[Annotation] [Ontology-editors] [Refgenome] Cell fractions
Karen Christie
kchris at genome.stanford.edu
Thu Feb 12 10:06:58 PST 2009
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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