Tools

Matrisome AnalyzeR is a web application developed by the Naba and Izzi labs that uses Matrisome lists to identify matrisome genes/proteins in -omic datasets and annotates and tabulates these molecules according to matrisome divisions and categories.

Using Matrisome AnalyzeR? Please cite: 

Petrov PB, Considine JM, Izzi, V, and Naba A. Matrisome AnalyzeR: A suite of tools to annotate and quantify ECM molecules in big datasets across organisms. Journal of Cell Science, 2023, 136 (17): jcs261255. https://doi.org/10.1242/jcs.261255

MatriCom is a web application developed by the Naba and Izzi labs to mine scRNA-Seq datasets and infer communications between ECM components and between different cell populations and the ECM. To impute interactions from expression data, MatriCom relies on a unique database, MatriComDB, that includes over 25,000 curated interactions involving matrisome components, with data on 80% of the ~1,000 genes that compose the mammalian matrisome. MatriCom offers the option to query open-access datasets sourced from large sequencing efforts (Tabula Sapiens, The Human Protein Atlas, HuBMAP) or to process user-generated datasets. 

Using MatriCom? Please cite: 

Coming soon!

MatrisomeDB is a web application originally developed by Dr. Naba and currently mainatained by the Naba lab in collaboration with the Gao lab. MatrisomeDB is a searchable collection of curated proteomic data on the ECM of healthy and diseased human and murine samples. 

Using MatrisomeDB? Please cite 

Shao X, Gomez CD, Kapoor N, Considine JM, Grams C, Gao Y, Naba A. MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database. Nucleic Acids Research, 2022, gkac1009. doi.org/10.1093/nar/gkac1009