[ensembl-dev] Orthologs table vs site mismatch

[Ewan Birney]

Just a quick gotcha - are you sure you are connecting to the right  
database version -
ie, 61?


On 10 Apr 2011, at 20:13, Tal Shay wrote:

> 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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