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Experimental Design and Bioinformatic Analysis of DNA Methylation Data

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1766))

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.

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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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Authors and Affiliations

  1. Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Science, Moscow, 117312, Russia

    Yulia Medvedeva

  2. Department of System Biology and Bioinformatics, Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, 119991, Russia

    Yulia Medvedeva

  3. Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia

    Yulia Medvedeva & Alexander Shershebnev

  4. School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA 01003, MA, USA

    Alexander Shershebnev

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  1. Josep Carreras Leukaemia, Research Institute, Badalona, Barcelona, Spain

    Tanya Vavouri

  2. IGTP, IMPPC, Badalona, Barcelona, Spain

    Miguel A. Peinado

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Medvedeva, Y., Shershebnev, A. (2018). Experimental Design and Bioinformatic Analysis of DNA Methylation Data. In: Vavouri, T., Peinado, M. (eds) CpG Islands. Methods in Molecular Biology, vol 1766. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7768-0_10

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  • DOI: https://doi.org/10.1007/978-1-4939-7768-0_10

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7767-3

  • Online ISBN: 978-1-4939-7768-0

  • eBook Packages: Springer Protocols

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