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 provide here, 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).

Resources

The following links give access to a collection of resources (data files and tables) on the matrisome and its generation. Presently, all posted files were generated in the context of the publication above, and most of them are reconfigured or extended versions of data files from this publication's supplemental data files.
 
(1) The human matrisome (.xlsx file) Based on Naba et al., 2011. Excel table with the annotated collection of human and murine matrisomal proteins.

UPDATED!
Like Tables S3A and B, but in addition, data on the orthologs from the respective other species are present in each table, facilitating cross-comparisons between the human and the murine matrisomes.
(2) The mouse matrisome (.xlsx file)
(3) Experimental coverage of the in silico matrisome NEW!
Proteomics data of extracellular matrix proteins identified in selected experimental conditions.

(4) Domain collections (.xlsx file) Collections of InterPro domains used as "defining" and "excluding with respect to matrisome membership (based on Table S2, Naba et al., 2011).

(5) Index flatfiles for (1) and (2) (.txt files) COMING SOON! Select indexes derived from the tables (1) and (2)

(6) Protein FASTA files Access to protein FASTA files of the sequences referenced in the matrisome tables (1) and (2).

(7) Commented workflow for deriving the in silico matrisome A detailed description of the bioinformatics workflow for arriving at the matrisomes is provided in Naba et al., 2011. We re-post it here with additional comments and explanatory notes that may be helpful for those wishing to establish a matrisome for another species following our methodology. Decision points in the workflow are highlighted and possibly less obvious aspects commented on in more detail.


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
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Alexandra Naba
Sebastian Hoersch
Richard O. Hynes

Karl R. Clauser
Steven A. Carr




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Last update: 20121130
Regarding technical issues with this site, please contact Alexandra Naba.