[go] Re: regulation of cell cycle vs. regulation of progression through cell cycle

[Eurie Hong]

I have a couple of questions -

Are the "regulation of cell cycle" and "regulation of progression  
through cell cycle" going to be specific for just regulating the rate  
at which the progression through the cell cycle occurs?  Then maybe  
they should be renamed "regulation of cell cycle phase" (cell cycle  
phase is GO:0022403)?

Or do we need to keep the structure of the regulation terms to mimic  
how the cell cycle branch is organized?

"regulation of cell cycle" - general grouping term for both molecular/ 
cellular events and temporal phasing
-- "regulation of cell cycle processes" - grouping term for all the  
regulation of processes
---- "regulation of cell cycle phase" - specific for going through  
the temporal phases

The mitotic - meiotic switch terms sound ok.  As long as there are  
synonyms to find them - most folks in the field do refer to "entry  
into meiosis" but there are positive and negative regulators of the  
process.

On Dec 6, 2007, at 6:25 AM, Valerie Wood wrote:

> Hi Tanya,
>
> Sorry for the delay.
>
> At first glance, I think that what you propsed is OK. You are  
> correct that the seperate terms were created to cope with the  
> switching between mitotic and meiotic cell-cycles, but your  
> solution of making these positive and negative regulatory terms  
> respectively seems logically consistant.
>
> I think however, there is a more fundamental problem in this  
> portion of the graph in that there is some confusion between  the  
> concurrent use of meiosis to describe 'meiotic division' and  
> meiosis as a 'developmental stage'
>
> I'm not sure if the terms created to cope with the switching  
> between mitotic and meiotic cell-cycles rather refer to a switch  
> between developmental stage
> for example "entry into meiosis" for yeast would include response  
> to pheromone, and conjugation etc, and gene products annotated to  
> these terms would not necessarily be considered be a 'cell-cycle '  
> genes.
>
> current child terms of "meiosis"  also include
> megasporogenesis (synonym megaspore development ) and these terms  
> do not appear to be referring specifically to meiosis as a cell  
> cycle process.
>
> This is essentially what I was trying to describe in
> SF 1831804 ] yeast meiotic development.
>
> Even some of the definitions of these terms seem to merge both  
> concepts into a single term.
>
> It might make sense to tackle both issues at the same time. I'm not  
> sure what the solution is....
>
> Val
>
>
>
>
> Tanya Berardini wrote:
>
>> Dear GO Consortium,
>>
>> As part of the 'regulates' project, we have come across a set of  
>> terms
>> in the cell cycle portion of the graph that seem problematic. We are
>> writing because we know that a lot of previous work has gone into  
>> this
>> part of the graph and want to be sure that our plan makes sense.  
>> We have
>> two sets of terms similar to these:
>>
>> term: regulation of cell cycle (simple term)
>> def:A cell cycle process that modulates the rate, extent or mode  
>> of the
>> cell cycle.
>>
>> term: regulation of progression through cell cycle (progression term)
>> def: Any process that modulates the rate or extent of progression
>> through the cell cycle.
>>
>> Our question is how does 'regulation of progression through cell  
>> cycle'
>> differ from 'regulation of cell cycle'?
>>
>> Note that 'cell cycle' itself is defined as "the progression  
>> of ...phases and events ...", implying that regulation of the cell  
>> cycle is regulation of progression through the cycle; the same  
>> holds for the types of cell cycle (i.e. its is_a children).
>>
>> cell cycle: The progression of biochemical and morphological  
>> phases and
>> events that occur in a cell during successive cell replication or
>> nuclear replication events. Canonically, the cell cycle comprises the
>> replication and segregation of genetic material followed by the  
>> division
>> of the cell, but in endocycles or syncytial cells nuclear  
>> replication or
>> nuclear division may not be followed by cell division.
>>
>> If they are indeed describing the same processes, the 'regulation  
>> of %'
>> and 'regulation of progression of %' terms should be merged. If not,
>> then we need to create a bona-fide biological process called
>> 'progression through cell cycle' and we need to differentiate that  
>> from
>> 'cell cycle' with a really good definition. Currently the progression
>> terms are only used in conjunction with regulation.
>>
>> The way we represent these in the graph is also inconsistent. An  
>> example
>> follows:
>>
>> Case 1: No direct link between the 'regulation of progression through
>> cell cycle' term and 'cell cycle' term exists.
>>
>> regulation of cell cycle
>> --[i]regulation of progression through cell cycle
>>
>>
>> Case 2: Direct link between 'regulation of progression through  
>> meiotic
>> cell cycle' and 'meiotic cell cycle' exists.
>>
>> regulation of meiotic cell cycle
>> --[i]regulation of progression through meiotic cell cycle
>>
>> meiotic cell cycle
>> --[p]regulation of progression through meiotic cell cycle
>>
>>
>> We propose:
>>
>> 1) Merging the 'regulation of progression through' terms
>> with their simpler parents when they exist.
>>
>> 2) Renaming the 'regulation of progression through' terms to their
>> simpler forms when the simpler parents do not exist since the parent
>> non-regulates terms are already defined as the progression of...
>>
>> 3) Moving 'cell cycle switching, meiotic to mitotic cell cycle' to
>> become an is_a 'negative regulation of meiotic cell cycle' and an  
>> is_a
>> 'positive regulation of mitotic cell cycle'.
>>
>> 4) Moving 'cell cycle switching, mitotic to meiotic cell cycle'
>> to be an is_a 'positive regulation of meiotic cell cycle' and an is_a
>> 'negative regulation of mitotic cell cycle'. We think that the  
>> last two
>> terms were why 'regulation of cell cycle' and 'regulation of  
>> progression through cell cycle' were originally created as  
>> distinct terms. However, the movement of these as in 3 and 4 makes  
>> more logical sense since the process they describe stops  
>> (negatively regulates) one type of cell cycle and initiates  
>> (positively regulates)
>> another.
>>