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Hi Ashok,<br>
<br>
Mapping between resources is a complicated process which
unfortunately exposes some edge cases like this one.<br>
<br>
To map Ensembl genes to EntrezGene ids, there is no direct mapping
available, hence we map via their respective transcripts, Ensembl
transcripts and RefSeq mRNAs.<br>
Where the data is available, we attempt to map based on genomic
coordinates, but when everything else fails, the sequences are
aligned.<br>
Only the best hit is kept, but we do allow for mismatches as we know
models can vary between Ensembl and RefSeq, in particular regarding
UTR regions.<br>
In this particular example, the Ensembl transcript
<meta charset="utf-8">
ENST00000618217 aligns very well against 3 separate RefSeq sequences<br>
<a class="moz-txt-link-freetext" href="http://e81.ensembl.org/Homo_sapiens/Transcript/Similarity?db=core;g=ENSG00000196873;r=9:68232003-68300015;t=ENST00000618217">http://e81.ensembl.org/Homo_sapiens/Transcript/Similarity?db=core;g=ENSG00000196873;r=9:68232003-68300015;t=ENST00000618217</a><br>
corresponding to CBDW1, CBDW2 and CBDW3<br>
Another transcript, ENST00000377342, aligns against 2 different
RefSeq sequences, corresponding to CBDW3 and CBDW5<br>
<a class="moz-txt-link-freetext" href="http://e81.ensembl.org/Homo_sapiens/Transcript/Similarity?db=core;g=ENSG00000196873;r=9:68232003-68300015;t=ENST00000377342">http://e81.ensembl.org/Homo_sapiens/Transcript/Similarity?db=core;g=ENSG00000196873;r=9:68232003-68300015;t=ENST00000377342</a><br>
<br>
As a result, we have not one but 4 different EntrezGene ids for the
same Ensembl gene.<br>
Note that all these RefSeq sequences are predicted sequences, as
noted by the XM_ prefix.<br>
This means that we would never use any of those EntrezGene ids to
name the gene.<br>
However, we still provide the initial mappings as these are our best
guess as to which RefSeq transcript corresponds to which Ensembl
transcript.<br>
<br>
We are hoping to improve these mappings by including genomic
coordinate information for predicted models, as this is already done
for the curated RefSeq (NM_ like identifiers)<br>
This is unlikely to be available before the end of the year though.<br>
<br>
For correct gene naming, we recommend using HGNC identifiers, as
these are obtained via curated direct mappings from HGNC, who update
them regularly.<br>
<br>
<br>
Hope this helps,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 03/09/2015 20:04, Ragavendran, Ashok
wrote:<br>
</div>
<blockquote
cite="mid:20150903190421.B77B61344EB_5E899B5B@hx-mx2.ebi.ac.uk"
type="cite">
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charset=windows-1252">
hello,<br>
I came upon this while using the Biomart interface. There are
errors mapping Ensembl Id to entrezgeneid. The ensembl id maps to
the wrong entrez, when I click the entrez link it shows a
different ensembl Id. Attached is a screenshot of the results. The
Ensembl ID refers to CBWD3, but the entrezgeneId are for
CBDW1,CBDW2,CBDW5 and CBDW3. The last result is the correct one,
All others are wrong and they actually have different Ensembl IDs,
which is what i wanted to retreive.<br>
<br>
Is there something I am missing??<br>
<br>
Cheers<br>
Ashok<br>
====== Text based Results from querying the gene id
ENSG00000196873 =======<br>
Ensembl Gene ID EntrezGene ID<br>
ENSG00000196873 55871<br>
ENSG00000196873 150472<br>
ENSG00000196873 220869<br>
ENSG00000196873 445571<br>
<br>
<br>
===== Screenshot of results: May not come through ===<br>
<br>
<img src="cid:part1.08080305.06000608@ebi.ac.uk" alt=""><br>
<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 moz-do-not-send="true" 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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