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geneontology / go-annotation

This repository hosts the tracker for issues pertaining to GO annotations.
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Matrix: amino acid metabolism/chromatin remodelling 6 #2417

Open ValWood opened 5 years ago

ValWood commented 5 years ago

Hi Tanya,

I'm not including TAIR in the rule building process, but If I see any obvious outliers I'll elt you know. These appear to be indirect for "chromatin remodelling"

HOG1 AT4G13940   methylation-dependent chromatin silencing   TAIR Arabidopsis thaliana IMP     protein TAIR:locus:2129256 PMID:15659630TAIR:Publication:501714540 20050404
HOG1 AT4G13940   posttranscriptional gene silencing   TAIR Arabidopsis thaliana IMP     protein TAIR:locus:2129256 PMID:9611181TAIR:Publication:2530 20030610
tberardini commented 5 years ago

@ValWood What should I do with these annotations? Anything? Or is this just informational?

ValWood commented 5 years ago

This is

adenosylhomocysteinase activity

so its part of the   | S-adenosylmethionine cycle so its affect on silencing is indirectly/upstream. (It would affect ALL methylation)

It's quite old: https://www.ncbi.nlm.nih.gov/pubmed/?term=Gene+silencing+and+homology-dependent+gene+silencing+in+Arabidopsis%3A+genetic+modifiers+and+DNA+methylation

(I couldn't access the abstract, or PubMed, via TAIR from the publication page?)

tberardini commented 5 years ago

Would 'causally upstream of' work?

HOG1 'causally upstream of' posttranscriptional gene silencing HOG1 'causally upstream of' methylation-dependent chromatin silencing

ValWood commented 5 years ago

It is causally upstream of I guess. I have asked a few times about similar issues..... I did not have a definitive answer.

I don't know if 'causally upstream of' should be used when something is a 'given'. For instance, would you annotate core transcription or translation as causally upstream of everything ? (I don't know the answer to this).

If we capture all causal relations we would annotate almost everything to almost everything: causal

So, I don't know where we begin and end with causality, so we opted not to use it at PomBase, and only too annotate "involved" in or "real regulation" (i.e control). Possibly we will eventually use "causally upstream" when the boundaries are clearer. So I don't think it would be incorrect, but I'm not sure when it is, and is not, appropriate.