<div dir="ltr">Hi
Ameya,<div><br></div><div>Thanks for your reply, is there a way to get around that and get the expected(/desired) results? From your description it sounds like that might not be so straightforward...</div><div><br></div><div>Kind regards,</div><div>Gerhard</div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Nov 9, 2020 at 3:15 PM Ameya Chaubal <<a href="mailto:ameya@ebi.ac.uk">ameya@ebi.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;">Hello Gerhard,<div><br></div><div>Within the system, genes identified as alleles get associated with the external references of each other.</div><div>From the biomart, this gets picked up as another attribute of a given Ensembl id and hence the mapping between the attributes.</div><div><br></div><div>Thanks,</div><div>Ameya</div><div><br><div><br><blockquote type="cite"><div>On 3 Nov 2020, at 14:07, Gerhard Burger <<a href="mailto:g.a.burger@lacdr.leidenuniv.nl" target="_blank">g.a.burger@lacdr.leidenuniv.nl</a>> wrote:</div><br><div><div dir="ltr">Hi ensemble-dev,<div><br></div><div>I'm trying to get entrizid for hgnc gene symbols, but I got some confusing results for CCL3L1, CCL3L1, HLA-DQA1, HLA-DQA2. I am using the following R code:</div><div><br></div><div> library(biomaRt)</div> ensembl <- useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl")<br> getBM(values = c("CCL3L1", "CCL3L3", "HLA-DQA1", "HLA-DQA2"),<br> attributes = c("entrezgene_id", "hgnc_symbol"),<br> filters = "hgnc_symbol", mart = ensembl)<div><br></div><div>which gives:</div><div><br></div><div> entrezgene_id hgnc_symbol<br> 1 6349 CCL3L1<br> 2 414062 CCL3L1<br> 3 6349 CCL3L3<br> 4 414062 CCL3L3<br> 5 3117 HLA-DQA1<br> 6 3117 HLA-DQA2<br> 7 3118 HLA-DQA2<br></div><div><br></div><div>However, when I look up these hgnc symbols online I believe the result should be:</div><div><br></div><div> entrezgene_id hgnc_symbol<br> 1 6349 CCL3L1<br> 2 414062 CCL3L3<br> 3 3117 HLA-DQA1<br> 4 3118 HLA-DQA2 <br></div><div><br></div><div>The online sources:</div><div><br></div><div>CCL3L1: <a href="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:10628" target="_blank">https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:10628</a><br></div><div>CCL3L3: <a href="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:30554" target="_blank">https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:30554</a></div><div>HLA-DQA1: <a href="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:4942" target="_blank">https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:4942</a><br></div><div>HLA-DQA2: <a href="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:4943" target="_blank">https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:4943</a><br></div><div><br></div><div>Also AnnotationDbi does give me the expected results:</div><div><br></div><div> require(AnnotationDbi)<br> require(org.Hs.eg.db)<br> AnnotationDbi::mapIds(org.Hs.eg.db, </div><div> keys=c("CCL3L1", "CCL3L3", "HLA-DQA1", "HLA- DQA2"), </div><div> column = "ENTREZID", keytype = "SYMBOL")<br></div><div><br></div><div>Am I doing something wrong or is this is bug?</div><div><br></div><div>(biomaRt version 2.44.4, ensemble version 101)</div><div><br></div><div>Kind regards,</div><div>Gerhard</div></div>
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