PRIN: a predicted rice interactome network.
PRIN: a predicted rice interactome network.
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DOI：
10.1186/1471-2105-12-161
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发表时间：
2011-05-16
影响因子：
3
通讯作者：
Chen M
中科院分区：
文献类型：
--
作者：
Gu H;Zhu P;Jiao Y;Meng Y;Chen M
蛋白质间相互作用在阐明生物分子功能、信号转导和代谢途径的分子机制中起着基础性作用。虽然酵母双杂交、亲和纯化和质谱等高通量技术在模式生物中得到了广泛应用，但植物蛋白质相互作用的研究进展缓慢。基于这个动机，我们的工作提出了一个计算方法来预测水稻蛋白质-蛋白质相互作用。为了更好地了解水稻蛋白质的相互作用，我们开发了PRIN，一个预测的水稻相互作用网络。PRIN的蛋白质-蛋白质相互作用数据是基于已经应用大规模蛋白质-蛋白质相互作用实验的六种模式生物的互作日志：酵母（酿酒酵母）、蠕虫（秀丽隐杆线虫）、果蝇（黑腹果蝇）、人（智人）、大肠杆菌K12和拟南芥。在一定的质量控制下，我们从5，049个大米蛋白中总共获得了76，585个非冗余大米蛋白相互作用对。进一步的分析表明，预测的大米蛋白质相互作用网络的拓扑结构与酵母的相似性高于其他5种生物。这可能并不奇怪，因为基于酵母的interrolog贡献了总相互作用的近74%。此外，GO注释，亚细胞定位信息和基因表达数据也映射到我们的网络进行验证。最后，开发了一个用户友好的Web界面，提供方便的数据库搜索和网络可视化。PRIN是第一个注释良好的重要模式植物水稻蛋白质相互作用数据库。它极大地扩展了目前可用的水稻蛋白质相互作用的数据与计算方法，这必将提供进一步的了解水稻功能基因组学和系统生物学。PRIN可在http://bis.zju.edu.cn/prin/上在线获得。
Protein-protein interactions play a fundamental role in elucidating the molecular mechanisms of biomolecular function, signal transductions and metabolic pathways of living organisms. Although high-throughput technologies such as yeast two-hybrid system and affinity purification followed by mass spectrometry are widely used in model organisms, the progress of protein-protein interactions detection in plants is rather slow. With this motivation, our work presents a computational approach to predict protein-protein interactions in Oryza sativa. To better understand the interactions of proteins in Oryza sativa, we have developed PRIN, a Predicted Rice Interactome Network. Protein-protein interaction data of PRIN are based on the interologs of six model organisms where large-scale protein-protein interaction experiments have been applied: yeast (Saccharomyces cerevisiae), worm (Caenorhabditis elegans), fruit fly (Drosophila melanogaster), human (Homo sapiens), Escherichia coli K12 and Arabidopsis thaliana. With certain quality controls, altogether we obtained 76,585 non-redundant rice protein interaction pairs among 5,049 rice proteins. Further analysis showed that the topology properties of predicted rice protein interaction network are more similar to yeast than to the other 5 organisms. This may not be surprising as the interologs based on yeast contribute nearly 74% of total interactions. In addition, GO annotation, subcellular localization information and gene expression data are also mapped to our network for validation. Finally, a user-friendly web interface was developed to offer convenient database search and network visualization. PRIN is the first well annotated protein interaction database for the important model plant Oryza sativa. It has greatly extended the current available protein-protein interaction data of rice with a computational approach, which will certainly provide further insights into rice functional genomics and systems biology. PRIN is available online at http://bis.zju.edu.cn/prin/.
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