[go] 'regulation of gene expression'

[Jim Hu]

Wrote my example of IMP and IGI before seeing Karen's reply.

GFF3 has a catch-all field that allows addition of new attributes.   
Is something like that worth considering?

On Aug 10, 2007, at 12:13 PM, 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
>>

=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


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