Samarasinghe Kasun W, Kotlyar Max, Vallet Sylvain D, Hayes Catherine, Naba Alexandra, Jurisica Igor, Lisacek Frédérique, Ricard-Blum Sylvie
SIB, Swiss Institute of Bioinformatics, Geneva, Switzerland.
Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada.
Nucleic Acids Res. 2025 Jan 6;53(D1):D1677-D1682. doi: 10.1093/nar/gkae1088.
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.
MatrixDB是国际分子交换联盟（IMEx）的成员之一，是一个经过整理的相互作用数据库，专注于由细胞外基质（ECM）成分建立的相互作用，这些成分包括蛋白质、蛋白聚糖、糖胺聚糖和ECM生物活性片段。MatrixDB的架构进行了升级，以简化相互作用数据的导出，允许版本控制和编程访问，并确保可持续性。该数据库的新版本包含的手动整理和实验支持的相互作用数量增加了一倍多。从综合相互作用数据库中导入了高可信度的预测相互作用，以扩大ECM相互作用组的覆盖范围。对五种物种（人类、小鼠、牛、鸟类和斑马鱼）的ECM和ECM相关蛋白进行了基质体划分和分类注释，这些用于ECM组学数据集的计算分析。来自Reactome通路知识库的生物通路也被添加到生物分子描述中。新的转录组学和扩展的蛋白质组学数据集被导入到MatrixDB中，以使用数据库中集成的新开发的内部网络浏览器生成细胞和组织特异性的ECM网络。MatrixDB可在https://matrixdb.univ-lyon1.fr免费获取。
