[annotation] Question about Isoform Annotation

[Doug howe]

Though it is a direct assay, you can only detect it's role in the GABA 
receptor activity when you introduce both subunit b and subunit c, so it 
still seems like an IGI to me, though I could see how you might go down 
either road.  Something like this perhaps:

Subunit b:
   'GABA receptor activity'   IDA   <--b has activity by itself
   'GABA receptor activity'   IGI    with gene ID for subunit c   <--b 
has altered activity when c is present

Subunit c:
  contributes_to 'GABA receptor activity'   IGI   with gene ID for 
subunit b  <--c doesn't have activity by itself
  'receptor complex'   IGI  with gene ID for subunit b

-Doug


Kimberly Van Auken wrote:
> 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
>>>
>>>
>>>
>>>
>>
>