StratomeX: Visual Analysis of Large-Scale Heterogeneous Genomics Data for Cancer Subtype Characterization
StratomeX: Visual Analysis of Large-Scale Heterogeneous Genomics Data for Cancer Subtype Characterization
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DOI：
10.1111/j.1467-8659.2012.03110.x
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发表时间：
2012-06-01
影响因子：
2.5
通讯作者：
Gehlenborg, N.
中科院分区：
文献类型：
--
作者：
Lex, A.;Streit, M.;Gehlenborg, N.
癌症亚型的识别和表征是基于对多个异质基因组数据集的综合分析的重要研究领域。由于没有支持此过程的工具，因此大部分工作都是使用即席脚本和静态绘图完成的，这不仅效率低下，而且限制了对数据的可视化探索。为了解决这个问题，我们开发了StratomeX，这是一个集成的可视化工具，允许研究人员探索多种基因组数据类型(如基因表达、DNA甲基化或拷贝数数据)中候选亚型的关系。StratomeX将数据集表示为列，将子类型表示为这些列中的砖。列之间的带状物连接砖块，以显示数据集之间的子类型关系。向下钻取功能可实现详细的探索。StratomeX通过使用小倍数提供对候选亚型的功能和临床意义的见解，使研究人员能够评估亚型对分子途径或结果(如患者生存)的影响。针对这种多数据集、多视图场景中查看参数配置复杂的问题，提出了一种针对数据集依赖关系和数据视图关系的元可视化配置接口。StratomeX是与领域专家密切合作开发的。我们描述了案例研究，展示了研究人员如何使用该工具来探索大型数据集中的亚型，并展示了他们如何高效地复制文献中的发现并获得对数据的新见解。
Identification and characterization of cancer subtypes are important areas of research that are 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 relationships. 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.