<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Ivan<div>This is a well known issue with BioMart which we have fed back to the BioMart developers. If you take a look a this gene on the Ensembl website you will understand what is happening here:</div><div><br></div><div><a href="http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000072110;r=14:69340860-69446157">http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000072110;r=14:69340860-69446157</a></div><div><br></div><div><br></div><div>You will see that this gene has 21 transcripts. This corresponds to your first query in BioMart. When you add the attribute for UniProt accession, this essentially acts like a filter as you only retrieve transcripts that are protein coding (there are 14 protein coding transcripts which corresponds to your second query in BioMart). The tools we use to build the gene mart will not currently allow us to add a necessary left join to allow retrieval of all transcripts in the results whether protein coding or not. The reason you don't see this issue in the NCBI36 BioMart is because there were only 2 protein coding transcripts for this gene in in 2009 so you will retrieve everything. </div><div><br></div><div><a href="http://may2009.archive.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000072110;r=14:69340860-69446157">http://may2009.archive.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000072110;r=14:69340860-69446157</a></div><div><br></div><div>I hope this makes sense but please don't hesitate to get back to me if you require more information.</div><div>Regards</div><div>Rhoda</div><div><br></div><div><br><div><div>On 31 Jul 2012, at 20:24, Ivan Kel wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Greetings, <br><br>I am using Ensembl Biomart to map Ensembl Gene IDs to Transcript IDs and UniProt/SwissProt Accession numbers. <br>Surprisingly, in several cases the corresponding Transcript IDs found for a Gene ID deffer depending on whether or not I add the UniProt number to the search. <br>
To clarify here is an example:<br>Ensembl Gene ID: ENSG00000072110<br>Result using only GeneID and TranscriptID: <br><table style="position: static; z-index: auto; "><tbody><tr><th><font size="1">Ensembl Gene ID</font></th>
<th><font size="1">Ensembl Transcript ID</font></th>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000193403" target="_blank">ENST00000193403</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556083" target="_blank">ENST00000556083</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553882" target="_blank">ENST00000553882</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000394419" target="_blank">ENST00000394419</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000438964" target="_blank">ENST00000438964</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000376839" target="_blank">ENST00000376839</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000555075" target="_blank">ENST00000555075</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000538545" target="_blank">ENST00000538545</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000544964" target="_blank">ENST00000544964</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553290" target="_blank">ENST00000553290</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556432" target="_blank">ENST00000556432</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556343" target="_blank">ENST00000556343</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000555616" target="_blank">ENST00000555616</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556433" target="_blank">ENST00000556433</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000554508" target="_blank">ENST00000554508</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000554158" target="_blank">ENST00000554158</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553370" target="_blank">ENST00000553370</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553779" target="_blank">ENST00000553779</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556571" target="_blank">ENST00000556571</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553659" target="_blank">ENST00000553659</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556203" target="_blank">ENST00000556203</a></font></td></tr></tbody></table>
<br>Result using only GeneID and TranscriptID and UniProtID:<br><table><tbody><tr><th><font size="1">Ensembl Gene ID</font></th>
<th><font size="1">Ensembl Transcript ID</font></th>
<th><font size="1">UniProt/SwissProt Accession</font></th>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000193403" target="_blank">ENST00000193403</a></font></td>
<td><font size="1"><a href="http://www.uniprot.org/uniprot/P12814" target="_blank">P12814</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000394419" target="_blank">ENST00000394419</a></font></td>
<td><font size="1"><a href="http://www.uniprot.org/uniprot/P12814" target="_blank">P12814</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000438964" target="_blank">ENST00000438964</a></font></td>
<td><font size="1"><a href="http://www.uniprot.org/uniprot/P12814" target="_blank">P12814</a></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000376839" target="_blank">ENST00000376839</a></font></td>
<td><font size="1"><br></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000555075" target="_blank">ENST00000555075</a></font></td>
<td><font size="1"><br></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000538545" target="_blank">ENST00000538545</a></font></td>
<td><font size="1"><br></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000544964" target="_blank">ENST00000544964</a></font></td>
<td><font size="1"><br></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553290" target="_blank">ENST00000553290</a></font></td>
<td><font size="1"><br></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000555616" target="_blank">ENST00000555616</a></font></td>
<td><font size="1"><br></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556433" target="_blank">ENST00000556433</a></font></td>
<td><font size="1"><br></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553370" target="_blank">ENST00000553370</a></font></td>
<td><font size="1"><br></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553779" target="_blank">ENST00000553779</a></font></td>
<td><font size="1"><br></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556571" target="_blank">ENST00000556571</a></font></td>
<td><font size="1"><br></font></td>
</tr>
<tr>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110" target="_blank">ENSG00000072110</a></font></td>
<td><font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553659" target="_blank">ENST00000553659</a></font></td>
</tr></tbody></table><font size="1"> <br></font><br><br>Please notice that the transcripts found for the Gene ENSG00000072110 differ between the two cases (e.g. <font size="1"><a href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556083" target="_blank">ENST00000556083</a> is not present in the second results)</font>.<br>
<br>For this analysis I use the current Biomart version. This problem does not occur if I use the older Biomart (hg18, Biomart archive from 2009, NCBI36). <br><br>Am I missing something?<br><br>Thank you very much in advance.<br>
<br>Ivan<br><br>
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