Friday, May 11, 2012

Video Tip: Use Ensembl BioMart to Quickly Get Ortholog Information

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:

207630_s_at
221840_at
219228_at
204924_at
227613_at
223454_at
228962_at
214696_at
210732_s_at
212371_at
225390_s_at
227645_at
226652_at
221641_s_at
202055_at
226743_at
228393_s_at
225120_at
218515_at
202224_at
200614_at
212014_x_at
223461_at
209835_x_at
213315_x_at

Youtube - Get Orthologs via BioMart

1 comment:

  1. Hi there, Great post! It was vwery helpful (was going crazy with my probeset id's) I am a master's degree student in Bioinformatics. I was trying to get information from Biomart and i was wondering what exactly "Pathology (egenetics)" and "Cell type (egenetics)"
    is the meaning? I guess they refer to the expression of a particular gene in a particular cell type and/or pathology. how can i exactly read these results? Which is the source of these informations?
    Thanks again for your help

    ReplyDelete

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