Visualisation of BioPAX Networks using BioLayout Express (3D).
Visualisation of BioPAX Networks using BioLayout Express (3D).
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DOI：
10.12688/f1000research.5499.1
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发表时间：
2014
期刊：
影响因子：
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通讯作者：
Freeman TC
中科院分区：
文献类型：
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作者：
Wright DW;Angus T;Enright AJ;Freeman TC
BioLayout Express 3D是一款网络分析工具，用于可视化和分析来自生物数据的图表。事实证明，它在分析基因表达数据、生物学途径和其他一系列应用中都是强大的。在该工具的3.2版中，我们引入了导入、合并和显示BioPAX Level 3标准交换格式中可用的通路和蛋白质相互作用网络的功能。图形界面允许用户搜索存储在Path Commons数据库中的路径或交互数据。使用基因/蛋白质或路径名称的查询是通过cPath2客户端进行的，用户还可以定义他们希望检查的信息源和/或种类。系统会列出与查询匹配的数据，并且可以使用“高级”查询选项卡单独查看或合并各个记录。已通过将BioPAX实体类型映射到一系列字形来定义可视化方案。这些数据的图形可以在BioLayout中以2D或3D图形布局的形式查看和浏览，在这些图形布局中，可以编辑和/或导出它们，以便在其他工具中进行可视化和编辑。
BioLayout Express 3D is a network analysis tool designed for the visualisation and analysis of graphs derived from biological data. It has proved to be powerful in the analysis of gene expression data, biological pathways and in a range of other applications. In version 3.2 of the tool we have introduced the ability to import, merge and display pathways and protein interaction networks available in the BioPAX Level 3 standard exchange format. A graphical interface allows users to search for pathways or interaction data stored in the Pathway Commons database. Queries using either gene/protein or pathway names are made via the cPath2 client and users can also define the source and/or species of information that they wish to examine. Data matching a query are listed and individual records may be viewed in isolation or merged using an ‘Advanced’ query tab. A visualisation scheme has been defined by mapping BioPAX entity types to a range of glyphs. Graphs of these data can be viewed and explored within BioLayout as 2D or 3D graph layouts, where they can be edited and/or exported for visualisation and editing within other tools.