MatrisomeDB is a searchable database that integrates experimental proteomic data on the ECM composition of normal and diseased tissues.
It provides for each entry the list of tissues in which it was detected, a coverage map indicating the peptides detected, as well as the list of post-translational modifications identified. It also provides live cross-referencing to gene and protein databases for every ECM and ECM-associated genes.
MatrisomeDB is part of the larger Matrisome Project, an effort initiated by Dr. Naba during her postdoctoral training in the laboratory of Dr. Richard Hynes at MIT, in collaboration with members of the Bioinformatics & Computing Facility at the Koch Institute for Integrative Cancer Research at MIT, and Karl Clauser and Steve Carr at the Proteomics Platform of the Broad Institute.
The 2019 release of MatrisomeDB was developed through a collaborative effort between the Naba lab in the Department of Physiology and Biophysics at the University of Illinois at Chicago (UIC) and the Gao lab in the College of Pharmacy at UIC.
The 2022 release of MatrisomeDB(MatrisomeDB2.0) includes an expanded content, enhanced data visualization features including peptide and post-translational modification mapping onto domain-based representation and 3D structures of proteins, and an abstract-mining tool that generates an enrichment word cloud from abstracts of studies in which a queried protein is found with higher confidence and higher abundance relative to other studies in MatrisomeDB.
MatrisomeDB is expandable. If you have recently reported the results of a ECM proteomics study and would like to have your data integrated in MatrisomeDB, please contact us at firstname.lastname@example.org. Your data will help other researchers in the field to conduct better research. Together, we thrive. To submit your datasets and related meta-data to assist with the curation process, click HERE.