Question: biomaRt: Extracting data for a particular isoform (R/bioconductor)
gravatar for bsmith030465
2.8 years ago by
United States
bsmith03046590 wrote:


I was trying to extract the 5' UTR and 3'UTR coordinates for a particular isoform. My code is:



mart = useMart("ensembl")

getBM(attributes = c("5_utr_start","5_utr_end","3_utr_start","3_utr_end"),filters = "hgnc_symbol",value = "AAGAB",mart = ensembl)


Is there a way that I can specify that for the gene (AAGAB), I want information for isoform 001 (ie. AAGAB-001)? Else, how do I process the data given by my query above so that I can get this information?

Or should I be doing something else altogether?




bioconductor extract utr biomart • 1.1k views
ADD COMMENTlink modified 2.7 years ago by Biostar ♦♦ 20 • written 2.8 years ago by bsmith03046590

I suspect that specifying a query based on gene symbol is not the way to go.  You'll probably need to specify a transcript in the filter.  Do you know a transcript ID?

ADD REPLYlink written 2.8 years ago by Sean Davis24k

Thanks for the reply. So, if I want to get the details of "ENST00000538028", I should use something like:

ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")

xx <- getBM(attributes = c("5_utr_start","5_utr_end","3_utr_start","3_utr_end"),
                    filters = "ensembl_transcript_id",value = "ENST00000261880",mart = ensembl)


Am I using the right filters?

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by bsmith03046590

Looks right.  You might want to specify that ensembl_transcript_id in the attributes as well.

ADD REPLYlink written 2.8 years ago by Sean Davis24k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1165 users visited in the last hour