title: Analyzing epigenome data in context of genome evolution and human diseases.
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.
authors.affiliation: Max Planck Institute, Saarbrücken, Germany. lfbach@mpi-inf.mpg.de
authors.forename: Lars
authors.initials: L
authors.lastname: Feuerbach
authors.forename: Konstantin
authors.initials: K
authors.lastname: Halachev
authors.forename: Yassen
authors.initials: Y
authors.lastname: Assenov
authors.forename: Fabian
authors.initials: F
authors.lastname: Müller
authors.forename: Christoph
authors.initials: C
authors.lastname: Bock
authors.forename: Thomas
authors.initials: T
authors.lastname: Lengauer
mesh_terms: D000818:Animals; D002877:Chromosomes, Human / Q000235:genetics; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics; D003627:Data Interpretation, Statistical; D030541:Databases, Genetic; D004194:Disease / Q000235:genetics*; D057890:Epigenomics / Q000379:methods*; D019143:Evolution, Molecular; D005260:Female; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D051379:Mice; D010051:Ovarian Neoplasms / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D012984:Software