[ensembl-dev] Reg: ensembl__homolog files

[Premanand Achuthan]

Thanks Thomas,  managed to export via mart.   The earlier format (with 
both human & mouse gene identifiers in the 
'hsapiens_gene_ensembl__homolog_mmus__dm' file) was useful for our 
automated pipeline. However, it didn't take much time to do the mart 
export for all the ensembl genes. So, it should be okay.

Thanks
Prem



On 06/03/13 14:46, Thomas Maurel wrote:
> Dear Prem,
>
> In order improve scalability we have recently invested a lot of effort 
> in tidying up parts of the schema that we are not using as filters or 
> attributes on the biomart interface.
> Therefore we have removed this and other columns from the homolog 
> dimension tables. On the interface you can still obtain the human 
> ensembl gene id along with the corresponding mouse ortholog gene id. 
> Here is the query you can do on the interface 
> (http://www.ensembl.org/biomart/martview 
> <http://www.ensembl.org/biomart/index.html>):
>
> Database: "Ensembl Genes 70"
> Dataset: "Homo sapiens genes (GRCh37.p10)"
> 1) Filters:
> a) In Gene: Click on "ID list limit" and select "ensembl Gene ID(s)" 
> from the dropdown
> b) Paste your Human gene ids in the box.
> 2) Attributes:
> Homologs section:
> a) In Gene:
> Select "Ensembl Gene ID"
> b) In Orthologs, Mouse Orthologs:
> Select "Mouse Ensembl Gene ID"
>
> I hope this clarifies the situation but please get in contact if you 
> have further questions.
>
> Regards,
> Thomas
> On 6 Mar 2013, at 14:05, Premanand Achuthan wrote:
>
>> HI
>>
>> Have noticed that there is no human gene identifiers in the 
>> 'hsapiens_gene_ensembl__homolog_mmus__dm' file in e70. It used to be 
>> there in earlier versions (eg: e67).
>>
>> ftp://ftp.ensembl.org/pub/release-67/mysql/ensembl_mart_67/hsapiens_gene_ensembl__homolog_mmus__dm.txt.gz 
>> => Had 16 columns
>> ftp://ftp.ensembl.org/pub/release-70/mysql/ensembl_mart_70/hsapiens_gene_ensembl__homolog_mmus__dm.txt.gz 
>> => Has 13 columns
>>
>>
>> Looking for gene PTPN22 in e67
>>
>> *grep 'ENSG00000134242' hsapiens_gene_ensembl__homolog_mmus__dm.txt.e67*
>> 0.18300    3    297698    Eutheria    103716170 103663718    
>> ortholog_one2one *ENSG00000134242* \N    0.49670    71    \N 
>> *ENSMUSG00000027843* ENSMUSP00000029433    ENSP00000352833    71
>>
>>
>> *grep 'ENSG00000134242' hsapiens_gene_ensembl__homolog_mmus__dm.txt.e70*
>> Returns nothing, but grep on it's mouse ortholog 'ENSMUSG00000027843' 
>> gives result.
>> *grep 'ENSMUSG00000027843' hsapiens_gene_ensembl__homolog_mmus__dm.e70*
>> 0.18290    3    477787    Eutheria    103859795 103912247    
>> ortholog_one2one    0.49100    71 *ENSMUSG00000027843* 
>> ENSMUSP00000029433    ENSP00000352833    71
>>
>> Wondering why the human gene identifier column is not available 
>> anymore. Could you please point me to the changelogs in Ensembl where 
>> I can get more info about this change.
>>
>> Thanks
>> Prem
>>
>>
>>
>> ==
>> premanand.achuthan at cimr.cam.ac.uk
>> JDRF/WT Diabetes and Inflammation Laboratory (DIL)
>> Cambridge Institute for Medical Research (CIMR)
>> Wellcome Trust/MRC Building
>> Addenbrooke's Hospital Hills Road Cambridge CB2 0XY
>>
>>
>>
>>
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>
> --
> Thomas Maurel
> Bioinformatician - Ensembl Production Team
> European Bioinformatics Institute (EMBL-EBI)
> Wellcome Trust Genome Campus, Hinxton
> Cambridge - CB10 1SD - UK
>
>
>
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