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Matrix Biol DOI:10.1016/j.matbio.2015.06.003

The extracellular matrix: Tools and insights for the "omics" era.

Publication TypeJournal Article
Year of Publication2016
AuthorsNaba, A, Clauser, KR, Ding, H, Whittaker, CA, Carr, SA, Hynes, RO
JournalMatrix Biol
Volume49
Pages10-24
Date Published2016 Jan
ISSN1569-1802
KeywordsAnimals, Computational Biology, Databases, Protein, Extracellular Matrix, Extracellular Matrix Proteins, Humans, Internet, Neoplasms, Organ Specificity, Proteomics
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.

URLhttp://linkinghub.elsevier.com/retrieve/pii/S0945-053X(15)00121-3
DOI10.1016/j.matbio.2015.06.003
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/26163349?dopt=Abstract

Alternate JournalMatrix Biol.
PubMed ID26163349
PubMed Central IDPMC5013529
Grant ListP30 CA014051 / CA / NCI NIH HHS / United States
P30-CA14051 / CA / NCI NIH HHS / United States
U54 CA163109 / CA / NCI NIH HHS / United States
/ / Howard Hughes Medical Institute / United States
U54 CA126515 / CA / NCI NIH HHS / United States
CA163109 / CA / NCI NIH HHS / United States