[go] 'regulation of gene expression'

[Jane Lomax]

The suggested definition for gene expression from the SF item is:

"The processes by which a gene's coding sequence is converted into a
mature gene product or products (proteins or RNA). This includes the
production of an RNA transcript as well as any processing to produce a
mature RNA product or an mRNA (for protein-coding genes) and the
translation of that mRNA into protein. Some protein processing events may
be included when they are required to form an active form of a product 
from an inactive precursor form."

Jane


On Mon, 13 Aug 2007, Harold Drabkin wrote:

> I didn't mean for my comments to take us too far off the topic of introducing 
> the "regulation of gene expression" term, other than to raise thoughts about 
> some logical consequences or questions that might pop up when one sees a gene 
> product annotated to "regulation of gene expression" (namely, WHICH gene).
>
> I think other questions that the term may raise  will be dependent upon what 
> we define as "gene expression", and how one assays that expression
> Expression:
> Transcription.... ok
> translation.... ok
> gene_product activity.... ?? So, if protein x blocks the phosphorylation of 
> protein Y, which if phosphorylated, has kinase activity, it X involved in the 
> expression of the Y gene??  ; I wouldn't think so (Y is expressed just fine; 
> but Y's activity has been blocked).
>
> So, if one measures expression at the transcription level (RT-PCR, Northern, 
> etc.), translation level (protein immuniP, etc,), or activity level (enzyme 
> assay) one may get very different pictures
>
> So will gene expression be defined as anything that effects the "functional 
> presence" of the gene product?
>
>
> hjd
>
>
> Michelle Gwinn Giglio wrote:
>> 
>> 
>> Hi all,
>> 
>> I agree with Karen that "with" is not the place for this.
>> 
>> I also want to point out that we discussed a closely related topic of 
>> capturing "targets" at the St. Croix meeting in reference to some needs 
>> from the PAMGO group who wished to link the GO terms for various protein 
>> secretion systems to the proteins that they secrete - this is currently not 
>> allowed in GO annotation policy.  In that discussion also came up the 
>> possibility of capturing enzyme substrates.  We suggested an "acted_upon" 
>> qualifer or something else along those lines. See page 48 of the St. Crox 
>> minutes.
>> 
>> Then at the Cambrige meeting I seem to recall that David and Chris had 
>> started work on a new format for the association file that would allow the 
>> capture of this kind of information on the "slots" model.  And I remember 
>> asking David about the "acted_upon" issue being solved by this and he 
>> confirmed it would be.  But I can't find anything about that in the meeting 
>> notes.
>> 
>> I am all for capturing the information - I think it is important.  But just 
>> finding a good way is the issue.
>> 
>> Michelle
>> 
>> 
>> 
>

Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

p: +44 1223 492516
f: +44 1223 494468