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Volumn 36, Issue 16, 2008, Pages 5376-5390

The cis-regulatory map of Shewanella genomes

Author keywords

[No Author keywords available]

Indexed keywords

DNA; METAL ION; PALINDROMIC DNA; TRANSCRIPTION FACTOR;

EID: 52649145421     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn515     Document Type: Article
Times cited : (13)

References (65)
  • 1
    • 9144270496 scopus 로고    scopus 로고
    • Salgado,H, Gama-Castro,S, Martinez-Antonio,A, Diaz-Peredo,E, Sanchez-Solano,F, Peralta-Gil,M, Garcia-Alonso,D, Jiminez-Jacinto,V, Santos-Zavaleta,A, Bonavides-Martinez,C. 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
    • Salgado,H., Gama-Castro,S., Martinez-Antonio,A., Diaz-Peredo,E., Sanchez-Solano,F., Peralta-Gil,M., Garcia-Alonso,D., Jiminez-Jacinto,V., Santos-Zavaleta,A., Bonavides-Martinez,C. 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.
  • 2
    • 33644873438 scopus 로고    scopus 로고
    • 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. et al, 2006) RegulonDB version 5.0, Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Res, 34, D394-D397
    • 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. et al. (2006) RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Res., 34, D394-D397.
  • 5
    • 0025372992 scopus 로고
    • Identification of consensus patterns in unaligned DNA sequences known to be functionally related
    • Hertz,G.Z., Hartzell,G.W. III and Stormo,G.D. (1990) Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput. Appl. Biosci., 6, 81-92.
    • (1990) Comput. Appl. Biosci , vol.6 , pp. 81-92
    • Hertz, G.Z.1    Hartzell III, G.W.2    Stormo, G.D.3
  • 7
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • Bailey,T.L. and Elkan,C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol., 2, 28-36.
    • (1994) Proc. Int. Conf. Intell. Syst. Mol. Biol , vol.2 , pp. 28-36
    • Bailey, T.L.1    Elkan, C.2
  • 8
    • 0344906814 scopus 로고    scopus 로고
    • Combining phylogenetic data with co-regulated genes to identify regulatory motifs
    • Wang,T. and Stormo,G.D. (2003) Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bio informatics, 19, 2369-2380.
    • (2003) Bio informatics , vol.19 , pp. 2369-2380
    • Wang, T.1    Stormo, G.D.2
  • 9
    • 0344237358 scopus 로고    scopus 로고
    • Computational identification of the Spo0A-phosphate regulon that is essential for the cellular differentiation and development in Gram-positive spore-forming bacteria
    • Liu,J., Tan,K. and Stormo,G.D. (2003) Computational identification of the Spo0A-phosphate regulon that is essential for the cellular differentiation and development in Gram-positive spore-forming bacteria. Nucleic Acids Res., 31, 6891-6903.
    • (2003) Nucleic Acids Res , vol.31 , pp. 6891-6903
    • Liu, J.1    Tan, K.2    Stormo, G.D.3
  • 12
    • 0037015025 scopus 로고    scopus 로고
    • Identification of the binding sites of regulatory proteins in bacterial genomes
    • Li,H., Rhodius,V., Gross,C. and Siggia,E.D. (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    Rhodius, V.2    Gross, C.3    Siggia, E.D.4
  • 13
    • 12244259677 scopus 로고    scopus 로고
    • Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites
    • Qin,Z.S., McCue,L.A., Thompson,W., Mayerhofer,L., Lawrence,C.E. and Liu,J.S. (2003) Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites. Nat. Biotechnol. 21, 45-439.
    • (2003) Nat. Biotechnol , vol.21 , pp. 45-439
    • Qin, Z.S.1    McCue, L.A.2    Thompson, W.3    Mayerhofer, L.4    Lawrence, C.E.5    Liu, J.S.6
  • 14
    • 0036798220 scopus 로고    scopus 로고
    • Factors influencing the identification of transcription factor binding sites by cross-species comparison
    • McCue,L.A., Thompson,W., Carmack,C.S. and Lawrence,C.E. (2002) Factors influencing the identification of transcription factor binding sites by cross-species comparison. Genome Res., 12, 1523-1532.
    • (2002) Genome Res , vol.12 , pp. 1523-1532
    • McCue, L.A.1    Thompson, W.2    Carmack, C.S.3    Lawrence, C.E.4
  • 15
    • 27544485238 scopus 로고    scopus 로고
    • Combining phylogenetic motif discovery and motif clustering to predict co-regulated genes
    • Jensen,S.T., Shen,L. and Liu,J.S. (2005) Combining phylogenetic motif discovery and motif clustering to predict co-regulated genes. Bioinformatics, 21, 3832-3839.
    • (2005) Bioinformatics , vol.21 , pp. 3832-3839
    • Jensen, S.T.1    Shen, L.2    Liu, J.S.3
  • 16
    • 3543068251 scopus 로고    scopus 로고
    • Regulog analysis: Detection of conserved regulatory networks across bacteria: Application to Staphylococcus aureus
    • Alkema,W.B., Lenhard,B. and Wasserman,W.W. (2004) Regulog analysis: detection of conserved regulatory networks across bacteria: Application to Staphylococcus aureus. Genome Res., 14, 1362-1373.
    • (2004) Genome Res , vol.14 , pp. 1362-1373
    • Alkema, W.B.1    Lenhard, B.2    Wasserman, W.W.3
  • 17
    • 0642340506 scopus 로고    scopus 로고
    • Genome wide identification of regulatory motifs in Bacillus subtilis
    • Mwangi,M.M. and Siggia,E.D. (2003) Genome wide identification of regulatory motifs in Bacillus subtilis. BMC Bioinformatics, 4 18.
    • (2003) BMC Bioinformatics , vol.4 , pp. 18
    • Mwangi, M.M.1    Siggia, E.D.2
  • 18
    • 2942529158 scopus 로고    scopus 로고
    • Bioinformatic identification of novel regulatory DNA sequence motifs in Streptomyces coelicolor
    • Studholme,D.J., Bentley,S.D. and Kormanec,J. (2004) Bioinformatic identification of novel regulatory DNA sequence motifs in Streptomyces coelicolor. BMC Microbiol., 4, 14.
    • (2004) BMC Microbiol , vol.4 , pp. 14
    • Studholme, D.J.1    Bentley, S.D.2    Kormanec, J.3
  • 19
    • 0036107903 scopus 로고    scopus 로고
    • Discovery of regulatory elements by a computational method for phylogenetic footprinting
    • Blanchette,M. and Tompa,M. (2002) Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res., 12, 739-748.
    • (2002) Genome Res , vol.12 , pp. 739-748
    • Blanchette, M.1    Tompa, M.2
  • 20
    • 33750218960 scopus 로고    scopus 로고
    • PhyloGibbs: A Gibbs sampling motif finder that incorporates phylogeny
    • Siddharthan,R., Siggia,E.D. and van Nimwegen,E. (2005) PhyloGibbs: A Gibbs sampling motif finder that incorporates phylogeny. PLoS Comput. Biol., 1, e67.
    • (2005) PLoS Comput. Biol , vol.1
    • Siddharthan, R.1    Siggia, E.D.2    van Nimwegen, E.3
  • 21
    • 28444484981 scopus 로고    scopus 로고
    • Identifying the conserved network of cis-regulatory sites of a eukaryotic genome
    • Wang,T. and Stormo,G.D. (2005) Identifying the conserved network of cis-regulatory sites of a eukaryotic genome. Proc. Natl Acad. Sci. USA, 102, 17400-17405.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 17400-17405
    • Wang, T.1    Stormo, G.D.2
  • 23
    • 33645832957 scopus 로고    scopus 로고
    • Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups
    • Wels,M., Francke,C., Kerkhoven,R., Kleerebezem,M. and Siezen,R.J. (2006) Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups. Nucleic Acids Res., 34, 1947-1958.
    • (2006) Nucleic Acids Res , vol.34 , pp. 1947-1958
    • Wels, M.1    Francke, C.2    Kerkhoven, R.3    Kleerebezem, M.4    Siezen, R.J.5
  • 24
    • 32044434639 scopus 로고    scopus 로고
    • Rhodopseudomonas palustris regulons detected by cross-species analysis of alphaproteobacterial genomes
    • Conlan,S., Lawrence,C. and McCue,L.A. (2005) Rhodopseudomonas palustris regulons detected by cross-species analysis of alphaproteobacterial genomes. Appl. Environ. Microbiol., 71, 7442-7452.
    • (2005) Appl. Environ. Microbiol , vol.71 , pp. 7442-7452
    • Conlan, S.1    Lawrence, C.2    McCue, L.A.3
  • 30
    • 33745005291 scopus 로고    scopus 로고
    • Global transcriptome analysis of the cold shock response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold shock proteins
    • Gao,H., Yang,Z.K., Wu,L., Thompson,D.K. and Zhou,J. (2006) Global transcriptome analysis of the cold shock response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold shock proteins. J. Bacteriol., 188, 4560-4569.
    • (2006) J. Bacteriol , vol.188 , pp. 4560-4569
    • Gao, H.1    Yang, Z.K.2    Wu, L.3    Thompson, D.K.4    Zhou, J.5
  • 32
    • 0032826179 scopus 로고    scopus 로고
    • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    • Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
    • (1999) Bioinformatics , vol.15 , pp. 563-577
    • Hertz, G.Z.1    Stormo, G.D.2
  • 33
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 34
    • 0030683599 scopus 로고    scopus 로고
    • PAML a program package for phylogenetic analysis by maximum likelihood
    • Yang,Z. (1997) PAML a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci., 13, 555-556.
    • (1997) Comput. Appl. Biosci , vol.13 , pp. 555-556
    • Yang, Z.1
  • 35
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: Improvement in accuracy of multiple sequence alignment
    • Katoh,K., Kuma,K., Toh,H. and Miyata,T. (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res., 33, 511-518.
    • (2005) Nucleic Acids Res , vol.33 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 37
    • 0038781885 scopus 로고    scopus 로고
    • Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes
    • Cooper,G.M., Brudno,M., Green,E.D., Batzoglou,S. and Sidow,A. (2003) Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. Genome Res., 13, 813-820.
    • (2003) Genome Res , vol.13 , pp. 813-820
    • Cooper, G.M.1    Brudno, M.2    Green, E.D.3    Batzoglou, S.4    Sidow, A.5
  • 38
    • 0036468362 scopus 로고    scopus 로고
    • Prokaryotic transcription regulators: More than just the helix-turn-helix motif
    • Huffman,J.L. and Brennan,R.G. (2002) Prokaryotic transcription regulators: More than just the helix-turn-helix motif. Curr. Opin. Struct. Biol., 12, 98-106.
    • (2002) Curr. Opin. Struct. Biol , vol.12 , pp. 98-106
    • Huffman, J.L.1    Brennan, R.G.2
  • 41
    • 14644388890 scopus 로고    scopus 로고
    • Making connections between novel transcription factors and their DNA motifs
    • Tan,K., McCue,L.A. and Stormo,G.D. (2005) Making connections between novel transcription factors and their DNA motifs. Genome Res., 15, 312-320.
    • (2005) Genome Res , vol.15 , pp. 312-320
    • Tan, K.1    McCue, L.A.2    Stormo, G.D.3
  • 42
    • 0034785443 scopus 로고    scopus 로고
    • Identifying regulatory networks by combinatorial analysis of promoter elements
    • Pilpel,Y., Sudarsanam,P. and Church,G.M. (2001) Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet. 29, 153-159.
    • (2001) Nat. Genet , vol.29 , pp. 153-159
    • Pilpel, Y.1    Sudarsanam, P.2    Church, G.M.3
  • 43
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genomewide studies
    • Storey,J.D. and Tibshirani,R. (2003) Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA, 100, 9440-9445.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2
  • 44
    • 0344153727 scopus 로고    scopus 로고
    • Genomic regulatory regions: Insights from comparative sequence analysis
    • Cooper,G.M. and Sidow,A. (2003) Genomic regulatory regions: Insights from comparative sequence analysis. Curr. Opin. Genet. Dev., 13 604-610.
    • (2003) Curr. Opin. Genet. Dev , vol.13 , pp. 604-610
    • Cooper, G.M.1    Sidow, A.2
  • 45
    • 1842667855 scopus 로고    scopus 로고
    • Characterization of evolutionary rates and constraints in three mammalian genomes
    • Cooper,G.M., Brudno,M., Stone,E.A., Dubchak,I., Batzoglou,S. and Sidow,A. (2004) Characterization of evolutionary rates and constraints in three mammalian genomes. Genome Res., 14, 539-548.
    • (2004) Genome Res , vol.14 , pp. 539-548
    • Cooper, G.M.1    Brudno, M.2    Stone, E.A.3    Dubchak, I.4    Batzoglou, S.5    Sidow, A.6
  • 46
    • 0036144777 scopus 로고    scopus 로고
    • The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: An empirical and simulation study
    • Nekrutenko,A., Makova,K.D. and Li,W.H. (2002) The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: An empirical and simulation study. Genome Res., 12, 198-202.
    • (2002) Genome Res , vol.12 , pp. 198-202
    • Nekrutenko, A.1    Makova, K.D.2    Li, W.H.3
  • 47
    • 14644390333 scopus 로고    scopus 로고
    • A model of the statistical power of comparative genome sequence analysis
    • Eddy,S.R. (2005) A model of the statistical power of comparative genome sequence analysis. PLoS Biol., 3, e10.
    • (2005) PLoS Biol , vol.3
    • Eddy, S.R.1
  • 48
    • 0036156696 scopus 로고    scopus 로고
    • Transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of Shewanella oneidensis: Possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress
    • Thompson,D.K., Beliaev,A.S., Giometti,C.S., Tollaksen,S.L., Khare,T., Lies,D.P., Nealson,K.H., Lim,H., Yates,J. III, Brandt,C.C. et al. (2002) Transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of Shewanella oneidensis: Possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress. Appl. Environ. Microbiol., 68, 881-892.
    • (2002) Appl. Environ. Microbiol , vol.68 , pp. 881-892
    • Thompson, D.K.1    Beliaev, A.S.2    Giometti, C.S.3    Tollaksen, S.L.4    Khare, T.5    Lies, D.P.6    Nealson, K.H.7    Lim, H.8    Yates III, J.9    Brandt, C.C.10
  • 49
    • 33747148392 scopus 로고    scopus 로고
    • Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA
    • Cho,B.K., Knight,E.M. and Palsson,B.O. (2006) Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA. Microbiology 152, 2207-2219.
    • (2006) Microbiology , vol.152 , pp. 2207-2219
    • Cho, B.K.1    Knight, E.M.2    Palsson, B.O.3
  • 53
    • 33750215315 scopus 로고    scopus 로고
    • Transcriptional monitoring of steady state and effects of anaerobic phases in chemostat cultures of the filamentous fungus Trichoderma, reesei
    • Rautio,J.J., Smit,B.A., Wiebe,M., Penttila,M. and Saloheimo,M. (2006) Transcriptional monitoring of steady state and effects of anaerobic phases in chemostat cultures of the filamentous fungus Trichoderma, reesei. BMC Genomics, 7, 247.
    • (2006) BMC Genomics , vol.7 , pp. 247
    • Rautio, J.J.1    Smit, B.A.2    Wiebe, M.3    Penttila, M.4    Saloheimo, M.5
  • 54
    • 33646113855 scopus 로고    scopus 로고
    • Evolutionary dynamics of prokaryotic transcriptional regulatory networks
    • Madan Babu,M., Teichmann,S.A. and Aravind,L. (2006) Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J. Mol. Biol., 358, 614-633.
    • (2006) J. Mol. Biol , vol.358 , pp. 614-633
    • Madan Babu, M.1    Teichmann, S.A.2    Aravind, L.3
  • 55
    • 33746207758 scopus 로고    scopus 로고
    • Bacterial regulatory networks are extremely flexible in evolution
    • Lozada-Chavez,I., Janga,S.C. and Collado-Vides,J. (2006) Bacterial regulatory networks are extremely flexible in evolution. Nucleic Acids Res., 34, 3434-3445.
    • (2006) Nucleic Acids Res , vol.34 , pp. 3434-3445
    • Lozada-Chavez, I.1    Janga, S.C.2    Collado-Vides, J.3
  • 56
    • 28944433798 scopus 로고    scopus 로고
    • Insights on biology and evolution from microbial genome sequencing
    • Fraser-Liggett,C.M. (2005) Insights on biology and evolution from microbial genome sequencing. Genome Res., 15, 1603-1610.
    • (2005) Genome Res , vol.15 , pp. 1603-1610
    • Fraser-Liggett, C.M.1
  • 57
    • 25844498846 scopus 로고    scopus 로고
    • Trade-offs in detecting evolutionarily constrained sequence by comparative genomics
    • Stone,E.A., Cooper,G.M. and Sidow,A. (2005) Trade-offs in detecting evolutionarily constrained sequence by comparative genomics. Annu. Rev. Genomics Hum. Genet., 6, 143-164.
    • (2005) Annu. Rev. Genomics Hum. Genet , vol.6 , pp. 143-164
    • Stone, E.A.1    Cooper, G.M.2    Sidow, A.3
  • 60
    • 0035859803 scopus 로고    scopus 로고
    • Do mRNAs act as direct sensors of small molecules to control their expression?
    • Stormo,G.D. and Ji,Y. (2001) Do mRNAs act as direct sensors of small molecules to control their expression? Proc. Natl Acad. Sci. USA, 98, 9465-9467.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 9465-9467
    • Stormo, G.D.1    Ji, Y.2
  • 61
    • 0033765362 scopus 로고    scopus 로고
    • Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs
    • Rivas,E. and Eddy,S.R. (2000) Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. Bioinformatics, 16, 583-605.
    • (2000) Bioinformatics , vol.16 , pp. 583-605
    • Rivas, E.1    Eddy, S.R.2
  • 62
    • 0021718304 scopus 로고
    • Structure and autoregulation of the metJ regulatory gene in Escherichia coli
    • Saint-Girons,I., Duchange,N., Cohen,G.N. and Zakin,M.M. (1984) Structure and autoregulation of the metJ regulatory gene in Escherichia coli. J. Biol. Chem., 259, 14282-14285.
    • (1984) J. Biol. Chem , vol.259 , pp. 14282-14285
    • Saint-Girons, I.1    Duchange, N.2    Cohen, G.N.3    Zakin, M.M.4
  • 63
    • 0021398988 scopus 로고
    • Positive and negative control of the glnA ntrBC regulon in Klebsiella pneumoniae
    • Alvarez-Morales,A., Dixon,R. and Merrick,M. (1984) Positive and negative control of the glnA ntrBC regulon in Klebsiella pneumoniae. EMBO J. 3, 501-507.
    • (1984) EMBO J , vol.3 , pp. 501-507
    • Alvarez-Morales, A.1    Dixon, R.2    Merrick, M.3
  • 64
    • 0020416355 scopus 로고
    • Regulation and autoregulation by lexA protein
    • Brent,R. (1982) Regulation and autoregulation by lexA protein. Biochimie, 64, 565-569.
    • (1982) Biochimie , vol.64 , pp. 565-569
    • Brent, R.1


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