Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks
Baumbach J, Tauch A, Rahmann S (2009)
BRIEFINGS IN BIOINFORMATICS 10(1): 75-83.
Zeitschriftenaufsatz
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Autor*in
Baumbach, Jan;
Tauch, AndreasUniBi;
Rahmann, Sven
Einrichtung
Abstract / Bemerkung
To handle changing environmental surroundings and to manage unfavorable conditions, microbial organisms have evolved complex transcriptional regulatory networks. To comprehensively analyze these gene regulatory networks, several online available databases and analysis platforms have been implemented and established. In this article, we address the typical cycle of scientific knowledge exploration and integration in the area of procaryotic transcriptional gene regulation. We briefly review five popular, publicly available systems that support (i) the integration of existing knowledge, (ii) visualization capabilities and (iii) computer analysis to predict promising wet lab targets. We exemplify the benefits of such integrated data analysis platforms by means of four application cases exemplarily performed with the corynebacterial reference database CoryneRegNet.
Erscheinungsjahr
2009
Zeitschriftentitel
BRIEFINGS IN BIOINFORMATICS
Band
10
Ausgabe
1
Seite(n)
75-83
ISSN
1467-5463
eISSN
1477-4054
Page URI
https://pub.uni-bielefeld.de/record/1635928
Zitieren
Baumbach J, Tauch A, Rahmann S. Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks. BRIEFINGS IN BIOINFORMATICS. 2009;10(1):75-83.
Baumbach, J., Tauch, A., & Rahmann, S. (2009). Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks. BRIEFINGS IN BIOINFORMATICS, 10(1), 75-83. https://doi.org/10.1093/bib/bbn055
Baumbach, Jan, Tauch, Andreas, and Rahmann, Sven. 2009. “Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks”. BRIEFINGS IN BIOINFORMATICS 10 (1): 75-83.
Baumbach, J., Tauch, A., and Rahmann, S. (2009). Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks. BRIEFINGS IN BIOINFORMATICS 10, 75-83.
Baumbach, J., Tauch, A., & Rahmann, S., 2009. Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks. BRIEFINGS IN BIOINFORMATICS, 10(1), p 75-83.
J. Baumbach, A. Tauch, and S. Rahmann, “Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks”, BRIEFINGS IN BIOINFORMATICS, vol. 10, 2009, pp. 75-83.
Baumbach, J., Tauch, A., Rahmann, S.: Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks. BRIEFINGS IN BIOINFORMATICS. 10, 75-83 (2009).
Baumbach, Jan, Tauch, Andreas, and Rahmann, Sven. “Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks”. BRIEFINGS IN BIOINFORMATICS 10.1 (2009): 75-83.
Daten bereitgestellt von European Bioinformatics Institute (EBI)
9 Zitationen in Europe PMC
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Addressing the problems with life-science databases for traditional uses and systems biology.
Philippi S, Kohler J., Nat. Rev. Genet. 7(6), 2006
PMID: 16682980
Philippi S, Kohler J., Nat. Rev. Genet. 7(6), 2006
PMID: 16682980
RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.
Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muniz-Rascado L, Martinez-Flores I, Salgado H, Bonavides-Martinez C, Abreu-Goodger C, Rodriguez-Penagos C, Miranda-Rios J, Morett E, Merino E, Huerta AM, Trevino-Quintanilla L, Collado-Vides J., Nucleic Acids Res. 36(Database issue), 2007
PMID: 18158297
Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muniz-Rascado L, Martinez-Flores I, Salgado H, Bonavides-Martinez C, Abreu-Goodger C, Rodriguez-Penagos C, Miranda-Rios J, Morett E, Merino E, Huerta AM, Trevino-Quintanilla L, Collado-Vides J., Nucleic Acids Res. 36(Database issue), 2007
PMID: 18158297
RegulonDB: a database on transcriptional regulation in Escherichia coli.
Huerta AM, Salgado H, Thieffry D, Collado-Vides J., Nucleic Acids Res. 26(1), 1998
PMID: 9399800
Huerta AM, Salgado H, Thieffry D, Collado-Vides J., Nucleic Acids Res. 26(1), 1998
PMID: 9399800
RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12.
Salgado H, Gama-Castro S, Martinez-Antonio A, Diaz-Peredo E, Sanchez-Solano F, Peralta-Gil M, Garcia-Alonso D, Jimenez-Jacinto V, Santos-Zavaleta A, Bonavides-Martinez C, Collado-Vides J., Nucleic Acids Res. 32(Database issue), 2004
PMID: 14681419
Salgado H, Gama-Castro S, Martinez-Antonio A, Diaz-Peredo E, Sanchez-Solano F, Peralta-Gil M, Garcia-Alonso D, Jimenez-Jacinto V, Santos-Zavaleta A, Bonavides-Martinez C, Collado-Vides J., Nucleic Acids Res. 32(Database issue), 2004
PMID: 14681419
RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions.
Salgado H, Gama-Castro S, Peralta-Gil M, Diaz-Peredo E, Sanchez-Solano F, Santos-Zavaleta A, Martinez-Flores I, Jimenez-Jacinto V, Bonavides-Martinez C, Segura-Salazar J, Martinez-Antonio A, Collado-Vides J., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381895
Salgado H, Gama-Castro S, Peralta-Gil M, Diaz-Peredo E, Sanchez-Solano F, Santos-Zavaleta A, Martinez-Flores I, Jimenez-Jacinto V, Bonavides-Martinez C, Segura-Salazar J, Martinez-Antonio A, Collado-Vides J., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381895
RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli.
Salgado H, Santos A, Garza-Ramos U, van Helden J, Diaz E, Collado-Vides J., Nucleic Acids Res. 27(1), 1999
PMID: 9847141
Salgado H, Santos A, Garza-Ramos U, van Helden J, Diaz E, Collado-Vides J., Nucleic Acids Res. 27(1), 1999
PMID: 9847141
RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12.
Salgado H, Santos-Zavaleta A, Gama-Castro S, Millan-Zarate D, Blattner FR, Collado-Vides J., Nucleic Acids Res. 28(1), 2000
PMID: 10592182
Salgado H, Santos-Zavaleta A, Gama-Castro S, Millan-Zarate D, Blattner FR, Collado-Vides J., Nucleic Acids Res. 28(1), 2000
PMID: 10592182
RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12.
Salgado H, Santos-Zavaleta A, Gama-Castro S, Millan-Zarate D, Diaz-Peredo E, Sanchez-Solano F, Perez-Rueda E, Bonavides-Martinez C, Collado-Vides J., Nucleic Acids Res. 29(1), 2001
PMID: 11125053
Salgado H, Santos-Zavaleta A, Gama-Castro S, Millan-Zarate D, Diaz-Peredo E, Sanchez-Solano F, Perez-Rueda E, Bonavides-Martinez C, Collado-Vides J., Nucleic Acids Res. 29(1), 2001
PMID: 11125053
MtbRegList, a database dedicated to the analysis of transcriptional regulation in Mycobacterium tuberculosis.
Jacques PE, Gervais AL, Cantin M, Lucier JF, Dallaire G, Drouin G, Gaudreau L, Goulet J, Brzezinski R., Bioinformatics 21(10), 2005
PMID: 15722376
Jacques PE, Gervais AL, Cantin M, Lucier JF, Dallaire G, Drouin G, Gaudreau L, Goulet J, Brzezinski R., Bioinformatics 21(10), 2005
PMID: 15722376
PRODORIC: prokaryotic database of gene regulation.
Munch R, Hiller K, Barg H, Heldt D, Linz S, Wingender E, Jahn D., Nucleic Acids Res. 31(1), 2003
PMID: 12519998
Munch R, Hiller K, Barg H, Heldt D, Linz S, Wingender E, Jahn D., Nucleic Acids Res. 31(1), 2003
PMID: 12519998
DBTBS: a database of Bacillus subtilis promoters and transcription factors.
Ishii T, Yoshida K, Terai G, Fujita Y, Nakai K., Nucleic Acids Res. 29(1), 2001
PMID: 11125112
Ishii T, Yoshida K, Terai G, Fujita Y, Nakai K., Nucleic Acids Res. 29(1), 2001
PMID: 11125112
DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics.
Makita Y, Nakao M, Ogasawara N, Nakai K., Nucleic Acids Res. 32(Database issue), 2004
PMID: 14681362
Makita Y, Nakao M, Ogasawara N, Nakai K., Nucleic Acids Res. 32(Database issue), 2004
PMID: 14681362
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information.
Sierro N, Makita Y, de Hoon M, Nakai K., Nucleic Acids Res. 36(Database issue), 2007
PMID: 17962296
Sierro N, Makita Y, de Hoon M, Nakai K., Nucleic Acids Res. 36(Database issue), 2007
PMID: 17962296
CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks.
Baumbach J., BMC Bioinformatics 8(), 2007
PMID: 17986320
Baumbach J., BMC Bioinformatics 8(), 2007
PMID: 17986320
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
Baumbach J, Brinkrolf K, Czaja LF, Rahmann S, Tauch A., BMC Genomics 7(), 2006
PMID: 16478536
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