ArticleNucleic acids research2019
MatrixDB: integration of new data with a focus on glycosaminoglycan interactions.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed.
- BRD2 impedes iPSC reprogramming by regulating lipid biosynthesis and the matrisome via its ET tail.Communications biology · 2026Article
- A guide to building the matrisome interactome: from computational predictions to experimental validation.The FEBS journal · 2026Review
- Scaling Large Language Models for Next-Generation Single-Cell Analysis.bioRxiv : the preprint server for biology · 2026Article
- Mining Alzheimer's Interactomes, Macromolecular Complexes and Pathways for Drug Discovery.Proteomics · 2025Review
- Phase-separating fusion proteins drive cancer by upsetting transcription regulation.Genome biology · 2025Article
- SPP1 + macrophages facilitate pancreatic cancer progression via ITGB6-mediated interactions: evidence from integrated multi-omics analysis and experimental validation.Immunologic research · 2025Article
- MatriCom, a single-cell RNA-sequencing data mining tool to infer cell-extracellular matrix interactions.Journal of cell science · 2025Article
- What Have Data Standards Ever Done for Us?Molecular & cellular proteomics : MCP · 2025Review
- Development and Validation of an Extracellular Matrix Gene Expression Signature for Prognostic Prediction in Patients with Uveal Melanoma.International journal of molecular sciences · 2025Article
- Human bone tissue-derived ECM hydrogels: Controlling physicochemical, biochemical, and biological properties through processing parameters.Bioactive materials · 2025Article
- Mechanisms of assembly and remodelling of the extracellular matrix.Nature reviews. Molecular cell biology · 2024Review
- Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy.Database : the journal of biological databases and curation · 2024Article
- Matrisome proteomics reveals novel mediators of muscle remodeling with aerobic exercise training.Matrix biology plus · 2024Article
- Glycosaminoglycans: Participants in Microvascular Coagulation of Sepsis.Thrombosis and haemostasis · 2024Review
- The epithelial adherens junction component PLEKHA7 regulates ECM remodeling and cell behavior through miRNA-mediated regulation of MMP1 and LOX.bioRxiv : the preprint server for biology · 2024Article
- Decoding glycosylation potential from protein structure across human glycoproteins with a multi-view recurrent neural network.bioRxiv : the preprint server for biology · 2024Article
- Discovery of immunotherapy targets for pediatric solid and brain tumors by exon-level expression.Nature communications · 2024Article
- Discovery of immunotherapy targets for pediatric solid and brain tumors by exon-level expression.Research square · 2024Article
- Web-Based Resources to Investigate Protease Function.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Hyaluronidase-induced matrix remodeling contributes to long-term synaptic changes.Frontiers in neural circuits · 2024Article
19 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MatrixDB (http://matrixdb.univ-lyon1.fr/) is an interaction database focused on biomolecular interactions established by extracellular matrix (ECM) proteins and glycosaminoglycans (GAGs). It is an active member of the International Molecular Exchange (IMEx) consortium (https://www.imexconsortium.org/). It has adopted the HUPO Proteomics Standards Initiative standards for annotating and exchanging interaction data, either at the MIMIx (The Minimum Information about a Molecular Interaction eXperiment) or IMEx level. The following items related to GAGs have been added in the updated version of MatrixDB: (i) cross-references of GAG sequences to the GlyTouCan database, (ii) representation of GAG sequences in different formats (IUPAC and GlycoCT) and as SNFG (Symbol Nomenclature For Glycans) images and (iii) the GAG Builder online tool to build 3D models of GAG sequences from GlycoCT codes. The database schema has been improved to represent n-ary experiments. Gene expression data, imported from Expression Atlas (https://www.ebi.ac.uk/gxa/home), quantitative ECM proteomic datasets (http://matrisomeproject.mit.edu/ecm-atlas), and a new visualization tool of the 3D structures of biomolecules, based on the PDB Component Library and LiteMol, have also been added. A new advanced query interface now allows users to mine MatrixDB data using combinations of criteria, in order to build specific interaction networks related to diseases, biological processes, molecular functions or publications.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.