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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
GeneMergeResource, data analysis service, production service resource, analysis service resource, software application, service resource, software resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Web-based and standalone application that returns a wide range of functional genomic data for a given set of study genes and provides rank scores for over-representation of particular functions or categories in the data. It uses the hypergeometric test statistic which returns statistically correct results for samples of all sizes and is the #2 fastest GO tool available (Khatri and Draghici, 2005). GeneMerge can be used with any discrete, locus-based annotation data, including, literature references, genetic interactions, mutant phenotypes as well as traditional Gene Ontology queries. GeneMerge is particularly useful for the analysis of microarray data and other large biological datasets. The big advantage of GeneMerge over other similar programs is that you are not limited to analyzing your data from the perspective of a pre-packaged set of gene-association data. You can download or create gene-association files to analyze your data from an unlimited number of perspectives. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatiblegene, genomics, functional genomic data, analysis, post-genomic analysis, data mining, hypothesis testing, statistical analysis, slimmer-type tool, term enrichment, text mining, false discovery rate, bonferroni correction, false discovery rate and bonferroni correction, perl, microarraySCR_005744(GeneMerge, RRID:SCR_005744)Harvard University; Cambridge; United States related to: Gene Ontology, listed by: Gene Ontology ToolsPMID:12724301Last checked downnlx_149203http://genemerge.cbcb.umd.edu/
MetaGeneProfilerResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Meta Gene Profiler (MetaGP) is a web application tool for discovering differentially expressed gene sets (meta genes) from the gene set library registered in our database. Once user submits gene expression profiles which are categorized into subtypes of conditioned experiments, or a list of genes with the valid pvalues, MetaGP assigns the integrated p-value to each gene set by combining the statistical evidences of genes that are obtained from gene-level analysis of significance. The current version supports the nine Affymetrix GeneChip arrays for the three organisms (human, mouse and rat). The significances of GO terms are graphically mapped onto the directed acyclic graph (DAG). The navigation systems of GO hierarchy enable us to summarize the significance of interesting sub-graphs on the web browser. Platform: Online toolgene, gene expression, differentially expressed, gene ontology, meta gene, gene set, statistical analysisSCR_005794(MetaGeneProfiler, RRID:SCR_005794)Institute of Statistical Mathematics; Tokyo; Japan related to: Gene Ontology, listed by: Gene Ontology ToolsLast checked downnlx_149271
Expression ProfilerResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice.other analysis, cluster, analysis, visualization, gene expression, genomic, gene ontology, gene association, microarray, protein-protein interaction, geneSCR_005821(Expression Profiler, RRID:SCR_005821)European Bioinformatics Institute Estonian Science Foundation, European Union, Wellcome Trustrelated to: Gene Ontology, listed by: Gene Ontology ToolsPMID:15215431Last checked downnlx_149323
PubSearchResource, service resource, software resource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. PubSearch is a web-based literature curation tool, allowing curators to search and annotate genes to keywords from articles. It has a simple mySQL database backend and uses a set of Java Servlets and JSPs for querying, modifying, and adding gene, gene-annotation, and literature information. PubSearch can be downloaded from GMOD. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatiblegene, annotate, editor, literature curation tool, literature, ontology or annotation editorSCR_005830(PubSearch, RRID:SCR_005830)TAIR , Stanford University; Stanford; California NHGRIrelated to: Gene Ontology, listed by: Gene Ontology ToolsLast checked downnlx_149338
Candidate Genes to Inherited DiseasesResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of candidate genes for mapped inherited human diseases. Candidate priorities are automatically established by a data mining algorithm that extracts putative genes in the chromosomal region where the disease is mapped, and evaluates their possible relation to the disease based on the phenotype of the disorder. Data analysis uses a scoring system developed for the possible functional relations of human genes to genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene. Methodology can be divided in two parts: the association of genes to phenotypic features, and the identification of candidate genes on a chromosonal region by homology. This is an analysis of relations between phenotypic features and chemical objects, and from chemical objects to protein function terms, based on the whole MEDLINE and RefSeq databases.function, gene, genetic, chromosome, disease, disorder, genome, homology, human, phenotype, protein, region, candidate gene, database, data warehouse, data setSCR_008190(Candidate Genes to Inherited Diseases, RRID:SCR_008190) EMBL - Bork Group , European Molecular Biology Laboratory related to: Gene Ontology, listed by: 3DVC, Gene Ontology ToolsPMID:16115313Last checked downnif-0000-21162http://www.bork.embl-heidelberg.de/g2d/, http://www.ogic.ca/projects/g2d_2/
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