Rito Tiago, Deane Charlotte M, Reinert Gesine
Department of Statistics, University of Oxford, Oxford United Kingdom.
J Comput Biol. 2012 Jun;19(6):785-95. doi: 10.1089/cmb.2012.0054.
Here we present an in-depth analysis of the protein age patterns found in the edge and triangle subgraphs of the yeast protein-protein interaction network (PIN). We assess their statistical significance both according to what would be expected by chance given the node frequencies found in the yeast PIN, and also, for the case of triangles, given the age frequencies observed in the currently available pairwise data. We find that pairwise interactions between Old proteins are over-represented even when controlling for high degree, and triangle interactions between Old proteins are over-represented even when controlling for pairwise interaction frequencies. There is evidence for negative selection of interactions between Middle-aged and Old proteins within triangles, despite pairwise Middle-Old interactions being common. Most triangles consist solely of vertices with high degree. Our findings point towards an architecture of the yeast PIN that is highly heterogeneous, having connected clumps which contain a large number of interacting Old proteins along with selective age-dependent interaction patterns. Supplementary Material is available online (www.liebertonline.com/cmb).
在此，我们对酵母蛋白质-蛋白质相互作用网络（PIN）的边和三角形子图中发现的蛋白质年龄模式进行了深入分析。我们根据酵母PIN中发现的节点频率，按随机预期情况评估其统计显著性，对于三角形的情况，还根据当前可用的成对数据中观察到的年龄频率进行评估。我们发现，即使在控制高连接度的情况下，老年蛋白质之间的成对相互作用也过度存在，并且即使在控制成对相互作用频率的情况下，老年蛋白质之间的三角形相互作用也过度存在。尽管中年与老年蛋白质之间的成对相互作用很常见，但有证据表明三角形内中年与老年蛋白质之间的相互作用存在负选择。大多数三角形仅由高连接度的顶点组成。我们的研究结果表明酵母PIN的结构高度异质，具有连接的团块，其中包含大量相互作用的老年蛋白质以及选择性的年龄依赖性相互作用模式。补充材料可在线获取（www.liebertonline.com/cmb）。
