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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Oct 12, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
MINTResource, data or information resource, databaseA database that focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The curated data can be analyzed in the context of the high throughput data and viewed graphically with the MINT Viewer. This collection of molecular interaction databases can be used to search for, analyze and graphically display molecular interaction networks and pathways from a wide variety of species. MINT is comprised of separate database components. HomoMINT, is an inferred human protein interatction database. Domino, is database of domain peptide interactions. VirusMINT explores the interactions of viral proteins with human proteins. The MINT connect viewer allows you to enter a list of proteins (e.g. proteins in a pathway) to retrieve, display and download a network with all the interactions connecting them.protein-protein interaction, protein, interaction, virus, peptide, organelle co-localization, pathway, molecular interaction, papillomavirus, epstein-barr virus, hepatitis b virus, hepatitis c virus, human adenovirus, human herpesvirus, human immunodeficiency virus, influenza a virus, vaccinia virus, simian virus 40, virus strains, virus protein, orthologous protein, network, proteomics, orthologSCR_001523(MINT, RRID:SCR_001523)University of Rome Tor Vergata; Rome; Italy AIRC Associazione Italiana per la Ricerca sul Cancro, ENFIN, European Union, HUPO Proteomics Standards Initiative, IMEx - The International Molecular Exchange Consortium, Interaction Proteome Projectrelated to: MPIDB, TissueNet - The Database of Human Tissue Protein-Protein Interactions, InteroPorc, Interaction Reference Index, Pathway Commons, ConsensusPathDB, VirusMINT, PSICQUIC Registry, Agile Protein Interactomes DataServer, uses: IntAct, PSI-MI, listed by: re3data.org, affiliated with: IMEx - The International Molecular Exchange Consortium, works_with: IMEx - The International Molecular Exchange ConsortiumReferences (8)Last checked upnlx_152821
MatrixDBResource, service resource, data or information resource, production service resource, databaseFreely available database focused on interactions established by extracellular proteins and polysaccharides, taking into account the multimeric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data. It includes interaction data extracted from the literature by manual curation, and offers access to relevant data involving extracellular proteins provided by the IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database. The database reports mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. Interactions with lipids and cations are also reported. MatrixDB is focused on mammalian interactions, but aims to integrate interaction datasets of model organisms when available. MatrixDB provides direct links to databases recapitulating mutations in genes encoding extracellular proteins, to UniGene and to the Human Protein Atlas that shows expression and localization of proteins in a large variety of normal human tissues and cells. MatrixDB allows researchers to perform customized queries and to build tissue- and disease-specific interaction networks that can be visualized and analyzed with Cytoscape or Medusa. Statistics (2013): 2283 extracellular matrix interactions including 2095 protein-protein and 169 protein-glycosaminoglycan interactions.extracellular, protein fragment, biomolecule, cation, cleavage, collagen, glycosaminoglycan, human, interaction, laminin, lipid, mammalian, matricryptin, matrikin, matrix, molecule, monomer, mulimerization, multimer, polysaccharide, protein, protein-carbohydrate interaction, protein-protein interaction, recognition, thrombospondin, interactome, extracellular protein, protein-polysaccharide interaction, extracellular interaction, molecular interaction, model organism, inorganic, small molecule-protein, small molecule, extracellular matrix protein, protein-glycosaminoglycan interactionSCR_001727(MatrixDB, RRID:SCR_001727)Claude Bernard University Lyon 1; Lyon; France European Unionrelated to: IMEx - The International Molecular Exchange Consortium, Gene Ontology, PSI-MI, HPRD - Human Protein Reference Database, Interaction Reference Index, ConsensusPathDB, IMEx - The International Molecular Exchange Consortium, PSICQUIC Registry, IntAct, listed by: re3data.orgReferences (2)Last checked upnif-0000-10226http://matrixdb.ibcp.fr/
G:ProfilerResource, analysis service resource, software resource, data analysis service, service resource, production service resourceA web-based toolset for functional profiling of gene lists from large-scale experiments. It has a simple web interface with powerful visualization. It currently supports 85 species, including mammals, fungi, plants, insects, etc, from the Ensembl and Ensembl Genomes databases. g:Profiler consists of the following tools: * g:GOSt retrieves most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs to a user-specified group of genes, proteins or microarray probes. g:GOSt also allows analysis of ranked or ordered lists of genes, visual browsing of GO graph structure, interactive visualization of retrieved results, and many other features. Multiple testing corrections are applied to extract only statistically important results. * g:Convert allows conversion between gene or protein names, database IDs and microarray probes of more than 100 types. A mix of various IDs may be presented as input; output options include HTML, text and XLS spreadsheet. * g:Orth retrieves orthologs for a given set of genes, proteins or probes in a selected organism. Graphical representation also shows orthologs present in all g:Profiler organisms. * g:Sorter searches for similar expression profiles to a given gene, protein or probe in a large set of public microarray datasets from the Gene Expression Omnibus (GEO) database. * g:Cocoa provides a compact interface for comparing enrichments of multiple gene lists. Platform: Online toolgene, high-throughput, genomics, visualization, statistical analysis, slimmer-type tool, term enrichment, protein interaction, functional similarity, analysis, coexpression, gene id, network enrichment analysis, orthology mapping, genomic locus, ontology or annotation visualization, other analysis, ortholog, functional profile, gene list, ontology, pathway, transcription factor, microrna, regulatory motif, protein-protein interaction, biomolecule, gene expression, gene, homology, single nucleotide polymorphism, dna polymorphism, chromosome, network analysis, disease gene, rSCR_006809(G:Profiler, RRID:SCR_006809)BIIT - Bioinformatics Algorithmics and Data Mining Group EITSA, ENFIN, ERDF through EXCS funding projects, ETF7437 MEM, European Union, FP6 COBRED, University of Tartu; Tartu; Estoniarelated to: Gene Ontology, Ensembl, Ensembl Genomes, listed by: Gene Ontology Tools, OMICtoolsReferences (2)Last checked upnif-0000-31975, OMICS_02223
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