Uncovering the co-evolutionary network among prokaryotic genes.
Uncovering the co-evolutionary network among prokaryotic genes.
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DOI：
10.1093/bioinformatics/bts396
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发表时间：
2012-09-15
期刊：
影响因子：
--
通讯作者：
Pupko T
中科院分区：
文献类型：
--
作者：
Cohen O;Ashkenazy H;Burstein D;Pupko T
动机：收益和损失的相关事件使得能够推断共同进化关系。重建原核生物中的协同进化相互作用网络有助于阐明基因间的功能关联。结果：我们开发了一种新的概率方法检测基因对之间的共同进化的相互作用。利用这种方法，我们推断了4593个直向同源基因簇（COG）之间的协同进化网络。的共同进化的相互作用的数量有很大的不同，COG。超过40%的人被发现与至少一个伴侣共同进化。我们将共同进化关系的网络划分为簇，并发现了具有明确定义功能的基因的多个模块化组装。最后，我们测量了共同进化关系与其他细胞关系（如基因组邻近性、基因融合倾向、共表达、蛋白质-蛋白质相互作用和代谢连接）相一致的程度。我们的研究结果表明，共同进化的关系只有部分重叠与这些其他类型的网络。我们的研究结果表明，原核生物中推断的协同进化网络是高度信息化的，有助于揭示基因之间的功能关系，通常显示无法从其他网络类型中提取的信号。可用性和实现：在GPL许可下作为开源提供。联系人：talp@post.tau.ac.il。补充信息：补充数据可在Bioinformatics在线获得。
Motivation: Correlated events of gains and losses enable inference of co-evolution relations. The reconstruction of the co-evolutionary interactions network in prokaryotic species may elucidate functional associations among genes. Results: We developed a novel probabilistic methodology for the detection of co-evolutionary interactions between pairs of genes. Using this method we inferred the co-evolutionary network among 4593 Clusters of Orthologous Genes (COGs). The number of co-evolutionary interactions substantially differed among COGs. Over 40% were found to co-evolve with at least one partner. We partitioned the network of co-evolutionary relations into clusters and uncovered multiple modular assemblies of genes with clearly defined functions. Finally, we measured the extent to which co-evolutionary relations coincide with other cellular relations such as genomic proximity, gene fusion propensity, co-expression, protein–protein interactions and metabolic connections. Our results show that co-evolutionary relations only partially overlap with these other types of networks. Our results suggest that the inferred co-evolutionary network in prokaryotes is highly informative towards revealing functional relations among genes, often showing signals that cannot be extracted from other network types. Availability and implementation: Available under GPL license as open source. Contact: talp@post.tau.ac.il. Supplementary information: Supplementary data are available at Bioinformatics online.
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