[Annotation] IMP or IGI for deficiencies

[Karen Christie]

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
>
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