Dear All,

I have performed a knockdown studies in HLE-B3 cells. I have used gene targeting siRNA, non targeting siRNA and healthy cells with no siRNA in my experiment. On doing analysis I have done three different comparisons: gene targeting siRNA vs non targeting siRNA; gene targeting siRNA vs WT and NTC siRNA vs WT. However, on doing IPA analysis of differentially expressed genes between the above mentioned groups using Qiagen software I am seeing some pathways are overlapping in all three categories. My question is how would I get to know which pathway is legitimate? what should be the best startegy to do the analysis. Please help