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

Neva C Durand¹, James T Robinson², Muhammad S Shamim³, Ido Machol³, Jill P Mesirov⁴, Eric S Lander⁵, Erez Lieberman Aiden⁶

Affiliations

¹ The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA; Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
² The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
³ The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA.
⁴ Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
⁵ Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
⁶ The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA; Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA. Electronic address: erez@erez.com.

PMID: 27467250
PMCID: PMC5596920
DOI: 10.1016/j.cels.2015.07.012

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

Neva C Durand et al. Cell Syst. 2016 Jul.

. 2016 Jul;3(1):99-101.

doi: 10.1016/j.cels.2015.07.012.

Authors

Neva C Durand¹, James T Robinson², Muhammad S Shamim³, Ido Machol³, Jill P Mesirov⁴, Eric S Lander⁵, Erez Lieberman Aiden⁶

Affiliations

¹ The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA; Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
² The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
³ The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA.
⁴ Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
⁵ Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
⁶ The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA; Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA. Electronic address: erez@erez.com.

PMID: 27467250
PMCID: PMC5596920
DOI: 10.1016/j.cels.2015.07.012

Abstract

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.

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Figures

**Figure 1. Juicebox enables exploration of contact maps at many resolutions**
Here, we see a screenshot of Juicebox zoomed into 5-Kb resolution on chromosome 3. The toolbar at the top allows users to quickly navigate between different chromosomes, views, normalizations, and resolutions. Users can load one-dimensional tracks and compare them to features seen in the heatmap. Two-dimensional features can be superimposed on the main map. Several peaks are annotated (cyan), each peak indicating the presence of a chromatin loop. A peak in the CTCF track, indicating CTCF binding, is seen at most loop anchors. At the top right, a mini-map shows the whole chromosome at low resolution. Below, hover text shows additional data for one of the highlighted peaks.

See this image and copyright information in PMC

Comment in

Minute-Made Data Analysis: Tools for Rapid Interrogation of Hi-C Contacts.
Rowley MJ, Corces VG. Rowley MJ, et al. Mol Cell. 2016 Oct 6;64(1):9-11. doi: 10.1016/j.molcel.2016.09.029. Mol Cell. 2016. PMID: 27716489 Free PMC article.

References

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1. Lieberman-Aiden E, van Berkum N, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie B, Sabo P, Dorschner M, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326:289–293. - PMC - PubMed
1. Paulsen J, Sandve GK, Gundersen S, Lien TG, Trengereid K, Hovig E. HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization. Bioinformatics. 2014;30:1620–1622. - PMC - PubMed
1. Rao SSP, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, Aiden EL. A Threedimensional Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell. 2014;159:1665–1680. - PMC - PubMed
1. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttan M, Lander ES, Getz G, Mesirov JP. Integrative Genomics Viewer. Nature Biotechnology. 2011;29:24–26. - PMC - PubMed

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

Affiliations

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

Authors

Affiliations

Abstract

Figures

Comment in

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources

Miscellaneous