Category Cross-Omics>Knowledge Bases/Databases/Tools

Abstract MatrixDB (Extracellular Matrix interactions DataBase) is a database that is focused on mammalian extracellular protein-protein and protein-carbohydrate interactions.

It takes into account the full interaction repertoire of the extracellular matrix involving full-length molecules, fragments and multimers.

MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions. Interactions with lipids and cations are also reported.

MatrixDB takes into account the influence of multimerization and limited cleavage on molecular recognition properties.

Specific entries are created for multimers (e.g.; collagens, laminins, thrombospondins) and fragments issued from extracellular matrix molecules displaying biological activities of their own (matrikins/matricryptins).

The links between monomers and the corresponding multimers and between matricryptins and their parent molecules are also indicated.

MatrixDB integrates interaction data from the Human Protein Reference Database (HPRD) with permission, from the BioGRID database (a general repository for interaction datasets), from publicly available databases of the IMex consortium (DIP, IntAct, MINT), from the manufacturer's in-house literature curation, and from experiments performed with protein and polysaccharide arrays probed by surface Plasmon Resonance.

Building MatrixDB --

1) Biomolecule sources - Protein data were imported from the UniProtKB/Swiss-Prot database and identified by UniProtKB/Swiss-Prot accession numbers. In order to list all the partners of a protein, interactions are associated by default to the accession number of the human protein.

The actual source species used in experiments is indicated in the page that reports interaction data. Intracellular and membrane proteins were included to obtain a comprehensive network of the partners of extracellular molecules.

Extracellular matrix (ECM) proteins were identified by the UniProtKB/Swiss-Prot keyword ‘extracellular matrix’ and by the GO terms ‘extracellular matrix’, ‘proteinaceous extracellular matrix’ and their child terms.

The proteins annotated with the GO terms ‘extracellular region’ and ‘extracellular space’, which are used for proteins found in biological fluids, were Not included because circulating molecules do Not directly contribute to the extracellular scaffold.

Additionally, 96 proteins were manually (re-)annotated through literature curation. Glycan-binding proteins were annotated with cross-references to the KEGG GLYCAN database when available.

The manufacturer created specific identifiers for fragments (PFRAG_number), multimers (MULT_number), cations (CAT_number), lipids (LIP_number) and GAGs (GAG_number), with cross-references to the ChEBI database when available.

2) Interaction sources - MatrixDB integrates 1,378 interactions from the Human Protein Reference Database (HPRD), 211 interactions from the Molecular INTeraction database (MINT), 46 interactions from the Database of Interacting Proteins (DIP), 232 interactions from IntAct and 839 from BioGRID involving at least one extracellular biomolecule of mammalian origin.

The manufacturer added 283 interactions from manual literature curation and 65 interactions from protein and Glycosaminoglycan (GAG) array experiments.

All interaction data, except those imported from HPRD and BioGRID, are reported according to the MIMIx standard (Minimum Information required for reporting a Molecular Interaction experiment).

The coverage of the extracellular interaction network is Not complete and MatrixDB is regularly updated.

Querying MatrixDB --

All members of a category (i.e. all the extracellular molecules, proteins, fragments, multimers, GAGs, lipids or cations) can be displayed.

Biomolecules can be searched by their common name, UniProtKB/Swiss-Prot (or CheBI for GAGs) accession number or gene name.

GO terms, UniProtKB/Swiss-Prot keywords, PubMed IDentifiers or author names can be used to query the database.

Interactions from each database can be retrieved. All the binding partners of a biomolecule are listed on the ‘Biomolecule Report’ page.

The list of experiments reporting an interaction is accessible on the ‘Association Report’ page.

Experimental data (binding site, kinetic and affinity constants) are displayed on the ‘Experiment Report’ page.

Selected molecules can be saved in a cart for building the corresponding interaction network.

A tutorial is available on-line and interaction data can be downloaded from the MatrixDB website in PSI-MI XML 2.5 and MITAB 2.5.

Visualization of Interaction Networks --

The manufacturer has developed a set of scripts based on Cytoscape (see G6G Abstract Number 20092), to visualize the extracellular interaction network or sub-networks.

Biomolecule types are shape- and color-coded. Besides non-covalent physical interactions, links are displayed between a multimer and its constitutive monomers, a fragment and its parent molecule, and the protein and Glycosaminoglycan (GAG) moieties of proteoglycans.

Sub-cellular localization of the biomolecules can be visualized.

Biomolecule and interaction data are imported into Cytoscape and displayed when clicking on a node (biomolecule) or on an edge (link) of the network.

Alternatively, interaction networks can be visualized on the MatrixDB website using Medusa (see G6G Abstract Number 20299).

System Requirements

Contact manufacturer.


Manufacturer Web Site MatrixDB

Price Contact manufacturer.

G6G Abstract Number 20486

G6G Manufacturer Number 104109