Abstract
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.
List of abbreviations
- API
- Application programming interface
- BED
- Browser Extensible Data
- ChIP
- Chromatin immunoprecipitation
- ESC
- embryonic stem cell
- FAQ
- Frequently Asked Questions
- GUI
- Graphical User Interface
- IGV
- Integrative Genomics Viewer
- MVVM
- Model-View-View Model
- NGS
- Next Generation Sequencing
- SVG
- Scalable Vector Graphics
- TSS
- Transcription start site