Video Tip: Convert Gene IDs with Biomart

I get asked frequently how to convert from one gene identifier to another. This can be tricky, especially when relying on gene symbols, as Will pointed out in a previous post a few years ago. There are several tools that can do this, including DAVID and the previously mentioned new Biomart ID Converter, but I still prefer using the Ensembl Biomart for this because of its added flexibility and annotation.

I've started putting together video screencasts for things like this, especially when several of the core's clients ask the same question. In this example, I'll show you how to quickly convert from the Affymetrix Mouse Gene 1.0 ST microarray probeset IDs to an Ensembl gene ID and gene symbol.



You can also do this programmatically in R using the biomaRt package in Bioconductor.

	# Fit your model on your expressionset and design matrix
	fit <- lmFit(eset, design)
	fit2 <- contrasts.fit(fit, contrast.matrix)
	fit2 <- eBayes(fit2)
	results <- topTable(fit2)
	# get biomart annotation
	library(biomaRt)
	mart <- useMart("ensembl", dataset="mmusculus_gene_ensembl")
	attributes <- c("affy_mogene_1_0_st_v1", "chromosome_name",
	"start_position","end_position", "ensembl_gene_id",
	"external_gene_id", "description")
	genes <- getBM(attributes=attributes, filters="affy_mogene_1_0_st_v1",
	values=topTable$ID, mart=mart, uniqueRows=T)

view raw ensembl-biomart.r hosted with ❤ by GitHub