Veres Daniel V, Gyurkó Dávid M, Thaler Benedek, Szalay Kristóf Z, Fazekas Dávid, Korcsmáros Tamás, Csermely Peter
Department of Medical Chemistry, Semmelweis University, Budapest, Hungary.
Department of Medical Chemistry, Semmelweis University, Budapest, Hungary Faculty of Electrical Engineering and Informatics, Budapest University of Technology and Economics, Budapest, Hungary.
Nucleic Acids Res. 2015 Jan;43(Database issue):D485-93. doi: 10.1093/nar/gku1007. Epub 2014 Oct 27.
Here we present ComPPI, a cellular compartment-specific database of proteins and their interactions enabling an extensive, compartmentalized protein-protein interaction network analysis (URL: http://ComPPI.LinkGroup.hu). ComPPI enables the user to filter biologically unlikely interactions, where the two interacting proteins have no common subcellular localizations and to predict novel properties, such as compartment-specific biological functions. ComPPI is an integrated database covering four species (S. cerevisiae, C. elegans, D. melanogaster and H. sapiens). The compilation of nine protein-protein interaction and eight subcellular localization data sets had four curation steps including a manually built, comprehensive hierarchical structure of >1600 subcellular localizations. ComPPI provides confidence scores for protein subcellular localizations and protein-protein interactions. ComPPI has user-friendly search options for individual proteins giving their subcellular localization, their interactions and the likelihood of their interactions considering the subcellular localization of their interacting partners. Download options of search results, whole-proteomes, organelle-specific interactomes and subcellular localization data are available on its website. Due to its novel features, ComPPI is useful for the analysis of experimental results in biochemistry and molecular biology, as well as for proteome-wide studies in bioinformatics and network science helping cellular biology, medicine and drug design.
在此，我们展示了ComPPI，这是一个特定于细胞区室的蛋白质及其相互作用的数据库，可实现广泛的、按区室划分的蛋白质-蛋白质相互作用网络分析（网址：http://ComPPI.LinkGroup.hu）。ComPPI能让用户筛选生物学上不太可能的相互作用，即相互作用的两种蛋白质没有共同的亚细胞定位，并预测新的特性，如区室特异性生物学功能。ComPPI是一个综合数据库，涵盖四种物种（酿酒酵母、秀丽隐杆线虫、黑腹果蝇和智人）。九个蛋白质-蛋白质相互作用数据集和八个亚细胞定位数据集的编纂有四个管理步骤，包括一个手动构建的、包含超过1600个亚细胞定位的全面层次结构。ComPPI为蛋白质亚细胞定位和蛋白质-蛋白质相互作用提供置信度分数。ComPPI为单个蛋白质提供了用户友好的搜索选项，给出它们的亚细胞定位、相互作用以及考虑其相互作用伙伴的亚细胞定位时其相互作用的可能性。其网站上提供搜索结果、全蛋白质组、细胞器特异性相互作用组和亚细胞定位数据的下载选项。由于其新颖的特性，ComPPI对于生物化学和分子生物学实验结果的分析以及生物信息学和网络科学中的蛋白质组范围研究很有用，有助于细胞生物学、医学和药物设计。
