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Review
. 2016 Jan;49:10-24.
doi: 10.1016/j.matbio.2015.06.003. Epub 2015 Jul 8.

The Extracellular Matrix: Tools and Insights for the "Omics" Era

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Free PMC article
Review

The Extracellular Matrix: Tools and Insights for the "Omics" Era

Alexandra Naba et al. Matrix Biol. .
Free PMC article

Abstract

The extracellular matrix (ECM) is a fundamental component of multicellular organisms that provides mechanical and chemical cues that orchestrate cellular and tissue organization and functions. Degradation, hyperproduction or alteration of the composition of the ECM cause or accompany numerous pathologies. Thus, a better characterization of ECM composition, metabolism, and biology can lead to the identification of novel prognostic and diagnostic markers and therapeutic opportunities. The development over the last few years of high-throughput ("omics") approaches has considerably accelerated the pace of discovery in life sciences. In this review, we describe new bioinformatic tools and experimental strategies for ECM research, and illustrate how these tools and approaches can be exploited to provide novel insights in our understanding of ECM biology. We also introduce a web platform "the matrisome project" and the database MatrisomeDB that compiles in silico and in vivo data on the matrisome, defined as the ensemble of genes encoding ECM and ECM-associated proteins. Finally, we present a first draft of an ECM atlas built by compiling proteomics data on the ECM composition of 14 different tissues and tumor types.

Keywords: Bioinformatics; ECM atlas; Extracellular matrix; Matrisome; MatrisomeDB; Proteomics.

Figures

Figure 1
Figure 1. Defining the matrisome
A. Definition of matrisome categories. The core matrisome comprises ECM glycoproteins, collagens and proteoglycans. Matrisome-associated proteins include ECM-affiliated proteins, ECM regulators and secreted factors [16, 17]. B. Pie charts represent the number of human genes encoding core matrisome and matrisome-associated proteins. “Hs” indicates genes in the human genome and “Mm”, genes in the murine genome.
Figure 2
Figure 2. Expression of collagen chains across 55 tissue and cellular proteomes
ProteomicsDB (April 2015 release) was interrogated with the 44 human collagen genes. The expression of 39 out of the 44 human collagen chains was reported in at least one of the 55 tissues or cell types for which global proteomics data were available. The five collagen chains not detected are: COL9A3, COL23A1, COL24A1, COL25A1, COL27A1.
Figure 3
Figure 3. Experimental coverage of the in silico of the matrisome
Bar chart represents, for each matrisome category, the percentage representation and number of ECM genes detected in one (lighter bars) or more than one (darker bars) tissue.

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