search

geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
Creative Commons Attribution 4.0 International
220 stars 40 forks source link

interleukin-27-mediated signaling pathway #5543

Closed gocentral closed 9 years ago

gocentral commented 15 years ago

Hi

please could the following term be created: GO:0019221 cytokine and chemokine mediated signaling pathway NTR: is_a interleukin-27-mediated signaling pathway

For use with gp130/IL6ST PMID:14764690

Thanks

Ruth

Reported by: RLovering

Original Ticket: "geneontology/ontology-requests/5561":https://sourceforge.net/p/geneontology/ontology-requests/5561

gocentral commented 15 years ago

Ruth and Midori,

I don't personally have any objection to this term, but David Hill pointed out on Friday that his view on signaling pathway terms is that they should be tied to a particular receptor, not to the ligand of the receptor. We do have, however, multiple terms of the 'X mediated signaling pathway' type already, which for certain ligands may actually apply to more than one receptor for the same ligand. This ambiguity is not always so good since gene products annotation to a particular 'X mediated signaling pathway' may in fact be in different pathways. But on the other hand, in some experiments, the data may refer to phosphorylation of intracellular signaling intermediates, but without identifying which actual cell surface receptor is involved, and so the ambiguity of the term allows easy annotation.

Given that IL-27 appears only to have one identified receptor, the heterodimer of IL27RA/IL6ST (IL6ST is otherwise known as gp130, a shared chain among several cytokine receptors, so the official name is somewhat misleading), either formulation of the term name works for me, but I would be happy to hear other opinions.

Thanks,

Alex

Original comment by: addiehl

gocentral commented 15 years ago

I've added the terms here and in the other item, in light of (a) your approval, or at least lack of objection; (b) the precedent of existing terms included to allow annotation where a receptor isn't known; and (c) your statement that IL-27 has only one known receptor, so the term is unambiguous, at least for the present.

interleukin-27-mediated signaling pathway GO:0070106 regulation of interleukin-27-mediated signaling pathway GO:0070107 negative regulation of interleukin-27-mediated signaling pathway GO:0070108 positive regulation of interleukin-27-mediated signaling pathway GO:0070109

Original comment by: mah11

gocentral commented 15 years ago

Original comment by: mah11