question about 'phase' terms

[gocentral]

I was wondering how the 'phase' terms are supposed to be used.

GO:0000084 S phase of mitotic cell cycle

the definition is

"Progression through S phase, the part of the mitotic cell cycle during which DNA synthesis takes place".

is this supposed to refer to regulators of progression.

For example, would you expect to see genes involved in DNA sythesis annotated to this term? or just the cell -cycle regulators of S-phase progression.

It seems like maybe the latter, and that this is supposed to be a regulation term?

If they are for 'regulators' what is the difference between

GO:0000084 S phase of mitotic cell cycle Progression through S phase, the part of the mitotic cell cycle during which DNA synthesis takes place.

and the child

GO:0007090 regulation of S phase of mitotic cell cycle

A cell cycle process that modulates the frequency, rate or extent of the progression through the S phase of mitotic cell cycle.

in terms of the genes that you would annotate to each, becasue they both sound as though they refer to 'regulation of progression'.

both of GO:0000084 child terms are regulation terms (although GO:0000115: S-phase-specific transcription in mitotic cell cycle doesn't specify this in the term, only in the definition)

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/4086":https://sourceforge.net/p/geneontology/ontology-requests/4086

[gocentral]

Logged In: YES user_id=436423 Originator: NO

huh. good question! I've been thinking of progression through x phase as including more than regulation, but I'm not really sure where to draw the line. Maybe a question for the annotation list -- see how others have actually been using the terms??

m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=546388 Originator: NO

This is a good question. One of course must have DNA synthesis; the S phase is the part of the cell cycle when DNA synthesis occurs.

Original comment by: hdrabkin

[gocentral]

Logged In: YES user_id=516865 Originator: YES

I used to concurrently annotate all DNA synthesis genes to S-phase, but during some analysis I am doing it looked odd.

These terms have always confused me. They aren't really refering to the physical processes which occur, they are referring to a period of time. Although they are defined as 'progression through'. this, and their position under 'cell cycle' makes it seem as though it should perhaps be used for the 'cell cycle regulators' rather than every gene which is involved in a process which occurs during the period referred to.

(of course some DNA replication proteins are also key cell cycle regulators, but others have no effect on cell cycle progression ....)

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=436423 Originator: NO

much work on regulation makes us think this is out of date

Original comment by: mah11

[gocentral]

• status: open --> closed-out-of-date

Original comment by: mah11

[gocentral]

• milestone: --> PomBase

Original comment by: mah11