Where Can I Find Out Whether A Microarray Platform Has A Probeset Against My Gene Of Interest

Question

[Ian Evans]

Is there some website or webpage that allows you to quickly see whether a particular microarray platform has probe sets against your gene of interest. I would be interested in finding out various Affymetrix, Agilent, Illumina platforms, and also for exon arrays. I know you can find this out from the annotation files made available by each provider separately, however I was wondering whether there was any company-independent source for this information.

[Ben]

Why not just use Ensembl biomart, enter your gene ID and select the probesets you're interested in under Attributes/External

[Neilfws]

This assumes that you're interested in the (limited) number of platforms provided in BioMart.

[polarise]

Do you have a particular reason why you are avoiding company-dependent information?

Answer 1

[Alex Paciorkowski]

Your best bet is going to the company product annotation and making a query there about coverage for your gene of interest, since they are the ones who make the array. You can also look in GEO data sets and see if the gene(s) of interest are included in the results. The methods for each experiment should tell you which array was used. But then I would still check with the manufacturer's annotations.