AtPIN: Arabidopsis thaliana protein interaction network.
AtPIN: Arabidopsis thaliana protein interaction network.
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DOI：
10.1186/1471-2105-10-454
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发表时间：
2009-12-31
影响因子：
3
通讯作者：
Silva-Filho MC
中科院分区：
文献类型：
--
作者：
Brandão MM;Dantas LL;Silva-Filho MC
蛋白质-蛋白质相互作用（PPIs）是生物体维持生命的最重要条件之一。为了研究拟南芥的PPI，我们开发了AtPIN，这是一个数据库和web界面，用于搜索和构建基于公开可用的蛋白质-蛋白质相互作用数据集的相互作用网络。所有的相互作用分为实验证明或预测。AtPIN数据库中的PPI呈现细胞室分类（C3），根据其相互作用证据和亚细胞定位将PPI分为4类。文献表明，一对真正相互作用的蛋白质通常被认为具有共同的细胞作用，具有共同相互作用伙伴的蛋白质有很高的机会共享共同的功能。在AtPIN中，由于其整体性，报告的PPI的可靠性指数可以根据两种蛋白质共同具有的相互作用伙伴的比例来假设。为此，我们实现了AtPIN数据库中存在的所有一级交互的功能相似度权重（FSW）计算。为了鉴定胞质谷氨酰基trna合成酶（Cyt-gluRS） （AT5G26710）的靶蛋白，我们将AtPIN搜索和酵母双杂交筛选两种方法结合起来。有趣的是，在实验筛选中也检测到被AtPIN预测为Cyt-gluRS靶蛋白的蛋白谷氨酰胺合成酶（AT5G35630）、抗病蛋白（AT3G50950）和锌指蛋白（AT5G24930）。AtPIN是一个友好且易于使用的工具，可以收集拟南芥PPIs，本体和亚细胞定位的信息，可能是绘制拟南芥蛋白质-蛋白质相互作用的有用且可靠的策略。AtPIN可以在http://bioinfo.esalq.usp.br/atpin上访问。
Protein-protein interactions (PPIs) constitute one of the most crucial conditions to sustain life in living organisms. To study PPI in Arabidopsis thaliana we have developed AtPIN, a database and web interface for searching and building interaction networks based on publicly available protein-protein interaction datasets. All interactions were divided into experimentally demonstrated or predicted. The PPIs in the AtPIN database present a cellular compartment classification (C3) which divides the PPI into 4 classes according to its interaction evidence and subcellular localization. It has been shown in the literature that a pair of genuine interacting proteins are generally expected to have a common cellular role and proteins that have common interaction partners have a high chance of sharing a common function. In AtPIN, due to its integrative profile, the reliability index for a reported PPI can be postulated in terms of the proportion of interaction partners that two proteins have in common. For this, we implement the Functional Similarity Weight (FSW) calculation for all first level interactions present in AtPIN database. In order to identify target proteins of cytosolic glutamyl-tRNA synthetase (Cyt-gluRS) (AT5G26710) we combined two approaches, AtPIN search and yeast two-hybrid screening. Interestingly, the proteins glutamine synthetase (AT5G35630), a disease resistance protein (AT3G50950) and a zinc finger protein (AT5G24930), which has been predicted as target proteins for Cyt-gluRS by AtPIN, were also detected in the experimental screening. AtPIN is a friendly and easy-to-use tool that aggregates information on Arabidopsis thaliana PPIs, ontology, and sub-cellular localization, and might be a useful and reliable strategy to map protein-protein interactions in Arabidopsis. AtPIN can be accessed at http://bioinfo.esalq.usp.br/atpin.
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