[Annotation] [Ontology-editors] [Refgenome] Cell fractions
Karen Christie
kchris at genome.stanford.edu
Thu Feb 12 10:46:18 PST 2009
OK, wasn't obvious from the original explanation, but makes sense to me.
-K
On Thu, 12 Feb 2009, Harold Drabkin wrote:
> For example, an antibody would have to be very specific for only one of
> protein product of 8 beta-tubulin genes in mouse (assuming one has
> demonstrated no cross-reactivity). So if one is 100% sure, fine; if not...
>
> hjd
>
> 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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>>>
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