Putting epigenome comparison into practice

NIH Epigenomics Roadmap Data Analysis and Coordination Center, Molecular and Human Genetics Department, Baylor College of Medicine, Houston, Texas, USA.
Nature Biotechnology (Impact Factor: 41.51). 10/2010; 28(10):1053-6. DOI: 10.1038/nbt1010-1053
Source: PubMed


Comparative analysis of epigenomes offers new opportunities to understand cellular differentiation, mutation effects and disease processes. But the scale and heterogeneity of epigenetic data present numerous computational challenges.

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    • "However, our current capability of interpreting epigenomic information is still primitive . The concept of using cross-species comparison to annotate epigenomic functions may revolutionize epigenomic analysis (Feng et al., 2010; Mikkelsen et al., 2010; Milosavljevic, 2010; Xiao et al., 2012). Indeed, by exploiting the link between evolutionary selection and regulatory functions, 'comparative epigenomics' have annotated epigenomes with unprecedented details (Xiao et al., 2012). "
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    ABSTRACT: We developed the Comparative Epigenome Browser (CEpBrowser) to allow the public to perform multi-species epigenomic analysis. The web-based CEpBrowser integrates, manages and visualizes sequencing-based epigenomic datasets. Five key features were developed to maximize the efficiency of interspecies epigenomic comparisons. Availability: CEpBrowser is a web application implemented with PHP, MySQL, C and Apache. URL: Contact: Supplementary information: Supplementary data are available at Bioinformatics online.
    Bioinformatics 03/2013; 29(9). DOI:10.1093/bioinformatics/btt114 · 4.98 Impact Factor
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    • "There are challenges regarding data integration, interpretation, and dissemination - as one would expect given that the technologies used are all relatively new. There is a critical need for the creation of a new generation of tools for interpretation of the numerous epigenetic datasets [81]. Briefly, in contrast to DNA sequence data, epigenomic data are not digital, differ in resolution, and are highly variable. "
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    ABSTRACT: Epigenetic changes are critical for development and progression of cancers, including breast cancer. Significant progress has been made in the basic understanding of how various epigenetic changes such as DNA methylation, histone modification, miRNA expression, and higher order chromatin structure affect gene expression. The present review will focus on methylation and demethylation of histones. While the acetylation of histones has been at the forefront of well-characterized post-translational modifications of histones, including the development of inhibitors targeting de-acetylating enzymes, the past few years have witnessed a dramatic increase in knowledge regarding the role of histone methylation/demethylation. This is an exciting and rapidly evolving area of research, with much promise for potential clinical intervention in several cancers including breast cancer. We also summarize efforts to identity DNA methylation signatures that could be prognostic and/or predictive markers in breast cancer, focusing on recent studies using genome-wide approaches. Finally, we briefly review the efforts made by both the National Institutes of Health Epigenome Project and The Cancer Genome Atlas, especially highlighting the study of breast cancer epigenetics, exciting technological advances, potential roadblocks, and future directions.
    Breast cancer research: BCR 11/2011; 13(6):225. DOI:10.1186/bcr2925 · 5.49 Impact Factor
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