[go] 'regulation of gene expression'

[Karen Christie]

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
>>>>>>>>
>>>>>>>> 
>>>>>>>> ------------------------------------------------------------------------------------------ 
>>>>>> 
>>>> 
>>> 
>>> 
>> 
>