Compilation of Genetics Resource Databases


Brain and Neuroscience
  • Neuroscience Information Framework - Website for identifying, locating, relating, accessing, integrating, and analyzing information from the neuroscience research enterprise
  • Allen Brain Atlas - Brain expression and other tools for mouse, human and non-human primates
  • Alliance of Genome Resources - An alliance of the Gene Ontology Consortium, Mouse Genome Database (MGD), FlyBase, WormBase, Saccharomyces Genome Database (SGD), Rat Genome Database (RGD), Zebrafish Information Network (ZFIN) to facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease
  • Brain Architecture Project - Integrated resource containing knowledge about nervous system architecture in multiple species, with a focus on mouse and human
  • Mouse Genome Informatics - International database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease
  • Brain Maps - Interactive multiresolution brain atlases based on over 20 million megapixels of sub-micron resolution, annotated, scanned images of serial sections of human, non-human primate, cat, rat, mouse, barn owl, opossum, red jungle fowl, spiny anteaters, platypus and goldfish brains
  • The Scalable Brain Atlas - A web-based display engine for different atlases created for mouse, macaque, and human
  • NITRC - The resource for neuroinformatics tools and resources
  • Laboratory of Neuroimaging Atlas - Website contains brain atlases for fetal and adult human, Alzheimer’s, monkey, vervet, mouse, and rat

Bioinformatics Platforms



Allen Human Brain Atlases

Other Human Brain Atlases

Human Connectome

  • Human Connectome Coordination Facility - The Connectome Coordination Facility houses and distributes public research data for a series of studies that focus on the connections within the human brain known as Human Connectome Projects.
  • ClinVar - ClinVar aggregates information about genomic variation and its relationship to human health
  • dbSNP - Database of single nucleotide polymorphisms (SNPs) and multiple small-scale variations that include insertions/deletions, microsatellites, and non-polymorphic variants
  • database of Genotypes and Phenotypes (dbGaP) - Platform for archiving and distributing data and results from studies that have investigated the interaction of genotype and phenotype in Humans
Twin Registries
  • Australian Twin Registry - The Australian Twin Registry is supported by a project grant from the National Health and Medical Research Council
  • Mid-Atlantic Twin Registry - The Mid-Atlantic Twin Registry (MATR, pronounced "matter") is a population-based registry of 37,000+ twins of all ages who were born in or live in North Carolina , South Carolina , and Virginia.
  • The Danish Twin Registry - The Danish Twin Registry (DTR) is one of the oldest twin registries in the world. It was established in the 1950'es with the aim of studying causes of cancer, and through the years it has gradually been expanded so that it now comprises twins born through more than 125 years.
  • National Twin Registry of Sri Lanka - NTR is an independent academic and research institution founded with the aim of establishing a register for twins in Sri Lanka , to facilitate study of twins. We aim to establish a centre of excellence for twin, sibling, family studies and genetic studies for the South Asian Region.
  • The Minnesota Twin Family Registry - Two longitudinal research studies of over 9800 individuals, including twins, siblings, and parents born in Minnesota from 1936 to 1955 and from 1971 to 1981.
  • Cardiff Study of all Wales and North West of England Twins (CaStANET) - CaStANET is a longitudinal study that followed children and adolescents to early adulthood. This study has collected behavioral and psychopathological information using self-, parent and teacher reports, and has focused on the contributions of genetic and environmental risk factors to the psychological health of young people.
  • Swedish Twin Registry - The Swedish Twin Registry was established in the 1960s and contains information about some 85,000 twin pairs for which zygosity is known, both mono- and dizygotic pairs. The registry covers older, middle, and younger cohorts. There are approximately 30 projects ongoing based on data from the registry.
  • The Finnish Twin Cohort Study - The twin panel consists of three nationwide samples of the Finnish twin pairs. Major studies include nicotine dependence, eating disorders and brain imaging and alcohol use.
Collaborative Opportunities and Behavioral Measures
  • Psychiatric Genetic Consortium (PGC) - The PGC unites investigators around the world to conduct meta- and mega-analyses of genome-wide genomic data for psychiatric disorders. Areas of focus include: autism, ADHD, bipolar disorder, major depressive disorder, schizophrenia, eating disorders, substance use disorders, obsessive-compusive disorder/Tourette's syndrome, and post-traumatic stress disorder (PTSD)
  • Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium - The CHARGE Consortium is conducting a meta-analysis of GWAS data for smoking cessation among subjects of European ancestry. This effort includes several prospective cohort studies such as ARIC, CHS, Rotterdam, Framingham, and Nurses' Health Study.
  • Pharmacogenetics of Nicotine Addiction Treatment - The goal of the Pharmacogenetics of Nicotine Addiction Treatment (PNAT) research program is to generate the evidence base to optimize treatment decisions for Individuals who want to quit smoking. The PNAT Consortium was formed in 2005 with funding from NIDA to identify the role of pharmacokinetic and pharmacodynamic gene variation in nicotine dependence phenotypes, with a focus on prospective smoking cessation and medication response.
  • PhenX Substance Abuse and Addiction Project (SAA) - PhenX measures that are relevant to substance abuse and addiction research are included in several research domains, including 14 measures in the Alcohol, Tobacco, and Other Substances domain, four measures in the Cancer domain, three measures in the Respiratory domain, and one measure each in the Reproductive Health, Oral Health, Environmental Exposures, and Infectious Diseases and Immunity domains.

Non-Human Primates

  • NIH Blueprint NHP Atlas - A suite of gene expression data, neuroanatomical data, and informatics tools for exploring the cellular and molecular architecture of the developing postnatal rhesus macaque brain.
  • McConnell Brain Imaging Centre - Atlases from the Average Macaque, Rhesus Macaque, and Cynomolgus Macaque
  • Rhesus Macaque Brain Atlases - These atlases enable the alignment of individual scans to improve localization and the statistical power of the results, and allow comparison of results between studies and institutions. A set of multi-subject atlas templates is constructed specifically for functional and structural imaging studies of rhesus macaque.


Brain Tissue

  • Macaque Brain Resource (MacBrainResource) - Macaque Brain Resource is a resource comprised of five distinct collections of macaque brain tissue available to investigators worldwide to provide a cost effective means for researchers to conduct de novo studies on the non-human primate brain



Allen Mouse Brain Atlases

  • Allen Brain Observatory - Standardized in vivo survey of physiological activity in the mouse visual cortex, featuring representations of visually evoked calcium responses from GCaMP6-expressing neurons in selected cortical layers, visual areas and Cre lines
  • Allen Cell Types Database - Database of neuronal cell types based on multimodal characterization of single cells to enable data-driven approaches to classification
  • Allen Developing Mouse Brain - Reference Atlas of the developing C57BL/6J mouse brain at Embryonic (E) and Postnatal (P) Days E11.5, E13.5, E15.5, E18.5, P4, P14 and P28
  • Allen Mouse Brain Atlas - Reference Atlas of the adult C57BL/6J mouse brain and high resolution gene expression atlas
  • Allen Spinal Cord Atlas - A gene expression atlas of mouse spinal cord at P4 and P56

Other Mouse Brain Atlases

  • EMBRYS - A database of gene expression patterns mapped in the wholemount mouse embryo (ICR strain) of mid- gestational stages (embryonic days E9.5, E10.5, E11.5), in which the most striking dynamics in pattern formation and organogenesis are observed
  • Gene Expression Database (GXD) - A collection of gene expression information during mouse development
  • Gene Expression Nervous System Atlas (GENSAT) - An NIH-funded, publicly available, gene expression atlas of the developing and adult CNS in mice
  • GenePaint - A digital atlas of gene expression patterns in the mouse
  • The Mouse Brain Library - High-resolution images and databases of brains from many genetically characterized strains of mice

Mouse Connectomes

  • Allen Mouse Brain Connectivity Atlas - High-resolution map of neural connections in the mouse brain, built on an array of transgenic mice genetically engineered to target specific cell types
Mouse Genome

Jackson Laboratory Resources

  • Mouse Genome Informatics Database - International database of biological resources for the mouse
  • Genes, Genome Features and Maps - A searchable database of mouse genes, DNA segments, cytogenetic markers and QTLs
  • Phenotypes and Mutant Alleles - The Phenotypes, Alleles & Disease Models project in MGI enables comparative phenotype analysis, searches for human disease models, and hypothesis generation by providing access to spontaneous, induced, and genetically engineered mutations and their strain-specific phenotypes.
  • Human Mouse Disease Connection - This database facilitate thes identification of published and potential mouse models of human disease, the discovery of candidate genes and the investigation of phenotypic similarity between mouse models and human patients
  • Gene Expression Database (GXD) - GXD collects and integrates the gene expression information in MGI. Its primary emphasis is on endogenous gene expression during mouse development
  • Recombinase (cre) Activity - This database contains expression and activity data for recombinase-containing transgenes and knock-in alleles
  • Functional Annotation - Provides functional annotations for mouse gene products using Gene Ontology
  • Strains, SNPs and Polymorphisms - Integrates comparative data on inbred strain characteristics including SNPs, polymorphisms, and quantitative phenotypes
  • Vertebrate Homology - Homology information for mouse, human, rat, chimp, dog and other species
  • Mouse Models of Human Cancer - Provides access to data and information on various resources dedicated to cancer
  • Batch Data and Analysis Tool - Access various Mouse Genome information in batch format
  • Optogenetics Resource Center - Database of different optogenetics resources
  • Knock-out Mouse Project Repository at JAX - KOMP's mission is to generate a targeted knockout mutation for every gene in the mouse genome
  • Nomenclature - Authoritative source of official names for mouse genes, alleles, and strains. Nomenclature follows the rules and guidelines established by the International Committee on Standardized Genetic Nomenclature for Mice


  • Mouse Phenome Database (MPD) - An NIH-funded, integrated resource to explore phenomics through genetics and genomics
  • International Mouse Phenotyping Consortium (IMPC) - Phenotype and characterize the function of 20 000 known and predicted mouse genes
  • Phenotypes and Mutant Alleles - The Phenotypes, Alleles & Disease Models project in MGI enables comparative phenotype analysis, searches for human disease models, and hypothesis generation by providing access to spontaneous, induced, and genetically engineered mutations and their strain-specific phenotypes.

Gene Editing in Mice

  • International Gene Trap Consortium (IGTC) - IGTC represents all publicly available gene-trap cell lines, which are available on a non-collaborative basis for nominal handling fees
  • IMPC - A world-wide consortium of institutions dedicated to the production and phenotyping of germ line transmission of targeted knockout mutations in embryonic stem cells for 20 000 known and predicted mouse genes
  • Knock-out Mouse Project Repository at JAX - KOMP's mission is to generate a targeted knockout mutation for every gene in the mouse genome
  • Mutant Mouse Regional Resource Centers (MMRRCs) - Distributes and cryopreserves genetically engineered mouse strains and mouse ES cell lines with potential value for the genetics and biomedical research community
  • International Mouse Strain Resource (IMSR) - Searchable online database of mouse strains, stocks, and mutant ES cell lines available worldwide, including inbred, mutant, and genetically engineered strains

Cre and Flp Driver Lines



  • Waxholm Standard Space - A coordinate-based reference space for the mapping and registration of neuroanatomical data in Sprague Dawley
Rat Genome
  • The Rat Genome Database - Genetic resources for rat (Genes, Strains, QTL, Function, Diseases, Phenotypes and Models, Genome Browser, Analysis and Visualization and Pathways
  • Rat Resource and Research Center - An NIH-funded Resource Center to supply biomedical investigators with the rat models, embryonic stem cells, related reagents, and protocols they require for their research

Other Species

  • Virtual Fly Brain - interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of Drosophila melanogaster
  • Atlas of Drosophila Development - Color illustrations that follow the main events of embryogenesis and post-embryonic development of Drosophila
  • Zebrafish Brain Atlas - Curated information and images of neuroanatomical structures in the developing zebrafish
  • McConnell Brain Imaging Centre - The Ovine Brain Atlas
  • Wormatlas - A description of anatomical location and function of 302 neurons in the adult Caenorhabditis elegans
Other Resources

Functional Annotation

Functional Annotation Resources

Sequence Data and Genome browsers

  • University of California at Santa Cruz Genome Browser - Provides reference sequences and working draft assemblies for large collection of genomes and access to the ENCODE and Neanderthal projects
  • Ensembl Genome Browser - Produces genome database for the eukaryotic and vertebrate organisms
  • NCBI Genome - This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations
  • Genbank - NIH genetic sequence database, an annotated collection of all publicly available DNA sequences
  • RefSeq - The Reference Sequence (RefSeq) collection provides a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins

Tissue-specific Information

Regulatory Elements

  • ENCODE - The ENCyclopedia Of DNA Elements provides information about the functional elements in the genome
  • PsychENCODE - Database of regulatory elements, epigenetic modifications, RNA and protein in the brain
  • Redfly Regulatory Element Database - Database of Drosophila transcriptional cis-regulatory modules and transcription factor binding sites
  • TRANSFAC - Database of eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes
  • TransmiR - Database for transcription factor-microRNA regulation
  • JASPAR - JASPAR is a collection of transcription factor DNA-binding preferences


  • DIANA-mirExTra - Analysis of expression data for microRNA function
  • MicroCosm Targets - Computationally predicted targets for microRNAs across many species
  • microT-CDS - MicroRNA target prediction
  • miRBase - Database of published miRNA sequences and annotation
  • miRanda - Predicted microRNA targets & target downregulation scores
  • mirPath - Incorporating microRNAs in pathways
  • miRTarBase - Experimentally validated microRNA-target interactions database
  • PicTar - Algorithm for the identification of microRNA targets
  • TarBase - Database of experimentally supported microRNA targets
  • TargetScan - predicted microRNA targets in human, mouse, fly, worm and fish



  • 4D Genome - Repository for chromatin interaction data

DNA methylation

Imaging resources

  • NITRC - The source for neuroimaging tools and resources

Viral vectors

  • National Gene Vector Biorepository (NGVB) - An NIH-funded Center to address the increasing needs of the research community for access to the use of viral transneuronal tracing tracers. This approach is the most widely used method to gain a circuit perspective on the functional architecture of the nervous system at a cellular level

Protein Resources

  • Antibody Registry - Provides a stable, traceable, permanent identifier to all antibody products created by large commercial vendors and individual laboratories
  • Protein Database - Databases of protein sequences and 3D structures of proteins
  • UniProt - a comprehensive, high-quality and freely accessible resource of protein sequence and functional information
  • Pharos - Pharos combines data on all human proteins from the over 100 data sources. Users are able to access, query, filter, and download any of this data from this portal.