[Annotation] [Refgenome] Cell fractions
Alexander Diehl
adiehl at informatics.jax.org
Wed Feb 11 06:23:07 PST 2009
[switched from ontology-editors to GO annotation list]
Chris,
I would justify ISS annotations for cell fraction based on the
assumption that physiochemical properties of proteins that determine
their fractionation are highly sequence dependent, and presumably
protein homologs/orthologs have a high degree of sequence similarity,
including the presence or absence of transmembrane domains, which
determines the protein's behavior in cell fractionation procedures in
most cases.
Also the argument can be made, that a term like "membrane fraction"
represents the unity of all membrane types in the cell (although this
may depend on the fractionation procedure in practice), and if we
believe ISS can be used to transfer, for instance, "plasma membrane"
annotations between species, why not "membrane fraction" annotations?
IMP annotations are similarly straight-forward. If one assays for an
enzyme activity in the soluble franction, and fails to find that
activity in the soluble fraction of cells of the same cell type from a
KO mouse with the putative enzyme missing, then an IMP annotation is
entirely appropriate. In particular this applies in cases where several
genes may have similar catalytic activity, but different cellular
expression patterns. Otherwise, depending on the strength of the data,
one could argue for an IDA here as well.
Harold may respond about the particular MGI IMP annotations you refer to.
IPI annotations are a type of IDA in any case, and NAS and TAS
annotations should ideally be replaces at some point.
Thanks,
Alex
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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--
Alexander D. Diehl, Ph.D.
Senior Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609
email: adiehl at informatics.jax.org
work: +1 (207) 288-6427
fax: +1 (207) 288-6131
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