Duplicates in Biomart Query, Ensembl ID maps to multiple Entrez genes.
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Entering edit mode
4.7 years ago
adam.faranda ▴ 110

When I run the following query on "ENSMUSG00000001175", I retrieve records for 2 corresponding entrezgene_id's (Calm1 and Calm2). The first record is correct, however the second record, "12314" is actually Calm2.

annot<-getBM(
  attributes = c(
    "ensembl_gene_id", "entrezgene_id",
    "mgi_symbol", "mgi_description", "chromosome_name"
  ),
  filters = "ensembl_gene_id",
  values="ENSMUSG00000001175",
  mart = useMart(
    "ensembl",
    dataset = "mmusculus_gene_ensembl"
  )
)

Query Results

> annot
     ensembl_gene_id entrezgene_id mgi_symbol mgi_description chromosome_name
1 ENSMUSG00000001175         12313      Calm1    calmodulin 1              12
2 ENSMUSG00000001175         12314      Calm1    calmodulin 1              12

The ncbi page for 12314 / Calm2, correctly cross references "ENSMUSG00000036438". Is there an additional filter I can specify to remove results like these?

Ensembl NCBI biomaRt • 1.4k views
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Entering edit mode

I'll pass this onto our team because I agree that this link to NCBI is wrong.

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