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Volumn 15, Issue 7, 2014, Pages

Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets

Author keywords

[No Author keywords available]

Indexed keywords

COHESIN; DNA; NUCLEIC ACID BINDING PROTEIN; PROTEIN THAP11; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR CTCF; TRANSCRIPTION FACTOR ETS; TRANSCRIPTION FACTOR JUNB; TRANSCRIPTION FACTOR JUND; UNCLASSIFIED DRUG;

EID: 84956912079     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-014-0412-4     Document Type: Article
Times cited : (49)

References (42)
  • 1
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M: An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74.
    • (2012) Nature , vol.489 , pp. 57-74
    • Bernstein, B.E.1    Birney, E.2    Dunham, I.3    Green, E.D.4    Gunter, C.5    Snyder, M.6
  • 2
    • 70449711243 scopus 로고    scopus 로고
    • Computation for ChIP-seq and RNA-seq studies
    • Pepke S, Wold B, Mortazavi A: Computation for ChIP-seq and RNA-seq studies. Nat Methods 2009, 6:S22-S32.
    • (2009) Nat Methods , vol.6 , pp. S22-S32
    • Pepke, S.1    Wold, B.2    Mortazavi, A.3
  • 3
    • 80052976954 scopus 로고    scopus 로고
    • ChIP-seq: technical considerations for obtaining high-quality data
    • 1529-2908
    • Kidder BL, Hu G, Zhao K: ChIP-seq: technical considerations for obtaining high-quality data. Nat Immunol 2011, 12:918-922. 1529-2908.
    • (2011) Nat Immunol , vol.12 , pp. 918-922
    • Kidder, B.L.1    Hu, G.2    Zhao, K.3
  • 6
    • 77955368935 scopus 로고    scopus 로고
    • Evaluation of algorithm performance in ChIP-seq peak detection
    • Wilbanks EG, Facciotti MT: Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One 2010, 5:e11471.
    • (2010) PLoS One , vol.5
    • Wilbanks, E.G.1    Facciotti, M.T.2
  • 7
    • 84866937220 scopus 로고    scopus 로고
    • Inferring direct DNA binding from ChIP-seq
    • Bailey TL, Machanick P: Inferring direct DNA binding from ChIP-seq. Nucleic Acids Res 2012, 40:e128.
    • (2012) Nucleic Acids Res , vol.40
    • Bailey, T.L.1    Machanick, P.2
  • 8
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • Bailey TL, Elkan C: Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 1994, 2:28-36.
    • (1994) Proc Int Conf Intell Syst Mol Biol , vol.2 , pp. 28-36
    • Bailey, T.L.1    Elkan, C.2
  • 9
    • 84883191963 scopus 로고    scopus 로고
    • oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-seq datasets
    • Kwon AT, Arenillas DJ, Hunt RW, Wasserman WW: oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-seq datasets. G3 2012, 2:987-1002.
    • (2012) G3 , vol.2 , pp. 987-1002
    • Kwon, A.T.1    Arenillas, D.J.2    Hunt, R.W.3    Wasserman, W.W.4
  • 10
    • 77952567987 scopus 로고    scopus 로고
    • Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
    • Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK: Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 2010, 38:576-589.
    • (2010) Mol Cell , vol.38 , pp. 576-589
    • Heinz, S.1    Benner, C.2    Spann, N.3    Bertolino, E.4    Lin, Y.C.5    Laslo, P.6    Cheng, J.X.7    Murre, C.8    Singh, H.9    Glass, C.K.10
  • 15
    • 84876588265 scopus 로고    scopus 로고
    • Modulation of gene expression via overlapping binding sites exerted by ZNF143, Notch1 and THAP11
    • Ngondo-Mbongo RP, Myslinski E, Aster JC, Carbon P: Modulation of gene expression via overlapping binding sites exerted by ZNF143, Notch1 and THAP11. Nucleic Acids Res 2013, 41:4000-4014.
    • (2013) Nucleic Acids Res , vol.41 , pp. 4000-4014
    • Ngondo-Mbongo, R.P.1    Myslinski, E.2    Aster, J.C.3    Carbon, P.4
  • 17
    • 80053197563 scopus 로고    scopus 로고
    • Genome-wide analysis of the relationships between DNaseI HS, histone modifications and gene expression reveals distinct modes of chromatin domains
    • Shu W, Chen H, Bo X, Wang S: Genome-wide analysis of the relationships between DNaseI HS, histone modifications and gene expression reveals distinct modes of chromatin domains. Nucleic Acids Res 2011, 39:7428-7443.
    • (2011) Nucleic Acids Res , vol.39 , pp. 7428-7443
    • Shu, W.1    Chen, H.2    Bo, X.3    Wang, S.4
  • 18
    • 84902057702 scopus 로고    scopus 로고
    • Improving analysis of transcription factor binding sites within ChIP-seq data based on topological motif enrichment
    • Worsley Hunt R, Mathelier A, Del Peso L, Wasserman WW: Improving analysis of transcription factor binding sites within ChIP-seq data based on topological motif enrichment. BMC Genomics 2014, 15:472.
    • (2014) BMC Genomics , vol.15 , pp. 472
    • Worsley Hunt, R.1    Mathelier, A.2    Del Peso, L.3    Wasserman, W.W.4
  • 22
    • 79956324593 scopus 로고    scopus 로고
    • Conserved, developmentally regulated mechanism couples chromosomal looping and heterochromatin barrier activity at the homeobox gene A locus
    • Kim YJ, Cecchini KR, Kim TH: Conserved, developmentally regulated mechanism couples chromosomal looping and heterochromatin barrier activity at the homeobox gene A locus. Proc Natl Acad Sci U S A 2011, 108:7391-7396.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 7391-7396
    • Kim, Y.J.1    Cecchini, K.R.2    Kim, T.H.3
  • 26
    • 84879643314 scopus 로고    scopus 로고
    • Cohesin and polycomb proteins functionally interact to control transcription at silenced and active genes
    • Schaaf CA, Misulovin Z, Gause M, Koenig A, Gohara DW, Watson A, Dorsett D: Cohesin and polycomb proteins functionally interact to control transcription at silenced and active genes. PLoS Genet 2013, 9:e1003560.
    • (2013) PLoS Genet , vol.9
    • Schaaf, C.A.1    Misulovin, Z.2    Gause, M.3    Koenig, A.4    Gohara, D.W.5    Watson, A.6    Dorsett, D.7
  • 29
    • 80052990473 scopus 로고    scopus 로고
    • Systematic bias in high-throughput sequencing data and its correction by BEADS
    • CheungMS, Down TA, Latorre I, Ahringer J: Systematic bias in high-throughput sequencing data and its correction by BEADS. Nucleic Acids Res 2011, 39:e103.
    • (2011) Nucleic Acids Res , vol.39
    • Cheung, M.S.1    Down, T.A.2    Latorre, I.3    Ahringer, J.4
  • 30
    • 84887478181 scopus 로고    scopus 로고
    • Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins
    • Teytelman L, Thurtle DM, Rine J, van Oudenaarden A: Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins. Proc Natl Acad Sci U S A 2013, 110:18602-18607.
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 18602-18607
    • Teytelman, L.1    Thurtle, D.M.2    Rine, J.3    van Oudenaarden, A.4
  • 36
    • 48249140621 scopus 로고    scopus 로고
    • FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology
    • Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, Jones SJ: FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 2008, 24:1729-1730.
    • (2008) Bioinformatics , vol.24 , pp. 1729-1730
    • Fejes, A.P.1    Robertson, G.2    Bilenky, M.3    Varhol, R.4    Bainbridge, M.5    Jones, S.J.6
  • 37
    • 84875608234 scopus 로고    scopus 로고
    • The UCSC genome browser and associated tools
    • Kuhn RM, Haussler D, Kent WJ: The UCSC genome browser and associated tools. Brief Bioinform 2013, 14:144-161.
    • (2013) Brief Bioinform , vol.14 , pp. 144-161
    • Kuhn, R.M.1    Haussler, D.2    Kent, W.J.3
  • 39
    • 0036677662 scopus 로고    scopus 로고
    • TFBS: Computational framework for transcription factor binding site analysis
    • Lenhard B, Wasserman WW: TFBS: Computational framework for transcription factor binding site analysis. Bioinformatics 2002, 18:1135-1136.
    • (2002) Bioinformatics , vol.18 , pp. 1135-1136
    • Lenhard, B.1    Wasserman, W.W.2
  • 40
    • 84863304598 scopus 로고    scopus 로고
    • 2141st edition. Vienna: R Foundation for Statistical Computing
    • R Core Team: R: A language and environment for statistical computing. 2141st edition. Vienna: R Foundation for Statistical Computing; 2014. http://www.R-project.org/.
    • (2014) R: A language and environment for statistical computing


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.