[go] 'regulation of gene expression'

[Harold Drabkin]

I think "directly regulates" may be worse.
It would have to be VERY restrictive

eg, mutation in gene_product x results in increased appearance of 
gene_product y.
Is X involved in the regulation of the  expression of gene Y?  That is 
the question.

How might X directly regulate the expression of Y? Is X a transcription 
factor? Is X a specific protease? Does X actually work on A, and A then 
works on B, and B then works on Y?

It is the same problem as the "biosynthesis" terms.

what is meant by "gene expression"? transcription? translation of an 
mRNA? turnover of the mRNA or of the protein?
very fuzzy
I can also see that the term would invoke requestions for "expression of 
X" and "expression of Y", like the biosynthesis terms did.

Perhaps if used, one needs to restrict the evidence code used with it to 
IEP and perhaps also allow a With field dbx ref for a gene_id if known 
or suspected


-Harold

Chris Mungall wrote:
>
> I agree with Karen -
>
> I sympathise with Harold's concerns. I wonder if the problem here may 
> be with "regulation". What if, say, the definition was changed to 
> "directly regulates". I don't have a clear answer yet for how we 
> should determine direct vs indirect. But it seems this may go some way 
> to addressing Harold's concerns. This is something we have to tackle 
> anyway for the "regulates" relation.
>
> In addition, we could have computable rules such as "IMP evidence for 
> regulation of gene expression is suspect".
>
> On Aug 9, 2007, at 12:42 PM, Karen Christie wrote:
>
>>
>>
>> I agree with you Harold that 'gene expression' isn't tremendously 
>> informative as a GO annotation, but then I don't think that 'cell' is 
>> particularly meaningful as a GO annotation either and we already have 
>> that term. However, I don't think usefulness in annotation is the 
>> only consideration for whether or not to add the term.
>>
>> I am in favor of adding this term because I think it does increase 
>> the accuracy of GO's representation of the biology.
>>
>> In addition, if I remember correctly from earlier discussions, it was 
>> also PATO people who wanted this term, and I can see that if PATO is 
>> leveraging off of GO to describe phenotypes, that it may be 
>> meaningful to say that a mutation of gene X affects the 'gene 
>> expression' of gene Y in a way that is broad enough that it does not 
>> specify how this is occurring.
>>
>> -Karen
>>
>>
>> On Tue, 7 Aug 2007, Harold Drabkin wrote:
>>
>>> IMHO, no;
>>> Some "experiments" do not give real information other than to help 
>>> you design what experiments will.
>>> Again, I am signing off on this with grave reservations.
>>>
>>> hjd
>>>
>>> Pascale Gaudet wrote:
>>>> But isn't it already more information than annotating to the root 
>>>> term?
>>>> Harold Drabkin wrote:
>>>>> Moi???
>>>>> Well; my feeling hasn't changed but everyone else thinks it's a 
>>>>> meaningful term. I like it a bit better than the " biosynthesis  
>>>>> of" terms. I still feel it doesn't say much if you say gene 
>>>>> product x is involved in the regulation of gene expression  based 
>>>>> on an observation that doing something to x causes the levels of 
>>>>> other gene products to change, without knowing actually what is 
>>>>> happening. Still seems like to me like making a term to use for 
>>>>> incomplete or ill-defined experiments. Just my take.
>>>>> hjd
>>>>> Jane Lomax wrote:
>>>>>> Actually, I was just waiting for Harold's blessing on this item...
>>>>>> Jane
>>>>>> Midori Harris wrote:
>>>>>>> So did I! I think what happened is simply that the SF item is 
>>>>>>> assigned to Jane, and she's been so busy with various2go 
>>>>>>> mappings and advocacy stuff that she hasn't had a chance to work 
>>>>>>> on her other SF things.
>>>>>>> m
>>>>>>> On Mon, 6 Aug 2007, David Hill wrote:
>>>>>>>> I thought it was going to be implemented.
>>>>>>>> David
>>>>>>>> Karen Christie wrote:
>>>>>>>>> Hi Tanya,
>>>>>>>>> There seems to be a stalled SF item on this topic:
>>>>>>>>> [ 1418820 ] gene expression
>>>>>>>>> https://sourceforge.net/tracker/index.php?func=detail&aid=1418820&group_id=36855&atid=440764 
>>>>>>>>> -Karen
>>>>>>>>> On Mon, 6 Aug 2007, Tanya Berardini wrote:
>>>>>>>>>> A (long) while back, we'd talked about having a term for 
>>>>>>>>>> 'regulation of gene expression'.  I've been searching the 
>>>>>>>>>> email archives without much luck hoping to find out what 
>>>>>>>>>> happened with respect to that item. The last I found was an 
>>>>>>>>>> action item from the Sept. 2002 (!) meeting.
>>>>>>>>>> Collective memory, please help out!
>>>>>>>>>> Thanks,
>>>>>>>>>> Tanya
>>>>>>>>>>
>>>>>>>>>> ------------------------------------------------------------------------------------------ 
>>>>>>>>>> Tanya Berardini, Ph.D.            tberardi at acoma.stanford.edu
>>>>>>>>>> The Arabidopsis Information Resource    FAX: (650) 325-6857
>>>>>>>>>> Carnegie Institution of Washington    Tel: (650) 325-1521 
>>>>>>>>>> ext. 325
>>>>>>>>>> Department of Plant Biology        URL: http://arabidopsis.org/
>>>>>>>>>> 260 Panama St.
>>>>>>>>>> Stanford, CA 94305
>>>>>>>>>>
>>>>>>>>>> ------------------------------------------------------------------------------------------ 
>>>>>>>>>>
>>>
>>
>