Question: R : Get Gene Symbol From Refseq Id - Biomart Problem
gravatar for Nicolas Rosewick
6.3 years ago by
Belgium, Brussels
Nicolas Rosewick8.6k wrote:


I've several refseq id that I want to convert to gene symbol. So in R with biomaRt :

mart<- useDataset("hsapiens_gene_ensembl", useMart("ensembl"))
refseq <- c("NM_001271003")
getBM(filters="refseq_mrna", attributes="external_gene_id", values=refseq, mart=mart)

gives me logical(0)

But the gene is well defined in pubmed (TFPI2) :

The gene is also in ensembl :;g=ENSG00000105825;r=7:93514709-93520303 but in external references, the refseq id : NM_001271003 is not reported..

So is there an another way to get the gene symbol from refseq id using R ?


ensembl refseq • 6.4k views
ADD COMMENTlink modified 6.3 years ago by Emily_Ensembl20k • written 6.3 years ago by Nicolas Rosewick8.6k
gravatar for Emily_Ensembl
6.3 years ago by
Emily_Ensembl20k wrote:

The Ref Seq ID that you refer to is indeed very similar to the Ensembl transcript ENST00000222543, however ENST00000222543 actually aligns to a different RefSeq mRNA, NM_006528. If you look at these alignments of NM_001271003 and NM_006528, you can see that NM_006528 perfectly corresponds to the exons of ENST00000222543 whereas NM_001271003 differs by 33bp in one exon and 18bp in another exon. Ensembl chose the RefSeq which was the best fit to our model.

ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by Emily_Ensembl20k
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