A method of screening a compound that treats a disease or disorder, comprising: measuring quantitatively protein activity of a plurality of master regulator proteins in a sample from said disease or disorder, wherein said measuring quantitatively protein activity of said plurality of master regulator proteins is based directly or indirectly on expression of regulons of said master regulator proteins, and wherein said measuring quantitatively protein activity of said plurality of master regulator proteins comprises computationally inferring protein activity of said plurality of master regulator proteins from gene expression profiles of regulons of said master regulator proteins, wherein said computationally inferring protein activity of said plurality of master regulator proteins is performed by the VIPER technique; exposing said sample to said compound; measuring quantitatively protein activity of said plurality of master regulator proteins in said compound-treated sample, wherein said measuring quantitatively protein activity of said plurality of master regulator proteins is based directly or indirectly on expression of regulons of said master regulator proteins, and wherein said measuring quantitatively protein activity of said plurality of master regulator proteins comprises computationally inferring protein activity of said plurality of master regulator proteins from gene expression profiles of regulons of said master regulator proteins, wherein said computationally inferring protein activity of said plurality of master regulator proteins is performed by the VIPER technique;; and assessing quantitatively inversion of protein activity of said plurality of master regulator proteins in said compound-treated sample compared to a sample from said disease or disorder without treatment with said compound or a model exposed to a vehicle used to deliver said compound. measuring quantitatively protein activity of a plurality of master regulator proteins in a sample from said disease or disorder, wherein said measuring quantitatively protein activity of said plurality of master regulator proteins is based directly or indirectly on expression of regulons of said master regulator proteins, and wherein said measuring quantitatively protein activity of said plurality of master regulator proteins comprises computationally inferring protein activity of said plurality of master regulator proteins from gene expression profiles of regulons of said master regulator proteins, wherein said computationally inferring protein activity of said plurality of master regulator proteins is performed by the VIPER technique; exposing said sample to said compound; measuring quantitatively protein activity of said plurality of master regulator proteins in said compound-treated sample, wherein said measuring quantitatively protein activity of said plurality of master regulator proteins is based directly or indirectly on expression of regulons of said master regulator proteins, and wherein said measuring quantitatively protein activity of said plurality of master regulator proteins comprises computationally inferring protein activity of said plurality of master regulator proteins from gene expression profiles of regulons of said master regulator proteins, wherein said computationally inferring protein activity of said plurality of master regulator proteins is performed by the VIPER technique;; and assessing quantitatively inversion of protein activity of said plurality of master regulator proteins in said compound-treated sample compared to a sample from said disease or disorder without treatment with said compound or a model exposed to a vehicle used to deliver said compound.