proposal for a evidence code

[Pankaj Jaiswal]

Dear All

I am sending this mail for your reference on what Michael and others are talking
about. The information about IGI and IMP (as GO evidence codes) is as follows
and see if makes justification and let me know.

Pankaj

IGI inferred from genetic interaction 
	#"Traditional" genetic interactions such as suppressors, synthetic lethals,
etc. 
	#Functional complementation 
	#Rescue experiments 
	#Inference about one gene drawn from the phenotype of a mutation in a different
gene 

    Comment: Includes any combination of alterations in the sequence (mutation)
or expression of more than one gene/gene product. This
    category can therefore cover any of the IMP experiments that are done in a
non-wild-type background, though we prefer to use it only
    when all mutations are documented. When redundant copies of a gene must all
be mutated to see an informative phenotype, that's
    IGI. (Yes, we know that means some organisms, such as mouse, will have far,
far more IGI than IMP annotations.) 

    We have also decided to use this category for situations where a mutation in
one gene (gene A) provides information about the
    function, process, or component of another gene (gene B; i.e. annotate gene
B using IGI). 

    We recommend making an entry in the "with" column when using this evidence
code (i.e. include an identifier for the "other" gene
    involved in the interaction). If more than one independent genetic
interaction supports the association, use separate lines for each. In
    cases where the gene of interest interacts simultaneously with more than one
other gene, put both/all of the interacting genes on the
    same line (separate identifiers by commas in the "with" column). To help
clarify: 

        GOterm   IGI    FB:gene1,FB:gene2

        means that the GO term is supported by evidence from its interaction
        with *both* of these genes; i.e. neither of these statements are true:

        GOterm  IGI     FB:gene1
        GOterm  IGI     FB:gene2 
       

    See the GO Annotation Guide for more information. 

IMP inferred from mutant phenotype
 
       #Any gene mutation/knockout 
       #Overexpression/ectopic expression of wild-type or mutant genes 
       #Anti-sense experiments 
       #RNAi experiments 
       #Specific protein inhibitors 
    Comment: anything that is concluded from looking at mutations or abnormal
levels of the product(s) only of the gene of interest is IMP
    (compare IGIs).

"Michael Ashburner (Genetics)" wrote:
> 
> Pankaj
> 
> Unless I am missing something, I think that is not appropriate for GO,
> which is for the annotation of gene_products (or genes as their surrogates).
> It may well be appropriate for TO. For the functions etc of gene products
> inferred from mutant phenoptypes we have, of course, already the evidence
> code "IMP".
> 
> Michael

-- 

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Pankaj Jaiswal, Ph.D.                                   
Postdoctoral Associate
Dept. of plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   http://ars-genome.cornell.edu/rice
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