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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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NTR: beta-arrestin-dependent dopamine receptor signaling pathway #28005

Open pgaudet opened 1 month ago

pgaudet commented 1 month ago

Following up on https://github.com/geneontology/go-ontology/issues/26959

After discussion with @hattrill we agree that we should look into creating a new term under 'GO:0007166 cell surface signaling pathway', based on the paper @raymond91125 cited, PMID: 25671228, and also PMID:35688404.

One problem is that there are no general beta-arrestin or GSK3 signaling pathway terms in GO, so no 'module' we can reuse. Beta-arrestin a an adaptor that seem to activate may different proteins; can a a pathway in which the receptor binds beta-arrestin be defined unambiguously?

The mechanism of signaling is not clear: PMID: 25671228, mentions PP2, Akt and GSK3A, while

PMID:35688404 mentions Akt, PI3K, MAP kinases but not GSK3

image

image

Are these the same pathway?

The first step would be with it to review the direct annotations to GO:0007212 dopamine receptor signaling pathway (39 EXP) and see if they can be made more precise with existing terms, or if we already need a new term.

@raymond91105 can you please set up an annotation review?

Thanks, Pascale

raymond91125 commented 1 month ago

@pgaudet For annotation review, is the proposal to make dopamine receptor signaling pathway do_not_annotate or obsolete or something else? Thanks.

raymond91125 commented 1 month ago

The PMID:25671228 figure above is about D2R whereas PMID:35688404 D1R. As indicated in PMID:28328745, G-protein independent arrestin signaling is quite varied regarding both upstream (many different 7TM receptors) and downstream (kinase and non-kinase).

Perhaps we could do: GO:0007166 cell surface signaling pathway ---GO:0007212 dopamine receptor signaling pathway (do_not_annotate) ------GO:0007191 adenylate cyclase-activating dopamine receptor signaling pathway (is_a G protein-coupled receptor signaling pathway) ------GO:0007195 adenylate cyclase-inhibiting dopamine receptor signaling pathway (is_a G protein-coupled receptor signaling pathway) ------GO:0060158 phospholipase C-activating dopamine receptor signaling pathway (is_a G protein-coupled receptor signaling pathway) ------GO:nnnnnnn beta-arrestin-dependent dopamine receptor signaling pathway (LD = 'dopamine receptor signaling pathway' and ('has part' some 'arrestin-family protein binding'))

pgaudet commented 1 month ago

This looks good to me. @hattrill ?