The Matrisome Project

The Matrisome Project is a collaborative effort between scientists from the Hynes Lab at the Koch Institute for Integrative Cancer Research at MIT and the Broad Institute of MIT and Harvard, aimed at defining bioinformatically and experimentally the ensemble of genes encoding the "matrisome", i.e. the ensemble of extracellular matrix and ECM-associated proteins (Naba et al, 2011).
The purpose of the Matrisome Project 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. Our aim is to facilitate the use of our protocols by other scientists and to allow their widespread use in future studies.

Contact: 
Alexandra Naba: anaba@mit.edu
Data Info: 
Description: 

Collection of resources (inventories of ECM domains used to define extracellular matrix proteins, sequence files and tables) on the human and mouse matrisomes.
Experimental coverage of the in silico matrisome: http://web.mit.edu/hyneslab/matrisome/page_experimentalData.html
This table summarizes experimental proteomic data mapped to the human in silico matrisome defined bioinformatically. The data presented in this table were published in Naba et al., Molecular and Cellular Proteomics, 2011 (doi: 10.1074/mcp.M111.014647). For detailed description of the material and methods used to generate these data, please refer to this publication.
 
In addition, the raw mass spectrometry data are deposited in MassIVE (http://proteomics.ucsd.edu/ProteoSAFe/datasets.jsp)
- Murine lung, murine colon and melanoma xenografts data (A375 and MA2 tumors): MSV000078494
- Human mammary carcinoma xenigrafts (MDA-MB-231 and LM2 tumors): MSV000078535
 

Publication Info: 
Date: 
Published online December 2011
Notes: 
The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices. Alexandra Naba, Karl R. Clauser, Sebastian Hoersch, Hui Liu, Steven A. Carr and Richard O. Hynes. Molecular and Cellular Proteomics, 2011 (doi: 10.1074/mcp.M111.014647). PMID:22159717
Date: 
September 2011
Notes: 
Overview of the Matrisome - An Inventory of Extracellular Matrix Constituents and Functions. Richard O. Hynes and Alexandra Naba In: Extracellular Matrix Biology. Hynes RO, Yamada KM (Editors). Cold Spring Harbor Perspectives in Biology, 2011. PMID:21937732.
Date: 
March 2014
Notes: 
Extracellular matrix signatures of human mammary carcinoma identify novel metastasis promoters. Alexandra Naba, Karl R. Clauser, John M. Lamar, Steven A. Carr, Richard O. Hynes. eLife, 2014, 3:e01308.
Tool Info: 
Name: 
Bioinformatic workflow for deriving in silico matrisomes
Description: 

Annotated bioinformatic workflow used to derive in silico matrisomes.