C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search

BMC Bioinformatics

Research

Jyotsna Dhawan¹  Surabhi Srivastava¹  Rakesh K Mishra¹  Divya Tej Sowpati¹ 

[1] CSIR- Centre for Cellular and Molecular Biology, Hyderabad, India;

关键词: Epigenetic patterns;    Chromatin state;    Visualization;    JavaScript;    Genome browser;    Web app;    ChIP-seq;    RNA-seq;   

DOI  :  10.1186/s12859-017-1786-6

来源: Springer

【 摘 要 】

BackgroundComparative 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.ResultsWe 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.ConclusionsC-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.

【 授权许可】

CC BY   
© The Author(s). 2017