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PomBase curation
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PMID:22267499 Ypa1, Ypa2 SIN signalling #3439

Open ValWood opened 1 year ago

ValWood commented 1 year ago

Ypa1, Ypa2
GO:0023057 negative regulation of SIN signalling GO:0008160 protein tyrosine phosphatase activator activity EXP PMID:22267499 prioritise

ValWood commented 1 year ago

in progress curs/291d614ef0c90bc4

ValWood commented 5 months ago

@PCarme a heads up that I changed ypa2 to regulation of SIN signalling, so it should fit into your model, I'm not sure how?

PCarme commented 5 months ago

Probably through the SIP complex which contains other PP2A subunits and dephosphorylates Cdc11 via Ppa3. I will have to search for the missing link there.

ValWood commented 5 months ago

I had this hanging around on my desktop:

So the MOR might also be relevant for inhibition ....

SIN regulators
PCarme commented 5 months ago

I just noticed that this paper is listed in the literature category on the ppa3 gene page image

although it contains no annotations regarding ppa3, which is only mentioned in the introduction. image

ValWood commented 5 months ago

We only began to do this gene extraction from publications recently. I guess this is because we get this info from the PubMed metadata (I gues ppa3 must be included in the keywords). We did decide (although I can't remember if a ticket was opened), that once a publication is curated in PomBAse, we could default to the gene list from Canto (which would remove this type of anomaly, in addition to the problem when a gene has conflicting names.

I will open a ticket for this if there isn't one. Opening this as a reminder.

@kimrutherford

ValWood commented 5 months ago

Although it's a bit weird because

https://pubmed.ncbi.nlm.nih.gov/?cmd=Search&term=(SPAC22H10.04+OR+ppa3+OR+ppg1)+AND+(pombe+OR+fission+yeast)

does not retrieve ANY fission yeast ppa3 publications???

PCarme commented 5 months ago

This is strange. It looks like the searchbar has a problem with ppa3 in pombe.

PCarme commented 5 months ago

And searching for ppa3 AND yeast only finds this paper about a plant protein (with some data with expression in yeast). https://pubmed.ncbi.nlm.nih.gov/29691313/

ValWood commented 5 months ago

Are there any true positives for ppa3? Part of the problem might be that people never call it ppa3 they call it PPA2 because its PPA2 catalytic subunit. I can't find a paper the uses ppa3.

This doesn't explain why ppa3 appears in the list, but it might be in the keywords for the paper, in which case it would appear, regardless of whether it has any annotation. The list, until recently was based on only curated papers, but recently we included anything PubMed retrieved.

PCarme commented 5 months ago

Are there any true positives for ppa3? Part of the problem might be that people never call it ppa3 they call it PPA2 because its PPA2 catalytic subunit. I can't find a paper the uses ppa3.

You're right, I can't find a single pombe paper with ppa3 in either the title or abstract.