Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
Proteomics. 2011 Jul;11(13):2672-82. doi: 10.1002/pmic.201000546. Epub 2011 Jun 1.
Protein-protein interaction networks are typically built with interactions collated from many experiments. These networks are thus composite and show all interactions that are currently known to occur in a cell. However, these representations are static and ignore the constant changes in protein-protein interactions. Here we present software for the generation and analysis of dynamic, four-dimensional (4-D) protein interaction networks. In this, time-course-derived abundance data are mapped onto three-dimensional networks to generate network movies. These networks can be navigated, manipulated and queried in real time. Two types of dynamic networks can be generated: a 4-D network that maps expression data onto protein nodes and one that employs 'real-time rendering' by which protein nodes and their interactions appear and disappear in association with temporal changes in expression data. We illustrate the utility of this software by the analysis of singlish interface date hub interactions during the yeast cell cycle. In this, we show that proteins MLC1 and YPT52 show strict temporal control of when their interaction partners are expressed. Since these proteins have one and two interaction interfaces, respectively, it suggests that temporal control of gene expression may be used to limit competition at the interaction interfaces of some hub proteins. The software and movies of the 4-D networks are available at http://www.systemsbiology.org.au/downloads_geomi.html.
蛋白质-蛋白质相互作用网络通常是通过整合来自多个实验的相互作用构建而成的。因此，这些网络是复合的，展示了当前已知在细胞中发生的所有相互作用。然而，这些表示形式是静态的，忽略了蛋白质-蛋白质相互作用的不断变化。在这里，我们介绍了用于生成和分析动态、四维（4-D）蛋白质相互作用网络的软件。在这方面，时程衍生的丰度数据被映射到三维网络上，以生成网络电影。这些网络可以实时进行导航、操作和查询。可以生成两种类型的动态网络：一种是将表达数据映射到蛋白质节点的 4-D 网络，另一种是采用“实时渲染”，即蛋白质节点及其相互作用随着表达数据的时间变化而出现和消失。我们通过分析酵母细胞周期中 singlish 界面日期中心相互作用来展示该软件的实用性。在这方面，我们表明蛋白质 MLC1 和 YPT52 对其相互作用伙伴表达的时间有严格的控制。由于这两种蛋白质分别具有一个和两个相互作用界面，因此表明基因表达的时间控制可能用于限制某些中心蛋白相互作用界面的竞争。该软件和 4-D 网络的电影可在 http://www.systemsbiology.org.au/downloads_geomi.html 上获得。
