[annotation] Question about Isoform Annotation

[Kimberly Van Auken]

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
>>
>>
>>
>>
>