The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions

• DOI: 10.1186/s13059-018-1519-9
• Publication Date: 2018-10-04T10:54:47Z
• Authors: Yanli Wang; Fan Song; Bo Zhang; Lijun Zhang; Jie Xu; Da Kuang; Daofeng Li; Mayank N. K. Chou...; Yun Li; Ming Hu; Ross Hardison; Ting Wang; Feng Yue
• Keywords: QH301-705.5; Genome, Human; Method; Genetic Variation; QH426-470; Web Browser; Polymorphism, Single Nucleotide; 3D Genome Browser; Chromatin; Mice; Imaging, Three-Dimensional; chromatin conformation; Species Specificity; Hi-C; Neoplasms; Databases, Genetic; epigenomics; Genetics; Animals; Deoxyribonuclease I; Humans; DNA, Intergenic; Biology (General)

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.