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

[Valerie Wood]

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
>>>
>>>
>>>
>>> ------------------------------------------------------------------------ 
>>>
>>>
>>> _______________________________________________
>>> Go mailing list
>>> Go at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>   
>> _______________________________________________
>> Annotation mailing list
>> Annotation at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>
>>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Annotation mailing list
> Annotation at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/annotation
>   


-- 
---------------------------------------------------------------------------
Valerie Wood			 Tel: 01223 496909
S. pombe Genome Project		 Fax: 01223 494919 		       
Wellcome Trust Sanger Institute	 email: val at sanger.ac.uk
Wellcome Trust Genome Campus	 http://www.genedb.org/genedb/pombe 
Hinxton, Cambridge, CB10 1HH	 http://www.sanger.ac.uk/Projects/S_pombe



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.