Caleydo: Design and evaluation of a visual analysis framework for gene expression data in its biological context
Caleydo: Design and evaluation of a visual analysis framework for gene expression data in its biological context
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Caleydo：生物背景下基因表达数据可视化分析框架的设计和评估
DOI：
10.1109/pacificvis.2010.5429609
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发表时间：
2010
期刊：
影响因子：
--
通讯作者：
D. Schmalstieg
中科院分区：
文献类型：
--
作者：
A. Lex;M. Streit;E. Kruijff;D. Schmalstieg
我们工作的目标是支持专家在关于基因在疾病中的作用的假设生成过程中。为了更深入地了解基因之间复杂的相互依赖关系，将基因表达（测量）与途径结合起来是很重要的。路径是生物过程的模型，可在在线数据库中找到。在这些数据库中，大型网络被分解为更小的子图，以更好地映射。这种简化导致了上下文的丢失，因为途径是相互连接的，基因可以在分散在网络中的多个实例中出现。因此，我们的主要目标是提供所有相关信息，即，基因表达，表达和途径之间的关系，以及多个途径之间的关系。为了实现这一点，我们采用两种不同的多视图方法。传统的多视图用于大型数据集或高度交互式的可视化，而2.5D技术用于支持多个途径的无缝导航，这些途径同时链接到所包含基因的表达。这种方法有助于理解途径的相互联系，并使基因表达数据的非分散注意力的关系。我们与来自生命科学社区的一组用户一起评估了Caleydo。用户被要求执行三项任务：路径探索，基因表达分析和信息比较，有和没有视觉链接，这必须在四种不同的条件下进行。评估结果表明，该系统可以大大提高理解复杂的网络通路和基因表达调控的个体效应的过程。特别是可用的上下文信息和空间组织的质量被评为良好的2.5D设置。
The goal of our work is to support experts in the process of hypotheses generation concerning the roles of genes in diseases. For a deeper understanding of the complex interdependencies between genes, it is important to bring gene expressions (measurements) into context with pathways. Pathways, which are models of biological processes, are available in online databases. In these databases, large networks are decomposed into small sub-graphs for better manageability. This simplification results in a loss of context, as pathways are interconnected and genes can occur in multiple instances scattered over the network. Our main goal is therefore to present all relevant information, i.e., gene expressions, the relations between expression and pathways and between multiple pathways in a simple, yet effective way. To achieve this we employ two different multiple-view approaches. Traditional multiple views are used for large datasets or highly interactive visualizations, while a 2.5D technique is employed to support a seamless navigation of multiple pathways which simultaneously links to the expression of the contained genes. This approach facilitates the understanding of the interconnection of pathways, and enables a non-distracting relation to gene expression data. We evaluated Caleydo with a group of users from the life science community. Users were asked to perform three tasks: pathway exploration, gene expression analysis and information comparison with and without visual links, which had to be conducted in four different conditions. Evaluation results show that the system can improve the process of understanding the complex network of pathways and the individual effects of gene expression regulation considerably. Especially the quality of the available contextual information and the spatial organization was rated good for the presented 2.5D setup.
DOI：
10.1073/pnas.95.25.14863
发表时间：
1998-12-08
影响因子：
11.1
作者：
Eisen, MB;Spellman, PT;Botstein, D
通讯作者：
Botstein, D