QuIN

QuIN constructs and analyzes chromatin interaction networks from data such as ChIA-PET and HiC to characterize interactions among promoters, enhancers, and other regulatory elements and to prioritize regulatory targets using network theory.

Key Features:

• Network Construction and Visualization: Builds chromatin interaction networks and provides visual representations of interactions between distal genomic regulatory elements such as promoters and enhancers.
• Annotation Capabilities: Annotates interaction networks using user-provided private datasets and publicly available functional genomics data.
• Query Functionality: Supports queries of network components by gene name and by specific chromosome locations.
• Network-Based Analysis: Applies network theory measures to identify and prioritize critical regulatory targets, including exploration of direct and indirect interactions to infer distal gene targets influenced by non-coding regulatory elements.

Scientific Applications:

• Locus Prioritization: Prioritizes loci and regulatory targets relevant to cellular functions based on chromatin interaction topology.
• Regulatory Target Inference: Maps and analyzes chromatin interactions to infer relationships between distant regulatory elements and their target genes.
• Functional Genomics Integration: Integrates diverse interaction and functional genomics datasets to support analyses in functional genomics studies.

Methodology:

Implemented in Java and JavaScript, deployed on an Apache Tomcat web server with a MySQL backend, and released under the GPLv3 license.