Open pgaudet opened 3 years ago
I would be happy if "cAMP-mediated signalling" was obsoleted and made a related synonym of GO:0007188 adenylate cyclase-modulating" G protein-coupled receptor signaling pathway.
I just want people to find this pathway if they search on "cAMP-mediated signalling"
or merged...
I think we can also do the same merge with
Annotations are here: https://docs.google.com/spreadsheets/d/11VqCZrr_xy3pLGDBtEGksjncw1a1EDoOdif9V_ppO-U/edit#gid=0 (see also this analysis from 2017 https://docs.google.com/presentation/d/1xR6EFbRyCSwruXVeMYZtJfwWEbIr6U8zei8IwGG3OrA/edit#slide=id.g26be66c50c_0_91
Will might need to obsolete, because it looks like there are many receptors, as annotations are too inconsistent to merge: ligands and adenylate cyclases annotate to 'regulation of cAMP-mediated signaling' (since they are upstream). Also, phosphodiesterases, that degrade cAMP and stop the signaling, are often annotated to negative regulation of cAMP signaling.
There are not so many annotations
Group | Number of EXP annotations |
---|---|
AgBase | 3 |
dictyBase | 13 @pfey03 |
FlyBase | 3 @hattrill |
MGI | 6 @ukemi |
PomBase | 6 OK |
RGD | 37 @gthayman |
SGD | 3 @srengel |
UniProt | 30 |
WB | 1 @vanaukenk |
This really is a case where the start and end of the pathway would be useful to have. The 'canonical' ACA-activating GPCR pathway activates PKA, which activates gene expression, see https://docs.google.com/presentation/d/1xR6EFbRyCSwruXVeMYZtJfwWEbIr6U8zei8IwGG3OrA/edit#slide=id.g26cb322782_0_61 so - do we also need to merge/obsolete GO:0010737 protein kinase A signaling ? But other pathways also feed into PKA signaling.
Maybe we can do the cAMP bit and see PKA later ?
~I only see 2 direct annotations at PomBase? stm1 and pka1~
ignore 2 genes, multiple annotations
PomBase done!
another commonly used name for is GO:0007188 adenylate cyclase-modulating" G protein-coupled receptor signaling pathway in fission yeast is glucose-sensing PKA pathway
@ValWood We have a term for this, adenylate cyclase-activating glucose-activated G protein-coupled receptor signaling pathway
Yes "GO:0007188 adenylate cyclase-modulating" G protein-coupled receptor signaling pathway needs synonyms glucose-sensing PKA pathway (exact?) and cAMP-mediated signaling (related or broad? ) after merge?
Sorry I was talking about GO:0010619 - can you not use this ?
We already use this, https://www.pombase.org/term/GO:0010619 but it is no longer linked to "cAMP-mediated signalling" which used to be an ancestor and is what users are more likely to use in searching... All these terms need
either glucose-sensing PKA pathway and cAMP-mediated signaling
or just cAMP-mediated signaling as synonyms (depending whether they mention glucose or not)
I see links between those terms -
Do you want me to add
OK ?
Yes! thanks.
@pgaudet I know we said maybe exclude Dicty from GO:0019933 cAMP-mediated signaling' , but I need to check if it can really be excluded as cAMP also plays role in later development. not sure if anything is intracellular but need to check into that again to be really sure.
I checked and it's always via an extracellular receptor as far as I could find and cAMP is always secreted. So I think GO:0019933 can be 'not in Dictyostelium'
Added Never in taxon GO:0019933 cAMP-mediated signaling NCBITaxon:33083 Dictyostelids
THanks @pgaudet
We need to obsolete the following 4 terms:
The reason for obsoletion is that cAMP-mediated signaling is part of adenylate cyclase-activating G protein-coupled receptor signaling pathway. However many annotations are incorrect, ie not 'part of' adenylate cyclase-activating G protein-coupled receptor signaling pathway, but rather downstream targets.
Annotations are here (downloaded again today): https://docs.google.com/spreadsheets/d/11VqCZrr_xy3pLGDBtEGksjncw1a1EDoOdif9V_ppO-U/edit#gid=0
AgBase | 3 BHF-UCL | 1 CGD | 10 dictyBase | 40 FlyBase | 8 MGI | 14 ParkinsonsUK-UCL | 1 RGD | 44 SGD | 10 UniProt | 54 WB | 1
What about soluble adenylate cyclase? PMID:25308880
Isn't adenylate cyclase always soluble? I presume you would only use "adenylate cyclase-activating G protein-coupled receptor signaling pathway" if the adenylate cyclase is part of this pathway.
Is adenylate cyclase part of other pathways too? I presume there would be other terms for that?
This paper also helps: https://pubmed.ncbi.nlm.nih.gov/21490586/
sAC is distinct from the more widely studied source of cAMP, the transmembrane adenylyl cyclases (tmACs); its activity is uniquely regulated by bicarbonate anions, and it is distributed throughout the cytoplasm and in cellular organelles. Due to its unique localization and regulation, sAC has various functions in a variety of physiological systems that are distinct from tmACs
The authors also write
However, in a seeming conundrum, cAMP has also been implicated in a wide variety of often-contradictory physiological processes, including different aspects of metabolism, proliferation, apoptosis, differentiation, migration, development, ion transport, pH regulation, and gene expression. Only recently has it become clear how this single second messenger could simultaneously mediate so many processes. In current models of cyclic nucleotide signal transduction, cAMP is locally generated within independently regulated microdomains (most recently reviewed in 39).
supporting multiple pathways, in fact. I dont find any term(s) that would represent the other ACA/cAMP signaling pathways.
I already updated all Dicty from dictyBase on 22. Feb, hope it will soon come through with next EBI release
Thanks @pfey03 !
@pgaudet noticed I missed some regulation of cAMP mediated signaling and updating those today or tomorrow
Just to add to the soluble AC thread, I am currently looking at cAMP signaling in the mitochondrial matrix: https://pubmed.ncbi.nlm.nih.gov/29694829/
Thanks @hattrill let us know what you find, it sounds like we can create other pathways.
Where I dont know what to do is for PDE - it degrades cAMP, but would we be able to tell from which pathway cAMP was produced?
I think for my purposes as they stand (looking at PMID:25648146), I could do with a negative term for GO:0010738 regulation of protein kinase A signaling
In D.mel, it's not clear if the cAMP is generated in the mitochondrion or not as the sAC is unknown. So, I don't think I can point to a specific pathway.
For mammalian systems it seems like cAMP can be generated by sACs in the matrix.
SGD done.
AgBase done
dictyBase all checked and done
dictyBase | 3 FlyBase | 2 MGI | 6 RGD | 37 UniProt | 31 WB | 1
WB checked and updated.
done with dicty
Annotation Review is out-of-date and was closed
Hello,
Following on the Signaling workshop of the Fall 2017 (see slides here: https://docs.google.com/presentation/d/1xR6EFbRyCSwruXVeMYZtJfwWEbIr6U8zei8IwGG3OrA/edit#slide=id.g26be66c50c_0_6) and on #20487
"GO:0007188 adenylate cyclase-modulating" G protein-coupled receptor signaling pathway and "GO:0019933 cAMP mediated signalling" are 2 names for the same pathway