[Ontology-editors] [Refgenome] Cell fractions
Pankaj Jaiswal (OSU)
jaiswalp at science.oregonstate.edu
Thu Feb 12 10:12:01 PST 2009
I see your point, but GO annotations as I understand is for the generic
gene product and not necessarily the mutant form. The annotation
suggests that one is likely to find a given gene product (based on
evidence) in a given location (fraction) for a given SPECIES (it
may/may_not be the same location for a gene product from another species).
Therefore, you would have two annotation for an enzyme for example
Protein-X GO_MF(enzyme activity) IDA
Protein-X GO_CC(a-fraction) IMP
IMP annotation is fine, but where do we annotate that GO_CC was
confirmed by IEP (western).
Pankaj
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&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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>>>>
>>>
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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
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