Tag: gene

The Gene Ontology resource provides a computational representation of our current scientific knowledge about the functions of genes (or, more properly, the protein and non-coding RNA molecules produced by genes) from many different organisms, from hu ...

Ensembl aims to provide a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other vertebrates and model organisms. Ensembl is one of several well known genome browsers for the ...

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 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 ...

The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in miRBase represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence ...

GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. The complete release notes for the current version of GenBank are available on the NCBI ftp site. A new release is made every two months. G ...

The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications.

The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submissi ...

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.

Database that aims to advance understanding about how environmental exposures affect human health. It provides manually curated information about chemical–gene/protein interactions, chemical–disease and gene–disease relationships. These data are inte ...

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 PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function ...

GENCODE is a scientific project in genome research and part of the ENCODE (ENCyclopedia Of DNA Elements) scale-up project. The GENCODE consortium was initially formed as part of the pilot phase of the ENCODE project to identify and map all protein-co ...

Genetic, genomic and molecular information pertaining to the model organism Drosophila melanogaster and related sequences. This database also contains information relating to human disease models in Drosophila, the use of transgenic constructs contai ...

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 National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts publish ...

HGNC is responsible for approving unique symbols and names for human loci, including protein coding genes, ncRNA genes and pseudogenes, to allow unambiguous scientific communication.

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 ...

WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematod ...

VectorBase is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes (as well as a number of non-vector genomes for comparative analysis) providing an integrat ...

Gramene's purpose is to provide added value to plant genomics data sets available within the public sector, which will facilitate researchers' ability to understand the plant genomes and take advantage of genomic sequence known in one species for ide ...

The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation.

BioModels is a repository of computational models of biological processes. It allows users to search and retrieve mathematical models published in the literature. Many models are manually curated (to ensure reproducibility) and extensively cross-link ...

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 ...

The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available from TAIR includes the complete genome sequence along with gene structure, gene pro ...

The Entrez Global Query Cross-Database Search System is a federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. Entrez can effic ...

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 ...

eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the gene ...

SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. The Sequence Ontology is a set of terms and relationships used to describe the features and attributes of biological sequence. SO i ...

The Ensembl genome annotation system, developed jointly by EMBL-EBI and the Wellcome Trust Sanger Institute, has been used for the annotation, analysis and display of vertebrate genomes since 2000. Since 2009, the Ensembl site has been complemented b ...

Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as s ...

The Virus Pathogen Database and Analysis Resource (ViPR) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Center ...

The Rat Genome Database stores genetic, genomic, phenotype, and disease data generated from rat research. It provides access to corresponding data for eight other species, allowing cross-species comparison. Data curation is performed both manually an ...

Swiss Institute of Bioinformatics (SIB) coordinates research and education in bioinformatics throughout Switzerland and provides bioinformatics services to the national and international research community. ExPASy gives access to numerous repositorie ...

InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactio ...

A bioinformatic database of antimicrobial resistance genes, their products and associated phenotypes.

EBI Metagenomics has changed its name to MGnify to reflect a change in scope. This is a free-to-use resource aiming at supporting all metagenomics researchers. The service is an automated pipeline for the analysis and archiving of metagenomic data th ...

This database provides a list of insertion sequences (IS) isolated from bacteria and archae. It is organized into individual files containing their general features (name, size, origin, family.....) as well as their DNA and potential protein sequence ...

Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis which was created to improve knowledge of developmental and disease processes. Through curation and automated data provisioning from various sources, Xenbase aims ...

DIANA-TarBase is a reference database that indexes experimentally-supported microRNA (miRNA) targets. It integrates information on cell-type specific miRNA–gene regulation and includes miRNA-binding locations. The target data provided by DIANA-TarBas ...

PHI-Base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions. PHI-base catalogues experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete ...

Ontology-based annotation data can be submitted to the Gene Ontology Consortium and other projects (e.g. the Planteome project) in the Gene Association Format 2.1 (GAF 2.1). The annotation flat file format is comprised of 17 tab-delimited fields. Thi ...

ViralZone is a web resource for viral genes and families, providing detailed molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives easy access to UniProtKB/Swiss-Prot viral protein entries.

CAO ontology is designed for supporting the COG enrichment study by using Fisher's exact test. It is used for the ontology based application for statistical analysis on COG db.

The GO Annotation Database (GOA) provides Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal. GOA files contain a mixture of manual annotati ...

PomBase is a model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation as w ...

Ontology-based annotation data can be submitted to the Gene Ontology Consortium and other projects (e.g. the Planteome project) in the Gene Association Format 2.2 (GAF 2.2). The annotation flat file format is comprised of 17 tab-delimited fields. Thi ...

The Entrez Protein search and retrieval system contains protein entries that have been compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.

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.

TDR Targets integrates chemical and genomic information and allows users to prioritize targets and compounds to develop and repurpose new drugs and chemical tools for human pathogens. The TDR Target Project was started in 2005 after a call for applic ...

The GDP Database provides a public resource of gene disruptions of Drosophila genes using a single transposable element.

FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Its main focus is genomic and proteomics data for Drosophila and other insects. It provides access to integrated data at a number of d ...

HomoloGene is an automated system for the detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. HomoloGene takes protein sequences from differing species and compares them to one another (using blastp) an ...

A resource providing data on bioentities and their associated ontology terms for Plant Biology. The database provides access to ontology-based annotations of genes, phenotypes and germplasms from about 90 plant species. A number of internal and exter ...

This database enables the reliable identification of an individual Interferon Regulated Gene (IRG) or IRG signatures from high-throughput data sets (i.e. microarray, proteomic data etc.). It also assists in identifying regulatory elements, chromosoma ...

The Leiden Open Variation Database (LOVD) provides a flexible, freely available tool for gene-centered collection and display of DNA variations. LOVD also stores patient-centered data, NGS data, and variants outside of genes.

YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 ...

AnimalTFDB is a comprehensive animal transcription factor database. The resource is classification of transcription factors from 50 genomes from species including Homo sapiens and Caenorhabditis elegans. The database also has information on co-transc ...

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 ...

The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. The resource provides categorical information ...

Gene3D uses the information in CATH to predict the locations of structural domains on millions of protein sequences available in public databases. Sequence data from UniProtKB and Ensembl for domains with no experimentally determined structures are s ...

BioGRID ORCS is an open repository of CRISPR screens compiled through comprehensive curation efforts. Our current index is version 1.0.3 and searches more than 49 publications and 58,161 genes to return more than 895 CRISPR screens from 3 major model ...

The Genome Database for Rosaceae (GDR) is a curated and integrated web-based relational database providing centralized access to Rosaceae genomics and genetics data and analysis tools to facilitate cross-species utilization of data.

Minimum Information About an RNAi Experiment Tabular (MIARE) is a set of reporting guidelines that describes the minimum information that should be reported about an RNAi experiment to enable the unambiguous interpretation and reproduction of the res ...

The Aspergillus Genome Database is a resource for genomic sequence data as well as gene and protein information for Aspergilli. This publicly available repository is a central point of access to genome, transcriptome and polymorphism data for the fun ...

GSA is a data repository specialized for archiving raw sequence reads. It supports data generated from a variety of sequencing platforms ranging from Sanger sequencing machines to single-cell sequencing machines and provides data storing and sharing ...

The Molecular Modeling Database (MMDB), as part of the Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more.

The ribosomal RNA operon copy number database is a publicly available, curated resource for ribosomal operon (rrn) copy number information for Bacteria and Archaea.

Fly-FISH documents the expression and localization patterns of Drosophila mRNAs at the cellular and subcellular level during early embryogenesis and third instar larval tissues. A high-resolution, high-throughput fluorescence detection method is used ...

The purpose of this database is to collect and distribute statistical maps of the human brain. Such maps are acquired by scientist all around the world using brain imaging techniques such as MRI or PET in a combined effort to map the functions and st ...

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 ...

The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays and is automatically cross-ref ...

UNITE is primarily a fungal rDNA internal transcribed spacer (ITS) sequence database, although they also welcome additional genes and genetic markers. UNITE focuses on high-quality ITS sequences generated from fruiting bodies collected and identified ...

The e-Mouse Atlas of Gene Expression (EMAGE) is a freely available database of in situ gene expression patterns that allows users to perform online queries of mouse developmental gene expression. EMAGE is unique in providing both text-based descripti ...

ATTED-II is a coexpression database for plant species with parallel views of multiple coexpression data sets and network analysis tools. The user can find functional gene relationships and design experiments to identify gene functions by reverse gene ...

BloodSpot is a database of mRNA expression in healthy and malignant haematopoiesis and includes data from both humans and mice. The core function of BloodSpot is to provide an expression plot of genes in healthy and cancerous haematopoietic cells at ...

ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.

HumanMine integrates many types of data for Homo sapiens and Mus musculus. Users can run flexible queries, export results and analyse lists of data.

The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of ge ...

ionomicHUB provides curated ionomic data on many thousands of plant samples freely available to the public. It is an international collaborative cyber research environment to help identify and understand the genes and gene networks that function to c ...

AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-align ...

INDIGO enables the integration of annotations for the exploration and analysis of newly sequenced microbial genomes.

The Human Genetic Variation Database (HGVD) aims to provide a central resource to archive and display Japanese genetic variation and association between the variation and transcription level of genes. The database currently contains genetic variation ...

AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products.

The Vertebrate Genome Annotation (VEGA) database is a central repository for high quality manual annotation of vertebrate finished genome sequence.

TargetMine integrates many types of data for human, rat and mouse. Flexible queries, export of results and data analysis are available.

This is a database of comparative protein structure models of the MIP (Major Intrinsic Protein) family of proteins. The MIPs have been identified from the completed genome sequence of organisms available at NCBI.

PRODORIC is a comprehensive database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites.

FlyCircuit is a public database for online archiving, cell type inventory, browsing, searching, analysis and 3D visualization of individual neurons in the Drosophila brain. The FlyCircuit Database currently contains about 30,000 high resolution 3D br ...

The goal of the Gene Wiki is to apply community intelligence to the annotation of gene and protein function. The Gene Wiki is an informal collection of pages on human genes and proteins, and this effort to develop these pages is tightly coordinated w ...

ThaleMine enables you to analyze Arabidopsis thaliana genes, proteins, gene expression, protein-protein interactions, orthologs, and more. Use plain text or structured queries for interactive gene and protein reports.

The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biol ...

Minimum Information About an RNAi Experiment (MIARE) is a set of reporting guidelines that describes the minimum information that should be reported about an RNAi experiment to enable the unambiguous interpretation and reproduction of the results. MI ...

Aniseed is a database designed to offer a representation of ascidian embryonic development at the level of the genome (cis-regulatory sequences, spatial gene expression, protein annotation), of the cell (cell shapes, fate, lineage) or of the whole em ...

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).

PlanMine is an integrated web resource of data & tools to mine Planarian biology.

Gene Transcription Regulation Database (GTRD) is a database of transcription factor binding sites (TFBSs) identified by ChIP-seq experiments for human and mouse.

Corynebacterial Regulation Network a reference database and analysis platform for corynebacterial transcription factors and gene regulatory networks.

Knockout mutant mice strains. The KOMP repository is a resource of mouse embryonic stem (ES) cells containing a null mutation in every gene in the mouse genome. The KOMP collection of mice, ES Cells, and vectors are now distributed through the Mutant ...

Human Gene and Protein Database (HGPD) presents SDS-PAGE patterns and other informations of human genes and proteins.

HymenopteraMine integrates genomic data for bees, ants and the parasitoid jewel wasp. Expression and variation data are provided for A. mellifera.

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 ...

PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. The majority of these pathways are not found in any other path ...

Autism genetics KnowledgeBase, an evidence-based knowledgebase of autism genetics.

The HIV-1, human protein interaction data presented here are based on literature reports. This dataset is available in report pages per HIV-1 protein and is also integrated into Entrez Gene report pages for HIV-1 and human proteins.

The CHD7 database contains locus-specific, anonymised mutation data on both published and unpublished variants of the CHD7 gene related to the CHARGE syndrome phenotype. It can be searched for patients and their clinical phenotype or for mutations. I ...

Collaborative resource for the Bacillus community.

VBASE2 is an integrative database of germ-line variable genes from the immunoglobulin loci of human and mouse. All variable gene sequences are extracted from the EMBL-Bank.

International Dystrophic Epidermolysis Bullosa Patient Registry (DEB Register) provides phenotypic and genotypic information on DEB and the related COL7A1 mutations. The registry is intended to aid in disease diagnosis, genetic counseling, and discov ...

The Generic Feature Format Version 3 (GFF3) format was developed after earlier formats, although widely used, became fragmented into multiple incompatible dialects. The GFF3 format addresses the most common extensions to GFF, while preserving backwar ...

BovineMine integrates the bovine reference genome assembly with many other biological data sets, including genomes of other species. The sheep and goat genomes allow comparison across ruminants. Model organism data (human, mouse, rat) allow well-cura ...

The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast). This database covers metabolites described in textboo ...

ZebrafishMine is a tool to customize searches of Zebrafish-related biological data including genes, proteins, fish, and reagents

SigMol is a specialized repository of quorom sensing signaling molecules (QSSMs) in prokaryotes. SigMol harbors information on QSSMs pertaining to different quorum sensing signaling systems namely acylated homoserine lactones (AHLs), diketopiperazine ...

Orphanet Rare Diseases Ontology (ORDO) provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.

T1DBase focuses on two research areas in type 1 diabetes (T1D): the genetics of T1D susceptibility and beta cell biology.

The goal of MutDB is to annotate human variation data with protein structural information and other functionally relevant information, if available. The mutations are organized by gene. Click on the alphabet below to go alphabetically through the lis ...

Gene Signature DataBase (GeneSigDB) is a database of gene signatures (or gene sets) that have been extracted and manually curated from articles that are indexed by PubMed.

GermOnline is a cross-species database gateway focusing on high-throughput expression data relevant for germline development, the meiotic cell cycle and mitosis in healthy versus malignant cells. The portal provides access to the Saccharomyces Genomi ...

The aim of PEROXISOME database (PeroxisomeDB) is to gather, organise and integrate curated information on peroxisomal genes, their encoded proteins, their molecular function and metabolic pathway they belong to, and their related disorders.

The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic techno ...

HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.

The tumor-associated gene (TAG) database was designed to utilize information from well-characterized oncogenes and tumor suppressor genes to facilitate cancer research. All target genes were identified through text-mining approach from the PubMed dat ...

The database of human DNA Methylation and Cancer (MethyCancer) is developed to study interplay of DNA methylation, gene expression and cancer. It hosts both highly integrated data of DNA methylation, cancer-related gene, mutation and cancer informati ...

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 ...

CHOmine integrates many types of data for Cricetulus griseus, and CHO cells. You can run flexible queries, export results and analyse lists of data.

A comprehensive online knowledgebase for the monkey research community.

DPVweb provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences a ...

The Candidate Cancer Gene Database (CCGD) was developed to disseminate the results of transposon-based forward genetic screens in mice that identify candidate cancer genes. The purpose of the database is to allow cancer researchers to quickly determi ...

StellaBase is the Nematostella vectensis genomics database.

ABS: A database of Annotated regulatory Binding Sites from known binding sites identified in promoters of orthologous vertebrate genes.

ORDB began as a database of vertebrate OR genes and proteins and continues to support sequencing and analysis of these receptors by providing a comprehensive archive with search tools for this expanding family.

An integrated Omics data warehouse for Locust, Locusta migratoria

Dr.VIS collects and locates human disease-related viral integration sites. So far, about 600 sites covering 5 virus organisms and 11 human diseases are available. Integration sites in Dr.VIS are located against chromesome, cytoband, gene and refseq p ...

The DistiLD database aims to increase the usage of existing genome-wide association studies (GWAS) results by making it easy to query and visualize disease-associated SNPs and genes in their chromosomal context.

euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, ...

A genetic database for attention deficit hyperactivity disorder. ADHDgene aims to provide research community with a central genetic resource and analysis platform for ADHD, to help unveil the genetic basis of ADHD and to contribute to global mental h ...

ICDS database is a database containing ICDS detected by a similarity-based approach. The definition of each interrupted gene is provided as well as the ICDS genomic localisation with the surrounding sequence.

HuSiDa is a public database that serves as a depository for both, sequences of published functional siRNA molecules targeting human genes and important technical details of the corresponding gene silencing experiments. It aims at supporting the setup ...

Satellog is a database that catalogs all pure 1-16 repeat unit satellite repeats in the human genome along with supplementary data. Satellog analyzes each pure repeat in UniGene clusters for evidence of repeat polymorphism.

IVDB hosts complete genome sequences of influenza A virus generated by BGI and curates all other published influenza virus sequences after expert annotations. IVDB provides a series of tools and viewers for analyzing the viral genomes, genes, genetic ...

GenAtlas is a database containing information on human genes, markers and phenotypes.

NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web.

XenMine has been created to view, search and analyze Xenopus data, and provides essential information on gene expression changes and regulatory elements present in the genome. It contains published genomic datasets from both Xenopus tropicalis and Xe ...

TropGENE DB is a database that manages genetic and genomic information about tropical crops studied by Cirad. The database is organised into crop specific modules.

The D. melanogaster and eight other eukaryote model genomes, and gene predictions from several groups. Summaries of essential genome statistics include sizes, genes found and predicted, homology among genomes, phylogenetic trees of species, and compa ...

The MMRRC distributes and cryopreserves scientifically valuable, genetically engineered mouse strains and mouse ES cell lines with potential value for the genetics and biomedical research community. The Catalog provides information on the strains ava ...

EpoDB (Erythropoiesis database) is a database of genes that relate to vertebrate red blood cells. It includes DNA sequence, structural features, protein information, gene expression information and transcription factor binding sites.

mycoCLAP is a searchable resource for the knowledge and annotation of Characterized Lignocellulose-Active Proteins of fungal origin.

Integration, navigation, visualization, and analysis of gene interaction networks. This record has been marked as "Uncertain" because its homepage no longer exists. If you have any information on the current status of this resource, please contact us ...

Implemented the SNP discovery software autoSNP within a relational database to enable the efficient mining of the identified polymorphisms and the detailed interrogation of the data. AutoSNP was selected because it does not require sequence trace fil ...

SilkDB is a database of the integrated genome resource for the silkworm, Bombyx mori. This database provides access to not only genomic data including functional annotation of genes, gene products and chromosomal mapping, but also extensive biologica ...

The database provides a means of investigating alternative splicing and can be used for identifying alternative splicing - related motifs, such as the exonic splicing enhancer (ESE), the exonic splicing silencer (ESS) and other intronic splicing moti ...

The aim of this Oryza sativa database was first to display sequence information such as the T-DNA and Ds flanking sequence tags (FSTs) produced in the framework of the French genomics initiative Genoplante and the EU consortium Cereal Gene Tags. This ...

siRecords is a collection of a diverse range of mammalian RNAi experiments . After choosing a gene, researchers can find all siRNA records targeting the gene, design a new siRNA targeting it, or submit siRNAs that have been tested. The resource also ...

MEPD contains expression data of genes and regulatory elements assayed in the Japanese killifish Medaka (Oryzias latipes).

miRwayDB provides information on experimentally validated microRNA-pathway associations for pathophysiological conditions. Information includes disease condition, associated microRNAs, experimental sample types, regulation pattern (up/down), and path ...

This ontology is about human pseudogenes, extending the existing SO framework to incorporate additional attributes. Relationships between pseudogenes and segmental duplications are defined in this standard. To answer research questions and to annotat ...

The Agronomic Linked Data (AgroLD) is a knowledge-based system relying on Semantic Web technologies and exploiting standard domain ontologies, which integrates data about plant species of high interest for the plant science community. AgroLD is an RD ...

The IPD-NHKIR database provides a centralised repository for non-human KIR (NHKIR) sequences. Killer-cell Immunoglobulin-like Receptors (KIR) have been shown to be highly polymorphic at the allelic and haplotypic level. KIRs are members of the immuno ...

If a database is inadequate in terms of its description, unclear with respect to the terms of use, or is not downloadable, it may not be fully used, cited or rightly acknowledged by the (research) communities. This is even true for databases with hig ...

The Pig Genomic Informatics System (PigGIS) presents accurate pig gene annotations in all sequenced genomic regions. It integrates various available pig sequence data, including 3.84 million whole-genome-shortgun (WGS) reads and 0.7 million Expressed ...

The database is gene-centered and organized by paralog family. It focused on the paralogs and the duplication events in the evolution. The paralog families and paralogons can be searched by text or sequence, and are downloadable from the website in p ...

EPConDB is a resource of the Beta Cell Biology Consortium which displays information about genes expressed in cells of the pancreas and their transcriptional regulation.

The PGDBj Ortholog Database, created under the auspices of the Plant Genome Database Japan (PGDBj), contains information about orthologous genes in plants based on their corresponding amino acid sequence similarity. By placing PGDBj Ortholog Database ...

CnidBase, the Cnidarian Evolutionary Genomics Database, is a tool for investigating the evolutionary, developmental and ecological factors that affect gene expression and gene function in cnidarians.

Chickspress is a gene expression database for chicken tissues. Chickspress incorporates both NCBI and Ensembl gene models and links these gene sets with experimental gene expression data and QTL information. By linking gene models from both NCBI and ...

This server allows to access the complete genome of Bacillus subtilis. Additional data on gene mapping and codon usage have been added, as well as cross-references with the SWISS-PROT, ENZYME and HOBACGEN databases.

<<<!!!<<< This repository is no longer available>>>!!!>>>. Although the web pages are no longer available, you will still be able to download the final UniGene builds as static content from the FTP site https://ftp.ncbi.nlm.nih.gov/repository/UniGen ...

The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific m ...

OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms. Each gene in OGG has over 10 annota ...

OGG-Mm is the OGG Mus musculus (mouse) subset. The OGG (Ontology of Genes and Genomes) is a formal ontology of genes and genomes of biological organisms. OGG is developed by following OBO Foundry principles and aligning with the BFO top-level ontolog ...

This ontology was designed to help integrate species concepts with species occurrences, gene sequences, images, references and geographical information.

The TBestDB (a Taxonomically Broad EST database) database contains ~370,000 clustered EST sequences from 49 organisms, covering a taxonomically broad range of poorly studied, mainly unicellular eukaryotes, and includes experimental information, conse ...

CarpeDB serves as a novel source for epilepsy researchers by featuring scores of "epilepsy genes" and associated publications in one locus. Furthermore, multiple genes implicated in epilepsy are also implicated in other human disorders.

BenchSci is a free platform designed to help biomedical research scientists quickly and easily identify validated antibodies from publications. Using various filters including techniques, tissue, cell lines, and more, scientists can find out publishe ...

The glycobiology of Drosophila has been extensively studied in recent years, and much information has accumulated regarding glycan-related genes and proteins in Drosophila. The FlyGlycoDB ontology describes glycogenes of Drosophila and includes mutan ...

Genomics of fungal, oomycete and bacterial phytopathogens

The EuMMCR (European Mouse Mutant cell Repository) is the mouse ES cell distribution unit in Europe. The EuMMCR has been founded as distribution unit of EUCOMM (European Mouse Mutagenesis Program). The EuMMCR provides an online database to help users ...

The National Omics Data Encyclopedia (NODE) is big data library with complete and integrative data storage, safe and efficiency-guaranteed data management as well as comprehensive and user-friendly data service functions. NODE stores raw sequence dat ...

Expert-authored and peer-reviewed information on mammalian proteins involved in cellular signaling

GeneWeaver combines cross-species data and gene entity integration, scalable hierarchical analysis of user data with a community-built and curated data archive of gene sets and gene networks, and tools for data driven comparison of user-defined biolo ...

The need for a way to represent genes/gene products separately from annotations, as well as the need to use the evidence ontology has lead to the creation of the GPAD (Gene Product Annotation Data) and GPI (Gene Product Information) formats. Whilst G ...

The need for a way to represent genes/gene products separately from annotations, as well as the need to use the evidence ontology has lead to the creation of the GPAD (Gene Product Annotation Data) and GPI (Gene Product Information) formats, defined ...

The bigGenePred format stores annotation items that are a linked collection of exons, much as BED files indexed as bigBeds do. However, the bigGenePred format includes 8 additional fields that contain details about coding frames and other gene-specif ...

Oral Cancer Gene Database is an initiative of the Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai. The present database, version II, consists of 374 genes. It is developed as a user friendly site that would provide the s ...

The Fungal Genetics Stock Center has preserved and distributed strains of genetically characterized fungi since 1960. The collection includes over 20,000 accessioned strains of classical and genetically engineered mutants of key model, human, and pla ...

>>>!!!<<< Noticed 26.08.2020: The NCI CBIIT instance of the CGAP no longer exist on this website. The Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer has a new home at the NCI-funded Institute for Systems Biology Cancer Geno ...

The Cellular Phenotype database stores data derived from high-throughput phenotypic studies and it is being developed as part of the Systems Microscopy Network of Excellence project. The aim of the Cellular Phenotype database is to provide easy acces ...

The glycobiology of Drosophila has been extensively studied in recent years, and much information has accumulated regarding glycan-related genes and proteins in Drosophila. As a database for glycan-related genes in Drosophila, FlyGlycoDB provides spe ...

This is a data table format used in the PUMAdb workflow to transform a .pcl file into a .cdt (clustered data table) file which contains the original data, but reordered, to reflect the clustering.

JAX® Mice are the industry standard for animal model research, using precise genome solutions to better understand human disease. Our rigorous Animal Health Programs and stringent genetic quality standards ensure the reproducibility and validity of y ...

Wiki-Pi is a wiki resource centered on human protein-protein interactions. Wiki-Pi's intuitive search functionality allows you to retrieve and discover interactions effectively.

TPA is a database that contains sequences built from the existing primary sequence data in GenBank. TPA records are retrieved through the Nucleotide Database and feature information on the sequence, how it was cataloged, and proper way to cite the se ...

A small genotype data repository containing data used in recent papers from the Estonian Biocentre. Most of the data pertains to human population genetics. PDF files of the papers are also freely available.

PRIMESDB is a systems biology platform that is being developed to enable the collection, integration and analysis of state-of-the-art genomics, proteomics and mathematical modelling data being generated by the PRIMES project. PRIMES is investigating ...

>>> !!! the repository is offline !!! The current successor is https://www.lovd.nl/USH1C. <<< The database contains all the variants published as pathogenic mutations in the international literature up to November 2007. In addition, unpublished Ushe ...

The database aims to bridge the gap between agent repositories and studies documenting the effect of antimicrobial combination therapies. Most notably, our primary aim is to compile data on the combination of antimicrobial agents, namely natural prod ...

We offer a public platform to help researchers organize, share, and explore their research data. DataCenterHub provides a simple, standardized yet flexible platform to preserve and share data. In the future, this platform will offer data visualizati ...

The Organelle Genome Megasequencing Program (OGMP) provides mitochondrial, chloroplast, and mitochondrial plasmid genome data. OGMP tools allow direct comparison of OGMP and NCBI validated records. Includes GOBASE, a taxonomically broad organelle gen ...

The Alzheimer Disease & Frontotemporal Dementia Mutation Database (AD&FTDMDB) aims at collecting all known mutations in the genes related to Alzheimer disease (AD) and fromtotemporal dementias (FTD). Mutations are collected from the literature and fr ...

The Plant Metabolic Network (PMN) provides a broad network of plant metabolic pathway databases that contain curated information from the literature and computational analyses about the genes, enzymes, compounds, reactions, and pathways involved in p ...

NCBI PopSet collects DNA sequences to analyze the ways that populations are related by evolution. Such sequences indicate if populations originate from different members of the same species or from organisms of different species entirely.

>>>!!! <<< 2021-09-01: repository is offline >>>!!!<<< Background: Many studies have been conducted to detect quantitative trait loci (QTL) in dairy cattle. However, these studies are diverse in terms of their differing resource populations, marker ...

Project Achilles is a systematic effort aimed at identifying and cataloging genetic vulnerabilities across hundreds of genomically characterized cancer cell lines. The project uses genome-wide genetic perturbation reagents (shRNAs or Cas9/sgRNAs) to ...

HADb provides a complete and an up-to-date list of human genes and proteins involved directly or indirectly in autophagy as described in literature.

A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data.