ISOM2023 -RGD Data and Tools for Translational Research in Otitis Media  

This is a presentation from the 22nd International Symposium on Recent Advances in Otitis Media. This presentation offers a comprehensive overview of RGD as a valuable multispecies resource, specifically focusing on its significance in translational research and its application in otitis media studies using Chinchilla as model.

RGD: PhenoMiner Tool  

This is a presentation from the 35th IMGC meeting. The video talks about the PhenoMiner Tool that allows users to query and visualize quantitative phenotype data across rat strains and between studies. Begin by selecting rat strains, clinical measurements, measurement methods and/or experimental conditions to view and download the associated phenotype measurement data.

RGD: Disease Portals

RGD has numerous disease portals, where relationships between diseases and genes, QTLs and strains can be explored in all RGD species. Learn more about disease portals from this video by Jack Pugliese (RGD student intern).

RGD: A Multispecies Resource to Explore Complex Diseases

This Video is a presentation from RGD symposium at the 2021 Complex Trait Consortium (CTC) meeting and provides an overview of the RGD data and tools.

Rat Reference Sequence Update

Rat Reference mRatBN7.2 Update and Curation

This Video is a presentation from RGD symposium at the 2021 Complex Trait Consortium (CTC) meeting and provides an overview of the new rat reference genome.

Rat Strain Updates

Rat Strain Updates at the Rat Genome Database

This Video is a presentation from RGD symposium at the 2021 Complex Trait Consortium (CTC) meeting and provides a brief on the strain submission process, finding rat models and phenotypes and models portal at the RGD.

Quantitative Phenotype Data Curation for HRDP Strains at the Rat Genome Database

This Video is a presentation from RGD symposium at the 2021 Complex Trait Consortium (CTC) meeting and provides an overview of the quantitative and qualitative phenotype data curation and the Hybrid Rat Diversity Panel at the RGD.

Comparsion of Genomic Variants Discovery in HRDP Inbred Rat Strains With Two Rat Genome Reference

This Video is a presentation from RGD symposium at the 2021 Complex Trait Consortium (CTC) meeting and provides a comparison of genomic variants in Hybrid Rat Diversity Panel rat strains.

RGD Tools

JBrowse Genome Browser Video Tutorial

This video demonstrates how to use the RGD JBrowse Genome Browser. The JBrowse Genome Browser allows the user to view objects such as genes, variants, QTLs, and so forth in their genomic context. You can view versions for Rat, Human and Mouse.

MOET-Multi Ontology Enrichment Tool Video Tutorial

This video demonstrates how to use the RGD Multi Ontology Enrichment Tool. For a list of genes, find the terms from any or all of the ontologies used by RGD for gene curation (Disease, Pathway, Phenotype, GO, ChEBI) that are over-represented in the annotations for those genes, or for orthologs in other species using MOET.

OLGA-Object List Generator and Analyzer Video Tutorial

The purpose of OLGA is to build lists for rat genes, QTLs and strains. OLGA can also be used to query human and mouse genes and QTLs. Search for genomic data annotated to specific diseases, conditions and other queries. Multiple searches will allow you to refine your final result list to use for your own analysis or to send to another tool on the RGD website.

Variant Visualizer Video Tutorial

The examination of SNPs has undergone a recent change, and in response to this change, RGD has released the new Variant Visualizer tool (VarVis), taking the place of the old SNPlotyper tool. VarVis is a visualization and analysis tool for sequence variation. At the time the video was made, the tool contained 22 rat strains sequenced by 4 independent labs. Since then, additional strain sequences for rat, as well as human clinical variants from ClinVar have been added, but the basic steps to use the tool have largely remained the same.

When it Comes to the Rat Genome, Bigger is Better

RGD’s GViewer is an interactive tool which allows users to view genomic features such as genes and QTLs in the context of the entire genome.  Click this icon to access a short video tutorial on how to get started with RGD’s GViewer Tool.

Gene Annotator Tool Video Tutorial

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. This tool will retrieve annotations from any or all ontologies used at RGD for genes and their orthologs, as well as links to additional information at other databases.

Additional Informational Videos

RGD Presentations From Conferences

This playlist contains videos from some of the conferences attended by the RGD team recently.

Molecular Pathway Diagrams Video Tutorial

This video demonstrates how to use the RGD Molecular Pathway Diagrams. You can access the Ontology Report for the pathway, view the description for the pathway with it’s various interactions and components, and you can click on any of the pathway’s interactive features to view more information about that entity.

Ontology Analysis of Infectious Disease Genes at the Rat Genome Database

This video is a poster presentation from the 2021 Great Lakes Bioinformatics Conference. In this video, we demonstrate the utility of RGD tools in analyzing coronavirus disease genes. We can look at not only the enrichment profile of a disease gene set, but also the gene distribution between two selected ontologies. Click here for the poster

It’s Easy to Get Lost on the Biological Superhighway.  Thankfully, we Brought a Map

Biological pathways are complex networks made up of a wide variety of components interacting in many different ways.  Click this icon to access a short video tutorial which demonstrates how RGD’s Interactive Pathway Diagrams can help you explore and understand these important intermolecular networks.