CoryneRegNet: An ontology-based data warehouse of corynebacterial transcription factors and regulatory networks

Baumbach J, Brinkrolf K, Czaja LF, Rahmann S, Tauch A (2006)
BMC Genomics 7(1): 24.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Baumbach, Jan; Brinkrolf, KarinaUniBi; Czaja, Lisa F.; Rahmann, Sven; Tauch, AndreasUniBi
Erscheinungsjahr
2006
Zeitschriftentitel
BMC Genomics
Band
7
Ausgabe
1
Art.-Nr.
24
ISSN
1471-2164
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https://pub.uni-bielefeld.de/record/1773632

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Baumbach J, Brinkrolf K, Czaja LF, Rahmann S, Tauch A. CoryneRegNet: An ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. BMC Genomics. 2006;7(1): 24.
Baumbach, J., Brinkrolf, K., Czaja, L. F., Rahmann, S., & Tauch, A. (2006). CoryneRegNet: An ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. BMC Genomics, 7(1), 24. https://doi.org/10.1186/1471-2164-7-24
Baumbach, Jan, Brinkrolf, Karina, Czaja, Lisa F., Rahmann, Sven, and Tauch, Andreas. 2006. “CoryneRegNet: An ontology-based data warehouse of corynebacterial transcription factors and regulatory networks”. BMC Genomics 7 (1): 24.
Baumbach, J., Brinkrolf, K., Czaja, L. F., Rahmann, S., and Tauch, A. (2006). CoryneRegNet: An ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. BMC Genomics 7:24.
Baumbach, J., et al., 2006. CoryneRegNet: An ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. BMC Genomics, 7(1): 24.
J. Baumbach, et al., “CoryneRegNet: An ontology-based data warehouse of corynebacterial transcription factors and regulatory networks”, BMC Genomics, vol. 7, 2006, : 24.
Baumbach, J., Brinkrolf, K., Czaja, L.F., Rahmann, S., Tauch, A.: CoryneRegNet: An ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. BMC Genomics. 7, : 24 (2006).
Baumbach, Jan, Brinkrolf, Karina, Czaja, Lisa F., Rahmann, Sven, and Tauch, Andreas. “CoryneRegNet: An ontology-based data warehouse of corynebacterial transcription factors and regulatory networks”. BMC Genomics 7.1 (2006): 24.
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28 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Regulons of global transcription factors in Corynebacterium glutamicum.
Toyoda K, Inui M., Appl Microbiol Biotechnol 100(1), 2016
PMID: 26496920
CMRegNet-An interspecies reference database for corynebacterial and mycobacterial regulatory networks.
Abreu VA, Almeida S, Tiwari S, Hassan SS, Mariano D, Silva A, Baumbach J, Azevedo V, Röttger R., BMC Genomics 16(), 2015
PMID: 26062809
Genome wide identification of Acidithiobacillus ferrooxidans (ATCC 23270) transcription factors and comparative analysis of ArsR and MerR metal regulators.
Hödar C, Moreno P, di Genova A, Latorre M, Reyes-Jara A, Maass A, González M, Cambiazo V., Biometals 25(1), 2012
PMID: 21830017
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
Mitochondrial DNA as effective molecular markers for the genetic variation and phylogeny of the family Osteoglossidae.
Mu XD, Wang XJ, Song HM, Yang YX, Luo D, Gu DE, Xu M, Liu C, Luo JR, Hu YC., Gene 511(2), 2012
PMID: 23036711
The Zur regulon of Corynebacterium glutamicum ATCC 13032.
Schröder J, Jochmann N, Rodionov DA, Tauch A., BMC Genomics 11(), 2010
PMID: 20055984
The transcriptional regulators RamA and RamB are involved in the regulation of glycogen synthesis in Corynebacterium glutamicum.
Seibold GM, Hagmann CT, Schietzel M, Emer D, Auchter M, Schreiner J, Eikmanns BJ., Microbiology 156(pt 4), 2010
PMID: 20056699
Regulation by transcription factors in bacteria: beyond description.
Balleza E, López-Bojorquez LN, Martínez-Antonio A, Resendis-Antonio O, Lozada-Chávez I, Balderas-Martínez YI, Encarnación S, Collado-Vides J., FEMS Microbiol Rev 33(1), 2009
PMID: 19076632
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
Integration of prostate cancer clinical data using an ontology.
Min H, Manion FJ, Goralczyk E, Wong YN, Ross E, Beck JR., J Biomed Inform 42(6), 2009
PMID: 19497389
The LacI/GalR family transcriptional regulator UriR negatively controls uridine utilization of Corynebacterium glutamicum by binding to catabolite-responsive element (cre)-like sequences.
Brinkrolf K, Plöger S, Solle S, Brune I, Nentwich SS, Hüser AT, Kalinowski J, Pühler A, Tauch A., Microbiology 154(pt 4), 2008
PMID: 18375800
Linking Cytoscape and the corynebacterial reference database CoryneRegNet.
Baumbach J, Apeltsin L., BMC Genomics 9(), 2008
PMID: 18426593
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), 2007
PMID: 17229482
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, Hüser AT, Gerstmeir R, Eikmanns BJ, Kalinowski J, Pühler A, Tauch A., J Bacteriol 189(7), 2007
PMID: 17259312
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
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, Goesmann A., BMC Syst Biol 1(), 2007
PMID: 18034885

39 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
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
Transcription factors: structural families and principles of DNA recognition.
Pabo CO, Sauer RT., Annu. Rev. Biochem. 61(), 1992
PMID: 1497306
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
The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12.
Perez-Rueda E, Collado-Vides J., Nucleic Acids Res. 28(8), 2000
PMID: 10734204
Reconstruction of microbial transcriptional regulatory networks.
Herrgard MJ, Covert MW, Palsson BO., Curr. Opin. Biotechnol. 15(1), 2004
PMID: 15102470
Transcription regulation and environmental adaptation in bacteria.
Cases I, de Lorenzo V, Ouzounis CA., Trends Microbiol. 11(6), 2003
PMID: 12823939
Corynebacterium efficiens sp. nov., a glutamic-acid-producing species from soil and vegetables.
Fudou R, Jojima Y, Seto A, Yamada K, Kimura E, Nakamatsu T, Hiraishi A, Yamanaka S., Int. J. Syst. Evol. Microbiol. 52(Pt 4), 2002
PMID: 12148616
Industrial production of amino acids by coryneform bacteria.
Hermann T., J. Biotechnol. 104(1-3), 2003
PMID: 12948636
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
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
The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129.
Cerdeno-Tarraga AM, Efstratiou A, Dover LG, Holden MT, Pallen M, Bentley SD, Besra GS, Churcher C, James KD, De Zoysa A, Chillingworth T, Cronin A, Dowd L, Feltwell T, Hamlin N, Holroyd S, Jagels K, Moule S, Quail MA, Rabbinowitsch E, Rutherford KM, Thomson NR, Unwin L, Whitehead S, Barrell BG, Parkhill J., Nucleic Acids Res. 31(22), 2003
PMID: 14602910
Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens.
Nishio Y, Nakamura Y, Kawarabayasi Y, Usuda Y, Kimura E, Sugimoto S, Matsui K, Yamagishi A, Kikuchi H, Ikeo K, Gojobori T., Genome Res. 13(7), 2003
PMID: 12840036
The genome stability in Corynebacterium species due to lack of the recombinational repair system.
Nakamura Y, Nishio Y, Ikeo K, Gojobori T., Gene 317(1-2), 2003
PMID: 14604803
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 modulation of Escherichia coli RNA polymerase.
Ishihama A., Annu. Rev. Microbiol. 54(), 2000
PMID: 11018136
ppGpp: a global regulator in Escherichia coli.
Magnusson LU, Farewell A, Nystrom T., Trends Microbiol. 13(5), 2005
PMID: 15866041
Stringend control and ppGpp synthesis in Brevibacterium flavum during amino acid starvation
Ruklisha MP, Damberga BE, Shvinka JE., 1993
Growth control and ppGpp synthesis in Brevibacterium flavum cells at various medium mixing rates and aeration intensities
Ruklisha MP, Viesturs U, Labane L., 1995
Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalised Data Structures.
Koehler J, Rawlings C, Verrier P, Mitchell R, Skusa A, Ruegg A, Philippi S., In Silico Biol. (Gedrukt) 5(1), 2005
PMID: 15972003

Wiese R, Eiglsperger M, Kaufmann M., 2001
Database resources of the National Center for Biotechnology.
Wheeler DL, Church DM, Federhen S, Lash AE, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E, Tatusova TA, Wagner L., Nucleic Acids Res. 31(1), 2003
PMID: 12519941
The Corynebacterium glutamicum genome: features and impacts on biotechnological processes.
Ikeda M, Nakagawa S., Appl. Microbiol. Biotechnol. 62(2-3), 2003
PMID: 12743753
Database resources of the National Center for Biotechnology Information.
Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Church DM, DiCuccio M, Edgar R, Federhen S, Helmberg W, Kenton DL, Khovayko O, Lipman DJ, Madden TL, Maglott DR, Ostell J, Pontius JU, Pruitt KD, Schuler GD, Schriml LM, Sequeira E, Sherry ST, Sirotkin K, Starchenko G, Suzek TO, Tatusov R, Tatusova TA, Wagner L, Yaschenko E., Nucleic Acids Res. 33(Database issue), 2005
PMID: 15608222
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
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
Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes
Münch R, Hiller K, Grote A, Scheer M, Klein J, Schobert M, Jahn D., 2005
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
Conditional senescence in bacteria: death of the immortals.
Nystrom T., Mol. Microbiol. 48(1), 2003
PMID: 12657042
Structure and function of the feed-forward loop network motif.
Mangan S, Alon U., Proc. Natl. Acad. Sci. U.S.A. 100(21), 2003
PMID: 14530388
On the power of profiles for transcription factor binding site detection.
Rahmann S, Muller T, Vingron M., Stat Appl Genet Mol Biol 2(), 2003
PMID: 16646785
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