Chapter 7 – Mining the Epigenetic Landscape: Surface Mining or Deep Underground

With improvements in epigenomic profiling assays and with increasing amounts of epigenomic data in public repositories, new opportunities are available to understand normal epigenomes and their cancer-related perturbations. Nascent comparative epigenomic analyses have the potential to provide insights into cancer etiology, identify clinically relevant cancer biomarkers and therapeutic targets. Much of the epigenomic data generated by large consortium projects and small projects are now publicly available at epigenomic data portals. Several computational tools and methodological framework are developed to perform comparative epigenomic analysis. However, the methods for comparative epigenomic analysis are in their infancy and numerous challenges are faced when mining heterogeneous epigenomic datasets. In this chapter, we describe types of epigenomic data available in public repositories, epigenomic tools for comparative analysis, and address challenges faced when mining epigenomic datasets. We also illustrate the utility of mining epigenomic data by providing use cases that utilize publicly available data and tools to provide example into types of analysis that are possible.