Initiation of signal transduction: Difference between revisions
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==Current Terms== | ==Current Terms== |
Latest revision as of 12:21, 5 May 2014
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Current Terms
[Term] id: GO:0023036 name: initiation of signal transduction namespace: biological_process def: "The process in which 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. synonym: "signal reception" RELATED [] is_a: GO:0009987 ! cellular process relationship: part_of GO:0007165 ! signal transduction creation_date: 2010-02-16T09:30:50Z
initiation of signal transduction ; GO:0023036 signal initiation by diffusible mediator ; GO:0023038 initiation of adrenergic receptor signal transduction ; GO:0071876 signal initiation by amino acid ; GO:0023006 signal initiation by chemical mediator ; GO:0023047 signal initiation by lipid mediator ; GO:0023048 signal initiation by neurotransmitter ; GO:0023005 activation of dopamine receptor signaling pathway ; GO:0023004 signal initiation by protein/peptide mediator ; GO:0023049 initiation of Roundabout signal transduction ; GO:0035555 initiation of T cell receptor signaling ; GO:0023009 initiation of T cell receptor signaling by binding of a MHC complex to T cell receptor ; GO:0023012 ligand binding to T cell receptor ; GO:0023007 positive regulation of initiation of T cell receptor signaling ; GO:0023011 regulation of initiation of T cell receptor signaling ; GO:0023010 signal initiation by peptide hormone ; GO:0023055 signal initiation by light ; GO:0023037 signal initiation by mechanical effect ; GO:0023053 signal initiation by physical damage ; GO:0023039 signal initiation by stretch effect ; GO:0023054
Problems with the current term
- The comment states that the term can be used to annotate both ligands and receptors, however many of the children terms (E.g. initiation of signal transduction by mechanical effect) cover cases where the ligand is not a gene product.
- The definition is more geared to annotation of ligands rather than receptors.
- The definition does not state where initiation of signal transduction ends. At the February 2011 signaling workshop, we asked whether initiation of signal transduction ends with an activated receptor, or when an activated receptor has passed the signal to the next signaling molecule, and it wasn't possible to reach a standard for all pathways.
- With the addition of links between the function terms: 'receptor activity ; GO:0004872' and 'receptor agonist activity ; GO:0048018' and the process term 'signal transduction ; GO:0007165' a grouping term in process is not particularly useful.
Proposal Overview
- OBSOLETE 'initiation of signal transduction ; GO:0023036 and it's children.
- REPLACE the existing annotations with 'receptor activity' and 'receptor antagonist activity' terms, along with 'signal transduction terms'.
Proposal Specifics
initiation of signal transduction ; GO:0023036 consider: receptor activity ; GO:0004872 consider: receptor agonist activity ; GO:0004872 consider: signal transduction ; GO:0007165
signal initiation by diffusible mediator consider: paracrine signaling ; GO:0038001 consider: signal transduction ; GO:0007165 consider: receptor activity ; GO:0004872 consider: receptor agonist activity ; GO:0048018
initiation of adrenergic receptor signal transduction ; GO:0071876 consider: adrenergic receptor activity ; GO:0004935 consider: adrenergic receptor signaling pathway ; GO:0071875 consider: signal transduction ; GO:0007165 consider: cellular response to epinephrine stimulus ; GO:0071872 consider: cellular response to norepinephrine stimulus ; GO:0071874 consider: hormone activity ; GO:0005179
signal initiation by amino acid ; GO:0023006 consider: glutamate receptor activity ; GO:0008066 consider: glutamate signaling pathway ; GO:0007215 consider: cellular response to amino acid stimulus ; GO:0071230
signal initiation by chemical mediator ; GO:0023047 consider: signal transduction ; GO:0007165 consider: receptor activity ; GO:0004872 consider: cellular response to chemical stimulus ; GO:0070887
signal initiation by lipid mediator ; GO:0023048 consider: signal transduction ; GO:0007165 consider: bioactive lipid receptor activity ; GO:0045125
signal initiation by neurotransmitter ; GO:0023005 consider: signal transduction ; GO:0007165 consider: neurotransmitter receptor activity ; GO:0030594
signal initiation by light ; GO:0023037 consider: photoreceptor activity ; GO:0009881 consider: signal transduction ; GO:0007165 consider: blue light signaling pathway ; GO:0009785 consider: far-red light signaling pathway ; GO:0010018 consider: red or far-red light signaling pathway ; GO:0010017 consider: red light signaling pathway ; GO:0010161
activation of dopamine receptor signaling pathway ; GO:0023004 consider: signal transduction ; GO:0007165 consider: dopamine receptor signaling pathway ; GO:0007212 NB: Note that ligands are part of the signaling pathway.
signal initiation by protein/peptide mediator ; GO:0023049 consider: signal transduction ; GO:0007165 consider: receptor activity ; GO:0004872 consider: receptor agonist activity ; GO:0048018
initiation of Roundabout signal transduction ; GO:0035555 consider: signal transduction ; GO:0007165 consider: Roundabout signaling pathway ; GO:0035385 consider: Roundabout binding ; GO:0048495 NB: Note that ligands (SLIT in this case) are part of the signaling pathway.
initiation of T cell receptor signaling ; GO:0023009 consider: T cell receptor signaling pathway ; GO:0050852 consider: T cell receptor complex ; GO:0042101
initiation of T cell receptor signaling by binding of a MHC complex to T cell receptor ; GO:0023012 consider: T cell receptor signaling pathway ; GO:0050852 consider: T cell receptor complex ; GO:0042101
regulation of initiation of T cell receptor signaling ; GO:0023010 consider: regulation of T cell receptor signaling pathway ; GO:0050856
positive regulation of initiation of T cell receptor signaling ; GO:0023011 consider: positive regulation of T cell receptor signaling pathway ; GO:0050862
ligand binding to T cell receptor ; GO:0023007 consider: T cell receptor binding ; GO:0042608 consider: T cell receptor complex ; GO:0042101
signal initiation by peptide hormone ; GO:0023055 consider: hormone-mediated signaling pathway ; GO:0009755 consider: ligand-dependent nuclear receptor activity ; GO:0004879 consider: hormone activity ; GO:0005179
signal initiation by mechanical effect ; GO:0023053 consider: signal transduction ; GO:0007165 consider: cellular response to mechanical stimulus ; GO:0071260
signal initiation by physical damage ; GO:0023039 consider: signal transduction ; GO:0007165 consider: cellular response to stress ; GO:0033554
signal initiation by stretch effect ; GO:0023054 consider: signal transduction ; GO:0007165
Existing annotations
The low number of annotations to these terms agrees with the concern that the terms are confusing and poorly defined. Annotations are as follows:
initiation of signal transduction ; GO:0023036 (0 direct annotations) signal initiation by diffusible mediator ; GO:0023038 (0 direct annotations) initiation of adrenergic receptor signal transduction ; GO:0071876 (0 direct annotations) signal initiation by amino acid ; GO:0023006 (20 ISS and IMP annotations from UniProt for glutamate receptors) signal initiation by chemical mediator ; GO:0023047 (0 direct annotations) signal initiation by lipid mediator ; GO:0023048 (1 BHF-UCL) signal initiation by neurotransmitter ; GO:0023005 (4 annotations: 1 EA Ensembl, 3 manual BHF-UCL to purinoreceptors) activation of dopamine receptor signaling pathway ; GO:0023004 (0 direct annotations) signal initiation by protein/peptide mediator ; GO:0023049 (0 direct annotations) initiation of Roundabout signal transduction ; GO:0035555 (1 annotation: BHF-UCL to SLIT2) initiation of T cell receptor signaling ; GO:0023009 (0 direct annotations) initiation of T cell receptor signaling by binding of a MHC complex to T cell receptor ; GO:0023012 (0 direct annotations) ligand binding to T cell receptor ; GO:0023007 (0 direct annotations) positive regulation of initiation of T cell receptor signaling ; GO:0023011 (1 annotation: BHF-UCL) regulation of initiation of T cell receptor signaling ; GO:0023010 (0 direct annotations) signal initiation by peptide hormone ; GO:0023055 (0 direct annotations) signal initiation by light ; GO:0023037 (0 direct annotations) signal initiation by mechanical effect ; GO:0023053 (0 direct annotations) signal initiation by physical damage ; GO:0023039 (0 direct annotations) signal initiation by stretch effect ; GO:0023054 (0 direct annotations)
OUTCOME
Initiation of signal transduction terms were obsoleted from GO in May 2011 (version 1.1957).