Review annotations to histone modification BPs

[pgaudet]

Hi,

Histone modification BPs will be moved to MFs in the BP refactoring project.

Annotations are here: https://docs.google.com/spreadsheets/d/1LJTu3sZjwH7u3sD65KXf_e-l3A85cRKpeiYh2DVsRgg/edit#gid=1052081963

Enzymes We have started on the Annotation Call with the subset of 623 annotations to genes that fall in Panther families also annotated to some Enzyme MF (https://docs.google.com/spreadsheets/d/1LJTu3sZjwH7u3sD65KXf_e-l3A85cRKpeiYh2DVsRgg/edit#gid=909564179). These should be easier to either move to a MF or remove because they are redundant or incorrect. Remaining as of Aug 23

• ARUK-UCL 2
• BHF-UCL 9
• CACAO 17
• CAFA 1
• CGD 5
• ComplexPortal 17
• dictyBase 4
• FlyBase 108
• HGNC 3
• HGNC-UCL 2
• MGI 95
• PomBase 3
• RGD 9
• SGD 48
• UniProt 35
• WB 42
• ZFIN 24

dbTFs https://docs.google.com/spreadsheets/d/1LJTu3sZjwH7u3sD65KXf_e-l3A85cRKpeiYh2DVsRgg/edit#gid=1054149290 Likely to be incorrect; often some histone modifications are used as a mark for transcriptionally active chromatin.

• ARUK-UCL 3
• BHF-UCL 39
• CACAO 6
• CAFA 3
• CGD 2
• ComplexPortal 93
• FlyBase 71
• MGI 70
• RGD 2
• SGD 61
• UniProt 166
• WB 18
• ZFIN 6

coTFs https://docs.google.com/spreadsheets/d/1LJTu3sZjwH7u3sD65KXf_e-l3A85cRKpeiYh2DVsRgg/edit#gid=2078460474 Could be enzymes (lots of overlap); but in some cases, histone modifications are used as a mark for transcriptionally active chromatin.

• CACAO: 1
• ComplexPortal 22
• FlyBase 1
• SGD 2
• UniProt 8

[pgaudet]

The categories above only covers some of the annotations to be reviewed, but this is a good place to start.

[pgaudet]

@Antonialock (too many assigned, I could not assign you)

[srengel]

SGD done. a lot of the annotations in the spreadsheets for us had already been deleted back in April. are the spreadsheets old? just letting you know in case there is an issue where the annotations were obtained.

[hdrabkin]

@pgaudet where is the link to the list of new MFs you made? Can't find

[pgaudet]

https://wiki.geneontology.org/Annotation_Conf._Call_2022-08-16#Histone_modifications

Note that this is not comprehensive

[hattrill]

FlyBase done

[RLovering]

Hi

sorry to mave missed these discussion, I am happy to do the required changes but it would be helpful to have the link to the ontology discussion. https://docs.google.com/presentation/d/15fDBhmO54zSJms25aV5nX3kgSwsHMnWgdSuPdo-ukyw/edit#slide=id.gf4888089cb_0_0 Or is there a a page of guidance eg for proteins that bind to and regulate the activity of the histone modifying enzymes do we annotate as:

• regulating histone modification
• or as a histone..... activator/inhibitor
• and/or regulation of transcription

Thanks

Ruth

[Antonialock]

uniprot done for enzymes

[pfey03]

Dicty is done with the 4 annotations

[sandraorchard]

Complex Portal done (I think - hopefully didn't miss any). Curated at source so you'll have to wait for the next COmplex Portal release/data import to go through the system.

[marekskrzypek]

CGD done

[lreiser]

TAIR is done..

[Antonialock]

all sub-spreadsheets done for uniprot, would be good to regenerate the table to see what is left...

[lreiser]

TAIR done

[hattrill]

fb done

[jlewsmith]

CGD done

[gthayman]

RGD done.

[dsiegele]

CACAO is done. Except for two annotations that I couldn't find on Protein2GO, the CACAO annotations listed in the spreadsheet have been removed from Protein2GO. I may have removed the two missing annotations and forgotten to mark in the spreadsheet.

[pgaudet]

Thanks @dsiegele Just FYI, these annotations were in the 'Deleted' section in P2GO, so all CACAO annotations have been addressed.

Thanks, Pascale

[Antonialock]

uniprot done

[srengel]

SGD done.

[pgaudet]

@jlewsmith Can you please check PMID:36715154 - 3 annotations to regulation of histone acetylation; I think these can be changed to 'GO:0045815 transcriptional initiation-coupled chromatin remodeling'

Thanks, Pascale

[jlewsmith]

Hi Pascale,

I only found 2 annotations - but they've both been amended.

Best, Jodi

---

From: pgaudet @.> Sent: Wednesday, May 10, 2023 3:00 AM To: geneontology/go-annotation @.> Cc: Jodi Lew-Smith @.>; Mention @.> Subject: Re: [geneontology/go-annotation] Review annotations to histone modification BPs (Issue #4261)

@jlewsmithhttps://github.com/jlewsmith Can you please check PMID:36715154 - 3 annotations to regulation of histone acetylation; I think these can be changed to 'GO:0045815 transcriptional initiation-coupled chromatin remodeling'

Thanks, Pascale

— Reply to this email directly, view it on GitHubhttps://github.com/geneontology/go-annotation/issues/4261#issuecomment-1541454508, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AWBKZHLSILSW5FFXOJCVKO3XFM4JBANCNFSM57LR4GHQ. You are receiving this because you were mentioned.Message ID: @.***>

[pgaudet]

Hi @sandraorchard

There are about 50 annotations to PMID:18206972, that could probably be moved to 'GO:0045815 transcription initiation-coupled chromatin remodeling' - just wondering if that one was done and not yet in GO Central.

Thanks, Pascale

[sandraorchard]

They should be - desperately waiting for the release to be fixed so I can work out what I have done, and what still needs doing. Apologies Sandra

[pgaudet]

no worries!! It was just odd that a single paper was left. Thanks for checking.

[pgaudet]

Current status according to the spreadsheet:

Group	Number of EXP
GeneDB	23
MGI	33
SGD	1
WB	37

[srengel]

SGD done.