<div><br></div><div>Dear Ensembl users,</div><div><br></div><div>firstly, congratulations. Ensembl is a nice resource which we don't have in the bacterial world!</div><div><br></div><div>I have a question about some very highly expressed genes which are lacking annotations in the current Ensembl database v62.</div>
<div><br></div><div>I am using the edgeR bioconductor package to analyse human RNA-seq data. Some of the most important genes in the dataset</div><div>have Ensembl IDs, but no annotation attached (see examples below, eg. ENSG00000257107).</div>
<div><br></div><div>Are these old, too new or am I missing something here?</div><div><br></div><div>If I look up the gene on the Ensembl website I get. (<span class="Apple-style-span" style="color: rgb(85, 85, 85); font-family: 'Luxi Sans', Helvetica, Arial, Geneva, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); ">IDHistory_gene</span>)</div>
<div><span class="Apple-style-span" style="color: rgb(85, 85, 85); font-family: 'Luxi Sans', Helvetica, Arial, Geneva, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); ">Ensembl gene ENSG00000257107 is no longer in the database and has not been mapped to any newer identifiers</span></div>
<div><br></div><div>In fact, the edgeR ensembl database has about 52000 entries, but the bioMart export only gives me about 22000 entries with annotation.</div><div>Surely at least the important highly expressed genes must have been mapped to other identifiers if they have been removed ?</div>
<div><br></div><div><br></div><div><br></div><div><br></div><div>Thanks for any help!</div><div>Regards,</div><div>Colin</div><div><br></div><div><font class="Apple-style-span" size="3">
<table frame="VOID" cellspacing="0" cols="4" rules="NONE" border="0">
<colgroup><col width="129"><col width="86"><col width="86"><col width="86"></colgroup>
<tbody>
<tr>
<td width="129" height="17" align="LEFT">ENSG00000196565</td>
<td width="86" align="LEFT">HBG2</td>
<td width="86" align="CENTER">11</td>
<td width="86" align="LEFT">hemoglobin, gamma G [Source:HGNC Symbol;Acc:4832]</td>
</tr>
<tr>
<td height="17" align="LEFT">ENSG00000188536</td>
<td align="LEFT">HBA2</td>
<td align="CENTER">16</td>
<td align="LEFT">hemoglobin, alpha 2 [Source:HGNC Symbol;Acc:4824]</td>
</tr>
<tr>
<td height="17" align="LEFT">ENSG00000244734</td>
<td align="LEFT">HBB</td>
<td align="CENTER">11</td>
<td align="LEFT">hemoglobin, beta [Source:HGNC Symbol;Acc:4827]</td>
</tr>
<tr>
<td height="17" align="LEFT">ENSG00000206172</td>
<td align="LEFT">HBA1</td>
<td align="CENTER">16</td>
<td align="LEFT">hemoglobin, alpha 1 [Source:HGNC Symbol;Acc:4823]</td>
</tr>
<tr>
<td height="17" align="LEFT">ENSG00000257107</td>
<td align="LEFT"></td><td align="CENTER"><br></td>
<td align="LEFT"><br></td>
</tr>
<tr>
<td height="17" align="LEFT">ENSG00000255592</td>
<td align="LEFT"><br></td>
<td align="CENTER"><br></td>
<td align="LEFT"><br></td>
</tr>
<tr>
<td height="17" align="LEFT">ENSG00000210082</td>
<td align="LEFT"><br></td>
<td align="CENTER"><br></td>
<td align="LEFT"><br></td>
</tr>
<tr>
<td height="17" align="LEFT">ENSG00000211459</td>
<td align="LEFT"><br></td>
<td align="CENTER"><br></td>
<td align="LEFT"><br></td>
</tr>
<tr>
<td height="17" align="LEFT">ENSG00000105372</td>
<td align="LEFT">RPS19</td>
<td align="CENTER">19</td>
<td align="LEFT">ribosomal protein S19 [Source:HGNC Symbol;Acc:10402]</td>
</tr>
<tr>
<td height="17" align="LEFT">ENSG00000198712</td>
<td align="LEFT">MT-CO2</td>
<td align="CENTER">MT</td>
<td align="LEFT">mitochondrially encoded cytochrome c oxidase II [Source:HGNC Symbol;Acc:7421]</td>
</tr>
</tbody>
</table></font></div><div><br></div><div><br></div><div><br></div>