how to retrieve mouse (mm10) gene information from Ensemble using Biomart inR

Question

[M K]

I am tying to retrieve mouse mm10 gene information using biomart library in R, but I don't know how to do that

(The information that I need are mm10.knownGene.name, mm10.knownGene.chrom, mm10.knownGene.strand, mm10.knownGene.txStart, mm10.knownGene.txEnd and mm10.kgXref.geneSymbol)

source("http://bioconductor.org/biocLite.R")
biocLite("biomaRt")

library(biomaRt)

mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl")
listFilters(mouse)

getBM(attributes=c("ensembl_gene_id", "mgi_symbol"), filters= "mgi_symbol", mart=mouse)

[komal.rathi]

What is mm10.kgXref.geneSymbol?

[M K]

The kgXref.geneSymbol is the gene name that I got when downloaded the known gene from UCSC website using table browser

Answer 1

[komal.rathi]

If you just want mm10 symbol, chr, strand, transcript start & end, you could do this:

res <- getBM(attributes = c("ensembl_gene_id", "mgi_symbol","chromosome_name",'strand','transcript_start','transcript_end'), mart = mouse)

If you have list of genes:

#genesym is a character vector of gene symbols
res <- getBM(attributes = c("ensembl_gene_id", "mgi_symbol","chromosome_name",'strand','transcript_start','transcript_end'), filters = genesym, mart = mouse)

[M K]

Thanks Komal for helping me, I run that code and it works. But I have question about how can I assign the version release (i.e I am going to run this code with different species like human (hg19)) so here I don't know what release I will retrieve from ensemble. Is there any way to include release# in this code.

[Sakti]

The current Ensembl database should be mm10, the most up to date one. For changing genomic versions see my reply.

Answer 2

[Sakti]

library(biomaRt)
ensembl <- useMart("ensembl", dataset="mmusculus_gene_ensembl")
annot<-getBM(c("ensembl_gene_id", "mgi_symbol", "chromosome_name", "strand", "start_position", "end_position","gene_biotype"), mart=ensembl)

# For older biomart releases I have used
ensembl <- useMart("ENSEMBL_MART_ENSEMBL", dataset="mmusculus_gene_ensembl", host="jul2012.archive.ensembl.org")

#modify the host depending on when your genomic version was released, or which ensembl archive you want to use

[M K]

I got it. Thanks a lot Sakti.