[go] Boundary between IMP and IGI

[Valerie Wood]

The pombe community are very fond of 'localization dependency' 
experiments to dissect the
pathways involved in the function and formation of large proteinaceous 
complexes such as the spindle pole body, or the polarisome, or signaling 
networks like the SIN. For example:
PMID:12034771
PMID:11676915
PMID: 16775007
PMID: 10864871

I've curated these as IGI (in accordance with current documentation), 
but I'd be happy to move them to IMP as only a single gene is mutated. 
It has never bothered me too much that they are IGI because one could 
predict that if there is a 'localization dependency', and because the 
experiments are targeted at gene products known to exist in the same 
complex or pathway, and have the same phenotype when mutated, then the 
pair of genes would also display a genetic interaction (although these 
experiments don't show one).

If I did move these to IMP I would like to be able to continue to 
capture the 'gene product' which didn't localize properly in the 'with' 
column. But would be confusing because this is usually the allele for 
IMP. Alternatively I could just filter out this from the GO submission 
file (although it is biologically useful information).

Val






Karen Christie wrote:

> Boundary between IMP and IGI
> -------------------------------------------------------
>
> In response to the new draft of the evidence code documentation, some
> discussion came up between Midori and Val about the usage of the IGI
> versus the IMP evidence codes. As this issue was not a specific gripe
> of anyone on the Evidence Code Committee, it was not discussed.
>
> However, one of the goals of this revision was to have guidelines that
> make sense and I completely see the point that it doesn't really make
> sense to say that making an inference from a strain with one mutation
> is a genetic interaction, even when you are annotating a gene other
> than the one that is mutant.
>
> We were also asked to make a decision tree/flow chart for evidence
> code decisions (I have a draft I'll send out later), and I think it
> would be a much simpler decision if there was a clear line between 1
> mutant gene and multiple mutant genes.
>
> I think it would make a lot more sense if any annotations made on the
> basis of mutation, or comparison between alleles, of a single gene
> should use IMP.  Since we already allow use of the with field for IMP
> to record the mutant allele, it might make more sense to use IMP for
> any annotation based on a phenotype of a single gene and just record
> the mutant allele in the with field. Since not all groups track
> alleles, perhaps we should also allow with for IMP to contain the name
> of the gene without specifically designating an allele.
>
> Below is transcript of the discussion that occurred on this issue.
>
> -Karen
>
>
> **IMP:
>
>> mutation in gene B provides information about gene A being
>> annotated. For this type of experiment, use the IGI code.  and IGI:
>> Inference about one gene drawn from the phenotype of a mutation in a
>> different gene
>
>
> Midori (15 Jun 2007):
>   I have always disagreed with this usage: I've argued that IMP would be
>   more appropriate, because in the examples given, only one gene is
>   mutated, so the "combination of alterations" criterion for IGI is not
>   met. But it's an argument that I lost years ago. Oh well.
>
> Val (22 Jun 2007):
>   This is still a bit is unclear to me
>
>   "We also use this code for situations where a mutation in gene A
>   provides information about the function, process, or component of gene
>   B. If a mutation in gene A causes a mislocalization of gene B, gene A
>   is annotated to protein localization with gene B in the with/from
>   column using IGI."
>
>   In the protein localization example above a mutation in gene A is
>   providing information about gene A (protein localization) not about
>   gene B (the protein localized).
>
>   I have made a number of these type of annotations to 'protein
>   localization, (the fission yeast community are very keen on
>   localization dependency experiments for functionally connected gene
>   products). However, I thought I had used the wrong evidence code
>   (using the existing documentation) and that they should be IMP (I
>   wanted to capture the protein localized and at the time I had no other
>   way to do it). These were on my todo list to fix.  It now seems they
>   are OK as IGI, so I just wanted to double check.........
>
>   The original documentation says:
>   # Inference about one gene drawn from the phenotype of a mutation in a
>   different gene I don't have an example of this though. I forgot what
>   it is used for, although I used to know......
>
> Midori (22 Jun 2007, in response to Val):
>   > I have made a number of these type of annotations to 'protein
>   > localization, (the fission yeast community are very keen on
>   > localization dependency experiments for functionally connected gene
>   > products). However, I thought I had used the wrong evidence code
>   > (using the existing documentation) and that they should be IMP (I
>   > wanted to capture the protein localized and at the time I had no
>   > other way to do it). These were on my todo list to fix.  It now
>   > seems they are OK as IGI, so I just wanted to double check.........
>
>   Your annotations are consistent with the existing documentation. What
>   I'm saying is that I think the documentation should recommend IMP for
>   these.
>
>   I think I still wouldn't put B is 'with' with IMP, because a few
>   groups would put the allele of A used in the experiment, and others
>   would leave 'with' blank.
>
>   >  The original documentation says: # Inference about one gene drawn
>   > from the phenotype of a mutation in a different gene I don't have an
>   > example of this though. I forgot what it is used for, although I
>   > used to know......
>
>   I would also prefer to recommend IMP for these.
>
>



-- 
 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.