本文介绍了如何利用各种生物信息学工具，如BioGrid、IntAct、STRING和GeneMANIA等，从公开数据库中快速检索和整合蛋白质相互作用及功能网络数据。这些工具对于增强假设生成和理解蛋白质在生物系统中的具体角色至关重要。通过构建定制的蛋白质相互作用网络，研究人员能够从复合交互网络中获取更多关于特定生物学系统的深入信息，超越单一数据库或仅依赖原始文献的局限。
摘要：
The abundance of publicly available life science databases offers a wealth of information that can support interpretation of experimentally derived data and greatly enhance hypothesis generation. Protein interaction and functional networks are not simply new renditions of existing data: they provide the opportunity to gain insights into the specific physical and functional role a protein plays as part of the biological system. In this chapter, we describe different in silico tools that can quickly and conveniently retrieve data from existing data repositories and we discuss how the available tools are best utilized for different purposes. While emphasizing protein-protein interaction databases (e.g., BioGrid and IntAct), we also introduce metasearch platforms such as STRING and GeneMANIA, pathway databases (e.g., BioCarta and Pathway Commons), text mining approaches (e.g., PubMed and Chilibot), and resources for drug-protein interactions, genetic information for model organisms and gene expression information based on microarray data mining. Furthermore, we provide a simple step-by-step protocol for building customized protein-protein interaction networks in Cytoscape, a powerful network assembly and visualization program, integrating data retrieved from these various databases. As we illustrate, generation of composite interaction networks enables investigators to extract significantly more information about a given biological system than utilization of a single database or sole reliance on primary literature.
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