Phylogeny-guided interaction mapping in seven eukaryotes.
Phylogeny-guided interaction mapping in seven eukaryotes.
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DOI：
10.1186/1471-2105-10-393
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发表时间：
2009-11-30
影响因子：
3
通讯作者：
Tiuryn J
中科院分区：
文献类型：
--
作者：
Dutkowski J;Tiuryn J
组装可靠和完整的蛋白质-蛋白质相互作用（PPI）地图仍然是系统生物学的重大挑战之一。整合和优先考虑交互数据的计算方法可以极大地帮助实现这一目标。我们开发了一个贝叶斯推理框架，该框架使用系统发育关系来指导跨多个数据集和物种的PPI证据的整合，提供更准确的预测。我们应用我们的框架来协调七个真核生物相互作用组：H。sapiens，M. musculus、R. norvegicus、黑腹拟步行虫D. melanogaster、黑腹隐翅虫C. elegans，S. cerevisiae和A. thaliana.基于GO的综合质量评估表明，与输入数据相比，预测的相互作用组的得分增加了5%至44%。黄金标准MIPS、CYC 2008和HPRD数据集提供了进一步的支持。我们证明了在充分表征的酵母和人类复合物（26 S蛋白酶体，内体和外泌体）中恢复已知PPI的能力，并提出了与A. thaliana.我们的遗传学指导的方法相比，有利的两个标准方法映射跨物种的PPI。在选定的功能模块中的预测的详细分析揭示了特定的PPI档案之间的同源蛋白质，建立基于相互作用的蛋白质家族的分区。提供的证据还表明，核心复合物亚基内的相互作用通常比这些亚基之间的相互作用更保守，更容易准确地转移到其他生物体中。
The assembly of reliable and complete protein-protein interaction (PPI) maps remains one of the significant challenges in systems biology. Computational methods which integrate and prioritize interaction data can greatly aid in approaching this goal. We developed a Bayesian inference framework which uses phylogenetic relationships to guide the integration of PPI evidence across multiple datasets and species, providing more accurate predictions. We apply our framework to reconcile seven eukaryotic interactomes: H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. cerevisiae and A. thaliana. Comprehensive GO-based quality assessment indicates a 5% to 44% score increase in predicted interactomes compared to the input data. Further support is provided by gold-standard MIPS, CYC2008 and HPRD datasets. We demonstrate the ability to recover known PPIs in well-characterized yeast and human complexes (26S proteasome, endosome and exosome) and suggest possible new partners interacting with the putative SWI/SNF chromatin remodeling complex in A. thaliana. Our phylogeny-guided approach compares favorably to two standard methods for mapping PPIs across species. Detailed analysis of predictions in selected functional modules uncovers specific PPI profiles among homologous proteins, establishing interaction-based partitioning of protein families. Provided evidence also suggests that interactions within core complex subunits are in general more conserved and easier to transfer accurately to other organisms, than interactions between these subunits.
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