<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<div class="moz-cite-prefix">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. <br>
<br>
Thanks<br>
Prem<br>
<br>
<br>
<br>
On 06/03/13 14:46, Thomas Maurel wrote:<br>
</div>
<blockquote
cite="mid:568194E0-A132-4CFF-8B3E-4491E5AB1E18@ebi.ac.uk"
type="cite">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 moz-do-not-send="true"
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">
<meta http-equiv="content-type" content="text/html;
charset=ISO-8859-1">
<div bgcolor="#FFFFFF" text="#000000"> 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 moz-do-not-send="true" 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 moz-do-not-send="true" 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
moz-do-not-send="true"
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>
_______________________________________________<br>
Dev mailing list <a moz-do-not-send="true"
href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a
moz-do-not-send="true"
href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a moz-do-not-send="true"
href="http://www.ensembl.info/">http://www.ensembl.info/</a><br>
</blockquote>
</div>
<br>
<div apple-content-edited="true">
<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>
</div>
<br>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</body>
</html>