title: An integrative approach to inferring gene regulatory module networks.
abstract: BACKGROUND
  Gene regulatory networks (GRNs) provide insight into the mechanisms of differential gene expression at a system level. However, the methods for inference, functional analysis and visualization of gene regulatory modules and GRNs require the user to collect heterogeneous data from many sources using numerous bioinformatics tools. This makes the analysis expensive and time-consuming.
  
  
  RESULTS
  In this work, the BiologicalNetworks application-the data integration and network based research environment-was extended with tools for inference and analysis of gene regulatory modules and networks. The backend database of the application integrates public data on gene expression, pathways, transcription factor binding sites, gene and protein sequences, and functional annotations. Thus, all data essential for the gene regulation analysis can be mined publicly. In addition, the user's data can either be integrated in the database and become public, or kept private within the application. The capabilities to analyze multiple gene expression experiments are also provided.
  
  
  CONCLUSIONS
  The generated modular networks, regulatory modules and binding sites can be visualized and further analyzed within this same application. The developed tools were applied to the mouse model of asthma and the OCT4 regulatory network in embryonic stem cells. Developed methods and data are available through the Java application from BiologicalNetworks program at http://www.biologicalnetworks.org.
authors.affiliation: San Diego Supercomputer Center, University of California-San Diego, La Jolla, CA, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Baitaluk
authors.forename: Sergey
authors.initials: S
authors.lastname: Kozhenkov
authors.forename: Julia
authors.initials: J
authors.lastname: Ponomarenko
mesh_terms: D000818:Animals; D001249:Asthma / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D020407:Internet; D051379:Mice; D050814:Octamer Transcription Factor-3 / Q000235:genetics; D012984:Software
chemical_list: D050814:Octamer Transcription Factor-3; C494174:Pou5f1 protein, mouse