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

Yanli Wang; Fan Song; Bo Zhang; Lijun Zhang; Jie Xu; Da Kuang; Daofeng Li; Mayank N.K. Choudhary; Yun Li; Ming Hu; Ross Hardison; Ting Wang; Feng Yue

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

Yanli Wang, Fan Song, Bo Zhang, Lijun Zhang, Jie Xu, Da Kuang, Daofeng Li, Mayank N.K. Choudhary, Yun Li, Ming Hu, Ross Hardison, Ting Wang^*, Feng Yue

^*Corresponding author for this work

Biochemistry and Molecular Genetics

Research output: Contribution to journal › Article › peer-review

331 Scopus citations

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.

Original language	English (US)
Article number	151
Journal	Genome biology
Volume	19
Issue number	1
DOIs	https://doi.org/10.1186/s13059-018-1519-9
State	Published - Oct 4 2018

Funding

This work was supported by NIH grants R35GM124820, R01HG009906, and U01CA200060 (F.Y.). F.Y. is also supported by Leukemia Research Foundation, PhRMA Foundation, and Penn State CTSI. T.W. is also supported by NIH grants R01HG007175, R01HG007354, R01ES024992, U24ES026699, and U01HG009391. M.H. is partially supported by NIH U54DK107977. Y.L. is partially supported by NIH R01HG006292 and R01HL129132.

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

Access to Document

10.1186/s13059-018-1519-9

Cite this

@article{13da59a7ac664accb5249f35cf7a7afb,

title = "The 3D Genome Browser: A web-based browser for visualizing 3D genome organization and long-range chromatin interactions",

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.",

author = "Yanli Wang and Fan Song and Bo Zhang and Lijun Zhang and Jie Xu and Da Kuang and Daofeng Li and Choudhary, {Mayank N.K.} and Yun Li and Ming Hu and Ross Hardison and Ting Wang and Feng Yue",

note = "Publisher Copyright: {\textcopyright} 2018 The Author(s).",

year = "2018",

month = oct,

day = "4",

doi = "10.1186/s13059-018-1519-9",

language = "English (US)",

volume = "19",

journal = "Genome biology",

issn = "1474-7596",

publisher = "BioMed Central",

number = "1",

}

TY - JOUR

T1 - The 3D Genome Browser

T2 - A web-based browser for visualizing 3D genome organization and long-range chromatin interactions

AU - Wang, Yanli

AU - Song, Fan

AU - Zhang, Bo

AU - Zhang, Lijun

AU - Xu, Jie

AU - Kuang, Da

AU - Li, Daofeng

AU - Choudhary, Mayank N.K.

AU - Li, Yun

AU - Hu, Ming

AU - Hardison, Ross

AU - Wang, Ting

AU - Yue, Feng

PY - 2018/10/4

Y1 - 2018/10/4

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85054460140&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85054460140&partnerID=8YFLogxK

U2 - 10.1186/s13059-018-1519-9

DO - 10.1186/s13059-018-1519-9

M3 - Article

C2 - 30286773

AN - SCOPUS:85054460140

SN - 1474-7596

VL - 19

JO - Genome biology

JF - Genome biology

IS - 1

M1 - 151

ER -

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

Abstract

Funding

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this