Signaling - pointers from the community

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I have mailed the GO list asking for their pet peeves and ideas on prioritization. I will store the answers here.


G protein-mediated signaling

Pascale Gaudet, cc'd to Petra Fey

"Let me know which bits you do first. Dicty is widely used to study signaling: a lot of G protein, but loads of other pathways as well. We could probably also get an expert to help. "


Various cascades

Alex Diehl


"I've never been totally happy about naming, arrangement, and synonyms of the terms in the GO:0000165 MAPKKK cascade hierarchy. Similarly, the GO:0007259 JAK-STAT cascade ought to be reviewed as well. Also, the GO:0007249 I-kappaB kinase/NF-kappaB cascade hierarchy."


signal transducer

One of my pet peeves is the use of the term "signal transducer" activity, or rather, the inconsistent use of signal transducer activity. Sometimes it is used very loosely for any gene product involved in the signaling pathway and sometimes it is used very specifically, for gene products that get the whole thing rolling (like RAS and and RHO and other heterotrimeric G-proteins). I had a conversation with Jeremy Thorner, who works on pheromone and osmostress signaling, and according to him the latter is the more appropriate use of the term in regards to GO function. The function of the thing that binds the ligand is "receptor", anything like GTPase activating proteins and exchange factors (GAPs and GEFs) are "signal transducer regulator activity" and then things downstream are "kinases" and only the thing that binds the receptor and then triggers the rest of the signal transduction cascade would have the MF "signal transducer activity". Also, according to this line of thinking, "signal transducer activity" having children like "receptor activity" is a tpv.

However, having said all this, I only spoke to one expert and will be happy just to have a group of experts get together to straighten that part of the tree out.

Thank you! -Julie

Julie Park, Ph.D., Scientific Curator juliep at genome.stanford.edu