메뉴 건너뛰기




Volumn 21, Issue 22, 2005, Pages 4073-4083

Analysis of differentially-regulated genes within a regulatory network by GPS genome navigation

Author keywords

[No Author keywords available]

Indexed keywords

PHOP PROTEIN;

EID: 27944461068     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti672     Document Type: Article
Times cited : (35)

References (58)
  • 2
    • 0033536012 scopus 로고    scopus 로고
    • Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays
    • Alon,U. et al. (1999) Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl Acad. Sci. USA, 96, 6745-6750.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 6745-6750
    • Alon, U.1
  • 3
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology
    • The Gene Ontology Consortium
    • Ashburner,M. et al. (2000) Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 4
    • 19944433202 scopus 로고    scopus 로고
    • The simplicity of metazoan cell lineages
    • Azevedo,R.B. et al. (2005) The simplicity of metazoan cell lineages. Nature, 433, 152-156.
    • (2005) Nature , vol.433 , pp. 152-156
    • Azevedo, R.B.1
  • 5
    • 10744226222 scopus 로고    scopus 로고
    • Computational discovery of gene modules and regulatory networks
    • Bar-Joseph,Z. et al. (2003) Computational discovery of gene modules and regulatory networks. Nat. Biotechnol., 21, 1337-1342.
    • (2003) Nat. Biotechnol. , vol.21 , pp. 1337-1342
    • Bar-Joseph, Z.1
  • 6
    • 1942453302 scopus 로고    scopus 로고
    • Predicting gene expression from sequence
    • Beer,M.A. and Tavazoie,S. (2004) Predicting gene expression from sequence. Cell, 117, 185-198.
    • (2004) Cell , vol.117 , pp. 185-198
    • Beer, M.A.1    Tavazoie, S.2
  • 7
    • 0036371372 scopus 로고    scopus 로고
    • Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNA
    • RESEARCH0013
    • Benitez-Bellon,E. et al. (2002) Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNA. Genome Biol., 3, RESEARCH0013.
    • (2002) Genome Biol. , vol.3
    • Benitez-Bellon, E.1
  • 8
    • 0003297157 scopus 로고    scopus 로고
    • Pattern analysis
    • Pedrycz,W., Bonissone,P.P. and Ruspini,E.H. (eds), Institute of Physics Bristol
    • Bezdek,J.C. (1998) Pattern analysis. In Pedrycz,W., Bonissone,P.P. and Ruspini,E.H. (eds), Handbook of Fuzzy Computation. Institute of Physics, Bristol, pp. F6.1.1-F6.6.20.
    • (1998) Handbook of Fuzzy Computation
    • Bezdek, J.C.1
  • 11
    • 0042967741 scopus 로고    scopus 로고
    • Optimal structure identification with greedy search
    • Chickering,D.M. (2003) Optimal structure identification with greedy search. J. Mach. Learn. Res., 3, 507-554.
    • (2003) J. Mach. Learn. Res. , vol.3 , pp. 507-554
    • Chickering, D.M.1
  • 12
    • 0037453009 scopus 로고    scopus 로고
    • Integrating regulatory motif discovery and genome-wide expression analysis
    • Conlon,E.M. et al. (2003) Integrating regulatory motif discovery and genome-wide expression analysis. Proc. Natl Acad. Sci. USA, 100, 3339-3344.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 3339-3344
    • Conlon, E.M.1
  • 13
    • 8344276113 scopus 로고    scopus 로고
    • Elvira: An environment for probabilistic graphical models
    • Gamez,J.A.a.S.A. (ed.)
    • Consortium,E. (2002) Elvira: An environment for probabilistic graphical models. In Gamez,J.A.a.S.A. (ed.), 1st European Workshop an Probabilistic Graphical Models, pp. 222-230.
    • (2002) 1st European Workshop an Probabilistic Graphical Models , pp. 222-230
    • Consortium, E.1
  • 14
    • 0034893508 scopus 로고    scopus 로고
    • Structural mining of molecular biology data
    • Cook,D.J. et al. (2001) Structural mining of molecular biology data. IEEE Eng. Med. Biol. Mag., 20, 67-74.
    • (2001) IEEE Eng. Med. Biol. Mag. , vol.20 , pp. 67-74
    • Cook, D.J.1
  • 15
    • 0026003072 scopus 로고
    • Control site location and transcriptional regulation in Escherichia coli
    • Collado-Vides,J. et al. (1991) Control site location and transcriptional regulation in Escherichia coli. Microbiol. Rev., 55, 371-394.
    • (1991) Microbiol. Rev. , vol.55 , pp. 371-394
    • Collado-Vides, J.1
  • 16
    • 34249832377 scopus 로고
    • A Bayesian method for the induction of probabilistic networks from data
    • Cooper,G.F. and Herskovits,E. (1992) A Bayesian method for the induction of probabilistic networks from data. Machine Learning, 9, 309-347.
    • (1992) Machine Learning , vol.9 , pp. 309-347
    • Cooper, G.F.1    Herskovits, E.2
  • 17
    • 0036475811 scopus 로고    scopus 로고
    • Linguistic modeling by hierarchical systems of linguistic rules
    • Cordon,O. et al. (2002) Linguistic modeling by hierarchical systems of linguistic rules. IEEE Trans. Fuzzy Syst., 10, 2-20.
    • (2002) IEEE Trans. Fuzzy Syst. , vol.10 , pp. 2-20
    • Cordon, O.1
  • 18
    • 15344349017 scopus 로고    scopus 로고
    • A hybrid promoter analysis methodology for prokaryotic genomes
    • Cotik,V. et al. (2005) A hybrid promoter analysis methodology for prokaryotic genomes. Fuzzy Set. Syst., 152, 83-102.
    • (2005) Fuzzy Set. Syst. , vol.152 , pp. 83-102
    • Cotik, V.1
  • 19
    • 2142738304 scopus 로고    scopus 로고
    • WebLogo: A sequence logo generator
    • Crooks,G.E. et al. (2004) WebLogo: A sequence logo generator. Genome Res., 14, 1188-1190.
    • (2004) Genome Res. , vol.14 , pp. 1188-1190
    • Crooks, G.E.1
  • 21
    • 2342501446 scopus 로고    scopus 로고
    • Signal transduction cascade between EvgA/EvgS and PhoP/PhoQ two-component systems of Escherichia coli
    • Eguchi,Y. et al. (2004) Signal transduction cascade between EvgA/EvgS and PhoP/PhoQ two-component systems of Escherichia coli. J. Bacteriol., 186, 3006-3014.
    • (2004) J. Bacteriol. , vol.186 , pp. 3006-3014
    • Eguchi, Y.1
  • 24
    • 0037057374 scopus 로고    scopus 로고
    • Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering
    • RESEARCH0059
    • Gasch,A.P. and Eisen,M.B. (2002) Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol., 3, RESEARCH0059.
    • (2002) Genome Biol. , vol.3
    • Gasch, A.P.1    Eisen, M.B.2
  • 25
    • 0035105303 scopus 로고    scopus 로고
    • The pleiotropic two-component regulatory system PhoP-PhoQ
    • Groisman,E.A. (2001) The pleiotropic two-component regulatory system PhoP-PhoQ. J. Bacteriol., 183, 1835-1842.
    • (2001) J. Bacteriol. , vol.183 , pp. 1835-1842
    • Groisman, E.A.1
  • 26
    • 0242407438 scopus 로고    scopus 로고
    • Regulatory network of Escherichia coli: Consistency between literature knowledge and microarray profiles
    • Gutierrez-Rios,R.M. et al. (2003) Regulatory network of Escherichia coli: Consistency between literature knowledge and microarray profiles. Genome Res., 13, 2435-2443.
    • (2003) Genome Res. , vol.13 , pp. 2435-2443
    • Gutierrez-Rios, R.M.1
  • 27
    • 4444240880 scopus 로고    scopus 로고
    • Connecting two-component regulatory systems by a protein that protects a response regulator from dephosphorylation by its cognate sensor
    • Kato,A. and Groisman,E.A. (2004) Connecting two-component regulatory systems by a protein that protects a response regulator from dephosphorylation by its cognate sensor. Genes Dev., 18, 2302-2313.
    • (2004) Genes Dev. , vol.18 , pp. 2302-2313
    • Kato, A.1    Groisman, E.A.2
  • 28
    • 0037447083 scopus 로고    scopus 로고
    • Closing the loop: The PmrA/PmrB two-component system negatively controls expression of its posttranscriptional activator PmrD
    • Kato,A. et al. (2003) Closing the loop: The PmrA/PmrB two-component system negatively controls expression of its posttranscriptional activator PmrD. Proc. Natl Acad. Sci. USA, 100, 4706-4711.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 4706-4711
    • Kato, A.1
  • 29
    • 0031381525 scopus 로고    scopus 로고
    • Wrappers for feature subset selection
    • Kohavi,R. and John,G.H. (1997) Wrappers for feature subset selection. Artif. Intell., 97, 273-324.
    • (1997) Artif. Intell. , vol.97 , pp. 273-324
    • Kohavi, R.1    John, G.H.2
  • 30
    • 0030245966 scopus 로고    scopus 로고
    • Structure learning of Bayesian networks by genetic algorithms: A performance analysis of control parameters
    • Larranaga,P. and Poza,M. (1996) Structure learning of Bayesian networks by genetic algorithms: A performance analysis of control parameters. IEEE J. Pattern Anal. Mach. Intell., 18, 912-926.
    • (1996) IEEE J. Pattern Anal. Mach. Intell. , vol.18 , pp. 912-926
    • Larranaga, P.1    Poza, M.2
  • 31
    • 0142245627 scopus 로고    scopus 로고
    • Molecular characterization of the Mg2+-responsive PhoP-PhoQ regulon in Salmonella enterica
    • Lejona,S. et al. (2003) Molecular characterization of the Mg2+-responsive PhoP-PhoQ regulon in Salmonella enterica. J. Bacteriol., 185, 6287-6294.
    • (2003) J. Bacteriol. , vol.185 , pp. 6287-6294
    • Lejona, S.1
  • 32
    • 0035793042 scopus 로고    scopus 로고
    • Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection
    • Li,C. and Wong,W.H. (2001) Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proc. Natl Acad. Sci. USA, 98, 31-36.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 31-36
    • Li, C.1    Wong, W.H.2
  • 33
    • 0037015025 scopus 로고    scopus 로고
    • Identification of the binding sites of regulatory proteins in bacterial genomes
    • Li,H. et al. (2002) Identification of the binding sites of regulatory proteins in bacterial genomes. Proc. Natl. Acad. Sci. USA, 99, 11772-11777.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 11772-11777
    • Li, H.1
  • 34
    • 0242386460 scopus 로고    scopus 로고
    • Identifying global regulators in transcriptional regulatory networks in bacteria
    • Martinez-Antonio,A. and Collado-Vides,J. (2003) Identifying global regulators in transcriptional regulatory networks in bacteria. Curr. Opin. Microbiol., 6, 482-489.
    • (2003) Curr. Opin. Microbiol. , vol.6 , pp. 482-489
    • Martinez-Antonio, A.1    Collado-Vides, J.2
  • 35
    • 0038349356 scopus 로고    scopus 로고
    • Regulatory network of acid resistance genes in Escherichia coli
    • Masuda,N. and Church,G.M. (2003) Regulatory network of acid resistance genes in Escherichia coli. Mol. Microbiol., 48, 699-712.
    • (2003) Mol. Microbiol. , vol.48 , pp. 699-712
    • Masuda, N.1    Church, G.M.2
  • 36
    • 0035253676 scopus 로고    scopus 로고
    • Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes
    • McCue,L. et al. (2001) Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res., 29, 774-782.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 774-782
    • McCue, L.1
  • 37
    • 0038377583 scopus 로고    scopus 로고
    • Identification and molecular characterization of the Mg2+ stimulon of Escherichia coli
    • Minagawa,S. et al. (2003) Identification and molecular characterization of the Mg2+ stimulon of Escherichia coli. J. Bacteriol., 185, 3696-3702.
    • (2003) J. Bacteriol. , vol.185 , pp. 3696-3702
    • Minagawa, S.1
  • 39
    • 0036033707 scopus 로고    scopus 로고
    • Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12
    • Oshima,T. et al. (2002) Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12. Mol. Microbiol., 46, 281-291.
    • (2002) Mol. Microbiol. , vol.46 , pp. 281-291
    • Oshima, T.1
  • 40
    • 12244259677 scopus 로고    scopus 로고
    • Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites
    • Qin,Z.S. et al. (2003) Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites. Nat. Biotechnol., 21, 435-439.
    • (2003) Nat. Biotechnol. , vol.21 , pp. 435-439
    • Qin, Z.S.1
  • 42
    • 0042278534 scopus 로고    scopus 로고
    • Characterization of maximum probability points in the Multivariate Hypergeometric distribution
    • Requena,F. and Ciudad,N.M. (2000) Characterization of maximum probability points in the Multivariate Hypergeometric distribution. Stat. Probab. Lett., 50, 39-47.
    • (2000) Stat. Probab. Lett. , vol.50 , pp. 39-47
    • Requena, F.1    Ciudad, N.M.2
  • 44
    • 27944436470 scopus 로고    scopus 로고
    • Generalized analysis of promoters: A method for DNA sequence description
    • Coello Coello,C.a.L.G. (ed.), World Scientific
    • Romero Zaliz,R., Zwir,I. and Ruspini,E.H. (2004) Generalized analysis of promoters: A method for DNA sequence description. In Coello Coello,C.a.L.G. (ed.), Applications of Multi-Objective Evolutionary Algorithms. World Scientific, pp. 427-450.
    • (2004) Applications of Multi-Objective Evolutionary Algorithms , pp. 427-450
    • Romero Zaliz, R.1    Zwir, I.2    Ruspini, E.H.3
  • 45
    • 0036678794 scopus 로고    scopus 로고
    • Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics
    • Ronen,M. et al. (2002) Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics. Proc. Natl Acad. Sci. USA, 99, 10555-10560.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 10555-10560
    • Ronen, M.1
  • 47
    • 33750540500 scopus 로고    scopus 로고
    • Automated generation of qualitative representations of complex objects by hybrid soft-computing methods
    • Pal,S.K. and Pal,A. (eds), World Scientific, NJ
    • Ruspini,E.H.a.Z.I. (2001) Automated generation of qualitative representations of complex objects by hybrid soft-computing methods. In Pal,S.K. and Pal,A. (eds), Pattern Recognition: From Classical to Modern Approaches. World Scientific, NJ, pp. 612.
    • (2001) Pattern Recognition: From Classical to Modern Approaches , pp. 612
    • Ruspini, E.H.A.Z.I.1
  • 48
    • 9144270496 scopus 로고    scopus 로고
    • RegulonDB (version 4.0): Transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12
    • Salgado,H. et al. (2004) RegulonDB (version 4.0): Transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res., 32, D303-D306.
    • (2004) Nucleic Acids Res. , vol.32
    • Salgado, H.1
  • 49
    • 0003543769 scopus 로고    scopus 로고
    • Probabilits, analyse des donnes et statistiques
    • Technip, France
    • Saporta,G. (1996) Probabilits, analyse des donnes et statistiques, Technip, France.
    • (1996)
    • Saporta, G.1
  • 50
    • 4644343541 scopus 로고    scopus 로고
    • Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins
    • Shi,Y. et al. (2004) Transcriptional control of the antimicrobial peptide resistance ugtL gene by the Salmonella PhoP and SlyA regulatory proteins. J. Biol. Chem., 279, 38618-38625.
    • (2004) J. Biol. Chem. , vol.279 , pp. 38618-38625
    • Shi, Y.1
  • 51
    • 14244270197 scopus 로고    scopus 로고
    • Signal-dependent binding of the response regulators PhoP and PmrA to their target promoters in vivo
    • Shin,D. and Groisman,E.A. (2005) Signal-dependent binding of the response regulators PhoP and PmrA to their target promoters in vivo. J. Biol. Chem., 280, 4089-4094.
    • (2005) J. Biol. Chem. , vol.280 , pp. 4089-4094
    • Shin, D.1    Groisman, E.A.2
  • 52
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: Representation and discovery
    • Stormo,G.D. (2000) DNA binding sites: Representation and discovery. Bioinformatics, 16, 16-23.
    • (2000) Bioinformatics , vol.16 , pp. 16-23
    • Stormo, G.D.1
  • 53
    • 0033028596 scopus 로고    scopus 로고
    • Systematic determination of genetic network architecture
    • Tavazoie,S. et al. (1999) Systematic determination of genetic network architecture. Nat. Genet., 22, 281-285.
    • (1999) Nat. Genet. , vol.22 , pp. 281-285
    • Tavazoie, S.1
  • 54
    • 0036889029 scopus 로고    scopus 로고
    • Gene expression profiling of the pH response in Escherichia coli
    • Tucker,D.L. et al. (2002) Gene expression profiling of the pH response in Escherichia coli. J. Bacteriol., 184, 6551-6558.
    • (2002) J. Bacteriol. , vol.184 , pp. 6551-6558
    • Tucker, D.L.1
  • 55
    • 0034800371 scopus 로고    scopus 로고
    • Principal component analysis for clustering gene expression data
    • Yeung,K.Y. and Ruzzo,W.L. (2001) Principal component analysis for clustering gene expression data. Bioinformatics, 17, 763-774.
    • (2001) Bioinformatics , vol.17 , pp. 763-774
    • Yeung, K.Y.1    Ruzzo, W.L.2
  • 56
    • 0033318858 scopus 로고    scopus 로고
    • Multiobjective evolutionary algorithms: A comparative case study and the Strength Pareto approach
    • Zitzler,E. and Thiele,L. (1999) Multiobjective evolutionary algorithms: a comparative case study and the Strength Pareto approach. IEEE Trans. Evol. Comput., 3, 257-271.
    • (1999) IEEE Trans. Evol. Comput. , vol.3 , pp. 257-271
    • Zitzler, E.1    Thiele, L.2
  • 57
    • 0036972480 scopus 로고    scopus 로고
    • Automated biological sequence description by genetic multi-objective generalized clustering
    • Zwir,I. et al. (2002) Automated biological sequence description by genetic multi-objective generalized clustering. Ann. N. Y. Acad. Sci., 980, 65-82.
    • (2002) Ann. N. Y. Acad. Sci. , vol.980 , pp. 65-82
    • Zwir, I.1
  • 58
    • 14544307890 scopus 로고    scopus 로고
    • Dissecting the PhoP regulatory network of Escherichia coli and Salmonella enterica
    • Zwir,I. et al. (2005) Dissecting the PhoP regulatory network of Escherichia coli and Salmonella enterica. Proc. Natl Acad. Sci. USA, 102, 2862-2867.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 2862-2867
    • Zwir, I.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.