Generalized Venn diagrams:: a new method of visualizing complex genetic set relations
Generalized Venn diagrams:: a new method of visualizing complex genetic set relations
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DOI：
10.1093/bioinformatics/bti169
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发表时间：
2005-04-15
期刊：
影响因子：
5.8
通讯作者：
Buchholz, M
中科院分区：
文献类型：
--
作者：
Kestler, HA;M端ller, A;Buchholz, M
动机：微阵列实验产生大量数据。差异表达基因的未知或仅部分已知的功能背景可以通过经由GOMiner查询基因本体数据库来评估。生成的树表示很难解释，不适合这种类型的数据的可视化。需要有效地可视化这些复杂的集合关系的方法。结果：我们提出了一种基于维恩图的集合关系可视化方法。所提出的扩展增强了通常的概念维恩图，将集大小信息。集合和交集的基数由它们对应的圆（多边形）大小表示。为了避免局部最小值，通过进化优化来寻求该问题的解决方案。这种广义维恩图的方法已被实现为一个交互式的Java应用程序（VennMaster），专门设计用于与GOMiner的基因本体数据库的上下文中。
Motivation: Microarray experiments generate vast amounts of data. The unknown or only partially known functional context of differentially expressed genes may be assessed by querying the Gene Ontology database via GOMiner. Resulting tree representations are difficult to interpret and are not suited for visualization of this type of data. Methods are needed to effectively visualize these complex set relationships.Results: We present a visualization approach for set relationships based on Venn diagrams. The proposed extension enhances the usual notion of Venn diagrams by incorporating set size information. The cardinality of the sets and intersection sets is represented by their corresponding circle (polygon) sizes. To avoid local minima, solutions to this problem are sought by evolutionary optimization. This generalized Venn diagram approach has been implemented as an interactive Java application (VennMaster) specifically designed for use with GOMiner in the context of the Gene Ontology database.