Review annotations to 'regulation of protein x-merization activity' and children

[vanaukenk]

Hi,

There are a few more annotations to review for the x-merization activity terms. This ticket addresses the 'regulation of x-merization activity' terms which will be obsoleted.

Annotations to be reviewed are organized according to evidence code below and are in this Google spreadsheet:

https://docs.google.com/spreadsheets/d/18KdAXo95Ms7aYDbETTzwmHiaPm3cH6k8o-6uvEXYFlw

Further information about review of these annotations can be found in this Google doc:

https://docs.google.com/document/d/1JxzNwl1fr5Fj-IJy_Fo1lLfAlAQB8IxPDwwYKxIXBZo/edit#heading=h.oxlxrmsdkphr

Any questions or edge cases for annotation, please add a comment to the ticket and we'll discuss.

Please also remember to mark the spreadsheet when you're done, so we can calculate accurate metrics for review efforts for the grant.

If you have any trouble accessing the spreadsheet, please send a request for edit access.

Thank you!

[vanaukenk]

IDA

Annotations to regulation of protein x-merization activity and children with evidence code ECO:0000314 (IDA)

Issue: Need manual review to possibly change to 'regulation of protein complex assembly' or a child term; alternatively, can be removed.

UniProt - 6 BHF-UCL - 3 HGNC - 3 TAIR - 3 ParkinsonsUK-UCL - 2 ARUK-UCL - 1 dictyBase - 1 SGD - 1

[vanaukenk]

IMP

Annotations to regulation of protein x-merization activity and children with evidence code ECO:0000315 (IMP)

Issue: Need manual review to possibly change to 'regulation of protein complex assembly' or a child term; alternatively, can be removed.

UniProt - 8 BHF-UCL - 1 ARUK-UCL - 1 dictyBase - 1

[vanaukenk]

IPI

Annotations to regulation of protein x-merization activity and children with evidence code ECO:0000353 (IPI)

Issue: Need manual review to possibly change to 'regulation of protein complex assembly' or a child term; alternatively, can be removed.

UniProt - 2 HGNC - 1

[vanaukenk]

TAS

Annotations to regulation of protein x-merization activity and children with evidence code ECO:0000304 (TAS)

Issue: Need manual review to possibly change to experimental evidence of 'regulation of protein complex assembly' or a child term; alternatively, can be removed.

BHF-UCL - 1 ParkinsonsUK-UCL - 1

[srengel]

SGD done.

[pfey03]

I looked at my tgrC1 GO:0090073 (positive regulation of protein homodimerization activity) has_regulation_target tgrB1

TgrB1 only homodimerizes upon interaction with TgrC1; tgrC1 homodimerizes spontanously but tgrB1 cannot homodimerize to form the kin recognition complex without tgrC1.

How would I otherwise annotate this?How in GO CAM? Thanks!

[pfey03]

OK, the second annotation I just inspected. The phosphpducin phlp1is necessary for Gbeta/gamma dimerization, or complex formation. This I could annotate to regulation of complex formation has_input X I suppose Maybe I need to think for tgrB1 also about kin recognition complex and need to rethink these with extensions and their relations. Thanks!!

[EricaBakker]

Fixed the three assigned to TAIR. The spreadsheet was read only, so could not mark this in the document.

[tberardini]

I updated the TAIR lines on the spreadsheet. Can you please add write access for @ebakker2 in the GDrive for the future? Thanks.

[vanaukenk]

@pfey03

For the TgrC1 example, would 'positive regulation of protein complex assembly' also work?

https://www.ncbi.nlm.nih.gov/pubmed/24490801

[pgaudet]

UniProt annotations fixed or disputed in P2GO.

Thanks, Pascale

[pgaudet]

@pfey03 @vanaukenk Looks like TgrC1 and TgrB1 are a complex; I think the process annotation would be wrong in this case. Remove ?

[pgaudet]

@ebakker2 please email help-at-geneontology.org to give us the email you want to use to get access to the GO google drive.

Thanks, Pascale

[pfey03]

@vanaukenk @pgaudet I was off for a couple of days. Now I looked at a few papers I annotated in the past and this is what happens: tgrC1 spontaneously binds in one cell. When it encounters a matching tgrB1 bearing cell it causes tgrB1 also to cluster. Furthermore, it was found that tgrB1 has receptor activity and tgrC1 is the ligand; tgrB1 is phosphorylated upon interaction, which could be the mechanisms that it clusters when binding tgrC1. When matching clusters bind they form a GO:0098635 'protein complex involved in cell-cell adhesion' So I deleted the annotation now but I wish I could have annotated something like: tgrC1 positively_regulates GO:0042802 'identical protein binding' has_input tgrB1 Would that be acceptable in GO-CAM? Thanks!!

[pgaudet]

I think this is valid according to the GO-CAM specs; however this is a very mechanistic description of what is happening, I would say this is more granular than what we would like to capture with GO-CAMs.

@vanaukenk @thomaspd do you want to comment ?

Thanks, Pascale

[thomaspd]

Many of the examples look like direct interactions, so in these cases we should make an MF annotation.

[pgarmiri]

All the UniProt-EBI annotations have reviewed and fixed of removed accordingly. Thanks, Penelope

[RLovering]

BHF-UCL and HGNC-UCL done

[vanaukenk]

@pfey03 I agree with @pgaudet that this sounds like a more mechanistic representation than what we have in mind for GO-CAM. I wonder, though, if you could make a causal model using the MF of 'cell adhesion receptor activity' (although I think the definition here might need to be revised to include binding to another cell adhesion molecule)? http://amigo.geneontology.org/amigo/term/GO:0004895

[pfey03]

@vanaukenk Thanks Kimberly. Maybe the def of GO:0004895 should be widened.

But this tgrB/C complex is more than cel cell adhesion, the complex determines cell-cell recognition, the binding only happens in 'fitting' partner cells - kin recognition.

These genes are annotated to the processes cell-cell recognition and socially cooperative development, but functions to describe this cell-cell recognition are not available. Maybe a new term 'cell-cell recognition receptor activity' should be created, if determined that the cell-cell recognition is a function (I think so).

Should exist in other systems I would think. Thanks!

[BarbaraCzub]

ARUK-UCL done

[BarbaraCzub]

ParkinsonsUK-UCL done