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

Genome Biology. 2018;19(1):1-12 DOI 10.1186/s13059-018-1519-9

 

Journal Homepage

Journal Title: Genome Biology

ISSN: 1474-760X (Online)

Publisher: BMC

LCC Subject Category: Science: Biology (General): Genetics

Country of publisher: United Kingdom

Language of fulltext: English

Full-text formats available: PDF, HTML

 

AUTHORS


Yanli Wang (Bioinformatics and Genomics Program, The Pennsylvania State University)

Fan Song (Bioinformatics and Genomics Program, The Pennsylvania State University)

Bo Zhang (Bioinformatics and Genomics Program, The Pennsylvania State University)

Lijun Zhang (Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State Hershey)

Jie Xu (Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State Hershey)

Da Kuang (Department of Computer and Information Science, University of Pennsylvania)

Daofeng Li (Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine)

Mayank N. K. Choudhary (Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine)

Yun Li (Department of Genetics, University of North Carolina)

Ming Hu (Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation)

Ross Hardison (Center for Computational Biology and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University)

Ting Wang (Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine)

Feng Yue (Bioinformatics and Genomics Program, The Pennsylvania State University)

EDITORIAL INFORMATION

Blind peer review

Editorial Board

Instructions for authors

Time From Submission to Publication: 14 weeks

 

Abstract | Full Text

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.