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

Area of Science:

• Biochemistry
• Bioinformatics
• Molecular Biology

Background:

• The extracellular matrix (ECM) is crucial for tissue structure and function.
• Understanding ECM component interactions is vital for biological research.
• Existing databases may lack comprehensive, curated ECM interaction data.

Purpose of the Study:

• To present an upgraded version of the MatrixDB database.
• To enhance data accessibility, curation, and analytical capabilities for ECM interactions.
• To expand the coverage of the ECM interactome.

Main Methods:

• Database architecture upgrade for improved data export, versioning, and programmatic access.
• Integration of manually curated and experimentally-supported interactions, doubling previous content.
• Importation of high-confidence predicted interactions from the Integrated Interactions Database.
• Annotation of ECM proteins with matrisome categories and addition of Reactome pathways.
• Incorporation of transcriptomic and proteomic datasets for network generation via Network Explorer.

Main Results:

• MatrixDB now contains over twice the number of manually curated and experimentally-supported ECM interactions.
• Expanded coverage of the ECM interactome through imported predicted interactions.
• Enhanced annotation with matrisome divisions and biological pathways.
• Development of an in-house Network Explorer for generating cell- and tissue-specific ECM networks.

Conclusions:

• The upgraded MatrixDB provides a significantly enhanced resource for studying ECM interactions.
• Improved data accessibility and analytical tools facilitate computational analysis of ECM -omic datasets.
• MatrixDB serves as a valuable, freely available platform for the scientific community.