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.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
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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.
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BRIEFINGS IN BIOINFORMATICS
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10
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75-83
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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. doi:10.1093/bib/bbn055
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.

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R-based software for the integration of pathway data into bioinformatic algorithms.
Kramer F, Bayerlová M, Beißbarth T., Biology (Basel) 3(1), 2014
PMID: 24833336
Entropic Biological Score: a cell cycle investigation for GRNs inference.
Lopes FM, Ray SS, Hashimoto RF, Cesar RM., Gene 541(2), 2014
PMID: 24631265
How little do we actually know? On the size of gene regulatory networks.
Röttger R, Rückert U, Taubert J, Baumbach J., IEEE/ACM Trans Comput Biol Bioinform 9(5), 2012
PMID: 22585140
Computational methods for discovering gene networks from expression data.
Lee WP, Tzou WS., Brief Bioinform 10(4), 2009
PMID: 19505889
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
Functional genomics of pH homeostasis in Corynebacterium glutamicum revealed novel links between pH response, oxidative stress, iron homeostasis and methionine synthesis.
Follmann M, Ochrombel I, Krämer R, Trötschel C, Poetsch A, Rückert C, Hüser A, Persicke M, Seiferling D, Kalinowski J, Marin K., BMC Genomics 10(), 2009
PMID: 20025733

69 References

Daten bereitgestellt von Europe PubMed Central.

Survival versus maintenance of genetic stability: a conflict of priorities during stress.
Matic I, Taddei F, Radman M., Res. Microbiol. 155(5), 2004
PMID: 15207865
Gene regulatory network growth by duplication.
Teichmann SA, Babu MM., Nat. Genet. 36(5), 2004
PMID: 15107850
Structure and evolution of transcriptional regulatory networks.
Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA., Curr. Opin. Struct. Biol. 14(3), 2004
PMID: 15193307
Evolution of transcription factors and the gene regulatory network in Escherichia coli.
Madan Babu M, Teichmann SA., Nucleic Acids Res. 31(4), 2003
PMID: 12582243
Evolutionary dynamics of prokaryotic transcriptional regulatory networks.
Madan Babu M, Teichmann SA, Aravind L., J. Mol. Biol. 358(2), 2006
PMID: 16530225
Modular analysis of the transcriptional regulatory network of E. coli.
Resendis-Antonio O, Freyre-Gonzalez JA, Menchaca-Mendez R, Gutierrez-Rios RM, Martinez-Antonio A, Avila-Sanchez C, Collado-Vides J., Trends Genet. 21(1), 2005
PMID: 15680508
Transcription factors: structural families and principles of DNA recognition.
Pabo CO, Sauer RT., Annu. Rev. Biochem. 61(), 1992
PMID: 1497306
Reconstruction of microbial transcriptional regulatory networks.
Herrgard MJ, Covert MW, Palsson BO., Curr. Opin. Biotechnol. 15(1), 2004
PMID: 15102470
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
PEDRo: a database for storing, searching and disseminating experimental proteomics data.
Garwood K, McLaughlin T, Garwood C, Joens S, Morrison N, Taylor CF, Carroll K, Evans C, Whetton AD, Hart S, Stead D, Yin Z, Brown AJ, Hesketh A, Chater K, Hansson L, Mewissen M, Ghazal P, Howard J, Lilley KS, Gaskell SJ, Brass A, Hubbard SJ, Oliver SG, Paton NW., BMC Genomics 5(), 2004
PMID: 15377392
On the power of profiles for transcription factor binding site detection
Rahmann S, Mueller T, Vingron M., 2003
DNA binding sites: representation and discovery.
Stormo GD., Bioinformatics 16(1), 2000
PMID: 10812473
Unraveling the Web Services Web: an introduction to SOAP, WSDL, and UDDI
Curbera F, Duftler M, Khalaf R., 2002
Bacterial regulatory networks are extremely flexible in evolution.
Lozada-Chavez I, Janga SC, Collado-Vides J., Nucleic Acids Res. 34(12), 2006
PMID: 16840530
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
SCOP database in 2004: refinements integrate structure and sequence family data.
Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, Murzin AG., Nucleic Acids Res. 32(Database issue), 2004
PMID: 14681400
Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv.
Camus JC, Pryor MJ, Medigue C, Cole ST., Microbiology (Reading, Engl.) 148(Pt 10), 2002
PMID: 12368430
Database resources of the National Center for Biotechnology Information.
Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Ostell J, Miller V, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E., Nucleic Acids Res. 35(Database issue), 2006
PMID: 17170002
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes.
Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, Voss N, Stegmaier P, Lewicki-Potapov B, Saxel H, Kel AE, Wingender E., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381825
The TRANSFAC system on gene expression regulation.
Wingender E, Chen X, Fricke E, Geffers R, Hehl R, Liebich I, Krull M, Matys V, Michael H, Ohnhauser R, Pruss M, Schacherer F, Thiele S, Urbach S., Nucleic Acids Res. 29(1), 2001
PMID: 11125113
The Universal Protein Resource (UniProt).
Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS., Nucleic Acids Res. 33(Database issue), 2005
PMID: 15608167
Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes.
Munch R, Hiller K, Grote A, Scheer M, Klein J, Schobert M, Jahn D., Bioinformatics 21(22), 2005
PMID: 16109747
ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks.
Klein J, Leupold S, Munch R, Pommerenke C, Johl T, Karst U, Jansch L, Jahn D, Retter I., Nucleic Acids Res. 36(Web Server issue), 2008
PMID: 18440972
JVirGel: Calculation of virtual two-dimensional protein gels.
Hiller K, Schobert M, Hundertmark C, Jahn D, Munch R., Nucleic Acids Res. 31(13), 2003
PMID: 12824438
PrediSi: prediction of signal peptides and their cleavage positions.
Hiller K, Grote A, Scheer M, Munch R, Jahn D., Nucleic Acids Res. 32(Web Server issue), 2004
PMID: 15215414
JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information.
Scheer M, Klawonn F, Munch R, Grote A, Hiller K, Choi C, Koch I, Schobert M, Hartig E, Klages U, Jahn D., Nucleic Acids Res. 34(Web Server issue), 2006
PMID: 16845060
The transcriptional profile of early to middle sporulation in Bacillus subtilis.
Fawcett P, Eichenberger P, Losick R, Youngman P., Proc. Natl. Acad. Sci. U.S.A. 97(14), 2000
PMID: 10869437
Prediction of transcriptional terminators in Bacillus subtilis and related species.
de Hoon MJ, Makita Y, Nakai K, Miyano S., PLoS Comput. Biol. 1(3), 2005
PMID: 16110342
Fast index based algorithms and software for matching position specific scoring matrices.
Beckstette M, Homann R, Giegerich R, Kurtz S., BMC Bioinformatics 7(), 2006
PMID: 16930469
PoSSuMsearch: fast and sensitive matching of position specific scoring matrices using enhanced suffix arrays
Beckstette M, Strothmann D, Homann R, Giegerich R, Kurtz S., 2004
MoRAine – a web server for fast computational transcription factor binding motif reannotation
Baumbach J, Wittkop T, Weile J., 2008
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
CoryneCenter - an online resource for the integrated analysis of corynebacterial genome and transcriptome data.
Neuweger H, Baumbach J, Albaum S, Bekel T, Dondrup M, Huser AT, Kalinowski J, Oehm S, Puhler A, Rahmann S, Weile J, Goesmann A., BMC Syst Biol 1(), 2007
PMID: 18034885
Linking Cytoscape and the corynebacterial reference database CoryneRegNet.
Baumbach J, Apeltsin L., BMC Genomics 9(), 2008
PMID: 18426593
Exact and heuristic algorithms for weighted cluster editing.
Rahmann S, Wittkop T, Baumbach J, Martin M, Truss A, Bocker S., Comput Syst Bioinformatics Conf 6(), 2007
PMID: 17951842
Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing.
Wittkop T, Baumbach J, Lobo FP, Rahmann S., BMC Bioinformatics 8(), 2007
PMID: 17941985
CoryneRegNet 2: An integrative bioinformatics approach for reconstruction and comparison of transcriptional regulatory networks in prokaryotes
Baumbach J, Brinkrolf K, Wittkop T., 2006
Reconstruction of the evolutionary history of the LexA-binding sequence.
Mazon G, Erill I, Campoy S, Cortes P, Forano E, Barbe J., Microbiology (Reading, Engl.) 150(Pt 11), 2004
PMID: 15528664
MEME: discovering and analyzing DNA and protein sequence motifs.
Bailey TL, Williams N, Misleh C, Li WW., Nucleic Acids Res. 34(Web Server issue), 2006
PMID: 16845028
Analysis of computational approaches for motif discovery.
Li N, Tompa M., Algorithms Mol Biol 1(), 2006
PMID: 16722558
Assessing computational tools for the discovery of transcription factor binding sites.
Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Regnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z., Nat. Biotechnol. 23(1), 2005
PMID: 15637633
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
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
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
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
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
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
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
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
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
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
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
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
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

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