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bioRxiv · 10.1101/112268

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

Wang, Y.·Zhang, B.·Zhang, L.·An, L.·Xu, J.·Li, D.·Choudhary, M. N.·Li, Y.·Hu, M.·Hardison, R.·Wang, T.·Yue, F.
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Abstract

Recent advent of 3C-based technologies such as Hi-C and ChIA-PET provides us an opportunity to explore chromatin interactions and 3D genome organization in an unprecedented scale and resolution. However, it remains a challenge to visualize chromatin interaction data due to its size and complexity. Here, we introduce the 3D Genome Browser (http://3dgenome.org), which allows users to conveniently explore both publicly available and their own chromatin interaction data. Users can also seamlessly integrate other \"omics\" data sets, such as ChIP-Seq and RNA-Seq for the same genomic region, to gain a complete view of both regulatory landscape and 3D genome structure for any given gene. Finally, our browser provides multiple methods to link distal cis-regulatory elements with their potential target genes, including virtual 4C, ChIA-PET, Capture Hi-C and cross-cell-type correlation of proximal and distal DNA hypersensitive sites, and therefore represents a valuable resource for the study of gene regulation in mammalian genomes.

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Wang, Y., Zhang, B., Zhang, L., An, L., Xu, J., Li, D., Choudhary, M. N., Li, Y., Hu, M., Hardison, R., Wang, T., Yue, F.. 2017-02-27. The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions. https://doi.org/10.1101/112268

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