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

Yanli Wang, Bo Zhang, Lijun Zhang, Lin An, Jie Xu, Daofeng Li, Mayank NK Choudhary, Yun Li, Ming Hu, Ross Hardison, Ting Wang, Feng Yue
doi: https://doi.org/10.1101/112268
Yanli Wang
1Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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Bo Zhang
1Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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Lijun Zhang
2Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
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Lin An
1Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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Jie Xu
2Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
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Daofeng Li
3Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, 63110, USA
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Mayank NK Choudhary
3Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, 63110, USA
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Yun Li
4Department of Genetics, Department of Biostatistics, Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA
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Ming Hu
5Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
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Ross Hardison
6Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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Ting Wang
3Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, 63110, USA
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  • For correspondence: fyue@hmc.psu.edu twang@genetics.wustl.edu
Feng Yue
1Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
2Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
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  • For correspondence: fyue@hmc.psu.edu twang@genetics.wustl.edu
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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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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 27, 2017.
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The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions
Yanli Wang, Bo Zhang, Lijun Zhang, Lin An, Jie Xu, Daofeng Li, Mayank NK Choudhary, Yun Li, Ming Hu, Ross Hardison, Ting Wang, Feng Yue
bioRxiv 112268; doi: https://doi.org/10.1101/112268
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The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions
Yanli Wang, Bo Zhang, Lijun Zhang, Lin An, Jie Xu, Daofeng Li, Mayank NK Choudhary, Yun Li, Ming Hu, Ross Hardison, Ting Wang, Feng Yue
bioRxiv 112268; doi: https://doi.org/10.1101/112268

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