Entering edit mode
I have a list of somatic mutations from multiple samples. Each mutation has a statistic that indicates confidence, and one gene on one tumor can have multiple mutations.
I did Fisher's exact test with the pathway database downloaded from Broad Institute website, but do not feel very happy about this.
Either (1) Pathways that are significantly mutated (2) Define new pathways related to this particular cancer type would be interesting.
Could any one please recommend any tools?
AIthough your question of interest is not directed to the purposes of this group, i think MAFFINN tool (http://www.inetbio.org/muffinn/) probably is a valid option for your goal.
Best,
Efstathios