[go] Boundary between IMP and IGI
Paul Sternberg
pws at caltech.edu
Tue Sep 11 08:10:07 PDT 2007
I love genetic interactions but they are a less direct way of
inferring function so both are needed. (A gene in a bacterium can
interacts with a human gene, etc.).
Paul
On Sep 11, 2007, at 8:03 AM, Judith Blake wrote:
> I agree with Val. With multicellular organisms, perhaps even more
> particularly, it's a long trip between observable heritable
> phenotypes and understanding the precise genetic interactions that
> are producing them.
>
> Judy
>
> Valerie Wood wrote:
>> Benjamin Hitz wrote:
>>
>>>
>>> Do we really need IGI and IMP? Is the only difference
>>> technically that IGI = double (or 2+?) mutant, IPI = single mutant?
>>
>>
>> We need.
>>
>> These are *very* different types of biological data. The IMP the
>> annotation is derived in some way directly from the *observable
>> phenotype*, but with IGI it is an inference from the the actual
>> *interaction* (the phenotype may be suppressed or the cell may be
>> dead).
>>
>> Our current use of IGI includes things which aren't 'truly'
>> genetic interactions but on the whole, it is likely that most
>> databases have recorded non- canonical use and these can be
>> filtered (i.e functional complementation by a heterologous system
>> can be filtered because the 'with' column will contain a entry
>> from another taxon.
>>
>> Val
>>
>>
>>
>>
>>>
>>> Ben
>>>
>>> On Sep 10, 2007, at 4:18 PM, 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.
>>>
>>>
>>> --
>>> Ben Hitz
>>> Senior Scientific Programmer ** Saccharomyces Genome Database **
>>> GO Consortium
>>> Stanford University ** hitz at genome.stanford.edu
>>>
>>>
>>>
>>>
>>
>>
>>
>
>
Paul W. Sternberg
Thomas Hunt Morgan Professor of Biology
HHMI and Division of Biology 156-29, Caltech
1200 E. Calif Blvd., Pasadena CA 91125
tel 626-395-2181 fax 626-568-8012 email pws at caltech.edu
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