cell cycle regulation (sorry)

[gocentral]

I think we may have a (small) problem with some of the cell cycle regulates rearrangement.

Previously we had a term for 'progression through cell cycle'

this excluded the cell cycle arrest terms which refer to halting the cell cycle and switching to a differrnt mode of growth

for me this affects in the current implementation cell cycle arrest in response to pheromone cell cycle arrest in response to nitrogen starvation

which are both related to the transition between mitotic and meiotic growth, and are not generally considered to be 'cell cycle regulators' in the way which the previos terms annotated to

the 'progression of cell cycle'

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/4774":https://sourceforge.net/p/geneontology/ontology-requests/4774

[gocentral]

• labels: --> Other term-related request
• assigned_to: nobody --> tairtb

Original comment by: mah11

[gocentral]

Logged In: YES user_id=579762 Originator: NO

We propose that we rework the relationships of the 'cell cycle arrest in response to %' terms so that it is clear that they not only are related to cell cycle arrest but also to cell cycle switching.

How about something like this:

cell cycle switching, mitotic to meiotic cell cycle --[i]mitotic to meiotic cell cycle switching in response to pheromone ; GO:new1 -----[p]cell cycle arrest in response to pheromone --[i]mitotic to meiotic cell cycle switching in response to nitrogen starvation ; GO:new2 -----[p]cell cycle arrest in response to nitrogen starvation

(retain existing parentage to 'cell cycle arrest')

This will work only if what you say above is always true. When cell cycle arrest in response to pheromone occurs, it always has to be a part of this switch. Same goes for cell cycle arrest in response to nitrogen starvation. The cell cycle arrest terms should still be is_a cell cycle arrest. Since these processes stop the cell cycle, we cannot see how they are not, in fact, regulation of cell cycle children.

Tanya and David

Original comment by: tberardini

[gocentral]

Logged In: YES user_id=516865 Originator: YES

Cell cycle arrest in response to nitrogen starvation is not always part of the mitotic/meitic switch, this is dependent on the presence of cells of the opposite mating type. Can also result in G0 (stationary phase).

My problem was that the progression terms, as I understood them, referred specifically to canonical regulators of cell cycle progression (i.e. between G1/S/G2 and M) and did not include switching between cell cycles, which is a much broader type of cell cycle regulation.). Although it might be that this is OK. I will get a cell cycle expert to check my annotations shortly. If I have any issues I can probably solve them by getting a new, more specific child term.

(The switching between cell cycles includes lots of things like pheromone receptors

Since the merge, of progression with general regulation we now have no way to distinguish these regulators which the cell cycle community would consider to be 'call cycle regulators' they are now all lumped together with lots of other stuff.

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=631592 Originator: NO

Hi Val,

OK, so we've thought about this. It seems like what you need is a term called 'regulation of cell cycle switching', 'regulation of cell cycle switching, mitotic to meiotic'. We could create this. Then we could make a parent of this called 'regulation of cell cycle process'. We could then group all the regulation terms that are currently under the cell cycle as children of this. This would be similar to having a term like 'cell cycle regulator', which is an obsolete molecular function term. We would have to check, but we may be able to make 'cell cycle regulator' a related synonym to the new term. How's that???

David & Tanya

Original comment by: ukemi

[gocentral]

Logged In: YES user_id=516865 Originator: YES

I'm not sure. I might still have the same problem because it seems like the terms

'regulation of cell cycle switching'

would not necessarily be cell cycle regulators.

You could, for example potentially annotate a transcription factor which switched on the genes involved in the mitotic/meiotic switch to 'regulation of cell cycle switching', and this would then be annotateed to 'regulation of cell cycle process' but this would not be considered a canonical cell cycle regulator.

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=579762 Originator: NO

Hi Val,

Yes, it's Sourceforge Friday!

Perhaps the problem stems from the parentage of 'cell cycle arrest.' What if we moved 'cell cycle arrest' to be is_a 'cell cycle process' and NOT 'negative regulation of cell cycle'? This would mean that the arrest is an active process in and of itself and not a regulatory process.

If you mentally edit out 'cell cycle arrest' from the current children of 'regulation of cell cycle,' would annotations to the remaining children make sense?

T & D

Original comment by: tberardini

[gocentral]

Logged In: YES user_id=516865 Originator: YES

I think that works Val

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=579762 Originator: NO

DONE!!!!

Original comment by: tberardini

[gocentral]

• status: open --> closed-fixed

Original comment by: tberardini

[gocentral]

• milestone: --> PomBase

Original comment by: mah11