CpG Islands pp 175-194 | Cite as

Experimental Design and Bioinformatic Analysis of DNA Methylation Data

  • Yulia Medvedeva
  • Alexander Shershebnev
Part of the Methods in Molecular Biology book series (MIMB, volume 1766)


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 planning 



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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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Yulia Medvedeva
    • 1
    • 2
    • 3
  • Alexander Shershebnev
    • 3
    • 4
  1. 1.Institute of BioengineeringResearch Center of Biotechnology, Russian Academy of ScienceMoscowRussia
  2. 2.Department of System Biology and BioinformaticsVavilov Institute of General Genetics, Russian Academy of ScienceMoscowRussia
  3. 3.Department of Biological and Medical PhysicsMoscow Institute of Physics and TechnologyDolgoprudnyRussia
  4. 4.School of Public Health and Health SciencesUniversity of MassachusettsAmherstUSA

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