MatrixDB

MatrixDB catalogs interactions between extracellular proteins and polysaccharides, with a focus on extracellular matrix proteins and glycosaminoglycans to support analysis of ECM molecular interactions.

Key Features:

• Multimeric interaction curation: Reports interactions involving individual polypeptide chains and multimers, treating multimers as permanent complexes when appropriate.
• Data integration from experimental sources: Integrates experimental data from original laboratory research, literature curation, imported IMEx datasets, and the Human Protein Reference Database.
• Standards compliance and consortium participation: Participates in the IMEx consortium and adheres to HUPO Proteomics Standards Initiative formats for data annotation and exchange.
• Species coverage: Focuses primarily on mammalian interactions while incorporating model organism datasets as they become available.
• Query-driven network construction and visualization compatibility: Supports customized queries to construct tissue- and disease-specific interaction networks and enables network export/analysis with Cytoscape and Medusa, with an iNavigator component for network building and expansion.
• GAG representation and modeling: Cross-references GlyTouCan for glycosaminoglycan sequences and represents GAGs in IUPAC, GlycoCT, and SNFG image formats, with a GAG Builder for constructing 3D models from GlycoCT codes.
• Schema supporting complex experiments: Database schema supports n-ary experiments to represent complex interaction datasets.
• Expression and proteomics integration: Imports gene expression data from Expression Atlas and quantitative ECM proteomic datasets from the Matrisome Project.
• Advanced query mining: Enables mining by combinations of criteria including disease, biological process, molecular function, and publication.
• Cross-references to mutation and expression resources: Cross-references databases documenting mutations in genes encoding extracellular proteins, UniGene, and the Human Protein Atlas.

Scientific Applications:

• ECM interaction network analysis: Construction and analysis of extracellular matrix interaction networks to investigate biological processes and disease states.
• Protein–GAG interaction studies: Investigation of protein–glycosaminoglycan interactions using sequence representations and 3D GAG models.
• Contextualization with expression and proteomics data: Integration of Expression Atlas and Matrisome Project data to relate interactions to gene expression and quantitative ECM proteomics.
• Comparative studies: Comparative analysis across mammalian and available model organism interaction datasets.
• Molecular mechanism elucidation: Support for elucidating molecular mechanisms underlying physiological and pathological conditions involving the extracellular matrix.

Methodology:

Curation reports chain- and multimer-level interactions; imports data from literature, laboratories, IMEx databases and the Human Protein Reference Database; adheres to HUPO-PSI standards and participates in IMEx; schema supports n-ary experiments; cross-references GlyTouCan and represents GAGs in IUPAC, GlycoCT and SNFG formats with GAG Builder generating 3D models from GlycoCT; imports Expression Atlas and Matrisome Project datasets; supports network export for Cytoscape and Medusa and network construction via iNavigator.