Wright Derek W, Angus Tim, Enright Anton J, Freeman Tom C
The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, Scotland, EH25 9RG, UK.
EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
F1000Res. 2014 Oct 20;3:246. doi: 10.12688/f1000research.5499.1. eCollection 2014.
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.
BioLayout Express (3D)是一款网络分析工具，旨在可视化和分析源自生物数据的图表。事实证明，它在基因表达数据、生物途径及一系列其他应用的分析中功能强大。在该工具的3.2版本中，我们引入了导入、合并和显示以BioPAX Level 3标准交换格式提供的途径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Pathway Commons数据库中的途径或相互作用数据。使用基因/蛋白质或途径名称的查询通过cPath2客户端进行，用户还可以定义他们希望检查的信息的来源和/或物种。与查询匹配的数据会被列出，单个记录可以单独查看，也可以使用“高级”查询标签进行合并。通过将BioPAX实体类型映射到一系列符号，定义了一种可视化方案。这些数据的图表可以在BioLayout中作为二维或三维图形布局进行查看和探索，在其中可以进行编辑和/或导出，以便在其他工具中进行可视化和编辑。
