Lewis Anna C F, Jones Nick S, Porter Mason A, Deane Charlotte M
Department of Statistics, University of Oxford, Oxford, UK.
BMC Syst Biol. 2010 Jul 22;4:100. doi: 10.1186/1752-0509-4-100.
If biology is modular then clusters, or communities, of proteins derived using only protein interaction network structure should define protein modules with similar biological roles. We investigate the link between biological modules and network communities in yeast and its relationship to the scale at which we probe the network.
Our results demonstrate that the functional homogeneity of communities depends on the scale selected, and that almost all proteins lie in a functionally homogeneous community at some scale. We judge functional homogeneity using a novel test and three independent characterizations of protein function, and find a high degree of overlap between these measures. We show that a high mean clustering coefficient of a community can be used to identify those that are functionally homogeneous. By tracing the community membership of a protein through multiple scales we demonstrate how our approach could be useful to biologists focusing on a particular protein.
We show that there is no one scale of interest in the community structure of the yeast protein interaction network, but we can identify the range of resolution parameters that yield the most functionally coherent communities, and predict which communities are most likely to be functionally homogeneous.
如果生物学是模块化的，那么仅使用蛋白质相互作用网络结构衍生出的蛋白质簇或群落应该能定义具有相似生物学作用的蛋白质模块。我们研究了酵母中生物学模块与网络群落之间的联系，以及它与我们探测网络的尺度之间的关系。
我们的结果表明，群落的功能同质性取决于所选的尺度，并且几乎所有蛋白质在某些尺度下都处于功能同质的群落中。我们使用一种新颖的测试方法以及蛋白质功能的三种独立表征来判断功能同质性，并发现这些度量之间有高度的重叠。我们表明，群落的高平均聚类系数可用于识别功能同质的群落。通过在多个尺度上追踪蛋白质的群落成员身份，我们展示了我们的方法如何对专注于特定蛋白质的生物学家有用。
我们表明，酵母蛋白质相互作用网络的群落结构不存在单一感兴趣的尺度，但我们可以识别出产生功能最连贯群落的分辨率参数范围，并预测哪些群落最有可能是功能同质的。
