Question: Gene Locus to ENSEMBL ID
0
gravatar for Scott McKay
4 months ago by
Scott McKay20
Scott McKay20 wrote:

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

biomart R • 230 views
ADD COMMENTlink modified 12 weeks ago by Biostar ♦♦ 20 • written 4 months ago by Scott McKay20
1

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 REPLYlink written 4 months ago by Jean-Karim Heriche21k

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

ADD REPLYlink written 4 months ago by RamRS25k

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

ADD REPLYlink written 4 months ago by Scott McKay20
2
gravatar for Kevin Blighe
4 months ago by
Kevin Blighe54k
Kevin Blighe54k wrote:

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

ADD COMMENTlink written 4 months ago by Kevin Blighe54k
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