Differentially expressed genes analysis using IPA?

Question

[goyal.shiwali]

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

[ATpoint]

healthy cells with no siRNA in my experiment

But same treatment with empty vector, no? If not then you will mainly see the transfection and overexpression signature before anything else. It's stress to the cell to be transfected and overexpress a construct.

Towards the pathways, you really need to give examples. Pathway analysis is crude, and the same pathway can be triggered by different sets of genes. It's really just for hypothesis generation.