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Volumn 7, Issue 1, 2012, Pages 45-61

A computational pipeline for comparative ChIP-seq analyses

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EID: 84861133568     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2011.420     Document Type: Article
Times cited : (86)

References (48)
  • 2
    • 0035945567 scopus 로고    scopus 로고
    • Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
    • DOI 10.1038/35054095
    • Iyer, V.R. et al. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409, 533-538 (2001). (Pubitemid 32144361)
    • (2001) Nature , vol.409 , Issue.6819 , pp. 533-538
    • Iyer, V.R.1    Horak, C.E.2    Scafe, C.S.3    Botstein, D.4    Snyder, M.5    Brown, P.O.6
  • 3
    • 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. & Wold, B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497-1502 (2007). (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
  • 5
    • 33847271755 scopus 로고    scopus 로고
    • A core transcriptional network for early mesoderm development in Drosophila melanogaster
    • Sandmann, T. et al. A core transcriptional network for early mesoderm development in Drosophila melanogaster. Genes Dev. 21, 436-449 (2007).
    • (2007) Genes Dev. , vol.21 , pp. 436-449
    • Sandmann, T.1
  • 6
    • 70449132583 scopus 로고    scopus 로고
    • Combinatorial binding predicts spatio-temporal cis-regulatory activity
    • Zinzen, R.P., Girardot, C., Gagneur, J., Braun, M. & Furlong, E.E.M. Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature 462, 65-70 (2009).
    • (2009) Nature , vol.462 , pp. 65-70
    • Zinzen, R.P.1    Girardot, C.2    Gagneur, J.3    Braun, M.4    Furlong, E.E.M.5
  • 7
    • 77953763449 scopus 로고    scopus 로고
    • A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate
    • Lin, Y.C. et al. A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nat. Immunol. 11, 635-643 (2010).
    • (2010) Nat. Immunol. , vol.11 , pp. 635-643
    • Lin, Y.C.1
  • 8
    • 79551605803 scopus 로고    scopus 로고
    • Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages
    • Palii, C.G. et al. Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages. EMBO J. 30, 494-509 (2011).
    • (2011) EMBO J. , vol.30 , pp. 494-509
    • Palii, C.G.1
  • 9
    • 79955471381 scopus 로고    scopus 로고
    • High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species
    • He, Q. et al. High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species. Nat. Genet. 43, 414-420 (2011).
    • (2011) Nat. Genet. , vol.43 , pp. 414-420
    • He, Q.1
  • 10
    • 77953062527 scopus 로고    scopus 로고
    • Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding
    • Schmidt, D. et al. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 328, 1036-1040 (2010).
    • (2010) Science , vol.328 , pp. 1036-1040
    • Schmidt, D.1
  • 11
    • 77950566643 scopus 로고    scopus 로고
    • Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species
    • Bradley, R.K. et al. Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PLoS Biol. 8, e1000343 (2010).
    • (2010) PLoS Biol. , vol.8
    • Bradley, R.K.1
  • 12
    • 77954100084 scopus 로고    scopus 로고
    • Transposable elements have rewired the core regulatory network of human embryonic stem cells
    • Kunarso, G. et al. Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat. Genet. 42, 631-634 (2010).
    • (2010) Nat. Genet. , vol.42 , pp. 631-634
    • Kunarso, G.1
  • 13
    • 77957220857 scopus 로고    scopus 로고
    • Comparative epigenomic analysis of murine and human adipogenesis
    • Mikkelsen, T.S. et al. Comparative epigenomic analysis of murine and human adipogenesis. Cell 143, 156-169 (2010).
    • (2010) Cell , vol.143 , pp. 156-169
    • Mikkelsen, T.S.1
  • 14
    • 53849146020 scopus 로고    scopus 로고
    • Model-based analysis of ChIP-Seq (MACS)
    • Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
    • (2008) Genome Biol. , vol.9
    • Zhang, Y.1
  • 15
    • 77955368935 scopus 로고    scopus 로고
    • Evaluation of algorithm performance in ChIP-seq peak detection
    • Wilbanks, E.G. & Facciotti, M.T. Evaluation of algorithm performance in ChIP-seq peak detection. PLoS ONE 5, e11471 (2010).
    • (2010) PLoS ONE , vol.5
    • Wilbanks, E.G.1    Facciotti, M.T.2
  • 16
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Series B (Methodological) 57, 289-300 (1995).
    • (1995) J. R. Stat. Soc. Series B (Methodological) , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 17
    • 71849096141 scopus 로고    scopus 로고
    • How does multiple testing correction work?
    • Noble, W.S. How does multiple testing correction work? Nat. Biotechnol. 27, 1135-1137 (2009).
    • (2009) Nat. Biotechnol. , vol.27 , pp. 1135-1137
    • Noble, W.S.1
  • 18
    • 0037312921 scopus 로고    scopus 로고
    • Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease
    • DOI 10.1038/ng1071
    • Lohmueller, K.E., Pearce, C.L., Pike, M., Lander, E.S. & Hirschhorn, J.N. Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat. Genet. 33, 177-182 (2003). (Pubitemid 36177070)
    • (2003) Nature Genetics , vol.33 , Issue.2 , pp. 177-182
    • Lohmueller, K.E.1    Pearce, C.L.2    Pike, M.3    Lander, E.S.4    Hirschhorn, J.N.5
  • 19
    • 0034651005 scopus 로고    scopus 로고
    • The specifcity of protein-DNA crosslinking by formaldehyde: In vitro and in Drosophila embryos
    • Toth, J. & Biggin, M.D. The specifcity of protein-DNA crosslinking by formaldehyde: in vitro and in Drosophila embryos. Nucleic Acids Res. 28, e4 (2000).
    • (2000) Nucleic Acids Res. , vol.28
    • Toth, J.1    Biggin, M.D.2
  • 21
    • 14844341770 scopus 로고    scopus 로고
    • Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb
    • DOI 10.1242/dev.01613
    • Sagai, T., Hosoya, M., Mizushina, Y., Tamura, M. & Shiroishi, T. Elimination of a long-range cis-regulatory module causes complete loss of limb-specifc Shh expression and truncation of the mouse limb. Development 132, 797-803 (2005). (Pubitemid 40352838)
    • (2005) Development , vol.132 , Issue.4 , pp. 797-803
    • Sagai, T.1    Hosoya, M.2    Mizushina, Y.3    Tamura, M.4    Shiroishi, T.5
  • 22
    • 51149097760 scopus 로고    scopus 로고
    • Shadow enhancers as a source of evolutionary novelty
    • Hong, J.-W., Hendrix, D.A. & Levine, M.S. Shadow enhancers as a source of evolutionary novelty. Science 321, 1314 (2008).
    • (2008) Science , vol.321 , pp. 1314
    • Hong, J.-W.1    Hendrix, D.A.2    Levine, M.S.3
  • 23
    • 76749089660 scopus 로고    scopus 로고
    • A comprehensive map of insulator elements for the Drosophila genome
    • Nègre, N. et al. A comprehensive map of insulator elements for the Drosophila genome. PLoS Genet. 6, e1000814 (2010).
    • (2010) PLoS Genet. , vol.6
    • Nègre, N.1
  • 24
    • 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. et al. 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).
    • (2009) Genome Res. , vol.19 , pp. 24-32
    • Cuddapah, S.1
  • 25
    • 33645224575 scopus 로고    scopus 로고
    • GONOME: Measuring correlations between GO terms and genomic positions
    • Stanley, S.M., Bailey, T.L. & Mattick, J.S. GONOME: measuring correlations between GO terms and genomic positions. BMC Bioinformatics 7, 94 (2006).
    • (2006) BMC Bioinformatics , vol.7 , pp. 94
    • Stanley, S.M.1    Bailey, T.L.2    Mattick, J.S.3
  • 26
    • 76949094155 scopus 로고    scopus 로고
    • Developmental gene regulation in the era of genomics
    • Zeitlinger, J. & Stark, A. Developmental gene regulation in the era of genomics. Dev. Biol. 339, 230-239 (2010).
    • (2010) Dev. Biol. , vol.339 , pp. 230-239
    • Zeitlinger, J.1    Stark, A.2
  • 28
    • 77951610155 scopus 로고    scopus 로고
    • Genetic analysis of variation in transcription factor binding in yeast
    • Zheng, W., Zhao, H., Mancera, E., Steinmetz, L.M. & Snyder, M. Genetic analysis of variation in transcription factor binding in yeast. Nature 464, 1187-1191 (2010).
    • (2010) Nature , vol.464 , pp. 1187-1191
    • Zheng, W.1    Zhao, H.2    Mancera, E.3    Steinmetz, L.M.4    Snyder, M.5
  • 29
    • 71749103442 scopus 로고    scopus 로고
    • Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information
    • Meireles-Filho, A.C.A. & Stark, A. Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information. Curr. Opin. Genet. Dev. 19, 565-570 (2009).
    • (2009) Curr. Opin. Genet. Dev. , vol.19 , pp. 565-570
    • Meireles-Filho, A.C.A.1    Stark, A.2
  • 30
    • 77649225979 scopus 로고    scopus 로고
    • Genome-wide identifcation of binding sites defnes distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response
    • Zhong, M. et al. Genome-wide identifcation of binding sites defnes distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genet. 6, e1000848 (2010).
    • (2010) PLoS Genet. , vol.6
    • Zhong, M.1
  • 31
    • 33646510364 scopus 로고    scopus 로고
    • Genome-wide analysis of protein-DNA interactions
    • DOI 10.1146/annurev.genom.7.080505.115634
    • Kim, T.H. & Ren, B. Genome-wide analysis of protein-DNA interactions. Annu. Rev. Genomics Hum. Genet. 7, 81-102 (2006). (Pubitemid 44627923)
    • (2006) Annual Review of Genomics and Human Genetics , vol.7 , pp. 81-102
    • Kim, T.H.1    Ren, B.2
  • 32
    • 0037722938 scopus 로고    scopus 로고
    • Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling
    • DOI 10.1016/S0092-8674(03)00301-5
    • Zeitlinger, J. et al. Program-specifc distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. Cell 113, 395-404 (2003). (Pubitemid 36556120)
    • (2003) Cell , vol.113 , Issue.3 , pp. 395-404
    • Zeitlinger, J.1    Simon, I.2    Harbison, C.T.3    Hannett, N.M.4    Volkert, T.L.5    Fink, G.R.6    Young, R.A.7
  • 35
    • 0347125328 scopus 로고    scopus 로고
    • JASPAR: An open-access database for eukaryotic transcription factor binding profiles
    • Sandelin, A., Alkema, W., Engström, P., Wasserman, W.W. & Lenhard, B. JASPAR: an open-access database for eukaryotic transcription factor binding profles. Nucleic Acids Res. 32, D91-D94 (2004). (Pubitemid 38081611)
    • (2004) Nucleic Acids Research , vol.32 , Issue.DATABASE ISS.
    • Sandelin, A.1    Alkema, W.2    Engstrom, P.3    Wasserman, W.W.4    Lenhard, B.5
  • 37
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-effcient alignment of short DNA sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-effcient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
    • (2009) Genome Biol. , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 38
    • 77950941484 scopus 로고    scopus 로고
    • Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing
    • Horner, D.S. et al. Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Brief. Bioinformatics 11, 181-197 (2010).
    • (2010) Brief. Bioinformatics , vol.11 , pp. 181-197
    • Horner, D.S.1
  • 39
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/Map format and SAMtools
    • Li, H. et al. The sequence alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 40
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A fexible suite of utilities for comparing genomic features
    • Quinlan, A.R. & Hall, I.M. BEDTools: a fexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 41
    • 0036079158 scopus 로고    scopus 로고
    • The human genome browser at UCSC
    • Kent, W.J. et al. The human genome browser at UCSC. Genome Res. 12, 996-1006 (2002).
    • (2002) Genome Res. , vol.12 , pp. 996-1006
    • Kent, W.J.1
  • 42
    • 33747823564 scopus 로고    scopus 로고
    • MEME: Discovering and analyzing DNA and protein sequence motifs
    • DOI 10.1093/nar/gkl198
    • Bailey, T.L., Williams, N., Misleh, C. & Li, W.W. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 34, W369-W373 (2006). (Pubitemid 44529795)
    • (2006) Nucleic Acids Research , vol.34 , Issue.WEB. SERV. ISS.
    • Bailey, T.L.1    Williams, N.2    Misleh, C.3    Li, W.W.4
  • 43
    • 0031877016 scopus 로고    scopus 로고
    • Combining evidence using p-values: Application to sequence homology searches
    • Bailey, T.L. & Gribskov, M. Combining evidence using P-values: application to sequence homology searches. Bioinformatics 14, 48-54 (1998). (Pubitemid 28395676)
    • (1998) Bioinformatics , vol.14 , Issue.1 , pp. 48-54
    • Bailey, T.L.1    Gribskov, M.2
  • 44
    • 38549144819 scopus 로고    scopus 로고
    • A survey of DNA motif fnding algorithms
    • Das, M.K. & Dai, H.-K. A survey of DNA motif fnding algorithms. BMC Bioinformatics 8 (Suppl. 7): S21 (2007).
    • (2007) BMC Bioinformatics , vol.8 S21 , Issue.SUPPL. 7
    • Das, M.K.1    Dai, H.-K.2
  • 46
    • 70349267600 scopus 로고    scopus 로고
    • Mapping accessible chromatin regions using Sono-Seq
    • Auerbach, R.K. et al. Mapping accessible chromatin regions using Sono-Seq. Proc. Natl. Acad. Sci. USA 106, 14926-14931 (2009).
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 14926-14931
    • Auerbach, R.K.1
  • 47
    • 69249087790 scopus 로고    scopus 로고
    • Impact of chromatin structures on DNA processing for genomic analyses
    • Teytelman, L. et al. Impact of chromatin structures on DNA processing for genomic analyses. PLoS ONE 4, e6700 (2009).
    • (2009) PLoS ONE , vol.4
    • Teytelman, L.1
  • 48
    • 79951694175 scopus 로고    scopus 로고
    • Analyzing and minimizing PCR amplifcation bias in Illumina sequencing libraries
    • Aird, D. et al. Analyzing and minimizing PCR amplifcation bias in Illumina sequencing libraries. Genome Biol. 12, R18 (2011).
    • (2011) Genome Biol. , vol.12
    • Aird, D.1


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