Protein-protein interaction network-based detection of functionally similar proteins within species
Protein-protein interaction network-based detection of functionally similar proteins within species
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DOI：
10.1002/prot.24066
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发表时间：
2012-07-01
影响因子：
2.9
通讯作者：
Zhang, Deli
中科院分区：
文献类型：
--
作者：
Song, Baoxing;Wang, Fen;Zhang, Deli
虽然物种间功能相似蛋白已被广泛研究，但物种内显示低序列相似性的功能相似蛋白尚未被详细研究。这些蛋白质的鉴定对于理解生物功能、蛋白质家族的进化、共同进化的进展、趋同进化和其他无法通过检测跨物种功能相似的蛋白质来获得的蛋白质具有重要意义。在这里，我们探索了一种基于图论的检测物种内功能相似蛋白的方法。在用图表示蛋白质-蛋白质相互作用网络之后，我们使用1跳方法将图分割成子图。利用改进的最短路径方法检测物种中具有功能相似性的蛋白质，对这些子图进行比较，并找到符合条件的最优结果。利用7个蛋白相互作用网络和该方法，鉴定出了一些序列相似性较低、无法通过序列比对检测到的功能相似蛋白。通过对结果的分析，我们发现有时很难将同源进化与收敛进化区分开来。通过基因本体术语重叠对该方法的性能进行了评价，结果表明该方法具有较好的识别精度。蛋白质2012;(c) 2012 Wiley期刊有限公司
Although functionally similar proteins across species have been widely studied, functionally similar proteins within species showing low sequence similarity have not been examined in detail. Identification of these proteins is of significant importance for understanding biological functions, evolution of protein families, progression of co-evolution, and convergent evolution and others which cannot be obtained by detection of functionally similar proteins across species. Here, we explored a method of detecting functionally similar proteins within species based on graph theory. After denoting proteinprotein interaction networks using graphs, we split the graphs into subgraphs using the 1-hop method. Proteins with functional similarities in a species were detected using a method of modified shortest path to compare these subgraphs and to find the eligible optimal results. Using seven proteinprotein interaction networks and this method, some functionally similar proteins with low sequence similarity that cannot detected by sequence alignment were identified. By analyzing the results, we found that, sometimes, it is difficult to separate homologous from convergent evolution. Evaluation of the performance of our method by gene ontology term overlap showed that the precision of our method was excellent. Proteins 2012; (c) 2012 Wiley Periodicals, Inc.