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

doi:10.1016/j.cels.2015.07.012

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

doi: 10.1016/j.cels.2015.07.012.

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.

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Comment in

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References

1. Durand NC, Shamim MS, Machol I, Rao SSP, Huntley MH, Lander ES, Aiden EL. Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Cell Syst. 2016;3:95–98. - PMC - PubMed
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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[1] Durand NC, Shamim MS, Machol I, Rao SSP, Huntley MH, Lander ES, Aiden EL. Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Cell Syst. 2016;3:95–98. - PMC - PubMed

[2] Durand NC, Shamim MS, Machol I, Rao SSP, Huntley MH, Lander ES, Aiden EL. Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Cell Syst. 2016;3:95–98. - PMC - PubMed

[3] 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

[4] 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

[5] 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

[6] 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

[7] 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

[8] 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

[9] 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

[10] 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

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

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