메뉴 건너뛰기




Volumn 5, Issue 2, 2011, Pages 117-123

A short survey of computational analysis methods in analysing ChIP-seq data

Author keywords

Bioinformatics; CHIP Seq analysis; Comparative analysis; Next generation sequencing

Indexed keywords

RNA POLYMERASE II; STAT1 PROTEIN;

EID: 79955838994     PISSN: 14739542     EISSN: 14797364     Source Type: Journal    
DOI: 10.1186/1479-7364-5-2-117     Document Type: Review
Times cited : (19)

References (20)
  • 1
    • 70449711243 scopus 로고    scopus 로고
    • Computation for ChIP-seq and RNA-seq studies
    • Pepke, S., Wold, B. and Mortazavi, A. (2009), 'Computation for ChIP-seq and RNA-seq studies' Nat. Methods Vol. 6 (11 Suppl.) pp. S22-S32.
    • (2009) Nat. Methods , vol.6 , Issue.11 SUPPL.
    • Pepke, S.1    Wold, B.2    Mortazavi, A.3
  • 2
    • 60149112271 scopus 로고    scopus 로고
    • PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
    • Rozowsky J., Euskirchen, G., Auerbach, R.K., Zhang, Z.D., Gibson, T. et al. (2009) 'PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls' Nat. Biotechnol. Vol. 27 pp. 66-75.
    • (2009) Nat. Biotechnol. , vol.27 , pp. 66-75
    • Rozowsky, J.1    Euskirchen, G.2    Auerbach, R.K.3    Zhang, Z.D.4    Gibson, T.5
  • 3
    • 64249139132 scopus 로고    scopus 로고
    • RNA pol II accumulates at promoters of growth genes during developmental arrest
    • Baugh L.R. Demodena J. and Sternberg P.W (2009) 'RNA Pol II accumulates at promoters of growth genes during developmental arrest' Science Vol. 324 pp. 92-94.
    • (2009) Science , vol.324 , pp. 92-94
    • Baugh, L.R.1    Demodena, J.2    Sternberg, P.W.3
  • 4
    • 57449100870 scopus 로고    scopus 로고
    • Design and analysis of ChIP-seq experiments for DNA-binding proteins
    • Kharchenko, PV, Tolstorukov, M.Y and Park, P.J. (2008), 'Design and analysis of ChIP-seq experiments for DNA-binding proteins' Nat. Biotechnol. Vol. 26 pp. 1351-1359.
    • (2008) Nat. Biotechnol. , vol.26 , pp. 1351-1359
    • Kharchenko, P.V.1    Tolstorukov, M.Y.2    Park, P.J.3
  • 6
    • 55749094855 scopus 로고    scopus 로고
    • An integrated software system for analyzing ChIP-chip and ChIP-seq data
    • Ji, H., Jiang, H., Ma, W., Johnson, D.S., Myers, R.M. and Wong, W.H. (2008), 'An integrated software system for analyzing ChIP-chip and ChIP-seq data', Nat. Biotechnol. Vol. 26, pp. 1293-1300.
    • (2008) Nat. Biotechnol. , vol.26 , pp. 1293-1300
    • Ji, H.1    Jiang, H.2    Ma, W.3    Johnson, D.S.4    Myers, R.M.5    Wong, W.H.6
  • 7
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y. and Hochberg, Y. (1995), 'Controlling the false discovery rate: A practical and powerful approach to multiple testing'. J. R. Stat. Soc. Ser. B Vol. 57, pp. 289-300.
    • (1995) J. R. Stat. Soc. Ser. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 8
    • 52649157765 scopus 로고    scopus 로고
    • Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
    • Dohm, J.C., Lottaz, C., Borodina, T. and Himmelbauer, H. (2008), 'Substantial biases in ultra-short read data sets from high-throughput DNA sequencing', Nucleic Acids Res. Vol. 36, p. e105.
    • (2008) Nucleic Acids Res. , vol.36
    • Dohm, J.C.1    Lottaz, C.2    Borodina, T.3    Himmelbauer, H.4
  • 9
    • 65349122997 scopus 로고    scopus 로고
    • Inherent signals in sequencing-based chromatin-immunoprecipitation control libraries
    • Vega, V.B., Cheung, E., Palanisamy, N. and Sung, W.K. (2009), 'Inherent signals in sequencing-based Chromatin-ImmunoPrecipitation control libraries', PLoS One, Vol. 4, p. e5241.
    • (2009) PLoS One , vol.4
    • Vega, V.B.1    Cheung, E.2    Palanisamy, N.3    Sung, W.K.4
  • 11
    • 54949147307 scopus 로고    scopus 로고
    • F-seq: A feature density estimator for high-throughput sequence tags
    • Boyle, A.P., Guinney, J., Crawford, G.E. and Furey, T.S. (2008), 'F-Seq: A feature density estimator for high-throughput sequence tags', Bioinformatics Vol. 24, pp. 2537-2538.
    • (2008) Bioinformatics , vol.24 , pp. 2537-2538
    • Boyle, A.P.1    Guinney, J.2    Crawford, G.E.3    Furey, T.S.4
  • 12
    • 50849090969 scopus 로고    scopus 로고
    • Genome-wide analysis of transcription factor binding sites based on ChIP-seq data
    • Valouev, A., Johnson, D.S., Sundquist, A., Medina, C., Anton, E. et al. (2008), 'Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data', Nat. Methods Vol. 5, pp. 829-834.
    • (2008) Nat. Methods , vol.5 , pp. 829-834
    • Valouev, A.1    Johnson, D.S.2    Sundquist, A.3    Medina, C.4    Anton, E.5
  • 13
    • 77952857912 scopus 로고    scopus 로고
    • A signalnoise model for significance analysis of ChIP-seq with negative control
    • Xu, H., Handoko, L., Wei, X., Ye, C., Sheng, J. et al. (2010), 'A signalnoise model for significance analysis of ChIP-seq with negative control', Bioinformatics Vol. 26, pp. 1199-1204.
    • (2010) Bioinformatics , vol.26 , pp. 1199-1204
    • Xu, H.1    Handoko, L.2    Wei, X.3    Ye, C.4    Sheng, J.5
  • 14
    • 52649132425 scopus 로고    scopus 로고
    • Genome-wide identification of in vivo protein-DNA binding sites from ChIP-seq data
    • Jothi, R., Cuddapah, S., Barski, A., Cui, K. and Zhao, K. (2008), 'Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data', Nucleic Acids Res. Vol. 36, pp. 5221-5231.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 5221-5231
    • Jothi, R.1    Cuddapah, S.2    Barski, A.3    Cui, K.4    Zhao, K.5
  • 15
    • 67650711619 scopus 로고    scopus 로고
    • A clustering approach for identification of enriched domains from histone modification ChIP-seq data
    • Zang, C., Schones, D.E., Zeng, C., Cui, K., Zhao, K. et al. (2009), 'A clustering approach for identification of enriched domains from histone modification ChIP-Seq data', Bioinformatics Vol. 25, pp. 1952-1958.
    • (2009) Bioinformatics , vol.25 , pp. 1952-1958
    • Zang, C.1    Schones, D.E.2    Zeng, C.3    Cui, K.4    Zhao, K.5
  • 16
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein-DNA interactions
    • DOI 10.1126/science.1141319
    • Johnson, D.S., Mortazavi, A., Myers, R.M. and Wold, B. (2007), 'Genome-wide mapping of in vivo protein-DNA interactions', Science Vol. 316, pp. 1497-1502. (Pubitemid 46906620)
    • (2007) Science , vol.316 , Issue.5830 , pp. 1497-1502
    • Johnson, D.S.1    Mortazavi, A.2    Myers, R.M.3    Wold, B.4
  • 17
    • 60849117520 scopus 로고    scopus 로고
    • Empirical methods for controlling false positives and estimating confidence in ChIP-seq peaks
    • Nix, D.A., Courdy, S.J. and Boucher, K.M. (2008), 'Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks', BMC Bioinformatics Vol. 9, p. 523.
    • (2008) BMC Bioinformatics , vol.9 , pp. 523
    • Nix, D.A.1    Courdy, S.J.2    Boucher, K.M.3
  • 18
    • 53749092745 scopus 로고    scopus 로고
    • An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data
    • Xu, H., Wei, C.L., Lin, F. and Sung, W.K. (2008), 'An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data', Bioinformatics Vol. 24, pp. 2344-2349.
    • (2008) Bioinformatics , vol.24 , pp. 2344-2349
    • Xu, H.1    Wei, C.L.2    Lin, F.3    Sung, W.K.4
  • 19
    • 55549118625 scopus 로고    scopus 로고
    • ChromaSig: A probabilistic approach to finding common chromatin signatures in the human genome
    • Hon, G., Ren, B. and Wang, W. (2008), 'ChromaSig: A probabilistic approach to finding common chromatin signatures in the human genome'. PLoS Comput. Biol. Vol. 4, p. e1000201.
    • (2008) PLoS Comput. Biol. , vol.4
    • Hon, G.1    Ren, B.2    Wang, W.3
  • 20
    • 3543023310 scopus 로고    scopus 로고
    • Evidence for nucleosome depletion at active regulatory regions genome-wide
    • DOI 10.1038/ng1400
    • Lee, C.K., Shibata, Y., Rao, B., Strahl, B.D. and Lieb, J.D. (2004), 'Evidence for nucleosome depletion at active regulatory regions genomewide', Nat. Genet. Vol. 36, pp. 900-905. (Pubitemid 39014111)
    • (2004) Nature Genetics , vol.36 , Issue.8 , pp. 900-905
    • Lee, C.-K.1    Shibata, Y.2    Rao, B.3    Strahl, B.D.4    Lieb, J.D.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.