Thanks for getting my point. I just sent the same question in another mail.
Pankaj
Karen Christie wrote:
> Hi,
>
> I can see Harold's case for using IMP if you're comparing a protein
> activity in cell fractions prepared from wt versus mutant, and also
> agree that use of IMP in such a situation is what we agreed to at the
> 2006 Annotation Camp and in subsequent discussions.
>
> However, I am not following how the Western assay would need to be IMP.
> If you can identify the protein by Western, that seems like IDA. How is
> doing the same thing from the mutant even relevant?
>
> -Karen
>
>
> On Thu, 12 Feb 2009, Pascale Gaudet wrote:
>
>> What Harold says here is in complete agreement with the documentation:
>> http://geneontology.org/GO.evidence.shtml?all#imp
>> "The IMP evidence code covers those cases when the function, process
>> or cellular
>> localization of a gene product is inferred based on differences in the
>> function,
>> process, or cellular localization between two different alleles of the
>> corresponding
>> gene"
>>
>> As far as I know, most groups use IMP for component as described here.
>>
>> Pascale
>>
>> Harold Drabkin wrote:
>> I strongly disagree. Without the IMG you would not know what
>> protein you
>> are assaying. You have no other evidence to directly link the
>> the specific
>> gene product to the activity. Without the IMP, the assay just
>> says that this
>> activity is present, but it could be one of several proteins.
>> The IMP says
>> which one.
>>
>> hjd
>>
>>
>> Pankaj Jaiswal (OSU) wrote:
>> Harold,
>>
>> But I guess the confirmation that the activity was present in
>> the fraction-X was estimated by IDA / western. Whether it was
>> present/absent in mutant/reference is a different issue. The
>> confirmation is based on the exact experimental method i.e.
>> western/enzymatic assay of the fraction and not the genotype
>> (mutant/ref/WT) of the individual being assayed.
>>
>> I concur with Chris it should be limited to only IDA and IEP.
>>
>> Pankaj
>>
>> Harold Drabkin wrote:
>> No, not necessarily. If a cell-fractions from
>> mutant and wild type were examined for the presence
>> of the protein by either western or assay, the
>> difference between the mutant and wild type is the
>> basis for the IMP. Or, a western could be done and
>> it appears in a sample from one fraction in wild
>> type but not mutant. If the comparison is not made,
>> and it is some activity measurement in a crude
>> assay, the identify of the protein cannot be made.
>>
>> hd
>>
>> Chris Mungall wrote:
>> Following on from our call this morning
>> - it seems the cell fraction terms may
>> be around for a while yet. However, I
>> was wondering what people's opinions
>> were on evidence codes for fraction
>> terms. I'm not really sure how valid it
>> is to make an ISS to a fraction term. Or
>> an IMP. Shouldn't IDA be the only code
>> allowed?
>>
>> Here are some IMPs for microsome:
>>
>> http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?gptype=all&speciesdb=all&taxid=all&e
>>
>>
>> vcode=IMP&term_assocs=all&term=GO%3A0005792&action=filter<http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?gptype=all&speciesdb=all&taxid=all&
>>
>>
>> evcode=IMP&term_assocs=all&term=GO%3A0005792&action=filter>
>>
>> I followed up the mouse one and am not
>> really sure how the IMP is justified
>>
>> Here are some numbers for the genes
>> annotated to cell fractions using
>> different evidence codes
>>
>> +------------+---------------------------------------------+--------------------+------+-------
>>
>> --+ | acc
>> |
>> name
>> |
>> term_type
>> | code | n_genes
>>
>> |+------------+---------------------------------------------+--------------------+------+-------
>>
>> --+ | GO:0000267
>> | cell
>> fraction
>> |
>> cellular_component
>> | IDA | 3
>> | | GO:0000267 |
>> cell
>> fraction
>> |
>> cellular_component
>> | NAS | 1
>> | | GO:0000299 |
>> integral to
>> membrane of
>> membrane
>> fraction |
>> cellular_component
>> | IDA | 27
>> | | GO:0000299 |
>> integral to
>> membrane of
>> membrane
>> fraction |
>> cellular_component
>> | IPI | 2
>> | | GO:0000299 |
>> integral to
>> membrane of
>> membrane
>> fraction |
>> cellular_component
>> | ISA | 1
>> | | GO:0000299 |
>> integral to
>> membrane of
>> membrane
>> fraction |
>> cellular_component
>> | ISO | 2
>> | | GO:0000299 |
>> integral to
>> membrane of
>> membrane
>> fraction |
>> cellular_component
>> | ISS | 16
>> | | GO:0000299 |
>> integral to
>> membrane of
>> membrane
>> fraction |
>> cellular_component
>> | NAS | 1
>> | | GO:0000299 |
>> integral to
>> membrane of
>> membrane
>> fraction |
>> cellular_component
>> | TAS | 3
>> | | GO:0000300 |
>> peripheral to
>> membrane of
>> membrane
>> fraction |
>> cellular_component
>> | IDA | 28
>> | | GO:0000300 |
>> peripheral to
>> membrane of
>> membrane
>> fraction |
>> cellular_component
>> | IPI | 1
>> | | GO:0000300 |
>> peripheral to
>> membrane of
>> membrane
>> fraction |
>> cellular_component
>> | ISA | 1
>> | | GO:0000300 |
>> peripheral to
>> membrane of
>> membrane
>> fraction |
>> cellular_component
>> | ISO | 3
>> | | GO:0000300 |
>> peripheral to
>> membrane of
>> membrane
>> fraction |
>> cellular_component
>> | ISS | 6
>> | | GO:0005624 |
>> membrane
>> fraction
>> |
>> cellular_component
>> | IDA | 615
>> | | GO:0005624 |
>> membrane
>> fraction
>> |
>> cellular_component
>> | IGI | 1
>> | | GO:0005624 |
>> membrane
>> fraction
>> |
>> cellular_component
>> | IMP | 5
>> | | GO:0005624 |
>> membrane
>> fraction
>> |
>> cellular_component
>> | ISA | 4
>> | | GO:0005624 |
>> membrane
>> fraction
>> |
>> cellular_component
>> | ISO | 19
>> | | GO:0005624 |
>> membrane
>> fraction
>> |
>> cellular_component
>> | ISS | 280
>> | | GO:0005624 |
>> membrane
>> fraction
>> |
>> cellular_component
>> | NAS | 17
>> | | GO:0005624 |
>> membrane
>> fraction
>> |
>> cellular_component
>> | RCA | 2
>> | | GO:0005624 |
>> membrane
>> fraction
>> |
>> cellular_component
>> | TAS | 249
>> | | GO:0005625 |
>> soluble
>> fraction
>> |
>> cellular_component
>> | IDA | 428
>> | | GO:0005625 |
>> soluble
>> fraction
>> |
>> cellular_component
>> | IMP | 2
>> | | GO:0005625 |
>> soluble
>> fraction
>> |
>> cellular_component
>> | ISA | 1
>> | | GO:0005625 |
>> soluble
>> fraction
>> |
>> cellular_component
>> | ISO | 8
>> | | GO:0005625 |
>> soluble
>> fraction
>> |
>> cellular_component
>> | ISS | 99
>> | | GO:0005625 |
>> soluble
>> fraction
>> |
>> cellular_component
>> | NAS | 10
>> | | GO:0005625 |
>> soluble
>> fraction
>> |
>> cellular_component
>> | TAS | 135
>> | | GO:0005626 |
>> insoluble
>> fraction
>> |
>> cellular_component
>> | IDA | 65
>> | | GO:0005626 |
>> insoluble
>> fraction
>> |
>> cellular_component
>> | ISO | 1
>> | | GO:0005626 |
>> insoluble
>> fraction
>> |
>> cellular_component
>> | ISS | 32
>> | | GO:0005626 |
>> insoluble
>> fraction
>> |
>> cellular_component
>> | TAS | 5
>> | | GO:0005792 |
>> microsome
>> |
>> cellular_component
>> | IDA | 240
>> | | GO:0005792 |
>> microsome
>> |
>> cellular_component
>> | IMP | 5
>> | | GO:0005792 |
>> microsome
>> |
>> cellular_component
>> | IPI | 3
>> | | GO:0005792 |
>> microsome
>> |
>> cellular_component
>> | ISA | 2
>> | | GO:0005792 |
>> microsome
>> |
>> cellular_component
>> | ISO | 4
>> | | GO:0005792 |
>> microsome
>> |
>> cellular_component
>> | ISS | 105
>> | | GO:0005792 |
>> microsome
>> |
>> cellular_component
>> | NAS | 97
>> | | GO:0005792 |
>> microsome
>> |
>> cellular_component
>> | RCA | 1
>> | | GO:0005792 |
>> microsome
>> |
>> cellular_component
>> | TAS | 40
>> | | GO:0019717 |
>> synaptosome
>> |
>> cellular_component
>> | IDA | 77
>> | | GO:0019717 |
>> synaptosome
>> |
>> cellular_component
>> | IEP | 1
>> | | GO:0019717 |
>> synaptosome
>> |
>> cellular_component
>> | ISA | 1
>> | | GO:0019717 |
>> synaptosome
>> |
>> cellular_component
>> | ISO | 5
>> | | GO:0019717 |
>> synaptosome
>> |
>> cellular_component
>> | ISS | 34
>> | | GO:0019717 |
>> synaptosome
>> |
>> cellular_component
>> | NAS | 2
>> | | GO:0019718 |
>> rough
>> microsome
>> |
>> cellular_component
>> | IDA | 5
>> | | GO:0019719 |
>> smooth
>> microsome
>> |
>> cellular_component
>> | IDA | 1
>> | | GO:0042598 |
>> vesicular
>> fraction
>> |
>> cellular_component
>> | IDA | 12
>> | | GO:0042598 |
>> vesicular
>> fraction
>> |
>> cellular_component
>> | ISS | 7
>>
>> |+------------+---------------------------------------------+--------------------+------+-------
>>
>> --+ 53 rows in
>> set (36.97 sec)
>>
>>
>>
>> ------------------------------------------------------------------------
>>
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>>
>>
>>
--
Pankaj Jaiswal
Assistant Professor
Dept. of Botany and Plant Pathology
3082 Cordley Hall
Oregon State University
Corvallis, OR, 97331-2902, USA
Ph.: +1-541-737-8471
Fax: +1-541-737-3573
Web: www.gramene.org
www.plantontology.org