HiC-3DViewer: a new tool to visualize Hi-C data in 3D space
HiC-3DViewer: a new tool to visualize Hi-C data in 3D space
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HiC-3DViewer：在 3D 空间中可视化 Hi-C 数据的新工具
DOI：
10.1007/s40484-017-0091-8
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发表时间：
2017-06-01
影响因子：
3.1
通讯作者：
Gao, Juntao
中科院分区：
文献类型：
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作者：
Djekidel, Mohamed Nadhir;Wang, Mengjie;Gao, Juntao
背景尽管以前所未有的分辨率和比例绘制染色质结构图已经取得了重大进展，但我们还缺乏能够沿染色质三维结构进行直观可视化和导航的工具。到目前为止，人们所拥有的工具一般都是基于脚本的，或者提供的基本功能不容易实现基因组数据与3D染色质结构的集成，因此，许多科学家发现他们有义务破解为其他目的设计的工具，如蛋白质结构研究工具。方法我们介绍了HIC-3DViewer，这是一个基于浏览器的新的交互工具，旨在为研究人员提供直观的环境，以促进Hi-C数据的3D探索性分析以及许多有用的注释功能。在HIC-3DViewer与染色质构象研究相关的关键功能中，最重要的是一维到二维到三维的映射，以交互方式突出感兴趣的基因组区域。这一功能使调查人员能够在不同的层次/角度探索他们的数据。结果作为原理验证，我们应用HIC-3DViewer研究了Hi-C数据的质量，并展示了GATA1和GATA2沿基因组的空间结合。结论HIC-3DViewer作为一种用户友好的工具，可以可视化地显示染色质间/染色质内的相互作用，并使用户只需简单地点击鼠标，就可以灵活地定制3D结构的外观和感觉。HIC-3DViewer是用JAVASSCRIPT和PYTHON实现的，可以在http://bioinfo.au.tsinghua.edu.cn/member/nadhir/HiC3DViewer/.上免费获得补充信息(用户手册、演示数据)也可在该网站上找到。
BackgroundAlthough significant progress has been made to map chromatin structure at unprecedented resolution and scales, we are short of tools that enable the intuitive visualization and navigation along the three‐dimensional (3D) structure of chromatins. The available tools people have so far are generally script‐based or present basic features that do not easily enable the integration of genomic data along with 3D chromatin structure, hence, many scientists find themselves in the obligation to hack tools designed for other purposes such as tools for protein structure study.MethodsWe present HiC‐3DViewer, a new browser‐based interactive tool designed to provide an intuitive environment for investigators to facilitate the 3D exploratory analysis of Hi‐C data along with many useful annotation functionalities. Among the key features of HiC‐3DViewer relevant to chromatin conformation studies, the most important one is the 1D‐to‐2D‐to‐3D mapping, to highlight genomic regions of interest interactively. This feature enables investigators to explore their data at different levels/angels. Additionally, investigators can superpose different genomic signals (such as ChIP‐Seq, SNP) on the top of the 3D structure.ResultsAs a proof of principle we applied HiC‐3DViewer to investigate the quality of Hi‐C data and to show the spatial binding of GATA1 and GATA2 along the genome.ConclusionsAs a user‐friendly tool, HiC‐3DViewer enables the visualization of inter/intra‐chromatin interactions and gives users the flexibility to customize the look‐and‐feel of the 3D structure with a simple click. HiC‐3DViewer is implemented in Javascript and Python, and is freely available at: http://bioinfo.au.tsinghua.edu.cn/member/nadhir/HiC3DViewer/. Supplementary information (User Manual, demo data) is also available at this website.