Obsoletion request (maybe): GO:0005945 6-phosphofructokinase complex

[sjm41]

I didn't think GO made/had protein-containing complex terms for homomers (complexes containing repeats of the same subunit)? But maybe I'm wrong?

id: GO:0005945 name: 6-phosphofructokinase complex namespace: cellular_component def: "A protein complex that possesses 6-phosphofructokinase activity; homodimeric, homooctameric, and allosteric homotetrameric forms are known." [GOC:mah, GOC:vw, ISBN:0198506732] intersection_of: GO:0032991 ! protein-containing complex intersection_of: capable_of GO:0003872 ! 6-phosphofructokinase activity relationship: part_of GO:0005829 ! cytosol

[pgaudet]

In the most recently updated guidelines, we say homodimers are in scope: https://wiki.geneontology.org/Protein_complexes

[pgaudet]

Should this be rediscussed? I sent this to the ontology editors group some time ago, but maybe we want wider feedback?

[sjm41]

Thanks for pointing me to that doc. Maybe it's fine, and I just had the wrong understanding. Searching through the GO for 'homodimer', I do see more examples, so this isn't an isolated case. But I imagine there are many more homomers that could be added if these are really within scope.

[deustp01]

many more homomers that could be added

Many, many homomultimers, yes

[sjm41]

I notice we also have these two MF terms that relate to homodimers:

GO:0042802 identical protein binding
    |_GO:0042803 protein homodimerization activity

[pgaudet]

Right - I am not quite sure which complexes are really useful. @ValWood says she uses them to confirm that MF or BPs are correctly annotated; is this a common use case?

How else do you use GO complexes?

[sjm41]

How else do you use GO complexes? You mean generally? I think the most useful aspect is that allows you to annotate, and therefore group, different subunits within heteromers. FlyBase (at least) doesn't have systematic Complex Portal annotation (though we are starting to add more of these) and we don't use PRO at all, so annotating with GO-CC complex terms is our main method to do this.

And then of course, it's easy to compare heteromeric complex components between species using these GO complex terms. From that perspective, the most useful GO complex terms are those for conserved complexes.

[pgaudet]

So you dont use homomers ?

[sjm41]

I'm currently checking the FB policy for annotating homomeric complexes with @hattrill... I think we just use the MF terms I mentioned to annotate such cases, but Helen will know better.

[ValWood]

For PomBAse this is the main reason

FlyBase (at least) doesn't have systematic Complex Portal annotation

very few pombe entries in ComplexProtal, this is the only way we have to annotate complexes as most are initially via similarity. There is no annotation effort for complexes via Complex portal in most species so it will be a long time before this is comprehensive.

Very useful for QC too, tracking down missing complex components, and identifying missing orthologs and making sure that annotations across a complex are consistent.

I also use them to build networks which will eventually seed GO-CAMs

I'm ambivalent about monomer complexes (since we don't usually include dimers), but I don't think they do any harm, and I have used a few.

[deustp01]

So you dont use homomers ?

Reactome does, obsessively, because we want to catalog the molecular environment in which the enabling gene product carries out its enabling function. We also put protein : nonprotein cofactor complexes into our complex class but do not export those complexes to GO)

[ValWood]

Another use case https://scholar.google.com/scholar_url?url=https://royalsocietypublishing.org/doi/pdf/10.1098/rsob.130053%3Fdownload%3Dtrue&hl=en&sa=T&oi=ucasa&ct=ufr&ei=HEOpZc7HNKmu6rQPqourgAo&scisig=AFWwaeYCQiah33C4mhdDfT3DLC6i

I used them successfully in an enrichment of phenotypes (worked better than processes because complexes usually phenocopy each other)

Somewhere I have a whole list of use-cases from when GO once considered obsoleting them

[sandraorchard]

For Complex Portal they are used for searching and grouping so only really find the more top-level terms useful e.g. to find all the ubiquitin-ligase complexes, not the rather random collection of child terms this has collected. Can add more pombe to the Complex Portal if you send them over, as Flybase does.

[ValWood]

@sandraorchard I can do that! I will see if we can dig out a list of the ones with experimental data!

[pgaudet]

@sjm41 Should we close this? I dont think it's a high priority (although we should make clearer guidelines at some point)

[sjm41]

Yes, we can close this specific ticket.

I was under the (false) impression that homomeric complex terms were disallowed in GO and GO:0005945 was an oddity - e.g. see this recent obsoletion ticket - https://github.com/geneontology/go-announcements/issues/458 But seems I was wrong!

Yes, definitely would be good to have clearer guidelines going forward - e.g. there are LOTS of homomeric complexes in the metabolic pathways we're starting to annotate, and annotating these with the current set of available GO complex terms for 'homomers' is going to result in patchy/inconsistent annotation. Should we request new GO terms for every homomeric complex we encounter to increase consistency/coverage of annotation? Probably not.

[sjm41]

Tagging @rozaru retrospectively.