Sowpati Divya Tej, Srivastava Surabhi, Dhawan Jyotsna, Mishra Rakesh K
CSIR- Centre for Cellular and Molecular Biology, Hyderabad, India.
BMC Bioinformatics. 2017 Sep 13;18(Suppl 10):392. doi: 10.1186/s12859-017-1786-6.
Comparative epigenomic analysis across multiple genes presents a bottleneck for bench biologists working with NGS data. Despite the development of standardized peak analysis algorithms, the identification of novel epigenetic patterns and their visualization across gene subsets remains a challenge.
We developed a fast and interactive web app, C-State (Chromatin-State), to query and plot chromatin landscapes across multiple loci and cell types. C-State has an interactive, JavaScript-based graphical user interface and runs locally in modern web browsers that are pre-installed on all computers, thus eliminating the need for cumbersome data transfer, pre-processing and prior programming knowledge.
C-State is unique in its ability to extract and analyze multi-gene epigenetic information. It allows for powerful GUI-based pattern searching and visualization. We include a case study to demonstrate its potential for identifying user-defined epigenetic trends in context of gene expression profiles.
对多个基因进行比较表观基因组分析是从事NGS数据研究的实验生物学家面临的一个瓶颈。尽管已经开发出标准化的峰分析算法，但识别新的表观遗传模式并在基因子集间进行可视化展示仍然是一项挑战。
我们开发了一个快速且交互式的网络应用程序C-State（染色质状态），用于查询和绘制多个基因座和细胞类型的染色质图谱。C-State具有基于JavaScript的交互式图形用户界面，可在所有计算机上预先安装的现代网络浏览器中本地运行，从而无需进行繁琐的数据传输、预处理和预先的编程知识。
C-State在提取和分析多基因表观遗传信息方面具有独特能力。它允许基于强大的图形用户界面进行模式搜索和可视化展示。我们通过一个案例研究来证明其在基因表达谱背景下识别用户定义的表观遗传趋势的潜力。
