[Ontology-editors] [Refgenome] Cell fractions
Pankaj Jaiswal (OSU)
jaiswalp at science.oregonstate.edu
Wed Feb 11 16:56:13 PST 2009
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&evcode=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
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