Yao Qiuming, Xu Dong
Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA.
Methods Mol Biol. 2017;1558:127-138. doi: 10.1007/978-1-4939-6783-4_6.
Protein phosphorylation is one of the most pervasive protein post-translational modification events in plant cells. It is involved in many plant biological processes, such as plant growth, organ development, and plant immunology, by regulating or switching signaling and metabolic pathways. High-throughput experimental methods like mass spectrometry can easily characterize hundreds to thousands of phosphorylation events in a single experiment. With the increasing volume of the data sets, Plant Protein Phosphorylation DataBase (P3DB, http://p3db.org ) provides a comprehensive, systematic, and interactive online platform to deposit, query, analyze, and visualize these phosphorylation events in many plant species. It stores the protein phosphorylation sites in the context of identified mass spectra, phosphopeptides, and phosphoproteins contributed from various plant proteome studies. In addition, P3DB associates these plant phosphorylation sites to protein physicochemical information in the protein charts and tertiary structures, while various protein annotations from hierarchical kinase phosphatase families, protein domains, and gene ontology are also added into the database. P3DB not only provides rich information, but also interconnects and provides visualization of the data in networks, in systems biology context. Currently, P3DB includes the KiC (Kinase Client) assay network, the protein-protein interaction network, the kinase-substrate network, the phosphatase-substrate network, and the protein domain co-occurrence network. All of these are available to query for and visualize existing phosphorylation events. Although P3DB only hosts experimentally identified phosphorylation data, it provides a plant phosphorylation prediction model for any unknown queries on the fly. P3DB is an entry point to the plant phosphorylation community to deposit and visualize any customized data sets within this systems biology framework. Nowadays, P3DB has become one of the major bioinformatics platforms of protein phosphorylation in plant biology.
蛋白质磷酸化是植物细胞中最普遍的蛋白质翻译后修饰事件之一。它通过调节或切换信号传导和代谢途径，参与许多植物生物学过程，如植物生长、器官发育和植物免疫学。像质谱分析这样的高通量实验方法能够在单次实验中轻松表征数百至数千个磷酸化事件。随着数据集数量的不断增加，植物蛋白质磷酸化数据库（P3DB，http://p3db.org ）提供了一个全面、系统且交互式的在线平台，用于存储、查询、分析和可视化多种植物物种中的这些磷酸化事件。它在已鉴定的质谱、磷酸肽和来自各种植物蛋白质组研究的磷酸化蛋白质的背景下存储蛋白质磷酸化位点。此外，P3DB将这些植物磷酸化位点与蛋白质图表和三级结构中的蛋白质物理化学信息相关联，同时还将来自分层激酶磷酸酶家族、蛋白质结构域和基因本体的各种蛋白质注释添加到数据库中。P3DB不仅提供丰富的信息，还在系统生物学背景下将数据在网络中相互连接并提供可视化。目前，P3DB包括激酶客户端（KiC）分析网络、蛋白质 - 蛋白质相互作用网络、激酶 - 底物网络、磷酸酶 - 底物网络和蛋白质结构域共现网络。所有这些都可用于查询和可视化现有的磷酸化事件。虽然P3DB仅托管通过实验鉴定的磷酸化数据，但它可为任何未知查询即时提供植物磷酸化预测模型。P3DB是植物磷酸化领域在这个系统生物学框架内存储和可视化任何定制数据集的入口点。如今，P3DB已成为植物生物学中蛋白质磷酸化的主要生物信息学平台之一。
