R3WK60 last accessed: 2022-11-04

Rat Genome Database (RGD)
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:29.812536

rgd
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:29.812536

Other names: RGD, Rat Genome Database (RGD), rgd

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 and via an automated pipeline, giving RGD users integrated access to a wide variety of data to support their research.

Webpage:

https://rgd.mcw.edu/

Licence:

Name: Creative Commons Attribution 4.0 International (CC BY 4.0)
URL: https://creativecommons.org/licenses/by/4.0/

Publications: (8)

Publications
More detailed information about this field from each metasource.

The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease
PMID: 25355511
metasource: Fairsharing.org
version: FAIRsharing.org: RGD; Rat Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pfg82t; Last edited: Feb. 26, 2021, 8:39 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The Rat Genome Database, update 2007--easing the path from disease to data and back again
PMID: 17151068
metasource: Fairsharing.org
version: FAIRsharing.org: RGD; Rat Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pfg82t; Last edited: Feb. 26, 2021, 8:39 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:29.812536

The Rat Genome Database 2009: variation, ontologies and pathways
PMID: 18996890
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:29.812536

A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat
PMID: 10400928
metasource: Fairsharing.org
version: FAIRsharing.org: RGD; Rat Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pfg82t; Last edited: Feb. 26, 2021, 8:39 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform
PMID: 31713623
metasource: Fairsharing.org
version: FAIRsharing.org: RGD; Rat Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pfg82t; Last edited: Feb. 26, 2021, 8:39 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Rat Genome Database (RGD): mapping disease onto the genome
PMID: 11752273
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:29.812536

The Rat Genome Database (RGD): developments towards a phenome database
PMID: 15608243
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:29.812536

The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database
PMID: 27009807
metasource: Fairsharing.org
version: FAIRsharing.org: RGD; Rat Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pfg82t; Last edited: Feb. 26, 2021, 8:39 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease PubMed citations: 128.

128 articles citing: The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease

Comprehensive Assessment of Indian Variations in the Druggable Kinome Landscape Highlights Distinct Insights at the Sequence, Structure and Pharmacogenomic Stratum. PMID:35865963
Genomic changes underlying repeated niche shifts in an adaptive radiation. PMID:35398888
MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses. PMID:35380657
Invertebrate Model Organisms as a Platform to Investigate Rare Human Neurological Diseases. PMID:35256540
Machine learning prediction and tau-based screening identifies potential Alzheimer's disease genes relevant to immunity. PMID:35149761
Association of Genetic Variant at Chromosome 12q23.1 With Neuropathic Pain Susceptibility. PMID:34854908
Normalizing hyperactivity of the Gunn rat with bilirubin-induced neurological disorders via ketanserin. PMID:33790408
Trans-ethnic meta-analysis identifies new loci associated with longitudinal blood pressure traits. PMID:33603002
Characterizing modifier genes of cardiac fibrosis phenotype in hypertrophic cardiomyopathy. PMID:33529666
Sex-dimorphic genetic effects and novel loci for fasting glucose and insulin variability. PMID:33402679
Transforming the study of organisms: Phenomic data models and knowledge bases. PMID:33232313
Genetic Adaptation in New York City Rats. PMID:33211096
The lncRNA LOC102549805 (U1) modulates neurotoxicity of HIV-1 Tat protein. PMID:33033233
Music-listening regulates human microRNA expression. PMID:32867562
Genetic Liability for Internalizing Versus Externalizing Behavior Manifests in the Developing and Adult Hippocampus: Insight From a Meta-analysis of Transcriptional Profiling Studies in a Selectively Bred Rat Model. PMID:32762937
A comprehensive rat transcriptome built from large scale RNA-seq-based annotation. PMID:32749457
HISTome2: a database of histone proteins, modifiers for multiple organisms and epidrugs. PMID:32746900
Underlying Mechanism of Insulin Resistance: A Bioinformatics Analysis Based on Validated Related-Genes from Public Disease Databases. PMID:32651353
Differential methylation and expression of genes in the hypoxia-inducible factor 1 signaling pathway are associated with paclitaxel-induced peripheral neuropathy in breast cancer survivors and with preclinical models of chemotherapy-induced neuropathic pain. PMID:32586194
CYP2J2 Molecular Recognition: A New Axis for Therapeutic Design. PMID:32534953
Gene expression profiles for low-dose exposure to diethyl phthalate in rodents and humans: a translational study with implications for breast carcinogenesis. PMID:32341500
Ischaemic post-conditioning in rats: Responder and non-responder differ in transcriptome of mitochondrial proteins. PMID:32297702
A unified nomenclature for vertebrate olfactory receptors. PMID:32295537
Novel application of normalized pointwise mutual information (NPMI) to mine biomedical literature for gene sets associated with disease: use case in breast carcinogenesis. PMID:32274464
Predicting Outcomes of Rat Vascularized Composite Allotransplants through Quantitative Measurement of Chimerism with PCR-Amplified Short Tandem Repeat. PMID:32090131
Endothelial heterogeneity across distinct vascular beds during homeostasis and inflammation. PMID:31944177
Second Generation Nanoporous Silicon Nitride Membranes for High Toxin Clearance and Small Format Hemodialysis. PMID:31943849
Identification of infectious disease-associated host genes using machine learning techniques. PMID:31881961
The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform. PMID:31713623
The DisGeNET knowledge platform for disease genomics: 2019 update. PMID:31680165
Polyphenol Effects on Cholesterol Metabolism via Bile Acid Biosynthesis, CYP7A1: A Review. PMID:31661763
Using MARRVEL v1.2 for Bioinformatics Analysis of Human Genes and Variant Pathogenicity. PMID:31524990
A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. PMID:31494632
Epigenetic Regulation of Vascular Smooth Muscle Cells by Histone H3 Lysine 9 Dimethylation Attenuates Target Gene-Induction by Inflammatory Signaling. PMID:31434493
Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases. PMID:31328773
Camk2n1 Is a Negative Regulator of Blood Pressure, Left Ventricular Mass, Insulin Sensitivity, and Promotes Adiposity. PMID:31327268
A Novel Open Access Web Portal for Integrating Mechanistic and Toxicogenomic Study Results. PMID:31020328
Music-performance regulates microRNAs in professional musicians. PMID:30956902
Quantitative phenotype analysis to identify, validate and compare rat disease models. PMID:30938777
LasDB: A collective database for laboratory animal strain resources. PMID:30891576
Integrative Analysis of Genome and Expression Profile Data Reveals the Genetic Mechanism of the Diabetic Pathogenesis in Goto Kakizaki (GK) Rats. PMID:30687391
Drug repositioning for dengue haemorrhagic fever by integrating multiple omics analyses. PMID:30679503
BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language. PMID:30576488
Ensembl variation resources. PMID:30576484
RefSeq curation and annotation of stop codon recoding in vertebrates. PMID:30535227
Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer's Disease Data. PMID:30501127
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. PMID:30476213
MitoMiner v4.0: an updated database of mitochondrial localization evidence, phenotypes and diseases. PMID:30398659
RNAcentral: a hub of information for non-coding RNA sequences. PMID:30395267
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
Genenames.org: the HGNC and VGNC resources in 2019. PMID:30304474
H19 contributes to poor clinical features in NSCLC patients and leads to enhanced invasion in A549 cells through regulating miRNA-203-mediated epithelial-mesenchymal transition. PMID:30214583
Computational resources associating diseases with genotypes, phenotypes and exposures. PMID:30102366
MicroRNA interactome analysis predicts post-transcriptional regulation of ADRB2 and PPP3R1 in the hypercholesterolemic myocardium. PMID:29973623
Striatal Rgs4 regulates feeding and susceptibility to diet-induced obesity. PMID:29955167
Experimental evidence for rapid genomic adaptation to a new niche in an adaptive radiation. PMID:29942074
The Cellosaurus, a Cell-Line Knowledge Resource. PMID:29805321
A Primer for the Rat Genome Database (RGD). PMID:29761460
Identification of errors in the IEDB using ontologies. PMID:29688357
FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability. PMID:29688354
Transcriptomic characterization of MRI contrast with focus on the T1-w/T2-w ratio in the cerebral cortex. PMID:29567503
KMgene: a unified R package for gene-based association analysis for complex traits. PMID:29438558
ModuleDiscoverer: Identification of regulatory modules in protein-protein interaction networks. PMID:29323246
Resistant and susceptible chicken lines show distinctive responses to Newcastle disease virus infection in the lung transcriptome. PMID:29281979
Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat. PMID:29272997
Membrane Transporters for Bilirubin and Its Conjugates: A Systematic Review. PMID:29259555
eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality. PMID:29220476
In-Cardiome: integrated knowledgebase for coronary artery disease enabling translational research. PMID:29220465
Differential Expression of Ion Channels in Adult and Neonatal Rat Ventral Respiratory Column. PMID:29170997
Diagnostic and Prognostic Significance of Methionine Uptake and Methionine Positron Emission Tomography Imaging in Gliomas. PMID:29164057
Application of genome editing technologies in rats for human disease models. PMID:29158599
Genetics of hypertension: an assessment of progress in the spontaneously hypertensive rat. PMID:28916635
New Rodent Population Models May Inform Human Health Risk Assessment and Identification of Genetic Susceptibility to Environmental Exposures. PMID:28886592
Expression dynamics and relations with nearby genes of rat transposable elements across 11 organs, 4 developmental stages and both sexes. PMID:28851270
Rat Genome and Model Resources. PMID:28838068
Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse. PMID:28838066
Complement Factor B Is a Determinant of Both Metabolic and Cardiovascular Features of Metabolic Syndrome. PMID:28739975
A data-driven modeling approach to identify disease-specific multi-organ networks driving physiological dysregulation. PMID:28732007
Dynamic regulation of lysine acetylation: the balance between acetyltransferase and deacetylase activities. PMID:28701313
Classification and analysis of a large collection of in vivo bioassay descriptions. PMID:28678787
Gene2Function: An Integrated Online Resource for Gene Function Discovery. PMID:28663344
Naming CRISPR alleles: endonuclease-mediated mutation nomenclature across species. PMID:28589392
MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome. PMID:28502612
Prenatal Exposure to a Maternal High-Fat Diet Affects Histone Modification of Cardiometabolic Genes in Newborn Rats. PMID:28425976
The anatomy of phenotype ontologies: principles, properties and applications. PMID:28387809
Identifying genes for neurobehavioural traits in rodents: progress and pitfalls. PMID:28381599
BRIDG: a domain information model for translational and clinical protocol-driven research. PMID:28339791
ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics. PMID:28316655
Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions. PMID:28176778
Protein Bioinformatics Databases and Resources. PMID:28150231
RAIN: RNA-protein Association and Interaction Networks. PMID:28077569
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants. PMID:27924018
Ensembl 2017. PMID:27899575
Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse. PMID:27899570
Heterozygous connexin 50 mutation affects metabolic syndrome attributes in spontaneously hypertensive rat. PMID:27871290
Titin-truncating variants affect heart function in disease cohorts and the general population. PMID:27869827
Genetic profiling of two phenotypically distinct outbred rats derived from a colony of the Zucker fatty rats maintained at Tokyo Medical University. PMID:27795491
RNAcentral: a comprehensive database of non-coding RNA sequences. PMID:27794554
Strain survey and genetic analysis of vasoreactivity in mouse aorta. PMID:27764765
From integrative genomics to systems genetics in the rat to link genotypes to phenotypes. PMID:27736746
Disease, Models, Variants and Altered Pathways-Journeying RGD Through the Magnifying Glass. PMID:27602200
Predicted Molecular Effects of Sequence Variants Link to System Level of Disease. PMID:27536940
Uncovering the liver's role in immunity through RNA co-expression networks. PMID:27401171
Type 1 Interferons Induce Changes in Core Metabolism that Are Critical for Immune Function. PMID:27332732
An Integrated Data Driven Approach to Drug Repositioning Using Gene-Disease Associations. PMID:27196054
The Chinchilla Research Resource Database: resource for an otolaryngology disease model. PMID:27173523
Genome-Wide Analysis Identifies Germ-Line Risk Factors Associated with Canine Mammary Tumours. PMID:27158822
Candidate gene prioritization with Endeavour. PMID:27131783
JBrowse: a dynamic web platform for genome visualization and analysis. PMID:27072794
RegenBase: a knowledge base of spinal cord injury biology for translational research. PMID:27055827
Vaxar: A Web-Based Database of Laboratory Animal Responses to Vaccinations and Its Application in the Meta-Analysis of Different Animal Responses to Tuberculosis Vaccinations. PMID:27053566
Isolation of a Genomic Region Affecting Most Components of Metabolic Syndrome in a Chromosome-16 Congenic Rat Model. PMID:27031336
Assessing Concordance of Drug-Induced Transcriptional Response in Rodent Liver and Cultured Hepatocytes. PMID:27028627
Temporal Genetic Modifications after Controlled Cortical Impact--Understanding Traumatic Brain Injury through a Systematic Network Approach. PMID:26861311
New Wistar Kyoto and spontaneously hypertensive rat transgenic models with ubiquitous expression of green fluorescent protein. PMID:26769799
Ensembl 2016. PMID:26687719
GeneWeaver: data driven alignment of cross-species genomics in biology and disease. PMID:26656951
Mouse genome database 2016. PMID:26578600
Polygenic inheritance of cryptorchidism susceptibility in the LE/orl rat. PMID:26502805
Associating Multivariate Quantitative Phenotypes with Genetic Variants in Family Samples with a Novel Kernel Machine Regression Method. PMID:26482791
Orthology for comparative genomics in the mouse genome database. PMID:26223881
RefSeq curation and annotation of antizyme and antizyme inhibitor genes in vertebrates. PMID:26170238
Application of comparative biology in GO functional annotation: the mouse model. PMID:26141960
Genome-wide association studies and contribution to cardiovascular physiology. PMID:26106147
Cross-organism analysis using InterMine. PMID:26097192
2015 Guidelines for Establishing Genetically Modified Rat Models for Cardiovascular Research. PMID:25920443
Transparency in Research involving Animals: The Basel Declaration and new principles for reporting research in BJP manuscripts. PMID:25899710
The Rat Genome Database, update 2007--easing the path from disease to data and back again PubMed citations: 77.

77 articles citing: The Rat Genome Database, update 2007--easing the path from disease to data and back again

GABAA receptors in GtoPdb v.2021.3. PMID:35005623
Establishment and application of information resource of mutant mice in RIKEN BioResource Research Center. PMID:33455583
The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform. PMID:31713623
Use of Graph Database for the Integration of Heterogeneous Biological Data. PMID:28416946
A novel gene network analysis in liver tissues of diabetic rats in response to resistant starch treatment. PMID:25789210
Obesity gene atlas in mammals. PMID:25031655
GABAergic neurogliaform cells represent local sources of insulin in the cerebral cortex. PMID:24453306
Comprehensive analysis of single nucleotide polymorphisms in human microRNAs. PMID:24223755
Identification of QTLs involved in the development of amygdala kindling in the rat. PMID:23903052
Whole genome SNP genotyping and exome sequencing reveal novel genetic variants and putative causative genes in congenital hyperinsulinism. PMID:23869231
A novel rat model of hereditary hemochromatosis due to a mutation in transferrin receptor 2. PMID:23582421
Rat mir-155 generated from the lncRNA Bic is 'hidden' in the alternate genomic assembly and reveals the existence of novel mammalian miRNAs and clusters. PMID:23329697
Effects on gene expression in rat liver after administration of RXR agonists: UAB30, 4-methyl-UAB30, and Targretin (Bexarotene). PMID:23292798
Gene family matters: expanding the HGNC resource. PMID:23245209
Genetic basis of the impaired renal myogenic response in FHH rats. PMID:23220727
Using genome-wide expression profiling to define gene networks relevant to the study of complex traits: from RNA integrity to network topology. PMID:23195313
The UCSC Genome Browser database: extensions and updates 2013. PMID:23155063
A novel mutation causing nephronophthisis in the Lewis polycystic kidney rat localises to a conserved RCC1 domain in Nek8. PMID:22899815
Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report. PMID:22434826
MouseFinder: Candidate disease genes from mouse phenotype data. PMID:22331800
Catalog of microRNA seed polymorphisms in vertebrates. PMID:22303453
IntegromeDB: an integrated system and biological search engine. PMID:22260095
Channelpedia: an integrative and interactive database for ion channels. PMID:22232598
Phrenic motoneuron expression of serotonergic and glutamatergic receptors following upper cervical spinal cord injury. PMID:22227062
modMine: flexible access to modENCODE data. PMID:22080565
Disease Ontology: a backbone for disease semantic integration. PMID:22080554
GeneWeaver: a web-based system for integrative functional genomics. PMID:22080549
Integrated genomic approaches to identification of candidate genes underlying metabolic and cardiovascular phenotypes in the spontaneously hypertensive rat. PMID:21846806
Towards resolving the transcription factor network controlling myelin gene expression. PMID:21729871
The Strategies WDK: a graphical search interface and web development kit for functional genomics databases. PMID:21705364
Mitotic spindle proteomics in Chinese hamster ovary cells. PMID:21647379
Physical confirmation and mapping of overlapping rat mammary carcinoma susceptibility QTLs, Mcs2 and Mcs6. PMID:21625632
Animal models to guide clinical drug development in ADHD: lost in translation? PMID:21480864
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. PMID:21472436
Systematic polymorphism discovery after genome-wide identification of potential susceptibility loci in a hereditary rodent model of human hypertension. PMID:21428728
Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection. PMID:21304545
Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction. PMID:21171995
An ontology-based comparative anatomy information system. PMID:21146377
IUPHAR-DB: new receptors and tools for easy searching and visualization of pharmacological data. PMID:21087994
The RIKEN integrated database of mammals. PMID:21076152
Two new ArrayTrack libraries for personalized biomedical research. PMID:20946617
T1DBase: update 2011, organization and presentation of large-scale data sets for type 1 diabetes research. PMID:20937630
genenames.org: the HGNC resources in 2011. PMID:20929869
Meta-analysis of kindling-induced gene expression changes in the rat hippocampus. PMID:20582280
Identification of lipoprotein MslA as a neoteric virulence factor of Mycoplasma gallisepticum. PMID:20515935
Distribution of candidate genes for experimentally induced arthritis in rats. PMID:20196835
HDAPD: a web tool for searching the disease-associated protein structures. PMID:20158919
The mammalian phenotype ontology: enabling robust annotation and comparative analysis. PMID:20052305
Quantitative organellar proteomics analysis of rough endoplasmic reticulum from normal and acute pancreatitis rat pancreas. PMID:19954227
BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. PMID:19919682
Nme protein family evolutionary history, a vertebrate perspective. PMID:19852809
The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community. PMID:19773420
The spontaneously hypertensive rat model of ADHD--the importance of selecting the appropriate reference strain. PMID:19698722
Linking genes to diseases: it's all in the data. PMID:19678910
OmicBrowse: a Flash-based high-performance graphics interface for genomic resources. PMID:19528066
A major QTL for acute ethanol sensitivity in the alcohol tolerant and non-tolerant selected rat lines. PMID:19500156
Practical application of ontologies to annotate and analyse large scale raw mouse phenotype data. PMID:19426459
ABT-510 is an effective chemopreventive agent in the mouse 4-nitroquinoline 1-oxide model of oral carcinogenesis. PMID:19336725
MitoMiner, an integrated database for the storage and analysis of mitochondrial proteomics data. PMID:19208617
PhenoGO: an integrated resource for the multiscale mining of clinical and biological data. PMID:19208196
BioMart--biological queries made easy. PMID:19144180
Genotype-phenotype databases: challenges and solutions for the post-genomic era. PMID:19065136
Behavioral and genetic evidence for a novel animal model of Attention-Deficit/Hyperactivity Disorder Predominantly Inattentive Subtype. PMID:19046438
Genome and proteome annotation: organization, interpretation and integration. PMID:19019817
The UCSC Genome Browser Database: update 2009. PMID:18996895
IUPHAR-DB: the IUPHAR database of G protein-coupled receptors and ion channels. PMID:18948278
The Protein Feature Ontology: a tool for the unification of protein feature annotations. PMID:18936051
OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology. PMID:18925933
Advanced genomic data mining. PMID:18818719
Global liver proteomics of rats exposed for 5 days to phenobarbital identifies changes associated with cancer and with CYP metabolism. PMID:18796496
A gene wiki for community annotation of gene function. PMID:18613750
Onto-CC: a web server for identifying Gene Ontology conceptual clusters. PMID:18544607
What everybody should know about the rat genome and its online resources. PMID:18443589
Comparative genome mapping of the deer mouse (Peromyscus maniculatus) reveals greater similarity to rat (Rattus norvegicus) than to the lab mouse (Mus musculus). PMID:18302785
RGST - Rat Gene Symbol Tracker, a database for defining official rat gene symbols. PMID:18215257
Switch-like genes populate cell communication pathways and are enriched for extracellular proteins. PMID:18177501
Magnetic resonance imaging as a tool for in vivo and ex vivo anatomical phenotyping in experimental genetic models. PMID:17437283
The Rat Genome Database 2009: variation, ontologies and pathways PubMed citations: 49.

49 articles citing: The Rat Genome Database 2009: variation, ontologies and pathways

Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies. PMID:35639796
Single-cell RNA-seq identifies unique transcriptional landscapes of human nucleus pulposus and annulus fibrosus cells. PMID:32943704
The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform. PMID:31713623
HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology. PMID:31255713
A new approach to identifying hypertension-associated genes in the mesenteric artery of spontaneously hypertensive rats and stroke-prone spontaneously hypertensive rats. PMID:30882592
Evaluating whole genome sequence data from the Genetic Absence Epilepsy Rat from Strasbourg and its related non-epileptic strain. PMID:28708842
Drug repurposing for aging research using model organisms. PMID:28620943
histoneHMM: Differential analysis of histone modifications with broad genomic footprints. PMID:25884684
Similarity-based search of model organism, disease and drug effect phenotypes. PMID:25763178
OntoMate: a text-mining tool aiding curation at the Rat Genome Database. PMID:25619558
Community structure detection for overlapping modules through mathematical programming in protein interaction networks. PMID:25412367
Identifying roles of "Jun-Chen-Zuo-Shi" component herbs of QiShenYiQi formula in treating acute myocardial ischemia by network pharmacology. PMID:25342960
GeneSense: a new approach for human gene annotation integrated with protein-protein interaction networks. PMID:24667292
Differential evolutionary constraints in the evolution of chemoreceptors: a murine and human case study. PMID:24587745
The pathway ontology - updates and applications. PMID:24499703
RefSeq: an update on mammalian reference sequences. PMID:24259432
Quantification of the impact of PSI:Biology according to the annotations of the determined structures. PMID:24139526
Targeting the endothelial progenitor cell surface proteome to identify novel mechanisms that mediate angiogenic efficacy in a rodent model of vascular disease. PMID:24022221
Genetic and phenotypic characterization of a Japanese wild-derived DOB/Oda rat strain. PMID:23896813
An integrative, translational approach to understanding rare and orphan genetically based diseases. PMID:23853703
Community Structure Analysis of Gene Interaction Networks in Duchenne Muscular Dystrophy. PMID:23840633
CHD@ZJU: a knowledgebase providing network-based research platform on coronary heart disease. PMID:23818526
PosMed: Ranking genes and bioresources based on Semantic Web Association Study. PMID:23761449
STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation. PMID:23409969
Novel genes underlying beta cell survival in metabolic stress. PMID:23390342
Rat mir-155 generated from the lncRNA Bic is 'hidden' in the alternate genomic assembly and reveals the existence of novel mammalian miRNAs and clusters. PMID:23329697
Exploring genetic, genomic, and phenotypic data at the rat genome database. PMID:23255149
Genenames.org: the HGNC resources in 2013. PMID:23161694
IUPHAR-DB: updated database content and new features. PMID:23087376
The long path from QTL to gene. PMID:23049490
CD36-deficient congenic strains show improved glucose tolerance and distinct shifts in metabolic and transcriptomic profiles. PMID:22473311
The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse. PMID:22075990
The emerging role for rat models in gene discovery. PMID:21732192
Animal models to guide clinical drug development in ADHD: lost in translation? PMID:21480864
The Rat Genome Database pathway portal. PMID:21478484
Analyses of copy number variation of GK rat reveal new putative type 2 diabetes susceptibility loci. PMID:21124896
The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. PMID:21051359
Genomic architecture of MHC-linked odorant receptor gene repertoires among 16 vertebrate species. PMID:20680261
Pharmacogenetic interaction between dexamethasone and Cd36-deficient segment of spontaneously hypertensive rat chromosome 4 affects triacylglycerol and cholesterol distribution into lipoprotein fractions. PMID:20398376
Online tools for understanding rat physiology. PMID:20056729
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. PMID:20015972
The Protein Naming Utility: a rules database for protein nomenclature. PMID:20007151
The UCSC Genome Browser. PMID:19957273
The rat genome database curators: who, what, where, why. PMID:19956751
NBRP databases: databases of biological resources in Japan. PMID:19934255
The Proteomics Identifications database: 2010 update. PMID:19906717
Ensembl's 10th year. PMID:19906699
Next generation software for functional trend analysis. PMID:19717575
PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning. PMID:19468046
A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat PubMed citations: 47.

47 articles citing: A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat

The tweety Gene Family: From Embryo to Disease. PMID:34262434
Genetic boundary and gene flow between 2 parapatric subspecies of brown rats. PMID:33391367
Predicted rat interactome database and gene set linkage analysis. PMID:33216897
Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats. PMID:32398234
The differences in brain stem transcriptional profiling in hypertensive ISIAH and normotensive WAG rats. PMID:32039698
A High-Resolution Genetic Map for the Laboratory Rat. PMID:29760201
Epidemiological Distribution of Rodents as Potent Reservoirs for Infectious Diseases in the Provinces of Mazandaran, Gilan and Golestan, Northern Iran. PMID:28626537
Mapping of Mcs30, a new mammary carcinoma susceptibility quantitative trait locus (QTL30) on rat chromosome 12: identification of fry as a candidate Mcs gene. PMID:24023717
A novel mutation causing nephronophthisis in the Lewis polycystic kidney rat localises to a conserved RCC1 domain in Nek8. PMID:22899815
Evolution of the genomic recombination rate in murid rodents. PMID:21149647
A novel active endogenous retrovirus family contributes to genome variability in rat inbred strains. PMID:19887576
Genetic determinants of hypertension: an update. PMID:18959837
Genetically hypertensive Brown Norway congenic rat strains suggest intermediate traits underlying genetic hypertension. PMID:18925692
A set of highly informative rat simple sequence length polymorphism (SSLP) markers and genetically defined rat strains. PMID:16584579
The multigene family of fatty acid-binding proteins (FABPs): function, structure and polymorphism. PMID:16424607
Efficient single nucleotide polymorphism discovery in laboratory rat strains using wild rat-derived SNP candidates. PMID:16316463
RECORD: a novel method for ordering loci on a genetic linkage map. PMID:16228189
Tools and strategies for physiological genomics: the Rat Genome Database. PMID:16106031
A comprehensive expressed sequence tag linkage map for tiger salamander and Mexican axolotl: enabling gene mapping and comparative genomics in Ambystoma. PMID:16079226
The Rat Genome Database (RGD): developments towards a phenome database. PMID:15608243
Integrating linkage and radiation hybrid mapping data for bovine chromosome 15. PMID:15473903
Genetic variation in coding regions between and within commonly used inbred rat strains. PMID:15231744
BAC resources for the rat genome project. PMID:15060022
Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome. PMID:15060021
Integration of the rat recombination and EST maps in the rat genomic sequence and comparative mapping analysis with the mouse genome. PMID:15060020
High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. PMID:15060019
Integrative genomics: in silico coupling of rat physiology and complex traits with mouse and human data. PMID:15060006
Comparative recombination rates in the rat, mouse, and human genomes. PMID:15059993
Terminological mapping for high throughput comparative biology of phenotypes. PMID:14992504
Functional genomics in rodent models of hypertension. PMID:14678491
Application of chromosomal substitution techniques in gene-function discovery. PMID:14678490
Sequencing and chromosomal localization of Fabp6 and an intronless Fabp6 segment in the rat. PMID:12974472
A new framework marker-based linkage map and SDPs for the rat HXB/BXH strain set. PMID:12925886
Marker-assisted congenic screening (MACS): a database tool for the efficient production and characterization of congenic lines. PMID:12856287
OntoBlast function: From sequence similarities directly to potential functional annotations by ontology terms. PMID:12824422
The comprehensive mouse radiation hybrid map densely cross-referenced to the recombination map: a tool to support the sequence assemblies. PMID:12529315
RTPrimerDB: the real-time PCR primer and probe database. PMID:12519963
Lymphopenia in the BB rat model of type 1 diabetes is due to a mutation in a novel immune-associated nucleotide (Ian)-related gene. PMID:12097339
Expression and fine mapping of murine vasoactive intestinal peptide receptor 1. PMID:11859927
Rat Genome Database (RGD): mapping disease onto the genome. PMID:11752273
Automated construction of high-density comparative maps between rat, human, and mouse. PMID:11691858
Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. PMID:11483586
Genetic rat models of hypertension: relationship to human hypertension. PMID:11276399
Generation of a high-density rat EST map. PMID:11230173
Strategy for uncovering complex determinants of hypertension using animal models. PMID:10981152
A radiation hybrid map of the cat genome: implications for comparative mapping. PMID:10810092
Interspersed repetitive sequence (IRS)-PCR for typing of whole genome radiation hybrid panels. PMID:10606675
The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform PubMed citations: 39.

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

Body Composition and Metabolic Changes in a Lyon Hypertensive Congenic Rat and Identification of Ercc6l2 as a Positional Candidate Gene. PMID:35812759
Centralizing neurofibromatosis experimental tool knowledge with the NF Research Tools Database. PMID:35735230
Preventive aerobic training preserves sympathovagal function and improves DNA repair capacity of peripheral blood mononuclear cells in rats with cardiomyopathy. PMID:35440673
SwissBioPics-an interactive library of cell images for the visualization of subcellular location data. PMID:35411389
TNF-α Induced Myotube Atrophy in C2C12 Cell Line Uncovers Putative Inflammatory-Related lncRNAs Mediating Muscle Wasting. PMID:35409236
Harmonizing model organism data in the Alliance of Genome Resources. PMID:35380658
MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses. PMID:35380657
Systems genetics in the rat HXB/BXH family identifies Tti2 as a pleiotropic quantitative trait gene for adult hippocampal neurogenesis and serum glucose. PMID:35377872
Generation and network analysis of an RNA-seq transcriptional atlas for the rat. PMID:35265836
Genome-wide linkage analysis combined with genome sequencing in large families with intracranial aneurysms. PMID:35228681
Analysis of Genomic Alternative Splicing Patterns in Rat under Heat Stress Based on RNA-Seq Data. PMID:35205403
Exercise-Induced Extracellular Vesicles Delay the Progression of Prostate Cancer. PMID:35087866
Research-Relevant Conditions and Pathology of Laboratory Mice, Rats, Gerbils, Guinea Pigs, Hamsters, Naked Mole Rats, and Rabbits. PMID:34979559
The Human Disease Ontology 2022 update. PMID:34755882
The Rat Genome Database (RGD) facilitates genomic and phenotypic data integration across multiple species for biomedical research. PMID:34741192
Magnolol upregulates CHRM1 to attenuate Amyloid-β-triggered neuronal injury through regulating the cAMP/PKA/CREB pathway. PMID:34705126
Mouse Genome Informatics (MGI): latest news from MGD and GXD. PMID:34698891
Integrative Map of HIF1A Regulatory Elements and Variations. PMID:34680921
The human hepatocyte TXG-MAPr: gene co-expression network modules to support mechanism-based risk assessment. PMID:34626214
Domestication Explains Two-Thirds of Differential-Gene-Expression Variance between Domestic and Wild Animals; The Remaining One-Third Reflects Intraspecific and Interspecific Variation. PMID:34573632
Longitudinal peripheral tissue RNA-Seq transcriptomic profiling, hyperalgesia, and wound healing in the rat plantar surgical incision model. PMID:34499774
Development of mammary cancer in γ-irradiated F1 hybrids of susceptible Sprague-Dawley and resistant Copenhagen rats, with copy-number losses that pinpoint potential tumor suppressors. PMID:34388197
Coding variants in mouse and rat model organisms: mousepost and ratpost. PMID:34313794
Updates to HCOP: the HGNC comparison of orthology predictions tool. PMID:33959747
Advances in Genome Editing and Application to the Generation of Genetically Modified Rat Models. PMID:33959146
Dynamic miRNA changes during the process of epileptogenesis in an infantile and adult-onset model. PMID:33958654
The Cocaine and Oxycodone Biobanks, Two Repositories from Genetically Diverse and Behaviorally Characterized Rats for the Study of Addiction. PMID:33875455
Network-Based Analysis of Cognitive Impairment and Memory Deficits from Transcriptome Data. PMID:33713319
Ellagic Acid Affects Metabolic and Transcriptomic Profiles and Attenuates Features of Metabolic Syndrome in Adult Male Rats. PMID:33671116
Human pathways in animal models: possibilities and limitations. PMID:33524155
Frameshift Variant in Novel Adenosine-A1-Receptor Homolog Associated With Bovine Spastic Syndrome/Late-Onset Bovine Spastic Paresis in Holstein Sires. PMID:33329738
Longitudinal Transcriptomic Profiling in Carrageenan-Induced Rat Hind Paw Peripheral Inflammation and Hyperalgesia Reveals Progressive Recruitment of Innate Immune System Components. PMID:33227508
TCRD and Pharos 2021: mining the human proteome for disease biology. PMID:33156327
Genenames.org: the HGNC and VGNC resources in 2021. PMID:33152070
Protein ontology on the semantic web for knowledge discovery. PMID:33046717
Uncovering Potential Roles of Differentially Expressed Genes, Upstream Regulators, and Canonical Pathways in Endometriosis Using an In Silico Genomics Approach. PMID:32575462
Automated generation of gene summaries at the Alliance of Genome Resources. PMID:32559296
GJB4 and GJC3 variants in non-syndromic hearing impairment in Ghana. PMID:32524838
The 27th annual Nucleic Acids Research database issue and molecular biology database collection. PMID:31906604