CHiCP (Capture Hi-C Plotter) is a web-based tool designed for the interactive visualization of promoter capture Hi-C (PCHi-C) datasets. PCHi-C is a genomic technique that maps physical interactions between distal DNA regulatory elements and gene promoters across the genome. CHiCP allows researchers to explore these interaction maps, integrate public and user-defined genomic datasets, and gain insights into the regulatory mechanisms that govern gene expression.
The tool supports major HTML5 browsers and is freely accessible, providing a visual platform for the analysis of chromosomal interaction data. Researchers can overlay additional genomic annotations on the interaction maps, making it a powerful resource for understanding the spatial organization of the genome and its influence on gene regulation in various tissue types. The full source code is also available for customization and development
Interactive Visualization: CHiCP enables users to explore complex genomic interactions by generating detailed visual representations of chromosomal interaction maps. The interface is designed to be interactive, allowing users to zoom into specific areas of interest, overlay datasets, and examine different regulatory regions.
Integration with Genomic Datasets: In addition to promoter capture Hi-C data, users can integrate publicly available genomic annotations or upload their own datasets. This helps researchers correlate interaction maps with other genomic features, such as epigenetic marks, transcription factor binding sites, or gene expression data.
Open Source and Accessibility: CHiCP is open source, and its code is available on GitHub, allowing for further development or adaptation by researchers. It is freely accessible via most modern web browsers without the need for installation
Use in Research: The tool has been used in various studies to investigate the regulatory architecture of the genome, particularly in understanding diseases where gene regulation is disrupted. For example, it aids in uncovering how non-coding regions of DNA influence disease-associated genes by mediating long-range interactions.
By providing a platform to visually interpret and analyze the 3D architecture of the genome, CHiCP helps researchers uncover the functional relevance of DNA interactions, contributing to advances in genetics, epigenetics, and disease research.