[Annotation] [Go] Evidence code for gfp and phoA fusions?

[Alexander Diehl]

Jim, Val, David, and Pascale

I have used a similar approach at MGI, using a combination of ISM, IDA, 
and IC codes.  See Aqp2:

http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=markerGO&key=33522

-- Alex


Valerie Wood wrote:
>
>
> In these cases I have done
>
> i)    integral to membrane ISS TMM:whatever_its_called
> ii)    plasma membrane IDA
> iii)    integral to plasma membrane IC from GO:0016021|GO:0005886 (you 
> can put pipe separated GO ids in the "from" column, this was added 
> purely for this type of annotation.
>
> Its a bit clunky but at least you can pull the different annotation 
> sources apart..
>
> Val
>
>
> Pascale Gaudet wrote:
>> But, can you really see 'intrinsic to the membrane' by GFP?
>> I think you can only see that it's membrane, and you know it's 
>> intrinsic because there are TM domains (which would be ISM).
>> It's again one of those cases where the curator combines two 
>> different pieces of information to make an annotation. We should 
>> think of better ways to deal with this.
>>
>> Pascale
>>
>> David Hill wrote:
>>> Hi Jim,
>>>
>>> I would use IDA. As long as the purpose of the experiment is to show 
>>> the normal localization of the protein and the authors show no 
>>> reason to believe that the tags mislocalize the protein, then the 
>>> authors are looking at the normal distribution. Although these 
>>> experiments are subject to mislocalization due to the tags, like all 
>>> experiments are subject to artifact, I think we need to go with the 
>>> authors conclusions.
>>> I have annotated GFP fusions in mammalian cells using IDA.
>>>
>>> David
>>>
>>> Jim Hu wrote:
>>>> We have a lot of annotations that would be made to intrinsic to 
>>>> membrane based on expression of GFP and PhoA fusion proteins.  What 
>>>> evidence code would people use?
>>>>
>>>> Jim
>>>> =====================================
>>>> 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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>
>


-- 
Alexander D. Diehl, Ph.D.
Senior Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609

email:  adiehl at informatics.jax.org
work:  +1 (207) 288-6427
fax:  +1 (207) 288-6131