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StratomeX: Visual Analysis of Genomics Data for Cancer Subtype Characterization

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Published on Mar 8, 2012

Video for the EuroVis 2012 paper by Alexander Lex, Marc Streit, Hans-Jörg Schulz, Christian Partl, D. Schmalstieg, P. J. Park, and Nils Gehlenborg
For more info go to http://stratomex.caleydo.org

Identification and characterization of cancer subtypes is an important area of research that is based on the integrated analysis of multiple heterogeneous genomics datasets. Since there are no tools supporting this process, much of this work is done using ad-hoc scripts and static plots, which is inefficient and limits visual exploration of the data.
To address this, we have developed StratomeX, an integrative visualization tool that allows investigators to explore the relationships of candidate subtypes across multiple genomic data types such as gene expression, DNA methylation, or copy number data.
StratomeX represents datasets as columns and subtypes as bricks in these columns. Ribbons between the columns connect bricks to show subtype relationships across datasets. Drill-down features enable detailed exploration. StratomeX provides insights into the functional and clinical implications of candidate subtypes by employing small multiples, which allow investigators to assess the effect of subtypes on molecular pathways or outcomes such as patient survival. As the configuration of viewing parameters in such a multi-dataset, multi-view scenario is complex, we propose a meta visualization and configuration interface for dataset dependencies and data-view relations.
StratomeX is developed in close collaboration with domain experts. We describe case studies that illustrate how investigators used the tool to explore subtypes in large datasets and demonstrate how they efficiently replicated findings from the literature and gained new insights into the data.

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