DNA Methylation Microarrays_ Experimental Design and Statistical Analysis (2008)

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This book is intended to help researchers and students analyze high throughput epigenomic data, in particular DNA methylation microarray data, with sound statistics. It is divided into four parts. Part I, chapters 1 to 4, begins with an introduction to the basic statistics that is needed to comprehend the rest of the book. Chapters 2 and 3 are more biological and describe the wet bench technologies producing the data for analysis. Bioinformaticians and experimenters benefit by working closely together to design experiments with sufficient power and high quality. Chapter 4 preprocesses the data to remove systematic artifacts resulting from imperfection in the measurement. In Part II, chapters 5 and 6, the normalized data are then subject to conventional hypothesis-driven analysis looking for differential methylated loci between populations. Genomic tiling arrays may differ in their specific aims and a whole chapter is devoted to tiling arrays. Part III, chapters 7 to 10, concerns exploratory analysis, which prefill lead us to new hypotheses. In particular, functions and roles of unannotated DNA elements are associated with those of known ones by cluster and network analysis. Part IV, chapters 11 to 13, introduces the public online resources that facilitate justification and discussion of the findings.



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