[Ontology-editors] [Refgenome] Cell fractions
Harold Drabkin
hjd at informatics.jax.org
Thu Feb 12 07:19:27 PST 2009
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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