메뉴 건너뛰기




Volumn 242, Issue 1, 2006, Pages 135-141

The recognition and prediction of σ70 promoters in Escherichia coli K-12

Author keywords

Conservative hexamers segment; Position correlation scoring function (PCSF); Position correlation scoring matrix (PCSM); Promoter recognition

Indexed keywords

BACTERIUM; BIOLOGICAL ANALYSIS; PROTEIN;

EID: 33746925662     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2006.02.007     Document Type: Article
Times cited : (64)

References (44)
  • 1
    • 0031299508 scopus 로고    scopus 로고
    • Detection of eukaryotic promoters using markov transition matrices
    • Audic S., and Claverie J. Detection of eukaryotic promoters using markov transition matrices. Comput. Chem. 21 (1997) 223-227
    • (1997) Comput. Chem. , vol.21 , pp. 223-227
    • Audic, S.1    Claverie, J.2
  • 2
    • 0037352074 scopus 로고    scopus 로고
    • Computer model for recognition of functional transcription start sites in RNA polymerase II promoters of vertebrates
    • Bajic V.B., Seah S.H., Chong A., and Krishnam S.P.T. Computer model for recognition of functional transcription start sites in RNA polymerase II promoters of vertebrates. J. Molec. Graphic Model. 21 (2003) 323-332
    • (2003) J. Molec. Graphic Model. , vol.21 , pp. 323-332
    • Bajic, V.B.1    Seah, S.H.2    Chong, A.3    Krishnam, S.P.T.4
  • 3
    • 0030965301 scopus 로고    scopus 로고
    • Region 2.5 of the Escherichia coli RNA polymerase sigma70 subunit is responsible for the recognition of the 'extended-10' motif at promoters
    • Barne K.A., Bown J., Busby S.J., and Minchin S.D. Region 2.5 of the Escherichia coli RNA polymerase sigma70 subunit is responsible for the recognition of the 'extended-10' motif at promoters. EMBO J. 16 (1997) 4034-4040
    • (1997) EMBO J. , vol.16 , pp. 4034-4040
    • Barne, K.A.1    Bown, J.2    Busby, S.J.3    Minchin, S.D.4
  • 4
    • 0030451101 scopus 로고    scopus 로고
    • Computation of DNA structural variability-A new predictor of DNA regulatory regions
    • Benham C.J. Computation of DNA structural variability-A new predictor of DNA regulatory regions. CABIOS 12 (1996) 375-381
    • (1996) CABIOS , vol.12 , pp. 375-381
    • Benham, C.J.1
  • 5
    • 0025278259 scopus 로고
    • Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences
    • Bucher P. Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol. 212 (1990) 563-578
    • (1990) J. Mol. Biol. , vol.212 , pp. 563-578
    • Bucher, P.1
  • 6
    • 15844412591 scopus 로고    scopus 로고
    • Improving promoter prediction for the NNPP2.2 Algorithm: a case study using E-Coli DNA sequences
    • Burden S., Lin Y.X., and Zhang R. Improving promoter prediction for the NNPP2.2 Algorithm: a case study using E-Coli DNA sequences. Bioinformatics 21 (2005) 601-607
    • (2005) Bioinformatics , vol.21 , pp. 601-607
    • Burden, S.1    Lin, Y.X.2    Zhang, R.3
  • 7
    • 0034192263 scopus 로고    scopus 로고
    • DNA sequence elements located immediately upstream of the -10 hexamer in Escherichia coli promoters: a systematic study
    • Burr T., Mitchell J., Kolb A., Minchin S., and Busby S. DNA sequence elements located immediately upstream of the -10 hexamer in Escherichia coli promoters: a systematic study. Nucleic Acids Res. 28 (2000) 1864-1870
    • (2000) Nucleic Acids Res. , vol.28 , pp. 1864-1870
    • Burr, T.1    Mitchell, J.2    Kolb, A.3    Minchin, S.4    Busby, S.5
  • 8
    • 0030932088 scopus 로고    scopus 로고
    • PromFD 1.0: a computer program that predicts eukaryotic pol II promoters using strings and IMD matrices
    • Chen Q.K., Hertz G.Z., and Stormo G.D. PromFD 1.0: a computer program that predicts eukaryotic pol II promoters using strings and IMD matrices. CABIOS 13 (1997) 29-35
    • (1997) CABIOS , vol.13 , pp. 29-35
    • Chen, Q.K.1    Hertz, G.Z.2    Stormo, G.D.3
  • 9
    • 0025853156 scopus 로고
    • Neural network optimization for E. coli promoter prediction
    • Demeler B., and Zhou G. Neural network optimization for E. coli promoter prediction. Nucleic Acids Res. 19 (1991) 1593-1599
    • (1991) Nucleic Acids Res. , vol.19 , pp. 1593-1599
    • Demeler, B.1    Zhou, G.2
  • 10
    • 0033624446 scopus 로고    scopus 로고
    • Recognition of overlapping nucleotides by AraC and the sigma subunit of RNA polymerase
    • Dhiman A., and Schleif R. Recognition of overlapping nucleotides by AraC and the sigma subunit of RNA polymerase. J. Bacteriol. 182 (2000) 5076-5081
    • (2000) J. Bacteriol. , vol.182 , pp. 5076-5081
    • Dhiman, A.1    Schleif, R.2
  • 11
    • 0036123111 scopus 로고    scopus 로고
    • Computational detection and location of transcription start sites in mammalian genomic DNA
    • Down T.A., and Hubbard T.J.P. Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res. 12 (2002) 458-461
    • (2002) Genome Res. , vol.12 , pp. 458-461
    • Down, T.A.1    Hubbard, T.J.P.2
  • 12
    • 0033567215 scopus 로고    scopus 로고
    • Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit
    • Estrem S.T., Ross W., Gaal T., Chen Z.W., Niu W., Ebright R.H., and Gourse R.L. Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit. Genes. Dev. 13 (1999) 2134-2147
    • (1999) Genes. Dev. , vol.13 , pp. 2134-2147
    • Estrem, S.T.1    Ross, W.2    Gaal, T.3    Chen, Z.W.4    Niu, W.5    Ebright, R.H.6    Gourse, R.L.7
  • 14
    • 0022358896 scopus 로고
    • Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli
    • Galas D.J., Eggert M., and Waterman M.S. Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli. J. Mol. Biol. 186 (1985) 117-128
    • (1985) J. Mol. Biol. , vol.186 , pp. 117-128
    • Galas, D.J.1    Eggert, M.2    Waterman, M.S.3
  • 16
    • 33746877792 scopus 로고    scopus 로고
    • Gordon, J.J., Towsey, M.W., Hogan, J.M., Mathews, S.A., Timms, P., 2005. Improved prediction of bacterial transcription start sites. Bioinformatics (advance access published November 15, 2005).
  • 17
    • 0023650609 scopus 로고
    • Analysis of Escherichia coli promoter sequences
    • Harley C.B., and Reynolds R.P. Analysis of Escherichia coli promoter sequences. Nucleic Acids Res. 15 (1987) 2343-2361
    • (1987) Nucleic Acids Res. , vol.15 , pp. 2343-2361
    • Harley, C.B.1    Reynolds, R.P.2
  • 18
    • 0021111879 scopus 로고
    • Compilation and analysis of Escherichia coli promoter DNA sequences
    • Hawley D.K., and McClure W.R. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 11 (1983) 2237-2255
    • (1983) Nucleic Acids Res. , vol.11 , pp. 2237-2255
    • Hawley, D.K.1    McClure, W.R.2
  • 19
    • 0035171017 scopus 로고    scopus 로고
    • PromEC: an updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites
    • Hershherg R., Bejerano G., Santos-Zavaleta A., and Margalit H. PromEC: an updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites. Nucleic Acids Res. 29 (2001) 277
    • (2001) Nucleic Acids Res. , vol.29 , pp. 277
    • Hershherg, R.1    Bejerano, G.2    Santos-Zavaleta, A.3    Margalit, H.4
  • 20
    • 0141758085 scopus 로고    scopus 로고
    • Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals
    • Huerta A.M., and Collado-Vides J. Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals. J. Mol. Biol. 333 (2003) 261-278
    • (2003) J. Mol. Biol. , vol.333 , pp. 261-278
    • Huerta, A.M.1    Collado-Vides, J.2
  • 21
    • 27644499659 scopus 로고    scopus 로고
    • Measuring similarities between transcription factor binding sites
    • Kielbasa S.M., Gonze D., and Herzel H. Measuring similarities between transcription factor binding sites. BMC Bioinform. 6 (2005) 237
    • (2005) BMC Bioinform. , vol.6 , pp. 237
    • Kielbasa, S.M.1    Gonze, D.2    Herzel, H.3
  • 22
    • 0027295666 scopus 로고
    • The minus 35-recognition region of Escherichia coli sigma 70 is inessential for initiation of transcription at an "Extended minus 10" promoter
    • Kumar A., Malloch R.A., Fujita N., Smillie D.A., Ishihama A., and Hayward R.S. The minus 35-recognition region of Escherichia coli sigma 70 is inessential for initiation of transcription at an "Extended minus 10" promoter. J. Mol. Biol. 232 (1993) 406-418
    • (1993) J. Mol. Biol. , vol.232 , pp. 406-418
    • Kumar, A.1    Malloch, R.A.2    Fujita, N.3    Smillie, D.A.4    Ishihama, A.5    Hayward, R.S.6
  • 24
    • 0027230594 scopus 로고
    • Compilation of Escherichia coli mRNA promoter sequences
    • Lisser S., and Margalit H. Compilation of Escherichia coli mRNA promoter sequences. Nucleic Acids Res. 21 (1993) 1507-1516
    • (1993) Nucleic Acids Res. , vol.21 , pp. 1507-1516
    • Lisser, S.1    Margalit, H.2
  • 25
    • 0036124446 scopus 로고    scopus 로고
    • Consensus promoter identification in the human genome utilizing expressed gene markers and gene modeling
    • Liu R., and States D. Consensus promoter identification in the human genome utilizing expressed gene markers and gene modeling. Genome Res. 12 (2001) 462-469
    • (2001) Genome Res. , vol.12 , pp. 462-469
    • Liu, R.1    States, D.2
  • 26
    • 0141605202 scopus 로고    scopus 로고
    • Identification and analysis of 'extended -10' promoters in Escherichia coli
    • Mitchell J.E., Zheng D., Busby S.J., and Minchin S.D. Identification and analysis of 'extended -10' promoters in Escherichia coli. Nucleic Acids Res. 31 (2003) 4689-4695
    • (2003) Nucleic Acids Res. , vol.31 , pp. 4689-4695
    • Mitchell, J.E.1    Zheng, D.2    Busby, S.J.3    Minchin, S.D.4
  • 27
    • 0035252126 scopus 로고    scopus 로고
    • Identification and analysis of eukaryotic promoters: recent computational approaches
    • Ohler U., and Niemann H. Identification and analysis of eukaryotic promoters: recent computational approaches. Trends Genet. 17 (2001) 56-60
    • (2001) Trends Genet. , vol.17 , pp. 56-60
    • Ohler, U.1    Niemann, H.2
  • 28
    • 0033030389 scopus 로고    scopus 로고
    • Interpolated Markov chains for eukaryotic promoter recognition
    • Ohler U., Harbeck S., Niemann H., Nöth E., and Reese M. Interpolated Markov chains for eukaryotic promoter recognition. Bioinformatics 15 (1999) 362-369
    • (1999) Bioinformatics , vol.15 , pp. 362-369
    • Ohler, U.1    Harbeck, S.2    Niemann, H.3    Nöth, E.4    Reese, M.5
  • 29
    • 0343597687 scopus 로고
    • Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter
    • Pribnow D. Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter. Proc. Natl. Acad. Sci. USA 72 (1975) 784-788
    • (1975) Proc. Natl. Acad. Sci. USA , vol.72 , pp. 784-788
    • Pribnow, D.1
  • 30
    • 0027176699 scopus 로고
    • A simple method to forecast good promoters of Escherichia coli by means of doublet frequencies
    • Recknagel R.D., Weller K., and Köhler J.M. A simple method to forecast good promoters of Escherichia coli by means of doublet frequencies. J. Theor. Biol. 162 (1993) 75-80
    • (1993) J. Theor. Biol. , vol.162 , pp. 75-80
    • Recknagel, R.D.1    Weller, K.2    Köhler, J.M.3
  • 31
    • 0027761839 scopus 로고
    • A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase
    • Ross W., Gosink K.K., Salomon J., Igarashi K., Zou C., Ishihama A., et al. A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. Science 262 (1993) 1407-1413
    • (1993) Science , vol.262 , pp. 1407-1413
    • Ross, W.1    Gosink, K.K.2    Salomon, J.3    Igarashi, K.4    Zou, C.5    Ishihama, A.6
  • 34
    • 0034737325 scopus 로고    scopus 로고
    • Highly specific localization of promoter regions in large genomic sequences by promoterInspector: a novel context analysis approach
    • Scherf M., Klingenhoff A., and Werner T. Highly specific localization of promoter regions in large genomic sequences by promoterInspector: a novel context analysis approach. J. Mol. Biol. 297 (2000) 599-606
    • (2000) J. Mol. Biol. , vol.297 , pp. 599-606
    • Scherf, M.1    Klingenhoff, A.2    Werner, T.3
  • 35
    • 0017353007 scopus 로고
    • Interaction of RNA polymerase with promoters from bacteriophage fd
    • Seeburg P.H., Nusslein C., and Schaller H. Interaction of RNA polymerase with promoters from bacteriophage fd. Eur. J. Biochem. 74 (1977) 107-113
    • (1977) Eur. J. Biochem. , vol.74 , pp. 107-113
    • Seeburg, P.H.1    Nusslein, C.2    Schaller, H.3
  • 36
    • 0042622334 scopus 로고    scopus 로고
    • PromH: promoters identification using orthologous genomic sequences
    • Solovyev V., and Shahmuradov I.A. PromH: promoters identification using orthologous genomic sequences. Nucleic Acids Res. 31 (2003) 3540-3545
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3540-3545
    • Solovyev, V.1    Shahmuradov, I.A.2
  • 37
    • 0036081146 scopus 로고    scopus 로고
    • DBTSS: database of human transcriptional start sites and full-length cDNAs
    • Suzuki Y., Yamashita R., Nakai K., and Sugano S. DBTSS: database of human transcriptional start sites and full-length cDNAs. Nucleic Acids Res. 30 (2002) 328-331
    • (2002) Nucleic Acids Res. , vol.30 , pp. 328-331
    • Suzuki, Y.1    Yamashita, R.2    Nakai, K.3    Sugano, S.4
  • 38
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • Tatusov R.L., Koonin E.V., and Lipman D.J. A genomic perspective on protein families. Science 278 (1997) 631-637
    • (1997) Science , vol.278 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 39
    • 0031827572 scopus 로고    scopus 로고
    • Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12
    • Thieffry D., Salgado H., Huerta A.M., and Collado-Vides J. Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12. Bioinformatics 14 (1998) 391-400
    • (1998) Bioinformatics , vol.14 , pp. 391-400
    • Thieffry, D.1    Salgado, H.2    Huerta, A.M.3    Collado-Vides, J.4
  • 40
    • 4444337094 scopus 로고    scopus 로고
    • Stress-induced DNA duplex destabilization (SIDD) in the Escherichia coli genome: SIDD sites are closely associated with promoters
    • Wang H.Q., Noordewier M., and Benham C.J. Stress-induced DNA duplex destabilization (SIDD) in the Escherichia coli genome: SIDD sites are closely associated with promoters. Genome Res. 14 (2004) 1575-1584
    • (2004) Genome Res. , vol.14 , pp. 1575-1584
    • Wang, H.Q.1    Noordewier, M.2    Benham, C.J.3
  • 41
    • 1842584947 scopus 로고    scopus 로고
    • Applied bioinformatics for the identification of regulatory elements
    • Wasserman W.W., and Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nat. Rev. Genet. 5 (2004) 276-287
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 276-287
    • Wasserman, W.W.1    Sandelin, A.2
  • 42
    • 0028587703 scopus 로고
    • Promoter strength prediction based on occurrence frequencies of consensus patterns
    • Weller K., and Recknagel R.D. Promoter strength prediction based on occurrence frequencies of consensus patterns. J. Theor. Biol. 171 (1994) 355-359
    • (1994) J. Theor. Biol. , vol.171 , pp. 355-359
    • Weller, K.1    Recknagel, R.D.2
  • 43
    • 0032776529 scopus 로고    scopus 로고
    • Models for prediction and recognition of eukaryotic promoters
    • Werner T. Models for prediction and recognition of eukaryotic promoters. Mamm. Genome 10 (1999) 168-175
    • (1999) Mamm. Genome , vol.10 , pp. 168-175
    • Werner, T.1
  • 44
    • 0036733640 scopus 로고    scopus 로고
    • Computational prediction of eukaryotic protein-coding genes
    • Zhang M.Q. Computational prediction of eukaryotic protein-coding genes. Nat. Rev. Genet. 3 (2002) 698-709
    • (2002) Nat. Rev. Genet. , vol.3 , pp. 698-709
    • Zhang, M.Q.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.