Physical Module Networks: an integrative approach for reconstructing transcription regulation

• DOI: 10.1093/bioinformatics/btr222
• Publication Date: 2011-06-17T23:32:32Z
• Authors: Noa Novershtern; Aviv Regev; Nir Friedman
• Keywords: Gene regulatory network; Transcription

Abstract Motivation: Deciphering the complex mechanisms by which regulatory networks control gene expression remains a major challenge. While some studies infer regulation from dependencies between levels of putative regulators and their targets, others focus on measured physical interactions. Results: Here, we present Physical Module Networks, unified framework that combines Bayesian model describing modules co-expressed genes shared programs, interaction graph, protein–protein interactions protein-DNA binding events coherently underlie this regulation. Using synthetic data, demonstrate Network has similar recall improved precision compared to simple Network, as it omits many false positive regulators. Finally, show power Networks reconstruct meaningful pathways in genetically perturbed yeast during cell cycle, well response primary epithelial human cells infection with H1N1 influenza. Availability: The PMN software is available, free for academic use at http://www.compbio.cs.huji.ac.il/PMN/. Contact: [e-mail]; [e-mail]