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Volumn 13, Issue 1, 2012, Pages

An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING AFFINITY; BINDING SITE; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; DNA MICROARRAY; GENE MAPPING; HISTONE MODIFICATION; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; NORMAL DISTRIBUTION; PROMOTER REGION; PROTEIN DNA BINDING; QUANTITATIVE ANALYSIS; EVALUATION; FACTUAL DATABASE; GENETIC ASSOCIATION; INSTRUMENTATION; METABOLISM; METHODOLOGY; RECEIVER OPERATING CHARACTERISTIC; STANDARD;

EID: 84856078783     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-42     Document Type: Article
Times cited : (14)

References (40)
  • 1
    • 34548396885 scopus 로고    scopus 로고
    • ChIP-chip: Data, Model, and Analysis
    • 10.1111/j.1541-0420.2007.00768.x, 17825010
    • Zheng M, Barrera LO, Ren B, Wu YN. ChIP-chip: Data, Model, and Analysis. Biometrics 2007, 63(3):787-796. 10.1111/j.1541-0420.2007.00768.x, 17825010.
    • (2007) Biometrics , vol.63 , Issue.3 , pp. 787-796
    • Zheng, M.1    Barrera, L.O.2    Ren, B.3    Wu, Y.N.4
  • 2
    • 61449426211 scopus 로고    scopus 로고
    • Methylated DNA Immunoprecipitation (MeDIP)
    • 10.1007/978-1-59745-522-0_5, 18987806
    • Mohn F, Weber M, Schübeler D, Roloff T-C. Methylated DNA Immunoprecipitation (MeDIP). Methods Mol Biol 2009, 507:55-64. 10.1007/978-1-59745-522-0_5, 18987806.
    • (2009) Methods Mol Biol , vol.507 , pp. 55-64
    • Mohn, F.1    Weber, M.2    Schübeler, D.3    Roloff, T.-C.4
  • 4
    • 0348134871 scopus 로고    scopus 로고
    • Methyl-CpG binding proteins identify novel sites of epigenetic inactivation in human cancer
    • 10.1093/emboj/cdg604, 291845, 14633992
    • Ballestar E, Paz MF, Valle L, Wei S, Fraga MF, Espada J, Cigudosa JC, Huang TH-M, Esteller M. Methyl-CpG binding proteins identify novel sites of epigenetic inactivation in human cancer. The EMBO journal 2003, 22(23):6335-6345. 10.1093/emboj/cdg604, 291845, 14633992.
    • (2003) The EMBO journal , vol.22 , Issue.23 , pp. 6335-6345
    • Ballestar, E.1    Paz, M.F.2    Valle, L.3    Wei, S.4    Fraga, M.F.5    Espada, J.6    Cigudosa, J.C.7    Huang, T.H.-M.8    Esteller, M.9
  • 5
    • 33947315736 scopus 로고    scopus 로고
    • Cancer epigenomics: DNA methylomes and histone-modification maps
    • 10.1038/nrg2005, 17339880
    • Esteller M. Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet 2007, 8(4):286-298. 10.1038/nrg2005, 17339880.
    • (2007) Nat Rev Genet , vol.8 , Issue.4 , pp. 286-298
    • Esteller, M.1
  • 6
    • 77649197044 scopus 로고    scopus 로고
    • Differential DNA methylation correlates with differential expression of angiogenic factors in human heart failure
    • 10.1371/journal.pone.0008564, 2797324, 20084101
    • Movassagh M, Choy M-K, Goddard M, Bennett MR, Down TA, Foo RSY. Differential DNA methylation correlates with differential expression of angiogenic factors in human heart failure. PloS one 2010, 5(1):e8564. 10.1371/journal.pone.0008564, 2797324, 20084101.
    • (2010) PloS one , vol.5 , Issue.1
    • Movassagh, M.1    Choy, M.-K.2    Goddard, M.3    Bennett, M.R.4    Down, T.A.5    Foo, R.S.Y.6
  • 7
    • 50249165881 scopus 로고    scopus 로고
    • Epigenetic manifestations in diet-related disorders
    • 10.1159/000151237, 19776628
    • Mariman ECM. Epigenetic manifestations in diet-related disorders. Journal of nutrigenetics and nutrigenomics 2008, 1(5):232-239. 10.1159/000151237, 19776628.
    • (2008) Journal of nutrigenetics and nutrigenomics , vol.1 , Issue.5 , pp. 232-239
    • Mariman, E.C.M.1
  • 11
    • 33747874899 scopus 로고    scopus 로고
    • Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen microarrays
    • Scacheri PC, Crawford GE, Davis S. Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen microarrays. Methods Enzymol 2006, 411:270-282.
    • (2006) Methods Enzymol , vol.411 , pp. 270-282
    • Scacheri, P.C.1    Crawford, G.E.2    Davis, S.3
  • 16
    • 0242333835 scopus 로고    scopus 로고
    • Normalization of cDNA microarray data
    • 10.1016/S1046-2023(03)00155-5, 14597310
    • Smyth GK, Speed T. Normalization of cDNA microarray data. Methods 2003, 31(4):265-273. 10.1016/S1046-2023(03)00155-5, 14597310.
    • (2003) Methods , vol.31 , Issue.4 , pp. 265-273
    • Smyth, G.K.1    Speed, T.2
  • 17
    • 0037188875 scopus 로고    scopus 로고
    • Normalization and analysis of DNA microarray data by self-consistency and local regression
    • RESEARCH0037
    • Kepler TB, Crosby L, Morgan KT. Normalization and analysis of DNA microarray data by self-consistency and local regression. Genome Biol 2002, 3(7). RESEARCH0037.
    • (2002) Genome Biol , vol.3 , Issue.7
    • Kepler, T.B.1    Crosby, L.2    Morgan, K.T.3
  • 19
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide microarray data based on variance and bias
    • Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide microarray data based on variance and bias. Bioinformatics (Oxford, England) 2003, 19(2):185-193.
    • (2003) Bioinformatics (Oxford, England) , vol.19 , Issue.2 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 20
    • 0036376993 scopus 로고    scopus 로고
    • Statistical methods for identifying differentially expressed genes in replicated cDNA microarray
    • Dudoit S, Yang YH, Callow MJ. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray. Statistica Sinica 2002, 12:111-139.
    • (2002) Statistica Sinica , vol.12 , pp. 111-139
    • Dudoit, S.1    Yang, Y.H.2    Callow, M.J.3
  • 22
    • 11244346557 scopus 로고    scopus 로고
    • Variance stabilization applied to microarray data calibration and to the quantification of differential expression
    • Huber W, von Heydebreck A, Sültmann H, Poustka A, Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics (Oxford, England) 2002, 18(Suppl 1):S96-104.
    • (2002) Bioinformatics (Oxford, England) , vol.18 , Issue.SUPPL. 1
    • Huber, W.1    von Heydebreck, A.2    Sültmann, H.3    Poustka, A.4    Vingron, M.5
  • 24
    • 34447251894 scopus 로고    scopus 로고
    • Normalization and experimental design for ChIP-chip data
    • 10.1186/1471-2105-8-219, 1913544, 17592629
    • Peng S, Alekseyenko AA, Larschan E, Kuroda MI, Park PJ. Normalization and experimental design for ChIP-chip data. BMC bioinformatics 2007, 8:219. 10.1186/1471-2105-8-219, 1913544, 17592629.
    • (2007) BMC bioinformatics , vol.8 , pp. 219
    • Peng, S.1    Alekseyenko, A.A.2    Larschan, E.3    Kuroda, M.I.4    Park, P.J.5
  • 26
    • 70350210498 scopus 로고    scopus 로고
    • Identification of novel ER-alpha target genes in breast cancer cells: gene- and cell-selective co-regulator recruitment at target promoters determines the response to 17beta-estradiol and tamoxifen
    • Romano A, Adriaens M, Kuenen S, Delvoux B, Dunselman G, Evelo C, Groothuis P. Identification of novel ER-alpha target genes in breast cancer cells: gene- and cell-selective co-regulator recruitment at target promoters determines the response to 17beta-estradiol and tamoxifen. Mol Cell Endocrinol 2009, 314(1):90-100.
    • (2009) Mol Cell Endocrinol , vol.314 , Issue.1 , pp. 90-100
    • Romano, A.1    Adriaens, M.2    Kuenen, S.3    Delvoux, B.4    Dunselman, G.5    Evelo, C.6    Groothuis, P.7
  • 29
    • 1342294092 scopus 로고    scopus 로고
    • Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation
    • 10.1093/nar/30.4.e15, 100354, 11842121
    • Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic acids research 2002, 30(4):e15. 10.1093/nar/30.4.e15, 100354, 11842121.
    • (2002) Nucleic acids research , vol.30 , Issue.4
    • Yang, Y.H.1    Dudoit, S.2    Luu, P.3    Lin, D.M.4    Peng, V.5    Ngai, J.6    Speed, T.P.7
  • 30
    • 0035752668 scopus 로고    scopus 로고
    • Feature extraction and normalization algorithms for high-density oligonucleotide gene expression microarray data
    • Schadt EE, Li C, Ellis B, Wong WH. Feature extraction and normalization algorithms for high-density oligonucleotide gene expression microarray data. Journal of cellular biochemistry Supplement 2001, (Suppl 37):120-125.
    • (2001) Journal of cellular biochemistry Supplement , Issue.SUPPL. 37 , pp. 120-125
    • Schadt, E.E.1    Li, C.2    Ellis, B.3    Wong, W.H.4
  • 32
    • 25444453725 scopus 로고    scopus 로고
    • An adaptive method for cDNA microarray normalization
    • 10.1186/1471-2105-6-28, 552315, 15707486
    • Zhao Y, Li M-C, Simon R. An adaptive method for cDNA microarray normalization. BMC bioinformatics 2005, 6:28. 10.1186/1471-2105-6-28, 552315, 15707486.
    • (2005) BMC bioinformatics , vol.6 , pp. 28
    • Zhao, Y.1    Li, M.-C.2    Simon, R.3
  • 33
    • 53549104134 scopus 로고    scopus 로고
    • MEDME: an experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment
    • 10.1101/gr.080721.108, 2556264, 18765822
    • Pelizzola M, Koga Y, Urban AE, Krauthammer M, Weissman S, Halaban R, Molinaro AM. MEDME: an experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment. Genome research 2008, 18(10):1652-1659. 10.1101/gr.080721.108, 2556264, 18765822.
    • (2008) Genome research , vol.18 , Issue.10 , pp. 1652-1659
    • Pelizzola, M.1    Koga, Y.2    Urban, A.E.3    Krauthammer, M.4    Weissman, S.5    Halaban, R.6    Molinaro, A.M.7
  • 35
    • 84857801304 scopus 로고    scopus 로고
    • Bioinformatic interrogation of expression microarray data to identify nutritionally regulated genes potentially modulated by DNA methylation
    • 10.1007/s12263-008-0095-0, 2593010, 19034551
    • McKay JA, Adriaens ME, Ford D, Relton CL, Evelo CTA, Mathers JC. Bioinformatic interrogation of expression microarray data to identify nutritionally regulated genes potentially modulated by DNA methylation. Genes Nutr 2008, 3(3-4):167-171. 10.1007/s12263-008-0095-0, 2593010, 19034551.
    • (2008) Genes Nutr , vol.3 , Issue.3-4 , pp. 167-171
    • McKay, J.A.1    Adriaens, M.E.2    Ford, D.3    Relton, C.L.4    Evelo, C.T.A.5    Mathers, J.C.6
  • 36
    • 59549093642 scopus 로고    scopus 로고
    • ArrayQualityMetrics--a bioconductor package for quality assessment of microarray data
    • Kauffmann A, Gentleman R, Huber W. arrayQualityMetrics--a bioconductor package for quality assessment of microarray data. Bioinformatics (Oxford, England) 2009, 25(3):415-416.
    • (2009) Bioinformatics (Oxford, England) , vol.25 , Issue.3 , pp. 415-416
    • Kauffmann, A.1    Gentleman, R.2    Huber, W.3
  • 37
    • 57149113529 scopus 로고    scopus 로고
    • The MSL3 chromodomain directs a key targeting step for dosage compensation of the Drosophila melanogaster × chromosome
    • 10.1038/nsmb.1520, 22282294
    • Sural TH, Peng S, Li B, Workman JL, Park PJ, Kuroda MI. The MSL3 chromodomain directs a key targeting step for dosage compensation of the Drosophila melanogaster × chromosome. Nature structural & molecular biology 2008, 15(12):1318-1325. 10.1038/nsmb.1520, 22282294.
    • (2008) Nature structural & molecular biology , vol.15 , Issue.12 , pp. 1318-1325
    • Sural, T.H.1    Peng, S.2    Li, B.3    Workman, J.L.4    Park, P.J.5    Kuroda, M.I.6
  • 38
    • 68249158456 scopus 로고    scopus 로고
    • Drosophila MSL complex globally acetylates H4K16 on the male × chromosome for dosage compensation
    • 10.1038/nsmb.1644, 22282294
    • Gelbart ME, Larschan E, Peng S, Park PJ, Kuroda MI. Drosophila MSL complex globally acetylates H4K16 on the male × chromosome for dosage compensation. Nature structural & molecular biology 2009, 16(8):825-832. 10.1038/nsmb.1644, 22282294.
    • (2009) Nature structural & molecular biology , vol.16 , Issue.8 , pp. 825-832
    • Gelbart, M.E.1    Larschan, E.2    Peng, S.3    Park, P.J.4    Kuroda, M.I.5
  • 39
    • 0242333835 scopus 로고    scopus 로고
    • Normalization of cDNA microarray data
    • 10.1016/S1046-2023(03)00155-5, 14597310
    • Smyth GK, Speed TP. Normalization of cDNA microarray data. Methods 2003, 31:265-273. 10.1016/S1046-2023(03)00155-5, 14597310.
    • (2003) Methods , vol.31 , pp. 265-273
    • Smyth, G.K.1    Speed, T.P.2
  • 40
    • 34447277157 scopus 로고    scopus 로고
    • Ringo - an R/Bioconductor package for analyzing ChIP-chip readouts
    • 10.1186/1471-2105-8-221, 1906858, 17594472
    • Toedling J, Sklyar O, Huber W. Ringo - an R/Bioconductor package for analyzing ChIP-chip readouts. BMC Bioinformatics 2007, 8(1):221. 10.1186/1471-2105-8-221, 1906858, 17594472.
    • (2007) BMC Bioinformatics , vol.8 , Issue.1 , pp. 221
    • Toedling, J.1    Sklyar, O.2    Huber, W.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.