GeNGe: systematic generation of gene regulatory networks.
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.


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


BACKGROUND
Supplementary data are available at Bioinformatics online.
Hache
Hendrik
H
Vertebrate Genomics-Bioinformatics Group, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany. hache@molgen.mpg.de
Wierling
Christoph
C
Lehrach
Hans
H
Herwig
Ralf
R
D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D020407:Internet; D012984:Software; D014584:User-Computer Interface