Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.
Bioinformatics. 2017 Oct 15;33(20):3268-3275. doi: 10.1093/bioinformatics/btx371.
The Human Reference Epigenome Map, generated by the Roadmap Epigenomics Consortium, contains thousands of genome-wide epigenomic datasets that describe epigenomes of a variety of different human tissue and cell types. This map has allowed investigators to obtain a much deeper and more comprehensive view of our regulatory genome, e.g. defining regulatory elements including all promoters and enhancers for a given tissue or cell type. An outstanding task is to combine and compare different epigenomes in order to identify regions with epigenomic features specific to certain types of tissues or cells, e.g. lineage-specific regulatory elements. Currently available tools do not directly address this question. This need motivated us to develop a tool that allows investigators to easily identify regions with epigenetic features unique to specific epigenomes that they choose, making detection of common regulatory elements and/or cell type-specific regulatory elements an interactive and dynamic experience.
An online tool EpiCompare was developed to assist investigators in exploring the specificity of epigenomic features across selected tissue and cell types. Investigators can design their test by choosing different combinations of epigenomes, and choosing different classification algorithms provided by our tool. EpiCompare will then identify regions with specified epigenomic features, and provide a quality assessment of the predictions. Investigators can interact with EpiCompare by investigating Roadmap Epigenomics data, or uploading their own data for comparison. We demonstrate that by using specific combinations of epigenomes we can detect developmental lineage-specific enhancers. Finally, prediction results can be readily visualized and further explored in the WashU Epigenome Browser.
EpiCompare is freely available on the web at http://epigenome.wustl.edu/EpiCompare/.
Supplementary data are available at Bioinformatics online.
人类参考表观基因组图谱由 Roadmap Epigenomics 联盟生成,包含数千个全基因组表观基因组数据集,描述了各种不同人类组织和细胞类型的表观基因组。该图谱使研究人员能够更深入、更全面地了解我们的调控基因组,例如定义包括给定组织或细胞类型的所有启动子和增强子在内的调控元件。一项突出的任务是整合和比较不同的表观基因组,以识别具有特定组织或细胞类型表观基因组特征的区域,例如谱系特异性调控元件。目前可用的工具无法直接解决这个问题。这一需求促使我们开发了一种工具,使研究人员能够轻松识别他们选择的特定表观基因组特有的具有表观遗传特征的区域,从而使检测常见调控元件和/或细胞类型特异性调控元件成为一种交互式和动态的体验。
开发了一个在线工具 EpiCompare,以协助研究人员探索所选组织和细胞类型中表观基因组特征的特异性。研究人员可以通过选择不同的表观基因组组合,并选择我们工具提供的不同分类算法来设计他们的测试。EpiCompare 随后将识别具有指定表观基因组特征的区域,并提供预测的质量评估。研究人员可以通过研究 Roadmap Epigenomics 数据或上传自己的数据进行比较与 EpiCompare 进行交互。我们证明,通过使用特定的表观基因组组合,我们可以检测到发育谱系特异性增强子。最后,预测结果可以在 WashU Epigenome Browser 中轻松可视化和进一步探索。
EpiCompare 可在 http://epigenome.wustl.edu/EpiCompare/ 上免费在线使用。
补充数据可在 Bioinformatics 在线获取。