Hi there. I am writing after reviewing Biostar threads for information on pathway analysis. I could not find relevant answers on exome data in the context of pathway analysis (after mapping exome data to genes and then to relevant pathways)

I have also used DAVID and managed to get pathway maps in KEGG (but this only displays genes of significance without precisely identifying the relative signifance of p-values for the genes in the pathway)..and

I have used Webgestalt-v2 (Vanverbilt University) and PLINK for SNP-based pathway analysis before. These utilities worked beautifully, but I used for SNP-pathway analysis. Especially, Webgestalt-v2 allows input of SNP data by p-values, which can be used to trace the signifiance of genes within pathways, as well

At this time...

After reading some papers and also examining tutorials for atleast 3 softwares (GenGen, GSEA and Gene Pattern), I could not identify relevant points related to exome data and pathway analysis.

I would be very grateful if someone could share their experience in this regards. I can ofcourse, immmediately proceed to work with some of the above identified softwares but if there are other recommended softwares / utilities, then I would give them priority.

Thankyou in advance for a reply

Ali