HyperModules is a biological interaction network analysis algorithm to analyse gene mutations and clinical information. Specifically, HyperModules uses local network search heuristics to detect closely connected network regions (i.e. modules of genes and proteins) in which gene mutations correlate with clinical features.
Clinical features in HyperModules analysis comprise time values like patient survival, or discrete values like tumor stage or vital status. To establish statistical significance of clinical correlations in detected modules, HyperModules applies standard tests (Log-rank test, Fisher's exact test). Searches are repeated across many shuffled networks to correct for systematic biases originating from underlying network structure.
HyperModules was designed by Jüri Reimand and Gary Bader. The Java implementation for Cytoscape and command line software was created by Alvin Leung. For more info, please consult the [HyperModules website](http://baderlab.org/Software/HyperModules) and the original [http://www.nature.com/msb/journal/v9/n1/full/msb201268.html Paper] in Molecular Systems Biology (2013).
Please cite the HyperModules Cytoscape App paper in [Bioinformatics] (Apr 8 2014)(http://bioinformatics.oxfordjournals.org/content/early/2014/03/28/bioinformatics.btu172.abstract):
**HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery.** Leung A, Bader GD, Reimand J.
Bioinformatics (2014) [PubMed](http://www.ncbi.nlm.nih.gov/pubmed/24713437).
HyperModules is also available as stand-alone command line tool - please see the [http://baderlab.org/Software/HyperModules HyperModules] website.
**Please download the latest release of HyperModules (1.0.2) that addresses an important bug in module statistics.**
