Computer Laboratory, University of Cambridge, Cambridge CB3 0FD, UK.
Bioinformatics. 2013 May 1;29(9):1206-7. doi: 10.1093/bioinformatics/btt120. Epub 2013 Mar 18.
With the introduction of the Hi-C method new and fundamental properties of the nuclear architecture are emerging. The ability to interpret data generated by this method, which aims to capture the physical proximity between and within chromosomes, is crucial for uncovering the three dimensional structure of the nucleus. Providing researchers with tools for interactive visualization of Hi-C data can help in gaining new and important insights. Specifically, visual comparison can pinpoint changes in spatial organization between Hi-C datasets, originating from different cell lines or different species, or normalized by different methods. Here, we present CytoHiC, a Cytsocape plugin, which allow users to view and compare spatial maps of genomic landmarks, based on normalized Hi-C datasets. CytoHiC was developed to support intuitive visual comparison of Hi-C data and integration of additional genomic annotations.
The CytoHiC plugin, source code, user manual, example files and documentation are available at: http://apps.cytoscape.org/apps/cytohicplugin
随着 Hi-C 方法的引入，核架构的新的和基本性质正在出现。解释该方法生成的数据的能力对于揭示细胞核的三维结构至关重要，该方法旨在捕获染色体之间和内部的物理接近度。为研究人员提供用于交互式可视化 Hi-C 数据的工具可以帮助获得新的和重要的见解。具体来说，可视化比较可以指出源自不同细胞系或不同物种的 Hi-C 数据集之间，或通过不同方法归一化的空间组织的变化。在这里，我们展示了 CytoHiC，这是 Cytoscape 的一个插件，允许用户根据归一化的 Hi-C 数据集查看和比较基因组标记的空间图谱。CytoHiC 的开发是为了支持直观的 Hi-C 数据比较和集成其他基因组注释。
CytoHiC 插件、源代码、用户手册、示例文件和文档可在以下网址获得：http://apps.cytoscape.org/apps/cytohicplugin
