MatrixDB, the extracellular matrix interaction database

Area of Science:

• Biochemistry
• Bioinformatics
• Molecular Biology

Background:

• Extracellular protein and polysaccharide interactions are crucial for cellular functions but are underrepresented in biological databases.
• Existing databases lack comprehensive coverage of extracellular interactions, necessitating a specialized resource.

Purpose of the Study:

• To introduce MatrixDB, a freely accessible database dedicated to cataloging extracellular protein and polysaccharide interactions.
• To provide a centralized resource for researchers investigating the extracellular matrix and its associated molecular interactions.

Main Methods:

• Curation of interaction data, considering the multimeric nature of extracellular proteins.
• Adoption of Proteomics Standards Initiative-Molecular Interaction (PSI-MI) standards for data curation and exchange.
• Integration of experimental data, literature curation, and data from other reputable databases like the Human Protein Reference Database.

Main Results:

• MatrixDB offers a comprehensive collection of extracellular interactions, including those involving individual polypeptide chains and protein multimers.
• The database incorporates data from diverse sources, ensuring a rich and varied dataset.
• MatrixDB provides links to related resources for gene mutations, gene expression, and protein localization, enhancing its utility.

Conclusions:

• MatrixDB serves as a valuable and unique resource for studying extracellular interactions, filling a critical gap in biological data repositories.
• The database facilitates the construction and analysis of tissue- and disease-specific interaction networks.
• MatrixDB supports research in cell biology, disease mechanisms, and drug discovery by providing integrated and accessible interaction data.