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Volumn 8, Issue , 2007, Pages

CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks

Author keywords

[No Author keywords available]

Indexed keywords

CORYNEBACTERIUM GLUTAMICUM; DNA MICROARRAY ANALYSIS; ENVIRONMENTAL CONDITIONS; GENE REGULATORY NETWORKS; REGULATORY INTERACTIONS; SOAP-BASED WEB SERVICES; TRANSCRIPTIONAL REGULATION; TRANSCRIPTIONAL REGULATORY NETWORKS;

EID: 38049144241     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-429     Document Type: Article
Times cited : (60)

References (45)
  • 3
    • 2342648924 scopus 로고    scopus 로고
    • Integrating high-throughput and computational data elucidates bacterial networks
    • 10.1038/nature02456 15129285
    • Covert MW Knight EM Reed JL Herrgard MJ Palsson BO Integrating high-throughput and computational data elucidates bacterial networks Nature 2004, 429(6987):92-96. 10.1038/nature02456 15129285
    • (2004) Nature , vol.429 , Issue.6987 , pp. 92-96
    • Covert, M.W.1    Knight, E.M.2    Reed, J.L.3    Herrgard, M.J.4    Palsson, B.O.5
  • 4
    • 1242328740 scopus 로고    scopus 로고
    • Reconstruction of microbial transcriptional regulatory networks
    • 10.1016/j.copbio.2003.11.002 15102470
    • Herrgard MJ Covert MW Palsson B Reconstruction of microbial transcriptional regulatory networks Curr Opin Biotechnol 2004, 15:70-77. 10.1016/j.copbio.2003.11.002 15102470
    • (2004) Curr Opin Biotechnol , vol.15 , pp. 70-77
    • Herrgard, M.J.1    Covert, M.W.2    Palsson, B.3
  • 5
    • 0037406843 scopus 로고    scopus 로고
    • Thirteen years of building constraint-based in silico models of Escherichia coli
    • 154396 12700248 10.1128/JB.185.9.2692-2699.2003
    • Reed JL Palsson B Thirteen years of building constraint-based in silico models of Escherichia coli J Bacteriol 2003, 185(9):2692-2699. 154396 12700248 10.1128/JB.185.9.2692-2699.2003
    • (2003) J Bacteriol , vol.185 , Issue.9 , pp. 2692-2699
    • Reed, J.L.1    Palsson, B.2
  • 6
    • 30344484891 scopus 로고    scopus 로고
    • Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli
    • 10.1016/j.tim.2005.11.002 16311037
    • Martinez-Antonio A Janga SC Salgado H Collado-Vides J Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli Trends Microbiol 2006, 14:22-27. 10.1016/j.tim.2005.11.002 16311037
    • (2006) Trends Microbiol , vol.14 , pp. 22-27
    • Martinez-Antonio, A.1    Janga, S.C.2    Salgado, H.3    Collado-Vides, J.4
  • 7
    • 1642446957 scopus 로고    scopus 로고
    • From the sequence to cell modeling: Comprehensive functional genomics in Escherichia coli
    • 14761306
    • Mori H From the sequence to cell modeling: Comprehensive functional genomics in Escherichia coli J Biochem Mol Biol 2004, 37:83-92. 14761306
    • (2004) J Biochem Mol Biol , vol.37 , pp. 83-92
    • Mori, H.1
  • 8
    • 33644604851 scopus 로고    scopus 로고
    • CoryneRegNet: An ontology-based data warehouse of corynebacterial transcription factors and regulatory networks
    • 1382212 16478536 10.1186/1471-2164-7-24
    • Baumbach J Brinkrolf K Czaja L Rahmann S Tauch A CoryneRegNet: An ontology-based data warehouse of corynebacterial transcription factors and regulatory networks BMC Genomics 2006, 7:24. 1382212 16478536 10.1186/1471-2164-7-24
    • (2006) BMC Genomics , vol.7 , pp. 24
    • Baumbach, J.1    Brinkrolf, K.2    Czaja, L.3    Rahmann, S.4    Tauch, A.5
  • 9
    • 34047170261 scopus 로고    scopus 로고
    • CoryneRegNet 3.0-An interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli
    • 10.1016/j.jbiotec.2006.12.012 17229482
    • Baumbach J Wittkop T Rademacher K Rahmann S Brinkrolf K Tauch A CoryneRegNet 3.0-An interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli J Biotechnol 2007, 129(2):279-289. 10.1016/j.jbiotec.2006.12.012 17229482
    • (2007) J Biotechnol , vol.129 , Issue.2 , pp. 279-289
    • Baumbach, J.1    Wittkop, T.2    Rademacher, K.3    Rahmann, S.4    Brinkrolf, K.5    Tauch, A.6
  • 10
    • 33750959240 scopus 로고    scopus 로고
    • Fast index based algorithms and software for matching position specific scoring matrices
    • 1635428 16930469 10.1186/1471-2105-7-389
    • Beckstette M Homann R Giegerich R Kurtz S Fast index based algorithms and software for matching position specific scoring matrices BMC Bioinformatics 2006, 7:389. 1635428 16930469 10.1186/1471-2105-7-389
    • (2006) BMC Bioinformatics , vol.7 , pp. 389
    • Beckstette, M.1    Homann, R.2    Giegerich, R.3    Kurtz, S.4
  • 11
    • 2942606066 scopus 로고    scopus 로고
    • Structure and evolution of transcriptional regulatory networks
    • 10.1016/j.sbi.2004.05.004 15193307
    • Babu MM Luscombe NM Aravind L Gerstein M Teichmann SA Structure and evolution of transcriptional regulatory networks Curr Opin Struct Biol 2004, 14(3):283-291. 10.1016/j.sbi.2004.05.004 15193307
    • (2004) Curr Opin Struct Biol , vol.14 , Issue.3 , pp. 283-291
    • Babu, M.M.1    Luscombe, N.M.2    Aravind, L.3    Gerstein, M.4    Teichmann, S.A.5
  • 12
    • 33646113855 scopus 로고    scopus 로고
    • Evolutionary dynamics of prokaryotic transcriptional regulatory networks
    • 10.1016/j.jmb.2006.02.019 16530225
    • Babu MM Teichmann SA Aravind L Evolutionary dynamics of prokaryotic transcriptional regulatory networks J Mol Biol 2006, 358(2):614-633. 10.1016/j.jmb.2006.02.019 16530225
    • (2006) J Mol Biol , vol.358 , Issue.2 , pp. 614-633
    • Babu, M.M.1    Teichmann, S.A.2    Aravind, L.3
  • 13
    • 33746207758 scopus 로고    scopus 로고
    • Bacterial regulatory networks are extremely flexible in evolution
    • 1524901 16840530 10.1093/nar/gkl423
    • Lozada-Chavez I Janga SC Collado-Vides J Bacterial regulatory networks are extremely flexible in evolution Nucleic Acids Res 2006, 34(12):3434-3445. 1524901 16840530 10.1093/nar/gkl423
    • (2006) Nucleic Acids Res , vol.34 , Issue.12 , pp. 3434-3445
    • Lozada-Chavez, I.1    Janga, S.C.2    Collado-Vides, J.3
  • 16
    • 33646890640 scopus 로고    scopus 로고
    • Addressing the problems with life-science databases for traditional uses and systems biology
    • 10.1038/nrg1872 16682980
    • Philippi S Koehler J Addressing the problems with life-science databases for traditional uses and systems biology Nat Rev Genet 2006, 7(6):482-488. 10.1038/nrg1872 16682980
    • (2006) Nat Rev Genet , vol.7 , Issue.6 , pp. 482-488
    • Philippi, S.1    Koehler, J.2
  • 17
    • 0344065974 scopus 로고    scopus 로고
    • Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology
    • 10.1016/j.jbiotec.2003.08.007 14651858
    • Goesmann A Linke B Rupp O Krause L Bartels D Dondrup M McHardy AC Wilke A Puehler A Meyer F Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology J Biotechnol 2003, 106(2-3):157-167. 10.1016/ j.jbiotec.2003.08.007 14651858
    • (2003) J Biotechnol , vol.106 , Issue.2-3 , pp. 157-167
    • Goesmann, A.1    Linke, B.2    Rupp, O.3    Krause, L.4    Bartels, D.5    Dondrup, M.6    McHardy, A.C.7    Wilke, A.8    Puehler, A.9    Meyer, F.10
  • 20
    • 33846114132 scopus 로고    scopus 로고
    • BRENDA, AMENDA and FRENDA: The enzyme information system in 2007
    • (Database) 1899097 17202167 10.1093/nar/gkl972
    • Barthelmes J Ebeling C Chang A Schomburg I Schomburg D BRENDA, AMENDA and FRENDA: The enzyme information system in 2007 Nucleic Acids Res 2007, 35(Database):D511-D514. 1899097 17202167 10.1093/nar/gkl972
    • (2007) Nucleic Acids Res , vol.35
    • Barthelmes, J.1    Ebeling, C.2    Chang, A.3    Schomburg, I.4    Schomburg, D.5
  • 22
    • 19944389921 scopus 로고    scopus 로고
    • Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalised Data Structures
    • 15972003
    • Koehler J Rawlings C Verrier P Mitchell R Skusa A Ruegg A Philippi S Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalised Data Structures In Silico Biol 2005, 5(1):33-44. 15972003
    • (2005) In Silico Biol , vol.5 , Issue.1 , pp. 33-44
    • Koehler, J.1    Rawlings, C.2    Verrier, P.3    Mitchell, R.4    Skusa, A.5    Ruegg, A.6    Philippi, S.7
  • 23
    • 84874660315 scopus 로고    scopus 로고
    • MySQL
    • MySQL http://www.mysql.com
  • 25
    • 84874655117 scopus 로고    scopus 로고
    • PHP
    • PHP http://www.php.net
  • 26
    • 84874664207 scopus 로고    scopus 로고
    • Java
    • Java http://java.sun.com
  • 28
    • 84874650943 scopus 로고    scopus 로고
    • NuSOAP
    • NuSOAP http://sourceforge.net/projects/nusoap
  • 31
    • 0037935183 scopus 로고    scopus 로고
    • BioMOBY: An open source biological web services proposal
    • 10.1093/bib/3.4.331 12511062
    • Wilkinson MD Links M BioMOBY: An open source biological web services proposal Brief Bioinform 2002, 3(4):331-341. 10.1093/bib/3.4.331 12511062
    • (2002) Brief Bioinform , vol.3 , Issue.4 , pp. 331-341
    • Wilkinson, M.D.1    Links, M.2
  • 33
    • 0026257928 scopus 로고
    • Graph drawing by force-directed placement
    • 10.1002/spe.4380211102
    • Fruchterman TMJ Reingold EM Graph drawing by force-directed placement Software - Practice and Experience 1991, 21(11):1129-1164. 10.1002/ spe.4380211102
    • (1991) Software - Practice and Experience , vol.21 , Issue.11 , pp. 1129-1164
    • Fruchterman, T.M.J.1    Reingold, E.M.2
  • 34
    • 10244264813 scopus 로고    scopus 로고
    • Protein complex prediction via cost-based clustering
    • 15180928
    • King AD Przulj N Jurisica I Protein complex prediction via cost-based clustering Bioinformatics 2004, 20(17):3013-3020. http://10.1093/ bioinformatics/bth351 15180928
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 3013-3020
    • King, A.D.1    Przulj, N.2    Jurisica, I.3
  • 35
    • 84874660074 scopus 로고    scopus 로고
    • FORCE
    • FORCE http://gi.cebitec.uni-bielefeld.de/comet/force/
  • 38
    • 33644596184 scopus 로고    scopus 로고
    • The DtxR protein acting as dual transcriptional regulator directs a global regulatory network involved in iron metabolism of Corynebacterium glutamicum
    • 1382209 16469103 10.1186/1471-2164-7-21
    • Brune I Werner H Huser A Kalinowski J Puhler A Tauch A The DtxR protein acting as dual transcriptional regulator directs a global regulatory network involved in iron metabolism of Corynebacterium glutamicum BMC Genomics 2006, 7:21. 1382209 16469103 10.1186/1471-2164-7-21
    • (2006) BMC Genomics , vol.7 , pp. 21
    • Brune, I.1    Werner, H.2    Huser, A.3    Kalinowski, J.4    Puhler, A.5    Tauch, A.6
  • 39
    • 34147131102 scopus 로고    scopus 로고
    • The IclR-type transcriptional repressor LtbR regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer Corynebacterium glutamicum
    • 1855810 17259312 10.1128/JB.01876-06
    • Brune I Jochmann N Brinkrolf K Hueser AT Gerstmeir R Eikmanns BJ Kalinowski J Puehler A Tauch A The IclR-type transcriptional repressor LtbR regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer Corynebacterium glutamicum J Bacteriol 2007, 189(7):2720-2733. 1855810 17259312 10.1128/JB.01876-06
    • (2007) J Bacteriol , vol.189 , Issue.7 , pp. 2720-2733
    • Brune, I.1    Jochmann, N.2    Brinkrolf, K.3    Hueser, A.T.4    Gerstmeir, R.5    Eikmanns, B.J.6    Kalinowski, J.7    Puehler, A.8    Tauch, A.9
  • 40
    • 18444409651 scopus 로고    scopus 로고
    • The McbR repressor modulated by the effector substance S-adenosylhomocysteine controls directly the transcription of a regulon involved in sulphur metabolism of Corynebacterium glutamicum ATCC 13032
    • 10.1111/j.1365-2958.2005.04586.x 15853877
    • Rey DA Nentwich SS Koch DJ Rueckert C Puehler A Tauch A Kalinowski J The McbR repressor modulated by the effector substance S-adenosylhomocysteine controls directly the transcription of a regulon involved in sulphur metabolism of Corynebacterium glutamicum ATCC 13032 Mol Microbiol 2005, 56(4):871-887. 10.1111/j.1365-2958.2005.04586.x 15853877
    • (2005) Mol Microbiol , vol.56 , Issue.4 , pp. 871-887
    • Rey, D.A.1    Nentwich, S.S.2    Koch, D.J.3    Rueckert, C.4    Puehler, A.5    Tauch, A.6    Kalinowski, J.7
  • 41
    • 34347397183 scopus 로고    scopus 로고
    • The Extracytoplasmic Function-Type Sigma Factor SigM of Corynebacterium glutamicum ATCC 13032 Is Involved in Transcription of Disulfide Stress-Related Genes
    • 1913457 17483229 10.1128/JB.00382-07
    • Nakunst D Larisch C Hueser AT Tauch A Puehler A Kalinowski J The Extracytoplasmic Function-Type Sigma Factor SigM of Corynebacterium glutamicum ATCC 13032 Is Involved in Transcription of Disulfide Stress-Related Genes J Bacteriol 2007, 189(13):4696-4707. 1913457 17483229 10.1128/JB.00382-07
    • (2007) J Bacteriol , vol.189 , Issue.13 , pp. 4696-4707
    • Nakunst, D.1    Larisch, C.2    Hueser, A.T.3    Tauch, A.4    Puehler, A.5    Kalinowski, J.6
  • 42
    • 26944462003 scopus 로고    scopus 로고
    • The transcriptional regulator SsuR activates expression of the Corynebacterium glutamicum sulphonate utilization genes in the absence of sulphate
    • 10.1111/j.1365-2958.2005.04836.x 16194234
    • Koch DJ Rueckert C Albersmeier A Hueser AT Tauch A Puehler A Kalinowski J The transcriptional regulator SsuR activates expression of the Corynebacterium glutamicum sulphonate utilization genes in the absence of sulphate Mol Microbiol 2005, 58(2):480-494. 10.1111/ j.1365-2958.2005.04836.x 16194234
    • (2005) Mol Microbiol , vol.58 , Issue.2 , pp. 480-494
    • Koch, D.J.1    Rueckert, C.2    Albersmeier, A.3    Hueser, A.T.4    Tauch, A.5    Puehler, A.6    Kalinowski, J.7
  • 43
    • 0345359589 scopus 로고    scopus 로고
    • Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source
    • 10.1016/j.jbiotec.2003.08.006 14651867
    • Hueser AT Becker A Brune I Dondrup M Kalinowski J Plassmeier J Puehler A Wiegraebe I Tauch A Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source J Biotechnol 2003, 106(2-3):269-286. 10.1016/j.jbiotec.2003.08.006 14651867
    • (2003) J Biotechnol , vol.106 , Issue.2-3 , pp. 269-286
    • Hueser, A.T.1    Becker, A.2    Brune, I.3    Dondrup, M.4    Kalinowski, J.5    Plassmeier, J.6    Puehler, A.7    Wiegraebe, I.8    Tauch, A.9
  • 44
    • 33846837274 scopus 로고    scopus 로고
    • The alternative sigma factor SigB of Corynebacterium glutamicum modulates global gene expression during transition from exponential growth to stationary phase
    • 1779776 17204139 10.1186/1471-2164-8-4
    • Larisch C Nakunst D Hueser AT Tauch A Kalinowski J The alternative sigma factor SigB of Corynebacterium glutamicum modulates global gene expression during transition from exponential growth to stationary phase BMC Genomics 2007, 8:4. 1779776 17204139 10.1186/1471-2164-8-4
    • (2007) BMC Genomics , vol.8 , pp. 4
    • Larisch, C.1    Nakunst, D.2    Hueser, A.T.3    Tauch, A.4    Kalinowski, J.5
  • 45
    • 33846236542 scopus 로고    scopus 로고
    • Under the influence of the active deodorant ingredient 4-hydroxy-3-methoxybenzyl alcohol, the skin bacterium Corynebacterium jeikeium moderately responds with differential gene expression
    • 10.1016/j.jbiotec.2006.06.011 16890319
    • Brune I Becker A Paarmann D Albersmeier A Kalinowski J Puehler A Tauch A Under the influence of the active deodorant ingredient 4-hydroxy-3-methoxybenzyl alcohol, the skin bacterium Corynebacterium jeikeium moderately responds with differential gene expression J Biotechnol 2006, 127:21-33. 10.1016/j.jbiotec.2006.06.011 16890319
    • (2006) J Biotechnol , vol.127 , pp. 21-33
    • Brune, I.1    Becker, A.2    Paarmann, D.3    Albersmeier, A.4    Kalinowski, J.5    Puehler, A.6    Tauch, A.7


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