Tag: genotype and phenotype

Genome assemblies and aligned annotations for a wide range of vertebrates and model organisms, along with an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic datasets.

The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as Atrial septal defect. The HPO is currently being develope ...

The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public ...

MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. Data includes gene characterization, nomenclature, mapping, gene homo ...

The European Genome-phenome Archive (EGA) allows you to explore datasets from genomic studies, provided by a range of data providers. Access to datasets must be approved by the specified Data Access Committee (DAC).

DisGeNET is a discovery platform containing one of the largest collections available of genes and variants involved in human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models, and the scientific liter ...

The Database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. Such studies include genome-wide association studies, medical sequencing, molecular dia ...

The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relations ...

Online Mendelian Inheritance in Man. It is an authoritative compendium of human genes and phenotypes. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 15,000 genes. OMIM focuses on the relation ...

The Zebrafish Information Network, ZFIN, serves as the primary community database resource for the laboratory use of zebrafish. We develop and support integrated zebrafish genetic, genomic, developmental and physiological information and link this in ...

ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variat ...

PharmGKB is a resource that provides information about how human genetic variation affects response to medications. PharmGKB collects, curates and disseminates knowledge about clinically actionable gene-drug associations and genotype-phenotype relati ...

Characterizations of hundreds of strains of laboratory mice to facilitate translational discoveries and to assist in selection of strains for experimental studies. Data sets are voluntarily contributed by researchers or retrieved by us from public so ...

SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.

Genotype-Tissue Expression (GTEx) - database which helps to study the relationship between genetic variation and gene expression in human tissues.

The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the Solanaceae family, which includes species such as tomato, potato, pepper, petunia and eggplant.

CottonGen is a cotton community genomics, genetics and breeding database being developed to enable basic, translational and applied research in cotton. It is being built using the open-source Tripal database infrastructure. CottonGen supercedes Cotto ...

SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean. SoyBase contains genetic, physical and genomic sequence maps integrated with qualitati ...

PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to ...

Curated classification and nomenclature for all of the organisms in the public sequence databases. This currently represents about 10% of the described species of life on the planet.

The Arabidopsis Information Portal (Araport) is an open-access online community resource for Arabidopsis research. Araport enables biologists to navigate from the Arabidopsis thaliana Col-0 reference genome sequence to its associated annotation inclu ...

GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, association genetics, ...

PhenoM (Phenomics of yeast Mutants) stores, retrieves, visualises and data mines the quantitative single-cell measurements extracted from micrographs of temperature-sensitive mutant cells. PhenoM allows users to rapidly search and retrieve raw images ...

SNPeffect is a database for phenotyping human single nucleotide polymorphisms (SNPs). SNPeffect primarily focuses on the molecular characterization and annotation of disease and polymorphism variants in the human proteome. Further, SNPeffect holds pe ...

The GeneWeaver data and analytics website is a publically available resource for storing, curating and analyzing sets of genes from heterogeneous data sources. The system enables discovery of relationships among genes, variants, traits, drugs, enviro ...

SNPedia is a wiki resource of the functional consequences of human genetic variation as published in peer-reviewed studies. Entries are formatted to allow associations to be assigned to single genotypes as well as sets of genotypes (genosets). Curati ...

Cyclebase is a database to visualize and download results from genome-wide cell-cycle-related experiments. In addition to genome annotation, Cyclebase also provides mRNA data, protein expression data, and integrated cell-cycle phenotype information f ...

Online Mendelian Inheritance in Animals is a a database of inherited disorders, other (single-locus) traits, and genes in animal species (other than human and mouse).

GWAS Central stores genome-wide association study data. The database content comprises direct submissions received from GWAS authors and consortia in addition to actively gathered data sets from various public sources. GWAS data are discoverable from ...

The ITHANET Portal represents an expanding resource for clinicians and researchers dealing with haemoglobinopathies and a port of call for patients in search of professional advice. The ITHANET Portal integrates information on news, events, clinical ...

The EuroPhenome project provides access to raw and annotated mouse phenotyping data generated from primary pipelines such as EMPReSSlim and secondary procedures from specialist centres. Mutants of interest can be identified by searching the gene or t ...

The Leaf Senescence Database (LSD) is a comprehensive resource of senescence-associated genes (SAGs) and their corresponding mutants. LSD includes data types such as leaf senescence-associated transcriptomics, phenotype and interaction data.

DIDA (DIgenic diseases DAtabase) is a novel database that provides for the first time detailed information on genes and associated genetic variants involved in digenic diseases, the simplest form of oligogenic inheritance.

The IMPC is a confederation of international mouse phenotyping projects working towards the agreed goals of the consortium: To undertake the phenotyping of 20,000 mouse mutants over a ten year period, providing the first functional annotation of a ma ...

The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan. The Oryzabase consists of five parts, (1) genetic resource stock information, (2) gene dictionary, (3) chromosome maps, (4) mutant ima ...

Universal Mutation Database (UMD) is a database for mutations. UMD-predictor is a tool that enables functional annotation of variants to find the relevant ones.

The Microbial Genome Database for Comparative Analysis (MBGD) is a database for comparative genomics based on comprehensive orthology analysis of bacteria, archaea and unicellular eukaryotes. MBGD now contains 6318 genomes. To utilize the database fo ...

A portal to search variants (polymorphism) in UniProt Knowledgebase (UniProtKB) entries, and gives direct access to manual annotation on the genotype-phenotype relationship of each specific variant based on literature, as well as pre-computed informa ...

High-throughput screening using the CRISPR/Cas-9 system

Repository for clinicians and scientists working in the rare disorder community. It enables secure sharing of case records by clinicians and rare disease scientists and helps the user to find additional cases of the same unnamed disorder. The reposit ...

Attempt to summarize all known sequence variations in the human genome, to facilitate research into how genotypes affect common diseases, drug responses, and other complex phenotypes.

A database of phosphorylation-related SNP (phosSNP) which are non-synonymous SNP (nsSNP) that affect the protein phosphorylation status. Using an in-house developed kinase-specific phosphorylation site predictor (GPS 2.0), we computationally detected ...

NHLBI Exome Sequencing Project (ESP): Exome Variant Server (EVS) for browsing single nucleotide variation data from exome sequencing experiments mainly focused on heart, lung and blood disorders.

Mutant mouse lines held at MRC Harwell

Phenotypic data for Arabidopsis thaliana

Database for candidate genes for QTL for milk production traits in cattle

Genetic mutation database for rare diseases that enables to search, sort and filter genetic variants from clinically diagnosed individuals worldwide and make symptoms-based queries.

Database of phenotypes extracted from the scientific literature using text mining.

The Brassica Information Portal is a web repository for population and trait scoring information related to the Brassica breeding community. It provides information about quantitative trait loci and links curated Brassica phenotype experimental data ...

The Han Chinese Genomes Database (PGG.Han) serves as the central repository of the genomic data of the Han Chinese Genomes Project (Phase I). As is its current version, PGG.Han archives genomic data of 114,783 Han Chinese individuals (a.k.a. Han100 ...

PhenoModifier is a genetic modifier database for elucidating the genetic basis of human phenotypic variation. PhenoModifier provides a more complete spectrum of genetic factors contributing to human phenotypic variation and the portal has a broad sci ...

Using the MR-Base platform to investigate risk factors and drug targets for thousands of phenotypes | This repository contains the case studies associated with the manuscript "Using the MR-Base platform to investigate risk factors and drug targets fo ...

a database of curated and consistently annotated human gut metagenomes | GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. Its main purpose is to facilitate the reusability and acce ...

Cell type specificity of genetic traits

Gephebase is a manually-curated database compiling our accumulated knowledge of the genes and mutations that underlie natural, domesticated and experimental phenotypic variation in all Eukaryotes — mostly animals, plants and yeasts. Gephebase conso ...

The RAMEDIS system is a platform independent, web-based information system for rare metabolic diseases based on filed case reports. It was developed in close cooperation with clinical partners to allow them to collect information on rare metabolic di ...

An integrated omics knowledgebase for molecular breeding in rice. Rice Phenotype Search and Summary. Rice Genotype Search and Summary. Molecular Breeding Knowledge Database. Created with the Personal Edition of HelpNDoc: News and information abou ...

an adaptive immune receptor genotype and haplotype database. The adaptive immune receptor Genotype and Haplotype database. 11-Oct-2019 *NEW* - VDJbase is described in Nucleic Acids Research. VDJbase is a publicly available database that offers eas ...

Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization.

A database for disease/trait causal variants identified using summary statistics of genome-wide association studies. A GWAS fine-mapping pipeline used in CAUSALdb. CAUSALdb integrates large numbers of GWAS summary statistics and identifies credible ...

516 unique variants and 831 patients registered in an updated centralized Variome database | OPA1 (optic atrophy 1 (autosomal dominant)) | Autosomal dominant optic atrophy (DOA, Kjer type, MIM#165500) is characterized by moderate to severe loss of vi ...

BEable-GPS: Base Editable prediction of Global Pathogenic-related SNVs. Comparison of cytosine base editors and development of the BEable-GPS database for targeting pathogenic SNVs.

Massively parallel sequencing solutions for two common forensically used platforms | HIrisPlex-S Eye, Hair and Skin Colour DNA Phenotyping Webtool | 8px 9px 10px 11px 12px 13px 14px 15px 16px 17px 18px | With the advancement of DNA phenotyping as a t ...

an integrated database and analytic platform for de novo mutations in humans. De novo mutations (DNMs) significantly contribute to sporadic diseases, particularly in neuropsychiatric disorders. Whole-exome sequencing (WES) and whole-genome sequencin ...

A comprehensive database with multiple animal reference panels for genotype imputation.

Construction of a core collection of eggplant (Solanum melongena L.) based on genome-wide SNP and SSR genotypes. a DNA marker database for vegetables

Inherited glycophosphatidylinositol deficiency variant database.

A Curated Database with Taxonomic Profiling of the Healthy Mouse Gastrointestinal Microbiome. Murine microbiome database (MMDB) contains 16S rRNA gene-based microbiome taxonomic profiles of the healthy mouse gut microbiota with manually curated meta ...

a comprehensive database platform for identification and validation of disease related noncoding RNAs. Mar 26, 2020: ncRPheno was published on the journal of RNA Biology... ncRPheno is a comprehensive database that provides experimentally supported ...

GEnetic Antibiotic Resistance and Susceptibility Database.

Pan immune repertoire database (PIRD) collects raw and processed sequences of immunoglobulins (IGs) and T cell receptors (TCRs) of human and other vertebrate species with different phenotypes. You can check the detailed information of each sample in ...

CellTalkDB is a manually curated database of ligand-receptor interactions in humans and mice. CellTalkDB contains literature-supported ligand-receptor (LR) pairs for human and mouse, which are curated from protein-protein interactions (PPIs) in STRIN ...

A web application dedicated to genotyping members of Mycobacterium avium complex (MAC) including Mycobacterium avium subsp. paratuberculosis strains. Genotyping of Mycobacterium avium subsp. paratuberculosis (Map) is an indispensable tool for survei ...

Open-access high-throughput pipeline and database for rodent touchscreen-based cognitive assessment. Mousebytes-An-open-access-high-throughput-pipeline-and-database-for-rodent-touchscreen-based-data. This code is associated with the paper from Bera ...

Genome database that is purely based on the Semantic Web technology, which enables the integration of heterogeneous data and flexible semantic searches.

An online database for exploring over 2,000 Arabidopsis small RNA libraries.

ForageGrassBase is molecular resource for the forage grass meadow fescue (Festuca pratensis Huds.).

A Manually Curated Database for Identification of Noncoding RNA Variants Associated with Human Diseases. Jun 1, 2018: Startup of the ncRNAVar project.... Sep 10, 2019: The variant mapping was developed...

New open data resource for comparative studies of an old insect order. The Odonate Phenotypic DataBase is a resource for dragonfly and damselfly phenotypes. The database consists of a variety of morphological, behavioural, and bio-geographical infor ...

A data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information. The main web resource to explore human mitochondrial variability data and their pathological correlation. HmtVar is a manually-curate ...

A Comprehensive Hepatitis D Virus Database. Welcome to Hepatitis Delta Virus Database (HDVdb). The Hepatitis D Virus (HDV) Database, HDVdb contains comprehensive data on HDV genetic sequences that allows the researchers to investigate the genetic v ...

Taking advantage of a decade of Daphnia '-omics' data for gene annotation | Welcome to the Daphnia Stressor database

circVAR database is genome-wide archive of genetic variants for human circular RNAs Circular RNAs (circRNAs), the 3' and 5' ends of which are covalently linked, are a kind of widely distributed and abundant RNAs found in eukaryotic organisms in recen ...

database of traits of fish to promote advances in fish aquaculture. toff-project – Database of Traits OF Fish. TOFF (i.e. Traits OF Fish) is a curated database focusing on functional trait information for fish that aims at bringing together behavio ...

CellO (Cell Ontology-based classification) is a Python package for performing cell type classification of human RNA-seq data. CellO makes hierarchical predictions against the Cell Ontology. These classifiers were trained on nearly all of the human pr ...

A Literature-Curated Database of microRNA Expression Patterns, in Diabetic Microvascular Complications. miR2Diabetes aims to provide a comprehensive resource of miRNA dysregulation in diabetic microvascular complications (DMC). Each entry in the miR2 ...

lncRNA-associated ceRNA networks

High-throughput genetic screening based on CRISPR/Cas9 or RNA-interference (RNAi) enables the exploration of genes associated with the phenotype of interest on a large scale. The rapid accumulation of public available genetic screening data provides ...

Human metagenomic extrachromosomal mobile genetic elements

The availability of genetic variants, together with phenotypic annotations from model organisms, facilitates comparing these variants with equivalent variants in humans. However, existing databases and search tools do not make it easy to scan for equ ...

DDIEM - Drug Database for inborn errors of metabolism is a database on therapeutic strategies for inborn errors of metabolism. These strategies are classified by mechanism and outcome in DDIEM ontology. DDIEM uses this ontology to categorize the expe ...

PICEAdatabase is a web database for Picea omics and phenotypic information.

A genetic resource database for rubber tree genomic study | Molecular & Genetic Resources for Hevea tree

Integrative database and analysis platform that relates microbiome and phenotypic data. MANTA (Microbiota And pheNotype correlaTion Analysis platform) is an integrative database and analysis platform that relates microbiome and phenotypic data. MANT ...

FAIDARE: FAIR Data-finder for Agronomic Research. The purpose of this portal is to facilitate the discoverability of public data on plant biology from a federation of established data repositories. It is based on the Breeding API (BrAPI) specificat ...

ETph is a database for enhancer and their targets in pig and human.

A Comprehensive Protein-coding Gene Origination Database on the Evolutionary Timescale of Life.

CoFly is a gene coexpression database for the fruit fly Drosophila melanogaster

DINAX is a comprehensive database of inherited ataxias.

A unified and manually curated repertoire of GRIN variants. A CURATED DATABASE FOR GRIN VARIANTS.

A database for predicting pathogenicity of missense sequence variants of keratin genes associated with genodermatoses.

Quickomics is a tool for exploring omics data in an intuitive, interactive and informative manner.

MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes.

ColTapp is an automated image analysis application for efficient microbial colony growth dynamics quantification.

A web service for studying gene expression in human skeletal muscle. MuscleAtlasExplorer(BETA)2.

ADVP is a platform for the public community to browse, search and understand Alzheimer's Disease genetics findings easily. .

CoxBase is an online platform for epidemiological surveillance, visualization, analysis and typing of Coxiella burnetii genomic sequence.

Database for identifying, genotyping, and modelling the associations between single nucleotide polymorphisms (SNPs) in candidate genes and pathways that underlie inflammatory responses in humans.

FLHdb is database of variants of Familial Hemophagocytic Lymphohistiocytosis from the Clinical and Translational Bioinformatics Research Group at Vall Hebron Institute of Research (VHIR).

DODO is a graph database to facilitate access and interaction with disease and phenotype ontologies. The aim of DODO is to allow an easier way to interact and explore disease ontologies and their identifiers. The database is build on Neo4j and incorp ...

The MRC IEU OpenGWAS data infrastructure. The OpenGWAS database is constantly growing, but there may be studies that users have generated or need to include in their analyses that have not yet been incorporated.

A database of monosaccharide biosynthesis pathways. Monosaccharide Biosynthesis Pathways Database. Pathways for monosaccharide biosynthesis. Welcome to MonoPathDB, a database of biosynthesis pathways and enzymes for monosaccharides.

An international, open and dynamic library for up-to-date clinical information. Collect information about clinic management and research projects.

Novel disease-associated variants, common sequence variants, and results from newborn screening. The Pompe disease GAA variant database represents an effort to collect all known variants in the GAA gene and is maintained and provide by the Pompe cen ...

An Expanded Database of Ecological and Phenotypical Features of Microbes. Microbial communities are an incredibly fascinating and genetically diverse set of organisms that live with us, in us, and around us! Explore them all using the Microbe Direct ...

Genome-wide analysis of polymorphisms identified domestication-associated polymorphism desert carrying important rice grain size/weight QTL | By using SNP-Seek, you abide by the data use license stated | Query for SNPs from the 3000 genome project | ...

Phylogenize is a web tool that allows users to link microbial genes to environments, accounting for phylogeny. More specifically, given community composition data, phylogenize links genes in microbial genomes to either microbial prevalence in, or sp ...

In-silico functional characterization and drug-gene interactions of ACE2 gene network to understand its potential involvement in COVID-19 susceptibility.

Staphopia is a database focusing on the genomes of the bacterial pathogen Staphylococcus aureus. Life-threatening Methicillin-resistant S. aureus (MRSA) infections strike across our society, both in the community and hospital settings. In recent year ...

ATAV is a comprehensive platform for population-scale genomic analyses. ATAV stores variant and per site coverage data for all samples in a centralized database, which is efficiently queried by ATAV to support diagnostic analyses for trios and single ...

EpiGraphDB is an analytical platform and database to support data mining in epidemiology. The platform incorporates a graph of causal estimates generated by systematically applying Mendelian randomization to a wide array of phenotypes, and augments t ...

The variant call format provides efficient and robust storage of GWAS summary statistics. VCF vs plain text GWAS storage formats.

CONREL is a genome browser that allows for the exploration of consensus regulatory elements at different levels of abstraction. The total binding affinity of transcription factors on whole consensus region sequences is here fully exploited to charact ...

An interactive retrieval system for clinical trial studies with context-dependent protocol elements. Clinical trial protocol includes all the steps that should be conducted in clinical trial and all clinical trial start with development of the proto ...

A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize lines. This R script chara-2-sparse.R is used to convert a traditional character genotype matrix into an integer sparse genotype matrix. This R script can be used ...

Color Data is a user-friendly, open-access database with hereditary cancer and hereditary cardiovascular conditions datasets. Color Data is the largest public database of its kind, containing aggregated genetic and phenotypic information from 54,000 ...

A comprehensive genetic resource of nicotine and smoking. Genetic resources of nicotine and smoking. Genetic Resources Of Nicotine and Smoking (GRONS) is a database devoted to provide a comprehensive and systematic collection of cross-platform gene ...

Database Of Reconstructed MetAbolic Networks. We apologize for the inconvenience, but it appears that an internal error has occurred in the Dorman system. If this is the first time you have encountered this message, please use the Back button on you ...

A high-quality SNV database for interspecies genetic divergence investigation among macaques. A database for genetic divergence investigation among macaques. MACSNVdb is an open-access SNV database comprising ~74.51 million high-quality non-redunda ...

A toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions. GOMCL is a tool to cluster and extract summarized associations of Gene Ontology based functions in omics data. It clusters GO terms using MCL ba ...

Domestic Animal Diversity Information System is a communication and information tool for implementing strategies for the management of animal genetic resources. It provides the user with searchable databases of breed-related information and images, m ...

The Male Fertility Gene Atlas – A web tool for collecting and integrating data about epi-/genetic causes of male infertility. The Male Fertility Gene Atlas (MFGA) is a public platform for providing a fast, simple and straightforward access to OMICS ...

CHDGKB (A knowledgebase of non-syndromic congenital heart disease genetic variations) is a manually curated database of genetic variations associated with non syndromic congenital heart disease. CHDGKB contains a comprehensive information of genetic ...

An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Plasmodium falciparum Community Project. Dried blood spot collection. Photo credit: Will Hamilton. HiSeq machines at the Wellcome Trust Sanger Institute. Photo c ...

A framework for the annotation and prioritization of non-coding regulatory variants in whole-genome sequencing. Genomic Regulatory Elements ENcyclopedia. This is the home of the GREEN-DB and companion tools (GREEN-VARAN). Genomic Regulatory Elemen ...