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CoryneRegNet


NAR Molecular Biology Database Collection entry number 1167
Baumbach, Jan; Pauling, Josch; Röttger, Richard; Tauch, Andreas; Azevedo, Vasco
Center for Biotechnology, Bielefeld University, D-33594 Bielefeld, Germany

Database Description

CoryneRegNet is an ontology-based data warehouse for the reconstruction and visualization of transcriptional regulatory interactions in prokaryotes. To extend the biological content of CoryneRegNet, we added comprehensive data on transcriptional regulations in the model organism Escherichia coli K-12, originally deposited in the international reference database RegulonDB. The enhanced web interface of CoryneRegNet offers several types of search options. The results of a search are displayed in a table-based style and include a visualization of the genetic organization of the respective gene region. Information on DNA binding sites of transcriptional regulators is depicted by sequence logos. The results can also be displayed by several layouters implemented in the graphical user interface GraphVis, allowing, for instance, the visualization of genome-wide network reconstructions and the homology-based inter-species comparison of reconstructed gene regulatory networks.

References

1. Baumbach J, Wittkop T, Rademacher K, Rahmann S, Brinkrolf K, Tauch A. (2007) CoryneRegNet 3.0 - An interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli. J Biotechnol. 2007 (in press, http://dx.doi.org/10.1016/j.jbiotec.2006.12.012).
2. Baumbach J, Brinkrolf K, Wittkop T, Tauch A, Rahmann S (2006) CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes. Journal of Integrative Bioinformatics, 3(2):24, 2006.
3. Baumbach J, Brinkrolf K, Czaja LF, Rahmann S, Tauch A (2006) CoryneRegNet: An ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. BMC Genomics. 2006 Feb 14;7(1):24. (http://www.biomedcentral.com/1471-2164/7/24).


Go to the abstract in the NAR 2012 Database Issue.
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