[annotation] Question about Isoform Annotation

[Petri, Victoria]

Hi Kimberly,

I see it as a call for contributes_to for subunit C. 
I think that the complex - subunit b and subunit c - represents the
physiologically significant unit and therefore the physiologically
significant activity is the response profile exhibited by c when b is
present. The function of c is then to modulate the activity b would
otherwise have on its own and probably not the optimal response. In this
respect, b contributes to the 'proper' activity of the receptor complex.

Yes, the two subunits get the CC complex term which clarifies the
picture to the users that most likely encountered similar situations.

Best,

Victoria
 

Victoria Petri, Ph.D.
Research Scientist
Rat Genome Database 
(http://rgd.mcw.edu)
Bioinformatics Program
Human and Molecular Genetics Center
Medical College of Wisconsin 
8701 Watertown Plank Road, Milwaukee, WI 53226
(414) 456-7507
Fax (414) 456-6595 
vpetri at mcw.edu
vpetri at mail.brc.mcw.edu
 
-----Original Message-----
From: owner-annotation at genome.stanford.edu
[mailto:owner-annotation at genome.stanford.edu] On Behalf Of Kimberly Van
Auken
Sent: Friday, August 24, 2007 5:56 PM
To: dhowe at cs.uoregon.edu
Cc: annotation at genome.stanford.edu
Subject: Re: [annotation] Question about Isoform Annotation

Thanks, Doug.

I had thought about that, but neither of the gene products is mutant and

so I didn't
know if IGI was appropriate.

Perhaps Subunit C could get a contributes_to qualifier for an IDA 
annotation and
then I could annotate each of the subunits to the CC term receptor 
complex to fulfill
the contributes_to requirement that:

    All gene products annotated using contributes_to must also be 
annotated to a cellular
    component term representing the complex that possesses the activity.


--Kimberly


Doug howe wrote:

> Sounds like a possible IDA function annotation on Subunit B and a 
> 'contributes_to' function annotation by IGI on subunit C??
> -Doug
>
>
> Kimberly Van Auken wrote:
>
>> Hi--
>>
>> I'm trying to decide the best way to annotate information about the 
>> C. elegans GABA receptor.
>>
>> In C. elegans, functional GABA receptors are formed from one or more 
>> protein subunits encoded
>> by the same genomic locus, unc-49.
>>
>> To test functionality, the authors of the paper expressed subunits 
>> separately and then together
>> and measured the dose-response to, and response to continuous 
>> application of, GABA.   One subunit
>> has receptor activity on its own, one does not, and expression of 
>> both results in a response distinct
>> from that of the first on its own.  To summarize:
>>
>>    Subunit B:  responds
>>
>>    Subunit C: doesn't respond
>>
>>    Subunits B and C: respond with distinct profile
>>
>>
>> If this was just one isoform, I would annotate the protein to the 
>> appropriate receptor activity terms
>> using the IDA evidence code.  But is there any way to annotate this 
>> complexity using IDA?
>>
>> I can certainly annotate to the B isoform, but I don't want to make 
>> the same annotation to the C isoform.
>>
>> One way I can think to capture the complexity would be to annotate to

>> both B and C, but include the
>> other isoform in the WITH column for one B annotation and the only C 
>> annotation.
>>
>> Is the WITH column completely off-limits for IDA annotations?
>>
>> Any thoughts on this would be much appreciated!
>>
>> Thanks,
>> Kimberly
>>
>>
>>
>>
>