Wrzodek, Clemens and Schröder, Adrian and Dräger, Andreas and Wanke, Dierk and Berendzen, Kenneth W. and Kronfeld, Marcel and Harter, Klaus and Zell, Andreas

ModuleMaster: A new tool to decipher transcriptional regulatory networks

Biosystems vol. 99 (2010), no. 1, Elsevier, pp. 79-81


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. Availability: 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.


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BibTeX

@article{Wrzodek2010,
  author = {Wrzodek, Clemens and Schr\"oder, Adrian and Dr\"ager, Andreas and
	Wanke, Dierk and Berendzen, Kenneth W. and Kronfeld, Marcel and Harter,
	Klaus and Zell, Andreas},
  title = {{ModuleMaster}: A new tool to decipher transcriptional regulatory
	networks},
  journal = {Biosystems},
  year = {2010},
  volume = {99},
  pages = {79--81},
  number = {1},
  month = jan,
  abstract = {In this article we present ModuleMaster, a novel application for finding
	\emph{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.
	Availability: ModuleMaster is freely available to academics as a
	webstart application and for download at \url{http://www.ra.cs.uni-tuebingen.de/software/ModuleMaster/},
	including comprehensive documentation.},
  comment = {http://www.cogsys.cs.uni-tuebingen.de/software/ModuleMaster/},
  doi = {10.1016/j.biosystems.2009.09.005},
  issn = {0303-2647},
  keywords = {Gene regulation, Cis-regulatory modules, Regulatory sequence analysis,
	Matrix scan, Transcription factors},
  pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/wrzodek2010_ModuleMaster.pdf},
  publisher = {Elsevier},
  url = {http://dx.doi.org/10.1016/j.biosystems.2009.09.005}
}