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Merge terms under 'GO:0000991 transcription factor activity, core RNA polymerase II binding' and children #15798
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@krchristie @ValWood @RLovering @srengel Can you please have a look before I implement ? Thanks, Pascale |
Isn't that merging a more general term into a specific child? Are we sure all GO:0000990 annotations were meant to be for RNAPII? |
A quick glance at the FlyBase ones, I can see that they were probably made in a slightly different spirit - more aimed at capturing that they are regulating transcription but not DNA-binding TFs, I think. Will need a bit of time to review and re-house. |
1 and suggest using protein binding terms instead if appropriate, but also checking that they have the correct "general transcription initiation factor activity" or "cofactor activity" (since this is what most seem to be? If we move them now we will probably need to move them again later. Better to just get them to their final home? 2 GO:0000993 RNA polymerase II core binding Again, do we need this term. Why not just "protein binding" if demonstrated with the
but again, I think it is confusing to have both the "general/cofactor" term AND a RNA polymerase or TF binding term to describe the same activities. This is why we all got confused in the first place..... Personally I would obsolete or merge the binding branch into the cognate term in the non binding branch.... |
so I just moved all of these this week to GO:0000995 as the new “general RNA polymerase III transcription factor activity” pending the name change. but here you are saying I think we need the “GO:0000995 general RNA polymerase III transcription factor activity” |
So, I thought we would be getting rid of "transcription factor binding" terms and try to just use the simplified terms relating to your schema ? But if you can unambigously map to the other branch, that would be useful? |
Arghh I'm so confused ;!!! ;) |
yes, I checked. |
@ValWood I corrected geneontology/go-annotation#1734 |
This is done, it should trickle through shortly. |
You are right about the final home. For sure that protein binding branch is not really a solution. First: we don't have a term 'transcription factor activity', so it's really odd to have a precision on that.
So if we want to describe what types of protein a protein binds to, it should be to one of the 3. So anyways these will need to be reviewed (this is why I wanted to 'park' them there for now). I don't know if all the proteins in that list (see Google doc above) can have a home now. I think we're missing the elongation factor. (I can rescue that from the obsoletes). Can you spot anything else missing ? Thanks, Pascale |
I'm still confused GO:0000995 transcription factor activity, core RNA polymerase III binding -> merge into GO:0000994 RNA polymerase III core binding (5 manual annotations, excluding ISS) pombase but yesterday: Which term do I need (ID) for |
Hi @ValWood so the merge I propose above is irrelevant. Thanks for picking that up ! Pascale |
@pgaudet Wr the general pol II transcription initiation factors, though: |
@ValWood |
Did I say 28? |
I see 251 in QuickGO... |
For GO:0008134 transcription factor binding ? I see 943 EXP in QuickGO - and still 797 in AmiGO |
Hi Pascale I think merging would be great as this will reduce the our annotation workload. However, I also think that as suggested getting the transcription regulator terms available so that people can try to create additional GO terms based on the transcriptional activities would be great, so that people can go through the spreadsheet. Ruth |
should (and repressor term) https://www.ebi.ac.uk/QuickGO/term/GO:0003713 It seems to fit the definition? (Rather than the binding term?, or is this for something else? |
For example Rep2, is a co-activator for MBF transcription factor complex with the current proposal there is a loss of repressor/activator specificty |
@ValWood how are you trying to annotate Rep2? |
Actually it isn't a coactivator, it's part of a DNA binding TF complex but it also binds to another RNA pol II TF as part of the complex. I'm not so bothered about the binding term (we'll capture that with protein binding) GO ahead with the merge , but when I finish I don't plan to have anything annotated to |
Annotation guidelines presented at today's annotation call are here: |
This ticket is replaced by #16053
GO:0000989 transcription factor activity, transcription factor binding -> merge into GO:0008134 transcription factor binding (28 manual annotations, excluding ISS)
BHF-UCL
MGI
SGDUniProt
GO:0000990 transcription factor activity, core RNA polymerase binding -> merge into GO:0000993 RNA polymerase II core binding (21 manual annotations, excluding ISS)
CACAO, CAFA, FlyBase,
SGDGO:0000991 transcription factor activity, core RNA polymerase II binding -> merge into GO:0000993 RNA polymerase II core binding (26 manual annotations, excluding ISS) pombase
SGDGO:0000995 transcription factor activity, core RNA polymerase III binding -> merge into GO:0000994 RNA polymerase III core binding (5 manual annotations, excluding ISS) pombaseGO:0001076 transcription factor activity, RNA polymerase II transcription factor binding -> merge into GO:0001085 RNA polymerase II transcription factor binding (19 manual annotations, excluding ISS)
BHF-UCL
ComplexPortal
MGI
ParkinsonsUK-UCL
SGD
TAIR
UniProt
WB
GO:0001132 RNA polymerase II transcription factor activity, TBP-class protein binding -> merge into GO:0017025 TBP-class protein binding (6 manual annotations, excluding ISS) SGD
GO:0001181 transcription factor activity, core RNA polymerase I binding -> merge into GO:0001042 core RNA polymerase I binding (9 manual annotations, excluding ISS) SGD
GO:0001190 transcriptional activator activity, RNA polymerase II transcription factor binding -> merge into GO:0001085 RNA polymerase II transcription factor binding
BHF-UCL
CAFA
MGI
PomBase
SGD
TAIR
WB
GO:0001191 transcriptional repressor activity, RNA polymerase II transcription factor binding (44 manual annotations, excluding ISS)
-> merge into GO:0001085 RNA polymerase II transcription factor binding
BHF-UCL
CAFA
ComplexPortal
FlyBase
MGI
SGD
UniProt
GO:0038049 | transcription factor activity, ligand-activated RNA polymerase II transcription factor binding -> merge into GO:0035257 nuclear hormone receptor binding (1 manual annotations, excluding ISS) UniProt
Manual (non-ISS) annotations are here:
https://docs.google.com/spreadsheets/d/1Apv6MiftFCXKHKHVY_ebkZG8PH49PL1HlPsAFW-8LK4/edit#gid=0
There is no action needed if we merge, this is just to check that the merge is OK.
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