TY - JOUR T1 - C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search. JF - BMC Bioinformatics Y1 - 2017 A1 - Sowpati, Divya Tej A1 - Srivastava, Surabhi A1 - Dhawan, Jyotsna A1 - Mishra, Rakesh K KW - Algorithms KW - Embryonic Stem Cells KW - Epigenomics KW - Genes KW - Genomics KW - HeLa Cells KW - Humans KW - Internet KW - K562 Cells KW - Promoter Regions, Genetic KW - Software KW - Transcription, Genetic KW - Web Browser AB -

BACKGROUND: 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.

RESULTS: 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.

CONCLUSIONS: 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.

VL - 18 IS - Suppl 10 ER -