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
N1 - Funding Information:
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.
Publisher Copyright:
© 2018 The Author(s).
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
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 -