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Genome Biol. 2018 Oct 4;19(1):151. doi: 10.1186/s13059-018-1519-9.

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

Author information

1
Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, 16802, USA.
2
Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State Hershey, Hershey, PA, 17033, USA.
3
Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, 19104, USA.
4
Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63108, USA.
5
Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA.
6
Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27599, USA.
7
Department of Computer Science, University of North Carolina, Chapel Hill, NC, 27599, USA.
8
Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA.
9
Center for Computational Biology and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA, 16802, USA.
10
Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63108, USA. twang@genetics.wustl.edu.
11
Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, 16802, USA. fyue@hmc.psu.edu.
12
Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State Hershey, Hershey, PA, 17033, USA. fyue@hmc.psu.edu.

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.

PMID:
30286773
PMCID:
PMC6172833
DOI:
10.1186/s13059-018-1519-9
[Indexed for MEDLINE]
Free PMC Article

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