[go] 'regulation of gene expression'

[Karen Christie]

Commenting on a number of points that have been raised.

I don't think that it is reasonable to implement a restriction on which 
evidence codes can be used for a specific term. We have never done this 
for any other high level terms, many of which are equally uninformative if 
used as a GO annotation. We have always said that the granularity of the 
annotation reflects the state of knowledge and that annotations to high 
level terms generally mean that not much is known. So, I don't think we 
should implement any restrictions just for this term.

As for using the with column, I completely agree with Emily that this is 
NOT the place to put target information. At the St. Croix GO meeting we 
spent quite a lot of time discussing appropriate contents of the with 
field to make sure that it was consistently being used for things which 
are supporting evidence for how the annotation was made.

At the Cambridge Jan '07 meeting, we did discuss adding a column which 
would allow annotators to put info equivalent to MGI's structured notes 
into the annotation. If I remember correctly, a couple people were 
supposed to look into how to format this to allow flexibility, however I 
wasn't one of them so I have no idea about progress on this issue.

-Karen



On Fri, 10 Aug 2007, Jim Hu wrote:

> I'm relatively new to the group, but I think the term is useful if and only 
> if the target (direct or indirect) is specified.  From the pov of  an 
> experimentalist, I'd like to mine the annotations to find associations that 
> could be pushed down to lower nodes if more data was available.  In other 
> words, the ability of GO terms closer to the root to identify gaps in the 
> experimental literature is a good thing, since it suggests places where more 
> experiments are needed.
>
> A while ago I put up an SF query about whether terms that specify the target 
> in the term definition were too specific.  e.g.
> GO:0046011 ! regulation of oskar mRNA translation
>
> and it's two children would be lumped into regulation of mRNA translation and 
> given oskar mRNA as the target.  It sounds to me like the discussion is 
> coming around to my pov on this (I hope?!).  I can see why with may not be 
> appropriate, if the regulator is part of a complex that does the regulation, 
> then it seems like you could be getting into having two kinds of with, the 
> partner and the target.
>
> Adding a new field presumably opens another can of worms, but it sounds like 
> maybe one is needed.  But here I'm wading into waters best left to more 
> experienced GO people.
>
> Jim
>
> On Aug 10, 2007, at 9:42 AM, E Dimmer wrote:
>
>> Hi,
>> 
>> There is a large number of terms in GO which deserve more information 
>> regarding the 'target' of its gene product's activity, for instance:
>> -- negative regulation of ubiquitination
>> -- protein kinase activity
>> -- regulation of DNA binding
>> -- regulation of phosphorylation
>> -for all of these examples I have information on the specific target of a 
>> protein's action.
>> 
>> While I strongly feel that this target information should be captured -- is 
>> the 'with' the right place? We seem to have tried to be very strict on the 
>> contents of the 'with', so the type of value used is closely related to the 
>> type of evidence code applied in the annotation. I'm not sure that 
>> regulation of expression be an exception to this...
>> 
>> Emily
>> 
>> 
>> Pankaj Jaiswal wrote:
>>> 
>>> 
>>> Harold Drabkin wrote:
>>> 
>>>> 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
>>>> 
>>> 
>>> With field filling should be 'a must' because the regulation of expression 
>>> is always in context to another gene (product). However the code can also 
>>> be IPI, IGI, IMP besides IEP.
>>> 
>>> Pankaj
>> 
>> 
>> -- 
>> ************************************
>>   Emily Dimmer
>>   GOA Coordinator
>>   EMBL-EBI
>>   Wellcome Trust Genome Campus
>>   Hinxton
>>   Cambridge CB10 1SD, U.K.
>>   Tel:     +44 1223 494654
>>   Fax:    +44 1223 494468
>>   email:  edimmer at ebi.ac.uk
>> ************************************
>> 
>
> =====================================
> Jim Hu
> Associate Professor
> Dept. of Biochemistry and Biophysics
> 2128 TAMU
> Texas A&M Univ.
> College Station, TX 77843-2128
> 979-862-4054
>