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. 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