Question: Gviz and Biomart Gene ID
0
gravatar for shankasal
12 months ago by
shankasal10
shankasal10 wrote:

I'm trying to visualize a region on the mouse chromosome (genome mm10) that contains a the Il7r gene. For the life of me I cannot figure out how to switch the gene name from the Ensembl format (Eg. ENMUSG000...) to the "common" gene name (Eg. Il7r). I've tried a number of things including changing the $symbol in object fm (code shown below) to trying different filters in the bm object (code shown below).

In the Gviz User guide is states:

"The internal .getBMFeatureMAP is helpful to set up the feature mapping which is necessary because Ensembl used to call the gene symbol field external_gene_id in that release."

I can get the gene symbol to display Il7r if I use the mm9 genome, but not with the mm10 genome, since parameters have been changed.

I've been using this (http://useast.ensembl.org/biomart/martview/ca12e7079979ccf12cb1f6269e0e623a) to try and figure the right symbol name to use.

I've been using this (http://useast.ensembl.org/biomart/martservice?redirect=no&type=filters&dataset=mmusculus_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default) to try and determine the right filter.

Here's the code I'm using:

ensembl <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", 
               dataset = "mmusculus_gene_ensembl",
               host = "useast.ensembl.org", archive = FALSE, ensemblRedirect = FALSE,
               verbose = TRUE)

fm = Gviz:::.getBMFeatureMap()
fm["symbol"] = "ensembl_gene_id"

lim <- c(9450000, 9590000)

bm <- BiomartGeneRegionTrack(genome = "mm10", chromosome='chr15',
                            start=lim[1], end = lim[2], 
                            biomart = ensembl, filter=list("with_refseq_mrna"=TRUE), 
                            size = 4, name = "RefSeq",
                            protein_coding = "black", col.line = NULL, cex = 7,
                            collapseTranscripts = "longest", featureMap = fm)

AT <- GenomeAxisTrack()

plotTracks(list(bm, AT),
           from = lim[1], to = lim[2],
           transcriptAnnotation = "symbol", window = "auto", 
           cex.title = 1, fontsize = 10, type = "histogram")

Thanks for any help!!!

R • 518 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by shankasal10
0
gravatar for shankasal
12 months ago by
shankasal10
shankasal10 wrote:

I found a way to get the symbols that I want here:

https://support.bioconductor.org/p/95378/

Works well, but I figured there'd be an easier way???

ADD COMMENTlink written 12 months ago by shankasal10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 913 users visited in the last hour