NTR/MP regulation term (under txn)/community submission

[gocentral]

Could I have a term, negative regulation of GO:0000083 regulation of transcription involved in G1/S-phase of mitotic cell cycle standard aprents and defs.

Also, it seems that the term GO:0000083 regulation of transcription involved in G1/S-phase of mitotic cell cycle MUST be gene specific, and mitotic and so, should have the parents:

1. regulation of gene specific transcription from RNA polymerase II promoter
2. regulation of transcription form RNA polymerase II promoter, mitotic

(and the new neg reg term above would aklso need the -ve reg parernts)

v

(note to self yox1)

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/6849

[gocentral]

• summary: NTR/MP regulation term (under txn) --> NTR/MP regulation term (under txn)/community submission

Original comment by: ValWood

[gocentral]

should:

I GO:0000083 regulation of transcription involved in G1/S-phase of mitotic cell cycle I GO:0000114 regulation of transcription involved in G1 phase of mitotic cell cycle I GO:0000115 regulation of transcription involved in S-phase of mitotic cell cycle I GO:0000116 regulation of transcription involved in G2-phase of mitotic cell cycle I GO:0000117 regulation of transcription involved in G2/M-phase of mitotic cell cycle

also be children of: O:0046021 regulation of transcription from RNA polymerase II promoter, mitotic?

Original comment by: ValWood

[gocentral]

note to self remove IC to gene-specific transcription from RNA polymerase II promoter for nrm1 etc

Original comment by: ValWood

[gocentral]

• assigned_to: nobody --> tairtb

Original comment by: mah11

[gocentral]

Relevant comments from duplicate item (now closed): https://sourceforge.net/tracker/?func=detail&aid=2934951&group\_id=36855&atid=440764

Val:

GO:0000083 regulation of transcription involved in G1/S-phase of mitotic cell cycle

also please can these have the appropriate gene sepcific transcription from RNA pol II terms as parents

Jim Hu: This seems overly specific for GO to me.

Val: Maybe, but all of the other phase transcription terms exist.....and this particular one has been in GO since almost the beginning judging by the accession 0000083

They are useful terms to capture the gene products encoding controlling the various gene sets during the cell cycle. I imagine that eventually these types of annotations can be moved to column 16 annotations.....

Original comment by: tberardini

[gocentral]

Hi Tanya,

Can I get this term? (I'm cleaning out my log file)

Original comment by: ValWood

[gocentral]

i agree with Jim that these types of terms seem way too specific. i am not a fan of them at all. if all of the other phase transcription terms exist, then perhaps they should all be removed.

stacia

Original comment by: srengel

[gocentral]

I know this probably isn't ideal but it is useful information to capture. Downstream maybe it will be better as a cross-product between the transcrption process and the phase process, but this would in effect be equivalent to the composed term, and I don't have the capability to implement cross-products at annotation time right now..

In addition, this term was actually suggested by the author of the paper during community curation, so clearly a user think it useful to capture this information. Groups studying the transcriptional program do refer to the transcriptional waves via the phases they regulate. This gene and MBF specifically control the wave of transcription at G1/s. I can't think of any other way to do this.

My only other option would be to capture this with free text which would be impractical if the term is within the scope of GO

Original comment by: ValWood

[gocentral]

Could you both qualify what your objection is? is there something else apart from specificity?

thanks

Val

Original comment by: ValWood

[gocentral]

Just for the record, The title of the paper was he fission yeast homeodomain protein Yox1p binds to MBF and confines MBF-dependent cell-cycle transcription to G1-S via negative feedback.

and the first line is The regulation of the G1- to S-phase transition is critical for cell-cycle progression.

I think it is useful to capture the transcription which control the periodic waves of transcription in GO in this way......

Original comment by: ValWood

[gocentral]

Hi Stacia,

Do Val's additional comments affect your objections to the additions of this term (and the retention of the other existing similar ones) at all?

Thanks,

Tanya

Original comment by: tberardini

[gocentral]

Based on:

> Hi Val, > > I looked at the paper from which the 'DNA synthesis' annotation > came. I have removed that annotation, and replaced it with two > transcription-related annotations: > > - negative regulation of gene-specific transcription from RNA > polymerase II promoter > - regulation of transcription involved in G1/S-phase of mitotic cell > cycle > > These terms seem much more appropriate based on the evidence in the > paper. The changes will be visible online tomorrow. > > thanks, > stacia

As we are finding these terms useful, I think we are justified in having these terms, at least for now (also this seems to be the way the regulation group discussion is going). It may be at some point in the future these are done differently (i.e by cross products), at least this way we can capture the information and find it later.

VAl

Original comment by: ValWood

[gocentral]

Stacia, you may be able to use the new term instead of these 2 below? (would provide more information and less redundancy)

Tanya, maybe the term name should say regulation of gene-specific transcription involved in G1/S-phase of mitotic cell cycle?

Val

Original comment by: ValWood

[gocentral]

hi Val, no, i could not use the new term. i used the two separate terms on purpose.

these are specifically two different processes for this gene. it's (1) a repressor of gene-specific transcription from RNA polymerase II promoter that is not related to cell cycle, and (2) a regulator of periodic genes involved in G1/S-phase of mitotic cell cycle.

we have to be very careful about making assumptions about genes merely from glancing at their accumulated annotations without actually looking at the papers.

stacia

Original comment by: srengel

[gocentral]

so should it be postve regulation of of transcription involved in G1/S-phase of mitotic cell cycle? (the pombe subunit member is),

it is the gene above (Yox1) which has been identified as a negative regulator of MBF same as YOX1/ YML027W

Original comment by: ValWood

[gocentral]

the paper in question showed both positive and negative.

Original comment by: srengel

[gocentral]

This can be closed, out of date

Original comment by: ValWood

[gocentral]

• status: open --> closed

Original comment by: ValWood

[gocentral]

• milestone: --> PomBase

Original comment by: mah11