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PomBase curation
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Add to Noctua model G2/M #2900

Open ValWood opened 3 years ago

ValWood commented 3 years ago

Summary

Screenshot 2020-11-19 at 22 58 42

WHICH PUBLICATION IS THIS FROM?

CORE or unsorted

ValWood commented 3 years ago

Environmental stress module

Screenshot 2020-11-19 at 23 01 03

Tasks

or

pending https://github.com/PROconsortium/PRoteinOntology/issues/209

ValWood commented 3 years ago

Under moderate to high concentrations of hydrogen peroxide (naturally occurring, for example, in re-sponse to glucose arrest) nuclear accumulation of Pap1 is delayed until the expression of Atf1-dependent genes promotes its conversion to the active oxidized conformation that translocates into the nucleus and enhances Pap1-dependent gene expression (Madrid et al., 2004; Vivancos et al., 2006).

ValWood commented 3 years ago

https://github.com/pombase/curation/issues/2832

ValWood commented 3 years ago

ADD the geometry network

ValWood commented 3 years ago

DNA integrity checkpoints

Add a placeholder module

also note

A number of gene products including cdc18,cdt1,orp1,cut5,pol1 (possibly ctp1) function upstream of checkpoint signalling and are required for the checkpoint to occur.

This seems to be because they generate signals to indicate that replication is still in progress, and to halt the cell cycle. They are therefore "required" for the checkpoint. But, are they part of the checkpoint, or causally upstream?

I think this hinges upon whether they are sensors, or are they generating the signal recognised by the sensors?

ValWood commented 3 years ago

Questions for Jacky

from older ticket https://github.com/pombase/curation/issues/1047

GO terms and boundaries of processes. At the LEGO meeting JAcky was concerned the the G2/M term was too broad.

but I think we need to include all of these: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3475169/

We might need a term for the central control network

Is the difference to do with timing? location? drivers vs arrest? Most of the checkpoints can occur during Interphase, and seem to result in the sequestering of cdc25 in the cytoplasm. and then, presumably to achieve full Cdk activity cdc25 must be nuclear? are the "mitotic control network" events nuclear ? OR, should your "mitotic control network" the all be annotated to the term "G2/S transition" and the things which are more 'peripheral' (checkpoints) to =ve and -ve regulation of the transition?

old comment from JAcky I think what I m trying to distinguish what has the major effect (i.e. determines the timing/rate of a process) and how we differentiate this from all the other regulation

Also see https://github.com/geneontology/go-ontology/issues/15597

How to represent nutritional stress in GO https://github.com/pombase/curation/issues/2787

ValWood commented 3 years ago

Other issues

ValWood commented 3 years ago

Indirect examples

I did not annotate this to G2/M is that correct (it's just causally upstream) https://www.pombase.org/reference/PMID:22451489

I haven't included sal3 in the regulation of the transition. I'm assuming that this just happens constitutively when cdc25 is "available" (i.e unphosphorylated)...so as soon as cdc25 is released from rad24 which sequesters in the cytoplasm sal3 will transport into the nucleus. Sal3 isn't regulating per se (it doesn't change the timing, unless it is regulated to transport cdc25 at a specific point.....there is no evidence for this?) -[ ] Does that sound correct?

more explanation https://github.com/pombase/curation/issues/1047#issuecomment-246640080

ValWood commented 3 years ago

TOR module

current

Screenshot 2020-11-21 at 12 16 03 Screenshot 2020-11-21 at 12 08 31 Screenshot 2020-11-21 at 12 06 47 Screenshot 2020-11-21 at 12 05 48
ValWood commented 3 years ago

https://user-images.githubusercontent.com/7359272/38920513-550764ea-42eb-11e8-859e-7e5591feb8d4.jpg