Signaling Proposal January 2010
The edited graph was sent to the GO list on the 11th January 2010, for implementation on the 1st February 2010.
Edited Graph
The branch file containing the new structure can be downloaded by selecting the latest version at the top of this page: http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/signaling3.obo
This file can be loaded into OBO-Edit for viewing.
Please note that the graph was branched from the GO file in April of 2009 and has not yet been merged, so some of the changes that have been made in the live graph will not show in this branch. The graphs will be merged before the signaling changes are committed to the live repository.
New Terms Proposed:
id: GO:0023004 name: activation of dopamine receptor signaling pathway namespace: biological_process def: "Any process that initiates the dopamine receptor protein signaling pathway through stimulation of the dopamine receptor." [GOC:mtg_signaling] synonym: "initiation of dopamine receptor signaling pathway" RELATED [] synonym: "stimulation of dopamine receptor signaling pathway" EXACT [] is_a: GO:0023005 ! signal initiation by neurotransmitter is_a: GO:0060161 ! positive regulation of dopamine receptor signaling pathway created_by: Jennifer I Deegan creation_date: 2009-11-23T04:28:24Z [Term] id: GO:0023005 name: signal initiation by neurotransmitter namespace: biological_process def: "The process whereby a neurotransmitter signal causes activation of a receptor." [GOC:mtg_signal] is_a: GO:0023038 ! signal initiation by diffusible mediator created_by: Jennifer I Deegan creation_date: 2009-11-23T04:34:34Z [Term] id: GO:0023006 name: signal initiation by amino acid namespace: biological_process def: "The process whereby an amino acid signal causes activation of a receptor." [GOC:mtg_signal] is_a: GO:0023038 ! signal initiation by diffusible mediator created_by: Jennifer I Deegan creation_date: 2009-11-23T04:35:16Z [Term] id: GO:0023007 name: ligand binding to T cell receptor namespace: biological_process def: "Binding of a diffusable ligand to a T cell receptor as part of a signaling process." [GOC:jid, GOC:mtg_signal] is_a: GO:0050862 ! positive regulation of T cell receptor signaling pathway created_by: Jennifer I Deegan creation_date: 2009-11-30T04:42:10Z [Term] id: GO:0023009 name: initiation of T cell receptor signaling namespace: biological_process def: "The process whereby a signal causes activation of T cell receptor signaling." [GOC:mtg_signal] is_a: GO:0023049 ! signal initiation by protein/peptide mediator created_by: Jennifer I Deegan creation_date: 2009-12-02T11:07:14Z [Term] id: GO:0023010 name: regulation of initiation of T cell receptor signaling namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the initiation of T cell receptor signaling." [GOC:mtg_signal] is_a: GO:0023009 ! initiation of T cell receptor signaling created_by: Jennifer I Deegan creation_date: 2009-12-02T11:08:13Z [Term] id: GO:0023011 name: positive regulation of initiation of T cell receptor signaling namespace: biological_process def: "Any process that activates, maintains or increases the frequency, rate or extent of the initiation of T cell receptor signaling." [GOC:mtg_signal] is_a: GO:0023010 ! regulation of initiation of T cell receptor signaling created_by: Jennifer I Deegan creation_date: 2009-12-02T11:08:34Z [Term] id: GO:0023012 name: initiation of T cell receptor signaling by binding of a MHC complex to T cell receptor namespace: biological_process def: "The process whereby binding of an MHC complex to T cell receptor causes activation of T cell receptor signaling." [GOC:mtg_signal] is_a: GO:0023009 ! initiation of T cell receptor signaling relationship: has_part GO:0023023 ! MHC protein complex binding created_by: Jennifer I Deegan creation_date: 2009-12-02T11:10:16Z [Term] id: GO:0023013 name: signal transmission via an intracellular cascade namespace: biological_process def: "The process whereby a signal is conveyed via an intracellular cascade." [GOC:mtg_signal] is_a: GO:0023060 ! signal transmission created_by: Jennifer I Deegan creation_date: 2009-12-02T11:28:45Z [Term] id: GO:0023014 name: signal transmission via a phosphorylation event namespace: biological_process def: "The process whereby a signal is conveyed via a phosphorylation event." [GOC:mtg_signal] is_a: GO:0023060 ! signal transmission created_by: Jennifer I Deegan creation_date: 2009-12-02T11:32:55Z [Term] id: GO:0023015 name: signal transmission via a cis-phosphorylation event namespace: biological_process def: "The process whereby a signal is conveyed via a cis-phosphorylation event." [GOC:mtg_signal] is_a: GO:0023014 ! signal transmission via a phosphorylation event created_by: Jennifer I Deegan creation_date: 2009-12-02T11:33:24Z [Term] id: GO:0023016 name: signal transmission via a trans-phosphorylation event namespace: biological_process def: "The process whereby a signal is conveyed via a trans-phosphorylation event." [GOC:mtg_signal] is_a: GO:0023014 ! signal transmission via a phosphorylation event created_by: Jennifer I Deegan creation_date: 2009-12-02T11:33:35Z [Term] id: GO:0023017 name: signal transmission via diffusible molecule namespace: biological_process def: "The process whereby a signal is conveyed via a diffusible molecule." [GOC:mtg_signal] synonym: "signaling via diffusible mediator" EXACT [] is_a: GO:0023060 ! signal transmission created_by: Jennifer I Deegan creation_date: 2009-12-02T11:35:34Z [Term] id: GO:0023018 name: T cell activation of signal transmission via diffusible molecule namespace: biological_process def: "The process whereby signal transmission via a diffusible molecule is initiated by a T cell." [GOC:mtg_signal] is_a: GO:0023017 ! signal transmission via diffusible molecule created_by: Jennifer I Deegan creation_date: 2009-12-02T11:37:13Z [Term] id: GO:0023019 name: regulation of gene expression as a consequence of signal transmission namespace: biological_process def: "Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process whereby a signal is released and/or conveyed from one location to another." [GOC:mtg_signal] is_a: GO:0010468 ! regulation of gene expression is_a: GO:0023050 ! consequence of signal transmission created_by: Jennifer I Deegan creation_date: 2009-12-02T11:45:34Z [Term] id: GO:0023020 name: regulation of gene expression as a consequence of T cell signal transmission namespace: biological_process def: "Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process whereby a T cell signal is released and/or conveyed from one location to another." [GOC:mtg_signal] is_a: GO:0023019 ! regulation of gene expression as a consequence of signal transmission created_by: Jennifer I Deegan creation_date: 2009-12-02T11:46:15Z [Term] id: GO:0023021 name: termination of signal transduction namespace: biological_process def: "The signaling process whereby signal transduction is brought to an end rather than being reversibly modulated." [GOC:mtg_signal] comment: Note that this term encompasses both the control point when the instruction is given for the process to cease and the actual cessation of the process. A process can persist for some time after that signal that induced the process is withdrawn. is_a: GO:0023046 ! signaling process created_by: Jennifer I Deegan creation_date: 2009-12-02T11:48:19Z [Term] id: GO:0023022 name: termination of T cell signal transduction namespace: biological_process def: "The signaling process whereby T cell signal transduction is brought to an end rather than being reversibly modulated." [GOC:mtg_signal] is_a: GO:0023021 ! termination of signal transduction is_a: GO:0050860 ! negative regulation of T cell receptor signaling pathway created_by: Jennifer I Deegan creation_date: 2009-12-02T11:48:53Z [Term] id: GO:0023023 name: MHC protein complex binding namespace: molecular_function def: "Interacting selectively with the major histocompatibility complex." [GOC:mtg_signal] is_a: GO:0003823 ! antigen binding created_by: Jennifer I Deegan creation_date: 2009-12-07T04:27:53Z [Term] id: GO:0023024 name: MHC class I protein complex binding namespace: molecular_function def: "Interacting selectively with the class I major histocompatibility complex." [GOC:mtg_signal] is_a: GO:0023023 ! MHC protein complex binding created_by: Jennifer I Deegan creation_date: 2009-12-07T04:28:26Z [Term] id: GO:0023025 name: MHC class Ib protein complex binding namespace: molecular_function def: "Interacting selectively with the class Ib major histocompatibility complex." [GOC:mtg_signal] is_a: GO:0023023 ! MHC protein complex binding created_by: Jennifer I Deegan creation_date: 2009-12-07T04:28:51Z [Term] id: GO:0023026 name: MHC class II protein complex binding namespace: molecular_function def: "Interacting selectively with the class II major histocompatibility complex." [GOC:mtg_signal] is_a: GO:0023023 ! MHC protein complex binding created_by: Jennifer I Deegan creation_date: 2009-12-07T04:29:11Z [Term] id: GO:0023027 name: MHC class I protein binding, via antigen binding groove namespace: molecular_function def: "Interacting selectively with major histocompatibility complex class I molecules via the antigen binding groove." [GOC:mtg_signal] is_a: GO:0042288 ! MHC class I protein binding relationship: part_of GO:0023024 ! MHC class I protein complex binding created_by: Jennifer I Deegan creation_date: 2009-12-07T04:33:59Z [Term] id: GO:0023028 name: MHC class I protein binding, via lateral surface namespace: molecular_function def: "Interacting selectively with major histocompatibility complex class I molecules via the lateral surface." [GOC:mtg_signal] is_a: GO:0042288 ! MHC class I protein binding created_by: Jennifer I Deegan creation_date: 2009-12-07T04:34:16Z [Term] id: GO:0023029 name: MHC class Ib protein binding namespace: molecular_function def: "Interacting selectively with major histocompatibility complex class Ib molecules." [GOC:mtg_signal] is_a: GO:0042287 ! MHC protein binding created_by: Jennifer I Deegan creation_date: 2009-12-07T04:35:37Z [Term] id: GO:0023030 name: MHC class Ib protein binding, via antigen binding groove namespace: molecular_function def: "Interacting selectively with major histocompatibility complex class Ib molecules via the antigen binding groove." [GOC:mtg_signal] is_a: GO:0023029 ! MHC class Ib protein binding relationship: part_of GO:0023025 ! MHC class Ib protein complex binding created_by: Jennifer I Deegan creation_date: 2009-12-07T04:36:03Z [Term] id: GO:0023031 name: MHC class I protein binding, via lateral surface namespace: molecular_function def: "Interacting selectively with major histocompatibility complex class Ib molecules via the lateral surface." [GOC:mtg_signal] is_a: GO:0023029 ! MHC class Ib protein binding created_by: Jennifer I Deegan creation_date: 2009-12-07T04:36:25Z [Term] id: GO:0023032 name: behavioral signaling namespace: biological_process def: "The entirety of the behavioral process whereby information is sent between living organisms." [GOC:mtg_signal] is_a: GO:0023052 ! signaling created_by: Jennifer I Deegan creation_date: 2009-10-28T04:21:32Z [Term] id: GO:0023033 name: signaling pathway namespace: biological_process def: "The series of molecular events whereby information is sent from one location to another within a living organism or between living organisms." [GOC:mtg_signal] is_a: GO:0023052 ! signaling created_by: Jennifer I Deegan creation_date: 2009-10-28T04:21:54Z [Term] id: GO:0023034 name: intracellular signaling pathway namespace: biological_process alt_id: GO:0055128 def: "The series of molecular events whereby information is sent from one location to another within a living organism." [GOC:mtg_signal] synonym: "intercellular signaling" EXACT [] synonym: "intracellular signal transduction pathway" RELATED [] is_a: GO:0023033 ! signaling pathway created_by: Jennifer I Deegan creation_date: 2009-10-28T04:27:25Z [Term] id: GO:0023035 name: CD40 signaling pathway namespace: biological_process def: "Any series of molecular signals generated as a consequence of binding to the receptor CD40." [GOC:mtg_signal] is_a: GO:0023034 ! intracellular signaling pathway created_by: Jennifer I Deegan creation_date: 2009-10-28T04:44:32Z [Term] id: GO:0023036 name: initiation of signal transduction namespace: biological_process def: "The process whereby a signal causes activation of a receptor, for example, via a conformation change." [GOC:mtg_sig] comment: Note that this term is intended for the annotation of both ligands and receptors. is_a: GO:0023046 ! signaling process relationship: part_of GO:0007165 ! signal transduction created_by: jdeegan creation_date: 2009-03-23T10:03:58Z [Term] id: GO:0023037 name: signal initiation by light namespace: biological_process def: "The process whereby a light signal causes activation of a receptor." [GOC:mtg_signal] is_a: GO:0023036 ! initiation of signal transduction created_by: jdeegan creation_date: 2009-03-23T10:04:36Z [Term] id: GO:0023038 name: signal initiation by diffusible mediator namespace: biological_process def: "The process whereby a diffusible signal causes activation of a receptor." [GOC:mtg_signal] is_a: GO:0023036 ! initiation of signal transduction created_by: jdeegan creation_date: 2009-03-23T10:04:52Z [Term] id: GO:0023039 name: signal initiation by physical damage namespace: biological_process def: "The process whereby a physical damage signal causes activation of a receptor." [GOC:mtg_signal] is_a: GO:0023053 ! signal initiation by mechanical effect created_by: jdeegan creation_date: 2009-03-23T10:05:05Z [Term] id: GO:0023040 name: signaling via ionic flux namespace: biological_process def: "The process whereby information is sent from one location to another, within a living organism or between living organisms, via ionic flux." [GOC:mtg_signal] is_a: GO:0023017 ! signal transmission via diffusible molecule created_by: jdeegan creation_date: 2009-03-23T10:05:52Z [Term] id: GO:0023041 name: neuronal signal transduction namespace: biological_process def: "The process whereby an activated neuronal cell receptor conveys information down a signaling pathway, resulting in a change in the function or state of a cell. This process may be intracellular or intercellular." [GOC:mtg_signal] is_a: GO:0007165 ! signal transduction is_a: GO:0023040 ! signaling via ionic flux created_by: jdeegan creation_date: 2009-03-23T10:06:12Z [Term] id: GO:0023042 name: signaling via protein/peptide mediator namespace: biological_process def: "The process whereby information is sent from one location to another, within a living organism or between living organisms, via a protein/peptide mediator." [GOC:mtg_signal] is_a: GO:0023017 ! signal transmission via diffusible molecule created_by: jdeegan creation_date: 2009-03-23T10:06:27Z [Term] id: GO:0023043 name: signaling via lipid mediator namespace: biological_process def: "The process whereby information is sent from one location to another, within a living organism or between living organisms, via a lipid mediator." [GOC:mtg_signal] is_a: GO:0023017 ! signal transmission via diffusible molecule created_by: jdeegan creation_date: 2009-03-23T10:06:52Z [Term] id: GO:0023044 name: signaling via chemical mediator namespace: biological_process def: "The process whereby information is sent from one location to another, within a living organism or between living organisms, via a chemical mediator." [GOC:mtg_signal] is_a: GO:0023017 ! signal transmission via diffusible molecule created_by: jdeegan creation_date: 2009-03-23T10:07:13Z [Term] id: GO:0023045 name: signal transmission via conformational transition namespace: biological_process def: "The process whereby a signal is conveyed via a conformational transition." [GOC:mtg_signal] relationship: part_of GO:0023060 ! signal transmission created_by: Jennifer I Deegan creation_date: 2009-04-06T02:08:10Z [Term] id: GO:0023046 name: signaling process namespace: biological_process def: "Any biological process involved in the generation, transmission, reception, or interpretation of a signal. A signal is an entity used to transmit or convey information." [GOC:mtg_signaling] is_a: GO:0008150 ! biological_process relationship: part_of GO:0023052 ! signaling created_by: Jennifer I Deegan creation_date: 2009-04-06T02:22:22Z [Term] id: GO:0023047 name: signal initiation by chemical mediator namespace: biological_process def: "The process whereby a chemical signal causes activation of a receptor." [GOC:mtg_signal] is_a: GO:0023038 ! signal initiation by diffusible mediator created_by: Jennifer I Deegan creation_date: 2009-04-06T02:31:23Z [Term] id: GO:0023048 name: signal initiation by lipid mediator namespace: biological_process def: "The process whereby a lipid signal causes activation of a receptor." [GOC:mtg_signal] is_a: GO:0023038 ! signal initiation by diffusible mediator created_by: Jennifer I Deegan creation_date: 2009-04-06T02:32:08Z [Term] id: GO:0023049 name: signal initiation by protein/peptide mediator namespace: biological_process def: "The process whereby a protein/peptide signal causes activation of a receptor." [GOC:mtg_signal] is_a: GO:0023038 ! signal initiation by diffusible mediator created_by: Jennifer I Deegan creation_date: 2009-04-06T02:32:27Z [Term] id: GO:0023050 name: consequence of signal transmission namespace: biological_process def: "The steps whereby the downstream processes started by a signal are brought to a conclusion. Examples include destruction of cAMP by PDE, or endocytosis resulting from receptor phosphorylation. The termination process ends when the receptor has returned to its inactive state." [GOC:mtg_signaling] comment: Note that most or all examples of this process are regulation steps. synonym: "signal termination" EXACT [] relationship: part_of GO:0023060 ! signal transmission created_by: Jennifer I Deegan creation_date: 2009-07-13T04:14:59Z [Term] id: GO:0023051 name: regulation of signaling process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a signaling process." [GOC:mtg_signal] is_a: GO:0023046 ! signaling process created_by: Jennifer I Deegan creation_date: 2009-07-20T04:51:09Z [Term] id: GO:0023052 name: signaling namespace: biological_process def: "The entirety of a process whereby information is transmitted. This process begins with the initiation of the signal and ends when a response has been triggered." [GOC:mtg_signaling] comment: The synthesis of the signal is not, in general, considered to be part of this process, but in some cases it is. Synthesis of insulin is not considered to be part of the insulin signaling pathway, and the insulin is assumed to have been made before the signaling process starts. is_a: GO:0008150 ! biological_process created_by: Jennifer I Deegan creation_date: 2009-07-13T04:24:06Z [Term] id: GO:0023053 name: signal initiation by mechanical effect namespace: biological_process def: "The process whereby a mechanical signal causes activation of a receptor." [GOC:mtg_signal] is_a: GO:0023036 ! initiation of signal transduction created_by: Jennifer I Deegan creation_date: 2009-07-13T04:29:31Z [Term] id: GO:0023054 name: signal initiation by stretch effect namespace: biological_process def: "The process whereby a stretch signal causes activation of a receptor." [GOC:mtg_signal] is_a: GO:0023053 ! signal initiation by mechanical effect created_by: Jennifer I Deegan creation_date: 2009-07-13T04:30:50Z [Term] id: GO:0023055 name: signal initiation by peptide hormone namespace: biological_process def: "The process whereby a signal is initiated by a peptide hormone." [GOC:signaling] is_a: GO:0023049 ! signal initiation by protein/peptide mediator created_by: Jennifer I Deegan creation_date: 2009-07-13T04:36:37Z [Term] id: GO:0023056 name: positive regulation of signaling process namespace: biological_process def: "Any process that activates, maintains or increases the frequency, rate or extent of a signaling process." [GOC:mtg_signal] is_a: GO:0023051 ! regulation of signaling process created_by: Jennifer I Deegan creation_date: 2009-07-20T04:51:26Z [Term] id: GO:0023057 name: negative regulation of signaling process namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of a signaling process." [GOC:mtg_signal] is_a: GO:0023051 ! regulation of signaling process created_by: Jennifer I Deegan creation_date: 2009-07-20T04:51:56Z [Term] id: GO:0023058 name: adaptation of signaling pathway namespace: biological_process def: "The regulation of a signal transduction pathway in response to a stimulus upon prolonged exposure to that stimulus." [GOC:mtg_sig] is_a: GO:0009966 ! regulation of signal transduction created_by: Jennifer I Deegan creation_date: 2009-08-03T04:13:01Z [Term] id: GO:0023059 name: positive adaptation of signaling pathway namespace: biological_process def: "The positive regulation of a signal transduction pathway in response to a stimulus upon prolonged exposure to that stimulus." [GOC:mtg_sig] is_a: GO:0023056 ! positive regulation of signaling process is_a: GO:0023058 ! adaptation of signaling pathway created_by: Jennifer I Deegan creation_date: 2009-08-03T04:13:50Z [Term] id: GO:0023060 name: signal transmission namespace: biological_process def: "The process whereby a signal is released and/or conveyed from one location to another. The process terminates at the end of the sub-process of signal transduction, when the function of the cell has been altered as a consequence of receipt of the signal." [GOC:mtg_signal] is_a: GO:0023046 ! signaling process created_by: Jennifer I Deegan creation_date: 2009-09-02T04:15:57Z [Term] id: GO:0023061 name: signal release namespace: biological_process def: "The process whereby a signal is secreted or discharged into the extracellular medium from a cellular source." [GOC:mtg_signaling] is_a: GO:0023060 ! signal transmission created_by: Jennifer I Deegan creation_date: 2009-09-02T04:37:21Z [Term] id: GO:0023062 name: signal transmission via transcytosis namespace: biological_process def: "The process whereby a signal is conveyed via transcytosis." [GOC:mtg_signal] is_a: GO:0023060 ! signal transmission created_by: Jennifer I Deegan creation_date: 2009-09-02T04:37:35Z [Term] id: GO:0023063 name: signal transmission across a synapse namespace: biological_process def: "The process whereby a signal is conveyed across a synapse." [GOC:mtg_signal] is_a: GO:0023060 ! signal transmission created_by: Jennifer I Deegan creation_date: 2009-09-02T04:37:55Z [Term] id: GO:0023064 name: signal transmission along a neuron namespace: biological_process def: "The process whereby a signal is conveyed along a neuron." [GOC:mtg_signal] is_a: GO:0023060 ! signal transmission created_by: Jennifer I Deegan creation_date: 2009-09-02T04:38:21Z [Term] id: GO:0023065 name: signal transmission via blood namespace: biological_process def: "The process whereby a signal is conveyed via blood." [GOC:mtg_signal] is_a: GO:0023066 ! signal transmission via vascular system created_by: Jennifer I Deegan creation_date: 2009-09-02T04:40:22Z [Term] id: GO:0023066 name: signal transmission via vascular system namespace: biological_process def: "The process whereby a signal is conveyed via the vascular system." [GOC:mtg_signal] is_a: GO:0023060 ! signal transmission created_by: Jennifer I Deegan creation_date: 2009-09-02T04:41:09Z [Term] id: GO:0023067 name: signal transmission via lymphatic system namespace: biological_process def: "The process whereby a signal is conveyed via the lymphatic system." [GOC:mtg_signal] is_a: GO:0023066 ! signal transmission via vascular system created_by: Jennifer I Deegan creation_date: 2009-09-02T04:41:51Z [Term] id: GO:0023068 name: signal transmission via phloem namespace: biological_process def: "The process whereby a signal is conveyed via the phloem." [GOC:mtg_signal] is_a: GO:0023066 ! signal transmission via vascular system created_by: Jennifer I Deegan creation_date: 2009-09-02T04:42:27Z [Term] id: GO:0023069 name: signal transmission via xylem namespace: biological_process def: "The process whereby a signal is conveyed via the xylem." [GOC:mtg_signal] is_a: GO:0023066 ! signal transmission via vascular system created_by: Jennifer I Deegan creation_date: 2009-09-02T04:42:45Z [Term] id: GO:0023070 name: signal transmission via air namespace: biological_process def: "The process whereby a signal is conveyed via the air." [GOC:mtg_signal] is_a: GO:0023060 ! signal transmission created_by: Jennifer I Deegan creation_date: 2009-09-02T04:49:19Z