<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hello Gerhard,<div class=""><br class=""></div><div class="">Within the system, genes identified as alleles get associated with the external references of each other.</div><div class="">From the biomart, this gets picked up as another attribute of a given Ensembl id and hence the mapping between the attributes.</div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Ameya</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 3 Nov 2020, at 14:07, Gerhard Burger <<a href="mailto:g.a.burger@lacdr.leidenuniv.nl" class="">g.a.burger@lacdr.leidenuniv.nl</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi ensemble-dev,<div class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class=""> library(biomaRt)</div> ensembl <- useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl")<br class=""> getBM(values = c("CCL3L1", "CCL3L3", "HLA-DQA1", "HLA-DQA2"),<br class=""> attributes = c("entrezgene_id", "hgnc_symbol"),<br class=""> filters = "hgnc_symbol", mart = ensembl)<div class=""><br class=""></div><div class="">which gives:</div><div class=""><br class=""></div><div class=""> entrezgene_id hgnc_symbol<br class=""> 1 6349 CCL3L1<br class=""> 2 414062 CCL3L1<br class=""> 3 6349 CCL3L3<br class=""> 4 414062 CCL3L3<br class=""> 5 3117 HLA-DQA1<br class=""> 6 3117 HLA-DQA2<br class=""> 7 3118 HLA-DQA2<br class=""></div><div class=""><br class=""></div><div class="">However, when I look up these hgnc symbols online I believe the result should be:</div><div class=""><br class=""></div><div class=""> entrezgene_id hgnc_symbol<br class=""> 1 6349 CCL3L1<br class=""> 2 414062 CCL3L3<br class=""> 3 3117 HLA-DQA1<br class=""> 4 3118 HLA-DQA2 <br class=""></div><div class=""><br class=""></div><div class="">The online sources:</div><div class=""><br class=""></div><div class="">CCL3L1: <a href="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:10628" target="_blank" class="">https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:10628</a><br class=""></div><div class="">CCL3L3: <a href="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:30554" target="_blank" class="">https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:30554</a></div><div class="">HLA-DQA1: <a href="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:4942" target="_blank" class="">https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:4942</a><br class=""></div><div class="">HLA-DQA2: <a href="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:4943" target="_blank" class="">https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:4943</a><br class=""></div><div class=""><br class=""></div><div class="">Also AnnotationDbi does give me the expected results:</div><div class=""><br class=""></div><div class=""> require(AnnotationDbi)<br class=""> require(org.Hs.eg.db)<br class=""> AnnotationDbi::mapIds(org.Hs.eg.db, </div><div class=""> keys=c("CCL3L1", "CCL3L3", "HLA-DQA1", "HLA- DQA2"), </div><div class=""> column = "ENTREZID", keytype = "SYMBOL")<br class=""></div><div class=""><br class=""></div><div class="">Am I doing something wrong or is this is bug?</div><div class=""><br class=""></div><div class="">(biomaRt version 2.44.4, ensemble version 101)</div><div class=""><br class=""></div><div class="">Kind regards,</div><div class="">Gerhard</div></div>
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