MatrixDB 2024: an increased coverage of extracellular matrix interactions, a new Network Explorer and a new web interface
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.
Authors
- Kasun Samarasinghe (ORCID: https://orcid.org/0000-0002-0642-6841)
- Alexandra Naba (ORCID: https://orcid.org/0000-0002-4796-5614)
- Frédérique Lisacek (ORCID: https://orcid.org/0000-0002-0948-4537)
- Max Kotlyar (ORCID: https://orcid.org/0000-0002-1111-8667)
- Sylvie Ricard‐Blum (ORCID: https://orcid.org/0000-0001-9263-1851)
- Igor Jurišica (ORCID: https://orcid.org/0000-0002-2507-946X)
- Catherine Hayes (ORCID: https://orcid.org/0000-0002-3640-3237)
- Sylvain D. Vallet (ORCID: https://orcid.org/0000-0001-9885-7499)
Institutions
- Université Claude Bernard Lyon 1 (FR)
- SIB Swiss Institute of Bioinformatics (CH)
- Centre National de la Recherche Scientifique (FR)
- University Health Network (CA)
- University of Toronto (CA)
- Slovak Academy of Sciences (SK)
- Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR)
- Discovery Centre (CA)
- CEA Grenoble (FR)
- University of Illinois Chicago (US)
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (FR)
- Institute of Neuroimmunology of the Slovak Academy of Sciences (SK)
- Institut de Biologie Structurale (FR)
- Krembil Research Institute
- Université Grenoble Alpes (FR)
Publication Details
- Journal
- Nucleic Acids Research
- Published
- 2024-11-18
- DOI
- https://doi.org/10.1093/nar/gkae1088
- Citations
- 4
- Primary Topic
- Bioinformatics and Genomic Networks
- Type
- article
- Field-Weighted Citation Impact
- 0.94
Funders
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- Institut National Du Cancer
- National Institutes of Health
- National Human Genome Research Institute
- National Cancer Institute
- Office of Strategic Coordination