Evolutionary Genomics pp 431-467

Part of the Methods in Molecular Biology book series (MIMB, volume 856) | Cite as

Analyzing Epigenome Data in Context of Genome Evolution and Human Diseases

  • Lars Feuerbach
  • Konstantin Halachev
  • Yassen Assenov
  • Fabian Müller
  • Christoph Bock
  • Thomas Lengauer

Abstract

This chapter describes bioinformatic tools for analyzing epigenome differences between species and in diseased versus normal cells. We illustrate the interplay of several Web-based tools in a case study of CpG island evolution between human and mouse. Starting from a list of orthologous genes, we use the Galaxy Web service to obtain gene coordinates for both species. These data are further analyzed in EpiGRAPH, a Web-based tool that identifies statistically significant epigenetic differences between genome region sets. Finally, we outline how the use of the statistical programming language R enables deeper insights into the epigenetics of human diseases, which are difficult to obtain without writing custom scripts. In summary, our tutorial describes how Web-based tools provide an easy entry into epigenome data analysis while also highlighting the benefits of learning a scripting language in order to unlock the vast potential of public epigenome datasets.

Key words

Epigenomics Computational epigenetics DNA methylation CpG islands Comparative genomics Galaxy EpiGRAPH R statistical programming language 

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Lars Feuerbach
    • 1
  • Konstantin Halachev
    • 1
  • Yassen Assenov
    • 1
  • Fabian Müller
    • 1
    • 2
  • Christoph Bock
    • 1
    • 2
  • Thomas Lengauer
    • 1
  1. 1.Max Planck InstituteSaarbrückenGermany
  2. 2.Broad InstituteCambridgeUSA

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