Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

被引：1031

作者：

Durand, Neva C. ^{[1
,2
,3
,4
]}

Robinson, James T. ^{[1
,4
]}

Shamim, Muhammad S. ^{[1
,2
,3
]}

Machol, Ido ^{[1
,2
,3
]}

Mesirov, Jill P. ^{[4
]}

Lander, Eric S. ^{[4
,5
,6
]}

Aiden, Erez Lieberman ^{[1
,2
,3
,4
,7
]}

机构：

[1] Baylor Coll Med, Ctr Genome Architecture, Houston, TX 77030 USA

[2] Baylor Coll Med, Dept Mol & Human Genet, Houston, TX 77030 USA

[3] Rice Univ, Dept Computat & Appl Math, Dept Comp Sci, Houston, TX 77005 USA

[4] Broad Inst Harvard & Massachusetts Inst Technol, Cambridge, MA 02139 USA

[5] MIT, Dept Biol, 77 Massachusetts Ave, Cambridge, MA 02139 USA

[6] Harvard Med Sch, Dept Syst Biol, Boston, MA 02115 USA

[7] Rice Univ, Ctr Theoret Biol Phys, Houston, TX 77030 USA

来源：

CELL SYSTEMS | 2016年 / 3卷 / 01期

基金：

美国国家科学基金会;

关键词：

HUMAN GENOME; PRINCIPLES;

D O I：

10.1016/j.cels.2015.07.012

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Hi-C experiments study how genomes fold in 3D, generating contact maps containing features as small as 20 bp and as large as 200 Mb. Here we introduce Juicebox, a tool for exploring Hi-C and other contact map data. Juicebox allows users to zoom in and out of Hi-C maps interactively, just as a user of Google Earth might zoom in and out of a geographic map. Maps can be compared to one another, or to 1D tracks or 2D feature sets.

引用

页码：99 / 101

页数：3

共 50 条

[1] Juicebox.js']js Provides a Cloud-Based Visualization System for Hi-C Data
Robinson, James T.
Turner, Douglass
Durand, Neva C.
Thorvaldsdottir, Helga
Mesirov, Jill P.
Aiden, Erez Lieberman
[J]. CELL SYSTEMS, 2018, 6 (02) : 256 - +
[2] DiffGR: Detecting Differentially Interacting Genomic Regions from Hi-C Contact Maps
Liu, Huiling
Ma, Wenxiu
[J]. GENOMICS PROTEOMICS & BIOINFORMATICS, 2024, 22 (02)
[3] On the relations of phase separation and Hi-C maps to epigenetics
Singh, Prim B.
Newman, Andrew G.
[J]. ROYAL SOCIETY OPEN SCIENCE, 2020, 7 (03):
[4] Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization
Wolff, Joachim
Rabbani, Leily
Gilsbach, Ralf
Richard, Gautier
Manke, Thomas
Backofen, Rolf
Gruening, Bjoern A.
[J]. NUCLEIC ACIDS RESEARCH, 2020, 48 (W1) : W177 - W184
[5] HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps
Yan, Koon-Kiu
Yardimci, Galip Gurkan
Yan, Chengfei
Noble, William S.
Gerstein, Mark
[J]. BIOINFORMATICS, 2017, 33 (14) : 2199 - 2201
[6] Epiphany: predicting Hi-C contact maps from 1D epigenomic signals
Yang, Rui
Das, Arnav
Gao, Vianne R. R.
Karbalayghareh, Alireza
Noble, William S. S.
Bilmes, Jeffery A. A.
Leslie, Christina S. S.
[J]. GENOME BIOLOGY, 2023, 24 (01)
[7] Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture
Yaffe, Eitan
Tanay, Amos
[J]. NATURE GENETICS, 2011, 43 (11) : 1059 - U40
[8] EnHiC: learning fine-resolution Hi-C contact maps using a generative adversarial framework
Hu, Yangyang
Ma, Wenxiu
[J]. BIOINFORMATICS, 2021, 37 : I272 - I279
[9] Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture
Eitan Yaffe
Amos Tanay
[J]. Nature Genetics, 2011, 43 : 1059 - 1065
[10] Posterior inference of Hi-C contact frequency through sampling
Zhang, Yanlin
Cameron, Christopher J. F.
Blanchette, Mathieu
[J]. FRONTIERS IN BIOINFORMATICS, 2024, 3

← 1 2 3 4 5 →