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

[Ameya Chaubal]

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 <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 <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 <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 <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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