Epidaurus: Aggregation and integration analysis of prostate cancer epigenome

Liguo Wang, Haojie Huang, Gregory Dougherty, Yu Zhao, Asif Hossain, Jean-Pierre Kocher

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)e7
JournalNucleic Acids Research
Volume43
Issue number2
DOIs
StatePublished - Jan 30 2015

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Epigenomics
Prostatic Neoplasms
Androgen Receptors
Cell Line
Neoplasm Genes
Castration
Computational Biology
Genetic Promoter Regions
Histones
Up-Regulation
Software
Research
Datasets

ASJC Scopus subject areas

  • Genetics

Cite this

Epidaurus : Aggregation and integration analysis of prostate cancer epigenome. / Wang, Liguo; Huang, Haojie; Dougherty, Gregory; Zhao, Yu; Hossain, Asif; Kocher, Jean-Pierre.

In: Nucleic Acids Research, Vol. 43, No. 2, 30.01.2015, p. e7.

Research output: Contribution to journalArticle

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