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

Research output: Contribution to journalArticle

38 Citations (Scopus)

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 languageEnglish (US)
Article number151
JournalGenome biology
Volume19
Issue number1
DOIs
StatePublished - Oct 4 2018

Fingerprint

Web Browser
Chromatin
chromatin
genome
Genome
regulatory sequences
Information Storage and Retrieval
Base Pairing
Genes
genes
gene
methodology

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

Cite this

Wang, Yanli ; Song, Fan ; Zhang, Bo ; Zhang, Lijun ; Xu, Jie ; Kuang, Da ; Li, Daofeng ; Choudhary, Mayank N.K. ; Li, Yun ; Hu, Ming ; Hardison, Ross ; Wang, Ting ; Yue, Feng. / The 3D Genome Browser : A web-based browser for visualizing 3D genome organization and long-range chromatin interactions. In: Genome biology. 2018 ; Vol. 19, No. 1.
@article{a0de07d9dead47719f7b7ddf2ce9a1ad,
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",
year = "2018",
month = "10",
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",

}

Wang, Y, Song, F, Zhang, B, Zhang, L, Xu, J, Kuang, D, Li, D, Choudhary, MNK, Li, Y, Hu, M, Hardison, R, Wang, T & Yue, F 2018, 'The 3D Genome Browser: A web-based browser for visualizing 3D genome organization and long-range chromatin interactions', Genome biology, vol. 19, no. 1, 151. https://doi.org/10.1186/s13059-018-1519-9

The 3D Genome Browser : A web-based browser for visualizing 3D genome organization and long-range chromatin interactions. / Wang, Yanli; Song, Fan; Zhang, Bo; Zhang, Lijun; Xu, Jie; Kuang, Da; Li, Daofeng; Choudhary, Mayank N.K.; Li, Yun; Hu, Ming; Hardison, Ross; Wang, Ting; Yue, Feng.

In: Genome biology, Vol. 19, No. 1, 151, 04.10.2018.

Research output: Contribution to journalArticle

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

VL - 19

JO - Genome Biology

JF - Genome Biology

SN - 1474-7596

IS - 1

M1 - 151

ER -