[Annotation] IMP or IGI for deficiencies

[Doug howe]

Agree all around.
Thx.

Karen Christie wrote:
> Hi Doug,
>
> Yes, I think that in some cases I just wouldn't be comfortable making 
> an annotation from a multiple deficiency for the reasons you state, 
> that you may not know which gene(s) were causing the effect. In the 
> cases where you say that they rescue by re-introducing specific genes, 
> I think you can use IMP if they show that the phenotype is specific to 
> the one gene being annotated.
>
> I should also add that sometimes I am annotating from strains where it 
> is known that there are background mutations, usually markers 
> (typically auxotrophies, genes required for synthesis of histidine, 
> uracil, etc.), but that these genes do not affect the phenotype that 
> the GO annotation is based on. I ignore these for the purpose of 
> deciding between IMP and IGI.
>
> -Karen
>
>
>
>
> On Fri, 7 Nov 2008, Doug howe wrote:
>
>> Hi Karen,
>>  If a deficiency affects multiple gene, making any annotation is of 
>> course dependent upon your ability to discern which gene(s) may be 
>> involved in whatever you are annotating.  I guess it would typically 
>> be difficult to make any annotation with a Df mutant for that 
>> reason.  There are a few cases in zebrafish where a phenotype was 
>> rescued by re-introducing specific genes that were lost in the Df..so 
>> you at least think you know what gene to annotate.
>>
>> -Doug
>>
>> Karen Christie wrote:
>>> Hi,
>>>
>>> I think I'd be likely to use IGI for a "a deficiency mutant which is 
>>> known to affect more than one gene", barring some extenuating 
>>> circumstance.
>>>
>>> Generally, I use IMP for a single mutant affecting the gene of 
>>> interest, and IGI for most other genetic situations I can think of, 
>>> e.g. double or triple mutants, or a single mutant NOT in the gene 
>>> being annotated (as per GO guidelines which specify that making an 
>>> annotation for gene A based on a single mutation in gene B is IGI).
>>>
>>> -Karen
>>>
>>> On Fri, 7 Nov 2008, Doug howe wrote:
>>>
>>>> If an experiment uses a deficiency mutant which is known to affect 
>>>> more than one gene, should that be curated for GO using IMP or 
>>>> IGI?  Contrast that with basically the same experiment where the 
>>>> same genes were targeted individually with morpholinos/antisense 
>>>> techniques...the latter seems like IGI.
>>>> ?
>>>>
>>>> -- 
>>>> Doug Howe, Ph.D.
>>>> ZFIN Scientific Curator
>>>> Zebrafish Nomenclature Coordinator
>>>>
>>>> _______________________________________________
>>>> Annotation mailing list
>>>> Annotation at geneontology.org
>>>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>>>
>>>
>>
>> -- 
>> Doug Howe, Ph.D.
>> ZFIN Scientific Curator
>> Zebrafish Nomenclature Coordinator
>>
>> _______________________________________________
>> Annotation mailing list
>> Annotation at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>
>

-- 
Doug Howe, Ph.D.
ZFIN Scientific Curator
Zebrafish Nomenclature Coordinator