CpG Islands pp 123-135 | Cite as

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

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


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

Key words

DNA methylation Pancancer Data visualization TCGA The Cancer Genome Atlas 



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: 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.


  1. 1.
    Zhang J, Baran J, Cros A, Guberman JM, Haider S, Hsu J, Liang Y, Rivkin E, Wang J, Whitty B, Wong-Erasmus M, Yao L, Kasprzyk A (2011) International Cancer Genome Consortium Data Portal—a one-stop shop for cancer genomics data. Database (Oxford) 2011:bar026Google Scholar
  2. 2.
    Schroeder MP, Gonzalez-Perez A, Lopez-Bigas N (2013) Visualizing multidimensional cancer genomics data. Genome Med 5(1):9CrossRefGoogle Scholar
  3. 3.
    Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, Antipin Y, Reva B, Goldberg AP, Sander C, Schultz N (2012) The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov 2(5):401–404CrossRefGoogle Scholar
  4. 4.
    Cline MS, Craft B, Swatloski T, Goldman M, Ma S, Haussler D, Zhu J (2013) Exploring TCGA Pan-Cancer data at the UCSC Cancer Genomics Browser. Sci Rep 3:2652CrossRefGoogle Scholar
  5. 5.
    Speir ML, Zweig AS, Rosenbloom KR, Raney BJ, Paten B, Nejad P, Lee BT, Learned K, Karolchik D, Hinrichs AS, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Fujita PA, Eisenhart C, Diekhans M, Clawson H, Casper J, Barber GP, Haussler D, Kuhn RM, Kent WJ (2016) The UCSC Genome Browser database: 2016 update. Nucleic Acids Res 44(D1):D717–D725CrossRefGoogle Scholar
  6. 6.
    Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, Delano D, Zhang L, Schroth GP, Gunderson KL, Fan JB, Shen R (2011) High density DNA methylation array with single CpG site resolution. Genomics 98(4):288–295CrossRefGoogle Scholar
  7. 7.
    Zhu Y, Qiu P, Ji Y (2014) TCGA-assembler: open-source software for retrieving and processing TCGA data. Nat Methods 11(6):599–600CrossRefGoogle Scholar
  8. 8.
    Esteller M (2007) Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet 8(4):286–298CrossRefGoogle Scholar
  9. 9.
    Muller HM, Widschwendter A, Fiegl H, Ivarsson L, Goebel G, Perkmann E, Marth C, Widschwendter M (2003) DNA methylation in serum of breast cancer patients: an independent prognostic marker. Cancer Res 63(22):7641–7645PubMedGoogle Scholar
  10. 10.
    Frigola J, Song J, Stirzaker C, Hinshelwood RA, Peinado MA, Clark S (2006) Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band. Nat Genet 38(5):540–549CrossRefGoogle Scholar
  11. 11.
    Rauch T, Wang Z, Zhang X, Zhong X, Wu X, Lau SK, Kernstine KH, Riggs AD, Pfeifer GP (2007) Homeobox gene methylation in lung cancer studied by genome-wide analysis with a microarray-based methylated CpG island recovery assay. Proc Natl Acad Sci U S A 104(13):5527–5532CrossRefGoogle Scholar
  12. 12.
    Mayor R, Casadome L, Azuara D, Moreno V, Clark SJ, Capella G, Peinado MA (2009) Long-range epigenetic silencing at 2q14.2 affects most human colorectal cancers and may have application as a non-invasive biomarker of disease. Br J Cancer 100(10):1534–1539CrossRefGoogle Scholar

Copyright information

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

Authors and Affiliations

  • Izaskun Mallona
    • 1
    Email author
  • 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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