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Volumn 23, Issue 8, 2013, Pages 1295-1306

Inferring chromatin-bound protein complexes from genome-wide binding assays

Author keywords

[No Author keywords available]

Indexed keywords

ENHANCEOSOME; PROTEIN; SPACER DNA; TRANSCRIPTION FACTOR NANOG; ZINC FINGER PROTEIN;

EID: 84881171276     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.149419.112     Document Type: Article
Times cited : (30)

References (50)
  • 2
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman L. 2001. Random Forests. Mach Learn 45: 5-32.
    • (2001) Mach Learn , vol.45 , pp. 5-32
    • Breiman, L.1
  • 3
    • 1642529511 scopus 로고    scopus 로고
    • Metagenes and molecular pattern discovery using matrix factorization
    • Brunet JP, Tamayo P, Golub TR, Mesirov JP. 2004. Metagenes and molecular pattern discovery using matrix factorization. Proc Natl Acad Sci 101: 4164-4169.
    • (2004) Proc Natl Acad Sci , vol.101 , pp. 4164-4169
    • Brunet, J.P.1    Tamayo, P.2    Golub, T.R.3    Mesirov, J.P.4
  • 4
    • 84855895602 scopus 로고    scopus 로고
    • Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells
    • ChengC,GersteinM. 2011. Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells. Nucleic Acids Res 40: 553-568.
    • (2011) Nucleic Acids Res , vol.40 , pp. 553-568
    • Cheng, C.1    Gerstein, M.2
  • 6
    • 60149095014 scopus 로고    scopus 로고
    • Global analysis of the insulator binding protein ctcf in chromatin barrier regions reveals demarcation of active and repressive domains
    • Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, Zhao K. 2009. Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res 19: 24-32.
    • (2009) Genome Res , vol.19 , pp. 24-32
    • Cuddapah, S.1    Jothi, R.2    Schones, D.E.3    Roh, T.Y.4    Cui, K.5    Zhao, K.6
  • 7
    • 0034902130 scopus 로고    scopus 로고
    • Abundant gfp expression and ltp in hippocampal acute slices by in vivo injection of sindbis virus
    • D'Apuzzo M, Mandolesi G, Reis G, Schuman EM. 2001. Abundant GFP expression and LTP in hippocampal acute slices by in vivo injection of sindbis virus. J Neurophysiol 86: 1037-1042.
    • (2001) J Neurophysiol , vol.86 , pp. 1037-1042
    • D'Apuzzo, M.1    Mandolesi, G.2    Reis, G.3    Schuman, E.M.4
  • 8
    • 35348955882 scopus 로고    scopus 로고
    • A universal framework for regulatory element discovery across all genomes and data types
    • Elemento O, Slonim N, Tavazoie S. 2007. A universal framework for regulatory element discovery across all genomes and data types. Mol Cell 28: 337-350.
    • (2007) Mol Cell , vol.28 , pp. 337-350
    • Elemento, O.1    Slonim, N.2    Tavazoie, S.3
  • 9
    • 79955550445 scopus 로고    scopus 로고
    • A user's guide to the encyclopedia of dna elements (encode)
    • The ENCODE Project Consortium
    • The ENCODE Project Consortium. 2011. A user's guide to the Encyclopedia of DNA Elements (ENCODE). PLoS Biol 9: E1001046.
    • (2011) PLoS Biol , vol.9
  • 10
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of dna elements in the human genome
    • The ENCODE Project Consortium
    • The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
    • (2012) Nature , vol.489 , pp. 57-74
  • 11
    • 84857707318 scopus 로고    scopus 로고
    • Chromhmm: Automating chromatin-state discovery and characterization
    • Ernst J, Kellis M. 2012. ChromHMM: Automating chromatin-state discovery and characterization. Nat Methods 9: 215-216.
    • (2012) Nat Methods , vol.9 , pp. 215-216
    • Ernst, J.1    Kellis, M.2
  • 13
    • 77954069195 scopus 로고    scopus 로고
    • A flexible r package for nonnegative matrix factorization
    • Gaujoux R, Seoighe C. 2010. A flexible R package for nonnegative matrix factorization. BMC Bioinformatics 11: 367.
    • (2010) BMC Bioinformatics , vol.11 , pp. 367
    • Gaujoux, R.1    Seoighe, C.2
  • 15
    • 79959920881 scopus 로고    scopus 로고
    • An integrated chip-seq analysis platform with customizable workflows
    • Giannopoulou EG, Elemento O. 2011. An integrated ChIP-seq analysis platform with customizable workflows. BMC Bioinformatics 12: 277.
    • (2011) BMC Bioinformatics , vol.12 , pp. 277
    • Giannopoulou, E.G.1    Elemento, O.2
  • 17
    • 84867313376 scopus 로고    scopus 로고
    • I-cistarget: An integrative genomics method for the prediction of regulatory features and cis-regulatory modules
    • Herrmann C, Van de Sande B, Potier D, Aerts S. 2012. i-cisTarget: An integrative genomics method for the prediction of regulatory features and cis-regulatory modules. Nucleic Acids Res 40: E114.
    • (2012) Nucleic Acids Res , vol.40
    • Herrmann, C.1    Van De Sande, B.2    Potier, D.3    Aerts, S.4
  • 18
    • 84862785201 scopus 로고    scopus 로고
    • Unsupervised pattern discovery in human chromatin structure through genomic segmentation
    • Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes JA, Noble WS. 2012. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods 9: 473-476.
    • (2012) Nat Methods , vol.9 , pp. 473-476
    • Hoffman, M.M.1    Buske, O.J.2    Wang, J.3    Weng, Z.4    Bilmes, J.A.5    Noble, W.S.6
  • 19
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein-dna interactions
    • Johnson DS, Mortazavi A, Myers RM,Wold B. 2007. Genome-wide mapping of in vivo protein-DNA interactions. Science 316: 1497-1502.
    • (2007) Science , vol.316 , pp. 1497-1502
    • Johnson, D.S.1    Mortazavi, A.2    Myers, R.M.3    Wold, B.4
  • 21
    • 34547844077 scopus 로고    scopus 로고
    • Sparse non-negative matrix factorizations via alternating non-negativity-constrained least squares formicroarray data analysis
    • Kim H, Park H. 2007. Sparse non-negative matrix factorizations via alternating non-negativity-constrained least squares formicroarray data analysis. Bioinformatics 23: 1495-1502.
    • (2007) Bioinformatics , vol.23 , pp. 1495-1502
    • Kim, H.1    Park, H.2
  • 22
    • 40749104852 scopus 로고    scopus 로고
    • An extended transcriptional network for pluripotency of embryonic stem cells
    • Kim J, Chu J, Shen X,Wang J, Orkin SH. 2008. An extended transcriptional network for pluripotency of embryonic stem cells. Cell 132: 1049-1061.
    • (2008) Cell , vol.132 , pp. 1049-1061
    • Kim, J.1    Chu, J.2    Shen, X.3    Wang, J.4    Orkin, S.H.5
  • 23
    • 84655173624 scopus 로고    scopus 로고
    • Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells
    • Lee BK, Bhinge AA, Battenhouse A,McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS, et al. 2012. Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Res 22: 9-24.
    • (2012) Genome Res , vol.22 , pp. 9-24
    • Lee, B.K.1    Bhinge, A.A.2    Battenhouse, A.3    McDaniell, R.M.4    Liu, Z.5    Song, L.6    Ni, Y.7    Birney, E.8    Lieb, J.D.9    Furey, T.S.10
  • 24
    • 60349092237 scopus 로고    scopus 로고
    • Mapping cis- and trans-chromatin interaction networks using chromosome conformation capture (3c)
    • Miele A, Dekker J. 2009. Mapping cis- and trans-chromatin interaction networks using chromosome conformation capture (3C). Methods Mol Biol 464: 105-121.
    • (2009) Methods Mol Biol , vol.464 , pp. 105-121
    • Miele, A.1    Dekker, J.2
  • 26
    • 77951962545 scopus 로고    scopus 로고
    • Genomic binding profiles of functionally distinct rna polymerase iii transcription complexes in human cells
    • Moqtaderi Z,Wang J, Raha D, White RJ, Snyder M, Weng Z, Struhl K. 2010. Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nat StructMol Biol 17: 635-640.
    • (2010) Nat StructMol Biol , vol.17 , pp. 635-640
    • Moqtaderi, Z.1    Wang, J.2    Raha, D.3    White, R.J.4    Snyder, M.5    Weng, Z.6    Struhl, K.7
  • 27
    • 0033993821 scopus 로고    scopus 로고
    • Evi9 encodes a novel zinc finger protein that physically interacts with bcl6, a known human b-cell proto-oncogene product
    • Nakamura T, Yamazaki Y, Saiki Y, Moriyama M, Largaespada DA, Jenkins NA, Copeland NG. 2000. Evi9 encodes a novel zinc finger protein that physically interacts with BCL6, a known human B-cell proto-oncogene product. Mol Cell Biol 20: 3178-3186.
    • (2000) Mol Cell Biol , vol.20 , pp. 3178-3186
    • Nakamura, T.1    Yamazaki, Y.2    Saiki, Y.3    Moriyama, M.4    Largaespada, D.A.5    Jenkins, N.A.6    Copeland, N.G.7
  • 29
    • 35348887715 scopus 로고    scopus 로고
    • Mechanisms of transcription factor deregulation in lymphoid cell transformation
    • O'Neil J, Look AT. 2007. Mechanisms of transcription factor deregulation in lymphoid cell transformation. Oncogene 26: 6838-6849.
    • (2007) Oncogene , vol.26 , pp. 6838-6849
    • O'Neil, J.1    Look, A.T.2
  • 30
    • 76049125511 scopus 로고    scopus 로고
    • Chip-seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells
    • Ouyang Z, Zhou Q, Wong WH. 2009. ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc Natl Acad Sci 106: 21521-21526.
    • (2009) Proc Natl Acad Sci , vol.106 , pp. 21521-21526
    • Ouyang, Z.1    Zhou, Q.2    Wong, W.H.3
  • 33
    • 79953087743 scopus 로고    scopus 로고
    • Native fluorescence spectroscopic evaluation of chemotherapeutic effects on malignant cells using nonnegative matrix factorization analysis
    • Pu Y, Tang GC, Wang WB, Savage HE, Schantz SP, Alfano RR. 2011. Native fluorescence spectroscopic evaluation of chemotherapeutic effects on malignant cells using nonnegative matrix factorization analysis. Technol Cancer Res Treat 10: 113-120.
    • (2011) Technol Cancer Res Treat , vol.10 , pp. 113-120
    • Pu, Y.1    Tang, G.C.2    Wang, W.B.3    Savage, H.E.4    Schantz, S.P.5    Alfano, R.R.6
  • 34
    • 40449141957 scopus 로고    scopus 로고
    • Whole-genome maps of usf1 and usf2 binding and histone h3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders
    • Rada-Iglesias A, Ameur A, Kapranov P, Enroth S, Komorowski J, Gingeras TR, Wadelius C. 2008. Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders. Genome Res 18: 380-392.
    • (2008) Genome Res , vol.18 , pp. 380-392
    • Rada-Iglesias, A.1    Ameur, A.2    Kapranov, P.3    Enroth, S.4    Komorowski, J.5    Gingeras, T.R.6    Wadelius, C.7
  • 36
    • 84455200582 scopus 로고    scopus 로고
    • Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells
    • Ram O, Goren A, Amit I, Shoresh N, Yosef N, Ernst J, Kellis M, Gymrek M, Issner R, Coyne M, et al. 2011. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell 147: 1628-1639.
    • (2011) Cell , vol.147 , pp. 1628-1639
    • Ram, O.1    Goren, A.2    Amit, I.3    Shoresh, N.4    Yosef, N.5    Ernst, J.6    Kellis, M.7    Gymrek, M.8    Issner, R.9    Coyne, M.10
  • 39
    • 0032966918 scopus 로고    scopus 로고
    • Interaction between the two ubiquitously expressed transcription factorsnf-yand sp1
    • Roder K,Wolf SS, Larkin KJ, Schweizer M. 1999. Interaction between the two ubiquitously expressed transcription factorsNF-Yand Sp1. Gene 234: 61-69.
    • (1999) Gene , vol.234 , pp. 61-69
    • Roder, K.1    Wolf, S.S.2    Larkin, K.J.3    Schweizer, M.4
  • 40
    • 82055181847 scopus 로고    scopus 로고
    • Clustered chip-seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements
    • Rye M, Saetrom P, Handstad T, Drablos F. 2011. Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements. BMC Biol 9: 80.
    • (2011) BMC Biol , vol.9 , pp. 80
    • Rye, M.1    Saetrom, P.2    Handstad, T.3    Drablos, F.4
  • 42
    • 39049163024 scopus 로고    scopus 로고
    • Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site
    • Tabach Y, Brosh R, Buganim Y, Reiner A, Zuk O, Yitzhaky A, Koudritsky M, Rotter V, Domany E. 2007. Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site. PLoS ONE 2: E807.
    • (2007) PLoS ONE , vol.2
    • Tabach, Y.1    Brosh, R.2    Buganim, Y.3    Reiner, A.4    Zuk, O.5    Yitzhaky, A.6    Koudritsky, M.7    Rotter, V.8    Domany, E.9
  • 43
    • 0032751323 scopus 로고    scopus 로고
    • Transcriptional repression mediated by the human polycomb-group protein eed involves histone deacetylation
    • van der Vlag J, Otte AP. 1999. Transcriptional repression mediated by the human polycomb-group protein EED involves histone deacetylation. Nat Genet 23: 474-478.
    • (1999) Nat Genet , vol.23 , pp. 474-478
    • Van Der Vlag, J.1    Otte, A.P.2
  • 45
    • 84864929478 scopus 로고    scopus 로고
    • Computational inference of mrna stability from histone modification and transcriptome profiles
    • Wang C, Tian R, Zhao Q, Xu H, Meyer CA, Li C, Zhang Y, Liu XS. 2012a. Computational inference of mRNA stability from histone modification and transcriptome profiles. Nucleic Acids Res 40: 6414-6423.
    • (2012) Nucleic Acids Res , vol.40 , pp. 6414-6423
    • Wang, C.1    Tian, R.2    Zhao, Q.3    Xu, H.4    Meyer, C.A.5    Li, C.6    Zhang, Y.7    Liu, X.S.8
  • 48
    • 68149084884 scopus 로고    scopus 로고
    • Automated multidimensional phenotypic profiling using large public microarray repositories
    • Xu M, Li W, James GM, Mehan MR, Zhou XJ. 2009. Automated multidimensional phenotypic profiling using large public microarray repositories. Proc Natl Acad Sci 106: 12323-12328.
    • (2009) Proc Natl Acad Sci , vol.106 , pp. 12323-12328
    • Xu, M.1    Li, W.2    James, G.M.3    Mehan, M.R.4    Zhou, X.J.5
  • 49
    • 80051571400 scopus 로고    scopus 로고
    • Coassembly of rest and its cofactors at sites of gene repression in embryonic stem cells
    • Yu HB, Johnson R, Kunarso G, Stanton LW. 2011. Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells. Genome Res 21: 1284-1293.
    • (2011) Genome Res , vol.21 , pp. 1284-1293
    • Yu, H.B.1    Johnson, R.2    Kunarso, G.3    Stanton, L.W.4
  • 50
    • 4344669438 scopus 로고    scopus 로고
    • E protein silencing by the leukemogenic aml1-eto fusion protein
    • Zhang J, Kalkum M, Yamamura S, Chait BT, Roeder RG. 2004. E protein silencing by the leukemogenic AML1-ETO fusion protein. Science 305: 1286-1289.
    • (2004) Science , vol.305 , pp. 1286-1289
    • Zhang, J.1    Kalkum, M.2    Yamamura, S.3    Chait, B.T.4    Roeder, R.G.5


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