Rat genome database

RGD

Content
Description	The Rat Genome Database
Organisms	rat
Contact
Research center	Medical College of Wisconsin
Laboratory	Human Molecular and Genetics Center
Authors	Dr. Howard J Jacob
Primary citation	PMID 21296746
Access
Website	rgd.mcw.edu
Tools
Miscellaneous

The Rat Genome Database (RGD) is the premiere location for rat data including genomics, genetics, physiology and functional data. RGD is responsible for attaching biological information to the rat genome via ontology annotations assigned to genes and quantitative trait loci (QTL), and for consolidating rat strain data and making it available to the research community. RGD is working with groups such as the Programs for Genomic Applications at MCW and the National BioResource Project for the Rat in Japan to collect and make available comprehensive physiologic data for a variety of rat strains. They are also developing a suite of tools for mining and analyzing genomic, physiologic and functional data for the rat, and comparative data for rat, mouse and human.

RGD began as a collaborative effort between leading research institutions involved in rat genetic and genomic research. Its goal, as stated in RFA: HL-99-013 was the establishment of a Rat Genome Database, to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community. A secondary, but critical goal was to provide curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data.

The rat continues to be extensively used by researchers as a model organism for investigating the biology and pathophysiology of disease. In the past several years, there has been a rapid increase in rat genetic and genomic data. In addition to this, the Rat Genome Database has become a central point for information on the rat for research and now features information on not just genetics and genomics, but physiology and molecular biology as well. There are tools and data pages available for all of these fields that are curated by RGD staff.^[1]

Data

Reports

Individual object reports may be used to view detailed information on rat strains and rat, mouse, and human genes, markers, QTLs and references (these last link out to PubMed).

Reports for sequences and marker map data are separate from the report pages themselves, each with its own interfaces for bringing up these multi-object reports.

Genes

Gene reports include a comprehensive description of function and biological process as well as disease and phenotype information. Currently missing information types include the subcellular localization of the gene products, gene chemical interactions and information on which pathway/s a given gene participates in.

Initial gene records are imported from NCBI's Gene database on a weekly basis. RGD curators review the literature and manually curate GO, disease, phenotype and pathways for rat genes, disease and pathways for mouse genes, and disease, phenotype and pathways for human genes. In order to create access to as complete a dataset as possible, the site imports GO annotations for mouse and human genes from the GO consortium, rat electronic annotations from EBI's Gene Ontology Annotation group (GOA) and mouse phenotype annotations from MGI.

QTLs

RGD's staff manually curates the rat and human QTL records (either from the literature or from records directly submitted by researchers) and imports mouse QTL records from MGI. For rat and human QTLs, curation includes assigning phenotype and disease ontology annotations. Mouse QTL phenotype ontology anntotaions are also imported from MGI into the Rat Genome Database.

QTL reports provide phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes.

Strains

Strain reports include a comprehensive description of strain origin, disease, phenotype, genetics, immunology, behavior with links to related genes, QTLs, sub-strains, and strain sources. These records are manually curated from the literature or are submitted by researchers. Disease and phenotype annotations are manually assigned to rat strains. In addition to the standard inbred strains, RGD curates and provides data for congenic and transgenic strains. Where possible, the genomic positions of the introgressed region(s) are calculated and presented as data for these "mapped strains". There is no mouse strain data imported into this section of RGD.

Ontologies

Systematic naming has become very important in the organization and retrieval of genomic data. It is done through hierarchical term sets known as "ontologies", each with a searchable ID and a specific definition. These ontologies are dynamic, and respond to the changing needs of the research community. RGD houses these ontologies and also provides a browser interface for easy hierarchical navigation, including a view of both parent and child terms.

Genome Tools

These are the tools that the Rat Genome Database made specifically for genomics and are readily accessed through a tab at the top of RGD's home page.^[2]

Rat/Human/Mouse Genome Browsers

These tools allow the user to view the location of a genetic landmark (sequence, gene, locus, marker, and/or oligonucleotide) on the genome of either human, mouse, or rat. They also function to comparison between species, mostly between mouse and human using links.

Like many of the tools in RGD, this one links out to the curated RGD report pages for individual objects.

Gene Annotator

The Gene Annotator takes a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, and/or a chromosomal region, and retrieves annotation data from RGD in four different views.

Genome Viewer

Genome Viewer (or GViewer) retrieves a genome-level display of genes and QTLs, and mapped congenic strains annotated to one or more GO, phenotype, disease or pathway terms.

SNPlotyper

SNPlotyper is a visualization and analysis tool for Rat SNP data. Containing data for over 400 strains and SNP data from multiple sources, it enables users to view haplotype blocks shared between strains and identify informative (polymorphic) markers between two or more strains.

RatMine

RatMine enables the user to mine and analyze data from multiple databases including RGD, UniProtKB, Ensembl and more for annotations to function, biological process, cellular component, disease, phenotype, or metabolic pathway. These are annotated using the ontologies in RGD.

Overgo Probe Designer

Overgo probes are pairs of partially overlapping 22mer oligonucleotides derived from repeat-masked genomic sequence and used as high specific activity probes for genome mapping. The Overgo Probe Designer tool was created in order for users to submit their sequence of interest and get back optimized probe sequences containing the requisite 8 nucleotide overlap on their 3' ends.

ACP Haplotyper

ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non-conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.

Genome Scanner

The Genome Scanner tool is designed to assist researchers in selecting polymorphic markers for a genome scan of a cross between two strains. The tool uses the Allele Characterization Project dataset in combination with various genetic and Radiation Hybrid maps.

It also retrieves annotations from any or all ontologies used at RGD for genes and their orthologs, as well as links to additional information at other databases. Also, it provides the ability to analyze annotations within or across ontologies for the entered gene set.

VCMap

The Virtual Comparative Map (VCMap) is a downloadable tool that can be used to explore the syntenic relationships between rat, mouse and human genomes. A new version of VCMap is now available which also incorporates cow, pig and chicken, expanding both the versatility and utility of this valuable tool.

Other Rat Information Tools

Phenotypes and Models

This section of RGD focuses on strains and disease models in the rat, containing images, resources for creating and naming new rat strains, and even the sale of strains. Photos and resources for creating strains can be found under the "Meet Joe Rat" section.

The phenotypes portal provides access to PGA (PhysGen Program for Genomic Applications) and NBRP (National BioResource Project in Japan) data from a variety of phenotyping experiments.

A prominent piece of RGD's usefulness in researching phenotypes can be found in the tool PhenoMiner. This tool allows the user to analyze quantitative phenotype data across multiple methods, conditions, strains, and datasets.

The stains & models section includes resources on strain availability (and links to the institutions selling rats), disease models, animal husbandry.

Diseases

The direct way that RGD deals with diseases is to have various disease portals to locate rat, mouse, and human genes, rat and human QTLs, and rat strains associated with your disease of interest. Portals group diseases into respiratory, obesity/metabolic syndrome, cancer, diabetes, neurological, and immune/inflammatory diseases.

Knockouts

The PhysGen Knockout program ("Mechanistic Characterization of Genes for Hypertension and Renal Disease") aims to knock out a large number of genes nominated by genome wide association studies, then combine these gene knockouts (KO) with hypertensive and normotensive strains, and phenotypically characterize them. RGD provides data related to gene knockouts and provides contact information in order to nominate knockout genes.

Pathways

These are designed in order to help researchers and students explore metabolic, signaling, disease, regulatory, and drug pathways and related data with interactive diagrams that RGD has made available. These tend to fall under molecular or physiological pathways. Many of the molecular pathways have been grouped into suites.

The physiological pathways have a "zoom" feature that allows the user to view different levels of each pathway, down to the molecular. RGD annotations are available for each object in the molecular pathways only.

Grants

Active grants as of 2012:^[3]

• NATIONAL HEART, LUNG, AND BLOOD INSTITUTE
• NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES
• NATIONAL HUMAN GENOME RESEARCH INSTITUTE
• NATIONAL INSTITUTE ON DEAFNESS AND OTHER COMMUNICATION DISORDERS

Rat Community

RGD attempts to provide its users with connections to the rat research community and occasionally also use these same avenues to showcase the work of various faculty and staff at the Rat Genome Database. The website also provides links to resources for researchers, both within the site and outgoing to other websites.

This community has its own forum, Facebook page, a directory of rat research laboratories, a research publications page, and an archive of RGD's posters.

The community is also where many of RGD's video tutorials can be found, created by members of RGD's staff in order to assist researchers in operating the website's various tools.

Database Information

The genomic sequence is available under accession numbers AABR03000000 to AABR03137910 in the international sequence databases (GenBank, DDBJ and EMBL).

References