Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression.
Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression.
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DOI：
10.1186/1471-2164-10-288
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发表时间：
2009-06-29
期刊：
影响因子：
4.4
通讯作者：
Van de Peer Y
中科院分区：
文献类型：
--
作者：
De Bodt S;Proost S;Vandepoele K;Rouzé P;Van de Peer Y
大规模鉴定细胞不同组分之间的相互关系，如蛋白质之间的相互作用，最近引起了极大的兴趣。然而，解开大规模的蛋白质-蛋白质相互作用图是费力和昂贵的。此外，评估相互作用的可靠性可能很麻烦。在这项研究中，我们已经开发了一种计算方法，利用现有的知识，在不同的物种，通过正交关系，一方面，和功能关联数据，另一方面，在拟南芥蛋白质-蛋白质相互作用的预测和过滤。利用酵母、人、C. elegans和D.黑腹菌定位，生物过程和共表达数据被用作蛋白质-蛋白质相互作用的有力指标。所鉴定的相互作用组的功能库揭示了在保守的以及植物特异性生物过程中起作用的蛋白质之间的相互作用。我们观察到，虽然共同的机制（如肌动蛋白聚合）和组件（如ARPs，肌动蛋白相关蛋白）存在于不同的谱系之间，他们是活跃的特定过程，如生长，癌症转移和毛状体发育在酵母，人类和拟南芥，分别。我们的结论是整合的直系与功能关联数据是足够的预测蛋白质-蛋白质相互作用。通过这种方法，发现了大量具有不同生物学作用的新型蛋白质-蛋白质相互作用。总的来说，我们预测了一组可靠的蛋白质-蛋白质相互作用，适合进一步的计算和实验分析。
Large-scale identification of the interrelationships between different components of the cell, such as the interactions between proteins, has recently gained great interest. However, unraveling large-scale protein-protein interaction maps is laborious and expensive. Moreover, assessing the reliability of the interactions can be cumbersome. In this study, we have developed a computational method that exploits the existing knowledge on protein-protein interactions in diverse species through orthologous relations on the one hand, and functional association data on the other hand to predict and filter protein-protein interactions in Arabidopsis thaliana. A highly reliable set of protein-protein interactions is predicted through this integrative approach making use of existing protein-protein interaction data from yeast, human, C. elegans and D. melanogaster. Localization, biological process, and co-expression data are used as powerful indicators for protein-protein interactions. The functional repertoire of the identified interactome reveals interactions between proteins functioning in well-conserved as well as plant-specific biological processes. We observe that although common mechanisms (e.g. actin polymerization) and components (e.g. ARPs, actin-related proteins) exist between different lineages, they are active in specific processes such as growth, cancer metastasis and trichome development in yeast, human and Arabidopsis, respectively. We conclude that the integration of orthology with functional association data is adequate to predict protein-protein interactions. Through this approach, a high number of novel protein-protein interactions with diverse biological roles is discovered. Overall, we have predicted a reliable set of protein-protein interactions suitable for further computational as well as experimental analyses.
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影响因子：
14.9
作者：
Heazlewood, Joshua L.;Verboom, Robert E.;Millar, A. Harvey
通讯作者：
Millar, A. Harvey
影响因子：
14.9
作者：
Güldener U;Münsterkötter M;Oesterheld M;Pagel P;Ruepp A;Mewes HW;Stümpflen V
通讯作者：
Stümpflen V
影响因子：
14.9
作者：
Cui, Jian;Li, Peng;Li, Guang;Xu, Feng;Zhao, Chen;Li, Yuhua;Yang, Zhongnan;Wang, Guang;Yu, Qingbo;Li, Yixue;Shi, Tieliu
通讯作者：
Shi, Tieliu
影响因子：
12.3
作者：
Hart GT;Ramani AK;Marcotte EM
通讯作者：
Marcotte EM
影响因子：
64.8
作者：
Gavin, AC;Bösche, M;Superti-Furga, G
通讯作者：
Superti-Furga, G