ArticleNucleic acids research2015
MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
59 citing papers in PubMed.
- Article
- An Effective Computational Method for Predicting Self-Interacting Proteins Based on VGGNet Convolutional Neural Network and Gray-Level Co-occurrence Matrix.Evolutionary bioinformatics online · 2024Article
- HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence.Molecular cell · 2023Article
- SIPGCN: A Novel Deep Learning Model for Predicting Self-Interacting Proteins from Sequence Information Using Graph Convolutional Networks.Biomedicines · 2022Article
- ImitateDB: A database for domain and motif mimicry incorporating host and pathogen protein interactions.Amino acids · 2022Article
- Article
- A network view of human immune system and virus-human interaction.Frontiers in immunology · 2022Article
- Computational repurposing of therapeutic small molecules from cancer to pulmonary hypertension.Science advances · 2021Article
- Peptide Location Fingerprinting Reveals Tissue Region-Specific Differences in Protein Structures in an Ageing Human Organ.International journal of molecular sciences · 2021Article
- Applications and analytical tools of cell communication based on ligand-receptor interactions at single cell level.Cell & bioscience · 2021Review
- Peptide location fingerprinting reveals modification-associated biomarker candidates of ageing in human tissue proteomes.Aging cell · 2021Article
- Glycosaminoglycan-Protein Interactions: The First Draft of the Glycosaminoglycan Interactome.The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society · 2021Review
- Machine learning approaches and databases for prediction of drug-target interaction: a survey paper.Briefings in bioinformatics · 2021Review
- Network analysis of host-pathogen protein interactions in microbe induced cardiovascular diseases.In silico biology · 2021Article
- Article
- Towards a unified open access dataset of molecular interactions.Nature communications · 2020Review
- Three-Dimensional Structures of Carbohydrates and Where to Find Them.International journal of molecular sciences · 2020Review
- SZDB2.0: an updated comprehensive resource for schizophrenia research.Human genetics · 2020Article
- Databases and Bioinformatic Tools for Glycobiology and Glycoproteomics.International journal of molecular sciences · 2020Review
- Dynamic rewiring of the human interactome by interferon signaling.Genome biology · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MatrixDB (http://matrixdb.ibcp.fr) is a freely available database focused on interactions established by extracellular proteins and polysaccharides. It is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data, either at the MIMIx or IMEx level. MatrixDB content has been updated by curation and by importing extracellular interaction data from other IMEx databases. Other major changes include the creation of a new website and the development of a novel graphical navigator, iNavigator, to build and expand interaction networks. Filters may be applied to build sub-networks based on a list of biomolecules, a specified interaction detection method and/or an expression level by tissue, developmental stage, and health state (UniGene data). Any molecule of the network may be selected and its partners added to the network at any time. Networks may be exported under Cytoscape and tabular formats and as images, and may be saved for subsequent re-use.
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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.