A few weeks ago I showed you how to convert gene IDs with BioMart. Yesterday I hosted a workshop on the Ensembl Genome Browser, given by Dr. Bert Overduin from EBI-EMBL. He gave several examples of very useful tasks that you can do very quickly and easily using BioMart. One, in particular, is something that I'm doing for a client in the core right now.
Let's say you have a set of genes in one species and you want to know the orthologs in another species and gene expression probes in that species you can use to assay those orthologs. For example, Table 1 in this paper reports 25 gene expression probes that are dysregulated in humans when exposed to benzene. What if you only had the U133A/B Affymetrix probe IDs and wanted to know the gene names? What if you also wanted all the Ensembl gene IDs, names, and descriptions of the mouse orthologs for these human genes? Further, what are the mouse Affymetrix 430Av2 probe IDs that you can use to assay these genes' expression in mouse? All this can be accomplished for a list of genes in about 60 seconds using BioMart. See the video below. Watch it on Youtube in 1080p if you're having a hard time reading the text.
If you want to try this yourself, head to BioMart and copy the list of Affy probe IDs below:
Youtube - Get Orthologs via BioMart