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MatrixDB specifications


Unique identifier OMICS_02926
Name MatrixDB
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes


  • Primates
    • Homo sapiens


  • person_outline S. Ricard-Blum

Publications for MatrixDB

MatrixDB citations


Conditional deletion of RB1 in the Tie2 lineage leads to aortic valve regurgitation

PLoS One
PMCID: 5755794
PMID: 29304157
DOI: 10.1371/journal.pone.0190623
call_split See protocol

[…] loading scores were also grouped using k-means clustering (k = 4). Both algorithms were iterated 100 times to help assure convergence of the cluster centroids. ECM proteins were classified using the MatrixDB []. […]


Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder Enriched Interactions

Int J Mol Sci
PMCID: 5751360
PMID: 29257115
DOI: 10.3390/ijms18122761

[…] e raw data on the PPI were obtained from the mentha resource []. This resource integrates expert curated PPIs obtained from a comprehensive set of five primary databases: MINT [], IntAct [,], DIP [], MatrixDB [], and BioGRID []. We extracted all records from taxon 9606 (Homo sapiens) for this analysis. These records include 154,395 interactions that cover 15,870 proteins. Next, we mapped these pro […]


Modulation of FAK and Src adhesion signaling occurs independently of adhesion complex composition

PMCID: 4739608
PMID: 26833789
DOI: 10.1083/jcb.201508080

[…] ron, University of Edinburgh, Edinburgh, Scotland, UK) consisting of protein–protein interactions reported in the Protein Interaction Network Analysis platform (release date December 10, 2012; ), the MatrixDB database (release date April 20, 2012; ) and the literature-curated integrin adhesome (; ). FAK, β1 integrin and their associated interacting proteins were extracted and displayed as a networ […]


Meta Analysis of Large Scale Toxicogenomic Data Finds Neuronal Regeneration Related Protein and Cathepsin D to Be Novel Biomarkers of Drug Induced Toxicity

PLoS One
PMCID: 4559398
PMID: 26335687
DOI: 10.1371/journal.pone.0136698

[…] ere visualized using Cytoscape []. Rat PPIs from the following 13 sources were combined: BIND [], BIND_t [], BioGRID [], CORUM [], DIP [], HPRD [], IntAct [], MINT [], MPPI [], OPHID [], InnateDB [], MatrixDB [], and mentha []. Using the ortholog mapping relationships reported in the NCBI HomoloGene database [], we combined the most recent human PPIs [] with the rat PPIs. A total of 169,723 intera […]


Integrated inference and evaluation of host–fungi interaction networks

Front Microbiol
PMCID: 4523839
PMID: 26300851
DOI: 10.3389/fmicb.2015.00764

[…] interaction data of S. cerevisiae and H. sapiens were downloaded from the following 14 active partners of the International Molecular Exchange (IMEx) consortium ():DIP (), IntAct (), MBInfo, MINT (), MatrixDB (), Molecular Connections, I2D (), InnateDB (), UCL-BHF group, UCL London, UniProt Swiss-Prot group, SIB (), BioGRID (), MPact (), BIND (), and MPIDB ().PSICQUIC queries () were used to retri […]


The hierarchical organization of natural protein interaction networks confers self organization properties on pseudocells

BMC Syst Biol
PMCID: 4464023
PMID: 26050708
DOI: 10.1186/1752-0509-9-S3-S3

[…] cells. Both networks have been obtained from the resource mentha []. This resource integrates all the published information curated by the IMEx [] databases MINT [], Intact [], DIP [], BIOGRID [] and MatrixDB [] and uses a ranking procedure, similar to the one implemented in WI-PHI [], to offer human and yeast interactomes where each interaction is assigned a weight according to experimental suppo […]


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MatrixDB institution(s)
University Lyon, Institut de Chimie et Biochimie Moleculaires et Supramoleculaires (ICBMS), UMR 5246, University Lyon 1, CNRS, Villeurbanne, France; University Grenoble Alpes, CNRS, TIMC-IMAG / BCM, Grenoble, France; Department of Physiology and Biophysics, University of Illinois at Chicago, College of Medicine, Chicago, IL, USA; Centre de Recherches sur les Macromolecules Vegetales (CERMAV), UPR 5301 CNRS, University Grenoble Alpes, Grenoble, France
MatrixDB funding source(s)
Supported by Fondation pour la Recherche Medicale [DBI20141231336]; Institut Francais de Bioinformatique [ANR-11-INBS-0013, Glycomatrix project, call 2015]; GDR GAG [CNRS, GDR 3739, Structure, Fonction et Regulation des Glycosaminoglycanes]; Cross Disciplinary Program [email protected], within the framework ‘Investissements d’Avenir’ program [ANR-15IDEX-02].

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