[Ontology-editors] [Refgenome] Cell fractions
Harold Drabkin
hjd at informatics.jax.org
Thu Feb 12 07:21:45 PST 2009
Harold Drabkin wrote:
> I strongly disagree. Without the IMP 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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