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

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Genetic Variation

Part of the book series: Methods in Molecular Biology ((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.

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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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Authors and Affiliations

  1. Max-Planck-Institut für Informatik, Saarbrücken, Germany

    Christoph Bock, Greg Von Kuster & Thomas Lengauer

  2. Center for Comparative Genomics and Bioinformatics, Huck Institutes for Life Sciences, Penn State University, University Park, PA, USA

    Konstantin Halachev

  3. Departments of Biology and Mathematics & Computer Science, Emory University, Atlanta, GA, USA

    James Taylor & Anton Nekrutenko

Authors
  1. Christoph Bock
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  2. Greg Von Kuster
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  3. Konstantin Halachev
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  4. James Taylor
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  5. Anton Nekrutenko
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  6. Thomas Lengauer
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Corresponding author

Correspondence to Christoph Bock .

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Editors and Affiliations

  1. Medicines Research Centre, GlaxoSmithKline R&D Limited, Gunnels Wood Road, Stevenage, Hertfordshire, SG12NY, United Kingdom

    Michael R. Barnes

  2. Institute of Psychiatry, Social, Genetic & Developmental, King's College, Denmark Hill 111, London, SE58AF, United Kingdom

    Gerome Breen

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Bock, C., Von Kuster, G., Halachev, K., Taylor, J., Nekrutenko, A., Lengauer, T. (2010). Web-Based Analysis of (Epi-) Genome Data Using EpiGRAPH and Galaxy. In: Barnes, M., Breen, G. (eds) Genetic Variation. Methods in Molecular Biology, vol 628. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60327-367-1_15

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  • DOI: https://doi.org/10.1007/978-1-60327-367-1_15

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60327-366-4

  • Online ISBN: 978-1-60327-367-1

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