MatrixDB, a member of the International Molecular Exchange consortium (IMEx), is a curated interaction database focused on interactions established by extracellular matrix (ECM) constituents including proteins, proteoglycans, glycosaminoglycans and ECM bioactive fragments. The architecture of MatrixDB was upgraded to ease interaction data export, allow versioning and programmatic access and ensure sustainability. The new version of the database includes more than twice the number of manually curated and experimentally-supported interactions. High-confidence predicted interactions were imported from the Integrated Interactions Database to increase the coverage of the ECM interactome. ECM and ECM-associated proteins of five species (human, murine, bovine, avian and zebrafish) were annotated with matrisome divisions and categories, which are used for computational analyses of ECM -omic datasets. Biological pathways from the Reactome Pathway Knowledgebase were also added to the biomolecule description. New transcriptomic and expanded proteomic datasets were imported in MatrixDB to generate cell- and tissue-specific ECM networks using the newly developed in-house Network Explorer integrated in the database. MatrixDB is freely available at https://matrixdb.univ-lyon1.fr.

中文翻译：

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MatrixDB 2024：增加了细胞外基质相互作用的覆盖率，新的网络浏览器和新的 Web 界面


MatrixDB 是国际分子交换联盟 （IMEx） 的成员，是一个精选的相互作用数据库，专注于由细胞外基质 （ECM） 成分（包括蛋白质、蛋白聚糖、糖胺聚糖和 ECM 生物活性片段）建立的相互作用。MatrixDB 的架构进行了升级，以简化交互数据导出，允许版本控制和编程访问，并确保可持续性。新版本的数据库包含的手动策划和实验支持的交互数量是其两倍多。从集成交互数据库导入高置信度预测的交互，以增加 ECM 交互组的覆盖率。用基质体划分和类别注释了五个物种 （人、鼠、牛、禽和斑马鱼） 的 ECM 和 ECM 相关蛋白，用于 ECM 组学数据集的计算分析。来自 Reactome Pathway Knowledgebase 的生物通路也被添加到生物分子描述中。将新的转录组学和扩展的蛋白质组学数据集导入 MatrixDB，以使用集成在数据库中的新开发的内部 Network Explorer 生成细胞和组织特异性 ECM 网络。MatrixDB 在 https://matrixdb.univ-lyon1.fr 免费提供。