<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Prem,<div><br></div><div>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.</div><div>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 (<a href="http://www.ensembl.org/biomart/index.html">http://www.ensembl.org/biomart/martview</a>):</div><div><br></div><div>Database: "Ensembl Genes 70"</div><div>Dataset: "Homo sapiens genes (GRCh37.p10)"</div><div>1) Filters:</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>a) In Gene: Click on "ID list limit" and select "ensembl Gene ID(s)" from the dropdown</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>b) Paste your Human gene ids in the box.</div><div>2) Attributes:</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Homologs section:</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>a) In Gene: </div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Select "Ensembl Gene ID"</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>b) In Orthologs, Mouse Orthologs:</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Select "Mouse Ensembl Gene ID"</div><div><br></div><div>I hope this clarifies the situation but please get in contact if you have further questions.</div><div><br></div><div>Regards,</div><div>Thomas<br><div><div>On 6 Mar 2013, at 14:05, Premanand Achuthan wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
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HI<br>
<br>
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).<br>
<br>
<a class="moz-txt-link-freetext" href="ftp://ftp.ensembl.org/pub/release-67/mysql/ensembl_mart_67/hsapiens_gene_ensembl__homolog_mmus__dm.txt.gz">ftp://ftp.ensembl.org/pub/release-67/mysql/ensembl_mart_67/hsapiens_gene_ensembl__homolog_mmus__dm.txt.gz</a>
=> Had 16 columns<br>
<a class="moz-txt-link-freetext" href="ftp://ftp.ensembl.org/pub/release-70/mysql/ensembl_mart_70/hsapiens_gene_ensembl__homolog_mmus__dm.txt.gz">ftp://ftp.ensembl.org/pub/release-70/mysql/ensembl_mart_70/hsapiens_gene_ensembl__homolog_mmus__dm.txt.gz</a>
=> Has 13 columns<br>
<br>
<br>
Looking for gene PTPN22 in e67<br>
<br>
<b>grep 'ENSG00000134242'
hsapiens_gene_ensembl__homolog_mmus__dm.txt.e67</b><br>
0.18300 3 297698 Eutheria 103716170 103663718
ortholog_one2one <b>ENSG00000134242</b> \N 0.49670
71 \N <b>
ENSMUSG00000027843</b> ENSMUSP00000029433 ENSP00000352833
71<br>
<br>
<br>
<b>grep 'ENSG00000134242'
hsapiens_gene_ensembl__homolog_mmus__dm.txt.e70</b><br>
Returns nothing, but grep on it's mouse ortholog
'ENSMUSG00000027843' gives result.<br>
<b>grep 'ENSMUSG00000027843'
hsapiens_gene_ensembl__homolog_mmus__dm.e70</b><br>
0.18290 3 477787 Eutheria 103859795 103912247
ortholog_one2one 0.49100 71 <b>ENSMUSG00000027843</b>
ENSMUSP00000029433 ENSP00000352833 71<br>
<br>
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.<br>
<br>
Thanks<br>
Prem<br>
<br>
<br>
<br>
<font color="#666666">==<br>
</font><font color="#c0c0c0"><font color="#666666"><a class="moz-txt-link-abbreviated" href="mailto:premanand.achuthan@cimr.cam.ac.uk">premanand.achuthan@cimr.cam.ac.uk</a><br>
JDRF/WT Diabetes and Inflammation Laboratory (DIL)
<br>
Cambridge Institute for Medical Research (CIMR)
<br>
Wellcome Trust/MRC Building
<br>
Addenbrooke's Hospital Hills Road Cambridge CB2 0XY</font><br>
</font><br>
<br>
<br>
<br>
</div>
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>--</div><div>Thomas Maurel<br>Bioinformatician - Ensembl Production Team<br>European Bioinformatics Institute (EMBL-EBI)<br>Wellcome Trust Genome Campus, Hinxton<br>Cambridge - CB10 1SD - UK</div></div></span></div></div>
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