MPI für molekulare Genetik / Department of Vertebrate Genomics |
|GeNGe: systematic generation of gene regulatory networks. Bioinformatics.|
|Authors:||Hache, Hendrik; Wierling, Christoph; Lehrach, Hans; Herwig, Ralf|
|Date of Publication (YYYY-MM-DD):||2009-02-27|
|Title of Journal:||Bioinformatics|
|Issue / Number:||9|
|Full name of Issue-Editor(s):||Wren, Jonathan|
|Copyright:||2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
|Review Status:||not specified|
|Abstract / Description:||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|
|Comment of the Author/Creator:||Availability: Available online at http://genge.molgen.mpg.de
To whom correspondence should be addressed.
Supplementary information: Supplementary data are available at Bioinformatics online.
|External Publication Status:||published|
|Communicated by:||Hans Lehrach|
|Affiliations:||MPI für molekulare Genetik|
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