The Matrisome Project

Introduction

The extracellular matrix (ECM) is a fundamental and important component of metazoan organisms providing architectural support and anchorage for the cells. The ECM consists of a complex meshwork of highly cross-linked proteins and exists as interstitial forms within organs and as specialized forms, such as basement membranes underlying epithelia, vascular endothelium and surrounding certain other tissues and cell types.

In a research effort bringing together scientists from the Koch Institute for Integrative Cancer Research at MIT and the Broad Institute of MIT and Harvard, we characterized and predicted bioinformatically the ensemble of genes encoding the "matrisome", i.e. the ensemble of extracellular matrix and ECM-associated proteins (Naba et al, 2011). This effort was aided by a key feature of extracellular matrix proteins: their characteristic domain-based organization.

We have established a website to facilitate access to this information: http://matrisomeproject.mit.edu.

We provide there, in addition to the materials available in our publication, inventories of ECM domains used to define or exclude a protein from being categorized as extracellular matrix protein, additional resource files and annotations of the bioinformatic pipeline we use to derive the matrisomes from the human and mouse genomes.

The purpose of this web page is to provide information and resources relevant to research on ECM proteins and to be a platform for deploying data collections, methods, and protocols. This effort is aimed at further facilitating the use of our protocols by other scientists and to allow their widespread use in future studies.

Publications

1. 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. Mol. Cell. Prot.  2011. (Published on December 9, 2011, doi:10.1074/mcp.M111.014647). PMID:22159717
2. Hynes RO, Naba A. Overview of the Matrisome--An Inventory of Extracellular Matrix Constituents and Functions. Cold Spring Harbor Perspectives in Biology 2011 Sep. PMID:21937732. In: Hynes RO, Yamada KM (Editors). Extracellular Matrix Biology.  Cold Spring Harbor Perspectives in Biology 2011 Sep.
3. Naba A, Hoersch S, Hynes RO. Towards definition of an ECM parts list: An advance on GO categories. Matrix Biology 2012 Sep;31(7-8):371-372. (doi: 10.1016/j.matbio.2012.11.008).
   

Institutions and People

Contributors The Hynes Lab at The Koch Institute for Integrative Cancer Research at MIT		Collaborators Proteomics Platform of The Broad Institute of MIT and Harvard
Alexandra Naba Sebastian Hoersch Richard O. Hynes		Karl R. Clauser Steven A. Carr

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