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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
Human Gene Mutation DatabaseResource, data or information resource, databaseCurated database of known (published) gene lesions responsible for human inherited disease.gene, disease, gene lesion, mutation, deletion, insertion, duplication, rearrangement, nuclear gene, functional polymorphismSCR_001621(Human Gene Mutation Database, RRID:SCR_001621)Cardiff University; Wales; United Kingdom Inherited diseaserelated to: BIOBASE Corporation, Monarch Initiative, listed by: OMICtoolsReferences (11)Last checked upnlx_153887, OMICS_00281
VAASTResource, standalone software, data processing software, software application, sequence analysis software, data analysis software, software resourceA probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST combines elements of phylogenetic conservation, amino acid substitution, and aggregative approaches to variant prioritization into a single unified likelihood-framework that allows users to accurately identify damaged genes and deleterious variants. The software can score both coding (SNV, indel and splice site) and non-coding variants (SNV), evaluating the cumulative impact of both types of variants simultaneously. It can identify rare variants causing rare genetic diseases and can also use both rare and common variants to identify genes responsible for common diseases.sequence analysis software, genetic, variant classifier, amino acid substitution, disease, genome interpretation, variant prioritization, disease gene prioritization, genomic variationSCR_002179(VAAST, RRID:SCR_002179)Yandell Lab Portal related to: Opal Research, listed by: OMICtools, Genetic Analysis SoftwareReferences (2)Last checked upnlx_154686, OMICS_02134, SciRes_000138
GenevestigatorResource, data analysis service, commercial organization, database, analysis service resource, production service resource, service resource, data or information resourceA high performance search engine for gene expression that integrates thousands of manually curated public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts (diseases, drugs, tissues, cancers, genotypes, etc.). There are two basic analysis approaches: # for a gene of interest, identify which conditions affect its expression. # for condition(s) of interest, identify which genes are specifically expressed in this/these conditions. Genevestigator builds on the deep integration of data, both at the level of data normalization and on the level of sample annotations. This deep integration allows scientists to ask new types of questions that cannot be addressed using conventional tools.gene, genetic, animal, development, disease, meta-analysis, regulation, stage, microarray, rnaseq, visualization, gene expression, disease, drug, tissue, cancer, genotype, pharma, biomedical, conditions, genotype, anatomy, neoplasm, chemical, hormone, infection, model organism, organ, cell type, cell line, target, biomarker, similaritySCR_002358(Genevestigator, RRID:SCR_002358)Last checked upnif-0000-21172, nif-0000-21172, OMICS_00763
FunSimMatResource, data analysis service, data access protocol, production service resource, analysis service resource, database, web service, service resource, software resource, data or information resourceFunSimMat is a comprehensive resource of semantic and functional similarity values. It allows ranking disease candidate proteins for OMIM diseases and searching for functional similarity values for proteins (extracted from UniProt), and protein families (Pfam, SMART). FunSimMat provides several different semantic and functional similarity measures for each protein pair using the Gene Ontology annotation from UniProtKB and the Gene Ontology Annotation project at EBI (GOA). There are several search options available: Disease candidate prioritization: * Rank candidate proteins using any OMIM disease entry * Compare a list of proteins to any OMIM disease entry * Compare all human proteins to any OMIM disease entry Functional similarity: * Compare one protein / protein family to a list of proteins / protein families * Compare a list of GO terms to a list of proteins / protein families Semantic similarity: * For a list of GO terms, FunSimMat performs an all-against-all comparison and displays the semantic similarity values. FunSimMat provides an XML-RPC interface for performing automatic queries and processing of the results as well as a RestLike Interface. Platform: Online toolfunctional similarity value, protein family, protein similarity, semantic similarity value, similarity value, functional similarity, disease gene candidate prioritization, disease, protein, protein family, disease candidate prioritization, semantic similarity, gene ontology, visualization, annotation, database or data warehouseSCR_002729(FunSimMat, RRID:SCR_002729)Max-Planck-Institute for Informatics; Saarbrucken; Germany European Union, German National Genome Research Network, Klinische Forschergrupperelated to: Gene Ontology, listed by: Gene Ontology ToolsReferences (2)Last checked upnif-0000-02860
DiseaseMeth - The human disease methylation databaseResource, data analysis service, production service resource, analysis service resource, database, service resource, storage service resource, data repository, data or information resourceA human disease methylation database focused on the aberrant methylomes of human diseases. It provides a curated set of methylation information datasets and tools in the human genome. It provides a genome-scale landscape to show human methylaton information in a scalable and flexible manner. Currently, DiseaseMeth includes 175 datasets which are extracted from Methylation arrays and sequencing datasets and 14530 entries of scattered aberrant methylation information(72 diseases). DiseaseMeth supports analysis and visualization of these datasets, download for further analysis and can even easily import to the most popular genome browser: GBrowse of all version to date. The resource encourages deposition of outside datadisease, methylation, dna methylation, genome, gene, epigenetics, epigenomics, methylomeSCR_005942(DiseaseMeth - The human disease methylation database, RRID:SCR_005942)Harbin Medical University; Heilongjiang; China National Natural Science Foundation of China, Natural Science Foundation of Heilongjiang Province, Scientific Research Fund of Heilongjiang Provincial Education Department, State Key Laboratory of Urban Water Resource and Environmentlisted by: 3DVC, OMICtoolsPMID:22135302Last checked upnlx_151289, OMICS_01838
Comparative Toxicogenomics DatabaseResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceA public database that enhances understanding of the effects of environmental chemicals on human health. Integrated GO data and a GO browser add functionality to CTD by allowing users to understand biological functions, processes and cellular locations that are the targets of chemical exposures. CTD includes curated data describing cross-species chemical–gene/protein interactions, chemical–disease and gene–disease associations to illuminate molecular mechanisms underlying variable susceptibility and environmentally influenced diseases. These data will also provide insights into complex chemical–gene and protein interaction networks.environment, chemical, disease, gene, pathway, protein, interaction, animal model, ontology, annotation, toxin, ontology or annotation browserSCR_006530(Comparative Toxicogenomics Database, RRID:SCR_006530)Mount Desert Island Biological Laboratory , North Carolina State University; North Carolina; USA American Chemistry Council, NCRR, NIEHS, Pfizerrelated to: PharmGKB Ontology, Gene Ontology, BioRAT, Integrated Gene-Disease Interaction, OMICtools, Integrated Manually Extracted Annotation, used by: DisGeNET, NIF Data Federation, Monarch Initiative, listed by: 3DVC, Gene Ontology ToolsReferences (4)Last checked upnif-0000-02683, OMICS_01578
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