Initiation of signal transduction

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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).