Question

Gene Locus to ENSEMBL ID

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5.2 years ago

Scott McKay ▴ 30

Is there some way (biomaRt or not) that will allow me to convert the gene locus (NM_###) to it's ensembl gene id?

r biomart • 1.9k views

ADD COMMENT • link updated 5.1 years ago by Biostar 20 • written 5.2 years ago by Scott McKay ▴ 30

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Assuming this is about RefSeq accession numbers, note that NM prefixes are used for curated protein-coding transcripts, not genomic loci. Associating an accession number with the wrong entity type may mislead you.

ADD REPLY • link 5.2 years ago by Jean-Karim Heriche 27k

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What have you tried? Did you look at listAttributes() etc in biomaRt? Search for other packages such as org.Hs.eg.db?

ADD REPLY • link 5.2 years ago by Ram 44k

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I looked at searchAttributes(mart=ensembl, pattern=locus) and then searched the Attributes for some loci information but turned up nothing

ADD REPLY • link 5.2 years ago by Scott McKay ▴ 30

score 2 · Accepted Answer · 2019-10-06

If you want to convert RefSeq 'NM' or 'NR' identifiers, then use refseq_mrna or refseq_ncrna attributes, repectively, as I mention at the end of my answer, here: A: Affymetrix Human Genome U133 Plus 2.0 Array

Also a practical example shown here by another user: A: biomaRt doesn't convert refseq_rna to flybase_gene_id