Review annotations to GO:0070528 protein kinase C signaling & related

[pgaudet]

This ticket is for the review of GO:0007205 protein kinase C-activating G protein-coupled receptor signaling pathway

and GO:0070528 protein kinase C signaling GO:0090036 regulation of protein kinase C signaling GO:0090038 negative regulation of protein kinase C signaling GO:0090037 positive regulation of protein kinase C signaling

Note that there are 2 review Google sheets: one for GO:0007205 protein kinase C-activating G protein-coupled receptor signaling pathway and one for GO:0070528 protein kinase C signaling & children.

[pgaudet]

GO:0007205 protein kinase C-activating G protein-coupled receptor signaling pathway

MGI 2 RGD 10 UniProt 6 (done)

Obsoletion notice: https://github.com/geneontology/go-ontology/issues/28414 Annotations are here: https://docs.google.com/spreadsheets/d/1NsID-TLPcAWwNZFt_Jigf25hup9d_95KFuXQ-nC3n0M/edit?gid=0#gid=0

[pgaudet]

For GO:0070528 protein kinase C signaling GO:0090036 regulation of protein kinase C signaling GO:0090038 negative regulation of protein kinase C signaling GO:0090037 positive regulation of protein kinase C signaling

It looks like annotations are either:

• GO:0007205 protein kinase C-activating G protein-coupled receptor signaling pathway (or a child)
• GO:0141212 phospholipase C/protein kinase C signal transduction
• NTR positive regulation of phospholipase C/protein kinase C signal transduction
• activation of PKC without a known mechanism; annotations to be removed or changed to 'GO:0035556 intracellular signal transduction'

Annotations are here: https://docs.google.com/spreadsheets/d/1NsID-TLPcAWwNZFt_Jigf25hup9d_95KFuXQ-nC3n0M/edit?gid=0#gid=0

Impacted groups:

• 6 BHF
• 1 CGD
• 12 MGI
• 7 RGD
• 14 SGD
• 24 UniProt
• 7 WB

Thanks, Pascale

[jlewsmith]

CGD done

[LiNiMGI]

MGI done.

[vanaukenk]

I've removed the C. elegans annotations and didn't re-annotate to 'intracellular signal transduction' because I don't think that conveys the same information we were trying to capture with the 'negative regulation of protein kinase C signaling' annotations.

The paper describes genetic interactions between members of the PKA signaling pathway and pkc-3 in early embryo development, and while the mechanism is not studied in this paper, the conclusion of the genetic analysis is: "These results implicate a previously unknown negative crosstalk between the PKA signalling pathway and PKC-3 function."

I may try to capture this with genetic interaction curation at WB, instead.

[srengel]

SGD done.

[RLovering]

UCL done

[pgaudet]

Hi @vanaukenk Why can't you use cAMP/PKA signal transduction?

Figure 4 in the paper seems to descibe exactly this pathway

[Antonialock]

uniprot done

[vanaukenk]

@pgaudet The original annotations we had for this ticket were IGI annotations that were intended to capture that there seems to be some form (likely regulatory, but no mechanistic details were given) of cross-talk between members of the PKA signaling pathway and a protein kinase C signaling pathway.

While it is true that some of the genes in those annotations are members of a PKA signaling pathway, that's not what the original intent of the annotations was, so I think we're better off capturing the results of those experiments as genetic interactions in WB.

[pgaudet]

Thanks - terms have been obsoleted, the remaining annotations will appear in the gorules reports.