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

Methods Mol Biol. 2018;1766:123-135. doi: 10.1007/978-1-4939-7768-0_7.

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 .

Keywords: DNA methylation; Data visualization; Pancancer; TCGA; The Cancer Genome Atlas.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Atlases as Topic
  • Breast Neoplasms / genetics*
  • Colonic Neoplasms / genetics*
  • CpG Islands / genetics
  • DNA Methylation*
  • Data Visualization
  • Epigenesis, Genetic*
  • Estrogen Receptor alpha / genetics
  • Female
  • Genetic Association Studies
  • Genetic Heterogeneity
  • Genome, Human / genetics*
  • Homeodomain Proteins / genetics
  • Humans
  • Multigene Family

Substances

  • EN1 protein, human
  • Estrogen Receptor alpha
  • Homeodomain Proteins
  • estrogen receptor alpha, human
  • HoxA protein