The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions
Yanli Wang(Pennsylvania State University), Fan Song(Pennsylvania State University), Bo Zhang(Pennsylvania State University), Lijun Zhang(Penn State Milton S. Hershey Medical Center), Jie Xu(Penn State Milton S. Hershey Medical Center), Da Kuang(University of Pennsylvania), Daofeng Li(Washington University in St. Louis), Mayank Choudhary(Washington University in St. Louis), Yun Li(University of North Carolina at Chapel Hill), Ming Hu(Cleveland Clinic), Ross C. Hardison(Pennsylvania State University), Ting Wang(Washington University in St. Louis), Feng Yue(Pennsylvania State University)
Cited by 577Open Access
Abstract
Here, we introduce the 3D Genome Browser, http://3dgenome.org , which allows users to conveniently explore both their own and over 300 publicly available chromatin interaction data of different types. We design a new binary data format for Hi-C data that reduces the file size by at least a magnitude and allows users to visualize chromatin interactions over millions of base pairs within seconds. Our browser provides multiple methods linking distal cis-regulatory elements with their potential target genes. Users can seamlessly integrate thousands of other omics data to gain a comprehensive view of both regulatory landscape and 3D genome structure.
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