The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform

Abstract

Formed in late 1999, the Rat Genome Database (RGD, https://rgd.mcw.edu) will be 20 in 2020, the Year of the Rat. Because the laboratory rat, Rattus norvegicus, has been used as a model for complex human diseases such as cardiovascular disease, diabetes, cancer, neurological disorders and arthritis, among others, for >150 years, RGD has always been disease-focused and committed to providing data and tools for researchers doing comparative genomics and translational studies. At its inception, before the sequencing of the rat genome, RGD started with only a few data types localized on genetic and radiation hybrid (RH) maps and offered only a few tools for querying and consolidating that data. Since that time, RGD has expanded to include a wealth of structured and standardized genetic, genomic, phenotypic, and disease-related data for eight species, and a suite of innovative tools for querying, analyzing and visualizing this data. This article provides an overview of recent substantial additions and improvements to RGD’s data and tools that can assist researchers in finding and utilizing the data they need, whether their goal is to develop new precision models of disease or to more fully explore emerging details within a system or across multiple systems.

Longitudinal Transcriptomic Profiling in Carrageenan-Induced Rat Hind Paw Peripheral Inflammation and Hyperalgesia Reveals Progressive Recruitment of Innate Immune System Components

“…To determine pain-related transcriptions, we examined our dataset with the GO term of "sensory perception of pain", which consists of 194 genes from the Rat Genome Database. 50 This analysis identified 37…”

Uncovering Potential Roles of Differentially Expressed Genes, Upstream Regulators, and Canonical Pathways in Endometriosis Using an In Silico Genomics Approach

“…Aldosterone Signaling in Epithelial Cells Pathway: Aldosterone is a mineralocorticoid steroid hormone produced by the adrenal cortex. Aldosterone signaling primarily controls blood pressure and inflammation by regulating its target genes (FKBP5, IGF1, KRAS, PKCε, NCOA1, NCOR1, NEDD4L, SGK, and MR/NR3C2 as per RGD, https://rgd.mcw.edu [68] and IPA). Recent studies have shown the possible involvement of aldosterone in multiple gynecological problems and inflammatory disorders [69].…”

A Multi-Gene Synaptic Plasticity Array Identifies Candidate Molecular Underpinnings of Cognitive and Mood Deficits in Rats with Heart Failure

“…MOET provides an unbiased analysis of groups of genes within each brain region that are functionally related, co-occur and are statistically enriched in a given gene population. To identify functional classes of genes that are statistically over-represented amongst the genes that are differentially expressed during HF, MOET uses the Gene Ontology (GO) consortium, which provides detailed annotations of genes with respect to their known or putative molecular function, cellular localization and biological processes (Smith et al, 2020). where n is the number of genes in our list, N is the number of genes in the reference population, k is the number of genes annotated with this item in our list and M is the number of genes annotated with items in the reference population.…”

“…We then used the Multi Ontology Enrichment Tool (MOET), which provides an unbiased analysis of groups of genes within each brain region that are functionally related, co-occur and are statistically enriched in a given gene population. MOET uses the Gene Ontology (GO) consortium, in order to identify functional classes of genes that are statistically over-represented amongst the genes that are differentially expressed during HF (Smith et al, 2020). For this analysis, we focused on the PFC, DH and CeA, which are the three brain regions that showed the most significant changes in gene expression and are implicated in the measures of mood and memory used in our experiments (see Fig.7; results from the PVN and VH are shown in Supplementary Fig.1.…”