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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:
Hynes R.O and Naba A. Overview of the matrisome – an inventory of ECM constituents and functions. In Extracellular Matrix Biology (eds. R.O. Hynes and K.M. Yamada), Cold Spring Harbor Perspectives in Biology, 2012, 4(1):a004903. https://doi.org/10.1101/cshperspect.a004903
Naba A, Hoersch S, and Hynes R.O. Towards definition of an ECM parts list: an advance on GO categories. Matrix Biology, 2012, 31(7/8):371-372. https://doi.org/10.1016/j.matbio.2012.11.008
Gebauer J.M and Naba A. The matrisome of model organisms: from in-silico prediction to big-data annotation. In: Extracellular Matrix Omics. Biology of Extracellular Matrix, 2020, vol 7: 17-42, Springer. https://doi.org/10.1007/978-3-030-58330-9_2
Homo sapiens (human)
Naba A, Clauser KR, Hoersch S, Liu H, Carr SA, and Hynes RO. The matrisome: in-silico definition and in-vivo characterization by proteomics of normal and tumor extracellular matrices. Molecular and Cellular Proteomics, 2012, 11(4):M111.014647.
Mus musculus (mouse)
Naba A, Clauser KR, Hoersch S, Liu H, Carr SA, and Hynes RO. The matrisome: in-silico definition and in-vivo characterization by proteomics of normal and tumor extracellular matrices. Molecular and Cellular Proteomics, 2012, 11(4):M111.014647.
Danio rerio (zebrafish)
Nauroy P, Hughes S, Naba A, and Ruggiero F. The in-silico zebrafish matrisome: A new tool to study extracellular matrix gene and protein functions. Matrix Biology, 2018, 65:5-13.
Drosophila melanogaster (fruit fly)
Davis MN, Horne-Badovinac S, and Naba A. In-silico definition of the Drosophila melanogaster matrisome. Matrix Biology Plus, 2019, 100015.
Caenorhabditis elegans (nematode)
Teuscher A, Jongsma E, Davis MN, Statzer C, Gebauer JM, Naba A, and Ewald CY. In-silico characterization of the Caenorhabditis elegans matrisome and proposal of a novel collagen classification. Matrix Biology Plus, 2019, 100001.
Cote LE, Simental E, Reddien PW. Muscle functions as a connective tissue and source of extracellular matrix in planarians. Nat Commun. 2019, 10(1):1592.
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. https://doi.org/10.3389/fcell.2019.00035
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. https://doi.org/10.1016/j.jprot.2023.104891
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