I have performed several analysis to find which pathways are enriched in my data set, but they don't test activation or inactivation.
After observing the expression of one of those pathways I can observe an increase of the expression, however I was wondering if this implies activation of the pathway. I calculated the enrichment score (using GSEA) of the pathway but it is not designed to test if the pathway is activated or not, is it?
Is there any tool, to test activation/inactivation of a pathway?
I have found SIPA, ASSIGN, DART (on Bioconductor), but they all relay on KEGG, and I would like to be able to use also other pathways from Reactome or Biocarta. I would prefer using R but any tool/method is welcome.