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

Yanli Wang, Fan Song, Bo Zhang, Lijun Zhang, Jie Xu, Da Kuang, Daofeng Li, Mayank N.K. Choudhary, Yun Li, Ming Hu, Ross Hardison, Ting Wang*, Feng Yue

*Corresponding author for this work

Research output: Contribution to journalArticle

74 Scopus citations

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.

Original languageEnglish (US)
Article number151
JournalGenome biology
Volume19
Issue number1
DOIs
StatePublished - Oct 4 2018

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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    Wang, Y., Song, F., Zhang, B., Zhang, L., Xu, J., Kuang, D., Li, D., Choudhary, M. N. K., Li, Y., Hu, M., Hardison, R., Wang, T., & Yue, F. (2018). The 3D Genome Browser: A web-based browser for visualizing 3D genome organization and long-range chromatin interactions. Genome biology, 19(1), [151]. https://doi.org/10.1186/s13059-018-1519-9