Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.
Nat Protoc. 2011 Aug 11;6(9):1308-23. doi: 10.1038/nprot.2011.368.
To take full advantage of high-throughput genetic and physical interaction mapping projects, the raw interactions must first be assembled into models of cell structure and function. PanGIA (for physical and genetic interaction alignment) is a plug-in for the bioinformatics platform Cytoscape, designed to integrate physical and genetic interactions into hierarchical module maps. PanGIA identifies 'modules' as sets of proteins whose physical and genetic interaction data matches that of known protein complexes. Higher-order functional cooperativity and redundancy is identified by enrichment for genetic interactions across modules. This protocol begins with importing interaction networks into Cytoscape, followed by filtering and basic network visualization. Next, PanGIA is used to infer a set of modules and their functional inter-relationships. This module map is visualized in a number of intuitive ways, and modules are tested for functional enrichment and overlap with known complexes. The full protocol can be completed between 10 and 30 min, depending on the size of the data set being analyzed.
要充分利用高通量遗传和物理相互作用映射项目，必须首先将原始相互作用组装成细胞结构和功能的模型。PanGIA（物理和遗传相互作用比对）是 Cytoscape 生物信息学平台的一个插件，旨在将物理和遗传相互作用整合到层次模块图中。PanGIA 将“模块”定义为一组蛋白质，其物理和遗传相互作用数据与已知蛋白质复合物的数据相匹配。通过跨模块的遗传相互作用富集来识别更高阶的功能协同作用和冗余性。该方案从将相互作用网络导入 Cytoscape 开始，然后进行过滤和基本网络可视化。接下来，使用 PanGIA 推断一组模块及其功能关系。以多种直观的方式可视化模块图，并对模块进行功能富集和与已知复合物的重叠测试。完整的方案可以在 10 到 30 分钟之间完成，具体取决于正在分析的数据集的大小。
