CoryneRegNet 4.0: a reference database for corynebacterial gene regulatory networks

Baumbach J (2007)
BMC Bioinformatics 8(1): 429.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
Abstract / Bemerkung
Background: Detailed information on DNA-binding transcription factors (the key players in the regulation of gene expression) and on transcriptional regulatory interactions of microorganisms deduced from literature-derived knowledge, computer predictions and global DNA microarray hybridization experiments, has opened the way for the genome-wide analysis of transcriptional regulatory networks. The large-scale reconstruction of these networks allows the in silico analysis of cell behavior in response to changing environmental conditions. We previously published CoryneRegNet, an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. Initially, it was designed to provide methods for the analysis and visualization of the gene regulatory network of Corynebacterium glutamicum. Results: Now we introduce CoryneRegNet release 4.0, which integrates data on the gene regulatory networks of 4 corynebacteria, 2 mycobacteria and the model organism Escherichia coli K12. As the previous versions, CoryneRegNet provides a web-based user interface to access the database content, to allow various queries, and to support the reconstruction, analysis and visualization of regulatory networks at different hierarchical levels. In this article, we present the further improved database content of CoryneRegNet along with novel analysis features. The network visualization feature GraphVis now allows the inter-species comparisons of reconstructed gene regulatory networks and the projection of gene expression levels onto that networks. Therefore, we added stimulon data directly into the database, but also provide Web Service access to the DNA microarray analysis platform EMMA. Additionally, CoryneRegNet now provides a SOAP based Web Service server, which can easily be consumed by other bioinformatics software systems. Stimulons (imported from the database, or uploaded by the user) can be analyzed in the context of known transcriptional regulatory networks to predict putative contradictions or further gene regulatory interactions. Furthermore, it integrates protein clusters by means of heuristically solving the weighted graph cluster editing problem. In addition, it provides Web Service based access to up to date gene annotation data from GenDB. Conclusion: The release 4.0 of CoryneRegNet is a comprehensive system for the integrated analysis of procaryotic gene regulatory networks. It is a versatile systems biology platform to support the efficient and large-scale analysis of transcriptional regulation of gene expression in microorganisms. It is publicly available at http://www.CoryneRegNet.DE.
BMC Bioinformatics


Baumbach J. CoryneRegNet 4.0: a reference database for corynebacterial gene regulatory networks. BMC Bioinformatics. 2007;8(1):429.
Baumbach, J. (2007). CoryneRegNet 4.0: a reference database for corynebacterial gene regulatory networks. BMC Bioinformatics, 8(1), 429. doi:10.1186/1471-2105-8-429
Baumbach, J. (2007). CoryneRegNet 4.0: a reference database for corynebacterial gene regulatory networks. BMC Bioinformatics 8, 429.
Baumbach, J., 2007. CoryneRegNet 4.0: a reference database for corynebacterial gene regulatory networks. BMC Bioinformatics, 8(1), p 429.
J. Baumbach, “CoryneRegNet 4.0: a reference database for corynebacterial gene regulatory networks”, BMC Bioinformatics, vol. 8, 2007, pp. 429.
Baumbach, J.: CoryneRegNet 4.0: a reference database for corynebacterial gene regulatory networks. BMC Bioinformatics. 8, 429 (2007).
Baumbach, Jan. “CoryneRegNet 4.0: a reference database for corynebacterial gene regulatory networks”. BMC Bioinformatics 8.1 (2007): 429.
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39 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.
Novichkov PS, Laikova ON, Novichkova ES, Gelfand MS, Arkin AP, Dubchak I, Rodionov DA., Nucleic Acids Res 38(database issue), 2010
PMID: 19884135
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology.
Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R., Brief Bioinform 11(1), 2010
PMID: 19955237
PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes.
Grote A, Klein J, Retter I, Haddad I, Behling S, Bunk B, Biegler I, Yarmolinetz S, Jahn D, Münch R., Nucleic Acids Res 37(database issue), 2009
PMID: 18974177
Physiological adaptation of Corynebacterium glutamicum to benzoate as alternative carbon source - a membrane proteome-centric view.
Haussmann U, Qi SW, Wolters D, Rögner M, Liu SJ, Poetsch A., Proteomics 9(14), 2009
PMID: 19639586
Mechanisms and evolution of control logic in prokaryotic transcriptional regulation.
van Hijum SA, Medema MH, Kuipers OP., Microbiol Mol Biol Rev 73(3), 2009
PMID: 19721087
Linking Cytoscape and the corynebacterial reference database CoryneRegNet.
Baumbach J, Apeltsin L., BMC Genomics 9(), 2008
PMID: 18426593
Nitrogen control in Mycobacterium smegmatis: nitrogen-dependent expression of ammonium transport and assimilation proteins depends on the OmpR-type regulator GlnR.
Amon J, Bräu T, Grimrath A, Hänssler E, Hasselt K, Höller M, Jessberger N, Ott L, Szököl J, Titgemeyer F, Burkovski A., J Bacteriol 190(21), 2008
PMID: 18689485

45 References

Daten bereitgestellt von Europe PubMed Central.

SOAPlite library
From genomics to chemical genomics: new developments in KEGG.
Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381885
Unraveling the Web Services Web: An Introduction to SOAP, WSDL, and UDDI
Curbera F, Duftler M, Khalaf R, Nagy W, Mukhi N, Weerawarana S., 2002
BioMOBY: an open source biological web services proposal.
Wilkinson MD, Links M., Brief. Bioinformatics 3(4), 2002
PMID: 12511062
Exact and Heuristic Algorithms for Weighted Cluster Editing
Rahmann S, Wittkop T, Baumbach J, Martin M, Truss A, Boecker S., 2007
Graph drawing by force-directed placement
Fruchterman TMJ, Reingold EM., 1991
Protein complex prediction via cost-based clustering.
King AD, Przulj N, Jurisica I., Bioinformatics 20(17), 2004
PMID: 15180928
The COG database: an updated version includes eukaryotes.
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA., BMC Bioinformatics 4(), 2003
PMID: 12969510
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G., Nat. Genet. 25(1), 2000
PMID: 10802651
The IclR-type transcriptional repressor LtbR regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer Corynebacterium glutamicum.
Brune I, Jochmann N, Brinkrolf K, Huser AT, Gerstmeir R, Eikmanns BJ, Kalinowski J, Puhler A, Tauch A., J. Bacteriol. 189(7), 2007
PMID: 17259312
The transcriptional regulator SsuR activates expression of the Corynebacterium glutamicum sulphonate utilization genes in the absence of sulphate.
Koch DJ, Ruckert C, Albersmeier A, Huser AT, Tauch A, Puhler A, Kalinowski J., Mol. Microbiol. 58(2), 2005
PMID: 16194234
Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source.
Huser AT, Becker A, Brune I, Dondrup M, Kalinowski J, Plassmeier J, Puhler A, Wiegrabe I, Tauch A., J. Biotechnol. 106(2-3), 2003
PMID: 14651867


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