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Volumn 29, Issue 22, 2013, Pages 2884-2891

A-clustering: A novel method for the detection of co-regulated methylation regions, and regions associated with exposure

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; CLUSTER ANALYSIS; CPG ISLAND; DNA METHYLATION; ENVIRONMENTAL EXPOSURE; HUMAN; ARTICLE;

EID: 84890026239     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt498     Document Type: Article
Times cited : (73)

References (22)
  • 1
    • 0347320799 scopus 로고    scopus 로고
    • Methylation of cytochrome p4501a1 promoter in the lung is associated with tobacco smoking
    • Anttila, S. et al. (2003) Methylation of cytochrome p4501a1 promoter in the lung is associated with tobacco smoking. Cancer Res., 63, 8623-8628.
    • (2003) Cancer Res. , vol.63 , pp. 8623-8628
    • Anttila, S.1
  • 2
    • 79953152880 scopus 로고    scopus 로고
    • Accurate genome-scale percentage DNA methylation estimates from microarray data
    • Aryee, M.J. et al. (2011) Accurate genome-scale percentage DNA methylation estimates from microarray data. Bioinformatics, 12, 197-210.
    • (2011) Bioinformatics , vol.12 , pp. 197-210
    • Aryee, M.J.1
  • 3
    • 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. Royal Stat. Soc. B, 57, 289-300.
    • (1995) J. Royal Stat. Soc. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 4
    • 0035733108 scopus 로고    scopus 로고
    • The control of the false discovery rate in multiple testing under dependency
    • Benjamini, Y. and Yekutieli, D. (2001) The control of the false discovery rate in multiple testing under dependency. Ann. Stat., 29, 1165-1188.
    • (2001) Ann. Stat. , vol.29 , pp. 1165-1188
    • Benjamini, Y.1    Yekutieli, D.2
  • 5
    • 36749094097 scopus 로고    scopus 로고
    • Estimating the arm-wise false discovery rate in array comparative genomic hybridization experiments
    • Article32
    • Gaile, D.P. et al. (2007) Estimating the arm-wise false discovery rate in array comparative genomic hybridization experiments. Stat. Appl. Genet. Mol. Biol., 6. Article32.
    • (2007) Stat. Appl. Genet. Mol. Biol. , vol.6
    • Gaile, D.P.1
  • 6
    • 0023216891 scopus 로고
    • Cpg islands in vertebrate genomes
    • Gardiner-Garden, M. et al. (1987) Cpg islands in vertebrate genomes. J. Mol. Biol., 196, 261-282.
    • (1987) J. Mol. Biol. , vol.196 , pp. 261-282
    • Gardiner-Garden, M.1
  • 7
    • 84863338135 scopus 로고    scopus 로고
    • Environmental chemical exposures and human epigenetics
    • Hou, L. et al. (2012) Environmental chemical exposures and human epigenetics. Int. J. Epidemiol., 41, 79-105.
    • (2012) Int. J. Epidemiol. , vol.41 , pp. 79-105
    • Hou, L.1
  • 8
    • 84860637797 scopus 로고    scopus 로고
    • DNA methylation arrays as surrogate measures of cell mixture distribution
    • Houseman, E.A. et al. (2012) DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics, 13, 86.
    • (2012) BMC Bioinformatics , vol.13 , pp. 86
    • Houseman, E.A.1
  • 9
    • 59149084538 scopus 로고    scopus 로고
    • The human colon cancer methylome shows similar hypoand hypermethylation at conserved tissue-specific CpG island shores
    • Irizarry, R. et al. (2009) The human colon cancer methylome shows similar hypoand hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet., 41, 178-186.
    • (2009) Nat. Genet. , vol.41 , pp. 178-186
    • Irizarry, R.1
  • 11
    • 84870767737 scopus 로고    scopus 로고
    • Interindividual variability and co-regulation of DNA methylation differ among blood cell populations
    • Jacoby, M. et al. (2012) Interindividual variability and co-regulation of DNA methylation differ among blood cell populations. Epigenetics, 7, 35-34.
    • (2012) Epigenetics , vol.7 , pp. 35-34
    • Jacoby, M.1
  • 12
    • 84863386102 scopus 로고    scopus 로고
    • Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies
    • Jaffe, A.E. et al. (2012) Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. Int. J. Epidemiol., 41, 200-209.
    • (2012) Int. J. Epidemiol. , vol.41 , pp. 200-209
    • Jaffe, A.E.1
  • 13
    • 33845432928 scopus 로고    scopus 로고
    • Adjusting batch effects in microarray expression data using empirical Bayes methods
    • Johnson, W.E. et al. (2007) Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics, 8, 118-127.
    • (2007) Biostatistics , vol.8 , pp. 118-127
    • Johnson, W.E.1
  • 14
    • 84863986133 scopus 로고    scopus 로고
    • Functions of DNA methylation: Islands, start sites, gene bodies and beyond
    • Jones, P.A. (2012) Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat. Rev. Genet., 13, 484-492.
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 484-492
    • Jones, P.A.1
  • 15
    • 40549114662 scopus 로고    scopus 로고
    • CMARRT: A tool for the analysis of chip-chip data from tiling arrays by incorporating the correlation structure
    • Kuan, P.F. et al. (2008) CMARRT: a tool for the analysis of chip-chip data from tiling arrays by incorporating the correlation structure. Pac. Symp. Biocomput., 515-528.
    • (2008) Pac. Symp. Biocomput. , pp. 515-528
    • Kuan, P.F.1
  • 16
    • 34848914038 scopus 로고    scopus 로고
    • Capturing heterogeneity in gene expression studies by surrogate variable analysis
    • Leek, J.T. and Storey, J.D. (2007) Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet., 3, 1724-1735.
    • (2007) PLoS Genet. , vol.3 , pp. 1724-1735
    • Leek, J.T.1    Storey, J.D.2
  • 17
    • 77649173768 scopus 로고
    • Longitudinal data analysis using generalized linear models
    • Liang, K.Y. and Zeger, S.L. (1986) Longitudinal data analysis using generalized linear models. Biometrika, 73, 13-22.
    • (1986) Biometrika , vol.73 , pp. 13-22
    • Liang, K.Y.1    Zeger, S.L.2
  • 18
    • 84869421697 scopus 로고    scopus 로고
    • Comb-p: Software for combining, analyzing, grouping and correcting spatially correlated p-values
    • Pedersen, B.S. et al. (2012) Comb-p: software for combining, analyzing, grouping and correcting spatially correlated p-values. Bioinformatics, 28, 2986-2988.
    • (2012) Bioinformatics , vol.28 , pp. 2986-2988
    • Pedersen, B.S.1
  • 19
    • 79958754527 scopus 로고    scopus 로고
    • Validation of a DNA methylation microarray for 450, 000 CpG sites in the human genome
    • Sandoval, J. et al. (2011) Validation of a DNA methylation microarray for 450, 000 CpG sites in the human genome. Epigenetics, 6, 692-702.
    • (2011) Epigenetics , vol.6 , pp. 692-702
    • Sandoval, J.1
  • 20
    • 84876099049 scopus 로고    scopus 로고
    • Exposure to airborne particulate matter is associated with methylation pattern in the asthma pathway
    • Sofer, T. et al. (2013) Exposure to airborne particulate matter is associated with methylation pattern in the asthma pathway. Epigenomics, 5, 147-154.
    • (2013) Epigenomics , vol.5 , pp. 147-154
    • Sofer, T.1
  • 21
    • 84862266444 scopus 로고    scopus 로고
    • Complete pipeline for Infinium Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation
    • Touleimat, N. and Tost, J. (2012) Complete pipeline for Infinium Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation. Epigenomics, 4, 325-341.
    • (2012) Epigenomics , vol.4 , pp. 325-341
    • Touleimat, N.1    Tost, J.2
  • 22
    • 77956627119 scopus 로고    scopus 로고
    • Redefining CpG islands using hidden Markov models
    • Wu, H. et al. (2010) Redefining CpG islands using hidden Markov models. Biostatistics, 11, 499.
    • (2010) Biostatistics , vol.11 , pp. 499
    • Wu, H.1


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