[go] 'regulation of gene expression'

[Jim Hu]

Just to complicate things further, I imagine that regulation of  
expression of X terms are also assigned from IMP or IGI as well as  
IEP.  I was thinking that lots of the older E. coli regulation  
studies - e.g. the Jacob and Monod work that established the very  
idea of regulatory genes is based on inference from the presence or  
absence of phenotypes that indirectly measure the expression pattern.

Jim

On Aug 10, 2007, at 12:07 PM, Harold Drabkin wrote:

> 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.
>>
>
> This sort of came up many meetings ago, because we cannot put a new  
> term into the GO for each and every specific *instance*.   
> (regulation of (your favorite) mRNA translation, or biosynthesis  
> of ....fill in  your favorite item. Not only does this start down  
> an infinite expansion of the size of the DAG, but also moves away  
> from the idea of terms that would be useful to a broad range of  
> MODs, not just one or two.
> It isn't just the actual gene that you think is being regulated,  
> it's whether your gene product is directly participating in that  
> regulation process.
>
> an aside:.....
>
> We also discussed what and when to put something in the with field;  
> the idea was to ask the question "is there something missing if you  
> turned the annotation into a sentence... like, Product X has kinase  
> activity based on sequence similarity.  The question would be  
> "similarity to what?", wich is answered by the WITH field.
>
> IPI, IMP, and IGI all beg a question .. to/with/of WHAT? (based of  
> physical interaction with WHAT; based on (WHAT) mutant phenotype?;  
> based on genetic interaction with WHAT.
>
> I guess, if you use IEP, you could ask " .. based on the expression  
> pattern of WHAT?"
>
> (I realize the paradigm breaks with IEA and RCA, as the question  
> asked would be more along the lines of WHAT KIND (of electronic  
> annotation or computational analysis; by this one could make (not  
> that I am) an arguement that IDA would invoke WHAT KIND (of direct  
> assay). ..
>
> but I digress..
>
> The point is just how much can we put into an annotation?  How much  
> can we distill an experiment into a single line of 15 tab-delimited  
> fields? How much should we expect a user to refer to the PMID of  
> the annotation if it is of interest to them?
>
>
>> 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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