Genome-wide association studies (GWASs) have identified numerous single nucleotide polymorphisms (SNPs) that are associated with development of multifactorial diseases, such as coronary artery disease, rheumatoid arthritis, type 2 diabetes mellitus and cancers.
Contains the PheWAS results for 3,144 single-nucleotide polymorphisms (SNPs) present in the NHGRI GWAS Catalog as of 4/17/2012 in 13,835 European-ancestry individuals from five sites of the Electronic Medical Records and Genomics (eMERGE) network. A total of 1,358 EMR-derived phenotypes were analyzed for each SNP.
Allows users to share genetic variant data sets collected from large-scale population-sequencing projects, clinical diagnostic settings, and variant curation efforts. Beacon Network permits users to choose from a predetermined set of conditions that restrict potential data use on the basis of the consent of individuals represented in the data. It overcomes the inefficiency and expense experienced when data generators must transfer whole copies of their data sets into a single, centralized repository.
Gathers a manually curated resource of all published Genome-Wide Association Studies (GWAS) and association results. GWAS Catalog provides a dedicated mapping spreadsheet between all reported GWAS search interfaces and ontology terms. It allows users to identify the child terms included under each higher-level trait category on the GWAS. Moreover, the database can help in identifying causal variants, understand disease mechanisms, and establish targets for novel therapies.
Intends to collect, standardize and archive genetic association study data. GAD is a public repository of published genetic association studies that contains molecular, clinical and study parameters for more than 5,000 human genetic association studies. It aims to facilitate the studying of complex common human genetic disease in modern high-throughput assay systems and current annotated molecular nomenclature. All datasets can be downloaded from the website.
Provides access to a continuously updated knowledge base in human genome epidemiology, including information on population prevalence of genetic variants, gene-disease associations, gene-gene and gene- environment interactions, and evaluation of genetic tests. Since January 5, 2015, HuGE literature curation of the HuGE Navigator is completely automated, achieving 90% sensitivity and specificity compared to the previous semi-automatic curation process.
Archives and distributes the results of genotype-phenotype studies. dbGaP provides genomic data from cohort studies, clinical trials and other studies. This method is a highly utilized application for sharing individual-level data and summary level data such as allele frequencies. Data includes genotype, phenotype, exposure, expression array, epigenomic and pedigree data from genome-wide association studies (GWAS), sequencing studies and other largescale genomic studies.
Assists researchers to query UK Biobank results in an easy way without the need to incur in high computational costs. GeneAtlas contains significant and non-significant associations. It provides an unbiased view of phenotypegenotype associations across a large number of traits. This database can assist researchers working on complex traits genetics. It permits users to gain further insight into the genetic architecture of complex traits.
Deals with gene/human disease relationships. DisGeNET supplies a repository of about 130000 variant-disease associations (VDAs) and over 560000 gene-disease associations (GDAs) encompassing more than 17000 and 20000 diseases. Searches can be made by diseases, genes or variants and the database includes a feature which allows users to browse multiple databases such as Mouse Genome Database (MGD) or CLINVAR in their original context. Additionally, the platform proposes a plug-in that can be run through the Cytoscape software.
Depicts and integrates the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. AtPID predicts the Protein-protein interaction pairs by integrating several methods with the Naive Baysian Classifier. All other related information curated in the AtPID is manually extracted from published literatures and other resources from some expert biologists. AtPID collects 5564 mutants with significant morphological alterations which were manually curated to 167 plant ontology (PO) morphology categories and predicts 4457 high confidence gene-PO pairs with 1369 genes as the complement. These single/multiple-gene mutants are indexed and linked to 3919 genes.
Provides access to a collection of summary-level genetic association data. GWAS Central collates association data and study metadata from many disparate sources whose data are available in different formats and to differing degrees of detail. The database also provides a toolkit for the storage, mining and display of summary-level association data. It enables experimental biologists to explore and compare data in the genome-wide association study (GWAS) domain, from either a genotype or phenotype starting point.
Facilitates genome-wide Autism spectrum disorder (ASD) gene discovery. ASD is an evidence-weighted machine learning approach that utilizes a brain-specific functional interaction network. This brain-specific network integrates thousands of genomics experiments to create a genome-wide probabilistic graph representing how genes function together in pathways in the brain, or, conceptually, a molecular-level functional map of the brain.
Provides a comprehensive, regularly updated, collection of data from genetic association studies in cutaneous melanoma (CM), including random-effects meta-analysis results of all eligible polymorphisms. The updated database version includes data from 192 publications with information on 1114 significantly associated polymorphisms across 280 genes, along with new front-end and back-end capabilities. Various types of relationships between data are calculated and visualized as networks.
Combines collections of traits/diseases associated SNP (TASs) from current genome-wide association study (GWAS) and their comprehensive functional annotations, as well as disease classifications. GWASdb assists researchers and clinicians in optimizing the utility of the recent GWAS data and gain biological insights through an integrative, multi-dimensional functional annotation portal.
Offers information encompassing published genetic polymorphisms. VarySysDB is a database that provides separately annotated genetic polymorphisms for each H-inv transcripts (HITs), even from multiple transcripts forming a HIX. It (i) delivers an even greater understanding of the various biological processes, (ii) permits a detailed evaluation of how polymorphisms affect different phenotypes, and (iii) fosters a rich research environment focused on exploring the causes of genetic variation through genome-wide association studies.
The public web site of the Molecular and Functional Diversity in the Maize Genome project. Panzea provides access to the genotype, phenotype and polymorphism data produced by the project through user-friendly web-based database searches and data retrieval/visualization tools, as well as a wide variety of information and services related to maize diversity.
Provides tools for genotype-phenotype analysis, genomic diagnostics, and precision medicine across broad areas of disease. Monarch tools leverage this conceptual framework to help users understand and diagnose disease. Statistical similarity calculations enable comparison across species, biological scales, and community-specific vocabularies. Monarch supports researchers and clinicians using this data with visualization tools, application programming interfaces, and a rich web site. This suite of tools has developed four species-agnostic ontologies designed to unify their species-specific counterparts: GENO for genotypes, Uberpheno for phenotypes, UBERON for anatomy and MONDO for diseases. Monarch also contributes to the Gene Ontology, which also unifies gene function and subcellular anatomy across species.
Constitutes a resource on psychiatric diseases and their associated genes. PsyGeNET consists in a database and analysis tools. It contains information on depression, bipolar disorder, alcohol use disorders and cocaine. The database was developed by applying text mining tools to extract information from the scientific literature. The document describing the curation guidelines, providing a resource for the development and evaluation of text mining systems, is available in the web portal.