HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery

Summary: Correlating disease mutations with clinical and phenotypic information such as drug response or patient survival is an important goal of personalized cancer genomics and a first step in biomarker discovery. HyperModules is a network search algorithm that finds frequently mutated gene modules with significant clinical or phenotypic signatures from biomolecular interaction networks. Availability and implementation: HyperModules is available in Cytoscape App Store and as a command line tool at www.baderlab.org/Sofware/HyperModules. Contact: Juri.Reimand@utoronto.ca or Gary.Bader@utoronto.ca Supplementary information: Supplementary data are available at Bioinformatics online