multi-scale visualization tools for exploration of chromosome interaction data
TRANSCRIPT
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
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)
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
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
DNA in the Nucleus
https://upload.wikimedia.org/wikipedia/commons/7/7a/Basketball.png
https://upload.wikimedia.org/wikipedia/commons/7/7a/Basketball.pnghttp://simplemaps.com/resources/svg-us
Chromosome Interaction Data
Rao et al., Cell, 2014
Contact Matrix
3 Million x 3 Million Cells 1 KB resolution
Visualization Techniques
Yardımcı & Noble, Genome Biology, 2017
Global Interactions
Juicebox
HEATMAP
Yardımcı & Noble, Genome Biology, 2017
Global Interactions
Juicebox
HEATMAP
Yardımcı & Noble, Genome Biology, 2017
Global Interactions
Washington University Epigenome Browser
ARC DIAGRAM
Yardımcı & Noble, Genome Biology, 2017
Local Interactions
3D Genome Browser
HEATSTRIP
Yardımcı & Noble, Genome Biology, 2017
Local Interactions
Washington University Epigenome Browser
ARC DIAGRAM
Tasks
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
Technology
Cooler File
HDF5Pixi.js + D3.js + React
HiGlass Server
HiGlass Client
Django + RedisEBSChrome / Safari / Firefox EC2
https://github.com/mirnylab/cooler
Aggregation: sum adjacent cells to create lower resolution views
Tiling: partition matrices into 256x256 blocks that can be individually displayed
Dealing with Large Maps: HiGlass
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
Demo Time: http://higlass.io
Examples: http://higlass.io/examples/
Dealing with Many Features: HiPiler
1. View and compare featuresWithin and across maps
2. Do all of this in a web browserInteraction and low latency
Video: http://biorxiv.org/highwire/filestream/36210/field_highwire_adjunct_files/0/123588-1.mov
Take Aways
1. Good visualization comes at a cost: aggregation 2. Fast rendering is crucial: use advanced technologies 3. A flexible framework provides new opportunities
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