multi-scale visualization tools for exploration of chromosome interaction data
TRANSCRIPT
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Multi-Scale Visualization Tools for Exploration of Chromosome Interaction Data
Nils Gehlenborg, PhD
http://gehlenborglab.org
HARVARD MEDICAL SCHOOL DEPARTMENT OF BIOMEDICAL INFORMATICS
@nils_gehlenborg
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Acknowledgements
Peter Kerpedjiev, PhD Fritz Lekschas, MScHARVARD MEDICAL SCHOOL HARVARD SCHOOL OF ENGINEERING &
APPLIED SCIENCES
Funding provided by NIH COMMON FUND (U01 CA200059) NIH NATIONAL HUMAN GENOME RESEARCH INSTITUTE (R00 HG007583)
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Acknowledgements
Peter Kerpedjiev Fritz Lekschas Nezar Abdennur Benjamin Bach Chuck McCallum Kasper Dinkla Hendrik Strobelt Jacob M Luber
Scott B Ouellette Alaleh Ahzir Nikhil Kumar Jeewon Hwang Burak H Alver Hanspeter Pfister Leonid A Mirny Peter J Park
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Open Research
Demo Site: http://higlass.io
Code: https://github.com/hms-dbmi/higlass
Docker: https://hub.docker.com/r/gehlenborglab/higlass/
Preprint: http://biorxiv.org/content/early/2017/03/31/121889
HIGLASS
HIPILERDemo Site: https://flekschas.github.io/hipiler/ (beta)
Code: https://github.com/flekschas/hipiler
Preprint: http://biorxiv.org/content/early/2017/04/03/123588
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DNA in the Nucleus
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https://upload.wikimedia.org/wikipedia/commons/7/7a/Basketball.png
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https://upload.wikimedia.org/wikipedia/commons/7/7a/Basketball.pnghttp://simplemaps.com/resources/svg-us
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Chromosome Interaction Data
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Rao et al., Cell, 2014
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Contact Matrix
3 Million x 3 Million Cells 1 KB resolution
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Visualization Techniques
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Yardımcı & Noble, Genome Biology, 2017
Global Interactions
Juicebox
HEATMAP
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Yardımcı & Noble, Genome Biology, 2017
Global Interactions
Juicebox
HEATMAP
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Yardımcı & Noble, Genome Biology, 2017
Global Interactions
Washington University Epigenome Browser
ARC DIAGRAM
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Yardımcı & Noble, Genome Biology, 2017
Local Interactions
3D Genome Browser
HEATSTRIP
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Yardımcı & Noble, Genome Biology, 2017
Local Interactions
Washington University Epigenome Browser
ARC DIAGRAM
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Tasks
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1. View interactions at different scalesFrom genome to individual bins
2. Compare interactions across many conditions Two or more conditions
3. View and compare featuresWithin and across maps
4. Do all of this in a web browserInteraction and low latency
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Technology
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Cooler File
HDF5Pixi.js + D3.js + React
HiGlass Server
HiGlass Client
Django + RedisEBSChrome / Safari / Firefox EC2
https://github.com/mirnylab/cooler
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Aggregation: sum adjacent cells to create lower resolution views
Tiling: partition matrices into 256x256 blocks that can be individually displayed
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Dealing with Large Maps: HiGlass
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1. View interactions at different scalesFrom genome to individual bins
2. Compare interactions across many conditions Two or more conditions
3. Do all of this in a web browserInteraction and low latency
![Page 25: Multi-Scale Visualization Tools for Exploration of Chromosome Interaction Data](https://reader033.vdocuments.site/reader033/viewer/2022051404/5a64c6767f8b9ac21c8b5c43/html5/thumbnails/25.jpg)
Demo Time: http://higlass.io
Examples: http://higlass.io/examples/
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Dealing with Many Features: HiPiler
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1. View and compare featuresWithin and across maps
2. Do all of this in a web browserInteraction and low latency
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Video: http://biorxiv.org/highwire/filestream/36210/field_highwire_adjunct_files/0/123588-1.mov
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Take Aways
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1. Good visualization comes at a cost: aggregation 2. Fast rendering is crucial: use advanced technologies 3. A flexible framework provides new opportunities
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My lab is hiring postdocs!
HARVARD MEDICAL SCHOOL DEPARTMENT OF BIOMEDICAL INFORMATICS
http://gehlenborglab.org
Data visualization, analysis, and management for:
• exploration tools for data repositories • provenance graphs • genomic structural variants • dynamics of the 3D genome • cancer subtypes in patient cohorts