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Web-Based Analysis of (Epi-) Genome Data Using EpiGRAPH and Galaxy

  • Christoph Bock
  • Greg Von Kuster
  • Konstantin Halachev
  • James Taylor
  • Anton Nekrutenko
  • Thomas Lengauer
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 628)

Abstract

Modern life sciences are becoming increasingly data intensive, posing a significant challenge for most researchers and shifting the bottleneck of scientific discovery from data generation to data analysis. As a result, progress in genome research is increasingly impeded by bioinformatic hurdles. A new generation of powerful and easy-to-use genome analysis tools has been developed to address this issue, enabling biologists to perform complex bioinformatic analyses online - without having to learn a programming language or downloading and manually processing large datasets. In this tutorial paper, we describe the use of EpiGRAPH (http://epigraph.mpi-inf.mpg.de/) and Galaxy (http://galaxyproject.org/) for genome and epigenome analysis, and we illustrate how these two web services work together to identify epigenetic modifications that are characteristics of highly polymorphic (SNP-rich) promoters. This paper is supplemented with video tutorials (http://tinyurl.com/yc5xkqq), which provide a step-by-step guide through each example analysis.

Key words

Bioinformatics Genome analysis Statistics Machine learning Computational epigenetics Single nucleotide polymorphisms (SNPs) Evolutionary constraint 

Notes

Acknowledgments

We would like to thank Joachim Büch for maintaining the IT infrastructure of EpiGRAPH, Yoichi Yamada and Sascha Tierling for providing DNA methylation data, and Martina Paulsen as well as Jörn Walter for helpful discussions. EpiGRAPH is partially funded by the European Union through the CANCERDIP project (HEALTH-F2–2007-200620; http://www.cancerdip.eu/). Galaxy is supported by NSF Grant DBI-0543285 and NIH Grant 5R01HG003646–02 as well as by funds from the Huck Institutes for Life Sciences at Penn State University and Pennsylvania Department of Health.

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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Christoph Bock
    • 1
  • Greg Von Kuster
    • 1
  • Konstantin Halachev
    • 2
  • James Taylor
    • 3
  • Anton Nekrutenko
    • 3
  • Thomas Lengauer
    • 1
  1. 1.Max-Planck-Institut für InformatikSaarbrückenGermany
  2. 2.Center for Comparative Genomics and Bioinformatics, Huck Institutes for Life SciencesPenn State UniversityUniversity ParkUSA
  3. 3.Departments of Biology and Mathematics & Computer ScienceEmory UniversityAtlantaUSA

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