[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.







More information about the Dev mailing list