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Volumn 7, Issue 1, 2011, Pages

ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions

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EID: 79955676389     PISSN: None     EISSN: 17464811     Source Type: Journal    
DOI: 10.1186/1746-4811-7-11     Document Type: Article
Times cited : (48)

References (23)
  • 1
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein-DNA interactions
    • 10.1126/science.1141319, 17540862
    • Johnson D, Mortazavi A, Myers R, Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007, 316(5830):1497-1502. 10.1126/science.1141319, 17540862.
    • (2007) Science , vol.316 , Issue.5830 , pp. 1497-1502
    • Johnson, D.1    Mortazavi, A.2    Myers, R.3    Wold, B.4
  • 2
    • 65949090511 scopus 로고    scopus 로고
    • Target Genes of the MADS Transcription Factor SEPALLATA3: Integration of Developmental and Hormonal Pathways in the Arabidopsis Flower
    • Kaufmann K, Muino JM, Jauregui R, Airoldi CA, Smaczniak C, Krajewski P, Angenent GC. Target Genes of the MADS Transcription Factor SEPALLATA3: Integration of Developmental and Hormonal Pathways in the Arabidopsis Flower. Plos Biology 2009, 7(4):854-875.
    • (2009) Plos Biology , vol.7 , Issue.4 , pp. 854-875
    • Kaufmann, K.1    Muino, J.M.2    Jauregui, R.3    Airoldi, C.A.4    Smaczniak, C.5    Krajewski, P.6    Angenent, G.C.7
  • 3
    • 84979819147 scopus 로고    scopus 로고
    • Orchestration of the Floral Transition and Floral Development in Arabidopsis by the Bifunctional Transcription Factor APETALA2
    • 10.1105/tpc.110.075606, 20675573
    • Yant L, Mathieu J, Dinh TT, Ott F, Lanz C, Wollmann H, Chen X, Schmid M. Orchestration of the Floral Transition and Floral Development in Arabidopsis by the Bifunctional Transcription Factor APETALA2. Plant Cell 2010, 22(7):2156-2170. 10.1105/tpc.110.075606, 20675573.
    • (2010) Plant Cell , vol.22 , Issue.7 , pp. 2156-2170
    • Yant, L.1    Mathieu, J.2    Dinh, T.T.3    Ott, F.4    Lanz, C.5    Wollmann, H.6    Chen, X.7    Schmid, M.8
  • 4
    • 77749320166 scopus 로고    scopus 로고
    • Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP)
    • Kaufmann K, Muino JM, Osteras M, Farinelli L, Krajewski P, Angenent GC. Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP). Nat Protocols 2010, 5(3):457-472.
    • (2010) Nat Protocols , vol.5 , Issue.3 , pp. 457-472
    • Kaufmann, K.1    Muino, J.M.2    Osteras, M.3    Farinelli, L.4    Krajewski, P.5    Angenent, G.C.6
  • 5
    • 67650711615 scopus 로고    scopus 로고
    • SOAP2: an improved ultrafast tool for short read alignment
    • 10.1093/bioinformatics/btp336, 19497933
    • Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009, 25(15):1966-1967. 10.1093/bioinformatics/btp336, 19497933.
    • (2009) Bioinformatics , vol.25 , Issue.15 , pp. 1966-1967
    • Li, R.1    Yu, C.2    Li, Y.3    Lam, T.W.4    Yiu, S.M.5    Kristiansen, K.6    Wang, J.7
  • 6
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • 10.1093/bioinformatics/btp324, 2705234, 19451168
    • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25(14):1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
    • (2009) Bioinformatics , vol.25 , Issue.14 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 7
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • 10.1186/gb-2009-10-3-r25, 2690996, 19261174
    • Langmead B, Trapnell C, Pop M, Salzberg S. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 2009, 10(3):R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
    • (2009) Genome Biology , vol.10 , Issue.3
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.4
  • 8
    • 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 Meth 2009, 6(11s):S22-S32.
    • (2009) Nat Meth , vol.6 , Issue.11
    • Pepke, S.1    Wold, B.2    Mortazavi, A.3
  • 9
    • 77953176036 scopus 로고    scopus 로고
    • A scaling normalization method for differential expression analysis of RNA-seq data
    • 10.1186/gb-2010-11-3-r25, 2864565, 20196867
    • Robinson M, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology 2010, 11(3):R25. 10.1186/gb-2010-11-3-r25, 2864565, 20196867.
    • (2010) Genome Biology , vol.11 , Issue.3
    • Robinson, M.1    Oshlack, A.2
  • 12
    • 55749094855 scopus 로고    scopus 로고
    • An integrated software system for analyzing ChIP-chip and ChIP-seq data
    • Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH. An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotech 2008, 26(11):1293-1300.
    • (2008) Nat Biotech , vol.26 , Issue.11 , pp. 1293-1300
    • Ji, H.1    Jiang, H.2    Ma, W.3    Johnson, D.S.4    Myers, R.M.5    Wong, W.H.6
  • 16
    • 63949083912 scopus 로고    scopus 로고
    • Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G plus C)-biased genomes
    • 10.1038/nmeth.1311, 2664327, 19287394
    • Kozarewa I, Ning ZM, Quail MA, Sanders MJ, Berriman M, Turner DJ. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G plus C)-biased genomes. Nature Methods 2009, 6(4):291-295. 10.1038/nmeth.1311, 2664327, 19287394.
    • (2009) Nature Methods , vol.6 , Issue.4 , pp. 291-295
    • Kozarewa, I.1    Ning, Z.M.2    Quail, M.A.3    Sanders, M.J.4    Berriman, M.5    Turner, D.J.6
  • 20
    • 44649117905 scopus 로고    scopus 로고
    • Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells
    • 10.1016/j.cell.2008.04.043, 18555785
    • Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, et al. Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells. Cell 2008, 133(6):1106-1117. 10.1016/j.cell.2008.04.043, 18555785.
    • (2008) Cell , vol.133 , Issue.6 , pp. 1106-1117
    • Chen, X.1    Xu, H.2    Yuan, P.3    Fang, F.4    Huss, M.5    Vega, V.B.6    Wong, E.7    Orlov, Y.L.8    Zhang, W.9    Jiang, J.10
  • 21
    • 72249119297 scopus 로고    scopus 로고
    • Jarid2/Jumonji Coordinates Control of PRC2 Enzymatic Activity and Target Gene Occupancy in Pluripotent Cells
    • 10.1016/j.cell.2009.12.002, 2911953, 20064375
    • Peng JC, Valouev A, Swigut T, Zhang J, Zhao Y, Sidow A, Wysocka J. Jarid2/Jumonji Coordinates Control of PRC2 Enzymatic Activity and Target Gene Occupancy in Pluripotent Cells. Cell 2009, 139(7):1290-1302. 10.1016/j.cell.2009.12.002, 2911953, 20064375.
    • (2009) Cell , vol.139 , Issue.7 , pp. 1290-1302
    • Peng, J.C.1    Valouev, A.2    Swigut, T.3    Zhang, J.4    Zhao, Y.5    Sidow, A.6    Wysocka, J.7
  • 22
    • 0030052609 scopus 로고    scopus 로고
    • Permutation Tests for Multiple Loci Affecting a Quantitative Character
    • 1206957, 8770605
    • Doerge RW, Churchill GA. Permutation Tests for Multiple Loci Affecting a Quantitative Character. Genetics 1996, 142(1):285-294. 1206957, 8770605.
    • (1996) Genetics , vol.142 , Issue.1 , pp. 285-294
    • Doerge, R.W.1    Churchill, G.A.2
  • 23
    • 70349739736 scopus 로고    scopus 로고
    • The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets
    • 10.1093/bioinformatics/btp472, 2759552, 19654113
    • Nicol JW, Helt GA, Blanchard SG, Raja A, Loraine AE. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 2009, 25(20):2730-2731. 10.1093/bioinformatics/btp472, 2759552, 19654113.
    • (2009) Bioinformatics , vol.25 , Issue.20 , pp. 2730-2731
    • Nicol, J.W.1    Helt, G.A.2    Blanchard, S.G.3    Raja, A.4    Loraine, A.E.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.