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

BMC Bioinformatics. 2017 Sep 13;18(Suppl 10):392. doi: 10.1186/s12859-017-1786-6.


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.

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

MeSH terms

  • Algorithms
  • Embryonic Stem Cells / metabolism
  • Epigenomics*
  • Genes*
  • Genomics
  • HeLa Cells
  • Humans
  • Internet
  • K562 Cells
  • Promoter Regions, Genetic / genetics
  • Software*
  • Transcription, Genetic
  • Web Browser*