title: ModuleMaster: a new tool to decipher transcriptional regulatory networks.
abstract: In this article we present ModuleMaster, a novel application for finding cis-regulatory modules (CRMs) in sets of co-expressed genes. The application comes with a newly developed method which not only considers transcription factor binding information but also multivariate functional relationships between regulators and target genes to improve the detection of CRMs. Given only the results of a microarray and a subsequent clustering experiment, the program includes all necessary data and algorithms to perform every step to find CRMs. This workbench possesses an easy-to-use graphical user interface, together with job-processing and command-line options, making ModuleMaster a sophisticated program for large-scale batch processing. The detected CRMs can be visualized and evaluated in various ways, i.e., generating GraphML- and R-based whole regulatory network visualizations or generating SBML files for subsequent analytical processing and dynamic modeling.
  
  
  BACKGROUND
  ModuleMaster is freely available to academics as a webstart application and for download at http://www.ra.cs.uni-tuebingen.de/software/ModuleMaster/, including comprehensive documentation.
authors.affiliation: Center for Bioinformatics Tübingen (ZBIT), University of Tübingen, Sand 1, 72076 Tübingen, Germany. clemens.wrzodek@uni-tuebingen.de
authors.forename: Clemens
authors.initials: C
authors.lastname: Wrzodek
authors.forename: Adrian
authors.initials: A
authors.lastname: Schröder
authors.forename: Andreas
authors.initials: A
authors.lastname: Dräger
authors.forename: Dierk
authors.initials: D
authors.lastname: Wanke
authors.forename: Kenneth W
authors.initials: KW
authors.lastname: Berendzen
authors.forename: Marcel
authors.initials: M
authors.lastname: Kronfeld
authors.forename: Klaus
authors.initials: K
authors.lastname: Harter
authors.forename: Andreas
authors.initials: A
authors.lastname: Zell
mesh_terms: D000465:Algorithms; D000818:Animals; D003196:Computer Graphics; D003198:Computer Simulation; D005786:Gene Expression Regulation / Q000235:genetics*; D006801:Humans; D008957:Models, Genetic; D015398:Signal Transduction / Q000235:genetics*; D012984:Software; D012985:Software Design; D014158:Transcription, Genetic / Q000235:genetics*; D014584:User-Computer Interface