[ensembl-dev] Orthologs table vs site mismatch
Tal Shay
talshay at broadinstitute.org
Sun Apr 10 20:13:29 BST 2011
Hi,
I am trying to list all human genes with no mouse orthologs, and all
mouse genes with no human orthologs.
At first it seems like an SQL query of homology*homology_member will do
that,, but trying to compare the result list to the site, I see
orthologs in the ENSEMBL web site
that do not appear in the ENSEMBL-compara table homology.
Can anyone please tell me why is that, and in which table should I look
for those orthologs? Does that say anything abouth them, not being
included in the homology table?
E.G. between
PPY - Human gene: ENSG00000131096 (member id 2512486); mouse gene
ENSMUSG00000017311 (member id 1389651)
DSP - Human gene: ENSG00000096696 (member id 2480709); mouse gene
ENSMUSG00000054889 (member id 1078582)
IFIT - Human gene: ENSG00000185201 (member id 2341403); mouse gene
ENSMUSG00000059108 (member id 355717)
I am breaking my head over this, I assume it is trivial, but it is not
in the FAQ or the tutorial, so I'll be grateful for any insight.
Thanks,
Tal
More details -
In the ENSEMBL web site, I search each of the genes, and then ask for
its orthologs, of which the human mouse pairs are listed above.
In the database, I query the 'homology' table for homologies with the
human member id, and then search the resulting homologies id for the one
with the mouse homology id, but there is none.
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