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hi Magali,<br>
<br>
Thanks again for the prompt response. This again relates back to my previous post on the Entrez IDs and the webpage issue<br>
<br>
<i> <a class="moz-txt-link-freetext" href="http://useast.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=ENSMUSG00000106677;r=5:87459490-87490871;t=ENSMUST00000147854">
http://useast.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=ENSMUSG00000106677;r=5:87459490-87490871;t=ENSMUST00000147854</a></i><i><br>
</i><i><br>
</i><i> <a class="moz-txt-link-freetext" href="http://useast.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=ENSMUSG00000029268;r=5:87459490-87482260">
http://useast.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=ENSMUSG00000029268;r=5:87459490-87482260</a></i><br>
<br>
As you can see each of the genes above are assigned to only one MGI id which was misleading whereby I was unsure what the correct set of results were.
<br>
<br>
Does this mean we should not rely on the search results for a gene and for anything definite use the biomart tool instead??<br>
<br>
<b>Please don't get me wrong, I think that the Ensembl database is a really wonderful resource and I just wanted to bring these aspects to your attention in the hope that it helps in making it better.</b><br>
<br>
Furthermore, if I search using ensembl gene id for Ugt2a1 i get the following results<br>
<i> </i><i> Ensembl Gene ID Associated Gene Name MGI ID MGI symbol Ensembl Transcript ID</i><i><br>
</i><i> ENSMUSG00000106677 Ugt2a1 MGI:2149905 Ugt2a1 ENSMUST00000147854</i><br>
<br>
Whereas results from MGI data show that <i>ENSMUSG00000106677 </i>is associated with both MG1 ids.
<br>
>From MGI database:<br>
<small><br>
<i>MGI:2149905 Ugt2a1 O Gene UDP glucuronosyltransferase 2 family, polypeptide A1 43.56 5 87459490 87490871 - BB375653|AK140757|AF184901|BC048926 NM_053184 OTTMUST00000066277|OTTMUST00000138762
<b>ENSMUST00000079811|ENSMUST00000144144|ENSMUST00000147854</b> OTTMUSP00000033195|OTTMUSP00000072911 ENSMUSP00000078740|ENSMUSP00000114842|ENSMUSP00000114583 NP_444414</i></small><i>
</i><i><br>
</i><i><br>
</i><i><small>MGI:3576095 Ugt2a2 O Gene UDP glucuronosyltransferase 2 family, polypeptide A2 43.56 5 87459493 87482258 - BC058786|BC048920 NM_001024148 OTTMUST00000066277|OTTMUST00000138762
<b>ENSMUST00000144144|ENSMUST00000147854|ENSMUST00000079811 </b> OTTMUSP00000072911|OTTMUSP00000033195 ENSMUSP00000078740|ENSMUSP00000114842|ENSMUSP00000114583 NP_00101931</small></i><i>9</i><br>
<br>
I see their web page is inconsistent and only lists one of the Ensembl gene IDs, I will write them and see if they can correct the inconsitency.<br>
<br>
<br>
Thanks again for all your help.<br>
<br>
Cheers<br>
Ashok<br>
<br>
<br>
<div class="moz-cite-prefix">On 9/4/15 7:00 AM, <a class="moz-txt-link-abbreviated" href="mailto:dev-request@ensembl.org">
dev-request@ensembl.org</a> wrote:<br>
</div>
<blockquote cite="mid:mailman.1.1441364403.21930.dev@ensembl.org" type="cite">
<pre wrap="">Message: 1
Date: Fri, 04 Sep 2015 10:11:35 +0100
From: mag <a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:mr6@ebi.ac.uk"><mr6@ebi.ac.uk></a>
Subject: Re: [ensembl-dev] Bug?? Biomart mapping of Mouse ID to MGI
ids
To: <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:dev@ensembl.org">dev@ensembl.org</a>
Message-ID: <a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:55E96047.5010702@ebi.ac.uk"><55E96047.5010702@ebi.ac.uk></a>
Content-Type: text/plain; charset=windows-1252; format=flowed
Hi Ashok,
MGI mappings, like HGNC mappings, are direct mappings we import directly
from the source.
According to this database, both Ugt2a1 and Ugt2a2 map to the Ensembl gene.
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.informatics.jax.org/marker/MGI:2149905">http://www.informatics.jax.org/marker/MGI:2149905</a>
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.informatics.jax.org/marker/MGI:3576095">http://www.informatics.jax.org/marker/MGI:3576095</a>
Looking at the gene models, there is an overlap with ENSMUSG00000106677,
which corresponds to Ugt2a1.
I suspect MGI:2149905 needs to be updated to link to ENSMUSG00000106677
instead of ENSMUSG00000029268, but we cannot change it at our end.
If you have any experimental evidence to correct those mappings, please
contact MGI (<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:mgi-help@jax.org">mgi-help@jax.org</a>) to let them know.
Regards,
Magali
On 03/09/2015 21:34, Ragavendran, Ashok wrote:
</pre>
<blockquote type="cite" style="color: #000000;">
<pre wrap=""><span class="moz-txt-citetags">> </span>Hello,
<span class="moz-txt-citetags">> </span> I have come upon a subsequent bug where there is an erroneous
<span class="moz-txt-citetags">> </span>mapping of Ensembl Mouse ID to the corresponding MGI:ID using BioMart (
<span class="moz-txt-citetags">> </span>both in bioconductor and the Ensembl web interface). Please let me know
<span class="moz-txt-citetags">> </span>if I am missing something in this regard. Correct mapping should be only
<span class="moz-txt-citetags">> </span>to 3576095 and not to 2149905.
<span class="moz-txt-citetags">></span>
<span class="moz-txt-citetags">> </span> Cheers
<span class="moz-txt-citetags">> </span> Ashok
<span class="moz-txt-citetags">></span>
<span class="moz-txt-citetags">> </span>===== Text based Results from querying the gene id ENSMUSG00000029268
<span class="moz-txt-citetags">> </span>=======
<span class="moz-txt-citetags">></span>
<span class="moz-txt-citetags">> </span>Ensembl Gene ID Status (gene) MGI ID MGI symbol
<span class="moz-txt-citetags">> </span>ENSMUSG00000029268 KNOWN MGI:2149905 Ugt2a1
<span class="moz-txt-citetags">> </span>ENSMUSG00000029268 KNOWN MGI:3576095 Ugt2a2
<span class="moz-txt-citetags">></span>
</pre>
</blockquote>
<pre wrap="">
</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Ashok Ragavendran
Bioinformatics Specialist
Center for Human Genetic Research
Massachusetts General Hospital
Richard B. Simches Research Center
185 Cambridge St, Boston MA 02114
<a class="moz-txt-link-abbreviated" href="mailto:aragavendran@mgh.harvard.edu">aragavendran@mgh.harvard.edu</a>
ph: +1-617-726-1329</pre>
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