clean up of transcriptional regulation terms: p53 signaling

[pgaudet]

Finishing off https://github.com/geneontology/go-ontology/issues/12739

There are some terms related to the p53 pathway:

GO:0006978 | DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator GO:1902163 | negative regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator GO:1902162 | regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator GO:1902164 | positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator

25 EXP, 2 extensions, no mappings see https://github.com/geneontology/go-annotation/issues/4721

[pgaudet]

Hi @raymond91125

GO:0030330 DNA damage response, signal transduction by p53 class mediator has 2 children:

• GO:0006977 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest and GO:0006978 DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator

Can you see if you find evidence that these are 2 different pathways? or are they different read outs for the same pathway?

Thanks, Pascale

[raymond91125]

PMID:26931810 There are p21-dependent and independent cell cycle arrest caused by p53.

[pgaudet]

So then should it be merged with GO:0006977 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest?

https://www.nature.com/articles/ncomms14728#:~:text=By%20inhibiting%20CDK%20activity%2C%20p21,DNA%20damage%20is%20less%20clear.

[raymond91125]

p21 does have functions other than cell cycle arrest PMID:31438587. I'm not quite sure how that would affect our decision though.

[raymond91125]

Perhaps not surprisingly, DNA damage response is broad and complex with cross talking. Per PMID:36207426, DNA damage response, signal transduction by p53 class mediator can result in cell cycle arrest (p21-dependent and independent), apoptosis (p21-independent), and cellular senescence (p21-dependent and independent). I suggest that we merge up to GO:0030330 DNA damage response, signal transduction by p53 class mediator since it has only one child after merging GO:0006978 into GO:0006977. Although the siblings of GO:0030330, GO:0000077 DNA damage checkpoint signaling, and GO:0042772 DNA damage response, signal transduction resulting in transcription, are also in part mediated by p53.

[pgaudet]

Sounds good. Thanks for looking into this!

[raymond91125]

To summarize, we shall obsolete/replace these terms:

• [ ] GO:0006978 DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator -> GO:0030330 DNA damage response, signal transduction by p53 class mediator
• [ ] GO:1902163 negative regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator -> GO:0043518 negative regulation of DNA damage response, signal transduction by p53 class mediator
• [ ] GO:1902162 negulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator -> GO:0043516 regulation of DNA damage response, signal transduction by p53 class mediator
• [ ] GO:1902164 positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator -> GO:0043517 positive regulation of DNA damage response, signal transduction by p53 class mediator
• [ ] GO:0006977 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest -> GO:0030330 DNA damage response, signal transduction by p53 class mediator