[Ontology-editors] [Refgenome] Cell fractions
Harold Drabkin
hjd at informatics.jax.org
Wed Feb 11 06:53:06 PST 2009
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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