메뉴 건너뛰기




Volumn 25, Issue 16, 2009, Pages 2103-2109

Statistical detection of cooperative transcription factors with similarity adjustment

Author keywords

[No Author keywords available]

Indexed keywords

DNA; TRANSCRIPTION FACTOR;

EID: 68549111265     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp143     Document Type: Article
Times cited : (8)

References (53)
  • 1
    • 1842433988 scopus 로고    scopus 로고
    • Computational detection of cis-regulatory modules
    • Aerts,S. et al. (2003) Computational detection of cis-regulatory modules. Bioinformatics, 19 (Suppl. 2), ii5-ii14.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2
    • Aerts, S.1
  • 2
    • 0016518897 scopus 로고
    • Efficient string matching
    • Aho,A. and Corasick,M. (1975) Efficient string matching. CACM, 18, 333-340.
    • (1975) CACM , vol.18 , pp. 333-340
    • Aho, A.1    Corasick, M.2
  • 3
    • 0030986188 scopus 로고    scopus 로고
    • The hardwiring of development: Organization and function of genomic regulatory systems
    • Arnone,M. and Davidson,E. (1997) The hardwiring of development: organization and function of genomic regulatory systems. Development 124, 1851-1864.
    • (1997) Development , vol.124 , pp. 1851-1864
    • Arnone, M.1    Davidson, E.2
  • 4
    • 84972496740 scopus 로고
    • Poisson approximation and the Chen-Stein method
    • Arratia,R. et al. (1990) Poisson approximation and the Chen-Stein method. Stat. Sci., 5, 403-434.
    • (1990) Stat. Sci , vol.5 , pp. 403-434
    • Arratia, R.1
  • 5
    • 4043156577 scopus 로고    scopus 로고
    • Searching for statistically significant regulatory modules
    • Bailey,T. and Noble,W. (2003) Searching for statistically significant regulatory modules. Bioinformatics, 19, II16-II25.
    • (2003) Bioinformatics , vol.19
    • Bailey, T.1    Noble, W.2
  • 7
    • 12744263842 scopus 로고    scopus 로고
    • Computational identification of developmental enhancers: Conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura
    • Berman,B. et al. (2004) Computational identification of developmental enhancers: Conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol., 5, R61.
    • (2004) Genome Biol , vol.5
    • Berman, B.1
  • 8
    • 0037154273 scopus 로고    scopus 로고
    • Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome
    • Berman,B.P. et al. (2002) Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl Acad. Sci. USA, 99, 757-762.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 757-762
    • Berman, B.P.1
  • 9
    • 34548847506 scopus 로고    scopus 로고
    • A distance difference matrix approach to identifying transcription factors that regulate differential gene expression
    • Bleser,P.D. et al. (2007) A distance difference matrix approach to identifying transcription factors that regulate differential gene expression. Genome Biol., 8, R83.
    • (2007) Genome Biol , vol.8
    • Bleser, P.D.1
  • 10
    • 37849021289 scopus 로고    scopus 로고
    • Boeva,V. et al. (2007) Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules. Algorithms Mol. Biol., 2 13.
    • Boeva,V. et al. (2007) Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules. Algorithms Mol. Biol., 2 13.
  • 11
    • 0036607144 scopus 로고    scopus 로고
    • New computational approaches for analysis of cis-regulatory networks
    • Brown,C. et al. (2002) New computational approaches for analysis of cis-regulatory networks. Dev. Biol., 246, 86-102.
    • (2002) Dev. Biol , vol.246 , pp. 86-102
    • Brown, C.1
  • 12
    • 0001016345 scopus 로고
    • The composition of the deoxyribonucleic acid of salmon sperm
    • Chargaff,E. et al. (1951) The composition of the deoxyribonucleic acid of salmon sperm. J. Biol. Chem., 192, 223-230.
    • (1951) J. Biol. Chem , vol.192 , pp. 223-230
    • Chargaff, E.1
  • 13
    • 0001067389 scopus 로고
    • Poisson approximation for dependent trials
    • Chen,L.H.Y. (1975) Poisson approximation for dependent trials. Ann. Probab., 3, 534-545.
    • (1975) Ann. Probab , vol.3 , pp. 534-545
    • Chen, L.H.Y.1
  • 14
    • 0347987855 scopus 로고    scopus 로고
    • A self-organizing system of repressor gradients establishes segmental complexity in Drosophila
    • Clyde,D. et al. (2003) A self-organizing system of repressor gradients establishes segmental complexity in Drosophila. Nature, 426, 849-853.
    • (2003) Nature , vol.426 , pp. 849-853
    • Clyde, D.1
  • 15
    • 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
  • 16
    • 0031585995 scopus 로고    scopus 로고
    • A statistical model for locating regulatory regions in genomic DNA
    • Crowley,E. et al. (1997) A statistical model for locating regulatory regions in genomic DNA. J. Mol. Biol., 268, 8-14.
    • (1997) J. Mol. Biol , vol.268 , pp. 8-14
    • Crowley, E.1
  • 17
    • 0029935832 scopus 로고    scopus 로고
    • Coordinate positioning of MEF2 and myogenin binding sites
    • Fickett,J.W. (1996) Coordinate positioning of MEF2 and myogenin binding sites. Gene, 172, GC19-GC32.
    • (1996) Gene , vol.172
    • Fickett, J.W.1
  • 18
    • 0042121118 scopus 로고    scopus 로고
    • Cluster-buster: Finding dense clusters of motifs in DNA sequences
    • Frith,M. et al. (2003) Cluster-buster: Finding dense clusters of motifs in DNA sequences. Nucleic Acids Res., 31, 3666-3668.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3666-3668
    • Frith, M.1
  • 19
    • 0034777594 scopus 로고    scopus 로고
    • Detection of cis-element clusters in higher eukaryotic DNA
    • Frith,M.C. et al. (2001) Detection of cis-element clusters in higher eukaryotic DNA. Bioinformatics, 17, 878-889.
    • (2001) Bioinformatics , vol.17 , pp. 878-889
    • Frith, M.C.1
  • 20
    • 0037100636 scopus 로고    scopus 로고
    • Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences
    • Frith,M.C. et al. (2002) Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. Nucleic Acids Res., 30, 3214-3224.
    • (2002) Nucleic Acids Res , vol.30 , pp. 3214-3224
    • Frith, M.C.1
  • 21
    • 2542584654 scopus 로고    scopus 로고
    • Detection of functional DNA motifs via statistical overrepresentation
    • Frith,M.C. et al. (2004) Detection of functional DNA motifs via statistical overrepresentation. Nucleic Acids Res., 32, 1372-1381.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1372-1381
    • Frith, M.C.1
  • 22
    • 33746835021 scopus 로고    scopus 로고
    • Computational identification of transcriptional regulatory elements in DNA sequence
    • GuhaThakurta,D. (2006) Computational identification of transcriptional regulatory elements in DNA sequence. Nucleic Acids Res., 34, 3585-3598.
    • (2006) Nucleic Acids Res , vol.34 , pp. 3585-3598
    • GuhaThakurta, D.1
  • 23
    • 0034894539 scopus 로고    scopus 로고
    • Identifying target sites for cooperatively binding factors
    • GuhaThakurta,D. and Stormo,G.D. (2001) Identifying target sites for cooperatively binding factors. Bioinformatics, 17, 608-621.
    • (2001) Bioinformatics , vol.17 , pp. 608-621
    • GuhaThakurta, D.1    Stormo, G.D.2
  • 24
    • 18844396103 scopus 로고    scopus 로고
    • De novo cis-regulatory module elicitation for eukaryotic genomes
    • Gupta,M. and Liu,J.S. (2005) De novo cis-regulatory module elicitation for eukaryotic genomes. Proc. Natl Acad. Sci. USA, 102, 7079-7084.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 7079-7084
    • Gupta, M.1    Liu, J.S.2
  • 25
    • 0036796540 scopus 로고    scopus 로고
    • Predicting transcription factor synergism
    • Hannenhalli,S. and Levy,S. (2002) Predicting transcription factor synergism. Nucleic Acids Res., 30, 4278-4284.
    • (2002) Nucleic Acids Res , vol.30 , pp. 4278-4284
    • Hannenhalli, S.1    Levy, S.2
  • 26
    • 4544352942 scopus 로고    scopus 로고
    • Transcriptional regulatory code of a eukaryotic genome
    • Harbison,C.T. et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99-104.
    • (2004) Nature , vol.431 , pp. 99-104
    • Harbison, C.T.1
  • 27
    • 48549104329 scopus 로고    scopus 로고
    • Using transcription factor binding site co-occurrence to predict regulatory regions
    • Klein,H. and Vingron,M. (2007) Using transcription factor binding site co-occurrence to predict regulatory regions. Genome Inform., 18 109-118.
    • (2007) Genome Inform , vol.18 , pp. 109-118
    • Klein, H.1    Vingron, M.2
  • 28
    • 0032948782 scopus 로고    scopus 로고
    • Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity
    • Klingenhoff,A. et al. (1999) Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity. Bioinformatics, 15, 180-186.
    • (1999) Bioinformatics , vol.15 , pp. 180-186
    • Klingenhoff, A.1
  • 29
    • 4043089376 scopus 로고    scopus 로고
    • Searching for transcription factor binding site clusters: How true are true positives?
    • Krivan,W. (2004) Searching for transcription factor binding site clusters: How true are true positives? J. Bioinform. Comput. Biol. 2, 413-416.
    • (2004) J. Bioinform. Comput. Biol , vol.2 , pp. 413-416
    • Krivan, W.1
  • 30
    • 0037398319 scopus 로고    scopus 로고
    • Uniform clusters in Drosophila
    • Lifanov,A. et al. (2003) Uniform clusters in Drosophila. Genome Res., 13, 579-588.
    • (2003) Genome Res , vol.13 , pp. 579-588
    • Lifanov, A.1
  • 31
    • 26444566379 scopus 로고    scopus 로고
    • Manke,T. et al. (2005) Detecting functional modules of transcription factor binding sites in the human genome. In Lecture Notes in Computer Science. Springer, Berlin/Heidelberg.
    • Manke,T. et al. (2005) Detecting functional modules of transcription factor binding sites in the human genome. In Lecture Notes in Computer Science. Springer, Berlin/Heidelberg.
  • 32
    • 0037154218 scopus 로고    scopus 로고
    • Genome-wide analysis of clustered dorsal binding sites identifies putative target genes in the Drosophila embryo
    • Markstein,M. et al. (2002) Genome-wide analysis of clustered dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc. Natl Acad. Sci. USA, 99, 763-768.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 763-768
    • Markstein, M.1
  • 33
    • 0037208166 scopus 로고    scopus 로고
    • TRANSFAC(R): Transcriptional regulation, from patterns to profiles
    • Matys,V. et al. (2003) TRANSFAC(R): Transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.
    • (2003) Nucleic Acids Res , vol.31 , pp. 374-378
    • Matys, V.1
  • 34
    • 33644876958 scopus 로고    scopus 로고
    • Transfac(r) and its module transcompel(r): Transcriptional gene regulation in eukaryotes
    • Matys,V. et al. (2006) Transfac(r) and its module transcompel(r): transcriptional gene regulation in eukaryotes. Nucleic Acids Res., 34 (Suppl. 1), D108-D110.
    • (2006) Nucleic Acids Res , vol.34 , Issue.SUPPL. 1
    • Matys, V.1
  • 35
    • 34249676873 scopus 로고    scopus 로고
    • Clusterdraw web server: A tool to identify and visualize clusters of binding motifs for transcription factors
    • Papatsenko,D. (2007) Clusterdraw web server: A tool to identify and visualize clusters of binding motifs for transcription factors. Bioinformatics, 23, 1032-1034.
    • (2007) Bioinformatics , vol.23 , pp. 1032-1034
    • Papatsenko, D.1
  • 36
    • 85193596218 scopus 로고    scopus 로고
    • Extraction of functional binding sites from unique regulatory regions: The Drosophila early developmental enhancers, Preliminary version in Drosophila Workshop, Washington
    • Papatsenko,D. et al. (2002) Extraction of functional binding sites from unique regulatory regions: The Drosophila early developmental enhancers. Genome Res., 12, 470-481. [Preliminary version in Drosophila Workshop, Washington 2001].
    • (2001) Genome Res , vol.12 , pp. 470-481
    • Papatsenko, D.1
  • 37
    • 68549103287 scopus 로고    scopus 로고
    • Ph.D. Thesis, Library of the Free University of Berlin, IMPRS for Computional Biology and Scientific Computing, Max Planck Institute for Molecular Genetics
    • Pape,U.J. (2008) Statistics for Transcription Factor Binding Sites Ph.D. Thesis, Library of the Free University of Berlin, IMPRS for Computional Biology and Scientific Computing, Max Planck Institute for Molecular Genetics.
    • (2008) Statistics for Transcription Factor Binding Sites
    • Pape, U.J.1
  • 39
    • 34447503964 scopus 로고    scopus 로고
    • A new statistical model to select target sequences bound by transcription factors
    • Pape,U.J. et al. (2006) A new statistical model to select target sequences bound by transcription factors. Genome Inform., 17 134-140.
    • (2006) Genome Inform , vol.17 , pp. 134-140
    • Pape, U.J.1
  • 40
    • 47549096411 scopus 로고    scopus 로고
    • Compound Poisson approximation of number of occurrences of a position frequency matrix (PFM) on both strands
    • Pape,U.J. et al. (2008a) Compound Poisson approximation of number of occurrences of a position frequency matrix (PFM) on both strands. J. Comput. Biol., 15, 547-564.
    • (2008) J. Comput. Biol , vol.15 , pp. 547-564
    • Pape, U.J.1
  • 41
    • 38849122853 scopus 로고    scopus 로고
    • Natural similarity measures between position frequency matrices with an application to clustering
    • Pape,U.J. et al. (2008b) Natural similarity measures between position frequency matrices with an application to clustering. Bioinformatics, 24, 350-357.
    • (2008) Bioinformatics , vol.24 , pp. 350-357
    • Pape, U.J.1
  • 42
    • 0034785443 scopus 로고    scopus 로고
    • Identifying regulatory networks by combinatorial analysis of promoter elements
    • Pilpel,Y. et al. (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
  • 43
    • 33748690244 scopus 로고    scopus 로고
    • Dynamic programming algorithms for two statistical problems in computational biology
    • Springer, Heidelberg, pp
    • Rahmann,S. (2003) Dynamic programming algorithms for two statistical problems in computational biology. In Proceedings of the 3rd Workshop of Algorithms in Bioinformatics (WABI). Springer, Heidelberg, pp. 151-164.
    • (2003) Proceedings of the 3rd Workshop of Algorithms in Bioinformatics (WABI) , pp. 151-164
    • Rahmann, S.1
  • 44
    • 0037162497 scopus 로고    scopus 로고
    • Score: A computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data. site clustering over random expectation
    • Rebeiz,M. et al. (2002) Score: A computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data. site clustering over random expectation. Proc. Natl Acad. Sci. USA, 99, 9888-9893.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 9888-9893
    • Rebeiz, M.1
  • 45
    • 0042121137 scopus 로고    scopus 로고
    • Target explorer: An automated tool for the identification of new target genes for a specified set of transcription factors
    • Sosinsky,A. et al. (2003) Target explorer: An automated tool for the identification of new target genes for a specified set of transcription factors. Nucleic Acids Res., 31, 3589-3592.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3589-3592
    • Sosinsky, A.1
  • 46
    • 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
  • 47
    • 0030847502 scopus 로고    scopus 로고
    • A computational genomics approach to the identification of gene networks
    • Wagner,A. (1997) A computational genomics approach to the identification of gene networks. Nucleic Acids Res., 25, 3594-3604.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3594-3604
    • Wagner, A.1
  • 48
    • 0033394535 scopus 로고    scopus 로고
    • Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes
    • Wagner,A. (1999) Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes. Bioinformatics, 15, 776-784.
    • (1999) Bioinformatics , vol.15 , pp. 776-784
    • Wagner, A.1
  • 49
    • 0032562789 scopus 로고    scopus 로고
    • Identification of regulatory regions which confer muscle-specific gene expression
    • Wasserman,W. and Fickett,J. (1998) Identification of regulatory regions which confer muscle-specific gene expression. J. Mol. Biol., 278, 167-181.
    • (1998) J. Mol. Biol , vol.278 , pp. 167-181
    • Wasserman, W.1    Fickett, J.2
  • 50
    • 6744219613 scopus 로고    scopus 로고
    • Long range interaction of cis-DNA elements mediated by architectural transcription factor bach1
    • Yoshida,C. et al. (1999) Long range interaction of cis-DNA elements mediated by architectural transcription factor bach1. Genes Cells, 4, 643-655.
    • (1999) Genes Cells , vol.4 , pp. 643-655
    • Yoshida, C.1
  • 51
    • 33750217984 scopus 로고    scopus 로고
    • Computational analysis of tissue-specific combinatorial gene regulation: Predicting interaction between transcription factors in human tissues
    • Yu,X. et al. (2006) Computational analysis of tissue-specific combinatorial gene regulation: Predicting interaction between transcription factors in human tissues. Nucleic Acids Res., 34 4925-4936.
    • (2006) Nucleic Acids Res , vol.34 , pp. 4925-4936
    • Yu, X.1
  • 52
    • 0032549745 scopus 로고    scopus 로고
    • Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene
    • Yuh,C.-H. et al. (1998) Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene. Science, 279 1896-1902.
    • (1998) Science , vol.279 , pp. 1896-1902
    • Yuh, C.-H.1
  • 53
    • 4344607122 scopus 로고    scopus 로고
    • CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling
    • Zhou,Q. and Wong,W.H. (2004) CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling. Proc. Natl Acad. Sci., 101, 12114-12119.
    • (2004) Proc. Natl Acad. Sci , vol.101 , pp. 12114-12119
    • Zhou, Q.1    Wong, W.H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.