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

Bioinformatics. 2014 Aug 1;30(15):2230-2. doi: 10.1093/bioinformatics/btu172. Epub 2014 Apr 8.

Abstract

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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms*
  • Biomarkers, Tumor / genetics
  • Computer Graphics
  • Gene Regulatory Networks
  • Genomics
  • Humans
  • Internet
  • Mutation*
  • Neoplasms / genetics*
  • Neoplasms / metabolism*
  • Phenotype*
  • Protein Interaction Maps
  • Software*
  • Systems Biology / methods*

Substances

  • Biomarkers, Tumor