Identify cis-regulatory modules using promoter analysis and microarray expression data regression.

Clemens Wrzodek1, Adrian Schröder1, Andreas Dräger1, Dierk Wanke2, Kenneth Berendzen2, Marcel Kronfeld1, Klaus Harter2, Andreas Zell1

1Center for Bioinformatics Tübingen (ZBIT), Germany, 2Center for Plant Physiology Tübingen (ZMBP), Germany

Start ModuleMaster:
You may start ModuleMaster directly here as Java webstart application on almost every operating system. A basic implementation with very basic functionality, compared to the webstart version, is also available in our collection of webservices.

Short description:
ModuleMaster is 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. ModuleMaster is freely available to academics as a webstart application including comprehensive documentation.

You can start the ModuleMaster right away using Java webstart on any operating system.


Creative Commons License ModuleMaster is subject to the Creative Commons Namensnennung-Keine kommerzielle Nutzung 3.0 Deutschland Lizenz.

Citing ModuleMaster:
If you are using ModuleMaster, please cite us. You can find all ModuleMaster publications and BibTeX code in our publications section.

Usage information:
We would like to know who is using ModuleMaster. We will use this information only to keep track of downloads and to inform you about updates. Apart from this, your personal data will not be used for any other purpose nor divulged to third parties.

Please type the code:


Gene Expression Omnibus: ModuleMaster has been extended to smoothly work with GEO. Dataset can be downloaded and annotated automatically just by the GEO id from within ModuleMaster.
(wrzodek - 2009-19-11 10:22)
Annotate expression data: We have setted up a convenient webservice to annotate your expression data, for further use with ModuleMaster. Please use this function, before using the expression file in ModuleMaster, in order to achive a better mapping of expression values to transcription factors.
Please select ModuleMaster and Annotate expression data from the webservices menu.
(wrzodek - 2009-12-11 13:55)
Webservice: A basic version of ModuleMaster has been integrated into our webservices.   -  
(wrzodek - 2009-12-11 13:11)
Update: ModuleMaster has been updated to version 1.1.   -  
(wrzodek - 2009-02-11 16:32)
Documentation: A complete documentation is now available.   -  
(wrzodek - 2009-26-03 13:17)
First Release: Launch the application via Java webstart.   -  
(wrzodek - 2009-03-03 16:02)


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