title: Physical Module Networks: an integrative approach for reconstructing transcription regulation.
abstract: BACKGROUND
  Deciphering the complex mechanisms by which regulatory networks control gene expression remains a major challenge. While some studies infer regulation from dependencies between the expression levels of putative regulators and their targets, others focus on measured physical interactions.
  
  
  RESULTS
  Here, we present Physical Module Networks, a unified framework that combines a Bayesian model describing modules of co-expressed genes and their shared regulation programs, and a physical interaction graph, describing the protein-protein interactions and protein-DNA binding events that coherently underlie this regulation. Using synthetic data, we demonstrate that a Physical Module Network model has similar recall and improved precision compared to a simple Module Network, as it omits many false positive regulators. Finally, we show the power of Physical Module Networks to reconstruct meaningful regulatory pathways in the genetically perturbed yeast and during the yeast cell cycle, as well as during the response of primary epithelial human cells to infection with H1N1 influenza.
  
  
  BACKGROUND
  The PMN software is available, free for academic use at http://www.compbio.cs.huji.ac.il/PMN/.
  
  
  BACKGROUND
  aregev@broad.mit.edu; nirf@cs.huji.ac.il.
authors.affiliation: School of Computer Science, Hebrew University, Jerusalem 91904, Israel.
authors.forename: Noa
authors.initials: N
authors.lastname: Novershtern
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
authors.forename: Nir
authors.initials: N
authors.lastname: Friedman
mesh_terms: D001499:Bayes Theorem; D002453:Cell Cycle; D004847:Epithelial Cells / Q000378:metabolism / Q000821:virology; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000235:genetics / Q000378:metabolism; D007251:Influenza, Human / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D012984:Software
chemical_list: D029701:Saccharomyces cerevisiae Proteins