Wednesday, July 15, 2009

Gene ontology tool suggestions

I have used a few GO tools in the past, but after looking at the massive list of tools on the gene ontology page I'm hoping someone can give me a good suggestion for my problem.

Basically, I have several lists of GO terms (~4-15 terms per list) and I would like to see if at a "higher" branch they share a common molecular function. Ideally, a tool that could be run from the command line and outputs significance scores would be great, but a GUI tool would also work since I have about 70 lists that I would need to run.

Note, that this is slightly different than the usual over-representation analysis which usually takes a list of genes as input. In my problem I am starting with GO terms.

Any suggestions would really be welcome!