<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
<div id="divtagdefaultwrapper" style="font-size:12pt;color:#000000;background-color:#FFFFFF;font-family:Calibri,Arial,Helvetica,sans-serif;">
<p>Thanks for your reply. If those genes do occur in the database as cross references, where can I find a copy of them? Biomart doesn't seem to show genes with those symbols.</p>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> dev-bounces@ensembl.org <dev-bounces@ensembl.org> on behalf of Fergal <fergal@ebi.ac.uk><br>
<b>Sent:</b> Friday, 5 August 2016 6:12:06 PM<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] VEP Cache Gene List</font>
<div> </div>
</div>
<div>Hi Michael,
<div><br>
</div>
<div>These gene symbols do occur in the e75 human database, they are cross references in the otherfeatures database and come from the import of RefSeq gene models we did for e75. The gene symbols come from the RefSeq GTF files that were loaded as part of this
analysis.</div>
<div><br>
</div>
<div>With more recent imports (ones on GRCh38) the RefSeq annotation may have changed and the gene symbol may be updated as a result.</div>
<div><br>
</div>
<div>Thanks,</div>
<div><br>
</div>
<div>Fergal.</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div>On 4 Aug 2016, at 03:32, Michael Milton <<a href="mailto:michael.milton@unimelb.edu.au">michael.milton@unimelb.edu.au</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div dir="ltr" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;">
<div id="divtagdefaultwrapper">
<div style="margin-top: 0px; margin-bottom: 0px;">Yes we are using GRCh37. So we looked at the Ensembl release 75 genes (just using biomart) and there are still a number of gene symbols that VEP is outputting that don't occur in the GRCh37 Ensembl database
at all (as far as I can tell anyway).</div>
<div style="margin-top: 0px; margin-bottom: 0px;"><br>
</div>
<div style="margin-top: 0px; margin-bottom: 0px;">Namely:</div>
<div style="margin: 0px;">
<ul>
<li>ARMCX5-GPRASP2<br>
</li><li>C7orf10<br>
</li><li>PCDHGB5<br>
</li><li>PHOSPHO2-KLHL23<br>
</li><li>THEG5<br>
</li><li>UQCRHL<br>
</li><li>ZSCAN26</li></ul>
<div>There are others (100-200 I believe?) but this is just a small sample.<font face="Calibri"></font></div>
<div><br>
</div>
<div>Any ideas where these symbols are derived from?</div>
</div>
<p style="margin-top: 0px; margin-bottom: 0px; background-color: rgb(255, 255, 255);">
</p>
</div>
<hr tabindex="-1" style="display: inline-block; width: 705px;">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size: 11pt;"><b>From:</b><span class="Apple-converted-space"> </span><a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a><span class="Apple-converted-space"> </span><<a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a>>
on behalf of Will McLaren <<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>><br>
<b>Sent:</b><span class="Apple-converted-space"> </span>Wednesday, 3 August 2016 10:46:02 PM<br>
<b>To:</b><span class="Apple-converted-space"> </span>Ensembl developers list<br>
<b>Subject:</b><span class="Apple-converted-space"> </span>Re: [ensembl-dev] VEP Cache Gene List</font>
<div> </div>
</div>
<div>
<div dir="ltr">Hi Michael,
<div><br>
</div>
<div>I assume from this that you are using the GRCh37 assembly? Ensembl and therefore VEP annotations on GRCh37 were frozen at Ensembl release 75 as we have moved our main annotation pipelines to GRCh38.</div>
<div><br>
</div>
<div>See the about box on the RH side of <a href="http://grch37.ensembl.org/index.html" target="_blank" id="LPlnk150775">http://grch37.ensembl.org/index.html</a></div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 3 August 2016 at 06:41, Michael Milton<span class="Apple-converted-space"> </span><span dir="ltr"><<a href="mailto:michael.milton@unimelb.edu.au" target="_blank">michael.milton@unimelb.edu.au</a>></span><span class="Apple-converted-space"> </span>wrote:<br>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;">
<div dir="ltr">
<div style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;">
<div style="margin-top: 0px; margin-bottom: 0px;">Hi, I'm using VEP with a downloaded cache, and it seems that VEP is annotating some non-hgnc gene symbols or at least outdated symbols. I need a gene list including all possible genes that VEP could output for
a downstream application. Is there a definitive list of genes that VEP could output? Otherwise, what source is used to build the VEP cache?</div>
<div style="margin-top: 0px; margin-bottom: 0px;"><br>
</div>
<div style="margin-top: 0px; margin-bottom: 0px;">Some of the superceded gene symbols it's outputting, using the Ensembl 83 refseq cache, are:</div>
<p style="margin-top: 0px; margin-bottom: 0px;"></p>
<div style="color: rgb(33, 33, 33); font-size: 15px;">
<ul>
<li>GLTPD1<br>
</li><li>C1orf86<br>
</li><li>C7orf63<br>
</li><li>PCNXL3</li></ul>
</div>
Thanks!
<p style="margin-top: 0px; margin-bottom: 0px;"></p>
<div style="margin-top: 0px; margin-bottom: 0px;"><br>
</div>
</div>
</div>
<br>
_______________________________________________<br>
Dev mailing list <span class="Apple-converted-space"> </span><a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info:<span class="Apple-converted-space"> </span><a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog:<span class="Apple-converted-space"> </span><a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
<br>
</div>
</div>
</div>
_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info:<span class="Apple-converted-space"> </span><a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog:<span class="Apple-converted-space"> </span><a href="http://www.ensembl.info/">http://www.ensembl.info/</a></div>
</blockquote>
</div>
<br>
</div>
</body>
</html>