Label propagation defines signaling networks associated with recurrently mutated cancer genes

Each different tumor type has a distinct profile of genomic perturbations and each of these alterations causes unique changes to cellular homeostasis. Detailed analyses of these changes would reveal downstream effects of genomic alterations, contributing to our understanding of their roles in tumor development and progression. Across a range of tumor types, including bladder, lung, and endometrial carcinoma, we determined genes that are frequently altered in The Cancer Genome Atlas patient populations to study the effects of these alterations on signaling and regulatory pathways. To achieve this, we used a label propagation-based methodology to generate networks from gene expression signatures of mutations. Individual networks offered a comprehensive view of signaling changes represented by gene signatures, which in turn reflect the scope of molecular events that are perturbed in the presence of a given genomic alteration. Comparing different networks to each other revealed commonalities between them and biological pathways distinct genomic alterations converge on, highlighting the critical signaling events tumor dysregulate through multiple mechanisms. Finally, mutations inducing common changes to the signaling network were used to search for genomic markers of drug response, connecting shared perturbations to differential drug response.