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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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
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

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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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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.
Pauling J, Röttger R, Tauch A, Azevedo V, Baumbach J., Nucleic Acids Res 40(database issue), 2012
PMID: 22080556
EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data.
Dondrup M, Albaum SP, Griebel T, Henckel K, Jünemann S, Kahlke T, Kleindt CK, Küster H, Linke B, Mertens D, Mittard-Runte V, Neuweger H, Runte KJ, Tauch A, Tille F, Pühler A, Goesmann A., BMC Bioinformatics 10(), 2009
PMID: 19200358
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
PMID: 19297685
BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks.
Guziolowski C, Bourdé A, Moreews F, Siegel A., BMC Genomics 10(), 2009
PMID: 19470162
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
PMID: 19698148
Linking Cytoscape and the corynebacterial reference database CoryneRegNet.
Baumbach J, Apeltsin L., BMC Genomics 9(), 2008
PMID: 18426593
MeltDB: a software platform for the analysis and integration of metabolomics experiment data.
Neuweger H, Albaum SP, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A., Bioinformatics 24(23), 2008
PMID: 18765459

47 References

Daten bereitgestellt von Europe PubMed Central.

GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
EMMA: a platform for consistent storage and efficient analysis of microarray data.
Dondrup M, Goesmann A, Bartels D, Kalinowski J, Krause L, Linke B, Rupp O, Sczyrba A, Puhler A, Meyer F., J. Biotechnol. 106(2-3), 2003
PMID: 14651856
CoryneRegNet: an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks.
Baumbach J, Brinkrolf K, Czaja LF, Rahmann S, Tauch A., BMC Genomics 7(), 2006
PMID: 16478536
CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes
Baumbach J, Brinkrolf K, Wittkop T, Tauch A, Rahmann S., 2006
CoryneRegNet 3.0--an interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli.
Baumbach J, Wittkop T, Rademacher K, Rahmann S, Brinkrolf K, Tauch A., J. Biotechnol. 129(2), 2006
PMID: 17229482
Emerging Corynebacterium glutamicum systems biology.
Wendisch VF, Bott M, Kalinowski J, Oldiges M, Wiechert W., J. Biotechnol. 124(1), 2006
PMID: 16406159
The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins.
Kalinowski J, Bathe B, Bartels D, Bischoff N, Bott M, Burkovski A, Dusch N, Eggeling L, Eikmanns BJ, Gaigalat L, Goesmann A, Hartmann M, Huthmacher K, Kramer R, Linke B, McHardy AC, Meyer F, Mockel B, Pfefferle W, Puhler A, Rey DA, Ruckert C, Rupp O, Sahm H, Wendisch VF, Wiegrabe I, Tauch A., J. Biotechnol. 104(1-3), 2003
PMID: 12948626
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
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
Functional genomics and expression analysis of the Corynebacterium glutamicum fpr2-cysIXHDNYZ gene cluster involved in assimilatory sulphate reduction.
Ruckert C, Koch DJ, Rey DA, Albersmeier A, Mormann S, Puhler A, Kalinowski J., BMC Genomics 6(), 2005
PMID: 16159395
Graph-based analysis and visualization of experimental results with ONDEX.
Kohler J, Baumbach J, Taubert J, Specht M, Skusa A, Ruegg A, Rawlings C, Verrier P, Philippi S., Bioinformatics 22(11), 2006
PMID: 16533819
Comparative Mouse Genomics Centers Consortium: the Mouse Genotype Database.
Wiley JC, Prattipati M, Lin CP, Ladiges W., Mutat. Res. 595(1-2), 2006
PMID: 16442569
BioDAS website
AUTHOR UNKNOWN, 0
The distributed annotation system.
Dowell RD, Jokerst RM, Day A, Eddy SR, Stein L., BMC Bioinformatics 2(), 2001
PMID: 11667947
MyGrid website
AUTHOR UNKNOWN, 0
Taverna: a tool for building and running workflows of services.
Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P, Oinn T., Nucleic Acids Res. 34(Web Server issue), 2006
PMID: 16845108
BioMoby extensions to the Taverna workflow management and enactment software.
Kawas E, Senger M, Wilkinson MD., BMC Bioinformatics 7(), 2006
PMID: 17137515
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
SOAP-based services provided by the European Bioinformatics Institute.
Pillai S, Silventoinen V, Kallio K, Senger M, Sobhany S, Tate J, Velankar S, Golovin A, Henrick K, Rice P, Stoehr P, Lopez R., Nucleic Acids Res. 33(Web Server issue), 2005
PMID: 15980463
BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.
Barthelmes J, Ebeling C, Chang A, Schomburg I, Schomburg D., Nucleic Acids Res. 35(Database issue), 2007
PMID: 17202167
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
OBO-Edit--an ontology editor for biologists.
Day-Richter J, Harris MA, Haendel M; Gene Ontology OBO-Edit Working Group, Lewis S., Bioinformatics 23(16), 2007
PMID: 17545183
PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways.
Mlecnik B, Scheideler M, Hackl H, Hartler J, Sanchez-Cabo F, Trajanoski Z., Nucleic Acids Res. 33(Web Server issue), 2005
PMID: 15980551
Ultrafast de novo sequencing of Corynebacterium urealyticum using the Genome Sequencer 20 System
Tauch A, Trost E, Bekel T, Goesmann A, Ludewig U, Pühler A., 2006
Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora.
Tauch A, Kaiser O, Hain T, Goesmann A, Weisshaar B, Albersmeier A, Bekel T, Bischoff N, Brune I, Chakraborty T, Kalinowski J, Meyer F, Rupp O, Schneiker S, Viehoever P, Puhler A., J. Bacteriol. 187(13), 2005
PMID: 15968079
Interpolated Markov models for eukaryotic gene finding.
Salzberg SL, Pertea M, Delcher AL, Gardner MJ, Tettelin H., Genomics 59(1), 1999
PMID: 10395796
CRITICA: coding region identification tool invoking comparative analysis.
Badger JH, Olsen GJ, Woese CR., Mol. Biol. Evol. 16(4), 1999
PMID: 10331277
Development of joint application strategies for two microbial gene finders.
McHardy AC, Goesmann A, Puhler A, Meyer F., Bioinformatics 20(10), 2004
PMID: 14988122
GISMO--gene identification using a support vector machine for ORF classification.
Krause L, McHardy AC, Nattkemper TW, Puhler A, Stoye J, Meyer F., Nucleic Acids Res. 35(2), 2006
PMID: 17175534
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694
New developments in the InterPro database.
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Selengut JD, Sigrist CJ, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C., Nucleic Acids Res. 35(Database issue), 2007
PMID: 17202162
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 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
Funding high-throughput data sharing.
Ball CA, Sherlock G, Brazma A., Nat. Biotechnol. 22(9), 2004
PMID: 15340487
Design and implementation of microarray gene expression markup language (MAGE-ML).
Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, Shojatalab M, Pizarro A, White J, Hubley R, Deutsch E, Senger M, Aronow BJ, Robinson A, Bassett D, Stoeckert CJ Jr, Brazma A., Genome Biol. 3(9), 2002
PMID: 12225585
SOAPlite library website
AUTHOR UNKNOWN, 0
NuSOAP website
AUTHOR UNKNOWN, 0
Acetate metabolism and its regulation in Corynebacterium glutamicum.
Gerstmeir R, Wendisch VF, Schnicke S, Ruan H, Farwick M, Reinscheid D, Eikmanns BJ., J. Biotechnol. 104(1-3), 2003
PMID: 12948633
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