CoryneCenter: an online resource for the integrated analysis of corynebacterial genome and transcriptome data
Neuweger H, Baumbach J, Albaum S, Bekel T, Dondrup M, Hüser AT, Kalinowski J, Oehm S, Pühler A, Rahmann S, Weile J, et al. (2007)
BMC Systems Biology 1(1): 55.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
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Autor*in
Neuweger, HeikoUniBi;
Baumbach, Jan;
Albaum, StefanUniBi ;
Bekel, ThomasUniBi;
Dondrup, Michael;
Hüser, Andrea T.;
Kalinowski, JörnUniBi;
Oehm, SebastianUniBi;
Pühler, AlfredUniBi ;
Rahmann, Sven;
Weile, Jochen;
Goesmann, AlexanderUniBi
Einrichtung
Centrum für Biotechnologie > Arbeitsgruppe J. Kalinowski
Fakultät für Biologie
Technische Fakultät > Computational Genomics
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Arbeitsgruppe A. Pühler
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Centrum für Biotechnologie > Institut für Bioinformatik
Fakultät für Biologie
Technische Fakultät > Computational Genomics
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Arbeitsgruppe A. Pühler
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Centrum für Biotechnologie > Institut für Bioinformatik
Abstract / Bemerkung
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
Erscheinungsjahr
2007
Zeitschriftentitel
BMC Systems Biology
Band
1
Ausgabe
1
Art.-Nr.
55
ISSN
1752-0509
Page URI
https://pub.uni-bielefeld.de/record/1783754
Zitieren
Neuweger H, Baumbach J, Albaum S, et al. CoryneCenter: an online resource for the integrated analysis of corynebacterial genome and transcriptome data. BMC Systems Biology. 2007;1(1): 55.
Neuweger, H., Baumbach, J., Albaum, S., Bekel, T., Dondrup, M., Hüser, A. T., Kalinowski, J., et al. (2007). CoryneCenter: an online resource for the integrated analysis of corynebacterial genome and transcriptome data. BMC Systems Biology, 1(1), 55. https://doi.org/10.1186/1752-0509-1-55
Neuweger, Heiko, Baumbach, Jan, Albaum, Stefan, Bekel, Thomas, Dondrup, Michael, Hüser, Andrea T., Kalinowski, Jörn, et al. 2007. “CoryneCenter: an online resource for the integrated analysis of corynebacterial genome and transcriptome data”. BMC Systems Biology 1 (1): 55.
Neuweger, H., Baumbach, J., Albaum, S., Bekel, T., Dondrup, M., Hüser, A. T., Kalinowski, J., Oehm, S., Pühler, A., Rahmann, S., et al. (2007). CoryneCenter: an online resource for the integrated analysis of corynebacterial genome and transcriptome data. BMC Systems Biology 1:55.
Neuweger, H., et al., 2007. CoryneCenter: an online resource for the integrated analysis of corynebacterial genome and transcriptome data. BMC Systems Biology, 1(1): 55.
H. Neuweger, et al., “CoryneCenter: an online resource for the integrated analysis of corynebacterial genome and transcriptome data”, BMC Systems Biology, vol. 1, 2007, : 55.
Neuweger, H., Baumbach, J., Albaum, S., Bekel, T., Dondrup, M., Hüser, A.T., Kalinowski, J., Oehm, S., Pühler, A., Rahmann, S., Weile, J., Goesmann, A.: CoryneCenter: an online resource for the integrated analysis of corynebacterial genome and transcriptome data. BMC Systems Biology. 1, : 55 (2007).
Neuweger, Heiko, Baumbach, Jan, Albaum, Stefan, Bekel, Thomas, Dondrup, Michael, Hüser, Andrea T., Kalinowski, Jörn, Oehm, Sebastian, Pühler, Alfred, Rahmann, Sven, Weile, Jochen, and Goesmann, Alexander. “CoryneCenter: an online resource for the integrated analysis of corynebacterial genome and transcriptome data”. BMC Systems Biology 1.1 (2007): 55.
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Daten bereitgestellt von European Bioinformatics Institute (EBI)
9 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands.
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EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data.
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The Sequence Analysis and Management System -- SAMS-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies.
Bekel T, Henckel K, Küster H, Meyer F, Mittard Runte V, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Pühler A, Stoye J, Goesmann A., J Biotechnol 140(1-2), 2009
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Visualizing post genomics data-sets on customized pathway maps by ProMeTra-aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example.
Neuweger H, Persicke M, Albaum SP, Bekel T, Dondrup M, Hüser AT, Winnebald J, Schneider J, Kalinowski J, Goesmann A., BMC Syst Biol 3(), 2009
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Neuweger H, Albaum SP, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A., Bioinformatics 24(23), 2008
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SOAPlite library website
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NuSOAP website
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Acetate metabolism and its regulation in Corynebacterium glutamicum.
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RamA, the transcriptional regulator of acetate metabolism in Corynebacterium glutamicum, is subject to negative autoregulation.
Cramer A, Eikmanns BJ., J. Mol. Microbiol. Biotechnol. 12(1-2), 2007
PMID: 17183211
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Identification of RamA, a novel LuxR-type transcriptional regulator of genes involved in acetate metabolism of Corynebacterium glutamicum.
Cramer A, Gerstmeir R, Schaffer S, Bott M, Eikmanns BJ., J. Bacteriol. 188(7), 2006
PMID: 16547043
Cramer A, Gerstmeir R, Schaffer S, Bott M, Eikmanns BJ., J. Bacteriol. 188(7), 2006
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Identification and characterization of glxR, a gene involved in regulation of glyoxylate bypass in Corynebacterium glutamicum.
Kim HJ, Kim TH, Kim Y, Lee HS., J. Bacteriol. 186(11), 2004
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RamB, the transcriptional regulator of acetate metabolism in Corynebacterium glutamicum, is subject to regulation by RamA and RamB.
Cramer A, Auchter M, Frunzke J, Bott M, Eikmanns BJ., J. Bacteriol. 189(3), 2006
PMID: 17114251
Cramer A, Auchter M, Frunzke J, Bott M, Eikmanns BJ., J. Bacteriol. 189(3), 2006
PMID: 17114251
The DeoR-type regulator SugR represses expression of ptsG in Corynebacterium glutamicum.
Engels V, Wendisch VF., J. Bacteriol. 189(8), 2007
PMID: 17293426
Engels V, Wendisch VF., J. Bacteriol. 189(8), 2007
PMID: 17293426
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