[go] 'regulation of gene expression'

[Michelle Gwinn Giglio]

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





Karen Christie wrote:
> 
> 
> 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
>>