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Guided visual exploration of patient stratifications in cancer genomics
Nils GehlenborgHarvard Medical SchoolCenter for Biomedical Informatics
nils_gehlenborg!
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“In every chain of reasoning, the evidence of the last conclusion can be no greater than that of the weakest link of the chain, whatever may be the strength of the rest.”
- Thomas Reid, Essays on the Intellectual Powers of Man (1786)
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1.00 0.96 0.762.00 0.76 -0.143.00 -0.14 -0.914.00 -0.91 -0.845.00 -0.84 0.006.00 0.00 0.847.00 0.84 0.918.00 0.91 0.149.00 0.14 -0.7610.00 -0.76 -0.9611.00 -0.96 -0.28
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TCGAThe Cancer Genome Atlas
mRNA expression
microRNA expression
DNA methylation
protein expression
copy number variants
mutation calls
clinical parameters
Stratome
StratomeX
A Lex, M Streit, H-J Schulz, C Partl, D Schmalstieg, PJ Park, N Gehlenborg, “StratomeX: Visual Anal-ysis of Large-Scale Heterogeneous Genomics Data for Cancer Subtype Characterization“, Computer Graphics Forum 31:1175-1184 (2012)
M Streit, A Lex, S Gratzl, C Partl, D Schmalstieg, H Pfister, PJ Park, N Gehlenborg, “Guided Visual Exploration of Genomic Stratifications in Cancer“, Nature Methods 11:884-885 (2014)
Comparing Patient Sets across StratificationsPROBLEM 1
Comparing Patient Sets within StratificationsPROBLEM 2
Finding Relevant Stratifications and PathwaysPROBLEM 3
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Knowledge-driven Exploration
Data-driven Exploration
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Rank
VisualizeStratifications
Clinical Params Pathways
Guided Exploration
LineUp
S Gratzl, A Lex, N Gehlenborg, H Pfister and M Streit, “LineUp: Visual Analysis of Multi-Attribute Rankings“, IEEE Transactions on Visualization and Computer Graphics 19:2277-2286 (2013)
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VisualizeStratifications
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www.caleydo.org
www.caleydo.org
www.caleydo.org
Domino
S Gratzl, N Gehlenborg, A Lex, H Pfister and M Streit, “Domino: Extracting, Comparing, and Manipulating Subsets across Multiple Tabular Datasets“, IEEE Transactions on Visualization and Computer Graphics (2014)
MD Anderson Cancer Center
University of Rostock
Peter J Park
Michael S Noble, David Heiman, Firehose Team, Gad Getz
Terrence Wu, Ian Watson, Lynda Chin
Harvard Medical School
Broad Institute of MIT & Harvard
Christian Partl, Dieter SchmalstiegGraz University of Technology
Johannes Kepler University Linz Samuel Gratzl, Marc Streit
Hans-Jörg Schulz
Acknowledgements
Harvard SEAS Alexander Lex, Hanspeter Pfister
Funding NIH/NHGRI K99 HG007583 Pathway to Independence