[ensembl-dev] Possibly incorrect entrezgene ids for CCL3L1, CCL3L1, HLA-DQA2

[Gerhard Burger]

Hi  Ameya,

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...

Kind regards,
Gerhard



On Mon, Nov 9, 2020 at 3:15 PM Ameya Chaubal <ameya at ebi.ac.uk> wrote:

> Hello Gerhard,
>
> Within the system, genes identified as alleles get associated with the
> external references of each other.
> From the biomart, this gets picked up as another attribute of a given
> Ensembl id and hence the mapping between the attributes.
>
> Thanks,
> Ameya
>
>
> On 3 Nov 2020, at 14:07, Gerhard Burger <g.a.burger at lacdr.leidenuniv.nl>
> wrote:
>
> Hi ensemble-dev,
>
> 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:
>
>     library(biomaRt)
>     ensembl <- useEnsembl(biomart = "genes", dataset =
> "hsapiens_gene_ensembl")
>     getBM(values = c("CCL3L1", "CCL3L3", "HLA-DQA1", "HLA-DQA2"),
>                attributes = c("entrezgene_id", "hgnc_symbol"),
>                filters = "hgnc_symbol", mart = ensembl)
>
> which gives:
>
>       entrezgene_id hgnc_symbol
>     1            6349      CCL3L1
>     2        414062      CCL3L1
>     3            6349      CCL3L3
>     4        414062      CCL3L3
>     5            3117  HLA-DQA1
>     6            3117   HLA-DQA2
>     7            3118   HLA-DQA2
>
> However, when I look up these hgnc symbols online I believe the result
> should be:
>
>         entrezgene_id hgnc_symbol
>     1          6349      CCL3L1
>     2      414062      CCL3L3
>     3          3117  HLA-DQA1
>     4          3118  HLA-DQA2
>
> The online sources:
>
> CCL3L1:
> https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:10628
> CCL3L3:
> https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:30554
> HLA-DQA1:
> https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:4942
> HLA-DQA2:
> https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:4943
>
> Also AnnotationDbi does give me the expected results:
>
>     require(AnnotationDbi)
>     require(org.Hs.eg.db)
>     AnnotationDbi::mapIds(org.Hs.eg.db,
>         keys=c("CCL3L1", "CCL3L3", "HLA-DQA1", "HLA-  DQA2"),
>         column = "ENTREZID", keytype = "SYMBOL")
>
> Am I doing something wrong or is this is bug?
>
> (biomaRt version 2.44.4, ensemble version 101)
>
> Kind regards,
> Gerhard
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