figure out what these mean "regulation of transcription factor" -> pat1-stell model

[ValWood]

regulation of DNA-binding transcription factor activity (GO:0051090)

Gene name	Systematic ID	Product
cka1	SPAC23C11.11	serine/threonine protein kinase Cka1
ckb1	SPAC1851.03	CK2 family regulatory subunit Ckb1
pmk1	SPBC119.08	MAP kinase Pmk1
rad24	SPAC8E11.02c	14-3-3 protein Rad24
taf6	SPCC16C4.18c	SAGA complex/transcription factor TFIID complex histone H4-like subunit Taf6
tpx1	SPCC576.03c	thioredoxin peroxidase Tpx1
txl1	SPBC577.08c	thioredoxin-like I protein Txl1

most of these are NOT regulating the transcription factor activity....
geneontology/go-ontology#16152

and this is a really mixed bag of random activities

[ValWood]

• taf6 GO:0051090 | regulation of DNA-binding transcription factor activity | IEA with IPR011442
  Action, filtered IPR011442 mapping.

• cka1

• ckb1
  surplus to
  GO:0004674 | protein serine/threonine kinase activity | IDA |
  has substrate rrn7 involved in negative regulation of transcription by RNA polymerase II | IDA | Moreira-Ramos S et al. (2015)

[ValWood]

• rad24
  regulation of DNA-binding transcription factor activity (GO:0051090)

ACTION: removed this and linked existing MF to BP (but in artemis, hasn't yet been through Canto)

surplus to

protein binding

  | rad24 binds transcription factor ste11 phosphorylated 1 (Schizosaccharomyces pombe) binds ste11 part_of negative regulation of transcription by RNA polymerase II
  | rad24

This annotation was quite correct based on what the papers says (inhibits ste11 activity" but they assay expression. Anyway the other annotation captures the model better at the MF level:
and sometime we will know it is cytosolic sequestration (presumably), and we can refine

[ValWood]

• tpx1, I think this acts directly on pap1 (oxidation status) if so, this should be an MF annotation?

• txl1
  has
  GO:0004791 | thioredoxin-disulfide reductase activity | has substrate pap1

need to add F-P link to

negative regulation of transcription from RNA polymerase II promoter in response to oxidative stress

and delete

negative regulation of DNA-binding transcription factor activity
  | regulates pap1 during cellular response to oxidative stress

[ValWood]

• pmk1

"positive regulation of DNA-binding transcription factor activity"

should be "positive regulation of transcription from RNA polymerase II promoter"

and F-P connection.

changed process to
GO:0045944 | positive regulation of transcription by RNA polymerase II
(existing was correct, but I think we are moving in this direction for GO that is we don't know if it acts directly, we say it regulates the process rather than the gene product).

From other papers we actually do know that pap1 directly acts on Atf1 so we will get this connection (and I kept the atf1 target anyway)

[ValWood]

@Antonialock do you agree?
I think these are old.

"regulation of DNA-binding transcription factor activity" are really a function terms masquerading as processes

[ValWood]

I will do the changes, but I'd like you to look to see if you would annotate the same?
could you look at this tomorrow should only tke 5-10 mins.

[Antonialock]

should cka1/ckb1 change to negative regulation of DNA-templated transcription, initiation ?

atf1 yes looks odd

rad24 - yes looks like it should be a function, paper is still uncurated (I think rad24 sequesters several proteins)

tpx1 - looks like paper might need reading again to overhaul GO terms. Looks a bit complicated at a glance but doesn't look like they are right. Probably same with txl1

[ValWood]

• tpx1 /tx11 is done:

[ValWood]

I'll had this over to you.

No hurry but it would be nice to capture the data in the model for pat1-ste11, and you have that one

[Antonialock]

Closed? -- Antonia Lock, PhD PomBase Biocurator, http://www.pombase.org Department of Genetics, Evolution and Environment, The Darwin Building, University College London London WC1E 6BT, UK

[ValWood]

actually, we don't really need the ticket anyway. you have the paper with the model in your list. Close?

[Antonialock]

I suppose ? -- Antonia Lock, PhD PomBase Biocurator, http://www.pombase.org Department of Genetics, Evolution and Environment, The Darwin Building, University College London London WC1E 6BT, UK

[ValWood]

your call ;)

[Antonialock]

ok close, thee are too many tickboxes spread out over multiple comments in this ticket ;)