[go] 'regulation of gene expression'

[Harold Drabkin]

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
>
>
>