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CpG Islands pp 123-135 | Cite as

The Pancancer DNA Methylation Trackhub: A Window to The Cancer Genome Atlas Epigenomics Data

  • Izaskun Mallona
  • Alberto Sierco
  • Miguel A. Peinado
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1766)

Abstract

The Cancer Genome Atlas (TCGA) epigenome data includes the DNA methylation status of tumor and normal tissues of large cohorts for dozens of cancer types. Due to the moderately large data sizes, retrieving and analyzing them requires basic programming skills. Simple data browsing (e.g., candidate gene search) is hampered by the scarcity of easy-to-use data browsers addressed to the broad community of biomedical researchers. We propose a new visualization method depicting the overall DNA methylation status at each TCGA cohort while emphasizing its heterogeneity, thus facilitating the evaluation of the cohort variability and the normal versus tumor differences. Implemented as a trackhub integrated to the University of California Santa Cruz (UCSC) genome browser, it can be easily added to any genome-wide annotation layer.

To exemplify the trackhub usage we evaluate local DNA methylation boundaries, the aberrant DNA methylation of a CpG island located at the estrogen receptor 1 (ESR1) in breast and colon cancer, and the hypermethylation of the Homeobox HOXA gene cluster and the EN1 gene in multiple cancer types. The DNA methylation pancancer trackhub is freely available at http://maplab.cat/tcga_450k_trackhub.

Key words

DNA methylation Pancancer Data visualization TCGA The Cancer Genome Atlas 

Notes

Acknowledgments

We thank Iñaki Martinez de Ilarduya for his excellent technical support. The trackhub published here is based upon data generated by the TCGA Research Network: http://cancergenome.nih.gov/. This work was supported by the Spanish Ministry of Economy and Competitiveness [SAF2011/23638 and SAF2015-64521-R to M.A.P.]. CERCA Program/Generalitat de Catalunya.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Izaskun Mallona
    • 1
  • Alberto Sierco
    • 1
  • Miguel A. Peinado
    • 2
  1. 1.Predictive and Personalized Medicine of Cancer ProgramHealth Research Institute Germans Trias i Pujol (IGTP)BadalonaSpain
  2. 2.IGTPIMPPCBadalonaSpain

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