Introduction to Data Types in Epigenomics

  • Francesco Marabita
  • Jesper Tegnér
  • David Gomez-Cabrero
Chapter
Part of the Translational Bioinformatics book series (TRBIO, volume 7)

Abstract

The epigenome is the collection of all epigenetic modifications occurring on a genome. To properly generate, analyze, and understand epigenomic data has become increasingly important in basic and applied research, because epigenomic modifications have been broadly associated with differentiation, development, and disease processes, thereby also constituting attractive drug targets. In this chapter, we introduce the reader to the different aspects of epigenomics (e.g., DNA methylation and histone marks, among others), by briefly reviewing the most relevant underlying biological concepts and by describing the different experimental protocols and the analysis of the associated data types. Furthermore, for each type of epigenetic modification we describe the most relevant analysis pipelines, data repositories, and other resources. We conclude that any epigenomic investigation needs to carefully align the selection of the experimental protocols with the subsequent bioinformatics analysis and vice versa, as the effect sizes can be small and thereby escape detection if an integrative design is not well considered.

Keywords

Epigenomics DNA methylation Histone modifications ChIP-seq Bioinformatics 
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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Francesco Marabita
    • 1
  • Jesper Tegnér
    • 1
  • David Gomez-Cabrero
    • 1
  1. 1.Department of Medicine, Unit of Computational MedicineKarolinska Institutet, Center for Molecular Medicine, Karolinska University HospitalSolna, StockholmSweden

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