Fig. 4

Drug module characterization. a Drug module enrichment analysis based on the Hallmark gene set (odds ratios in color, p values < 0.05 are marked with a white dot). For simplicity, three drug classes are shown: drugs affecting mitosis, RTK signaling, and ERK/MAPK signaling. b Distribution of the enrichment scores in the Hallmark collection gene sets. Overall, higher enrichment scores are obtained using modules than using full signatures (PCGs and NCGs) (the gene universe used here is that of Reactome). c Similarly, number of Hallmark-drug pairs at different enrichment scores. We show the pairs found only with the modules (PCMs and NCMs, red), only with correlations (PCGs and NCGs, blue), or in both (orange). d A view of Lestaurtinib (CEP-701) module. For illustrative purposes, two out-of-the-module (non-correlated) proteins are shown (gray), one being very central and one being peripheral but acting as a “bridging” node. e TCGA enrichment analysis of PCMs in four types of cancer: SKCM (Cutaneous Melanoma), PAAD (Pancreatic Adenocarcinoma), GBM (Glioblastoma Multiforme), and BRCA (Breast Carcinoma)