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Question: Get gene symbols from gene ids for mouse using BioMart
1
gravatar for nikitavlassenko
2.6 years ago by
nikitavlassenko • 50
nikitavlassenko • 50 wrote:

I am trying to get gene symbols for gene ids that I got for mouse datasets. Gene ids look like that: 0610009B22Rik. The code that I am trying to utilize is the following one: 

ensembl <- useMart("ensembl", dataset="mmusculus_gene_ensembl")
mouse_gene_ids <- dataset[, 1]
foo <- getBM(attributes=c('ensembl_gene_id',
                      'external_gene_name'),
         filters = 'genedb',
         values = mouse_gene_ids,
         mart = ensembl)

I am getting zero results as an output after the query runs. I guess filters parameter is wrong. Any suggestions would be greatly appreciated.
gene ids biomart mouse gene symbols • 8.1k views
ADD COMMENT • link •
modified 2.6 years ago • written 2.6 years ago by nikitavlassenko • 50
7
gravatar for Mike Smith
2.6 years ago by
Mike Smith • 1.5k
EMBL Heidelberg / de.NBI
Mike Smith • 1.5k wrote:

The filter you need is mgi_symbol e.g.

library(biomaRt)

ensembl <- useMart("ensembl", dataset="mmusculus_gene_ensembl")
mouse_gene_ids  <- "0610009B22Rik"

foo <- getBM(attributes=c('ensembl_gene_id',
                          'external_gene_name'),
             filters = 'mgi_symbol',
             values = mouse_gene_ids,
             mart = ensembl)

Here's the result:

> foo
     ensembl_gene_id external_gene_name
1 ENSMUSG00000007777      0610009B22Rik

I find the best way to choose the correct filter is to start with the Ensembl BioMart web interface, use the examples in the Filters -> external references ID list dropdown list to find the format I'm using, and then hit the XML button near the top. This will let you see the filter name required by biomaRt
ADD COMMENT • link written 2.6 years ago by Mike Smith • 1.5k 
library(biomaRt)
listMarts()
ensembl=useMart("ensembl")
datasets <- listDatasets(ensembl)
head(datasets)
ensembl = useDataset("mmusculus_gene_ensembl", mart = ensembl)
entrzID=c("14455", "80904", "94275")
filters = listFilters(ensembl)
filters[1:50,]
getBM(attributes = c("ensembl_gene_id", "external_gene_name"), filters = "mgi_symbol", values = entrzID, mart = ensembl)

output:

[1] ensembl_gene_id    external_gene_name
<0 rows> (or 0-length row.names)

Why can't I get any gene symbol

ADD REPLY • link modified 13 months ago • written 13 months ago by Kai_Qi • 100
1

Perhaps you want to try the entrezgene_id filter instead?

getBM(attributes = c("ensembl_gene_id", "external_gene_name"), 
       filters = "entrezgene_id", 
       values = entrzID, 
       mart = ensembl)

     ensembl_gene_id external_gene_name
1 ENSMUSG00000040415               Dtx3
2 ENSMUSG00000025151             Maged1
ADD REPLY • link written 13 months ago by Mike Smith • 1.5k

Yes. I tried it and it works.

Thank you so much for the help!

ADD REPLY • link written 13 months ago by Kai_Qi • 100
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