CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands

Pauling J, Rottger R, Tauch A, Azevedo V, Baumbach J (2012)
Nucleic Acids Research 40(D1): D610-D614.

Zeitschriftenaufsatz | Veröffentlicht| Englisch
 
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Autor/in
Pauling, Josch; Rottger, Richard; Tauch, AndreasUniBi; Azevedo, Vasco; Baumbach, Jan
Abstract / Bemerkung
Post-genomic analysis techniques such as next-generation sequencing have produced vast amounts of data about micro organisms including genetic sequences, their functional annotations and gene regulatory interactions. The latter are genetic mechanisms that control a cell's characteristics, for instance, pathogenicity as well as survival and reproduction strategies. CoryneRegNet is the reference database and analysis platform for corynebacterial gene regulatory networks. In this article we introduce the updated version 6.0 of CoryneRegNet and describe the updated database content which includes, 6352 corynebacterial regulatory interactions compared with 4928 interactions in release 5.0 and 3235 regulations in release 4.0, respectively. We also demonstrate how we support the community by integrating analysis and visualization features for transiently imported custom data, such as gene regulatory interactions. Furthermore, with release 6.0, we provide easy-to-use functions that allow the user to submit data for persistent storage with the CoryneRegNet database. Thus, it offers important options to its users in terms of community demands. CoryneRegNet is publicly available at http://www.coryneregnet.de.
Erscheinungsjahr
2012
Zeitschriftentitel
Nucleic Acids Research
Band
40
Ausgabe
D1
Seite(n)
D610-D614
ISSN
0305-1048
eISSN
1362-4962
Page URI
https://pub.uni-bielefeld.de/record/2471873

Zitieren

Pauling J, Rottger R, Tauch A, Azevedo V, Baumbach J. CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands. Nucleic Acids Research. 2012;40(D1):D610-D614.
Pauling, J., Rottger, R., Tauch, A., Azevedo, V., & Baumbach, J. (2012). CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands. Nucleic Acids Research, 40(D1), D610-D614. doi:10.1093/nar/gkr883
Pauling, J., Rottger, R., Tauch, A., Azevedo, V., and Baumbach, J. (2012). CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands. Nucleic Acids Research 40, D610-D614.
Pauling, J., et al., 2012. CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands. Nucleic Acids Research, 40(D1), p D610-D614.
J. Pauling, et al., “CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands”, Nucleic Acids Research, vol. 40, 2012, pp. D610-D614.
Pauling, J., Rottger, R., Tauch, A., Azevedo, V., Baumbach, J.: CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands. Nucleic Acids Research. 40, D610-D614 (2012).
Pauling, Josch, Rottger, Richard, Tauch, Andreas, Azevedo, Vasco, and Baumbach, Jan. “CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands”. Nucleic Acids Research 40.D1 (2012): D610-D614.

35 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Identifying the Growth Modulon of Corynebacterium glutamicum.
Haas T, Graf M, Nieß A, Busche T, Kalinowski J, Blombach B, Takors R., Front Microbiol 10(), 2019
PMID: 31134020
PRODORIC2: the bacterial gene regulation database in 2018.
Eckweiler D, Dudek CA, Hartlich J, Brötje D, Jahn D., Nucleic Acids Res 46(d1), 2018
PMID: 29136200
Deciphering the Adaptation of Corynebacterium glutamicum in Transition from Aerobiosis via Microaerobiosis to Anaerobiosis.
Lange J, Münch E, Müller J, Busche T, Kalinowski J, Takors R, Blombach B., Genes (Basel) 9(6), 2018
PMID: 29899275
Comparative analysis of the Corynebacterium glutamicum transcriptome in response to changes in dissolved oxygen levels.
Liu X, Yang S, Wang F, Dai X, Yang Y, Bai Z., J Ind Microbiol Biotechnol 44(2), 2017
PMID: 27844170
A new genome-scale metabolic model of Corynebacterium glutamicum and its application.
Zhang Y, Cai J, Shang X, Wang B, Liu S, Chai X, Tan T, Zhang Y, Wen T., Biotechnol Biofuels 10(), 2017
PMID: 28680478
Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Changes.
Desai JS, Sartor RC, Lawas LM, Jagadish SVK, Doherty CJ., Sci Rep 7(1), 2017
PMID: 29222512
Regulons of global transcription factors in Corynebacterium glutamicum.
Toyoda K, Inui M., Appl Microbiol Biotechnol 100(1), 2016
PMID: 26496920
Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria.
Ibarra-Arellano MA, Campos-González AI, Treviño-Quintanilla LG, Tauch A, Freyre-González JA., Database (Oxford) 2016(), 2016
PMID: 27242034
Assessment of transfer methods for comparative genomics of regulatory networks in bacteria.
Kılıç S, Erill I., BMC Bioinformatics 17 Suppl 8(), 2016
PMID: 27586594
Parametric bootstrapping for biological sequence motifs.
O'Neill PK, Erill I., BMC Bioinformatics 17(1), 2016
PMID: 27716039
Absolute quantification of Corynebacterium glutamicum glycolytic and anaplerotic enzymes by QconCAT.
Voges R, Corsten S, Wiechert W, Noack S., J Proteomics 113(), 2015
PMID: 25451015
Ribosome binding site libraries and pathway modules for shikimic acid synthesis with Corynebacterium glutamicum.
Zhang B, Zhou N, Liu YM, Liu C, Lou CB, Jiang CY, Liu SJ., Microb Cell Fact 14(), 2015
PMID: 25981633
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
Biosensor-driven adaptive laboratory evolution of l-valine production in Corynebacterium glutamicum.
Mahr R, Gätgens C, Gätgens J, Polen T, Kalinowski J, Frunzke J., Metab Eng 32(), 2015
PMID: 26453945
CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria.
Kiliç S, White ER, Sagitova DM, Cornish JP, Erill I., Nucleic Acids Res 42(database issue), 2014
PMID: 24234444
Network portal: a database for storage, analysis and visualization of biological networks.
Turkarslan S, Wurtmann EJ, Wu WJ, Jiang N, Bare JC, Foley K, Reiss DJ, Novichkov P, Baliga NS., Nucleic Acids Res 42(database issue), 2014
PMID: 24271392
On the limits of computational functional genomics for bacterial lifestyle prediction.
Barbosa E, Röttger R, Hauschild AC, Azevedo V, Baumbach J., Brief Funct Genomics 13(5), 2014
PMID: 24855068
Comparative genomics and evolution of regulons of the LacI-family transcription factors.
Ravcheev DA, Khoroshkin MS, Laikova ON, Tsoy OV, Sernova NV, Petrova SA, Rakhmaninova AB, Novichkov PS, Gelfand MS, Rodionov DA., Front Microbiol 5(), 2014
PMID: 24966856
σ(ECF) factors of gram-positive bacteria: a focus on Bacillus subtilis and the CMNR group.
Souza BM, Castro TL, Carvalho RD, Seyffert N, Silva A, Miyoshi A, Azevedo V., Virulence 5(5), 2014
PMID: 24921931
Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models.
Faria JP, Overbeek R, Xia F, Rocha M, Rocha I, Henry CS., Brief Bioinform 15(4), 2014
PMID: 23422247
Label-free proteomic analysis to confirm the predicted proteome of Corynebacterium pseudotuberculosis under nitrosative stress mediated by nitric oxide.
Silva WM, Carvalho RD, Soares SC, Bastos IF, Folador EL, Souza GH, Le Loir Y, Miyoshi A, Silva A, Azevedo V., BMC Genomics 15(), 2014
PMID: 25477071
High-resolution detection of DNA binding sites of the global transcriptional regulator GlxR in Corynebacterium glutamicum.
Jungwirth B, Sala C, Kohl TA, Uplekar S, Baumbach J, Cole ST, Pühler A, Tauch A., Microbiology 159(pt 1), 2013
PMID: 23103979
Corynebacterium glutamicum promoters: a practical approach.
Pátek M, Holátko J, Busche T, Kalinowski J, Nešvera J., Microb Biotechnol 6(2), 2013
PMID: 23305350
Systems metabolic engineering of xylose-utilizing Corynebacterium glutamicum for production of 1,5-diaminopentane.
Buschke N, Becker J, Schäfer R, Kiefer P, Biedendieck R, Wittmann C., Biotechnol J 8(5), 2013
PMID: 23447448
Proteome response of Corynebacterium glutamicum to high concentration of industrially relevant C₄ and C₅ dicarboxylic acids.
Vasco-Cárdenas MF, Baños S, Ramos A, Martín JF, Barreiro C., J Proteomics 85(), 2013
PMID: 23624027
Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032.
Mentz A, Neshat A, Pfeifer-Sancar K, Pühler A, Rückert C, Kalinowski J., BMC Genomics 14(), 2013
PMID: 24138339
Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique.
Pfeifer-Sancar K, Mentz A, Rückert C, Kalinowski J., BMC Genomics 14(), 2013
PMID: 24341750
On the trail of EHEC/EAEC--unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria.
Pauling J, Röttger R, Neuner A, Salgado H, Collado-Vides J, Kalaghatgi P, Azevedo V, Tauch A, Pühler A, Baumbach J., Integr Biol (Camb) 4(7), 2012
PMID: 22318347
A Role for Sigma Factor σ(E) in Corynebacterium pseudotuberculosis Resistance to Nitric Oxide/Peroxide Stress.
Pacheco LG, Castro TL, Carvalho RD, Moraes PM, Dorella FA, Carvalho NB, Slade SE, Scrivens JH, Feelisch M, Meyer R, Miyoshi A, Oliveira SC, Dowson CG, Azevedo V., Front Microbiol 3(), 2012
PMID: 22514549

27 References

Daten bereitgestellt von Europe PubMed Central.

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units).
Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muniz-Rascado L, Solano-Lira H, Jimenez-Jacinto V, Weiss V, Garcia-Sotelo JS, Lopez-Fuentes A, Porron-Sotelo L, Alquicira-Hernandez S, Medina-Rivera A, Martinez-Flores I, Alquicira-Hernandez K, Martinez-Adame R, Bonavides-Martinez C, Miranda-Rios J, Huerta AM, Mendoza-Vargas A, Collado-Torres L, Taboada B, Vega-Alvarado L, Olvera M, Olvera L, Grande R, Morett E, Collado-Vides J., Nucleic Acids Res. 39(Database issue), 2010
PMID: 21051347
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 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
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 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
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
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
PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes.
Grote A, Klein J, Retter I, Haddad I, Behling S, Bunk B, Biegler I, Yarmolinetz S, Jahn D, Munch R., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18974177
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
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 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
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
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
Evidence for reductive genome evolution and lateral acquisition of virulence functions in two Corynebacterium pseudotuberculosis strains.
Ruiz JC, D'Afonseca V, Silva A, Ali A, Pinto AC, Santos AR, Rocha AA, Lopes DO, Dorella FA, Pacheco LG, Costa MP, Turk MZ, Seyffert N, Moraes PM, Soares SC, Almeida SS, Castro TL, Abreu VA, Trost E, Baumbach J, Tauch A, Schneider MP, McCulloch J, Cerdeira LT, Ramos RT, Zerlotini A, Dominitini A, Resende DM, Coser EM, Oliveira LM, Pedrosa AL, Vieira CU, Guimaraes CT, Bartholomeu DC, Oliveira DM, Santos FR, Rabelo EM, Lobo FP, Franco GR, Costa AF, Castro IM, Dias SR, Ferro JA, Ortega JM, Paiva LV, Goulart LR, Almeida JF, Ferro MI, Carneiro NP, Falcao PR, Grynberg P, Teixeira SM, Brommonschenkel S, Oliveira SC, Meyer R, Moore RJ, Miyoshi A, Oliveira GC, Azevedo V., PLoS ONE 6(4), 2011
PMID: 21533164
Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study.
Cerdeira LT, Carneiro AR, Ramos RT, de Almeida SS, D'Afonseca V, Schneider MP, Baumbach J, Tauch A, McCulloch JA, Azevedo VA, Silva A., J. Microbiol. Methods 86(2), 2011
PMID: 21620904
Comprehensive cluster analysis with Transitivity Clustering.
Wittkop T, Emig D, Truss A, Albrecht M, Bocker S, Baumbach J., Nat Protoc 6(3), 2011
PMID: 21372810
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
MicrobesOnline: an integrated portal for comparative and functional genomics.
Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, Friedland GD, Huang KH, Keller K, Novichkov PS, Dubchak IL, Alm EJ, Arkin AP., Nucleic Acids Res. 38(Database issue), 2009
PMID: 19906701

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