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

[Judith Blake]

Valerie Wood wrote:
>
> Pascale..
you say
"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."

isn't this classicly 'IC'  ?

Judy
> 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).
>> c
>>
>> 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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>>>>
>>>>
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>
>