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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)

Physical Resource or Software Tool Software

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
JASPARResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceOpen source database of curated, non-redundant set of profiles derived from published collections of experimentally defined transcription factor binding sites for multicellular eukaryotes. Consists of open data access, non-redundancy and quality. JASPAR CORE is smaller set that is non-redundant and curated. Collection of transcription factor DNA-binding preferences, modeled as matrices. These can be converted into Position Weight Matrices (PWMs or PSSMs), used for scanning genomic sequences. Web interface for browsing, searching and subset selection, online sequence analysis utility and suite of programming tools for genome-wide and comparative genomic analysis of regulatory regions. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval.structural class, transcription factor binding site, profile, regulatory region, genome, genomic, matrix, transcription factor, binding site, dnaSCR_003030(JASPAR, RRID:SCR_003030) Karolinska Institutet; Stockholm; Sweden , University of Copenhagen; Copenhagen; Denmark Carlsberg Foundation, EMBRACEa Sixth Framework Network of Excellence, European Union, Novo Nordisk Foundation, Sars Centrerelated to: Babelomics, listed by: OMICtools, re3data.orgReferences (3)Last checked downnif-0000-03061, OMICS_00538http://129.177.120.189/cgi-bin/jaspar2010/jaspar_db.pl, http://jaspar.cgb.ki.se
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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