QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks

• DOI: 10.1371/journal.pcbi.1004809
• Publication Date: 2016-06-23T18:22:36Z
• Authors: Asa Thibodeau; Eladio J. Márquez; Oscar Luo; Yijun Ruan; Francesca Menghi; Dong-Guk Shin; Michael L. Stitzel; Paola Vera-Licona; Duygu Ucar
• Keywords: 0301 basic medicine; 570; Internet; Binding Sites; QH301-705.5; Life Sciences; Polymorphism, Single Nucleotide; Chromatin; 004; Epigenesis, Genetic; User-Computer Interface; 03 medical and health sciences; Protein Interaction Mapping; Medicine and Health Sciences; Data Mining; Regulatory Elements, Transcriptional; Biology (General); Software; Research Article; Protein Binding; Signal Transduction

Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for mapping interactions between DNA regions, e.g., ChIA-PET and HiC, can generate genome-wide maps of interactions between regulatory elements. These interaction datasets are important resources to infer distal gene targets of non-coding regulatory elements and to facilitate prioritization of critical loci for important cellular functions. With the increasing diversity and complexity of genomic information and public ontologies, making sense of these datasets demands integrative and easy-to-use software tools. Moreover, network representation of chromatin interaction maps enables effective data visualization, integration, and mining. Currently, there is no software that can take full advantage of network theory approaches for the analysis of chromatin interaction datasets. To fill this gap, we developed a web-based application, QuIN, which enables: 1) building and visualizing chromatin interaction networks, 2) annotating networks with user-provided private and publicly available functional genomics and interaction datasets, 3) querying network components based on gene name or chromosome location, and 4) utilizing network based measures to identify and prioritize critical regulatory targets and their direct and indirect interactions.QuIN's web server is available at http://quin.jax.org QuIN is developed in Java and JavaScript, utilizing an Apache Tomcat web server and MySQL database and the source code is available under the GPLV3 license available on GitHub: https://github.com/UcarLab/QuIN/.