title: Analysis of genome-wide DNA methylation profiles by BeadChip technology.
abstract: This chapter covers the genome-wide DNA methylation analysis using microarray platforms, such as Illumina Infinium HumanMethylation27 BeadChips or HumanMethylation450 BeadChips. Using our previously published ovarian cancer dataset (Bauerschlag et al., Oncology 80:12-20, 2011), we introduce the underlying design principles of these methylation array platforms and describe common yet effective bioinformatic strategies for data analysis, including data preprocessing, clustering methods, and differential methylation tests. We also describe the downstream analytic techniques for the results derived from the methylation array, i.e., gene set enrichment analysis and sequence-based motif analysis, which can be utilized for generating biological hypotheses.
authors.affiliation: Institute for Biomedical Engineering-Cell Biology, RWTH Aachen University Medical School, Aachen, Germany.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Lin
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Wagner
authors.forename: Martin
authors.initials: M
authors.lastname: Zenke
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D018899:CpG Islands / Q000235:genetics*; D019175:DNA Methylation / Q000235:genetics*; D015894:Genome, Human; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods