCW e-journal:J. Mol. Evolo.2000\, v50\, p397-412 "Review article on EGF receptors and ligands", PubMed:12814936 "Review article"]
related_synonym: "EGF/neuregulin signaling pathway" []
is_a: PW:0000168 ! growth factor signaling pathway

[Term]
id: PW:0000171
name: disease pathways related to polyQ repeats
def: "A family of neurodegenerative and other inherited diseases that are caused by the expansion of a polyglutamine tract (polyQ) in the associated disease proteins. The diseases are manifested as distinct neuropathies and multiple pathways are perturbed. " [PubMed:2004\, v.20(3)\, 146-154 "Article in Trends in Genetics"]
comment: Definition adapted from an article in Trends in Genetics
is_a: PW:0000014 ! neurodegenerative disease pathway

[Term]
id: PW:0000172
name: spinobulbar muscular atrophy
def: "An inherited neurodegenerative disease caused by an expanded polyQ tract. Various pathways are disrupted and contribute to the manifestation of the condition." [PubMed:2004\, v. 20(3)\, 146-154. "From an article in Trends in Genetics"]
related_synonym: "SBMA" []
is_a: PW:0000173 ! spinocerebellar ataxia

[Term]
id: PW:0000173
name: spinocerebellar ataxia
def: "An inherited form of neurodegenerative disease caused by an expanded polyQ tract. Several types are grouped under SCA, types 1-3, 6, 7 and 17.Various pathways are disrupted and contribute to the manifestation of the condition." [PubMed:2004\, v.20(3)\, 146-154. "From an article in Trends in genetics"]
related_synonym: "SCA" []
is_a: PW:0000171 ! disease pathways related to polyQ repeats

[Term]
id: PW:0000174
name: metabolic syndrome
def: "The metabolic syndrome is a multiphenotypic condition with concurrent features of several diseases and metabolic abnormalities. Insulin resistance, obesity and hypertension are considered risk factors. Alterations in lipid, glucose and cholesterol metabolic pathways among others, can contribute to the multifactorial metabolic syndrome and the conditions associated with it. " [PubMed:2004\, v. 17\, 38047; PMID\: 16932765 "From an article in Physiological Genomics, review article in PubMed"]
is_a: PW:0000020 ! cardiovascular disease pathway

[Term]
id: PW:0000175
name: familial combined hyperlipidemia
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"]
related_synonym: "FCHL" []
is_a: PW:0000174 ! metabolic syndrome

[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 ! disease pathway

[Term]
id: PW:0000177
name: diabetic nephropathy pathway
def: "A common complication of diabetes and a leading cause of end stage renal diseases affecting a number of pathways, particularly the thiol and anti-oxidant pathways." [InPress:Manuscript "From an article in press - HMGC affiliated authors."]
is_a: PW:0000176 ! diabetes pathway
is_a: PW:0000300 ! renal disease, renal disorder pathway

[Term]
id: PW:0000178
name: neurological disorder disease pathway
def: "Neurological disorders are a group of disorders that involve the central nervous system (brain, brainstem and cerebellum), the peripheral nervous system (including cranial nerves), and the autonomic nervous system (parts of which are located in both central and peripheral nervous system). Major branches are headache, stupor and coma, dementia, seizure, sleep disorders, trauma, infections, neoplasms, neuro-ophthalmology, movement disorders, demyelinating diseases, spinal cord disorders, and disorders of peripheral nerves, muscle and neuromuscular junctions. Many mental illnesses are believed to be neurological disorders of the central nervous system, but they are classified separately. They are not traditionally listed as neurological diseases because their causes are not definitely determined as biological, although there are good reasons to suspect that bipolar disorder and schizophrenia have neuro-chemical causes." [OneLook:www.onelook.com "Online collection of dictionaries - Wikipedia"]
is_a: PW:0000013 ! disease pathway

[Term]
id: PW:0000179
name: tuberous sclerosis complex disease pathway
def: "An autosomal dominant condition that often leads to seizure and other neurological symptoms and that may be linked to deregulations in the mTOR signaling pathway." [PubMed:2004\, v.29(1)\, 32-38. "Definition derived from an article in TIBS discussing the mTOR signaling pathway"]
related_synonym: "TSC" []
is_a: PW:0000178 ! neurological disorder disease pathway

[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/or levels of nutrients." [PubMed:2004\, v. 29(1)\, 32-38. "From an article in TIBS"]
is_a: PW:0000003 ! signaling pathway

[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." [InHouse:InHouse PW dictionary "Definition compiled by the PW editorial team based on the information from a number of sources"]
is_a: PW:0000004 ! regulatory pathway

[Term]
id: PW:0000182
name: lysosomes based pathway of protein degradation
def: "A protein degradation pathway that involves proteases residing in lysosomes and exhibiting optimal activity at an acidic pH (e.g., cathepsins). " [PubMed:2003\, v. 285\, f1-f8. "American Journal of Physiology, Renal Physiology"]
is_a: PW:0000325 ! protein degradation pathway

[Term]
id: PW:0000183
name: the proteolytic pathway involving calcium-dependent proteases
def: "A protein degradation pathway that involves calcium-dependent proteases  (e.g., calpains) ," [PubMed:2003\, v. 285\, f1-f8. "From a review article published in American Journal of Physiology, Renal Physiology"]
is_a: PW:0000325 ! protein degradation pathway

[Term]
id: PW:0000184
name: terpenoid biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of terpenoids. The terpenoids, sometimes referred to as isoprenoids, are a class of naturally occurring chemicals derived from five-carbon isoprene units assembled and modified in thousands of ways. Most are multicyclic structures which differ from one another not only in functional groups, but also in their basic carbon skeletons. Terpenoids of different sizes and composition are found in all classes of living things, and are the largest group of natural products. They play a role in traditional herbal remedies and are under investigation for antibacterial, antineoplastic and other pharmaceutical effects. " [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000185
name: limonene and pinene degradation pathway
def: "Those metabolic reactions involved in the degradation of limonene -  an essential oil, a monocyclic terpene, found in the peel of oranges and lemons, and pinene - a terpene found in turpentine and many essential oils, used as a solvent and in the manufacture of camphor, insecticides, and synthetic pine oil." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000186
name: streptomycin biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of streptomycin - the first of the aminoglycoside antibiotics to be isolated, derived from Streptomyces griseus; it is effective against a wide variety of aerobic gram-negative bacilli and some gram-positive bacteria, including mycobacteria. Its use is now limited because of the emergence of resistant strains." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000187
name: erythromycin biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of erythromycin -   an intermediate spectrum macrolide (a chemical compound characterized by a large lactone ring containing multiple keto and hydroxyl groups) antibiotic, produced by Streptomyces erythreus, effective against most gram-positive and certain gram-negative bacteria, such as Neisseria species and Haemophilus influenzae, and against spirochetes, some rickettsias, and Entamoeba; it is also highly effective against Mycoplasma pneumoniae. It is used especially in patients allergic to penicillin and in those with penicillin-resistant infections and legionnaires' disease; administered orally or topically. " [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000188
name: pentose and glucuronate interconversion pathway
def: "The series or metabolic reactions involved in the interconversions of pentose and glucuronate as depicted in the KEGG diagrams. " [KEGG:http\://www.genome.ad.jp/kegg/pathway/map/map00040.html "Based on the entry found at KEGG"]
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000189
name: folate mediated one-carbon metabolic pathway
def: "Folate mediated one-carbon metabolism refers to the various metabolic reactions/pathways that use folate compounds to transfer one-carbon units for the biosynthesis of a number of biomolecules in the cytoplasm and mitochondrion." [PubMed:PMID\: 15166809 ; PMID\: 11001804; PMID\: 15298442 "Review articles in PubMed"]
is_a: PW:0000140 ! pathway of folate cycle/metabolism

[Term]
id: PW:0000190
name: porphyrin and chlorophyll metabolic pathway
def: "Those reactions involved in the synthesis, utilization and/or degradation of porphyrin - any of a group of compounds containing the porphin structure, four pyrrole rings connected by methylidyne bridges in a cyclic configuration, to which a variety of side chains may be attached - and chlorophyll - any of a group of green magnesium-containing porphyrin derivatives occurring in all photosynthetic organisms." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins

[Term]
id: PW:0000191
name: keratan sulfate biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of keratan sulfate - a glycosaminoglycan found in the cornea, in cartilage, and in the nucleus pulposus and also as the accumulation product in Morquio's syndrome. It consists of repeating disaccharide units in specific linkage, each composed of a sulfated N-acetylglucosamine residue linked to one of galactose, which is usually sulfated. There are two forms, keratan sulfate I and keratan sulfate II, which differ in carbohydrate content and localization; the former occurs in the cornea and the latter in skeletal tissues. " [OneLook:www.onelook.com "Online collection of dictionaries."]
is_a: PW:0000157 ! glycosaminoglycan metabolic pathway

[Term]
id: PW:0000192
name: N-Glycans biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of N-Glycans. N-Glycans are found attached to the R-group nitrogen of asparagine." [PW InHouse Dictionary:InHouse dictionary "PW InHouse dictionary"]
is_a: PW:0000146 ! glycan metabolic pathway

[Term]
id: PW:0000193
name: N-Glycan degradation pathway
def: "Those metabolic reactions involved in the degradation of N-Glycans. N-Glycans are found attached to the R-group nitrogen of asparagine." [XPW InHouse Dictionary:InHouse Dictionary "PW  InHouse dictionary"]
is_a: PW:0000146 ! glycan metabolic pathway

[Term]
id: PW:0000194
name: O-Glycans biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of O-Glycans. O-linked glycans are used to modify proteins at serine or threonine residues." [PW InHouse dictionary:PW]
is_a: PW:0000146 ! glycan metabolic pathway

[Term]
id: PW:0000195
name: chondroitin sulfate biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of chondroitin, Chondroitin is a mucopolysaccharide occurring in sulfated form in various animal tissues (as cartilage)." [OneLook:www.onelook.com "Online collection if dictionaries."]
is_a: PW:0000157 ! glycosaminoglycan metabolic pathway

[Term]
id: PW:0000196
name: globoside metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of globoside - a glycosphingolipid containing acetylated amino sugars and simple hexoses of the general composition N-acetylgalactosamine-galactose-galactose-glucose-ceramide; it accumulates in tissues in Sandhoff's disease, but not in Tay-Sachs disease." [OneLook:www.onelook.com "Online collection of dictionaries - Dorland's."]
is_a: PW:0000197 ! glycosphingolipid metabolic pathway

[Term]
id: PW:0000197
name: glycosphingolipid metabolic pathway
def: "Those metabolic reactions  involved in the synthesis, utilization and/or degradation of glycosphinholipids - any sphingolipid in which the head group is a mono- or oligosaccharide unit. Examples include the cerebrosides, globosides and gangliosides." [OneLook:www.onelook.com "Online collection of dictionaries - Dorland's."]
is_a: PW:0000010 ! lipid metabolic pathway

[Term]
id: PW:0000198
name: p38 MAPK pathway
def: "A SAPK MAPK pathway that plays an important role in inflammation and may be involved in several forms of cancer." [PubMed:PMID\: 14570565 ;  15102355 . "Review articles on p38 pathway"]
is_a: PW:0000312 ! stress-regulated MAPK signaling pathway

[Term]
id: PW:0000199
name: the Wnt/calcium signaling pathway
def: "A Wnt mediated pathway that is involved in the regulation of cell-cell adhesion and motility." [PubMed:PMID\:12573432\,  10858654]
related_synonym: "the Wnt/Ca(II) pathway" []
is_a: PW:0000597 ! non-canonical Wnt signaling pathway

[Term]
id: PW:0000200
name: the planar cell polarity Wnt signaling pathway
def: "The planar cell polarity (PCP) Wnt signaling pathway plays an essential in morphogenesis through the regulation of tissues patterning." [PubMed:PMID\: 12573432; 16765615]
related_synonym: "PCP Wnt signaling pathway" []
is_a: PW:0000597 ! non-canonical Wnt signaling pathway

[Term]
id: PW:0000201
name: canonical Wnt signaling pathway
def: "Wnt signaling pathway is involved in many developmental processes. In the conventional or canonical Wnt pathway,  beta-catenin is a central component required for the  transcriptional comtrol of Wnt signaling target genes." [PubMed:PMID\: 12573432; 15001769; 18432252]
related_synonym: "beta-catenin dependent Wnt signaling pathway" []
is_a: PW:0000008 ! Wnt signaling pathway

[Term]
id: PW:0000202
name: homologous recombination pathway of double-strand break repair
def: "A specific pathway for repair of double-strand breaks. It is thought to be involved in repair of breaks generated in meiotic prophase, or during cell cycle specific phases such as the S and G2 phases." [PubMed:Cell\, 2004\, v. 117\, p 171-184 "Article on double strand repair pathways"]
is_a: PW:0000131 ! double strand break repair pathway

[Term]
id: PW:0000203
name: non-homologous end joining pathway of double-strand break repair
def: "A specific pathway for repair of double-strand breaks. Possibly constitutive, it is the most important pathways in mammalian cells and plays an important role in mitotically replicating cells." [PubMed:Cell\, 2004\, v. 117\, 171-184. "Article published in Cell on the double-strand specific break repair pathways.", PubMed:PMID\: 12947387 "Review article in Oncogene, 002"]
related_synonym: "NHEJ pathway of double-strand break repair" []
is_a: PW:0000131 ! double strand break repair pathway

[Term]
id: PW:0000204
name: Notch signaling pathway
def: "Notch signaling pathway regulates processes involved in early embryonic development. It plays an important role in cell fate determination. Target genes of Notch have been implicated in angiogenesis, somitogenesis, gliogenesis. Deregulation of the Notch signaling pathway underlies a broad spectrum of diseases and clinical conditions." [PubMed:Several articles in PubMed "Based on a number of review articles"]
is_a: PW:0000332 ! cell-cell signaling pathway

[Term]
id: PW:0000205
name: dentatorubral-pallidoluysian atrophy disease pathway
def: "Dentatorubral-pallidoluysian atrophy (DRPLA) is caused by an expanded trinucleotide repeat in the DRPLA gene. A very rare condition, it can be sporadic or autosomal dominant inherited. Three forms of DRPLA have been clinically classified:  the ataxo-choreoathetoid form, the pseudo-Huntington form, and the myoclonic epilepsy form. " [NCBI:OMIM database "Definition compiled based on the information available at OMIM"]
related_synonym: "DRPLA" []
is_a: PW:0000171 ! disease pathways related to polyQ repeats

[Term]
id: PW:0000206
name: transforming growth factor-beta signaling pathway
def: "Transforming growth factor pathway regulates numerous cellular processes such as proliferation, differentiation, migration and cell death. The SMAD dependent pathway represents the core signaling cascade mediated by the TGF-beta superfamily. Mutations in TGF - beta family are responsible for a number of human diseases." [PubMed:TIBS\, 2004\, v29 (5)\, p267-273. "Article introduction"]
related_synonym: "TGF- beta signaling pathway - SMAD dependent" []
is_a: PW:0000329 ! transforming growth factor -beta superfamily mediated signaling pathway

[Term]
id: PW:0000207
name: central obesity with hypertension
is_a: PW:0000174 ! metabolic syndrome

[Term]
id: PW:0000208
name: diabetes type 2 pathway
is_a: PW:0000174 ! metabolic syndrome
is_a: PW:0000176 ! diabetes pathway

[Term]
id: PW:0000209
name: JAK-STAT signaling pathway
def: "The JAK/STAT pathway involve signaling from cytokine or growth factor receptor(s) to the nucleus via Janus kinases (Jak) and the signal transducers and activators of transcription (STAT) families of proteins. Deregulation of the pathway can lead to various conditions and diseases." [PubMed:14737178; 14668806; 12039028 "Articles in PubMed"]
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000210
name: SMAD dependent signaling pathways
def: "The core intracellular  signaling cascade mediated  by the TGF-beta superfamily. SMAD proteins function by carrying signals from the cell surface to the nucleus. There are eight vertebrate SMAD proteins and they are activated  by two types of  TGF-beta receptors in response to TGF cytokines binding.There are two known SMAD-dependent TGF-beta signaling pathways. SMAP pathways can also be activated via NGF signalign pathways" [PubMed:Science\, 2002\, v296\, p1564-7; PMID\: 14534577.PMID\: 15009204 "Articles in Science and Nature, Eur. J. Biochem"]
is_obsolete: true

[Term]
id: PW:0000211
name: amines and polyamines metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of amines and polyamines. Amines are organic compounds where the nitrogen atom of the amino functional group is attached via single bonds to one, two or three alkyl or aryl groups.  Polyamines contain one or more amine groups. " [OneLook:www.onelook.com "Online collection of dictionaries - Wikipedia."]
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000212
name: betaine biosynthetic pathway I
is_a: PW:0000211 ! amines and polyamines metabolic pathway

[Term]
id: PW:0000213
name: betaine biosynthetic pathway II
is_a: PW:0000211 ! amines and polyamines metabolic pathway

[Term]
id: PW:0000214
name: polyamine biosynthetic pathway I
is_a: PW:0000211 ! amines and polyamines metabolic pathway

[Term]
id: PW:0000215
name: polyamine biosynthetic pathway II
is_a: PW:0000211 ! amines and polyamines metabolic pathway

[Term]
id: PW:0000216
name: spermine metabolic pathway
is_a: PW:0000211 ! amines and polyamines metabolic pathway

[Term]
id: PW:0000217
name: metabolic pathway of prosthetic groups, electron carriers and reductants
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of molecules whose role or function is as prosthetic groups, electron carriers or reductants.  " [InHouse :PW InHouse dictionary "Definition compiled by the PW editorial board."]
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000218
name: heme biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of heme - an iron-containing compound where the iron is complexed within a porphyrin heterocyclic ring. There are several kinds of heme depending on the composition of their side chain. Heme serves as a prosthetic group for a number of proteins." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000217 ! metabolic pathway of prosthetic groups, electron carriers and reductants

[Term]
id: PW:0000219
name: NAD biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of NAD - nicotinamide adenine dinucleotide. NAD is used extensively in glycolysis and the citric acid cycle of cellular respiration. " [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000217 ! metabolic pathway of prosthetic groups, electron carriers and reductants

[Term]
id: PW:0000220
name: pyridine nucleotide biosynthetic pathway
is_a: PW:0000217 ! metabolic pathway of prosthetic groups, electron carriers and reductants

[Term]
id: PW:0000221
name: thioredoxin pathway
is_a: PW:0000217 ! metabolic pathway of prosthetic groups, electron carriers and reductants

[Term]
id: PW:0000222
name: UDP-N-acetylgalactosamine biosynthetic pathway
is_a: PW:0000211 ! amines and polyamines metabolic pathway

[Term]
id: PW:0000223
name: UDP-N-acetylglucosamine biosynthetic pathway
is_a: PW:0000211 ! amines and polyamines metabolic pathway

[Term]
id: PW:0000224
name: N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminic acid dissimilation pathway
def: "Those metabolic reactions leading to the decomposition of N-acetylglucosamine - an acetylated amino sugar that is an important moiety of glycoproteins, N-acetylmannosamine - the acetylated derivative of mannnosamine, and N-acetylneuraminic acid - the most common form of sialic acid in mammals." [OneLook:www.onelook.com "Online collection of dictionaries."]
is_a: PW:0000211 ! amines and polyamines metabolic pathway

[Term]
id: PW:0000225
name: citrulline degradation pathway
def: "Those metabolic reactions involved in the degradation of citrulline - alpha-amino delta-carbamido normal valeric acid, Citrulline is made from ornithine in the urea cycle; it also is a by-product of nitric oxide synthase catalyzed reactions." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000211 ! amines and polyamines metabolic pathway

[Term]
id: PW:0000226
name: putrescine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of putrescine - chemical name: tetra-methylene-diamine. A polyamine first found in decaying animal tissues but now known to occur in almost all tissues and in cultures of certain bacteria." [OneLook:www.onelook.com "Online collection of dictionaries - Dorland's Medical Dictionary"]
is_a: PW:0000211 ! amines and polyamines metabolic pathway

[Term]
id: PW:0000227
name: G protein signaling pathway via Galphas family
def: "Based on sequence similarity, the Galpha genes have been grouped into four classes. Exchange of GDP to GTP promoted through binding to receptors dissociates the heterotrimeric Galpa/beta/gamma complex. GTP-bound Galpha can then interact with downstream effectors. Lipid modification of Galpha regulates membrane localization and interactions with specific effectors." [PubMed:PMID\: 12040175; PMID\: 15747061 "Review articles"]
is_a: PW:0000125 ! G protein signaling pathway
is_a: PW:0000491 ! vasopressin signaling pathway
is_a: PW:0000528 ! Angiotensin II signaling pathway through the AT2 receptor

[Term]
id: PW:0000228
name: G protein signaling pathway via Galphai family
def: "Based on sequence similarity, the Galpha genes have been grouped into four classes. Exchange of GDP to GTP promoted through binding to receptors dissociates the heterotrimeric Galpa/beta/gamma complex. GTP-bound Galpha can then interact with downstream effectors. Lipid modification of Galpha regulates membrane localization and interactions with specific effectors." [PubMed:PMID\: 12040175; PMID\: 15747061 "Review articles"]
is_a: PW:0000125 ! G protein signaling pathway
is_a: PW:0000494 ! oxytocin signaling pathway
is_a: PW:0000527 ! Angiotensin II signaling pathway through the AT1 receptor
is_a: PW:0000528 ! Angiotensin II signaling pathway through the AT2 receptor
is_a: PW:0000586 ! orexin/hypocretin signaling pathway through the orexin/hypocretin receptor 2

[Term]
id: PW:0000229
name: G protein signaling pathway via Galphaq family
def: "Based on sequence similarity, the Galpha genes have been grouped into four classes. Exchange of GDP to GTP promoted through binding to receptors dissociates the heterotrimeric Galpa/beta/gamma complex. GTP-bound Galpha can then interact with downstream effectors. Lipid modification of Galpha regulates membrane localization and interactions with specific effectors." [PubMed:PMID\: 12040175; PMID\: 15747061 "Review articles"]
is_a: PW:0000125 ! G protein signaling pathway
is_a: PW:0000491 ! vasopressin signaling pathway
is_a: PW:0000494 ! oxytocin signaling pathway
is_a: PW:0000527 ! Angiotensin II signaling pathway through the AT1 receptor
is_a: PW:0000585 ! orexin/hypocretin signaling pathway through the orexin/hypocretin receptor 1
is_a: PW:0000586 ! orexin/hypocretin signaling pathway through the orexin/hypocretin receptor 2

[Term]
id: PW:0000230
name: G protein signaling pathway via Galpha12/Galpha13 family
def: "Based on sequence similarity, the Galpha genes have been grouped into four classes. Exchange of GDP to GTP promoted through binding to receptors dissociates the heterotrimeric Galpa/beta/gamma complex. GTP-bound Galpha can then interact with downstream effectors. Lipid modification of Galpha regulates membrane localization and interactions with specific effectors." [PubMed:PMID\: 12040175; PMID\: 15747061 "Review articles"]
is_a: PW:0000125 ! G protein signaling pathway
is_a: PW:0000527 ! Angiotensin II signaling pathway through the AT1 receptor

[Term]
id: PW:0000231
name: Rap1 pathways
def: "A very close relative of Ras, Rap1 mediated pathway  appears to control diverse processes such as modulation of growth and differentiation, secretion, integrin linked cell adhesion, morphogenesis." [PubMed:Nature Reviews\, Mol. Cell Biology\, 2001\, v2\, p369-77. "Review article"]
is_obsolete: true

[Term]
id: PW:0000232
name: phosphatidylinositol 3-kinase-Akt signaling pathway
def: "Phosphatidylinositol 3-kinase-Akt signaling pathway involving PI3K class I enzymes and particularly class IA controls various processes such as cell growth, proliferation and survival. Class IA enzymes couples to receptor tyrosine kinases or their adaptors; class IB couples to G-protein coupled receptor mainly via Galphai. The range of catalytic-regulatory subunit combinations is greater for class IA than class IB. Deregulation of the pathway has been linked to various forms of cancer." [PubMed:15143962 \, 15023437\, 14737178]
related_synonym: "phosphoinositide 3-kinase-Akt signaling pathway" []
related_synonym: "PI3K-Akt signaling pathway" []
is_a: PW:0000595 ! phosphatidylinositol 3-kinase signaling pathway

[Term]
id: PW:0000233
name: tumor necrosis factor signaling pathway
def: "Tumor necrosis factor (Tnf) signaling pathway plays pivotal roles in immunity, cell proliferation, differentiation and apoptosis through the activation of several downstream signaling pathways. NF-kB is the major pathway activated by Tnf; otherr pathways such as JNK and P3b MAPK or apoptosis can also be activated. Deregulation of Tnf signaling has been implicated in a great number of human diseases - cerebral malaria, cancer, multiple sclerosis - are a few examples." [PubMed:PMID\:12040173\, 12655295 "Review article"]
related_synonym: "TNF signaling pathway" []
related_synonym: "TNFalpha signaling pathway" []
is_a: PW:0000236 ! tumor necrosis factor superfamily signaling pathway

[Term]
id: PW:0000234
name: innate immune response pathway
def: "The innate immune response  - a universal and ancient form of host defense against infection - covers several areas of defense against pathogenic microbes where recognition relies on germline-encoded receptors." [PubMed:PMID\: 11861602 "Review article in Annual Review of Immunology"]
is_a: PW:0000023 ! immune response pathway

[Term]
id: PW:0000235
name: adaptive immune response pathway
def: "The adaptive immune response is an evolutionarily newer mechanism that involves gene rearrangements and generation of receptors, and thus provides a greater variability, specific recognition of foreign antigens, immunological memory of infection and pathogen-specific adaptor proteins. The adaptive response is responsible for autoimmunity, allergy and rejection of grafts." [PubMed:PMID\: 11861602 "Review article"]
is_a: PW:0000023 ! immune response pathway

[Term]
id: PW:0000236
name: tumor necrosis factor superfamily signaling pathway
def: "Members of TNF superfamily mediate autoimmunity and inflammation, cell proliferation, survival or apoptosis through a number of signaling mechanisms that involve activation of nuclear factor-kappaB, of caspases or of mitogen-activated protein kinases. TNF superfamily has been implicated in a wide range of human diseases including tumorigenesis, septic shock, diabetes, rheumatoid arthritis, other inflammatory conditions." [PubMed:PMID\: 14555214\,  11796220\, 11239407 "Review article"]
related_synonym: "TNF superfamily signaling pathways" []
is_a: PW:0000577 ! cytokine and chemokine signaling pathway

[Term]
id: PW:0000237
name: stress response pathway
is_a: PW:0000004 ! regulatory pathway

[Term]
id: PW:0000238
name: insulin-like growth factor signaling pathway
def: "Processes regulated by insulin and insulin-like growth factor signaling systems include growth and survival of many tissues; for example, neuron and retina, bone, pancreatic beta-cells. Insulin is best known for its role in the regulation of blood glucose. Deregulation of the systems is implicated in a number of metabolic disorders." [PubMed:PMID\: 12169433 "Review article"]
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000239
name: diabetes type 1 pathway
is_a: PW:0000176 ! diabetes pathway

[Term]
id: PW:0000240
name: neuropsychiatric disease pathway
is_a: PW:0000013 ! disease pathway

[Term]
id: PW:0000241
name: schizophrenia pathway
def: "Schizophrenia is a psychiatric diagnosis denoting a persistent, often chronic, mental illness variously affecting behavior, thinking, and emotion. The term schizophrenia comes from the Greek words schizo, (split or divide) and phrenos, (mind) and is best translated as \"shattered mind\"." [OneLook:www.onelook.com "Online collection of dictionaries - Wikipedia"]
is_a: PW:0000240 ! neuropsychiatric disease pathway

[Term]
id: PW:0000242
name: bipolar disorder pathway
def: "As categorized by the DSM-IV, bipolar disorder is a form of mood disorder characterized by a variation of mood between a phase of manic or hypomanic elation, hyperactivity and hyper imagination, and a depressive phase of inhibition, slowness to conceive ideas and move, and anxiety or sadness. Together these form what is commonly known as manic depression. Manic depression, with its two principal sub-types, bipolar disorder and major depression, was first clinically described near the end of the 19th century by psychiatrist Emil Kraepelin, who published his account of the disease in his Textbook of Psychiatry. DSM-IV is the Diagnostic and Statistical Manual of Mental Disorders, published by the American Psychiatric Association, is the handbook used most often in diagnosing mental disorders in the United States and other countries." [OneLook:www.onelook.com "Online collection of dictionaries - Wikipedia"]
is_a: PW:0000240 ! neuropsychiatric disease pathway

[Term]
id: PW:0000243
name: vascular endothelial growth factor signaling pathway
def: "The VEGF family  of cytokines plays key roles in angiogenesis and lymphangiogenesis. Through their receptors VEGFs can initiate a diverse and complex network of signaling cascades. Deregulation of VEGFs mediated pathways, mostly through upregulation of VEGFs expression, has been implicated in a number of conditions, primarily cancer. " [OneLook\, PubMed:PMID\: 15563310; PMID\: 15544039 "Review articles,"]
related_synonym: "VEGF signaling pathways" []
is_a: PW:0000168 ! growth factor signaling pathway

[Term]
id: PW:0000244
name: Angiotensin II signaling pathway
def: "Angiotensin II signaling pathways play a critical role in the control of cardiovascular and renal homeostasis. Angiotensin II pathway can also contribute to cardiovascular diseases such as hypertension, atherosclerosis and heart failure." [PubMed:PMID\: 15638741\, PMID\: 15883759 "Review article"]
is_a: PW:0000245 ! angiotensin signaling pathway

[Term]
id: PW:0000245
name: angiotensin signaling pathway
def: "Angiotensin peptides Ang II, Ang III, Ang IV and Ang (1-7) generated from a single precursor protein - angiotensinogen - regulate an array of physiological and pathophysiological processes." [PubMed:PMID\: 12676163; PMID\: 12676165\, 15638741 "Several review articles in PubMed"]
is_a: PW:0000467 ! peptide and protein hormone signaling pathway
is_a: PW:0000492 ! renin-angiotensin system signaling pathway

[Term]
id: PW:0000246
name: Rheb mediated signaling pathway
def: "The Rheb family of proteins plays an essential role in the regulation of cell growth and cell cycle. Rheb could be a mediator of the mTOR signaling pathway. The results have been shown for Drosophila but remained to be established for mammals." [PubMed:PMID\: 15240005 "Review article on Rheb"]
is_a: PW:0000158 ! Ras family signaling pathway

[Term]
id: PW:0000247
name: transforming growth factor-beta signaling pathway - SMAD independent
def: "TGF-beta can activate signaling cascades others than the SMAD mediated ones, including MAPK pathways such as Erk, p38 and JNK. The mechanisms of MAPK pathways activation by TGF-beta are not well understood." [PubMed:PMID\: 14534577]
related_synonym: "SMAD independent TGF-beta signaling pathway" []
is_a: PW:0000206 ! transforming growth factor-beta signaling pathway

[Term]
id: PW:0000248
name: steroid biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of steroids - any of a group of lipids that contain a hydrogenated cyclopentanoperhydrophenanthrene ring system. They include progesterone, adrenocortical hormones, the gonadal hormones, cardiac aglycones, bile acids, sterols (such as cholesterol), saponins, also some carcinogenic hydrocarbons." [OneLook:www.onelook.com "Online collection of dictionaries - Dorland's."]
is_a: PW:0000010 ! lipid metabolic pathway

[Term]
id: PW:0000249
name: lipopolysaccharide biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of lipopolysaccharides - a complex of lipid and polysaccharide." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000146 ! glycan metabolic pathway

[Term]
id: PW:0000250
name: peptidoglycan biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of peptidoglycan - a high-molecular-weight polymer that forms the tough, rigid structure of bacterial cell walls. It is made up of three parts: (1) a backbone, composed of alternating N-acetylglucosamine and N-acetylmuramic acid; (2) a set of identical tetrapeptide side-chains attached to N-acetylmuramic acid; and (3) a set of identical peptide cross-bridges. The backbone is the same in all bacterial species; however, the tetrapeptide side-chains and the peptide cross-bridges vary from species to species." [OneLook:www.onelook.com "Online collection of dictionaries - Dorland's"]
is_a: PW:0000146 ! glycan metabolic pathway

[Term]
id: PW:0000251
name: diterpenoid biosynthetic pathway
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000252
name: monoterpenoid biosynthetic pathway
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000253
name: indole and ipecac alkaloid biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of indole and ipecac. Indole is a heterocyclic compound, obtained from coal tar, and produced by the decomposition of tryptophan in the intestine, being partly responsible for the peculiar odor of the feces. It is also found in cultures of Vibrio cholerae and other bacteria; a color test for its production is used in classifying enteric bacteria. Ipecac is derived from the dried rhizome and roots of Cephaelis ipecacuanha or of C. acuminata. It is a mixture of alkaloids, primarily emetine and cephaelin." [OneLook:www.onelook.com "Online collection of dictionaries - Dorland's and other Internet resources."]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000254
name: penicillins and cephalosporins biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of penicillin and cephalosporins. The former is the best known antibiotic which blocks the cross linking reaction in peptidoglycan synthesis, thus destroying the bacterial cell wall. The latter represents a broad class of antibiotics similar to penicillin, both chemically and in mode of action." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000255
name: beta-Lactam resistance pathway
def: "Those pathways that confer to an organism resistance to the action of beta-lactams - a class of broad spectrum antibiotics that are structurally and pharmacologically related to penicillins and cephalosporins." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000256
name: polyketides biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of polyketides. Polyketides are a group of secondary metabolites made by microorganisms that possess a broad range of pharmacologically important activities such as antimicrobial, antifungal, antiparasitic and antitumor." [Internet:http\://linux1.nii.res.in/~pksdb/polyketide.html "Online information on polyketides"]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000257
name: polyketide sugar biosynthetic pathway
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000258
name: tetracycline biosynthetic pathway
def: "Those metabolic reactions involved in the synthesis of tetracycline - any of a group of biosynthetic antibiotics. Some are isolated from certain species of Streptomyces and others are produced semisynthetically by catalytic hydrogenation of chlortetracycline or oxytetracycline. The group includes chlortetracycline, oxytetracycline, tetracycline. " [OneLook:www.onelook.com "Online collection of dictionaries - Dorland's Medical Dictionary"]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000259
name: clavulanic acid biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of clavulanic acid.  Clavulanic acid is a beta-lactam antibiotic produced by a bacterium of the genus Streptomyces (S. clavuligerus) that is a beta-lactamase inhibitor and is usually used in the form of its clavulanate salt of potassium especially in combination with amoxicillin " [Internet:Google "Definition compiled from a number of Web sources."]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000260
name: puromycin biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of puromycin - an antibiotic produced by Streptomyces alboniger, which has been used experimentally as an antineoplastic because of its ability to inhibit protein synthesis; it also has trypanosomicidal and amebicidal activity and was formerly used in the treatment of African trypanosomiasis and amebic dysentery." [OneLook:www.onelook.com "Online collection of dictionaries - Dorland'sn"]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000261
name: neuronal secretory pathway
def: "The unique morphology of the neuron defies the classical organization of secretory pathways. The neuronal secretory pathway represents the intracellular trafficking route for proteins involved in synaptic transmission and plasticity as well as for lipids necessary for outgrowth and remodeling of the somatodendritic compartment. Neurons possess both somatic and dendritic Golgi compartments." [PubMed:PMID\: 15232591 "Review article"]
is_a: PW:0000059 ! pathway pertinent to signaling in the brain

[Term]
id: PW:0000262
name: altered metabolic pathway
def: "Those metabolic pathways that deviate from what their normal course should be. Aberrant metabolic pathways, alone or in combination with other pathways, underlie many conditions, disorders and/or diseases." [PW Dictionary:InHouse dictionary "Definition compiled from many sources."]
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000263
name: altered regulatory pathway
def: "Those regulatory pathways that deviate from what their normal course should be. Aberrant regulatory pathways, alone or in combination with other pathways underlie many conditions, disorders and/or diseases." [PW Dictionary:InHouse Dictionary "Definition compiled from many sources"]
is_a: PW:0000004 ! regulatory pathway

[Term]
id: PW:0000264
name: altered signaling pathway
def: "Those signaling pathways that deviate from what their normal course should be. Aberrant signaling pathways, alone or in combination with other pathways underlie many conditions, disorders and/or diseases." [PW Dictionary:InHouse Dictionary "Definition compiled from many sources."]
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000265
name: Creutzfeldt-Jakob disease
def: "Creutzfeldt-Jakob disease -  a rare prion disease, associated with a number of different mutations of the prion protein gene, existing in sporadic, familial (as an autosomal dominant), and infectious forms, with onset usually in middle life, and having a wide variety of clinical and pathological features. The most commonly seen are varying degrees of spongiform degeneration of neurons, neuronal loss, gliosis, and amyloid plaque formation, accompanied by rapidly progressive dementia, myoclonus, motor disturbances." [OneLook:www.onelook.com "Online collection of dictionaries - Dorland's."]
related_synonym: "CJD" []
is_a: PW:0000019 ! prion diseases pathway

[Term]
id: PW:0000266
name: Gerstmann-Strussler syndrome, Gerstmann-Strussler-Scheinker syndrome
def: "Gerstmann-Strussler syndrome,   Gerstmann-Strussler-Scheinker syndrome - a group of rare prion diseases, of autosomal dominant inheritance but linked to different mutations of the prion protein gene. Common characteristics include cognitive and motor disturbances, the presence of multicentric amyloid plaques in the brain. Its manifestations include cerebellar ataxia and dementia, rigidity, tremor, memory loss and others, depending on the form of the condition." [OneLook:www.onelook.com "Online collection of dictionaries - adapted from Dorland's."]
is_a: PW:0000019 ! prion diseases pathway

[Term]
id: PW:0000267
name: fatal familial insomnia
def: "Fatal familial insomnia - an inherited prion disease, transmitted as an autosomal dominant trait, affecting primarily the ventral and dorsomedial nuclei of the thalamus and characterized by progressive insomnia, hallucinations, stupor, and coma ending in death within 6 months to 3 years of onset; autonomic and motor disturbances are also present." [OneLook:www.onelook.com "Online collection of dictionaries - Dorland's."]
is_a: PW:0000019 ! prion diseases pathway

[Term]
id: PW:0000268
name: kuru
def: "Kuru - an infectious form of prion disease with a long incubation period, found only among the Fore and neighboring peoples of New Guinea. It is thought to be associated with ritual cannibalism. Its manifestations include truncal and limb ataxia, tremor, others; ends invariably in death. Amyloid plaques are present in about two thirds of affected individuals." [OneLook:www.onelook.com "Online collection of dictionaries - adapted from Dorland's."]
is_a: PW:0000019 ! prion diseases pathway

[Term]
id: PW:0000269
name: protein folding pathway
def: "Those reactions and molecular interactions 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 ! pathways of protein folding, sorting, modification, degradation

[Term]
id: PW:0000270
name: presynaptic differentiation
is_a: PW:0000261 ! neuronal secretory pathway

[Term]
id: PW:0000271
name: postsynaptic differentiation
is_a: PW:0000261 ! neuronal secretory pathway

[Term]
id: PW:0000272
name: neuron-to-neuron signaling pathways
is_a: PW:0000059 ! pathway pertinent to signaling in the brain

[Term]
id: PW:0000273
name: neuron-to-neuron signaling pathway via the electrical synapse
def: "A simpler pathway of neuron-to-neuron signaling involving the direct flow of ionic currents. It is a reciprocal pathway involving membrane-to-membrane apposition known as gap junction." [PubMed:Annu. Rev. Neurosci. 2004\, v27\, p393-418. "Review article"]
is_a: PW:0000272 ! neuron-to-neuron signaling pathways

[Term]
id: PW:0000274
name: neuron-to-neuron signaling pathway via the chemical synapse
def: "A neurotransmitter-releasing pathway of neuron-to-neuron communication. It involves fusion of neurotransmitter-filled synaptic vesicles with the plasma membrane, activation of postsynaptic receptors. It also involves recycling and re-release of synaptic vesicles." [PubMed :Annu. Rev. Neursci. 2003\, v26\, 701-28.]
related_synonym: "Neurotransmission pathway" []
is_a: PW:0000272 ! neuron-to-neuron signaling pathways

[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 ! regulatory pathway

[Term]
id: PW:0000276
name: non-apoptotic cell death pathway
is_a: PW:0000275 ! cell death pathway

[Term]
id: PW:0000277
name: senescence pathway
is_a: PW:0000276 ! non-apoptotic cell death pathway

[Term]
id: PW:0000278
name: autophagy pathway
def: "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:0000009 ! programmed cell death pathway

[Term]
id: PW:0000279
name: necrosis pathway
def: "Necrosis represents the sum of the morphological changes indicative of cell death and caused by the progressive degradative action of enzymes; it may affect groups of cells or part of a structure or an organ. There are many causes of necrosis including injury, infection, cancer, infarction, inflammation, others. There are several distinctive morphologic patterns of necrosis." [Onelook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000276 ! non-apoptotic cell death pathway

[Term]
id: PW:0000280
name: secretory pathway
is_a: PW:0000426 ! protein sorting pathway

[Term]
id: PW:0000281
name: endocytic pathway
is_a: PW:0000426 ! protein sorting pathway

[Term]
id: PW:0000282
name: benzoate degradation pathway
def: "Those enzymatic reactions involved in the degradation of benzoate - a salt of benzoic acid or benzene carboxylic acid, a fungistatic compound widely used as a food preservative." [InHouse:PW dictionary "A compiled definition"]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000283
name: altered glycan metabolic pathway
def: "Those metabolic pathways involving glycan that deviate from what their normal course should be. Aberrant glycan metabolic pathways, alone or in combination with other pathways, underlie various diseases." [PubMed:PMID\: 15459677 "Review article on glycomics and drug development"]
is_a: PW:0000146 ! glycan metabolic pathway
is_a: PW:0000262 ! altered metabolic pathway

[Term]
id: PW:0000284
name: altered glycosaminoglycan pathway
def: "Those metabolic pathways involving glycosaminoglycans that deviate from what their normal course should be. Aberrant glycosaminoglycan pathways, alone or in combination with other pathways underlie various diseases." [PubMed:PMID\: 15459677 "Review article on glycomics and drug development"]
is_a: PW:0000157 ! glycosaminoglycan metabolic pathway
is_a: PW:0000283 ! altered glycan metabolic pathway

[Term]
id: PW:0000285
name: altered heparan sulfate pathway
def: "Those metabolic pathways involving heparan sulfate (HS) that deviate from what their normal course should be. Aberrant HS pathways, alone or in combination with other pathways may be involved in diseases. An example is the potential role of HS in Alzheimer's disease." [PubMed:PMID\: 14530380 "Heparan sulfate interacts with BACE1 and affects the processing of amyloid precursor protein"]
is_a: PW:0000284 ! altered glycosaminoglycan pathway
is_a: PW:0000524 ! heparan sulfate biosynthetic pathway

[Term]
id: PW:0000286
name: integrin 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 ! cell-cell signaling pathway

[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 ! programmed cell death pathway
is_a: PW:0000289 ! altered cell death pathway

[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 ! intrinsic apoptotic pathway
is_a: PW:0000287 ! altered programmed cell death

[Term]
id: PW:0000289
name: altered cell death pathway
def: "Those pathways of cell death that deviate from what their normal course should be. Aberrant pathways of cell death, alone or in combination with other pathways underlie various diseases." [PW:Inhouse "Definition compiled by the PW editorial board."]
is_a: PW:0000263 ! altered regulatory pathway
is_a: PW:0000275 ! cell death pathway

[Term]
id: PW:0000290
name: altered pathway of replication, gene expression and protein biosynthesis
def: "Those pathways of replication, gene expression and protein biosynthesis that deviate from what their normal course should be. Aberrant pathways of replication, gene expression and protein biosynthesis, alone or in combination with other pathways underlie various diseases." [PW:Inhouse "Definition compiled by the PW editorial board."]
is_a: PW:0000085 ! pathways of replication, gene expression, protein biosynthesis
is_a: PW:0000263 ! altered regulatory pathway

[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 ! double strand break repair pathway
is_a: PW:0000292 ! altered DNA repair pathway

[Term]
id: PW:0000292
name: altered DNA repair pathway
def: "Those pathways of DNA repair that deviate from what their normal course should be. Aberrant pathways of DNA repair, alone or in combination with other pathways underlie various diseases." [PW:InHouse "Definition compiled by the PW editorial board."]
is_a: PW:0000099 ! DNA repair pathway
is_a: PW:0000290 ! altered pathway of replication, gene expression and protein biosynthesis

[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 ! pathways of protein folding, sorting, modification, degradation
is_a: PW:0000263 ! altered regulatory pathway

[Term]
id: PW:0000294
name: altered ubiquitin/proteasome degradation pathway
def: "An ubiquitin/proteasome degradation pathway that deviates from what its normal course should be. Aberrations in the pathway have been implicated in a number of diseases. Examples include certain malignancies, disorders of the immune and inflammatory responses and neurodegeneration." [PubMed:PMID\: 14556719 "Review article in Neuron"]
is_a: PW:0000144 ! ubiquitin/proteasome degradation pathway
is_a: PW:0000418 ! altered ubiquitin, ubiquitin-like degradation pathway

[Term]
id: PW:0000295
name: altered integrin 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 article in Cardiovascular Research, 2004."]
is_a: PW:0000286 ! integrin signaling pathway
is_a: PW:0000336 ! altered cell-cell signaling pathway

[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 ! cardiomyopathy

[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"]
related_synonym: "PDGF signaling pathway" []
is_a: PW:0000168 ! growth factor signaling pathway

[Term]
id: PW:0000298
name: altered growth factor signaling pathway
def: "Those growth factor mediated signaling pathways that deviate from what their normal course should be. Aberrant growth factor mediated pathways, alone or in combination with other pathways underlie various diseases." [PW:InHouse3 "Definition compiled by the PW editorial board."]
is_a: PW:0000168 ! growth factor signaling pathway
is_a: PW:0000264 ! altered signaling pathway

[Term]
id: PW:0000299
name: myocardial infarction
def: "Myocardial infarction, commonly known as heart attack, is a serious, sudden heart condition characterized by varying degrees of chest pain, weakness, sweating, nausea, and vomiting, sometimes causing loss of consciousness. It occurs when parts of the heart muscle die because they are not supplied with enough blood." [OneLook:www.onelook.org "Online collection of dictionaries - Wikipedia"]
is_a: PW:0000020 ! cardiovascular disease pathway

[Term]
id: PW:0000300
name: renal disease, renal disorder pathway
def: "The congenital and acquired diseases affecting the kidney. " [PW:InHouse "Definition compiled by the PW editorial board"]
is_a: PW:0000013 ! disease pathway

[Term]
id: PW:0000301
name: renal failure
def: "Renal failure implies the loss of kidney function. It can be acute and rapidly progressing, or chronic with slow progression. Chronic renal failure may involve a number of kidney diseases and end-stage renal failure is the ultimate consequence." [Onelook:www.onelook.com "Online collection of dictionaries - Wikipedia"]
is_a: PW:0000300 ! renal disease, renal disorder pathway

[Term]
id: PW:0000302
name: glomerulonephritis
def: "Glomerulonephritis is accompanied by inflammation of the capillary loops in the glomeruli of the kidney. It occurs in acute, subacute, and chronic forms and may be secondary to hemolytic streptococcal infection. Evidence also supports possible immune or autoimmune mechanisms." [Onelook:www.onelook.org "Online collection of dictionaries - Dorland's."]
is_a: PW:0000300 ! renal disease, renal disorder pathway

[Term]
id: PW:0000303
name: p53-dependent G1/S DNA damage checkpoint pathway
is_a: PW:0000095 ! G1/S DNA damage checkpoint pathway

[Term]
id: PW:0000304
name: p53-independent G1/S DNA damage checkpoint pathway
def: "The p53-independent pathway of CDKs inhibition." [InHouse:PW dictionary "Definition compiled by the PW editorial board based on the information at the Reactome."]
is_a: PW:0000095 ! G1/S DNA damage checkpoint pathway

[Term]
id: PW:0000305
name: altered carbohydrate metabolic pathway
def: "Those pathways of carbohydrate metabolism that deviate from what their normal course should be. Aberrant carbohydrate metabolic pathways, alone or in combination with other pathways, underlie various diseases." [InHouse:PW dictionary "Definition compiled by the PW editorial board."]
is_a: PW:0000005 ! carbohydrate metabolic pathway
is_a: PW:0000262 ! altered metabolic pathway

[Term]
id: PW:0000306
name: altered galactose metabolic pathway
def: "Those pathways of galactose metabolism that deviate from what their normal course should be. 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 ! galactose metabolic pathway
is_a: PW:0000305 ! altered carbohydrate metabolic pathway

[Term]
id: PW:0000307
name: coagulative necrosis pathway
def: "Coagulative necrosis is typically seen in hypoxic environments. Cell outlines remain after cell death and can be observed by light microscopy (e.g. myocardial infarction, infarct of the spleen)." [Onelook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000279 ! necrosis pathway

[Term]
id: PW:0000308
name: liquefactive necrosis pathway
def: "Liquefactive necrosis is associated with cellular destruction and pus formation (e.g. pneumonia)." [onelook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000279 ! necrosis pathway

[Term]
id: PW:0000309
name: caseous necrosis pathway
def: "Caseous necrosis is a mix of coagulative necrosis and liquefactive necrosis (e.g. tuberculosis)." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000279 ! necrosis pathway

[Term]
id: PW:0000310
name: fatty necrosis pathway
def: "Fatty necrosis results from the action of lipases on fatty tissues (e.g. acute pancreatitis)." [Onelook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000279 ! necrosis pathway

[Term]
id: PW:0000311
name: fibrinoid necrosis pathway
def: "Fibrinoid necrosis involves the deposition of fibrin and other plasma proteins in the walls of afferent renal arterioles in malignant hypertension, often accompanied by an inflammatory infiltrate within the walls and thrombosis of the vessel lumen. " [Onelook:www.onelook.com]
is_a: PW:0000279 ! necrosis pathway

[Term]
id: PW:0000312
name: stress-regulated MAPK signaling pathway
def: "A group of MAPK signaling pathways that are responding to stress or injury." [PubMed :PMID\: 10209154 ; PMID\: 14570565 "Two review articles on MAPK"]
related_synonym: "SAPK signaling pathway" []
is_a: PW:0000007 ! mitogen activated protein kinase signaling pathway

[Term]
id: PW:0000313
name: c-Jun N-terminal kinases MAPK signaling pathway
def: "A stress induced MAPK pathway that regulates an array of processes such as gene expression, cell migration, cytoskeletal organization, apoptosis." [PubMed :PMID\: 15102441 "Review article on the JNK MAPK pathway"]
related_synonym: "JNK signaling pathway" []
is_a: PW:0000312 ! stress-regulated MAPK signaling pathway

[Term]
id: PW:0000314
name: calcium/calmodulin dependent signaling pathway
def: "Those signaling pathways that are mediated through the binding of calmodulin - a multifunctional calcium transducer - to its target effectors." [PubMed:PMID\: 10884684 \, PMID\: 14671000 "Review articles"]
related_synonym: "Ca/CaM dependent signaling pathways" []
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000315
name: calcineurin signaling pathway
def: "Calcineurin - a calcium/calmodulin dependent serine/threonine phosphatase - plays important regulatory roles in cardiac muscle growth and differentiation, memory processes and apoptosis." [PuvMed:PMID\: 15232210 \, "Article in PubMed, Molecules and Cells"]
is_a: PW:0000314 ! calcium/calmodulin dependent signaling pathway

[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"]
related_synonym: "Ca/CaM dependent CaMKs pathway" []
is_a: PW:0000314 ! calcium/calmodulin dependent signaling pathway

[Term]
id: PW:0000317
name: nuclear factor of activated T-cells signaling pathway
def: "Members of the NFAT family of transcription factors, once de-phosphorylated by calcineurin translocate from the cytoplasm to the nucleus where they induce the transcription of genes involved in the immune response, cell-cell interactions. NFAT signaling is believed to play important roles in the development and function of the cardiovascular system." [pUBmED:PMID\: 11983154 \,PMID\: 12975316 "Review articles in Cell, Genes and Development"]
related_synonym: "NFAT signaling pathway" []
is_a: PW:0000315 ! calcineurin signaling pathway

[Term]
id: PW:0000318
name: altered calcium/calmodulin dependent pathway
def: "Those calcium/CaM dependent pathways that deviate from what their normal course should be. Aberrant calcium/CaM dependent pathways, alone or in combination with other pathways underlie many diseases. One example is the potential role disruptions within these pathways play in cardiac hypertrophy." [PW dictionary:InHouse PW "Definition compiled by the PW editorial board"]
related_synonym: "altered Ca/CaM dependent pathway" []
is_a: PW:0000264 ! altered signaling pathway
is_a: PW:0000314 ! calcium/calmodulin dependent signaling pathway

[Term]
id: PW:0000319
name: altered calcineurin signaling pathway
def: "A calcineurin signaling pathway that deviates from what its normal course should be. Aberrant calcineurin pathway, alone or in combination with other pathways underlie various diseases. One example is the role a constitutively active calcineurin plays in cardiac hypertrophy, via the NFAT pathway." [PubMed:PMID\: 15276472 "Review article in Cardiovascular Research"]
is_a: PW:0000315 ! calcineurin signaling pathway
is_a: PW:0000318 ! altered calcium/calmodulin dependent pathway

[Term]
id: PW:0000320
name: novobiocin biosynthetic pathway
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000321
name: altered Hedgehog signaling pathway
def: "A Hedgehog signaling pathway that deviates from what its normal course should be. Aberrant Hedgehog signaling pathway has been involved in a number of human cancers." [PubMed:PMID\: 12495844\, PMID\: 15205520. "Articles on Hedgehog signaling and human diseases."]
is_a: PW:0000122 ! Hedgehog signaling pathway
is_a: PW:0000264 ! altered signaling pathway

[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 ! cell-cell signaling pathway

[Term]
id: PW:0000323
name: altered ephrin - ephrin receptor bidirectional signaling pathway
def: "An Eph/ephrin bidirectional axis that deviates from what its normal course should be. Aberrant Eph/ephrins axis has been implicated in a number of human cancers. " [PubMed:PMID\: 15561600 "A survey article A survey article on the role of eph-ephrin axis in cancer"]
is_a: PW:0000322 ! ephrin - ephrin receptor bidirectional signaling axis
is_a: PW:0000336 ! altered cell-cell signaling pathway

[Term]
id: PW:0000324
name: altered Notch signaling pathway
def: "A Notch signaling pathway that deviates from what its normal course should be. Aberrant Notch signaling pathway has been implicated in a number of human cancers." [PubMed:PMID\: 14988924\, 15288257\,PMID\: 11549580. "Various articles on Notch signaling pathway and diseases"]
is_a: PW:0000204 ! Notch signaling pathway
is_a: PW:0000336 ! altered cell-cell signaling pathway

[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 ! pathways of protein folding, sorting, modification, degradation

[Term]
id: PW:0000326
name: altered protein degradation pathway
is_a: PW:0000293 ! altered pathway of protein folding, sorting, modification and degradation
is_a: PW:0000325 ! protein degradation pathway

[Term]
id: PW:0000327
name: protein disulphide bond pathway
def: "The pathways involved in the formation, reduction and isomerization of disulphide bonds in proteins. Disulphide bonds are essential for the stability of proteins that are secreted or are localized to organelles of the secretory pathway." [PubMed:PMID\: 10754564 "Review article in Trends in Cell Biology"]
is_a: PW:0000269 ! protein folding pathway

[Term]
id: PW:0000328
name: fibroblast growth factor signaling pathway
related_synonym: "FGF signaling pathway" []
is_a: PW:0000168 ! growth factor signaling pathway

[Term]
id: PW:0000329
name: transforming growth factor -beta superfamily mediated signaling pathway
def: "The TGF-beta superfamily of growth factors regulates a broad spectrum of processes such as angiogenesis, embryonic development, cell differentiation, proliferation, wound healing. Binding to two types of serine/threonine receptors and activation of Smad proteins is a common theme. However, ligand-receptor interaction and the identity of the activated Smad protein(s) appear to be member specific." [PubMed:PMID\: 15473857 "Review article and references therein"]
related_synonym: "TGF-beta superfamily mediated signaling pathways" []
is_a: PW:0000168 ! growth factor signaling pathway

[Term]
id: PW:0000330
name: Bone morphogenetic proteins signaling pathway
def: "The bone morphogenetic proteins (BMP) are related to TGF-beta and activins and are members of the TGF-beta superfamily. The BMP signaling pathway plays important roles in induction and patterning of the mesoderm. BMP pathway cross-talks to other pathways such as TGF-beta, Wnt, MAPK, Notch, JAK-STAT and others." [PubMed:PMID\: 15368350 "Review article in J Cell Biochem"]
related_synonym: "BMP signaling pathway - SMAD dependent" []
is_a: PW:0000329 ! transforming growth factor -beta superfamily mediated signaling pathway

[Term]
id: PW:0000331
name: activin signaling pathway
is_a: PW:0000329 ! transforming growth factor -beta superfamily mediated signaling pathway

[Term]
id: PW:0000332
name: cell-cell signaling pathway
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000333
name: cadherins signaling pathway
is_a: PW:0000332 ! cell-cell signaling pathway

[Term]
id: PW:0000334
name: connexins signaling pathway
is_a: PW:0000332 ! cell-cell signaling pathway

[Term]
id: PW:0000335
name: altered transforming growth factor-beta superfamily mediated signaling pathway
def: "Those TGF-beta superfamily mediated signaling pathways that deviate from what their normal course should be. Alone or in combination with other pathways they underlie many types of cancer, renal conditions, pulmonary hypertension." [PW dictionary:InHouse PW dictionary "Definition compiled by the PW editorial board."]
is_a: PW:0000298 ! altered growth factor signaling pathway
is_a: PW:0000329 ! transforming growth factor -beta superfamily mediated signaling pathway

[Term]
id: PW:0000336
name: altered cell-cell signaling pathway
def: "Those cell-cell signaling pathways that deviate from what their normal course should be." [PW dictionary:InHouse PW dictionary "Definition compiled by the PW editorial board."]
is_a: PW:0000264 ! altered signaling pathway
is_a: PW:0000332 ! cell-cell signaling pathway

[Term]
id: PW:0000337
name: selectin signaling pathway
def: "Selectins represent a small family of lectin-like adhesion receptors that mediate cell-cell interactions via calcium-dependent recognition of sialylated glycans. The exact role of this signaling pathway is not well known." [PubMed:PMID\: "Review article"]
is_a: PW:0000332 ! cell-cell signaling pathway

[Term]
id: PW:0000338
name: altered cadherins mediated signaling pathway
is_a: PW:0000333 ! cadherins signaling pathway

[Term]
id: PW:0000339
name: altered connexins mediated signaling pathway
is_a: PW:0000334 ! connexins signaling pathway

[Term]
id: PW:0000340
name: altered Notch signaling pathway involving the main players
def: "An altered Notch signaling pathway due to mutation(s) in the main players. They include receptor(s), ligand(s), and members of the CSL complex." [InHouse:PW dictionary "Definition compiled by the PW editorial board"]
is_a: PW:0000324 ! altered Notch signaling pathway

[Term]
id: PW:0000341
name: altered Notch signaling pathway involving the macromolecules modifying the main players
def: "An altered Notch signaling pathway due to mutation(s) in the enzymes, macromolecules that act upon the main players. They include proteases, elements of the proteo- and glucosaminoglycan metabolic pathways,  ubiquitin ligases, other proteins that modulate availability, sensitivity, endocytosis of ligands/receptors." [InHouse:PW dictionary "Definition compiled by the PW editorial board"]
is_a: PW:0000324 ! altered Notch signaling pathway

[Term]
id: PW:0000342
name: altered Notch signaling pathway involving target gene(s)
def: "An altered Notch signaling pathway due to mutation(s) in the target gene(s). They may include members of the HES and HERP families of basic helix-loop-helix (bHLH) transcriptional repressors." [InHouse:PW dictionary "Definition compiled by the PW editorial boardd."]
is_a: PW:0000324 ! altered Notch signaling pathway

[Term]
id: PW:0000343
name: altered Notch signaling pathway involving promoters
def: "An altered Notch signaling pathway due to mutation(s) in the promoters of target gene(s)." [InHouse:PW dictionary "Definition compiled by the PW editorial board."]
is_a: PW:0000324 ! altered Notch signaling pathway

[Term]
id: PW:0000344
name: cerebrovascular disease pathway
is_a: PW:0000013 ! disease pathway

[Term]
id: PW:0000345
name: cerebral arterial diseases
is_a: PW:0000344 ! cerebrovascular disease pathway

[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 ! cerebral arterial diseases

[Term]
id: PW:0000347
name: cardiovascular abnormalities
is_a: PW:0000020 ! cardiovascular disease pathway

[Term]
id: PW:0000348
name: congenital heart defects
is_a: PW:0000347 ! cardiovascular abnormalities

[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 ! congenital heart defects

[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"]
related_synonym: "altered VEGF signaling pathways" []
is_a: PW:0000243 ! vascular endothelial growth factor signaling pathway
is_a: PW:0000298 ! altered growth factor signaling pathway

[Term]
id: PW:0000351
name: altered vascular endothelial growth factor signaling pathway involving the main players
def: "An altered VEGF signaling pathway due to mutation(s) in the main players. They include the various VEGF molecules and VEGF receptors." [InHouse:InHouse PW dictionary "Definition compiled by the PW editorial board"]
related_synonym: "altered VEGF signaling pathway involving the main players" []
is_a: PW:0000350 ! altered vascular endothelial growth factor signaling pathway

[Term]
id: PW:0000352
name: altered vascular endothelial growth factor signaling pathway involving the macromolecules modifying the main players
def: "An altered VEGF signaling pathway due to mutation(s) in the enzymes that process VEGF, such as the plasmin and furin-like proteases." [InHouse:In House PW dictionary "Definition compiled by the PW editorial board"]
related_synonym: "altered VEGF signaling pathway involving the macromolecules modifying the main players" []
is_a: PW:0000350 ! altered vascular endothelial growth factor signaling pathway

[Term]
id: PW:0000353
name: altered vascular endothelial growth factor signaling pathway involving proteins affecting its expression
def: "An altered VEGF signaling pathway due to mutation(s), any activity change in the proteins that regulate VEGF expression. They include transcription factors  such as the hypoxia-inducible factor and the many proteins impacting on the stability and/or activity of these factors. " [InHouse :InHouse PW dictionary "Definition compiled by the PW editorial board."]
related_synonym: "altered VEGF signaling pathway involving proteins affecting its expression" []
is_a: PW:0000350 ! altered vascular endothelial growth factor signaling pathway

[Term]
id: PW:0000354
name: glycerophospholipid metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation pf glycerophospholipids - amphipathic lipids with a glycerol backbone." [InHouse:PW InHouse dictionary "Definition compiled by the PW editorial board."]
is_a: PW:0000153 ! glycerolipid metabolic pathway
is_a: PW:0000155 ! phospholipid metabolic pathway

[Term]
id: PW:0000355
name: homeostasis pathway
def: "Those pathways involved in the maintenance of the internal environment of an organism, the adequate levels of substances and nutrients, the stability of normal body states and the feedback regulatory mechanisms that control them." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000004 ! regulatory pathway

[Term]
id: PW:0000356
name: oxygen homeostasis pathway
is_a: PW:0000355 ! homeostasis pathway

[Term]
id: PW:0000357
name: energy homeostasis pathway
def: "Those pathways involved in the balance between energy uptake and energy expenditure. Disturbance of this equilibrium has been linked to various forms of human obesity. " [PubMed:PMID\: 15703762 \, PMID\: 11239410 "Review articles on obesity."]
is_a: PW:0000355 ! homeostasis pathway

[Term]
id: PW:0000358
name: altered homeostasis pathway
def: "Those homeostatic pathways that deviate from what their normal course should be. Aberrant homeostatic pathways, alone or in combination with other pathways, underlie many conditions, disorders and/or diseases." [PW dictionary:PW InHouse dictionary "Definition compiled by the PW editorial board."]
is_a: PW:0000263 ! altered regulatory pathway
is_a: PW:0000355 ! homeostasis pathway

[Term]
id: PW:0000359
name: altered energy homeostasis pathway
def: "Those pathways of energy homeostasis that deviate from what their normal course should be. Obesity in particular has been associated with disturbances in the control of energy balance." [PubMed :PMID\: 15703762 \,PMID\: 11239410 "Review articles on obesity"]
is_a: PW:0000357 ! energy homeostasis pathway
is_a: PW:0000358 ! altered homeostasis pathway

[Term]
id: PW:0000360
name: the chronic hypoxic response - the hypoxia inducible factor - alpha pathway
def: "The chronic hypoxic response is mediated by the hypoxia-inducible transcription factor. It involves changes in the expression of genes that play important roles in angiogenesis and erythropoiesis. " [PubMed:PMID\: 11181957  PMID\: 12603312 \, PMID\: 14597660\, PMID\: 15031665 . "Review articles in PubMed."]
related_synonym: "the chronic hypoxic response - the HIF-alpha pathway" []
is_a: PW:0000356 ! oxygen homeostasis pathway

[Term]
id: PW:0000361
name: altered oxygen homeostasis pathway
is_a: PW:0000356 ! oxygen homeostasis pathway
is_a: PW:0000358 ! altered homeostasis pathway

[Term]
id: PW:0000362
name: the acute hypoxic response - the ion channels pathway
def: "The acute hypoxic response is mediated through the activity of excitable cells via oxygen-sensing ion channels. " [PubMed:PMID\: 11181957 "Review article in PubMed"]
is_a: PW:0000356 ! oxygen homeostasis pathway

[Term]
id: PW:0000363
name: leptin system pathway
def: "Leptin acts on two populations of hypothalamic neurons that express orexigenic (feeding inducing) and anorexigenic genes, respectively. Leptin reduces the expression of genes from the former and enhances the expression of genes from the latter neurons. Leptin mediated response acts primarily via Jak-dependent activation of STAT." [PubMed:PMID\: 12079865\, PMID\: 11239410 . "Review article  - Ann. N.Y. Acd. Sci."]
is_a: PW:0000357 ! energy homeostasis pathway
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000364
name: altered leptin system pathway
is_a: PW:0000359 ! altered energy homeostasis pathway
is_a: PW:0000363 ! leptin system pathway
is_a: PW:0000511 ! altered peptide and protein hormone signaling pathway

[Term]
id: PW:0000365
name: melanocortin system pathway
def: "The melanocortin dependent system is involved in a diverse number of pathways such as pigmentation, steroidogenesis, sexual function, energy homeostasis. Its implication in energy homeostasis is of particular interest as alterations of this system have been associated with obesity." [PubMed:PMID\: 12556347 \,PMID\: 15189116 \,PMID\: 11874690 "Review articles in PubMed"]
is_a: PW:0000357 ! energy homeostasis pathway
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000366
name: altered melanocortin system pathway
def: "A melanocortin dependent system pathway that deviates from what its normal course should be. Mutations in the prohormone gene PMOC and a modifying enzyme PC1 are linked to obesity." [PubMed :v "review article on PMOC"]
is_a: PW:0000359 ! altered energy homeostasis pathway
is_a: PW:0000365 ! melanocortin system pathway
is_a: PW:0000511 ! altered peptide and protein hormone signaling pathway

[Term]
id: PW:0000367
name: altered JAK-STAT signaling pathway
def: "JAK-STAT signaling pathways that deviate from what their normal course should be. " [InHouse:PW InHouse dictionary "Definition compiled by the PW editorial group"]
is_a: PW:0000209 ! JAK-STAT signaling pathway
is_a: PW:0000264 ! altered signaling pathway

[Term]
id: PW:0000368
name: Non-STAT, JAK dependent pathway
def: "Those pathways dependent on activation by JAK kinases but independent of STAT proteins." [PubMed:PMID\: 12884916 "Review article regarding non-STAT JAK signaling pathway"]
is_a: PW:0000209 ! JAK-STAT signaling pathway

[Term]
id: PW:0000369
name: the ARE-Nrf mediated pathway of drug-metabolizing enzyme expression
def: "The ARE-Nrf mediated pathway regulates the expression of phase II drug-metabolizing enzymes." [PubMed:15252150 [ "Review article in PubMed"]
is_a: PW:0000124 ! cellular detoxification pathway
is_a: PW:0000378 ! oxidative stress response pathways

[Term]
id: PW:0000370
name: the XRE-AhR mediated pathway of drug-metabolizing enzyme expression
def: "The XRE-AhR mediated pathway regulates the expression of phase I and phase II drug-metabolizing enzymes." [PubMed:PMID\: 15627472 \, PMID\: 15451023 "Articles in PubMed"]
is_a: PW:0000124 ! cellular detoxification pathway

[Term]
id: PW:0000371
name: calcium homeostasis pathway
is_a: PW:0000589 ! metal homeostasis pathway

[Term]
id: PW:0000372
name: altered calcium homeostasis pathway
is_a: PW:0000358 ! altered homeostasis pathway
is_a: PW:0000371 ! calcium homeostasis pathway

[Term]
id: PW:0000373
name: glutathione conjugation pathway
def: "The glutathione conjugation of endogenous and exogenous electrophilic compounds represents a major pathway 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 ! cellular detoxification pathway
is_a: PW:0000378 ! oxidative stress response pathways

[Term]
id: PW:0000374
name: alternate pathways of glutathione conjugates processing
def: "Pathways of glutathione conjugates processing other than the mercapturic acid pathway" [InHouse dictionary:PW InHouse dictionary "Definition compiled by the PW editorial board based on a number of articles"]
is_a: PW:0000373 ! glutathione conjugation pathway

[Term]
id: PW:0000375
name: 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 ! cellular detoxification pathway

[Term]
id: PW:0000376
name: cytochrome P450-independent bioactivation pathway
is_a: PW:0000124 ! cellular detoxification pathway

[Term]
id: PW:0000377
name: glutathione conjugates processing - the mercapturic acid pathway
def: "The mercapturic acid pathway of glutathione conjugates processing involves the sequential cleavage of glutamyl and glycine residues of glutathione followed by cysteine N-acetylation." [MCW book:QV 600 C335t 2001 "Casarett"]
is_a: PW:0000373 ! glutathione conjugation pathway

[Term]
id: PW:0000378
name: oxidative stress response pathways
def: "Oxidative stress occurs when the redox balance between pro- and anti-oxidants is upset due to an increase in endogenous or exogenous pro-oxidant stimuli. The response triggers the upregulation of antioxidant and detoxification systems. Oxidants can also act as second messengers to trigger a variety of cellular signaling pathways." [InHouse:PW InHouse dictionary "Definition compiled by the PW editorial board."]
is_a: PW:0000237 ! stress response pathway

[Term]
id: PW:0000379
name: endoplasmic reticulum stress  - the unfolded protein response pathway
def: "Inhibition of protein folding or its disruption by mutant proteins in the endoplasmic reticulum triggers a signal transduction response known 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"]
related_synonym: "ER stress - UPR pathway" []
is_a: PW:0000237 ! stress response pathway
is_a: PW:0000269 ! protein folding pathway

[Term]
id: PW:0000380
name: transport pathway for the elimination of drugs, endogenous or exogenous compounds and metabolites
is_a: PW:0000103 ! transport pathway
is_a: PW:0000124 ! cellular detoxification pathway
is_a: PW:0000378 ! oxidative stress response pathways

[Term]
id: PW:0000381
name: multidrug resistance-associated protein mediated transport pathway
related_synonym: "MRP mediated pathway" []
is_a: PW:0000380 ! transport pathway for the elimination of drugs, endogenous or exogenous compounds and metabolites

[Term]
id: PW:0000382
name: multidrug resistance protein mediated transport pathway
related_synonym: "MDR mediated pathway" []
is_a: PW:0000380 ! transport pathway for the elimination of drugs, endogenous or exogenous compounds and metabolites

[Term]
id: PW:0000383
name: multispecific organic anion transporter mediated transport pathway
related_synonym: "OAT mediated pathway" []
is_a: PW:0000380 ! transport pathway for the elimination of drugs, endogenous or exogenous compounds and metabolites

[Term]
id: PW:0000384
name: G2/M DNA damage checkpoint pathway
is_a: PW:0000096 ! G2/M checkpoint pathway

[Term]
id: PW:0000385
name: G2/M DNA replication checkpoint pathway
is_a: PW:0000096 ! G2/M checkpoint pathway

[Term]
id: PW:0000386
name: Rap1 mediated signaling pathway
def: "A very close relative of Ras, Rap1 mediated pathway  appears to control diverse processes such as modulation of growth and differentiation, secretion, integrin linked cell adhesion, morphogenesis." [PubMed :PMID\: 11331911 "Review article"]
is_a: PW:0000158 ! Ras family signaling pathway

[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 ! small G proteins - the Ras superfamily signaling pathway

[Term]
id: PW:0000388
name: Reelin signaling pathway
def: "Reelin signaling pathway regulates neuronal positioning and may also play a role in synaptic plasticity. The reelin gene appears to be downregulated in the schizophrenic brains but the link between the reelin pathway and the disease remains to be established." [PubMed:PMID\: 14993361; PMID\: 12764038;PMID\: 14715136 "Articles on Reelin"]
is_a: PW:0000059 ! pathway pertinent to signaling in the brain

[Term]
id: PW:0000389
name: altered pathway pertinent to signaling in the brain
is_a: PW:0000059 ! pathway pertinent to signaling in the brain
is_a: PW:0000264 ! altered signaling pathway

[Term]
id: PW:0000390
name: altered Reelin signaling pathway
is_a: PW:0000388 ! Reelin signaling pathway
is_a: PW:0000389 ! altered pathway pertinent to signaling in the brain

[Term]
id: PW:0000391
name: altered small G proteins - the Ras superfamily - mediated signaling pathway
is_a: PW:0000006 ! small G proteins - the Ras superfamily signaling pathway
is_a: PW:0000264 ! altered signaling pathway

[Term]
id: PW:0000392
name: altered Ras mediated signaling pathway
def: "A Ras mediated signaling pathway that deviates from what its normal course should be. Aberrant Ras mediated signaling pathways have been implicated in a number of human cancers and deregulation of Ras has been reported even in the absence of mutations. " [PubMed:PMID\: 11027944]
is_a: PW:0000391 ! altered small G proteins - the Ras superfamily - mediated signaling pathway
is_a: PW:0000525 ! Ras mediated signaling pathway

[Term]
id: PW:0000393
name: altered mTOR signaling pathway
is_a: PW:0000180 ! mTOR signaling pathway

[Term]
id: PW:0000394
name: dopamine signaling pathway
related_synonym: "dopaminergic pathway" []
is_a: PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse

[Term]
id: PW:0000395
name: altered dopamine signaling pathway
related_synonym: "altered dopaminergic pathway" []
is_a: PW:0000389 ! altered pathway pertinent to signaling in the brain
is_a: PW:0000394 ! dopamine signaling pathway

[Term]
id: PW:0000396
name: spermidine metabolic pathway
is_a: PW:0000211 ! amines and polyamines metabolic pathway

[Term]
id: PW:0000397
name: Vitamin B12 (cobalamin) metabolic pathway
is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins

[Term]
id: PW:0000398
name: homocysteine metabolic pathway
def: "Homocysteine 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"]
related_synonym: "Hcy metabolism" []
is_a: PW:0000132 ! metabolic pathway of other amino acids

[Term]
id: PW:0000399
name: remethylation pathway of homocysteine metabolism - cobalamin dependent
is_a: PW:0000398 ! homocysteine metabolic pathway

[Term]
id: PW:0000400
name: transulfuration pathway of homocysteine metabolism
def: "The transulfuration pathway is one of the two routes of homocysteine metabolism. It allows for the transfer of sulfur from methionine to cysteine. 70% of cysteine is then converted to glutathione and the remainder ends up as either taurine or pyruvate and sulfate." [MCW library book:Homocysteine in Health and Disease - edited by Ralph Carmel and Donald W Jacobsen "Cambridge University Press, 2001"]
is_a: PW:0000398 ! homocysteine metabolic pathway

[Term]
id: PW:0000401
name: remethylation pathway of homocysteine metabolism - cobalamin independent, betaine dependent
is_a: PW:0000398 ! homocysteine metabolic pathway

[Term]
id: PW:0000402
name: altered metabolic pathway of other amino acids
def: "Those metabolic pathways of amino acids other than the common amino acids that deviate from what their normal course should be. Aberrant metabolic pathways of other amino acids, alone or in combination with other pathways, underlie various diseases." [InHouse :PW InHouse dictionary "Definition compiled by the PW editorial board"]
is_a: PW:0000132 ! metabolic pathway of other amino acids
is_a: PW:0000262 ! altered metabolic pathway

[Term]
id: PW:0000403
name: altered amino acid metabolic pathway
def: "Those pathways of amino acid metabolism that deviate from what their normal course should be. Aberrant amino acid metabolic pathways, alone or in combination with other pathways, underlie various diseases." [InHouse :PW InHouse dictionary "Definition compiled by the PW editorial board"]
is_a: PW:0000011 ! amino acid metabolic pathway
is_a: PW:0000262 ! altered metabolic pathway

[Term]
id: PW:0000404
name: creatine metabolic pathway
def: "Those enzymatic reactions involved in the metabolism of creatine. Officially methyl guanidino-acetic acid formed from arginine and glycine and the methyl group of methionine, creatine supplies energy to muscle cells." [PubMed; Onelook:PMID\: 10893433; www.onelook.com "Review article in PubMed, Wikipedia"]
is_a: PW:0000033 ! energy metabolic pathway
is_a: PW:0000132 ! metabolic pathway of other amino acids

[Term]
id: PW:0000405
name: synaptic vesicle exocytosis - neurotransmitter release pathway
def: "Release of neurotrasmitters is mediated through the exocytosis of neurotrasnmiter-filled synaptic vesicles. Synaptic vesicle trafficking cycle is composed of a number of steps that culminate in calcium-triggered fusion and release." [PubMed:PMID\: 10488439; PMID\: 15217342 "Review articles in PubMed"]
relationship: part_of PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse

[Term]
id: PW:0000406
name: metabolic pathway pertinent to the brain
is_a: PW:0000002 ! classic metabolic pathway

[Term]
id: PW:0000407
name: neurotransmitter metabolic pathway
is_a: PW:0000406 ! metabolic pathway pertinent to the brain

[Term]
id: PW:0000408
name: acetylcholine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of acetylcholine - an ester of choline and acetic acid that acts as a neurotransmitter in both the peripheral nervous system and the central nervous system." [OneLook:www.onelook.com "Online collection of dictionaries - Wikipedia"]
is_a: PW:0000436 ! primary amine neurotransmitter metabolic pathway

[Term]
id: PW:0000409
name: dopamine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of dopamine that acts as a neurotransmitter and a neurohormone. Dopamine has multiple functions in the brain." [OneLook:www.onelook.com "Online collection of dictionaries - Wikipedia"]
is_a: PW:0000443 ! catecholamine neurotransmitter metabolic pathway

[Term]
id: PW:0000410
name: serotonin metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of serotonin - an amine neurotransmitter that is believed to play important roles in a number of conditions such as depression, bipolar disorder, anxiety." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000444 ! indoleamine and related compounds neurotransmitter metabolic pathway

[Term]
id: PW:0000411
name: histamine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of histamine - a biogenic amine that acts as a neurotransmitter and is also involved in the local immune responses. " [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000444 ! indoleamine and related compounds neurotransmitter metabolic pathway

[Term]
id: PW:0000412
name: gamma-aminobutyric acid metabolic pathway
related_synonym: "GABA metabolism" []
is_a: PW:0000446 ! inhibitory neurotransmitter metabolic pathway

[Term]
id: PW:0000413
name: heme catabolic pathway
def: "Those metabolic reactions involved in the degradation of heme - an iron-containing compound where the iron is complexed within a porphyrin heterocyclic ring, There are several kinds of hemes depending on the composition of their side chain. Heme serves as a prosthetic group for a number of proteins." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000217 ! metabolic pathway of prosthetic groups, electron carriers and reductants

[Term]
id: PW:0000414
name: protein degradation pathway via the 'core' 20S proteasome pathway
def: "The 'core' 20S proteasome degrades oxidized and/or unfolded proteins in an ATP and ubiquitin independent manner. The association with the 19S regulatory cap yields the 26S proteasome which has substrate selectivity and ATP and ubiquitin-dependent activity." [PubMed:PMID\: 9212076; "Review articles"]
is_a: PW:0000325 ! protein degradation pathway

[Term]
id: PW:0000415
name: proteasome degradation pathway involving cullin-dependent ubiquitin ligases
def: "A proteasome degradation pathway mediated by cullins. Cullins are components of E3 ligase complexes and substrates for Nedd8 - a ubiquitin-like molecule. Neddylation is thought to modulate the activity of cullins." [PubMed:PMID\: 10806345; PMID\: 15021886 "Review articles in PubMed"]
is_a: PW:0000144 ! ubiquitin/proteasome degradation pathway

[Term]
id: PW:0000416
name: sentrinization pathway
def: "A pathway of protein modification via conjugation with sentrin - a family of ubiquitin-like protein. Sentrinization does not target proteins to the proteasome, rather it targets proteins to particular cellular compartments." [PubMed:PMID\: 10806345; 15808504 "Review articles in PubMed"]
related_synonym: "SUMO modification pathway" []
related_synonym: "sumoylation pathway" []
is_a: PW:0000433 ! protein modification pathway via conjugation with ubiquitin and ubiqutin-like molecules

[Term]
id: PW:0000417
name: ubiquitin, ubiquitin-like/proteasome degradation pathway
def: "The pathway for the ATP-dependent non-lysosomal proteolysis catalyzed by the 26S proteasome and for which ubiquitylation, the post-translational covalent conjugation of ubiquitin, or ubiquitin-like, to target proteins is a key signal." [PubMed:PMID\: 10993052 "Review article in Pubmed"]
is_a: PW:0000325 ! protein degradation pathway

[Term]
id: PW:0000418
name: altered ubiquitin, ubiquitin-like degradation pathway
is_a: PW:0000326 ! altered protein degradation pathway
is_a: PW:0000417 ! ubiquitin, ubiquitin-like/proteasome degradation pathway

[Term]
id: PW:0000419
name: water transport pathway
is_a: PW:0000103 ! transport pathway

[Term]
id: PW:0000420
name: altered c-Jun N-terminal kinase MAPK signaling pathway
related_synonym: "altered JNK signaling pathway" []
is_a: PW:0000313 ! c-Jun N-terminal kinases MAPK signaling pathway
is_a: PW:0000422 ! altered stress-regulated MAPK pathway

[Term]
id: PW:0000421
name: altered mitogen activated protein kinase pathway
def: "A mitogen activated protein kinase pathway that deviates from what its normal course should be. Altered MAAPK pathways have been linked to a spectrum of conditions. " [PW InHouse dictionary:InHouse "definition compiled by the PW editorial board"]
related_synonym: "altered MAPK signaling pathway" []
is_a: PW:0000007 ! mitogen activated protein kinase signaling pathway
is_a: PW:0000264 ! altered signaling pathway

[Term]
id: PW:0000422
name: altered stress-regulated MAPK pathway
related_synonym: "altered SAPK pathways" []
is_a: PW:0000312 ! stress-regulated MAPK signaling pathway
is_a: PW:0000421 ! altered mitogen activated protein kinase pathway

[Term]
id: PW:0000423
name: surfactant homeostasis pathway
is_a: PW:0000355 ! homeostasis pathway

[Term]
id: PW:0000424
name: altered surfactant homeostasis pathway
def: "A surfactant homeostatic pathway that deviates from what its normal course should be. Mutations in surfactant proteins and in ABCA3 - a member of the ABC transporters have been implicated in the altered pathway and associated with conditions such as Respiratory Distress Syndrome (RDS) in newborns and lung diseases in infants." [PubMed:15985750 "Review article in PubMed"]
is_a: PW:0000358 ! altered homeostasis pathway
is_a: PW:0000423 ! surfactant homeostasis pathway

[Term]
id: PW:0000425
name: diabetic retinopathy pathway
def: "High glucose-mediated oxidative stress effects on the expression of vascular endothelial growth factor are thought to play a role in diabetic retinopathy" [PubMed:PMID\: 16026270]
is_a: PW:0000176 ! diabetes pathway

[Term]
id: PW:0000426
name: protein sorting pathway
is_a: PW:0000181 ! pathways of protein folding, sorting, modification, degradation
is_a: PW:0000535 ! protein transport pathway

[Term]
id: PW:0000427
name: molybdenum cofactor biosynthetic pathway
is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins

[Term]
id: PW:0000428
name: altered molybdenum cofactor biosynthetic pathway
is_a: PW:0000427 ! molybdenum cofactor biosynthetic pathway
is_a: PW:0000429 ! altered metabolic pathway of cofactors and vitamins

[Term]
id: PW:0000429
name: altered metabolic pathway of cofactors and vitamins
is_a: PW:0000135 ! metabolic pathway of cofactors and vitamins
is_a: PW:0000262 ! altered metabolic pathway

[Term]
id: PW:0000430
name: killed term
is_obsolete: true

[Term]
id: PW:0000431
name: another killed term
is_obsolete: true

[Term]
id: PW:0000432
name: protein modification pathway
is_a: PW:0000181 ! pathways of protein folding, sorting, modification, degradation

[Term]
id: PW:0000433
name: protein modification pathway via conjugation with ubiquitin and ubiqutin-like molecules
def: "Conjugation of proteins with ubiquitin and ubiquitin-like molecules proceeds via a similar cascade-like, enzyme-driven mechanism but of diverse functionality.  " [PubMed:PMID\: 10806345 "Review article in PubMed"]
is_a: PW:0000432 ! protein modification pathway

[Term]
id: PW:0000434
name: ubiquitination pathway
def: "A pathway of protein modification via conjugation with ubiquitin. Ubiquitination is primarily involved in targeting protein to the proteasome for degradation. It is also involved in membrane protein trafficking." [PubMed:PMID\: 10806345 "Review article in PubMed"]
is_a: PW:0000433 ! protein modification pathway via conjugation with ubiquitin and ubiqutin-like molecules

[Term]
id: PW:0000435
name: neddylation pathway
def: "A pathway of protein modification via conjugation with Nedd8  - a ubiquitin-like protein. All Nedd8 targets appear to be members of the cullin family. Cullins participate in the assembly of various E3 ligase complexes. Neddylation pathway is important for embryogenesis and cell cycle control in metazoa, embryonic development in animals." [PubMed:10806345; 15021886 "Review articles in PubMed"]
is_a: PW:0000433 ! protein modification pathway via conjugation with ubiquitin and ubiqutin-like molecules

[Term]
id: PW:0000436
name: primary amine neurotransmitter metabolic pathway
is_a: PW:0000407 ! neurotransmitter metabolic pathway

[Term]
id: PW:0000437
name: amino acid neurotransmitter metabolic pathway
is_a: PW:0000407 ! neurotransmitter metabolic pathway

[Term]
id: PW:0000438
name: alanine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of alanine. Alanine is a non-essential amino acid with roles in glucose and protein metabolism." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000028 ! alanine and aspartate metabolic pathway

[Term]
id: PW:0000439
name: aspartate metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of aspartate/aspartic acid. Aspartic acid is a non-essential amino acid with roles in glucose, protein and nucleotide metabolism. In the brain, it can act as a neurotransmitter. " [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000028 ! alanine and aspartate metabolic pathway
is_a: PW:0000445 ! excitatory neurotransmitter metabolic pathway

[Term]
id: PW:0000440
name: glycine metabolic pathway
is_a: PW:0000047 ! glycine, serine and threonine metabolic pathway
is_a: PW:0000446 ! inhibitory neurotransmitter metabolic pathway

[Term]
id: PW:0000441
name: epinephrine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of epinephrine - a catecholamine derived from the amino acids phenylalanine and tyrosine. It acts as a hormone and a neurotransmitter." [OneLook:www.onelook.com "Online collection of dictionaries - Wikipedia"]
related_synonym: "adrenaline metabolism" []
is_a: PW:0000443 ! catecholamine neurotransmitter metabolic pathway

[Term]
id: PW:0000442
name: norepinephrine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of norepinephrine - a catecholamine derived from the amino acid tyrosine. It acts as a hormone and a neurotransmitter." [OneLook:www.onelook.com "Online collection of dictionaries - Wikipedia"]
related_synonym: "noradrenaline metabolism" []
is_a: PW:0000443 ! catecholamine neurotransmitter metabolic pathway

[Term]
id: PW:0000443
name: catecholamine neurotransmitter metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of catecholamines - chemical compounds derived from tyrosine. Epinephrine, norepinephrine and dopamine are among the most abundant and are produced primarily from the adrenal medulla and the postganglionic fibers of the sympathetic nervous system." [OneLook:www\,onelook.com "Online collection of dictionaries - Wikipedia"]
is_a: PW:0000436 ! primary amine neurotransmitter metabolic pathway

[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 ! primary amine neurotransmitter metabolic pathway

[Term]
id: PW:0000445
name: excitatory neurotransmitter metabolic pathway
is_a: PW:0000437 ! amino acid neurotransmitter metabolic pathway

[Term]
id: PW:0000446
name: inhibitory neurotransmitter metabolic pathway
is_a: PW:0000437 ! amino acid neurotransmitter metabolic pathway

[Term]
id: PW:0000447
name: peptide neurotransmitter metabolic pathway
is_a: PW:0000407 ! neurotransmitter metabolic pathway

[Term]
id: PW:0000448
name: neuropeptide Y metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of neuropeptide Y." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000447 ! peptide neurotransmitter metabolic pathway

[Term]
id: PW:0000449
name: enkephalin metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of enkephalins." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000447 ! peptide neurotransmitter metabolic pathway

[Term]
id: PW:0000450
name: neurotensin metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of neurotensin." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000447 ! peptide neurotransmitter metabolic pathway

[Term]
id: PW:0000451
name: beta-endorphin metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of beta-endorphine - a peptide neurotransmitter that may play a role in depression." [OneLook:www.onelook.com "Online collection of articles"]
is_a: PW:0000447 ! peptide neurotransmitter metabolic pathway

[Term]
id: PW:0000452
name: substance P metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of substance P - a  short-chain polypeptide that acts as a neurotransmitter and a neuromodulator." [OneLook:www\,onelook.com "Online collection of articles - Wikipedia"]
is_a: PW:0000447 ! peptide neurotransmitter metabolic pathway

[Term]
id: PW:0000453
name: sterol biosynthetic pathway
related_synonym: "steroid alcohol" []
is_a: PW:0000248 ! steroid biosynthetic pathway

[Term]
id: PW:0000454
name: cholesterol biosynthetic pathway
is_a: PW:0000453 ! sterol biosynthetic pathway

[Term]
id: PW:0000455
name: Excitatory synaptic transmission pathway
related_synonym: "Excitatory neurotransmission pathway" []
is_a: PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse

[Term]
id: PW:0000456
name: Inhibitory synaptic transmission pathway
related_synonym: "Inhibitory neurotransmission pathway" []
is_a: PW:0000274 ! neuron-to-neuron signaling pathway via the chemical synapse

[Term]
id: PW:0000457
name: angiotensin III signaling pathway
def: "Angiotensin III is derived from angiotensin II through the action of aminopeptidase A and in turn is cleaved by aminopeptidase N to generate angiotensin IV. Angiotensin III appears to function in a manner similar to angiotensin II. It plays a role in vasoconstriction and the control of arterial blood pressure. Angiotensin III may be the effective angiotensin peptide in the central nervous system." [PubMed: 10961935\, PMID\: 11295571 "Review article in PubMed"]
is_a: PW:0000245 ! angiotensin signaling pathway

[Term]
id: PW:0000458
name: angiotensin IV signaling pathway
def: "Angiotensin IV is derived from angiotensin III through the action of aminopeptidase N. The receptor for angiotensin IV has been shown to be the insulin-regulated membrane aminopeptidase. Studies suggest that angiotensin IV signaling activates a number of intracellular second messenger systems and plays a role in vascular remodeling and memory." [PubMed:PMID\: 15549174 \,  PMID  12591177 "Review articles in PubMed"]
is_a: PW:0000245 ! angiotensin signaling pathway

[Term]
id: PW:0000459
name: apelin signaling pathway
def: "apelin signaling pathway 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 ! signaling pathway

[Term]
id: PW:0000460
name: arachidonic acid metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of arachidonic acid - a polyunsaturated fatty acid." [OneLook:www.onelook.com "Wikipedia at OneLook"]
is_a: PW:0000058 ! fatty acid metabolic pathway

[Term]
id: PW:0000461
name: cyclooxygenase mediated pathway of arachidonic acid metabolism
def: "The cyclooxygase pathway is one of the three major routes of arachidonic acid oxygenation." [PubMed:PMID\: 15896353 "Review article"]
is_a: PW:0000460 ! arachidonic acid metabolic pathway

[Term]
id: PW:0000462
name: lipoxygenase mediated pathway of arachidonic acid metabolism
def: "lipoxygenase pathway is one of three major routes of arachidonic acid oxygenation" [PubMed :PMID\: 15896353 "Review article"]
is_a: PW:0000460 ! arachidonic acid metabolic pathway

[Term]
id: PW:0000463
name: cytochrome P450 monooxygenase mediated pathway of arachidonic acid metabolism
def: "cytochrome P450 monooxygenase pathway is one the three major routes of arachidonic acid oxygenation." [PubMed:PMID\: 15896353 "Review article"]
is_a: PW:0000460 ! arachidonic acid metabolic pathway

[Term]
id: PW:0000464
name: leukotriene metabolic pathway
is_a: PW:0000462 ! lipoxygenase mediated pathway of arachidonic acid metabolism
is_a: PW:0000485 ! eicosanoids metabolic pathway

[Term]
id: PW:0000465
name: hormone signaling pathway
def: "Hormones are a class of molecules that are used as messengers between cells and serve as signals to the target cell. Vertebrate hormones belong to three classes: amine and amino acid derived, peptide and protein hormones, and lipid and phospholipid derived hormones." [OneLook:www.onelook.com "online collection of dictionaries - wikipedia"]
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000466
name: amine and amino acid-derived hormone signaling pathway
is_a: PW:0000465 ! hormone signaling pathway

[Term]
id: PW:0000467
name: peptide and protein hormone signaling pathway
is_a: PW:0000465 ! hormone signaling pathway

[Term]
id: PW:0000468
name: steroid hormone signaling pathway
def: "steroid hormones - steroids that act as hormones - can be grouped into several categories depending on the receptor to which they bind." [OneLook:www.onelook.com "Online collection of dictionaries -wikipedia"]
is_a: PW:0000469 ! lipid hormone signaling pathway

[Term]
id: PW:0000469
name: lipid hormone signaling pathway
def: "The main categories of lipid hormones are the eicosanoids derived from arachidonic acid metabolism and the cholesterol derived steroid hormones." [OneLook:www.onelook.com "Online collection of dictionaries - wikipedia"]
is_a: PW:0000465 ! hormone signaling pathway

[Term]
id: PW:0000470
name: natriuretic peptide signaling pathway
def: "The natriuretic peptide family consists of three peptide hormones of diverse roles in cardiovascular as well as neuroendocrine and renal functions." [PubMed:PMID\: 15911062 PMID\: 15758553; PMID\: 15246247; "Review articles in PubMed"]
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000471
name: atrial natriuretic peptide signaling pathway
def: "Atrial natriuretic peptide hormone pathway plays important roles in the regulation of body fluid volume and blood pressure. " [PubMed:PMID\: 15911062 PMID\: 15758553; PMID\: 15246247 "Review articles in PubMed"]
related_synonym: "ANP signaling pathway" []
is_a: PW:0000470 ! natriuretic peptide signaling pathway

[Term]
id: PW:0000472
name: brain natriuretic peptide signaling pathway
def: "brain natriuretic peptide signaling pathway appears to elicit cardiovascular, renal and endocrine functions similar to those elicited by the atrial natriuretic peptide." [PubMed:PMID\: 15911062 PMID\: 15758553; PMID\: 1524624 "Review articles in PubMed"]
related_synonym: "BNP signaling pathway" []
is_a: PW:0000470 ! natriuretic peptide signaling pathway

[Term]
id: PW:0000473
name: C-type natriuretic peptide signaling pathway
def: "The role of the C-type signaling pathway is not well established. The receptor for the C-type natriuretic peptide, unlike the receptors for the other two types of peptides, is non-guanylyl cyclase receptor that appears to couple to adenylyl cyclase inhibition/phospholipase C activation via Gi family of G-protein. " [PubMed:PMID\: 15911062 PMID\: 15758553; PMID\: 15246247; PMID\: 15911072 "Review articles in PubMed"]
related_synonym: "C-type brain natriuretic peptide signaling pathway" []
related_synonym: "CNP signaling pathway" []
is_a: PW:0000470 ! natriuretic peptide signaling pathway

[Term]
id: PW:0000474
name: coagulation cascade pathway
def: "The coagulation cascade is the series of events proceeding via either the tissue factor or the contact activation pathway and leading to the formation of fibrin 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"]
related_synonym: "secondary hemostasis" []
relationship: part_of PW:0000475 ! hemostasis pathway

[Term]
id: PW:0000475
name: hemostasis pathway
def: "Hemostasis is the response to blood vessel injury to prevent blood loss via platelet mediated primary homeostasis and the secondary homeostasis of coagulation. The latter is a complex cascade which is triggered by the innate immune response and inflammation." [Various:PubMed\, Wikipedia\, Reactome]
related_synonym: "haemostasis pathway" []
is_a: PW:0000476 ! cardiovascular system homeostasis pathway

[Term]
id: PW:0000476
name: cardiovascular system homeostasis pathway
is_a: PW:0000355 ! homeostasis pathway

[Term]
id: PW:0000477
name: natural anticoagulant pathway
is_a: PW:0000476 ! cardiovascular system homeostasis pathway

[Term]
id: PW:0000478
name: tissue factor pathway inhibitor
related_synonym: "TFPI" []
is_a: PW:0000477 ! natural anticoagulant pathway

[Term]
id: PW:0000479
name: heparin-antithrombin pathway
is_a: PW:0000477 ! natural anticoagulant pathway

[Term]
id: PW:0000480
name: protein C anticoagulant pathway
is_a: PW:0000477 ! natural anticoagulant pathway

[Term]
id: PW:0000481
name: fibrinolytic cascade pathway
is_a: PW:0000476 ! cardiovascular system homeostasis pathway

[Term]
id: PW:0000482
name: lipoprotein metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of lipoproteins - any of the protein-lipid complexes. In the blood lipoproteins carry fats essential for the cell. Genetic variability and environmental (nongenetic) factors contribute to alterations in the homeostasis of lipid metabolic pathways and constitute cardiovascular disease risk." [PubMed:PMID\: 16011471 "Review article in PubMed"]
is_a: PW:0000010 ! lipid metabolic pathway

[Term]
id: PW:0000483
name: altered lipid metabolic pathway
def: "Those lipid metabolic pathways that deviate from what their normal course should be. Aberrant lipid metabolic pathways, alone or in combination with other pathways underlie a number of diseases." [InHouse:PW InHouse dictionary]
is_a: PW:0000010 ! lipid metabolic pathway
is_a: PW:0000262 ! altered metabolic pathway

[Term]
id: PW:0000484
name: altered lipoprotein metabolic pathway
def: "Those lipoprotein metabolic pathways that deviate from what their normal course should be. Aberrant lipoprotein metabolic pathways, alone or in combination with other pathways underlie several diseases." [In House:PW In House dictionary]
is_a: PW:0000482 ! lipoprotein metabolic pathway
is_a: PW:0000483 ! altered lipid metabolic pathway

[Term]
id: PW:0000485
name: eicosanoids metabolic pathway
def: "eicosanoids are molecules derived from omegoa-3 or omega-6 fats that can act as hormones. The prostaglandins, prostacyclins, the leukotrienes and the thromboxanes constitute the four eicosanoid families." [OneLook:www.onelook.com "Online collection of dictionaries - wikipedia"]
is_a: PW:0000460 ! arachidonic acid metabolic pathway

[Term]
id: PW:0000486
name: major histocompatibility complex class I antigen presentation pathway
def: "Antigen processing and presentation by MHC class I molecules primarily involves peptides derived from endogenous, cytosolic proteins. " [PubMed:16181325 "Review article on MHC I pathway"]
related_synonym: "MHC class I antigen presentation pathway" []
is_a: PW:0000235 ! adaptive immune response pathway

[Term]
id: PW:0000487
name: major histocompatibility complex class 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 ! adaptive immune response pathway

[Term]
id: PW:0000488
name: antigen processing pathway
def: "Antigen processing pathway engages the proteosomal machinery in the cytosol, ER specific proteases as well as chaperones for loading the HMC class I molecules with the 8-10 amino acid peptides " [PubMed:16181325 "Review article on MHC class I complex pathway"]
relationship: part_of PW:0000486 ! major histocompatibility complex class I antigen presentation pathway

[Term]
id: PW:0000489
name: angiopoietin signaling pathway
def: "Angiopoietin signaling pathway is involved in the regulation of angiogenic remodeling. Recent studies suggest that the pathway may also be involved in lymphangiogenesis and possibly in the development of hematopoietic system." [PubMed:PMID\: 16225862 "Review article on angiopoietin pathway in angiogenic remodeling and possibly in lymphangiogenesis"]
is_a: PW:0000168 ! growth factor signaling pathway

[Term]
id: PW:0000490
name: transforming growth factor-beta signaling pathway - SMAD dependent
is_a: PW:0000206 ! transforming growth factor-beta signaling pathway

[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 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000492
name: renin-angiotensin system signaling pathway
def: "The renin-angiotensin system (RAS) generates a number of bioactive peptides with diverse physiological and pathophysiological functions. RAS exerts vasoconstriction, vasodilation or vascular remodeling, cell proliferation or anti-proliferation effects, depending on which angiotensin peptide generates the signaling. Some of these features are also shared by the kallikrein-kinin system (KKS); the two systems can interact and cross-talk. " [PubMed:PMID\: 15883759   PMID\: 15638741 \,  PMID\: 12676165 \, PMID\: 12793984 \, PMID\: 16816138 "Several review articles."]
related_synonym: "RAS system signaling pathway" []
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000493
name: corticotropin-releasing hormone signaling pathway
related_synonym: "CRH" []
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000494
name: oxytocin signaling pathway
def: "The peptide hormone oxytocin plays a central role in parturition, lactation and sexual behavior." [PubMed:PMID\: 14624682 "Review"]
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000495
name: Gas6 - Axl signaling axis
def: "Gas6, a vitamin K-dependent growth factor signals through the Axl subfamily of tyrosine kinase receptors. The Gas6-Axl axis appears to be involved in growth and survival of various cell types as well as in tissue remodeling and regeneration. Deregulation of the axis is involved in a number of conditions, particularly renal." [Pubmed:PMID\: 16285961  PMID\: 11290560 ; PMID\: 16362042 "Review articles in Pubmed"]
related_synonym: "Gas6-Axl signaling system" []
is_a: PW:0000168 ! growth factor signaling pathway

[Term]
id: PW:0000496
name: exogenous pathway
relationship: part_of PW:0000482 ! lipoprotein metabolic pathway

[Term]
id: PW:0000497
name: endogenous pathway
relationship: part_of PW:0000482 ! lipoprotein metabolic pathway

[Term]
id: PW:0000498
name: reverse cholesterol transport pathway
def: "Reverse cholesterol transport (RCT) is the pathway by which cholesterol from extrahepatic cells/tissue is transported to the liver for excretion. The pathway may prevent the development of atherosclerosis by reducing the accumulation of cholesterol in the wall of arteries." [PubMed:PMID\: 16258026 "Review article"]
related_synonym: "RCT pathway" []
related_synonym: "selective cholesterol uptake pathway" []
is_a: PW:0000103 ! transport pathway
relationship: part_of PW:0000482 ! lipoprotein metabolic pathway

[Term]
id: PW:0000499
name: Nuclear Factor Kappa B signaling pathway
def: "Nuclear Factor Kappa B (NF-kB) signaling plays an essential role in the mammalian immune system. The classical or canonical pathway, downstream but not exclusively of tumor necrosis factor/receptor 1 signaling, is regarded as a paradigm of NF-kB signaling. The classical and the non-classical or alternative pathway, downstream of a subset of Tnf/receptor superfamily, share similar sets of core components, albeit in distinct ways." [PubMed:PMID\: 15371334\, 18267068\, 17072321 "Review articles"]
related_synonym: "NF-kappaB signaling pathway" []
related_synonym: "NF-kB signaling pathway" []
is_a: PW:0000233 ! tumor necrosis factor signaling pathway

[Term]
id: PW:0000500
name: tyrosine-derived hormone signaling pathway
is_a: PW:0000466 ! amine and amino acid-derived hormone signaling pathway

[Term]
id: PW:0000501
name: thyroid hormone signaling pathway
is_a: PW:0000500 ! tyrosine-derived hormone signaling pathway

[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 ! innate immune response pathway

[Term]
id: PW:0000503
name: classical complement pathway
is_a: PW:0000502 ! complement system pathway

[Term]
id: PW:0000504
name: mannose-binding lectin complement pathway
is_a: PW:0000502 ! complement system pathway

[Term]
id: PW:0000505
name: alternative complement pathway
is_a: PW:0000502 ! complement system pathway

[Term]
id: PW:0000506
name: endothelin signaling pathway
def: "Endothelins represent a family of three vasoconstrictor peptides that play a role in several intracellular signaling pathways and have been associated with hypertension, heart failure and myocardial infarction." [PubMed:PMID\: 16269952\, PMID\: 15124920 "Review articles in PubMed"]
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000507
name: estrogen signaling pathway
def: "Estrogens are a class of steroid hormones that constitutes the females sex hormones." [OneLook:www.onelook.com "Online collection of dictionaries - wikipedia"]
is_a: PW:0000567 ! sex steroids signaling pathway

[Term]
id: PW:0000508
name: platelet aggregation pathway
related_synonym: "primary hemostasis" []
relationship: part_of PW:0000475 ! hemostasis pathway

[Term]
id: PW:0000509
name: altered hormone signaling pathway
is_a: PW:0000264 ! altered signaling pathway
is_a: PW:0000465 ! hormone signaling pathway

[Term]
id: PW:0000510
name: altered insulin-like growth factor signaling pathway
is_a: PW:0000238 ! insulin-like growth factor signaling pathway
is_a: PW:0000511 ! altered peptide and protein hormone signaling pathway

[Term]
id: PW:0000511
name: altered peptide and protein hormone signaling pathway
is_a: PW:0000467 ! peptide and protein hormone signaling pathway
is_a: PW:0000509 ! altered hormone signaling pathway

[Term]
id: PW:0000512
name: Interleukin mediated signaling pathway
is_a: PW:0000577 ! cytokine and chemokine signaling pathway

[Term]
id: PW:0000513
name: Interleukin signaling pathway via interleukin-10 family members
is_a: PW:0000512 ! Interleukin mediated signaling pathway

[Term]
id: PW:0000514
name: Interleukin signaling pathway via interleukin-6 family members
is_a: PW:0000512 ! Interleukin mediated signaling pathway

[Term]
id: PW:0000515
name: Interleukin-10 signaling pathway
is_a: PW:0000513 ! Interleukin signaling pathway via interleukin-10 family members

[Term]
id: PW:0000516
name: Interleukin-6 signaling pathway
is_a: PW:0000514 ! Interleukin signaling pathway via interleukin-6 family members

[Term]
id: PW:0000517
name: arterial occlusive disease pathway
def: "A pathway leading to a general or specific artery occlusion." [MeSH:Medical Subject Headings]
is_a: PW:0000020 ! cardiovascular disease pathway

[Term]
id: PW:0000518
name: Atherosclerosis pathway
def: "A pathway leading to the thickening of medium and large arteries. While lipoprotein related pathways are of interest, monogenic conditions such as those linked to mutations in the laminin gene may also provide clues regarding atherosclerosis pathways." [PubMed:PMID\: 15205220 "Article on laminopathies and atherosclerosis"]
is_a: PW:0000517 ! arterial occlusive disease pathway

[Term]
id: PW:0000519
name: 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane degradation pathway
def: "Those enzymatic reactions involved in the degradation of DDT - a chlorinated organic insecticide and environmental pollutant, Although 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."]
related_synonym: "DDT degradation pathway" []
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000520
name: 2,4-dichlorobenzoate degradation pathway
def: "Those enzymatic reactions involved in the degradation of 2,4-dichlorobenzoate - a key intermediate in the aerobic degradation of over 200 polychlorinated biphenyls. " [KEGG:http\://umbbd.msi.umn.edu/dcb/dcb_map.html "Adapted from KEGG"]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000521
name: 1,2-dichloroethane degradation pathway
def: "Those enzymatic reactions involved in the degradation of 1,2-dichloroethane - a moderately reactive alkylating compound." [KEGG:http\://umbbd.msi.umn.edu/dce/dce_map.html "Adapted from the link at KEGG"]
is_a: PW:0000107 ! xenobiotics biodegradation pathway

[Term]
id: PW:0000522
name: flavonoid biosynthetic pathway
def: "Those enzymatic reactions involved in the biosynthesis of flavonoids - a class of plant secondary metabolites generally known for their antioxidant activity." [OneLook:www.onelook.com "Online collections of dictionaries - wikipedia"]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000523
name: linoleic acid metabolic pathway
def: "Those enzymatic reactions involved in the synthesis and degradation of linoleic acid - an unsaturated omega-6 fatty acid." [OneLook:http\://www.onelook.com "Online collection of dictionaries - wikipedia"]
is_a: PW:0000058 ! fatty acid metabolic pathway

[Term]
id: PW:0000524
name: heparan sulfate biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of heparan sulfate.  Heparan sulfate is a glycosaminoglycan occurring in the cell membrane of most cells. It consists of repeating disaccharide units in specific linkage, each composed of a glucosamine residue linked to an uronic acid, either glucuronic acid or L-iduronic acid, which may be sulfated." [OneLook:www.onelook.com "Online collection of dictionaries - Dorland's"]
is_a: PW:0000157 ! glycosaminoglycan metabolic pathway

[Term]
id: PW:0000525
name: Ras mediated signaling pathway
is_a: PW:0000158 ! Ras family signaling pathway

[Term]
id: PW:0000526
name: kallikrein-kinin system signaling pathway
def: "The kallikrein-kinin system (KKA) generates a number of bioactive peptides with diverse physiological and pathophysiological functions. These features are also shared by the renin-angiotensin system (RAS); the two systems can interact and cross-talk." [XX:PMID\: 12558525\, PMID\: 12793984  PMID\: 16177542\, PMID\: 12676165]
related_synonym: "KKS system signaling pathway" []
is_a: PW:0000003 ! signaling pathway

[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 pleiotropic effects, on angiotensin receptors, angiotensin type 2 receptor."]
is_a: PW:0000244 ! Angiotensin II signaling pathway

[Term]
id: PW:0000528
name: Angiotensin II signaling pathway 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 pathologies. AT2 receptor appears to function in a G-protein dependent as well as independent manner." [PubMed : 10977869\, 15158138\,  16286568 \, 12734384 "Articles on the pleiotropic AT1 receptor, all angiotensin receptors"]
is_a: PW:0000244 ! Angiotensin II signaling pathway

[Term]
id: PW:0000529
name: angiotensin (1-7) signaling pathway
def: "Angiotensin (1-7) is derived from angiotensin II through the action of angiotensin converting enzyme 2 (ACE2) or from angiotensin I through the action of neutral endopeptidase (NEP). Angiotensin (1-7) signaling appears to have a vasodilatory effect but the exact action of this peptide in humans remains to be established," [PubMed:PMID\: 15687842\, PMID\: 16520407\, PMID\: 15962175 "Review articles in PubMed"]
is_a: PW:0000245 ! angiotensin signaling pathway

[Term]
id: PW:0000530
name: Angiotensin III signaling pathway 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." [PubMed:PubMed 11100981\,]
is_a: PW:0000457 ! angiotensin III signaling pathway

[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 ! angiotensin III signaling pathway

[Term]
id: PW:0000532
name: glycogen biosynthetic pathway
def: "Those metabolic reactions leading to the biosynthesis of glycogen, a highly branched polysaccharide that constitutes 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"]
related_synonym: "glycogenesis" []
is_a: PW:0000533 ! glycogen metabolic pathway
is_a: PW:0000557 ! glucose storage pathway

[Term]
id: PW:0000533
name: glycogen metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of glycogen, a highly branched polysaccharide that constitutes the major storage form of glucose in the cell." [InHouse:www.rgd.mcw "Definition compiled by the PW editorial board."]
is_a: PW:0000005 ! carbohydrate metabolic pathway

[Term]
id: PW:0000534
name: glycogen degradation pathway
def: "Those metabolic reactions involved in the breakdown of glycogen to glucose-6-phosphate. This is a three step, exergonic pathway." [OneLook:www.onelook.com "Online collection of dictionaries; wikipedia"]
related_synonym: "glycogenolysis " []
is_a: PW:0000533 ! glycogen metabolic pathway

[Term]
id: PW:0000535
name: protein transport pathway
is_a: PW:0000103 ! transport pathway

[Term]
id: PW:0000536
name: constitutive secretory pathway
is_a: PW:0000280 ! secretory pathway

[Term]
id: PW:0000537
name: regulated secretory pathway
is_a: PW:0000280 ! secretory pathway

[Term]
id: PW:0000538
name: nuclear protein import pathway
is_a: PW:0000535 ! protein transport pathway

[Term]
id: PW:0000539
name: ghrelin system pathway
def: "Ghrelin is an appetite-stimulating hormone secreted primarily from the stomach in response to fasting that can downregulate energy expenditure and lead to weight increase." [PubMef:PMID\: 17202582; PMID\: 16550252 "Review articles in PubMed, also OneLook - Wikipedia"]
is_a: PW:0000357 ! energy homeostasis pathway
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000540
name: obesity disease pathway
def: "Obesity, usually defined as 20% or more excess body weight, constitutes a major public health problem and an independent risk factor for a number of conditions such as hypertension and diabetes. Deregulation of energy homeostasis, of various metabolic and signaling pathways, genetic and environmental aspects, all can contribute to the development of an obese state." [OneLook:www.onelook.com "Online collection of dictionaries"]
is_a: PW:0000013 ! disease pathway

[Term]
id: PW:0000541
name: signaling pathways involving second messengers
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000542
name: adenosine monophosphate-activated protein kinase (AMPK) signaling pathway
def: "AMPK senses changes in cellular energy as ATP: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]
related_synonym: "5'AMP-activated protein kinase" []
related_synonym: "AMPK signaling pathway" []
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000543
name: protein kinase A (PKA) signaling pathway
related_synonym: "cAMP-dependent protein kinase A signaling pathway" []
related_synonym: "cAMP/PKA signaling pathway" []
is_a: PW:0000541 ! signaling pathways involving second messengers

[Term]
id: PW:0000544
name: altered reverse cholesterol transport pathway
def: "An impaired pathway of reverse cholesterol transport and efflux can pose a risk for the development of cardiovascular disease. This varies in severity and manifestation depending on which gene in the pathway is affected." [PubMed:PMID\: 16258026 "Review article"]
related_synonym: "altered RCT pathway" []
is_a: PW:0000484 ! altered lipoprotein metabolic pathway
is_a: PW:0000498 ! reverse cholesterol transport pathway
is_a: PW:0000545 ! altered transport pathway

[Term]
id: PW:0000545
name: altered transport pathway
is_a: PW:0000103 ! transport pathway
is_a: PW:0000263 ! altered regulatory pathway

[Term]
id: PW:0000546
name: mRNA decay pathways
def: "The pathways of mRNA quality control thereby erroneous mRNA is degraded in the nucleus or cytoplasm, or normal mRNA accumulated in the nucleus is degraded." [PubMed:PMID\: 15933735]
related_synonym: "mRNA quality control pathways" []
related_synonym: "mRNA surveillance pathways" []
is_a: PW:0000085 ! pathways of replication, gene expression, protein biosynthesis

[Term]
id: PW:0000547
name: exosome mediated mRNA decay pathway
def: "The nuclear exosome pathway degrades erroneous mRNA as well as normal mRNA that has accumulated in the nucleus." [PubMed:PMID\: 15933735]
related_synonym: "exosome mediated mRNA degradation pathway" []
is_a: PW:0000546 ! mRNA decay pathways

[Term]
id: PW:0000548
name: nonsense-mediated mRNA decay pathway
def: "The nonsense-mediated decay pathway (NMD) degrades mRNA that contains a premature translation termination codon (PTC) and is one of the best characterized systems in eukaryotes." [PubMed:PMID\: 15933735; PMID\: 17010613 "Reviews in PubMed"]
related_synonym: "NMD pathway" []
is_a: PW:0000546 ! mRNA decay pathways

[Term]
id: PW:0000549
name: nonstop mRNA decay pathway
def: "The nonstop mRNA decay pathway degrades mRNA that lacks a translation termination codon." [PubMed:PMID\: 15933735]
is_a: PW:0000546 ! mRNA decay pathways

[Term]
id: PW:0000550
name: Staufen-mediated mRNA decay pathway
def: "Staufen-mediated mRNA decay pathway (SMD) is a rather novel pathway identified in mammals. Staufen (Stau)1 is thought to be involved in mRNA localization and it has recently been shown to be involved in mRNA decay. It shares some of the features of the nonsense-mediated mRNA decay pathway (NMD) but does not require components essential for NMD." [PubMed:PMID\: 15933735; PMID\: 15809649; PMID\: 15680326 "Review articles in PubMed"]
related_synonym: "SMD pathway" []
is_a: PW:0000546 ! mRNA decay pathways

[Term]
id: PW:0000551
name: altered mRNA decay pathway
def: "An mRNA decay pathway that deviates from what its normal course should be. An aberrant mRNA decay pathway would lead to the translation of erroneous mRNA with potentially serious consequences." [InHouse PW:InHouse PW "Definition compiled by the PW editorial team"]
is_a: PW:0000290 ! altered pathway of replication, gene expression and protein biosynthesis
is_a: PW:0000546 ! mRNA decay pathways

[Term]
id: PW:0000552
name: brassinosteroid biosynthetic pathway
def: "Those metabolic reactions involved in the biosynthesis of brassinosteroidd or brassins, a group of plant hormones released in response to low oxygen and sugar, or to root stresses. " [KEGG\, OneLook:http\://www.onelook.com "Wikipedia"]
is_a: PW:0000147 ! metabolic pathway of secondary metabolites

[Term]
id: PW:0000553
name: glucose homeostasis pathway
def: "Those pathways involved in the balanced maintenance of  glucose levels, transport and processing as demanded by the needs of the cells, tissues and organs. Glucose is an important and the most efficient fuel source.  Disruption of glucose homeostasis underlies many complex disorders." [PubMed:PMID\: 15466941 "Review article on the cellular fate of glucose"]
is_a: PW:0000355 ! homeostasis pathway

[Term]
id: PW:0000554
name: glucose transport pathway
def: "Glucose diffusion into cells requires specific transporter proteins. Two families of hexose transporters facilitate glucose transport down its concentration gradient. " [PubMed:PMID\: 15466941 ; PMID\: 15449578 "Review articles"]
is_a: PW:0000575 ! sugar transport pathway
relationship: part_of PW:0000553 ! glucose homeostasis pathway

[Term]
id: PW:0000555
name: glucose utilization pathway
def: "The various pathways thereby glucose is oxidized to produce energy, is converted to other molecules or is stored for further use. " [PubMed:PMID\: 15466941 "Review article on the cellular fate of glucose"]
relationship: part_of PW:0000553 ! glucose homeostasis pathway

[Term]
id: PW:0000556
name: glucose oxidation pathway
def: "The various pathways thereby glucose is converted to other compounds to yield primarily ATP. The final oxidation of glucose to carbon dioxide and water produces a net of 38 molecules of ATP per molecule of glucose." [PubMed:PMID\: 15466941 "Review article on the cellular fate of glucose."]
is_a: PW:0000555 ! glucose utilization pathway

[Term]
id: PW:0000557
name: glucose storage pathway
def: "Glycogen is the major form of glucose storage. Excess glucose is converted into glycogen - a highly branched polysaccharide. When glucose is rapidly needed, glycogen can be broken down via glycogenolysis." [PubMed:PMID\: 15466941 "Review article on the cellular fate of glucose"]
is_a: PW:0000555 ! glucose utilization pathway

[Term]
id: PW:0000558
name: glucose conversion pathway
is_a: PW:0000555 ! glucose utilization pathway

[Term]
id: PW:0000559
name: hexosamine biosynthetic pathway
def: "The formation of nucleotide hexosamines, primarily UDP-N-acetylglucosamine, constitutes the final step in the hexosamine biosynthetic pathway which provides substrates for glycosylation of proteins. In addition to glycoproteins that are either secreted from the cell or inserted into the plasma membrane, O-linked glycosylation of nuclear and/or cytosolic proteins confers a signaling dimension to the hexosamine biosynthetic pathway." [PubMed:PMID\: 15466941; PMID\: 16885148 "Review articles in PubMed"]
is_a: PW:0000558 ! glucose conversion pathway
is_a: PW:0000570 ! hexosamine metabolic pathway

[Term]
id: PW:0000560
name: facilitative sugar transporter mediated glucose transport pathway
def: "The GLUT family contains 14 members in mammals which can be grouped into 3 classes based on sequence similarities. The members of group I and of group III transporters facilitate glucose transport. " [PubMed:PMID\: 15466941 ; PMID\: 15449578 "Review articles in PubMed"]
related_synonym: "GLUT mediated glucose transport pathway" []
is_a: PW:0000554 ! glucose transport pathway

[Term]
id: PW:0000561
name: sodium-glucose cotransporter mediated glucose transport pathway
def: "The sodium-glucose or the sodium-dependent glucose cotransporters are characterized by the presence of 14 transmembrane alpha-helices.  The N- and C-termini are responsible for permeating sodium and sugar, respectively. " [PubMed:PMID\: 15466941 ; PMID\: 15449578 "Review articles in PubMed"]
related_synonym: "SGLT mediated glucose transport pathway" []
is_a: PW:0000554 ! glucose transport pathway

[Term]
id: PW:0000562
name: growth hormone signaling pathway
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000563
name: adiponectin signaling pathway
def: "Adiponectin signaling, a hormone secreted by the adipose tissue, impacts on metabolic pathways such as glucose and lipid metabolism, possibly via activation of AMPK pathway. Its deregulations has been linked to obesity, cardiovascular diseases, diabetes and metabolic syndrome. " [PubMed:PMID\: 16823476; PMID\: 16634986; PMID\: 17140553 "Review articles on adiponectins"]
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000564
name: androgen signaling pathway
def: "Androgens are a class of steroid hormones that constitutes the male sex hormones. They are also the precursors of female sex hormones, the estrogens." [OneLook:www.onelook.com "Online collection of dictionaries - wikipedia"]
is_a: PW:0000567 ! sex steroids signaling pathway

[Term]
id: PW:0000565
name: eicosanoids signaling pathway
def: "eicosanoids are molecules derived from omegoa-3 or omega-6 fats that can act as hormones. " [OneLook:www.onelook.com "Online collection of dictionaries - wikipedia"]
is_a: PW:0000469 ! lipid hormone signaling pathway

[Term]
id: PW:0000566
name: corticosteroid signaling pathway
def: "conrticosteroids group together glucocorticoids and mineralocorticoids. In each group the most important molecules are cortisol and aldosterone, respectively." [OneLook:www.onelook.com "Online collection of dictionaries - wikipedia"]
is_a: PW:0000468 ! steroid hormone signaling pathway

[Term]
id: PW:0000567
name: sex steroids signaling pathway
def: "sex steroid mediated signaling pathways have important roles in the development and/or maintenance of sex-specific characteristics or attributes." [OneLook:www.onelook.com "Online collection of dictionaries - wikipedia"]
is_a: PW:0000468 ! steroid hormone signaling pathway

[Term]
id: PW:0000568
name: aldosterone signaling pathway
def: "aldosterone signaling through the mineralocorticoid receptor plays an important role in the balance of fluids and electrolytes in the body. Its biosynthesis is primarily regulated by the renin-angiotenin system and potassium ions concentration. " [PubMed:PMID\: 16002531  PMID\: 17293689 ; "Review articles in PubMed"]
is_a: PW:0000566 ! corticosteroid signaling pathway

[Term]
id: PW:0000569
name: cortisol signaling pathway
is_a: PW:0000566 ! corticosteroid signaling pathway

[Term]
id: PW:0000570
name: hexosamine metabolic pathway
def: "Those metabolic reactions involved in the synthesis, utilization and/or degradation of hexosamines, amino sugars created by adding an amino group to a hexose. Hexosamines, particularly N-acetylglucosamine, are used to modify proteins." [PubMed\, Onelook:NCBI\, www.onelook.com "Various sources"]
is_a: PW:0000152 ! aminosugars metabolic pathway

[Term]
id: PW:0000571
name: neurotrophic factor signaling pathway
def: "signaling pathways activated by neurotropins - a family of growth factors that are involved in differentiation of progenitor cells, survival and differentiation of particular cells, neuronal survival." [OneLook:www.onelook.com "Online collection of dictionaries - wikipedia"]
is_a: PW:0000168 ! growth factor signaling pathway

[Term]
id: PW:0000572
name: brain-derived neurotrophic factor signaling pathway
def: "brain-derived neurotrophic factor signaling pathway plays important roles in the growth, differentiation and survival of neurons." [OneLook:www.onelook.com "online collection of dictionaries- wikipedia"]
related_synonym: "BDNF signaling pathway" []
is_a: PW:0000571 ! neurotrophic factor signaling pathway

[Term]
id: PW:0000573
name: pentose phosphate pathway - oxidative phase
def: "The oxidative (linear) phase of the pentose phosphate pathway involves the oxidation and decarboxylation of glucose-6-phosphate to produce the 5 carbon sugar ribulose-5-phosphate and the generation of NADPH." [OneLook\, PubMed:www.oneloook.com; http\://www.ncbi.nlm.nih.gov/sites/entrez "Various online resources and PubMed articles"]
is_a: PW:0000045 ! pentose phosphate pathway
is_a: PW:0000556 ! glucose oxidation pathway

[Term]
id: PW:0000574
name: pentose phosphate pathway - non-oxidative phase
def: "The non-oxidative (circular) phase of the pentose phosphate pathway involves conversion of  ribulose-5-phosphate to ribose-5-phosphate, important in the synthesis of nucleotides and nucleic acid, or to 3 or 6 carbon sugars. " [OneLookc\, PubMed:www.oneloook.com; http\://www.ncbi.nlm.nih.gov/sites/entrez "Various online resources and articles in Pubmed"]
is_a: PW:0000045 ! pentose phosphate pathway

[Term]
id: PW:0000575
name: sugar transport pathway
def: "Those pathways that mediate the transport of sugars across the cell membrane. Transport of glucose, one of the major energy sources in the cell, is an important aspect of sugar transport pathway." [Online\, Pubmed:http\://www.yahoo.com; http\://www.ncbi.nlm.nih.gov/ "Various resources"]
related_synonym: "carbohydrate transport pathway" []
is_a: PW:0000103 ! transport pathway

[Term]
id: PW:0000576
name: facilitative sugar transporter mediated transport pathway
def: "The GLUT family contains 14 members in mammals which can be grouped into 3 classes based on sequence similarities. These transporters are characterized by the presence of 12 transmembrane alpha helices. Of the 14 members of the GLUT  family, 11 have been shown to be involved in sugar transport pathway." [PubMed:PMID\: 15466941 ; PMID\: 15449578 "Review articles in PubMed"]
related_synonym: "GLUT mediated sugar transport pathway" []
is_a: PW:0000575 ! sugar transport pathway

[Term]
id: PW:0000577
name: cytokine and chemokine signaling pathway
def: "Cytokines are small proteins released by the cell and acting as intercellular mediators. Chemokines are a subset of cytokine that can attract and activate leukocytes; they can further be subdivided based on the arrangement of their conserved cysteines.  Binding to cognate receptors triggers numerous downstream signaling cascades." [Onelook\, PubMed:www.onelook.com;]
is_a: PW:0000003 ! signaling pathway

[Term]
id: PW:0000578
name: scatter factor/hepatocyte growth factor signaling pathway
def: "scatter factor/hepatocyte signaling impacts on various biological processes such as proliferation and survival, morphogenesis and motility. SF/HGF and its receptor c-Met have also been implicated in tumor growth and angiogenesis." [PubMed:PMID\: 16212809 ;PMID\: 16778093 "Review articles"]
related_synonym: "HGF/SF signaling pathway" []
related_synonym: "SF/HGF signaling pathway" []
is_a: PW:0000168 ! growth factor signaling pathway

[Term]
id: PW:0000579
name: somatostatin signaling pathway
def: "Somatostatin signaling through its receptors regulates processes such as proliferation, secretion and motility via inhibition of growth hormone and factor. The potential anti-tumor activity of somatostatin has led to the development and clinical use of its analogs." [OubMed:PMID\: 16625838; PMID\: 15153426; PMID\: 15078190;  PMID\: 15853632 "Review articles in PubMed"]
related_synonym: "somatotropin release inhibitory factor" []
related_synonym: "SRIF" []
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000580
name: translation initiation pathway
def: "Translation initiation is the first of the three stages of translation pathway in eukaryotes." [PubMed:PMID\: 17680008]
relationship: part_of PW:0000101 ! translation pathway

[Term]
id: PW:0000581
name: translation elongation pathway
def: "Translation elongation is the second of the three stages of translation pathway in eukaryotes." [PubMed:PMID\: 17680008]
relationship: part_of PW:0000101 ! translation pathway

[Term]
id: PW:0000582
name: translation termination pathway
def: "Translation termination is the third of the three stages of translation pathway in eukaryotes." [PubMed:PMID\: 17680008]
relationship: part_of PW:0000101 ! translation pathway

[Term]
id: PW:0000583
name: orexin/hypocretin signaling pathway
def: "The orexin/hypocretin signaling appears to play a role in the stimulation of food intake. Alterations of the system are associated with the narcolepsy sleep disorder." [OneLook\, PubMed:www.onelook.com; PMID\: 17299454 "Review article"]
is_a: PW:0000467 ! peptide and protein hormone signaling pathway

[Term]
id: PW:0000584
name: altered orexin/hypocretin signaling pathway
def: "An orexin/hypocretin signaling pathway that deviates from what its normal course should be. Alterations in orexin/hypocretin signaling pathway have been linked to narcolepsy. It may also play a role in obesity." [PubMed:PMID\: 17299454]
is_a: PW:0000511 ! altered peptide and protein hormone signaling pathway
is_a: PW:0000583 ! orexin/hypocretin signaling pathway

[Term]
id: PW:0000585
name: orexin/hypocretin signaling pathway through the orexin/hypocretin receptor 1
def: "Orexin/hypocretin signaling through receptor 1 couples to Galphaq class of G proteins. Orexin/hypocretin receptor 1 primarily binds orexin A. Orexin A and B are derived from prepro-orexin precursor." [PubMed:PMID\: 17299454 "Review article"]
is_a: PW:0000583 ! orexin/hypocretin signaling pathway

[Term]
id: PW:0000586
name: orexin/hypocretin signaling pathway through the orexin/hypocretin receptor 2
def: "Orexin/hypocretin signaling through receptor 2 couples to Galphaq and the inhibitory Galphai classes of G proteins. Orexin/hypocretin receptor 2 binds both orexin A and B derived from the prepro-orexin precursor." [PubMed:PMID\: 17299454 "Review article"]
is_a: PW:0000583 ! orexin/hypocretin signaling pathway

[Term]
id: PW:0000587
name: narcolepsy disease pathway
def: "Narcolepsy is a neurological condition characterized by excessive day sleep, an inability to maintain awake states. Dysfunction of the orexin/hypocretin signaling pathway has been linked to this condition." [PubMed:PMID\: 17299454 "Review article"]
is_a: PW:0000178 ! neurological disorder disease pathway

[Term]
id: PW:0000588
name: altered adiponectin signaling pathway
def: "An adiponectin signaling pathway that deviates from what its normal course should be. Deregulations in adiponectin signaling pathways have been linked to obesity, cardiovascular diseases, diabetes and metabolic syndrome. " [PubMed:PMID\: 16823476; PMID\: 16634986; PMID\: 17140553 "Review articles in  PubMed"]
is_a: PW:0000511 ! altered peptide and protein hormone signaling pathway
is_a: PW:0000563 ! adiponectin signaling pathway

[Term]
id: PW:0000589
name: metal homeostasis pathway
def: "Those pathways involved in the proper balance of metal ion levels, uptake and transport, utilization and storage as demanded by the needs of cells, tissues and organs. Disruption of metal ion homeostasis can have toxic and harmful consequences." [InHouse:PW-InHouse "definition based on a number of PubMed and other references"]
is_a: PW:0000355 ! homeostasis pathway

[Term]
id: PW:0000590
name: iron homeostasis pathway
def: "Those pathways involved in the proper balance of iron levels, uptake and transport, utilization and storage as needed by cells, tissues and organs. Iron is essential for many life processes but its reactivity makes it potentially dangerous." [PubMed:PMID\: 17194590; PMID\: 17014365; PMID\: 17367269]
is_a: PW:0000589 ! metal homeostasis pathway

[Term]
id: PW:0000591
name: iron transport pathway
is_a: PW:0000593 ! metal ion transport pathway
relationship: part_of PW:0000590 ! iron homeostasis pathway

[Term]
id: PW:0000592
name: iron storage pathway
relationship: part_of PW:0000590 ! iron homeostasis pathway

[Term]
id: PW:0000593
name: metal ion transport pathway
def: "Those pathways that mediate the uptake and transport of metal ions. Metal ion transport pathways are important aspects of metal ion homeostasis." [InHouse:PW-InHouse "Definition based on PubMed and other references"]
is_a: PW:0000103 ! transport pathway

[Term]
id: PW:0000594
name: altered glucose homeostasis pathway
is_a: PW:0000358 ! altered homeostasis pathway
is_a: PW:0000553 ! glucose homeostasis pathway

[Term]
id: PW:0000595
name: phosphatidylinositol 3-kinase signaling pathway
def: "Phosphatidylinositol kinases represent a family of lipid kinases that phosphorylate the 3' position of the inositol ring in target substrates. They are grouped into three classes: class I further subdivied into subclass A abd B, class II and class III. By far the best known and characterized is class I, particularly IA that signals downstream of receptor tyrosine kinases and engages the Akt family of kinases." [PubMed:PMID\: 17052169\, 17641274\, 16847462]
related_synonym: "phosphoinositide 3-kinase signaling pathway" []
related_synonym: "PI3K signaling pathway" []
is_a: PW:0000541 ! signaling pathways involving second messengers

[Term]
id: PW:0000596
name: altered insulin signaling pathway
def: "An insulin signaling pathway that deviates from what its normal course should be. Deregulation of insulin signaling can have profound health consequences due to its potential to alter glucose and energy homeostasis." [InHouse:PW dictionary]
is_a: PW:0000143 ! insulin signaling pathway
is_a: PW:0000511 ! altered peptide and protein hormone signaling pathway

[Term]
id: PW:0000597
name: non-canonical Wnt signaling pathway
def: "The non-canonical Wnt signaling pathway groups the various Wnt signaling routes that are beta-catenin independent." [PubMed:PMID\: 16019432; 18432252]
related_synonym: "beta-catenin independent Wnt signaling pathway" []
is_a: PW:0000008 ! Wnt signaling pathway

[Term]
id: PW:0000598
name: altered Wnt signaling pathway
def: "A Wnt signaling pathway that deviates from what its norma course should be. Deregulation of Wnt signalng has been implicated in several cancers as well as diseases other than cancer." [PubMed:PMID\: 18188179; 18432252]
is_a: PW:0000008 ! Wnt signaling pathway
is_a: PW:0000264 ! altered signaling pathway

[Term]
id: PW:0000599
name: altered canonical Wnt signaling pathway
def: "A canonical Wnt signaling pathway that deviates from what its normal course should be. Mutations in core components of the canonical pathway have been implicated in several cancers as well as diseases other than cancer." [PubMed:PMID\: 18188179; 18432252]
is_a: PW:0000201 ! canonical Wnt signaling pathway
is_a: PW:0000598 ! altered Wnt signaling pathway

[Term]
id: PW:0000600
name: altered non-canonical Wnt signaling pathway
def: "A non-canonical Wnt signaling pathway that deviates from what its normal course should be. Deregulation of the beta-catenin independent pathway appears to play a role in the biology of tumors." [PubMed:PMID\: 18271916]
is_a: PW:0000597 ! non-canonical Wnt signaling pathway
is_a: PW:0000598 ! altered Wnt signaling pathway

[Typedef]
id: part_of
name: part_pf