MatrixDB 2024: an increased coverage of extracellular matrix interactions, a new Network Explorer and a new web interface

Abstract

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.

Graphical Abstract

Figure 1.

Number of experimentally-supported interactions in MatrixDB releases. The plot shows the increase in the total number of experimental interactions (black), and in the number of experimental protein-protein (white) and protein-GAG (blue) interactions. The ‘protein’ category includes monomeric proteins and individual polypeptide chains of multimers (e.g. α chains of collagens).

Figure 2.

Interaction networks of several molecular proteoforms of human collagens. Network of selected native trimeric collagens, individual collagen a chains and collagen matrikines/matricryptins. It has been built using the Network Explorer using ‘Collagen’, ‘Multimers’ and ‘Homo sapiens’ as filters. The biomolecules are color-coded (protein: orange, glycosaminoglycan (GAG): blue, multimer: purple, protein fragment (PFRAG): yellow, grey: small molecule).

Figure 3.

Interaction networks of human fibronectin generated using the Network Explorer of MatrixDB. (A) Fibronectin network comprising experimental interactions only. The small network located in the bottom left corner comprises an isoform of fibronectin (P02751–12) and its three partners. The biomolecules are color-coded (protein: orange, glycosaminoglycan (GAG): blue, multimer: purple, protein fragment (PFRAG): yellow). (B) Fibronectin network comprising both experimental (black links) and predicted interactions (red links). (C) Fibronectin network in blood vessel generated by filtering the entire network with proteomic data (normalized spectral abundance factor 501). (D) Fibronectin network in the eye generated by filtering the entire network with proteomic data (normalized spectral abundance factor 501).