Overall, this study generated two main outputs: (i) proposed a data-driven framework for elucidating the mechanism of action of pleiotropic natural products using transcriptome data and protein interactome and (ii) demonstrated that plant-derived drugs (actein, indole-3-carbinol, withaferin A and CKI) are capable of simultaneously regulating multiple carcinogenesis processes in breast cancer. This evidence concerns the gene CHKA and breast cancer.