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Volumn 28, Issue 5, 2012, Pages 701-708

De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae

Author keywords

[No Author keywords available]

Indexed keywords

SACCHAROMYCES CEREVISIAE;

EID: 84863286971     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts002     Document Type: Article
Times cited : (13)

References (36)
  • 1
    • 57749121616 scopus 로고    scopus 로고
    • Alibrary of yeast transcription factor motifs reveals a widespread function for RSC3 in targeting nucleosome exclusion at promoters
    • Badis,G. et al. (2008)Alibrary of yeast transcription factor motifs reveals a widespread function for RSC3 in targeting nucleosome exclusion at promoters. Mol. Cell, 32, 878-887.
    • (2008) Mol. Cell , vol.32 , pp. 878-887
    • Badis, G.1
  • 2
    • 33745449162 scopus 로고    scopus 로고
    • Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast
    • Balaji,S. et al. (2006) Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. J. Mol. Biol., 360, 213-227.
    • (2006) J. Mol. Biol. , vol.360 , pp. 213-227
    • Balaji, S.1
  • 3
    • 0345099564 scopus 로고    scopus 로고
    • Identifying cooperativity among transcription factors controlling the cell cycle in yeast
    • Banerjee,N. and Zhang,M.Q. (2003) Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Res., 31, 7024-7031.
    • (2003) Nucleic Acids Res , vol.31 , pp. 7024-7031
    • Banerjee, N.1    Zhang, M.Q.2
  • 4
    • 33750882505 scopus 로고    scopus 로고
    • Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
    • Berger,M.F. et al. (2006) Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat. Biotechnol., 24, 1429-1435.
    • (2006) Nat. Biotechnol. , vol.24 , pp. 1429-1435
    • Berger, M.F.1
  • 5
    • 1242316281 scopus 로고    scopus 로고
    • ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
    • Buck,M.J. and Lieb,J.D. (2004) ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics, 83, 349-360.
    • (2004) Genomics , vol.83 , pp. 349-360
    • Buck, M.J.1    Lieb, J.D.2
  • 6
    • 34047191812 scopus 로고    scopus 로고
    • Protein binding microarrays for the characterization of DNA-protein interactions
    • Bulyk,M.L. (2007) Protein binding microarrays for the characterization of DNA-protein interactions. Adv. Biochem. Eng. Biotechnol., 104, 65-85.
    • (2007) Adv. Biochem. Eng. Biotechnol. , vol.104 , pp. 65-85
    • Bulyk, M.L.1
  • 7
    • 0033028741 scopus 로고    scopus 로고
    • Quantifying DNA-protein interactions by double-stranded DNA arrays
    • Bulyk,M.L. et al. (1999) Quantifying DNA-protein interactions by double-stranded DNA arrays. Nat. Biotechnol., 17, 573-577.
    • (1999) Nat. Biotechnol. , vol.17 , pp. 573-577
    • Bulyk, M.L.1
  • 8
    • 0035912721 scopus 로고    scopus 로고
    • Exploring the DNA-binding specificities of zinc fingers with DNA microarrays
    • Bulyk,M.L. et al. (2001) Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc. Natl. Acad. Sci. USA, 98, 7158-7163.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 7158-7163
    • Bulyk, M.L.1
  • 9
    • 33748694308 scopus 로고    scopus 로고
    • Identification of transcription factor cooperativity via stochastic system model
    • Chang,Y.H. et al. (2006) Identification of transcription factor cooperativity via stochastic system model. Bioinformatics, 22, 2276-2282.
    • (2006) Bioinformatics , vol.22 , pp. 2276-2282
    • Chang, Y.H.1
  • 10
    • 40649107189 scopus 로고    scopus 로고
    • Discovering gapped binding sites of yeast transcription factors
    • Chen,C.Y. et al. (2008) Discovering gapped binding sites of yeast transcription factors. Proc. Natl. Acad. Sci. USA, 105, 2527-2532.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 2527-2532
    • Chen, C.Y.1
  • 11
    • 39149093082 scopus 로고    scopus 로고
    • Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae
    • Datta,D. and Zhao,H. (2008) Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae. Bioinformatics, 24, 545-552.
    • (2008) Bioinformatics , vol.24 , pp. 545-552
    • Datta, D.1    Zhao, H.2
  • 12
    • 1842607847 scopus 로고    scopus 로고
    • R Foundation for Statistical Computing, Vienna, Austria Development Core Team of
    • Development Core Team of R. (2005) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
    • (2005) R.R: A Language and Environment for Statistical Computing
  • 13
    • 34047230770 scopus 로고    scopus 로고
    • Discovering motifs in ranked lists of DNA sequences
    • Eden,E. et al. (2007) Discovering motifs in ranked lists of DNA sequences. PLoS Comput Biol., 3, e39.
    • (2007) PLoS Comput Biol , vol.3
    • Eden, E.1
  • 14
    • 70350731108 scopus 로고    scopus 로고
    • Distinguishing direct versus indirect transcription factor-DNA interactions
    • Gordân,R. et al. (2009) Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Res., 19, 2090-2100.
    • (2009) Genome Res , vol.19 , pp. 2090-2100
    • Gordân, R.1
  • 15
    • 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
  • 16
    • 0035449843 scopus 로고    scopus 로고
    • Recruitment of HU by piggyback: a special role of GalR in repressosome assembly
    • Kar,S. and Adhya,S. (2001) Recruitment of HU by piggyback: a special role of GalR in repressosome assembly. Genes Dev., 15, 2273-2281.
    • (2001) Genes Dev , vol.15 , pp. 2273-2281
    • Kar, S.1    Adhya, S.2
  • 17
    • 13544254744 scopus 로고    scopus 로고
    • Identifying combinatorial regulation of transcription factors and binding motifs
    • Kato,M. et al. (2004) Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol., 5, R56.
    • (2004) Genome Biol , vol.5
    • Kato, M.1
  • 18
    • 0037174671 scopus 로고    scopus 로고
    • Transcriptional regulatory networks in Saccharomyces cerevisiae
    • Lee,T.I. et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298, 799-804.
    • (2002) Science , vol.298 , pp. 799-804
    • Lee, T.I.1
  • 19
    • 33745128746 scopus 로고    scopus 로고
    • Inferring transcriptional modules from ChIP-chip, motif and microarray data
    • Lemmens,K. et al. (2006) Inferring transcriptional modules from ChIP-chip, motif and microarray data. Genome Biol., 7, R37.
    • (2006) Genome Biol , vol.7
    • Lemmens, K.1
  • 20
    • 33645769260 scopus 로고    scopus 로고
    • An improved map of conserved regulatory sites for Saccharomyces cerevisiae
    • MacIsaac,K.D. et al. (2006) An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics, 7, 113.
    • (2006) BMC Bioinformatics , vol.7 , pp. 113
    • MacIsaac, K.D.1
  • 21
    • 0141792394 scopus 로고    scopus 로고
    • Correlating protein-DNA and protein-protein interaction networks
    • Manke,T. et al. (2003) Correlating protein-DNA and protein-protein interaction networks. J. Mol. Biol., 333, 75-85.
    • (2003) J. Mol. Biol. , vol.333 , pp. 75-85
    • Manke, T.1
  • 22
    • 34247226079 scopus 로고    scopus 로고
    • Inferring condition-specific transcription factor function from DNA binding and gene expression data
    • McCord,R.P. et al. (2007) Inferring condition-specific transcription factor function from DNA binding and gene expression data. Mol. Syst. Biol., 3, 100.
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 100
    • McCord, R.P.1
  • 23
    • 9644268153 scopus 로고    scopus 로고
    • Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays
    • Mukherjee,S. et al. (2004) Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat. Genet., 36, 1331-1339.
    • (2004) Nat. Genet. , vol.36 , pp. 1331-1339
    • Mukherjee, S.1
  • 24
    • 33747879675 scopus 로고    scopus 로고
    • Informative priors based on transcription factor structural class improve de novo motif discovery
    • Narlikar,L. et al. (2006) Informative priors based on transcription factor structural class improve de novo motif discovery. Bioinformatics, 22, e384-e392.
    • (2006) Bioinformatics , vol.22
    • Narlikar, L.1
  • 25
    • 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
  • 26
    • 0034704248 scopus 로고    scopus 로고
    • Genome-wide location and function of DNA binding proteins
    • Ren,B. et al. (2000) Genome-wide location and function of DNA binding proteins. Science, 290, 2306-2309.
    • (2000) Science , vol.290 , pp. 2306-2309
    • Ren, B.1
  • 27
    • 46449123335 scopus 로고    scopus 로고
    • Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets
    • Linhart,C. et al. (2008) Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets. Genome Res., 18, 1180-1189.
    • (2008) Genome Res , vol.18 , pp. 1180-1189
    • Linhart, C.1
  • 28
    • 0031742022 scopus 로고    scopus 로고
    • Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
    • Spellman,P.T. et al. (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.T.1
  • 29
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
    • Subramanian,A. et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA, 102, 15545-15550.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 15545-15550
    • Subramanian, A.1
  • 30
    • 26444501081 scopus 로고    scopus 로고
    • Statistical methods for identifying yeast cell cycle transcription factors
    • Tsai,H.K. et al. (2005) Statistical methods for identifying yeast cell cycle transcription factors. Proc. Natl. Acad. Sci. USA, 102, 13532-13537.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 13532-13537
    • Tsai, H.K.1
  • 31
    • 34547557480 scopus 로고    scopus 로고
    • MYBS: a comprehensive web server for mining transcription factor binding sites in yeast
    • Tsai,H.K. et al. (2007) MYBS: a comprehensive web server for mining transcription factor binding sites in yeast. Nucleic Acids Res., 35, W221-W226.
    • (2007) Nucleic Acids Res , vol.35
    • Tsai, H.K.1
  • 32
    • 70350690683 scopus 로고    scopus 로고
    • Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data
    • Wang,Y. et al. (2009) Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Nucleic Acids Res., 37, 5943-5958.
    • (2009) Nucleic Acids Res , vol.37 , pp. 5943-5958
    • Wang, Y.1
  • 33
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of 'small-world' networks
    • Watts,D.J. and Strogatz,S.H. (1998) Collective dynamics of 'small-world' networks. Nature, 393, 440-442.
    • (1998) Nature , vol.393 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 34
    • 34447279700 scopus 로고    scopus 로고
    • Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data
    • Wu,W.S. et al. (2007) Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data. BMC Bioinformatics, 8, 188.
    • (2007) BMC Bioinformatics , vol.8 , pp. 188
    • Wu, W.S.1
  • 35
    • 33644855121 scopus 로고    scopus 로고
    • Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae
    • Yu,X. et al. (2006) Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae. Nucleic Acids Res., 34, 917-927.
    • (2006) Nucleic Acids Res , vol.34 , pp. 917-927
    • Yu, X.1
  • 36
    • 63849315606 scopus 로고    scopus 로고
    • High-resolution DNA-binding specificity analysis of yeast transcription factors
    • Zhu,C. et al. (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res., 19, 556-566.
    • (2009) Genome Res , vol.19 , pp. 556-566
    • Zhu, C.1


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