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In-silico prediction of the matrisome - An introduction
In-silico prediction of the matrisome - An introduction
Using characteristic features of ECM proteins (signal peptide, modular domain-based organization), we interrogated the genomes of model organisms and identified computationally the ensemble of genes encoding proteins containing these features and inferred their belonging to the ECM. This ensemble of genes constitutes the matrisome.
These genes can further be divided into 1) genes encoding core matrisome proteins, i.e., structural components of the ECM including ECM glycoproteins, collagens, and proteoglycans, and 2) genes encoding matrisome-associated proteins that either share structural features with core matrisome proteins (ECM-affiliated proteins), contribute to the homeostasis or remodeling of the ECM (ECM regulators), or bind to the ECM and modulate ECM signaling (secreted factors).
Key publications:
Key publications:
Hynes RO, Naba A. Overview of the Matrisome – An Inventory of Extracellular Matrix Constituents and Functions. Cold Spring Harbor Perspective in Biology, 2011, 4(1), a004903. Journal Access | PMC Access | Book Review
Naba A, Hoersch S, Hynes RO. Towards definition of an ECM parts list: An advance on GO categories. Matrix Biology, 2012, 31(7-8), 371-372. Journal Access | PMC Access
Gebauer JM, Naba A. The Matrisome of Model Organisms: From In-Silico Prediction to Big-Data Annotation. In: Extracellular Matrix Omics. Biology of Extracellular Matrix, 2020, 7, 17-42. Chapter Access
Naba A, Clauser KR, Hoersch S, Liu H, Carr SA, Hynes RO. The Matrisome: In Silico Definition and In Vivo Characterization by Proteomics of Normal and Tumor Extracellular Matrices. Molecular & Cellular Proteomics, 2011, 11(4), M111.014647. Journal Access | PMC Access | F1000 Recommendation
Naba A, Clauser KR, Hoersch S, Liu H, Carr SA, Hynes RO. The Matrisome: In Silico Definition and In Vivo Characterization by Proteomics of Normal and Tumor Extracellular Matrices. Molecular & Cellular Proteomics, 2011, 11(4), M111.014647. Journal Access | PMC Access | F1000 Recommendation
Nauroy P, Hughes S, Naba A, Ruggiero F. The in-silico zebrafish matrisome: A new tool to study extracellular matrix gene and protein functions. Matrix Biology, 2017, 65, 5-13. Journal Access
Davis MN, Horne-Badovinac S, Naba A. In-silico definition of the Drosophila melanogaster matrisome. Matrix Biology Plus, 2019, 4, 100015. Journal Access | PMC Access
Teuscher AC, Jongsma E, Davis MN, Statzer C, Gebauer JM, Naba A, Ewald CY. The in-silico characterization of the Caenorhabditis elegans matrisome and proposal of a novel collagen classification. Matrix Biology Plus, 2019, 1, 100001. Journal Access | PMC Access
Cote LE, Simental E, Reddien PW. Muscle functions as a connective tissue and source of extracellular matrix in planarians. Nature Communications, 2019, 10(1): 1592. Journal Access | PMC Access
Bergheim BG, Cole AG, Rettel M, Stein F, Redl S, Hess MW, Ikmi A, Özbek S. Molecular dynamics of the matrisome across sea anemone life history. Elife, 2025, 14:105319. Journal Access | PMC Access
Huss DJ, Saias S, Hamamah S, Singh JM, Wang J, Dave M, Kim J, Eberwine J, Lansford R. Avian primordial germ cells contribute to and interact with the extracellular matrix during early migration. Front Cell Dev Biol, 2019, 7:35. Journal Access | PMC Access
Sacher F, Feregrino C, Tschopp P, Ewald CY. Extracellular matrix gene expression signatures as cell type and cell state identifiers. Matrix Biology Plus, 2021, 10:100069. Journal Access | PMC Access
Listrat A, Boby C, Tournayre J, Jousse C. Bovine extracellular matrix proteins and potential role in meat quality: First in silico Bos taurus compendium. Journal of Proteomics, 2023, 279:104891. Journal Access
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