메뉴 건너뛰기




Volumn 13, Issue 1, 2012, Pages

Normalization of ChIP-seq data with control

Author keywords

[No Author keywords available]

Indexed keywords

CONTROL SAMPLES; ERROR RATE CONTROL; ESTIMATION PRECISION; HISTONE MODIFICATION; MATCHING CONTROL; NORMALIZATION FACTORS; PROTEIN-DNA INTERACTIONS; STATISTICAL PROPERTIES; TRANSCRIPTION FACTOR BINDING;

EID: 84864803359     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-199     Document Type: Article
Times cited : (75)

References (21)
  • 2
    • 77956885532 scopus 로고    scopus 로고
    • A ChIP-seq defined genome-wide map of vitamin D receptor binding: Associations with disease and evolution
    • 10.1101/gr.107920.110, 2945184, 20736230
    • Ramagopalan S, Heger A, Berlanga A, Maugeri N, Lincoln M, Burrell A, Handunnetthi L, Handel A, Disanto G, Orton S. A ChIP-seq defined genome-wide map of vitamin D receptor binding: Associations with disease and evolution. Genome Res 2010, 20(10):1352. 10.1101/gr.107920.110, 2945184, 20736230.
    • (2010) Genome Res , vol.20 , Issue.10 , pp. 1352
    • Ramagopalan, S.1    Heger, A.2    Berlanga, A.3    Maugeri, N.4    Lincoln, M.5    Burrell, A.6    Handunnetthi, L.7    Handel, A.8    Disanto, G.9    Orton, S.10
  • 3
    • 79955480674 scopus 로고    scopus 로고
    • Genome-wide analysis reveals novel molecular features of mouse recombination hotspots
    • 10.1038/nature09869, 3117304, 21460839
    • Smagulova F, Gregoretti I, Brick K, Khil P, Camerini-Otero R, Petukhova G. Genome-wide analysis reveals novel molecular features of mouse recombination hotspots. Nature 2011, 472(7343):375-378. 10.1038/nature09869, 3117304, 21460839.
    • (2011) Nature , vol.472 , Issue.7343 , pp. 375-378
    • Smagulova, F.1    Gregoretti, I.2    Brick, K.3    Khil, P.4    Camerini-Otero, R.5    Petukhova, G.6
  • 4
    • 70349312354 scopus 로고    scopus 로고
    • ChIP-seq: advantages and challenges of a maturing technology
    • 10.1038/nrg2641, 3191340, 19736561
    • Park P. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 2009, 10(10):669-680. 10.1038/nrg2641, 3191340, 19736561.
    • (2009) Nat Rev Genet , vol.10 , Issue.10 , pp. 669-680
    • Park, P.1
  • 5
    • 77952857912 scopus 로고    scopus 로고
    • A signal-noise model for significance analysis of ChIP-seq with negative control
    • 10.1093/bioinformatics/btq128, 20371496
    • Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei C, Lin F, Sung W. A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics 2010, 26(9):1199-1204. 10.1093/bioinformatics/btq128, 20371496.
    • (2010) Bioinformatics , vol.26 , Issue.9 , pp. 1199-1204
    • Xu, H.1    Handoko, L.2    Wei, X.3    Ye, C.4    Sheng, J.5    Wei, C.6    Lin, F.7    Sung, W.8
  • 6
    • 34547633677 scopus 로고    scopus 로고
    • Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
    • 10.1038/nmeth1068, 17558387
    • Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 2007, 4(8):651-657. 10.1038/nmeth1068, 17558387.
    • (2007) Nat Methods , vol.4 , Issue.8 , pp. 651-657
    • Robertson, G.1    Hirst, M.2    Bainbridge, M.3    Bilenky, M.4    Zhao, Y.5    Zeng, T.6    Euskirchen, G.7    Bernier, B.8    Varhol, R.9    Delaney, A.10
  • 7
    • 54949147307 scopus 로고    scopus 로고
    • F-Seq: a feature density estimator for high-throughput sequence tags
    • 10.1093/bioinformatics/btn480, 2732284, 18784119
    • Boyle A, Guinney J, Crawford G, Furey T. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics 2008, 24(21):2537. 10.1093/bioinformatics/btn480, 2732284, 18784119.
    • (2008) Bioinformatics , vol.24 , Issue.21 , pp. 2537
    • Boyle, A.1    Guinney, J.2    Crawford, G.3    Furey, T.4
  • 8
    • 52649157765 scopus 로고    scopus 로고
    • Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
    • 10.1093/nar/gkn425, 2532726, 18660515
    • Dohm J, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 2008, 36(16):e105. 10.1093/nar/gkn425, 2532726, 18660515.
    • (2008) Nucleic Acids Res , vol.36 , Issue.16
    • Dohm, J.1    Lottaz, C.2    Borodina, T.3    Himmelbauer, H.4
  • 11
    • 65349122997 scopus 로고    scopus 로고
    • Inherent signals in sequencing-based chromatin-immunoprecipitation control libraries
    • 10.1371/journal.pone.0005241, 2666154, 19367334
    • Vega V, Cheung E, Palanisamy N, Sung W. Inherent signals in sequencing-based chromatin-immunoprecipitation control libraries. PLoS One 2009, 4(4):e5241. 10.1371/journal.pone.0005241, 2666154, 19367334.
    • (2009) PLoS One , vol.4 , Issue.4
    • Vega, V.1    Cheung, E.2    Palanisamy, N.3    Sung, W.4
  • 12
    • 55749094855 scopus 로고    scopus 로고
    • An integrated software system for analyzing ChIP-chip and ChIP-seq data
    • 10.1038/nbt.1505, 2596672, 18978777
    • Ji H, Jiang H, Ma W, Johnson D, Myers R, Wong W. An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol 2008, 26(11):1293-1300. 10.1038/nbt.1505, 2596672, 18978777.
    • (2008) Nat Biotechnol , vol.26 , Issue.11 , pp. 1293-1300
    • Ji, H.1    Jiang, H.2    Ma, W.3    Johnson, D.4    Myers, R.5    Wong, W.6
  • 14
    • 57449100870 scopus 로고    scopus 로고
    • Design and analysis of ChIP-seq experiments for DNA-binding proteins
    • 10.1038/nbt.1508, 2597701, 19029915
    • Kharchenko P, Tolstorukov M, Park P. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol 2008, 26(12):1351-1359. 10.1038/nbt.1508, 2597701, 19029915.
    • (2008) Nat Biotechnol , vol.26 , Issue.12 , pp. 1351-1359
    • Kharchenko, P.1    Tolstorukov, M.2    Park, P.3
  • 15
    • 60849117520 scopus 로고    scopus 로고
    • Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks
    • 10.1186/1471-2105-9-523, 2628906, 19061503
    • Nix D, Courdy S, Boucher K. Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC Bioinformatics 2008, 9:523. 10.1186/1471-2105-9-523, 2628906, 19061503.
    • (2008) BMC Bioinformatics , vol.9 , pp. 523
    • Nix, D.1    Courdy, S.2    Boucher, K.3
  • 16
    • 52649132425 scopus 로고    scopus 로고
    • Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
    • 10.1093/nar/gkn488, 2532738, 18684996
    • Jothi R, Cuddapah S, Barski A, Cui K, Zhao K. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res 2008, 36(16):5221. 10.1093/nar/gkn488, 2532738, 18684996.
    • (2008) Nucleic Acids Res , vol.36 , Issue.16 , pp. 5221
    • Jothi, R.1    Cuddapah, S.2    Barski, A.3    Cui, K.4    Zhao, K.5
  • 17
    • 79960614727 scopus 로고    scopus 로고
    • ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
    • 10.1186/gb-2011-12-7-r67, 3218829, 21787385
    • Rashid N, Giresi P, Ibrahim J, Sun W, Lieb J. ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions. Genome Biol 2011, 12(7):R67. 10.1186/gb-2011-12-7-r67, 3218829, 21787385.
    • (2011) Genome Biol , vol.12 , Issue.7
    • Rashid, N.1    Giresi, P.2    Ibrahim, J.3    Sun, W.4    Lieb, J.5
  • 18
    • 77649225979 scopus 로고    scopus 로고
    • Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response
    • 10.1371/journal.pgen.1000848, 2824807, 20174564
    • Zhong M, Niu W, Lu Z, Sarov M, Murray J, Janette J, Raha D, Sheaffer K, Lam H, Preston E. Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genet 2010, 6(2):e1000848. 10.1371/journal.pgen.1000848, 2824807, 20174564.
    • (2010) PLoS Genet , vol.6 , Issue.2
    • Zhong, M.1    Niu, W.2    Lu, Z.3    Sarov, M.4    Murray, J.5    Janette, J.6    Raha, D.7    Sheaffer, K.8    Lam, H.9    Preston, E.10
  • 19
    • 77951610155 scopus 로고    scopus 로고
    • Genetic analysis of variation in transcription factor binding in yeast
    • 10.1038/nature08934, 2941147, 20237471
    • Zheng W, Zhao H, Mancera E, Steinmetz L, Snyder M. Genetic analysis of variation in transcription factor binding in yeast. Nature 2010, 464(7292):1187-1191. 10.1038/nature08934, 2941147, 20237471.
    • (2010) Nature , vol.464 , Issue.7292 , pp. 1187-1191
    • Zheng, W.1    Zhao, H.2    Mancera, E.3    Steinmetz, L.4    Snyder, M.5
  • 21
    • 0345822598 scopus 로고    scopus 로고
    • The positive false discovery rate: A Bayesian interpretation and the q-value
    • Storey J. The positive false discovery rate: A Bayesian interpretation and the q-value. Ann Stat 2003, 31:2013-2035.
    • (2003) Ann Stat , vol.31 , pp. 2013-2035
    • Storey, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.