13 DNA Methylation Arrays: Methods and Analysis

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[22]  A. Bird,et al.  Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation. , 1999, Genes & development.

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[34]  G. Liang,et al.  Methylation-sensitive single-nucleotide primer extension (Ms-SNuPE) for quantitative measurement of DNA methylation , 2007, Nature Protocols.

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[38]  S. Dudoit,et al.  Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. , 2002, Nucleic acids research.

[39]  A. DeMarzo,et al.  Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes (COMPARE-MS) for the rapid, sensitive and quantitative detection of DNA methylation , 2006, Nucleic acids research.

[40]  M. Nelson,et al.  Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases. , 1994, Nucleic acids research.

[41]  Tim Hui-Ming Huang,et al.  Methylation microarray analysis of late-stage ovarian carcinomas distinguishes progression-free survival in patients and identifies candidate epigenetic markers. , 2002, Clinical cancer research : an official journal of the American Association for Cancer Research.

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[44]  Wei Jiang,et al.  High-throughput DNA methylation profiling using universal bead arrays. , 2006, Genome research.

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[48]  Christoph Grunau,et al.  Bisulfite genomic sequencing: systematic investigation of critical experimental parameters , 2001, Nucleic Acids Res..

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[51]  B. Ylstra,et al.  BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH) , 2006, Nucleic acids research.

[52]  Tim Hui-Ming Huang,et al.  Applications of CpG island microarrays for high-throughput analysis of DNA methylation. , 2002, The Journal of nutrition.

[53]  J. Lieb,et al.  ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. , 2004, Genomics.

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[57]  J. Herman,et al.  Synergy of demethylation and histone deacetylase inhibition in the re-expression of genes silenced in cancer , 1999, Nature Genetics.

[58]  A. Olek,et al.  A modified and improved method for bisulphite based cytosine methylation analysis. , 1996, Nucleic acids research.

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[61]  A. Bird,et al.  DNA binding selectivity of MeCP2 due to a requirement for A/T sequences adjacent to methyl-CpG. , 2005, Molecular cell.

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[63]  Monika Milewski,et al.  Decoding randomly ordered DNA arrays. , 2004, Genome research.

[64]  Dong Xu,et al.  Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. , 2007, Cancer research.

[65]  K. Robertson.  DNA methylation and human disease , 2005, Nature Reviews Genetics.

[66]  V. P. Collins,et al.  MMASS: an optimized array-based method for assessing CpG island methylation , 2006, Nucleic acids research.

[67]  M. Narro,et al.  Epigenomic Changes during Leukemia Cell Differentiation: Analysis of Histone Acetylation and Cytosine Methylation Using CpG Island Microarrays , 2004, Journal of Pharmacology and Experimental Therapeutics.

[68]  T. Rauch,et al.  MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells. , 2006, Cancer research.

[69]  M. Wigler,et al.  Cloning the differences between two complex genomes , 1993, Science.

[70]  W. Doerfler,et al.  DNA methylation and gene activity. , 1983, Annual review of biochemistry.

[71]  A. Bird.  CpG-rich islands and the function of DNA methylation , 1986, Nature.

[72]  Manel Esteller,et al.  DNA methylation: a profile of methods and applications. , 2002, BioTechniques.

[73]  Henrik Bengtsson,et al.  Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method , 2006, BMC Bioinformatics.

[74]  Ernest Fraenkel,et al.  High-resolution computational models of genome binding events , 2006, Nature Biotechnology.

[75]  T. Sekiya,et al.  Isolation of DNA fragments associated with methylated CpG islands in human adenocarcinomas of the lung using a methylated DNA binding column and denaturing gradient gel electrophoresis. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[76]  A. Feinberg,et al.  Hypomethylation distinguishes genes of some human cancers from their normal counterparts , 1983, Nature.

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[78]  J. Herman,et al.  A gene hypermethylation profile of human cancer. , 2001, Cancer research.

[79]  T. Rauch,et al.  Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer , 2005, Laboratory Investigation.

[80]  C. M. Chen,et al.  A novel technique for the identification of CpG islands exhibiting altered methylation patterns (ICEAMP). , 2001, Nucleic acids research.