Accurate differential analysis of transcription factor activity from gene expression

We present EPEE (Effector and Perturbation Estimation Engine), a method for differential analysis of transcription factor (TF) activity from gene expression data. EPEE addresses two principal challenges in the field, namely incorporating context-specific TF-gene regulatory networks, and accounting for the fact that TF activity inference is intrinsically coupled for all TFs that share targets. Our validations in well-studied immune and cancer contexts show that addressing the overlap challenge and using state-of-the-art regulatory networks enable EPEE to consistently produce accurate results. (Accessible at: https://github.com/Cobanoglu-Lab/EPEE )