Univ Lyon, University Lyon 1, CNRS, ICBMS, UMR 5246, F-69622, Villeurbanne, France.
Curr Protoc. 2021 Apr;1(4):e47. doi: 10.1002/cpz1.47.
The interaction database MatrixDB reports protein-protein and protein-glycosaminoglycan interactions in human, mammalian, and model organisms, involving at least one extracellular matrix (ECM) constituent, namely full-length proteins, ECM multimeric proteins considered as stable complexes, proteoglycans, glycosaminoglycans (GAGs), and bioactive fragments called matricryptins, which are released upon limited proteolysis of ECM proteins. The current version of MatrixDB (as of October 2020) contains 106,543 experimentally supported interactions, with all types of biomolecules combined. MatrixDB is the only database focusing on the curation of ECM protein and GAG interactions. The iNavigator integrated in MatrixDB allows users to build interaction networks online and to filter them according to expression data, quantitative proteomics data, or interaction detection methods. MatrixDB belongs to the International Molecular Exchange (IMEx) consortium, and uses its curation rules to capture interaction data, which are available in standardized exchange formats according to the Human Proteome Organization-Proteomics Standards Initiative (HUPO-PSI). © 2021 Wiley Periodicals LLC. Basic Protocol 1: Browse MatrixDB Basic Protocol 2: Create a list of biomolecules of interest to build interaction networks Basic Protocol 3: Build and export interaction networks of selected biomolecules using the iNavigator Basic Protocol 4: Build specific interaction networks using the iNavigator widgets Basic Protocol 5: Generate 3D models of glycosaminoglycan oligosaccharides using the GAG Builder tool.
交互数据库 MatrixDB 报告了人类、哺乳动物和模式生物中的蛋白质-蛋白质和蛋白质-糖胺聚糖相互作用，涉及至少一种细胞外基质 (ECM) 成分，即全长蛋白质、被认为是稳定复合物的 ECM 多聚体蛋白、蛋白聚糖、糖胺聚糖 (GAG) 和生物活性片段称为基质细胞素，它们是 ECM 蛋白有限蛋白水解时释放的。截至 2020 年 10 月，MatrixDB 的当前版本包含 106,543 个经过实验验证的相互作用，所有类型的生物分子都包括在内。MatrixDB 是唯一专注于 ECM 蛋白和 GAG 相互作用的数据库。集成在 MatrixDB 中的 iNavigator 允许用户在线构建相互作用网络，并根据表达数据、定量蛋白质组学数据或相互作用检测方法对其进行过滤。MatrixDB 属于国际分子交换 (IMEx) 联盟，并使用其策展规则捕获相互作用数据，这些数据根据人类蛋白质组组织-蛋白质组学标准倡议 (HUPO-PSI) 以标准化的交换格式提供。© 2021 Wiley Periodicals LLC. 基础方案 1：浏览 MatrixDB 基础方案 2：创建感兴趣的生物分子列表，以构建相互作用网络 基础方案 3：使用 iNavigator 构建和导出选定生物分子的相互作用网络 基础方案 4：使用 iNavigator 小部件构建特定的相互作用网络 基础方案 5：使用 GAG Builder 工具生成糖胺聚糖低聚糖的 3D 模型。
