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

被引：228

作者：

Wang, Yanli ^{[1
]}

Song, Fan ^{[1
]}

Zhang, Bo ^{[1
]}

Zhang, Lijun ^{[2
]}

Xu, Jie ^{[2
]}

Kuang, Da ^{[3
]}

Li, Daofeng ^{[4
]}

Choudhary, Mayank N. K. ^{[4
]}

Li, Yun ^{[5
,6
,7
]}

Hu, Ming ^{[8
]}

Hardison, Ross ^{[9
]}

Wang, Ting ^{[4
]}

Yue, Feng ^{[1
,2
]}

机构：

[1] Penn State Univ, Bioinformat & Genom Program, State Coll, PA 16802 USA

[2] Penn State Hershey, Coll Med, Dept Biochem & Mol Biol, Hershey, PA 17033 USA

[3] Univ Penn, Dept Comp & Informat Sci, 200 S 33Rd St, Philadelphia, PA 19104 USA

[4] Washington Univ, Sch Med, Edison Family Ctr Genome Sci & Syst Biol, Dept Genet, St Louis, MO 63108 USA

[5] Univ N Carolina, Dept Genet, Chapel Hill, NC 27599 USA

[6] Univ N Carolina, Dept Biostat, Chapel Hill, NC 27599 USA

[7] Univ N Carolina, Dept Comp Sci, Chapel Hill, NC 27599 USA

[8] Cleveland Clin Fdn, Lerner Res Inst, Dept Quantitat Hlth Sci, Cleveland, OH 44195 USA

[9] Penn State Univ, Huck Inst Life Sci, Ctr Computat Biol & Bioinformat, State Coll, PA 16802 USA

来源：

GENOME BIOLOGY | 2018年 / 19卷

关键词：

HIGH-RESOLUTION; HI-C; CHROMOSOME CONFORMATION; PROMOTER CONTACTS; EPIGENOME BROWSER; HUMAN-CELLS; ARCHITECTURE; DOMAINS; LINEAGE; DIFFERENTIATION;

D O I：

10.1186/s13059-018-1519-9

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页数：12

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