Database

CoryneCenter – An online resource for the integrated analysis of corynebacterial genome and transcriptome data

Heiko Neuweger^2,3 , Jan Baumbach^1,2 , Stefan Albaum³ , Thomas Bekel³ , Michael Dondrup³ , Andrea T Hüser⁴ , Jörn Kalinowski⁴ , Sebastian Oehm^3,5 , Alfred Pühler⁶ , Sven Rahmann^1,7 , Jochen Weile^1,3 and Alexander Goesmann³

¹Computational Methods for Emerging Technologies group, Bielefeld University, Bielefeld, Germany

²International NRW Graduate School in Bioinformatics and Genome Research, Center for Biotechnology (CeBiTec), Bielefeld, Germany

³Bioinformatics Resource Facility, CeBiTec, Bielefeld, Germany

⁴Technology Platform Genomics, CeBiTec, Bielefeld, Germany

⁵DFG Graduiertenkolleg Bioinformatik, Bielefeld University, Bielefeld, Germany

⁶Lehrstuhl für Genetik, Bielefeld University, Bielefeld, Germany

⁷Bioinformatics for High-Throughput Technologies, Dortmund University, Dortmund, Germany

author email corresponding author email

BMC Systems Biology 2007, 1:55doi:10.1186/1752-0509-1-55

Published:	22 November 2007

Abstract

Background

The introduction of high-throughput genome sequencing and post-genome analysis technologies, e.g. DNA microarray approaches, has created the potential to unravel and scrutinize complex gene-regulatory networks on a large scale. The discovery of transcriptional regulatory interactions has become a major topic in modern functional genomics.

Results

To facilitate the analysis of gene-regulatory networks, we have developed CoryneCenter, a web-based resource for the systematic integration and analysis of genome, transcriptome, and gene regulatory information for prokaryotes, especially corynebacteria. For this purpose, we extended and combined the following systems into a common platform: (1) GenDB, an open source genome annotation system, (2) EMMA, a MAGE compliant application for high-throughput transcriptome data storage and analysis, and (3) CoryneRegNet, an ontology-based data warehouse designed to facilitate the reconstruction and analysis of gene regulatory interactions. We demonstrate the potential of CoryneCenter by means of an application example. Using microarray hybridization data, we compare the gene expression of Corynebacterium glutamicum under acetate and glucose feeding conditions: Known regulatory networks are confirmed, but moreover CoryneCenter points out additional regulatory interactions.

Conclusion

CoryneCenter provides more than the sum of its parts. Its novel analysis and visualization features significantly simplify the process of obtaining new biological insights into complex regulatory systems. Although the platform currently focusses on corynebacteria, the integrated tools are by no means restricted to these species, and the presented approach offers a general strategy for the analysis and verification of gene regulatory networks. CoryneCenter provides freely accessible projects with the underlying genome annotation, gene expression, and gene regulation data. The system is publicly available at http://www.CoryneCenter.de webcite.