Geo Profiles For Two Gene Symbols At Once?

Question

[Qdjm]

As a way of showing support for an inferred co-expression interaction, I want to be able to construct a URL-based query to GEO profiles that contains a GDS or a GSE identifier and two gene identifiers and get a webpage of that contains both their expression profiles, plus information about samples etc.

For example, I'd like to construct one URL to bring me to a webpage that contains the content of the TP53 profile in GDS3318 and the BARD1 profile in GDS3318. This URL doesn't have to link to GEO profiles, it could be a third-party webserver, if such a thing exists.

I know I could strip the two webpages and reconstruct my magic page but I was hoping for a more direct solution. Ideas?

Answer 1

[Sean Davis]

You could consider using the GEOquery Biodonductor package and R to do this, combined with a small CGI script. Note that GEOquery can work from cached files locally, so once a GDS/GSE has been downloaded once by GEOquery, it need not be downloaded again.

P.S. I am the author of said package, so take this with a grain of salt.

[Qdjm]

Hi Sean, Thanks for the pointer -- this looks like a very useful package. I was hoping that someone else had already set up the webserver you recommend but it's true, we could set up our own server to do it. Not an ideal solution though.