TitleC-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search.
Publication TypeJournal Article
Year of Publication2017
AuthorsSowpati DTej, Srivastava S, Dhawan J, Mishra RK
JournalBMC Bioinformatics
IssueSuppl 10
Date Published2017 Sep 13
KeywordsAlgorithms, Embryonic Stem Cells, Epigenomics, Genes, Genomics, HeLa Cells, Humans, Internet, K562 Cells, Promoter Regions, Genetic, Software, Transcription, Genetic, Web Browser

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.

Alternate JournalBMC Bioinformatics
PubMed ID28929968
PubMed Central IDPMC5606219