title: The extracellular matrix: Tools and insights for the "omics" era.
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.
authors.affiliation: David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: anaba@mit.edu.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Naba
authors.affiliation: Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Karl R
authors.initials: KR
authors.lastname: Clauser
authors.affiliation: David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Barbara K. Ostrom Bioinformatics and Computing facility at the Swanson Biotechnology Center, Cambridge, MA 02139, USA.
authors.forename: Huiming
authors.initials: H
authors.lastname: Ding
authors.affiliation: David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Barbara K. Ostrom Bioinformatics and Computing facility at the Swanson Biotechnology Center, Cambridge, MA 02139, USA.
authors.forename: Charles A
authors.initials: CA
authors.lastname: Whittaker
authors.affiliation: Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Steven A
authors.initials: SA
authors.lastname: Carr
authors.affiliation: David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: rohynes@mit.edu.
authors.forename: Richard O
authors.initials: RO
authors.lastname: Hynes
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D005109:Extracellular Matrix / Q000378:metabolism*; D016326:Extracellular Matrix Proteins / Q000378:metabolism*; D006801:Humans; D020407:Internet; D009369:Neoplasms / Q000378:metabolism; D009928:Organ Specificity; D040901:Proteomics / Q000379:methods*
chemical_list: D016326:Extracellular Matrix Proteins
keywords: Bioinformatics; ECM atlas; Extracellular matrix; Matrisome; MatrisomeDB; Proteomics