Introduction

Integrative analyses of epigenetic data promise a deeper understanding of the epigenome. Epidaurus is a bioinformatics tool used to effectively reveal inter-dataset relevance and differences through data aggregation, integration and visualization. In this study, we demonstrated the utility of Epidaurus in validating hypotheses and generating novel biological insights. In particular, we described the use of Epidaurus to (i) integrate epigenetic data from prostate cancer cell lines to validate the activation function of EZH2 in castration-resistant prostate cancer and to (ii) study the mechanism of androgen receptor (AR) binding deregulation induced by the knockdown of FOXA1. We found that EZH2's noncanonical activation function was reaffirmed by its association with active histone markers and the lack of association with repressive markers. More importantly, we revealed that the binding of AR was selectively reprogramed to promoter regions, leading to the up-regulation of hundreds of cancer-associated genes including EGFR. The prebuilt epigenetic dataset from commonly used cell lines (LNCaP, VCaP, LNCaP-Abl, MCF7, GM12878, K562, HeLa-S3, A549, HePG2) makes Epidaurus a useful online resource for epigenetic research. As standalone software, Epidaurus is specifically designed to process user customized datasets with both efficiency and convenience.

Publications

  1. Epidaurus: aggregation and integration analysis of prostate cancer epigenome.
    Cite this
    Wang L, Huang H, Dougherty G, Zhao Y, Hossain A, Kocher JP, 2015-01-01 - Nucleic acids research

Credits

  1. Liguo Wang
    Developer

    Division of Biomedical Statistics and Informatics, Mayo Clinic, United States of America

  2. Haojie Huang
    Developer

    Department of Biochemistry and Molecular Biology, Mayo Clinic, United States of America

  3. Gregory Dougherty
    Developer

    Division of Biomedical Statistics and Informatics, Mayo Clinic, United States of America

  4. Yu Zhao
    Developer

    Department of Biochemistry and Molecular Biology, Mayo Clinic, United States of America

  5. Asif Hossain
    Developer

    Division of Biomedical Statistics and Informatics, Mayo Clinic, United States of America

  6. Jean-Pierre A Kocher
    Investigator

    Division of Biomedical Statistics and Informatics, Mayo Clinic, United States of America

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Summary
AccessionBT002404
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByJean-Pierre A Kocher