CpG Islands pp 175-194 | Cite as
Experimental Design and Bioinformatic Analysis of DNA Methylation Data
Abstract
DNA methylation is a crucial regulatory mechanism of gene expression, affected in many human pathologies. Therefore, it is not surprising that nowadays, in the era of high-throughput methods, a lot of data sets representing DNA methylation in various conditions are available and the amount of such data keeps growing. In this chapter, we discuss those aspects of experiment planning and data analysis, which we consider the most important for reliability and reproducibility of DNA methylation studies: usage of replicates, data quality control at various stages, selection of a statistical model, and incorporation of DNA methylation into the multi-omics analysis.
Key words
DNA methylation Next generation sequencing Data analysis Quality control Experiment planningNotes
Acknowledgments
Y.A.M.’s work was supported by RSF grant 15-14-30002, and A.S.’s work was supported by RSF grant 14-45-00065. Y.A.M. wrote the manuscript, and A.S. wrote sections about quality control and contributed to others.
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