Su Sheng-Yao, Chen Shu-Hwa, Lu I-Hsuan, Chiang Yih-Shien, Wang Yu-Bin, Chen Pao-Yang, Lin Chung-Yen
Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan.
Institute of Information Science, Academia Sinica, Taipei, Taiwan.
BMC Genomics. 2016 Dec 22;17(Suppl 13):1027. doi: 10.1186/s12864-016-3326-6.
Bisulfite sequencing (BS-seq) has become a standard technology to profile genome-wide DNA methylation at single-base resolution. It allows researchers to conduct genome-wise cytosine methylation analyses on issues about genomic imprinting, transcriptional regulation, cellular development and differentiation. One single data from a BS-Seq experiment is resolved into many features according to the sequence contexts, making methylome data analysis and data visualization a complex task.
We developed a streamlined platform, TEA, for analyzing and visualizing data from whole-genome BS-Seq (WGBS) experiments conducted in the model plant Arabidopsis thaliana. To capture the essence of the genome methylation level and to meet the efficiency for running online, we introduce a straightforward method for measuring genome methylation in each sequence context by gene. The method is scripted in Java to process BS-Seq mapping results. Through a simple data uploading process, the TEA server deploys a web-based platform for deep analysis by linking data to an updated Arabidopsis annotation database and toolkits.
TEA is an intuitive and efficient online platform for analyzing the Arabidopsis genomic DNA methylation landscape. It provides several ways to help users exploit WGBS data. TEA is freely accessible for academic users at: http://tea.iis.sinica.edu.tw .
亚硫酸氢盐测序（BS-seq）已成为在单碱基分辨率下对全基因组DNA甲基化进行分析的标准技术。它使研究人员能够针对基因组印记、转录调控、细胞发育与分化等问题开展全基因组胞嘧啶甲基化分析。根据序列上下文，一个来自BS-Seq实验的单一数据会被解析为许多特征，这使得甲基化组数据分析和数据可视化成为一项复杂的任务。
我们开发了一个简化的平台TEA，用于分析和可视化在模式植物拟南芥中进行的全基因组BS-Seq（WGBS）实验数据。为了抓住基因组甲基化水平的本质并满足在线运行效率，我们引入了一种通过基因在每个序列上下文中测量基因组甲基化的直接方法。该方法用Java编写脚本以处理BS-Seq映射结果。通过简单的数据上传过程，TEA服务器通过将数据链接到更新的拟南芥注释数据库和工具包，部署了一个基于网络的深度分析平台。
TEA是一个直观且高效的在线平台，用于分析拟南芥基因组DNA甲基化图谱。它提供了多种方式来帮助用户利用WGBS数据。学术用户可通过以下网址免费访问TEA：http://tea.iis.sinica.edu.tw 。
