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Volumn 26, Issue 22, 2010, Pages 2849-2855

A statistical framework for Illumina DNA methylation arrays

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA METHYLATION; DNA MICROARRAY; GENETIC DATABASE; METHODOLOGY; STATISTICAL ANALYSIS;

EID: 78149262820     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq553     Document Type: Article
Times cited : (79)

References (34)
  • 1
    • 77949877704 scopus 로고    scopus 로고
    • High-throughput assessment of CpG site methylation for distinguishing between HCV-cirrhosis and HCV-associated hepatocellular carcinoma
    • Archer, K. et al. (2010) High-throughput assessment of CpG site methylation for distinguishing between HCV-cirrhosis and HCV-associated hepatocellular carcinoma. Mol. Genet. Genomics, 283, 341-349.
    • (2010) Mol. Genet. Genomics , vol.283 , pp. 341-349
    • Archer, K.1
  • 2
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J.R. Stat. Soc. Ser. B, 57, 289-300.
    • (1995) J. R. Stat. Soc. Ser. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 3
    • 33644649616 scopus 로고    scopus 로고
    • High-throughput DNA methylation profiling using universal bead arrays
    • Bibikova, M. et al. (2006) High-throughput DNA methylation profiling using universal bead arrays. Genome Res., 16, 383-393.
    • (2006) Genome Res. , vol.16 , pp. 383-393
    • Bibikova, M.1
  • 4
    • 33745156863 scopus 로고    scopus 로고
    • Some theory for Fisher's linear discriminant function, naive Bayes, and some alternatives when there are many more variables than observations
    • Bickel, P. and Levina, E. (2004) Some theory for Fisher's linear discriminant function, "naive Bayes", and some alternatives when there are many more variables than observations. Bernoulli, 10, 989-1010.
    • (2004) Bernoulli , vol.10 , pp. 989-1010
    • Bickel, P.1    Levina, E.2
  • 5
    • 70149099610 scopus 로고    scopus 로고
    • Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context
    • Christensen, B. et al. (2009) Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context. PLoS Genet., 5, e1000602.
    • (2009) PLoS Genet. , vol.5
    • Christensen, B.1
  • 6
    • 46949098742 scopus 로고    scopus 로고
    • ABayesian deconvolution strategy for immunoprecipitation based DNA methylome analysis
    • Down, T. et al. (2008)ABayesian deconvolution strategy for immunoprecipitation based DNA methylome analysis. Nat. Biotechnol., 26.
    • (2008) Nat. Biotechnol. , vol.26
    • Down, T.1
  • 7
    • 70349604003 scopus 로고    scopus 로고
    • Spike-in validation of an Illumina-specific variancestabilizing transformation
    • Dunning, M. et al. (2008a) Spike-in validation of an Illumina-specific variancestabilizing transformation. BMC Res. Notes, 1, 18.
    • (2008) BMC Res. Notes , vol.1 , pp. 18
    • Dunning, M.1
  • 8
    • 42049089192 scopus 로고    scopus 로고
    • Statistical issues in the analysis of Illumina data
    • Dunning, M. et al. (2008b) Statistical issues in the analysis of Illumina data. BMC Bioinformatics, 9, 85.
    • (2008) BMC Bioinformatics , vol.9 , pp. 85
    • Dunning, M.1
  • 9
    • 33947315736 scopus 로고    scopus 로고
    • Cancer epigenomics: DNA methylomes and histone-modifications maps
    • Esteller, M. (2007) Cancer epigenomics: DNA methylomes and histone-modifications maps. Nat. Rev. Genet., 8, 286-298.
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 286-298
    • Esteller, M.1
  • 10
    • 0035998835 scopus 로고    scopus 로고
    • Model-based clustering, discriminant analysis, and density estimation
    • Fraley, C. and Raftery, A. (2002) Model-based clustering, discriminant analysis, and density estimation. J. Am. Stat. Assoc., 97, 611-631.
    • (2002) J. Am. Stat. Assoc. , vol.97 , pp. 611-631
    • Fraley, C.1    Raftery, A.2
  • 11
    • 77957361278 scopus 로고    scopus 로고
    • Hepatocellular carcinoma displays distinct DNA methylation signatures with potential as clinical predictors
    • Hernandez-Vargas, H. et al. (2010) Hepatocellular carcinoma displays distinct DNA methylation signatures with potential as clinical predictors. PLoS One, 5, e9749.
    • (2010) PLoS One , vol.5
    • Hernandez-Vargas, H.1
  • 12
    • 52949118548 scopus 로고    scopus 로고
    • Model-based clustering of DNA methylation array data: a recursive-partitioning algorithm for high-dimensional data arising as a mixture of beta distribution
    • Houseman, A. et al. (2008) Model-based clustering of DNA methylation array data: a recursive-partitioning algorithm for high-dimensional data arising as a mixture of beta distribution. BMC Bioinformatics, 9, 365.
    • (2008) BMC Bioinformatics , vol.9 , pp. 365
    • Houseman, A.1
  • 13
    • 77949574043 scopus 로고    scopus 로고
    • DNA methylation profiles of ovarian epithelial carcinoma tumors and cell lines
    • Houshdaran, S. et al. (2009) DNA methylation profiles of ovarian epithelial carcinoma tumors and cell lines. PLoS ONE, 5, e9359.
    • (2009) PLoS ONE , vol.5
    • Houshdaran, S.1
  • 14
    • 78149238599 scopus 로고    scopus 로고
    • Illumina. Available at
    • Illumina (2006) GoldenGate methylation cancer panel I. Available at http://www.illumina.com/technology/goldengate_methylation_assay.ilmn.
    • (2006) GoldenGate methylation cancer panel I
  • 15
    • 43149098062 scopus 로고    scopus 로고
    • Comprehensive high-throughput arrays for relative methylation (CHARM)
    • Irizarry, R. et al. (2008) Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res., 18, 780-790.
    • (2008) Genome Res , vol.18 , pp. 780-790
    • Irizarry, R.1
  • 16
    • 59149084538 scopus 로고    scopus 로고
    • The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores
    • Irizarry, R. et al. (2009) The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet., 41, 178-186.
    • (2009) Nat. Genet. , vol.41 , pp. 178-186
    • Irizarry, R.1
  • 17
    • 18744410117 scopus 로고    scopus 로고
    • Applications of beta-mixture models in bioinformatics
    • Ji, Y. et al. (2005) Applications of beta-mixture models in bioinformatics. Bioinformatics, 21, 2118-2122.
    • (2005) Bioinformatics , vol.21 , pp. 2118-2122
    • Ji, Y.1
  • 19
    • 68149108556 scopus 로고    scopus 로고
    • Genome-wide screen of promoter methylation identifies novel markers in melanoma
    • Koga, Y. et al. (2009) Genome-wide screen of promoter methylation identifies novel markers in melanoma. Genome Res., 19, 1462-1470.
    • (2009) Genome Res. , vol.19 , pp. 1462-1470
    • Koga, Y.1
  • 20
    • 77249137168 scopus 로고    scopus 로고
    • Principles and challenges of genome-wide DNA methylation analysis
    • Laird, P. (2010) Principles and challenges of genome-wide DNA methylation analysis. Nat. Rev. Genet., 11, 191-203.
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 191-203
    • Laird, P.1
  • 21
    • 70349588328 scopus 로고    scopus 로고
    • Considerations for processing and analysis of Goldengate-based two-colour illumina platforms
    • Lynch, A. et al. (2009) Considerations for processing and analysis of Goldengate-based two-colour illumina platforms. Stat. Methods Med. Res., 18, 437-452.
    • (2009) Stat. Methods Med. Res. , vol.18 , pp. 437-452
    • Lynch, A.1
  • 22
    • 62349119224 scopus 로고    scopus 로고
    • Epigenetic profiling reveals etiologically distinct patterns of DNA methylation in head and neck squamous cell carcinoma
    • Marsit, C. et al. (2009) Epigenetic profiling reveals etiologically distinct patterns of DNA methylation in head and neck squamous cell carcinoma. Carcinogenesis, 30, 416-422.
    • (2009) Carcinogenesis , vol.30 , pp. 416-422
    • Marsit, C.1
  • 23
    • 34249029861 scopus 로고    scopus 로고
    • Penalized model-based clustering with application to variable selection
    • Pan, W. and Shen, X. (2007) Penalized model-based clustering with application to variable selection. J. Mach. Learn. Res., 80, 1145-1164.
    • (2007) J. Mach. Learn. Res. , vol.80 , pp. 1145-1164
    • Pan, W.1    Shen, X.2
  • 24
    • 20444491962 scopus 로고    scopus 로고
    • Discussion of Bayesian clustering with variable selection and transformation selection by liu et al
    • Raftery, A. (2003) Discussion of "Bayesian clustering with variable selection and transformation selection" by liu et al. Bayesian Stat., 7, 266-271.
    • (2003) Bayesian Stat. , vol.7 , pp. 266-271
    • Raftery, A.1
  • 25
    • 50649108994 scopus 로고    scopus 로고
    • An integrated resource for genome-wide identification and analysis of human tissue-specific differential methylated regions (tDMRs)
    • Rakyan, V. et al. (2008) An integrated resource for genome-wide identification and analysis of human tissue-specific differential methylated regions (tDMRs). Genome Res., 18, 1518-1529.
    • (2008) Genome Res. , vol.18 , pp. 1518-1529
    • Rakyan, V.1
  • 26
    • 77952881988 scopus 로고    scopus 로고
    • Weighted model-based clustering for remote sensing image analysis
    • Richards, J. et al. (2009) Weighted model-based clustering for remote sensing image analysis. Comput. Geosci., 14, 125-136.
    • (2009) Comput. Geosci. , vol.14 , pp. 125-136
    • Richards, J.1
  • 27
    • 0023453329 scopus 로고
    • Silhouettes: a graphical aid to the interpretation and validation of cluster analysis
    • Rousseeuwl, P. (1987) Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J. Comput. Appl. Math., 20, 53-65.
    • (1987) J. Comput. Appl. Math. , vol.20 , pp. 53-65
    • Rousseeuwl, P.1
  • 28
    • 3543133355 scopus 로고    scopus 로고
    • Interactively optimizing signal-to-noise ratios in expression profiling, project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays
    • Seo, J. et al. (2004) Interactively optimizing signal-to-noise ratios in expression profiling, project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays. Bioinfomatics, 20, 2534-2544.
    • (2004) Bioinfomatics , vol.20 , pp. 2534-2544
    • Seo, J.1
  • 29
    • 70449331456 scopus 로고    scopus 로고
    • Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis
    • Shen, R. et al. (2009) Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis. Bioinformatics, 25, 2906-2912.
    • (2009) Bioinformatics , vol.25 , pp. 2906-2912
    • Shen, R.1
  • 30
    • 4444237023 scopus 로고    scopus 로고
    • A comparison of cluster analysis methods using DNA methylation data
    • Siegmund, K. et al. (2004) A comparison of cluster analysis methods using DNA methylation data. Bioinformatics, 20, 1896-1904.
    • (2004) Bioinformatics , vol.20 , pp. 1896-1904
    • Siegmund, K.1
  • 31
    • 43749096785 scopus 로고    scopus 로고
    • Variable selection for model-based high dimensional clustering and its application to microarray data
    • Wang, S. and Zhu, J. (2008) Variable selection for model-based high dimensional clustering and its application to microarray data. Biometrics, 64, 440-448.
    • (2008) Biometrics , vol.64 , pp. 440-448
    • Wang, S.1    Zhu, J.2
  • 32
    • 44349153603 scopus 로고    scopus 로고
    • A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets
    • Wei, H. et al. (2008) A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets. Nucleic Acids Res., 36, 2926-2938.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 2926-2938
    • Wei, H.1
  • 33
    • 47849111914 scopus 로고    scopus 로고
    • On the necessity of different statistical treatment for Illumina BeadChip and Affymetrix GeneChip data and its significance for biological interpretation
    • Wong, W. et al. (2008) On the necessity of different statistical treatment for Illumina BeadChip and Affymetrix GeneChip data and its significance for biological interpretation. Biol. Direct, 3.
    • (2008) Biol. Direct. , vol.3
    • Wong, W.1
  • 34
    • 62549119576 scopus 로고    scopus 로고
    • Statistical methods of background correction for Illumina BeadArray data
    • Xie, Y. et al. (2009) Statistical methods of background correction for Illumina BeadArray data. Bioinformatics, 25, 751-757. 2855.
    • (2009) Bioinformatics , vol.25 , pp. 751-757
    • Xie, Y.1


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