Journal Article

GeNGe: systematic generation of gene regulatory networks

Hendrik Hache, Christoph Wierling, Hans Lehrach and Ralf Herwig

in Bioinformatics

Volume 25, issue 9, pages 1205-1207
Published in print May 2009 | ISSN: 1367-4803
Published online February 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp115

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Summary: The analysis of gene regulatory networks (GRNs) is a central goal of bioinformatics highly accelerated by the advent of new experimental techniques, such as RNA interference. A battery of reverse engineering methods has been developed in recent years to reconstruct the underlying GRNs from these and other experimental data. However, the performance of the individual methods is poorly understood and validation of algorithmic performances is still missing to a large extent. To enable such systematic validation, we have developed the web application GeNGe (GEne Network GEnerator), a controlled framework for the automatic generation of GRNs. The theoretical model for a GRN is a non-linear differential equation system. Networks can be user-defined or constructed in a modular way with the option to introduce global and local network perturbations. Resulting data can be used, e.g. as benchmark data for evaluating GRN reconstruction methods or for predicting effects of perturbations as theoretical counterparts of biological experiments.

Availability: Available online at http://genge.molgen.mpg.de

Contact: hache@molgen.mpg.de

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1386 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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