메뉴 건너뛰기




Volumn 4, Issue , 2016, Pages

From reads to regions: A Bioconductor workflow to detect differential binding in ChIP-seq data

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE; TRANSCRIPTION FACTOR;

EID: 84969611139     PISSN: 20461402     EISSN: 1759796X     Source Type: Journal    
DOI: 10.12688/f1000research.7016.2     Document Type: Article
Times cited : (18)

References (28)
  • 1
    • 8844271685 scopus 로고    scopus 로고
    • Faster cyclic loess: normalizing RNA arrays via linear models
    • 15166021
    • Ballman KV Grill DE Oberg AL : Faster cyclic loess: normalizing RNA arrays via linear models. Bioinformatics. 2004;20(16):2778-2786. 15166021 10.1093/bioinformatics/bth327
    • (2004) Bioinformatics , vol.20 , Issue.16 , pp. 2778-2786
    • Ballman, K.V.1    Grill, D.E.2    Oberg, A.L.3
  • 2
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Reference Source
    • Benjamini Y Hochberg Y : Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Royal Stat Soc B. 1995;57(1):289-300. Reference Source
    • (1995) J Royal Stat Soc B , vol.57 , Issue.1 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 3
    • 0036081355 scopus 로고    scopus 로고
    • Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    • 11752295, 99122
    • Edgar R Domrachev M Lash AE : Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002;30(1):207-210. 11752295 10.1093/nar/30.1.207 99122
    • (2002) Nucleic Acids Res , vol.30 , Issue.1 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 4
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium, 22955616, 3439153
    • ENCODE Project Consortium: An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57-74. 22955616 10.1038/nature11247 3439153
    • (2012) Nature , vol.489 , Issue.7414 , pp. 57-74
  • 5
    • 0036143404 scopus 로고    scopus 로고
    • Changes in gene expression profiles in developing B cells of murine bone marrow
    • 11779835, 155249
    • Hoffmann R Seidl T Neeb M : Changes in gene expression profiles in developing B cells of murine bone marrow. Genome Res. 2002;12(1):98-111. 11779835 10.1101/gr.201501 155249
    • (2002) Genome Res , vol.12 , Issue.1 , pp. 98-111
    • Hoffmann, R.1    Seidl, T.2    Neeb, M.3
  • 6
    • 84961289551 scopus 로고    scopus 로고
    • Orchestrating high-throughput genomic analysis with Bioconductor
    • 25633503, 4509590
    • Huber W Carey VJ Gentleman R : Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods. 2015;12(2):115-121. 25633503 10.1038/nmeth.3252 4509590
    • (2015) Nat Methods , vol.12 , Issue.2 , pp. 115-121
    • Huber, W.1    Carey, V.J.2    Gentleman, R.3
  • 7
    • 84874758781 scopus 로고    scopus 로고
    • ChIPseqR: analysis of ChIP-seq experiments
    • 21281468, 3045301
    • Humburg P Helliwell CA Bulger D : ChIPseqR: analysis of ChIP-seq experiments. BMC Bioinformatics. 2011;12:39. 21281468 10.1186/1471-2105-12-39 3045301
    • (2011) BMC Bioinformatics , vol.12 , pp. 39
    • Humburg, P.1    Helliwell, C.A.2    Bulger, D.3
  • 8
    • 84865280797 scopus 로고    scopus 로고
    • H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells
    • 22920947, 3473242
    • Karmodiya K Krebs AR Oulad-Abdelghani M : H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells. BMC Genomics. 2012;13:424. 22920947 10.1186/1471-2164-13-424 3473242
    • (2012) BMC Genomics , vol.13 , pp. 424
    • Karmodiya, K.1    Krebs, A.R.2    Oulad-Abdelghani, M.3
  • 9
    • 84922363112 scopus 로고    scopus 로고
    • Genome-wide and single-cell analyses reveal a context dependent relationship between CBP recruitment and gene expression
    • 25249627, 4191404
    • Kasper LH Qu C Obenauer JC : Genome-wide and single-cell analyses reveal a context dependent relationship between CBP recruitment and gene expression. Nucleic Acids Res. 2014;42(18):11363-11382. 25249627 10.1093/nar/gku827 4191404
    • (2014) Nucleic Acids Res , vol.42 , Issue.18 , pp. 11363-11382
    • Kasper, L.H.1    Qu, C.2    Obenauer, J.C.3
  • 10
    • 57449100870 scopus 로고    scopus 로고
    • Design and analysis of ChIP-seq experiments for DNA-binding proteins
    • 19029915, 2597701
    • Kharchenko PV Tolstorukov MY Park PJ : Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol. 2008;26(12):1351-1359. 19029915 10.1038/nbt.1508 2597701
    • (2008) Nat Biotechnol , vol.26 , Issue.12 , pp. 1351-1359
    • Kharchenko, P.V.1    Tolstorukov, M.Y.2    Park, P.J.3
  • 11
    • 84865777819 scopus 로고    scopus 로고
    • ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
    • 22955991, 3431496
    • Landt SG Marinov GK Kundaje A : ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012;22(9):1813-1831. 22955991 10.1101/gr.136184.111 3431496
    • (2012) Genome Res , vol.22 , Issue.9 , pp. 1813-1831
    • Landt, S.G.1    Marinov, G.K.2    Kundaje, A.3
  • 12
    • 67649837030 scopus 로고    scopus 로고
    • rtracklayer: an R package for interfacing with genome browsers
    • 19468054, 2705236
    • Lawrence M Gentleman R Carey V : rtracklayer: an R package for interfacing with genome browsers. Bioinformatics. 2009;25(14):1841-1842. 19468054 10.1093/bioinformatics/btp328 2705236
    • (2009) Bioinformatics , vol.25 , Issue.14 , pp. 1841-1842
    • Lawrence, M.1    Gentleman, R.2    Carey, V.3
  • 13
    • 84855177111 scopus 로고    scopus 로고
    • Detecting differential binding of transcription factors with ChIP-seq
    • 22057161, 3244766
    • Liang K Keles S : Detecting differential binding of transcription factors with ChIP-seq. Bioinformatics. 2012;28(1):121-122. 22057161 10.1093/bioinformatics/btr605 3244766
    • (2012) Bioinformatics , vol.28 , Issue.1 , pp. 121-122
    • Liang, K.1    Keles, S.2
  • 14
    • 84878580738 scopus 로고    scopus 로고
    • The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote
    • 23558742, 3664803
    • Liao Y Smyth GK Shi W : The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res. 2013;41(10):e108. 23558742 10.1093/nar/gkt214 3664803
    • (2013) Nucleic Acids Res , vol.41 , Issue.10 , pp. e108
    • Liao, Y.1    Smyth, G.K.2    Shi, W.3
  • 15
    • 84903210850 scopus 로고    scopus 로고
    • De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly
    • 24852250, 4066778
    • Lun AT Smyth GK : De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly. Nucleic Acids Res. 2014;42(11):e95. 24852250 10.1093/nar/gku351 4066778
    • (2014) Nucleic Acids Res , vol.42 , Issue.11 , pp. e95
    • Lun, A.T.1    Smyth, G.K.2
  • 16
    • 84963820955 scopus 로고    scopus 로고
    • csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows
    • 26578583, ; pii: gkv1191.
    • Lun AT Smyth GK : csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows. Nucleic Acids Res. 2015; pii: gkv1191. 26578583 10.1093/nar/gkv1191
    • (2015) Nucleic Acids Res
    • Lun, A.T.1    Smyth, G.K.2
  • 17
    • 84879198972 scopus 로고    scopus 로고
    • Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates
    • 23104842
    • Lund SP Nettleton D McCarthy DJ : Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates. Stat Appl Genet Mol Biol. 2012;11(5):1544-6115. 23104842 10.1515/1544-6115.1826
    • (2012) Stat Appl Genet Mol Biol , vol.11 , Issue.5 , pp. 1544-6115
    • Lund, S.P.1    Nettleton, D.2    McCarthy, D.J.3
  • 18
    • 84858041341 scopus 로고    scopus 로고
    • Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation
    • 22287627, 3378882
    • McCarthy DJ Chen Y Smyth GK : Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res. 2012;40(10):4288-4297. 22287627 10.1093/nar/gks042 3378882
    • (2012) Nucleic Acids Res , vol.40 , Issue.10 , pp. 4288-4297
    • McCarthy, D.J.1    Chen, Y.2    Smyth, G.K.3
  • 19
    • 84874231902 scopus 로고    scopus 로고
    • Global changes in the mammary epigenome are induced by hormonal cues and coordinated by Ezh2
    • 23375371
    • Pal B Bouras T Shi W : Global changes in the mammary epigenome are induced by hormonal cues and coordinated by Ezh2. Cell Rep. 2013;3(2):411-426. 23375371 10.1016/j.celrep.2012.12.020
    • (2013) Cell Rep , vol.3 , Issue.2 , pp. 411-426
    • Pal, B.1    Bouras, T.2    Shi, W.3
  • 20
    • 0037546954 scopus 로고    scopus 로고
    • Selective regulation of mature IgG1 transcription by CD86 and beta 2-adrenergic receptor stimulation
    • 12734361
    • Podojil JR Sanders VM : Selective regulation of mature IgG1 transcription by CD86 and beta 2-adrenergic receptor stimulation. J Immunol. 2003;170(10):5143-5151. 12734361 10.4049/jimmunol.170.10.5143
    • (2003) J Immunol , vol.170 , Issue.10 , pp. 5143-5151
    • Podojil, J.R.1    Sanders, V.M.2
  • 21
    • 84864147148 scopus 로고    scopus 로고
    • The B-cell identity factor Pax5 regulates distinct transcriptional programmes in early and late B lymphopoiesis
    • 22669466, 3400013
    • Revilla-I-Domingo R Bilic I Vilagos B : The B-cell identity factor Pax5 regulates distinct transcriptional programmes in early and late B lymphopoiesis. EMBO J. 2012;31(14):3130-3146. 22669466 10.1038/emboj.2012.155 3400013
    • (2012) EMBO J , vol.31 , Issue.14 , pp. 3130-3146
    • Revilla-I-Domingo, R.1    Bilic, I.2    Vilagos, B.3
  • 22
    • 75249087100 scopus 로고    scopus 로고
    • edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    • 19910308, 2796818
    • Robinson MD McCarthy DJ Smyth GK : edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139-140. 19910308 10.1093/bioinformatics/btp616 2796818
    • (2010) Bioinformatics , vol.26 , Issue.1 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 23
    • 77953176036 scopus 로고    scopus 로고
    • A scaling normalization method for differential expression analysis of RNA-seq data
    • 20196867, 2864565
    • Robinson MD Oshlack A : A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010;11(3):R25. 20196867 10.1186/gb-2010-11-3-r25 2864565
    • (2010) Genome Biol , vol.11 , Issue.3 , pp. R25
    • Robinson, M.D.1    Oshlack, A.2
  • 24
    • 84946100079 scopus 로고    scopus 로고
    • The UCSC Genome Browser database: 2015 update
    • 25428374, 4383971
    • Rosenbloom KR Armstrong J Barber GP : The UCSC Genome Browser database: 2015 update. Nucleic Acids Res. 2015;43(Database issue):D670-681. 25428374 10.1093/nar/gku1177 4383971
    • (2015) Nucleic Acids Res , vol.43 , Issue.DATABASE ISSUE , pp. D670-681
    • Rosenbloom, K.R.1    Armstrong, J.2    Barber, G.P.3
  • 25
    • 84856008906 scopus 로고    scopus 로고
    • Differential oestrogen receptor binding is associated with clinical outcome in breast cancer
    • 22217937, 3272464
    • Ross-Innes CS Stark R Teschendorff AE : Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature. 2012;481(7381):389-393. 22217937 10.1038/nature10730 3272464
    • (2012) Nature , vol.481 , Issue.7381 , pp. 389-393
    • Ross-Innes, C.S.1    Stark, R.2    Teschendorff, A.E.3
  • 26
    • 67649345185 scopus 로고
    • An improved Bonferroni procedure for multiple tests of significance
    • Simes RJ : An improved Bonferroni procedure for multiple tests of significance. Biometrika. 1986;73(3):751-754. 10.1093/biomet/73.3.751
    • (1986) Biometrika , vol.73 , Issue.3 , pp. 751-754
    • Simes, R.J.1
  • 27
    • 53849146020 scopus 로고    scopus 로고
    • Model-based analysis of ChIP-Seq (MACS)
    • 18798982, 2592715
    • Zhang Y Liu T Meyer CA : Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. 18798982 10.1186/gb-2008-9-9-r137 2592715
    • (2008) Genome Biol , vol.9 , Issue.9 , pp. R137
    • Zhang, Y.1    Liu, T.2    Meyer, C.A.3
  • 28
    • 77951947707 scopus 로고    scopus 로고
    • ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
    • 20459804, 3098059
    • Zhu LJ Gazin C Lawson ND : ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics. 2010;11:237. 20459804 10.1186/1471-2105-11-237 3098059
    • (2010) BMC Bioinformatics , vol.11 , pp. 237
    • Zhu, L.J.1    Gazin, C.2    Lawson, N.D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.