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

By Yanli Wang, F. Song, Bo Zhang, Lijun Zhang, Jie Xu, Dai-Yong Kuang, Daofeng Li, Mayank N. K. Choudhary, Yun Li, Ming Hu and 3 more. Genome Biology, 2017

528 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/a0339c0f79020a4f110313880451a139b637699d

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Citations in the corpus

Cooler: scalable storage for Hi-C data and other genomically-labeled arrays (2019, methodology): “Several custom binary formats have been developed for Hi-C data, including butlr (7), hic (8), and MRH (9).”
Functional mapping and annotation of genetic associations with FUMA (2017, methodology): “The availability of biological resources that can aid in the interpretation of GWAS results, such as Hi-C and ChIA-PET, have dramatically increased recently and several studies have identi ﬁ ed novel candidates from GWAS risk loci by integrating their results for example with chromatin interactions ”
Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis (2018, methodology): “In addition, we will explore the use of long-range chromatin interaction data, such as those available at The 3D Genome Browser (50) to improve TF target predictions.”
The UCSC Genome Browser database: 2021 update (2020, methodology): “Several tools already existed to view Hi-C data (JuiceBox (40), HiGlass (41), the 3D Genome Browser (42), and the WashU Epigenome Browser (43)), but there was no fully integrated solution to view the data in tandem with Genome Browser tracks or sessions.”
Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data (2017, unknown): “Although several other web-based Hi-C contact map browsers have been developed (Wang et al., 2017; Yardımcı and Noble, 2017), none of the tools that have been published to date support interactive zooming in real time, a critical feature that is essential to seamless exploration of the high…”