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Volumn 31, Issue 12, 2015, Pages 1889-1896

A novel statistical method for quantitative comparison of multiple ChIP-seq datasets

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE; PROTEIN BINDING; TRANSCRIPTION FACTOR;

EID: 84931078005     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv094     Document Type: Article
Times cited : (39)

References (21)
  • 1
    • 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 (Methodological), 57, 289-300
    • (1995) J. R. Stat. Soc. Ser. B (Methodological , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 2
    • 67649292737 scopus 로고    scopus 로고
    • Unlocking the secrets of the genome
    • Celniker, S.E. et al. (2009) Unlocking the secrets of the genome. Nature, 459, 927-930
    • (2009) Nature , vol.459 , pp. 927-930
    • Celniker, S.E.1
  • 3
    • 44649117905 scopus 로고    scopus 로고
    • Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
    • Chen, X. et al. (2008) Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell, 133, 1106-1117
    • (2008) Cell , vol.133 , pp. 1106-1117
    • Chen, X.1
  • 4
    • 2142732441 scopus 로고    scopus 로고
    • Large-scale simultaneous hypothesis testing
    • Efron, B. (2004) Large-scale simultaneous hypothesis testing. J. Am. Stat. Assoc., 99, 96-104
    • (2004) J. Am. Stat. Assoc , vol.99 , pp. 96-104
    • Efron, B.1
  • 5
    • 84899843749 scopus 로고    scopus 로고
    • A bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data
    • Feng, H., Conneely, K.N. and Wu, H. (2014) A bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data. Nucleic Acids Res., 42, e69
    • (2014) Nucleic Acids Res , Issue.42 , pp. e69
    • Feng, H.1    Conneely, K.N.2    Wu, H.3
  • 6
    • 28744458859 scopus 로고    scopus 로고
    • Bioconductor: Open software development for computational biology and bioinformatics
    • Gentleman, R.C. et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5, R80
    • (2004) Genome Biol , vol.5 , pp. R80
    • Gentleman, R.C.1
  • 7
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein-DNA interactions
    • Johnson, D. et al. (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science, 316, 1497
    • (2007) Science , vol.316 , pp. 1497
    • Johnson, D.1
  • 8
    • 74549114755 scopus 로고    scopus 로고
    • A practical comparison of methods for detecting transcription factor binding sites in chip-seq experiments
    • Laajala, T.D. et al. (2009) A practical comparison of methods for detecting transcription factor binding sites in chip-seq experiments. BMC Genomics, 10, 618
    • (2009) BMC Genomics , vol.10 , pp. 618
    • Laajala, T.D.1
  • 9
    • 84896735766 scopus 로고    scopus 로고
    • Voom: Precision weights unlock linear model analysis tools for RNA-seq read counts
    • Law, C.W. et al. (2013) Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol 2014, 15, R29
    • (2013) Genome Biol , vol.2014 , Issue.15 , pp. R29
    • Law, C.W.1
  • 10
    • 84855177111 scopus 로고    scopus 로고
    • Detecting differential binding of transcription factors with chip-seq
    • Liang, K. and Keles-, S. (2012) Detecting differential binding of transcription factors with chip-seq. Bioinformatics, 28, 121-122
    • (2012) Bioinformatics , Issue.28 , pp. 121-122
    • Liang, K.1    Keles-, S.2
  • 11
    • 84864545388 scopus 로고    scopus 로고
    • Chipnorm: A statistical method for normalizing and identifying differential regions in histone modification chip-seq libraries
    • Nair, N.U. et al. (2012) Chipnorm: a statistical method for normalizing and identifying differential regions in histone modification chip-seq libraries. PLoS one, 7, e39573
    • (2012) PLoS One , Issue.7 , pp. e39573
    • Nair, N.U.1
  • 12
    • 84862799740 scopus 로고    scopus 로고
    • Manorm: A robust model for quantitative comparison of chip-seq data sets
    • Shao, Z. et al. (2012) Manorm: a robust model for quantitative comparison of chip-seq data sets. Genome Biol., 13, R16
    • (2012) Genome Biol , Issue.13 , pp. R16
    • Shao, Z.1
  • 13
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
    • Article 3
    • Smyth, G.K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, 3, Article 3
    • (2004) Statistical Applications in Genetics and Molecular Biology , vol.3
    • Smyth, G.K.1
  • 15
    • 69849103628 scopus 로고    scopus 로고
    • Comparative study on chip-seq data: Normalization and binding pattern characterization
    • Taslim, C. et al. (2009) Comparative study on chip-seq data: normalization and binding pattern characterization. Bioinformatics, 25, 2334-2340
    • (2009) Bioinformatics , vol.25 , pp. 2334-2340
    • Taslim, C.1
  • 16
    • 79957869355 scopus 로고    scopus 로고
    • Dime: R-package for identifying differential chip-seq based on an ensemble of mixture models
    • Taslim, C., Huang, T. and Lin, S. (2011) Dime: R-package for identifying differential chip-seq based on an ensemble of mixture models. Bioinformatics, 27, 1569-1570
    • (2011) Bioinformatics , Issue.27 , pp. 1569-1570
    • Taslim, C.1    Huang, T.2    Lin, S.3
  • 17
    • 33846072868 scopus 로고    scopus 로고
    • The encode project at uc santa cruz
    • Thomas, D. et al. (2006) The encode project at uc santa cruz. Nucleic Acids Res., 35, D663
    • (2006) Nucleic Acids Res , vol.35 , pp. D663
    • Thomas, D.1
  • 18
    • 77955368935 scopus 로고    scopus 로고
    • Evaluation of algorithm performance in chip-seq peak detection
    • Wilbanks, E.G. and Facciotti, M.T. (2010) Evaluation of algorithm performance in chip-seq peak detection. PLoS One, 5, e11471
    • (2010) PLoS One , Issue.5 , pp. e11471
    • Wilbanks, E.G.1    Facciotti, M.T.2
  • 19
    • 84874912212 scopus 로고    scopus 로고
    • A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data
    • Wu, H., Wang, C. and Wu, Z. (2013) A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data. Biostatistics, 14, 232-243
    • (2013) Biostatistics , Issue.14 , pp. 232-243
    • Wu, H.1    Wang, C.2    Wu, Z.3
  • 20
    • 53749092745 scopus 로고    scopus 로고
    • An hmm approach to genome-wide identification of differential histone modification sites from chip-seq data
    • Xu, H. et al. (2008). An hmm approach to genome-wide identification of differential histone modification sites from chip-seq data. Bioinformatics, 24, 2344-2349
    • (2008) Bioinformatics , vol.24 , pp. 2344-2349
    • Xu, H.1
  • 21
    • 53849146020 scopus 로고    scopus 로고
    • Model-based analysis of chip-seq (macs)
    • Zhang, Y. et al. (2008) Model-based analysis of chip-seq (macs). Genome Biol., 9, R137
    • (2008) Genome Biol , vol.9 , pp. R137
    • Zhang, Y.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.