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Volumn 20, Issue 16, 2004, Pages 2799-2811

Regulatory motif finding by logic regression

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TRANSCRIPTION FACTOR;

EID: 8844253932     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth333     Document Type: Article
Times cited : (51)

References (30)
  • 2
    • 0002759539 scopus 로고
    • Unsupervised learning of multiple motifs in biopolymers using expectation maximization
    • Bailey,T. and Elkan,C. (1995) Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Mach. Learning, 21, 51-80.
    • (1995) Mach. Learning , vol.21 , pp. 51-80
    • Bailey, T.1    Elkan, C.2
  • 3
    • 4043156577 scopus 로고    scopus 로고
    • Searching for statistically significant regulatory modules
    • Bailey,T.L. and Noble,W.S. (2003) Searching for statistically significant regulatory modules. Bioinformatics, 19, ii16-ii25.
    • (2003) Bioinformatics , vol.19
    • Bailey, T.L.1    Noble, W.S.2
  • 4
    • 0035135420 scopus 로고    scopus 로고
    • Regulatory element detection using correlation with expression
    • Bussemaker,H., Li,H. and Siggia,E. (2001) Regulatory element detection using correlation with expression. Nat. Genet., 27, 167-171.
    • (2001) Nat. Genet. , vol.27 , pp. 167-171
    • Bussemaker, H.1    Li, H.2    Siggia, E.3
  • 5
    • 0030920037 scopus 로고    scopus 로고
    • The AFT1 transcriptional factor is differentially required for expression of high-affinity iron uptake genes in Saccharomyces cerevisiae
    • Casas,C., Aldea,M., Espinet,C., Gallego,C., Gil,R. and Herrero,E. (1997) The AFT1 transcriptional factor is differentially required for expression of high-affinity iron uptake genes in Saccharomyces cerevisiae. Yeast, 13, 621-637.
    • (1997) Yeast , vol.13 , pp. 621-637
    • Casas, C.1    Aldea, M.2    Espinet, C.3    Gallego, C.4    Gil, R.5    Herrero, E.6
  • 6
    • 0037453009 scopus 로고    scopus 로고
    • Integrating regulatory motif discovery and genome-wide expression analysis
    • Conlon,E., Liu,X., Lieb,J. and Liu,J. (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.1    Liu, X.2    Lieb, J.3    Liu, J.4
  • 8
    • 0034894539 scopus 로고    scopus 로고
    • Identifying target sites for cooperatively binding factors
    • GuhaThakurta,D. and Stormo,G. (2001) Identifying target sites for cooperatively binding factors. Bioinformatics, 17, 608-621.
    • (2001) Bioinformatics , vol.17 , pp. 608-621
    • GuhaThakurta, D.1    Stormo, G.2
  • 9
    • 0032826179 scopus 로고    scopus 로고
    • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    • Hertz,G. and Stormo,G. (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.1    Stormo, G.2
  • 11
    • 0036740483 scopus 로고    scopus 로고
    • Identification of regulatory elements using a feature selection method
    • Keleş,S., van der Laan,M. and Eisen,M. (2002) Identification of regulatory elements using a feature selection method. Bioinformatics, 18, 1167-1175.
    • (2002) Bioinformatics , vol.18 , pp. 1167-1175
    • Keleş, S.1    van der Laan, M.2    Eisen, M.3
  • 13
    • 0027912333 scopus 로고
    • Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
    • Lawrence,C., Altsclml,S., Boguski,M., Liu,A.N. and Wootton,J. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
    • (1993) Science , vol.262 , pp. 208-214
    • Lawrence, C.1    Altsclml, S.2    Boguski, M.3    Liu, A.N.4    Wootton, J.5
  • 14
    • 0025320805 scopus 로고
    • An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
    • Lawrence,C. and Reilly,A. (1990) An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Prot. Struct. Funct. Genet. 7, 41-51.
    • (1990) Prot. Struct. Funct. Genet. , vol.7 , pp. 41-51
    • Lawrence, C.1    Reilly, A.2
  • 15
    • 0034730161 scopus 로고    scopus 로고
    • Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis
    • Li,H., Bussemaker,H. and Siggia,E. (2000) Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis. Proc. Natl Acad. Sci., USA, 97, 10096-10100.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 10096-10100
    • Li, H.1    Bussemaker, H.2    Siggia, E.3
  • 16
    • 0036324753 scopus 로고    scopus 로고
    • An algorithm for finding protein-DNA binding sites with applications to chromatin immunoprecipitation microarray experiments
    • Liu,X., Brutlag,D. and Liu,J. (2002) An algorithm for finding protein-DNA binding sites with applications to chromatin immunoprecipitation microarray experiments. Nat. Biotechnol., 20 835-839.
    • (2002) Nat. Biotechnol. , vol.20 , pp. 835-839
    • Liu, X.1    Brutlag, D.2    Liu, J.3
  • 17
    • 0029144601 scopus 로고
    • Gibbs motif sampling: Detection of bacterial outer membrane protein repeats
    • Neuwald,A., Liu,J. and Lawrence,C. (1995) Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Sci., 4, 1618-1632.
    • (1995) Protein Sci. , vol.4 , pp. 1618-1632
    • Neuwald, A.1    Liu, J.2    Lawrence, C.3
  • 18
    • 0034785443 scopus 로고    scopus 로고
    • Identifying regulatory networks by combinatorial analysis of promoter elements
    • Pilpel,Y., Sudarsanam,P. and Church,G. (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.3
  • 22
    • 8844271879 scopus 로고    scopus 로고
    • A probabilistics method to detect regulatory modules
    • Sinha,S., van Nimwegen,E. and Siggia,E. (2003) A probabilistics method to detect regulatory modules. Bioinformatics, 1, 1-10.
    • (2003) Bioinformatics , vol.1 , pp. 1-10
    • Sinha, S.1    van Nimwegen, E.2    Siggia, E.3
  • 23
    • 0031742022 scopus 로고    scopus 로고
    • Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
    • Spellman,P., Sherlock,G., Zhang,M., Iyer,V., Anders,K., Eisen,M., Brown,P., Botstein,D. and Futcher,B. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell, 9, 3273-3297.
    • (1998) Mol. Biol. Cell , vol.9 , pp. 3273-3297
    • Spellman, P.1    Sherlock, G.2    Zhang, M.3    Iyer, V.4    Anders, K.5    Eisen, M.6    Brown, P.7    Botstein, D.8    Futcher, B.9
  • 24
    • 0033028596 scopus 로고    scopus 로고
    • Systematic determination of genetic network architecture
    • Tavazoie,S., Hughes,J., Campbell,M., Cho,R. and Church,G. (1999) Systematic determination of genetic network architecture. Nat. Genet., 22, 281-285.
    • (1999) Nat. Genet. , vol.22 , pp. 281-285
    • Tavazoie, S.1    Hughes, J.2    Campbell, M.3    Cho, R.4    Church, G.5
  • 25
    • 0033289316 scopus 로고    scopus 로고
    • An exact method for finding short motifs in sequences, with application to the ribosome binding site problem
    • AAAI, Heidelberg, Germany
    • Tompa,M. (1999) An exact method for finding short motifs in sequences, with application to the ribosome binding site problem. Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, AAAI, Heidelberg, Germany, pp. 262-271.
    • (1999) Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology , pp. 262-271
    • Tompa, M.1
  • 26
    • 0032483307 scopus 로고    scopus 로고
    • Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
    • van Helden,J., Andre,B, and Collado-Vides,J. (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies, J. Mol. Biol. 281, 827-842.
    • (1998) J. Mol. Biol. , vol.281 , pp. 827-842
    • van Helden, J.1    Andre, B.2    Collado-Vides, J.3
  • 27
    • 0034656326 scopus 로고    scopus 로고
    • Discovering regulatory elements in intergenie sequences by analysis of spaced dyads
    • van Helden,J., Rios,A.F. and Collado-Vides,J. (2000) Discovering regulatory elements in intergenie sequences by analysis of spaced dyads. Nucleic Acids Res., 28, 1801-1818.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 1801-1818
    • van Helden, J.1    Rios, A.F.2    Collado-Vides, J.3
  • 28
    • 0030054971 scopus 로고    scopus 로고
    • Iron-regulated DNA binding by the AFT1 protein controls the iron regulon in yeast
    • Yamaguchi-Iwai,Y., Stearman,R., Dancis,A., and Klausner,R. (1996) Iron-regulated DNA binding by the AFT1 protein controls the iron regulon in yeast. EMBO J., 15, 3377-3384.
    • (1996) EMBO J. , vol.15 , pp. 3377-3384
    • Yamaguchi-Iwai, Y.1    Stearman, R.2    Dancis, A.3    Klausner, R.4
  • 29
    • 0037166279 scopus 로고    scopus 로고
    • Subcellular localization of AFT1 transcription factor responds to iron status in Saccharomyces cerevisiae
    • Yamaguchi-Iwai,Y., Ueta,R., Fukunaka,A. and Sasaki,R. (2002) Subcellular localization of AFT1 transcription factor responds to iron status in Saccharomyces cerevisiae. J. Biol. Chem. 227, 18914-18918.
    • (2002) J. Biol. Chem. , vol.227 , pp. 18914-18918
    • Yamaguchi-Iwai, Y.1    Ueta, R.2    Fukunaka, A.3    Sasaki, R.4
  • 30
    • 0032861774 scopus 로고    scopus 로고
    • Scpd: A promoter database of yeast Saccharomyces cerevisiae
    • Zhu,J. and Zhang,M. (1999) Scpd: a promoter database of yeast Saccharomyces cerevisiae. Bioinformatics, 15, 607-611.
    • (1999) Bioinformatics , vol.15 , pp. 607-611
    • Zhu, J.1    Zhang, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.