RhesusBase
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A comprehensive online knowledgebase for the monkey research community.
Description
More detailed information about this field from each metasource.
A comprehensive online knowledgebase for the monkey research community.
metasource: Fairsharing.orgversion: FAIRsharing.org: RhesusBase; RhesusBase; DOI: https://doi.org/10.25504/FAIRsharing.qkrmth; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
With human-comparable genome sequence and the advantages as model animal, rhesus macaque poses a unique model in molecular and translational study of human diseases.It is significant to study human biology in the framework of well-annotated macaque genomic contexts,while key issues regarding this animal model remain poorly addressed-the limited genomic annotation,the putative gene structure, and scarce platform to handle genomics data in the era of next-generation sequencing (NGS). RhesusBase was thus developed to refine genome-wide macaque gene structures, to integrate macaque functional annotations,and to provide a 'one-stop' knowledgebase for the primate research community. 28.7% of the rhesus macaque transcripts were convincingly revised on the basis of ~1.2 billion RNA-Seq reads generatedby strand-specific mRNA sequencing in ten macaque tissues (covering >97.4% of macaque exons).Functional genomics annotations from >60 categories of public and in-house resources were integrated, and multiple interfaces were developed to update,retrieve, visualize, and download the RhesusBase meta-data (Zhang et al, Nucleic Acids Res, 2012).Following the rapid pace of NGS technologies, RhesusBase was updated on the transcriptome and regulatory annotations annually, with the current version of the database containing 172million functional annotation records derived from 1,761 NGS data sets. Especially, We developed Molecular Evolution Gateway, an NGS-orientedgenomic framework to access and visualize macaque annotations in reference to human orthologous genes and the associated regulations, and PopGateway, the firstgenome-wide effort to identify and visualize the population genetics profile in rhesus monkey. Overall, RhesusBase would help the primate research community to clarify the fundamental questions in human biology, underscore functionalgenes and regulatory regions in the primate evolution, and accelerate the pace of the human translational study.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://www.rhesusbase.orgWebpage
More detailed information about this field from each metasource.
http://www.rhesusbase.org
metasource: Fairsharing.orgversion: FAIRsharing.org: RhesusBase; RhesusBase; DOI: https://doi.org/10.25504/FAIRsharing.qkrmth; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://rhesusbase.cbi.pku.edu.cn/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Publications:
Publications
More detailed information about this field from each metasource.
Evolutionary interrogation of human biology in well-annotated genomic framework of rhesus macaque
PMID: 24577841
metasource: Fairsharing.org
version: FAIRsharing.org: RhesusBase; RhesusBase; DOI: https://doi.org/10.25504/FAIRsharing.qkrmth; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
RhesusBase: a knowledgebase for the monkey research community
PMID: 22965133
metasource: Fairsharing.org
version: FAIRsharing.org: RhesusBase; RhesusBase; DOI: https://doi.org/10.25504/FAIRsharing.qkrmth; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
RhesusBase PopGateway: Genome-Wide Population Genetics Atlas in Rhesus Macaque
PMID: 26882984
metasource: Fairsharing.org
version: FAIRsharing.org: RhesusBase; RhesusBase; DOI: https://doi.org/10.25504/FAIRsharing.qkrmth; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://dx.doi.org/10.1093/nar/gks835
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
Evolutionary interrogation of human biology in well-annotated genomic framework of rhesus macaque
PMID: 24577841
metasource: Fairsharing.org
version: FAIRsharing.org: RhesusBase; RhesusBase; DOI: https://doi.org/10.25504/FAIRsharing.qkrmth; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
RhesusBase: a knowledgebase for the monkey research community
PMID: 22965133
metasource: Fairsharing.org
version: FAIRsharing.org: RhesusBase; RhesusBase; DOI: https://doi.org/10.25504/FAIRsharing.qkrmth; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
RhesusBase PopGateway: Genome-Wide Population Genetics Atlas in Rhesus Macaque
PMID: 26882984
metasource: Fairsharing.org
version: FAIRsharing.org: RhesusBase; RhesusBase; DOI: https://doi.org/10.25504/FAIRsharing.qkrmth; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://dx.doi.org/10.1093/nar/gks835
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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Evolutionary interrogation of human biology in well-annotated genomic framework of rhesus macaque
PubMed citations: 24.
24 articles citing: Evolutionary interrogation of human biology in well-annotated genomic framework of rhesus macaque
Adaptive Proteome Diversification by Nonsynonymous A-to-I RNA Editing in Coleoid Cephalopods. PMID:34022057
Polyadenylation-related isoform switching in human evolution revealed by full-length transcript structure. PMID:33973996
Functional and Adaptive Significance of Promoter Mutations That Affect Divergent Myocardial Expressions of TRIM72 in Primates. PMID:33744959
Genetic Diversity, Inbreeding Level, and Genetic Load in Endangered Snub-Nosed Monkeys (Rhinopithecus). PMID:33384722
Histone deacetylase HDA-1 modulates mitochondrial stress response and longevity. PMID:32934238
Animal-ImputeDB: a comprehensive database with multiple animal reference panels for genotype imputation. PMID:31584087
Central role of IP3R2-mediated Ca2+ oscillation in self-renewal of liver cancer stem cells elucidated by high-signal ER sensor. PMID:31113961
Evolutionarily significant A-to-I RNA editing events originated through G-to-A mutations in primates. PMID:30712515
Characterization of spontaneously-developed non-alcoholic fatty liver disease in aged rhesus monkeys. PMID:30214501
Human exonization through differential nucleosome occupancy. PMID:30104384
Deficiency of PRKD2 triggers hyperinsulinemia and metabolic disorders. PMID:29789568
Isoform Evolution in Primates through Independent Combination of Alternative RNA Processing Events. PMID:28957512
Spliceosomal protein eftud2 mutation leads to p53-dependent apoptosis in zebrafish neural progenitors. PMID:27899647
RhesusBase PopGateway: Genome-Wide Population Genetics Atlas in Rhesus Macaque. PMID:26882984
Small activating RNA binds to the genomic target site in a seed-region-dependent manner. PMID:26873922
Selectively Constrained RNA Editing Regulation Crosstalks with piRNA Biogenesis in Primates. PMID:26341297
Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates. PMID:26177073
Functional Impact of RNA editing and ADARs on regulation of gene expression: perspectives from deep sequencing studies. PMID:25949793
GASS: genome structural annotation for Eukaryotes based on species similarity. PMID:25764973
Epigenetic modifications are associated with inter-species gene expression variation in primates. PMID:25468404
Comparative transcriptomics and metabolomics in a rhesus macaque drug administration study. PMID:25453034
Species differences in cannabinoid receptor 2 and receptor responses to cocaine self-administration in mice and rats. PMID:25374096
AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors. PMID:25262351
RNA editome in rhesus macaque shaped by purifying selection. PMID:24722121 -
RhesusBase: a knowledgebase for the monkey research community
PubMed citations: 23.
23 articles citing: RhesusBase: a knowledgebase for the monkey research community
Genomic resources for rhesus macaques (Macaca mulatta). PMID:34999909
Polyadenylation-related isoform switching in human evolution revealed by full-length transcript structure. PMID:33973996
MACSNVdb: a high-quality SNV database for interspecies genetic divergence investigation among macaques. PMID:32367112
Database Resources of the BIG Data Center in 2019. PMID:30365034
Comparative genome-wide survey of single nucleotide variation uncovers the genetic diversity and potential biomedical applications among six Macaca species. PMID:30314376
Characterization of spontaneously-developed non-alcoholic fatty liver disease in aged rhesus monkeys. PMID:30214501
Deficiency of PRKD2 triggers hyperinsulinemia and metabolic disorders. PMID:29789568
Transcriptome profiling of individual rhesus macaque oocytes and preimplantation embryos. PMID:29025079
dbCoRC: a database of core transcriptional regulatory circuitries modeled by H3K27ac ChIP-seq signals. PMID:28977473
Isoform Evolution in Primates through Independent Combination of Alternative RNA Processing Events. PMID:28957512
Extensive ceRNA-ceRNA interaction networks mediated by miRNAs regulate development in multiple rhesus tissues. PMID:27365046
RhesusBase PopGateway: Genome-Wide Population Genetics Atlas in Rhesus Macaque. PMID:26882984
Selectively Constrained RNA Editing Regulation Crosstalks with piRNA Biogenesis in Primates. PMID:26341297
Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates. PMID:26177073
The BioMart community portal: an innovative alternative to large, centralized data repositories. PMID:25897122
GASS: genome structural annotation for Eukaryotes based on species similarity. PMID:25764973
Lassa and Marburg viruses elicit distinct host transcriptional responses early after infection. PMID:25377889
Species differences in cannabinoid receptor 2 and receptor responses to cocaine self-administration in mice and rats. PMID:25374096
A new rhesus macaque assembly and annotation for next-generation sequencing analyses. PMID:25319552
AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors. PMID:25262351
RNA editome in rhesus macaque shaped by purifying selection. PMID:24722121
Evolutionary interrogation of human biology in well-annotated genomic framework of rhesus macaque. PMID:24577841
The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection. PMID:23203983 -
RhesusBase PopGateway: Genome-Wide Population Genetics Atlas in Rhesus Macaque
PubMed citations: 13.
13 articles citing: RhesusBase PopGateway: Genome-Wide Population Genetics Atlas in Rhesus Macaque
Genomic resources for rhesus macaques (Macaca mulatta). PMID:34999909
Polyadenylation-related isoform switching in human evolution revealed by full-length transcript structure. PMID:33973996
Genomic Copy Number Variation Study of Nine Macaca Species Provides New Insights into Their Genetic Divergence, Adaptation, and Biomedical Application. PMID:32970804
Animal-ImputeDB: a comprehensive database with multiple animal reference panels for genotype imputation. PMID:31584087
Evolutionarily significant A-to-I RNA editing events originated through G-to-A mutations in primates. PMID:30712515
Comparative genome-wide survey of single nucleotide variation uncovers the genetic diversity and potential biomedical applications among six Macaca species. PMID:30314376
Characterization of spontaneously-developed non-alcoholic fatty liver disease in aged rhesus monkeys. PMID:30214501
Population genomics of wild Chinese rhesus macaques reveals a dynamic demographic history and local adaptation, with implications for biomedical research. PMID:30165519
Computational resources associating diseases with genotypes, phenotypes and exposures. PMID:30102366
Deficiency of PRKD2 triggers hyperinsulinemia and metabolic disorders. PMID:29789568
Identification and characterization of short tandem repeats in the Tibetan macaque genome based on resequencing data. PMID:29643326
Isoform Evolution in Primates through Independent Combination of Alternative RNA Processing Events. PMID:28957512
Genomic Tools for the Use of Nonhuman Primates in Translational Research. PMID:28838069 - http://dx.doi.org/10.1093/nar/gks835
Tags:
Tags
More detailed information about this field from each metasource.
gene
metasource: Fairsharing.org
version: FAIRsharing.org: RhesusBase; RhesusBase; DOI: https://doi.org/10.25504/FAIRsharing.qkrmth; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
gene model annotation
metasource: Fairsharing.org
version: FAIRsharing.org: RhesusBase; RhesusBase; DOI: https://doi.org/10.25504/FAIRsharing.qkrmth; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
pseudogene
metasource: Fairsharing.org
version: FAIRsharing.org: RhesusBase; RhesusBase; DOI: https://doi.org/10.25504/FAIRsharing.qkrmth; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
human and other vertebrate genomes
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
model organisms, comparative genomics
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Tags
More detailed information about this field from each metasource.
gene
metasource: Fairsharing.orgversion: FAIRsharing.org: RhesusBase; RhesusBase; DOI: https://doi.org/10.25504/FAIRsharing.qkrmth; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
gene model annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: RhesusBase; RhesusBase; DOI: https://doi.org/10.25504/FAIRsharing.qkrmth; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
pseudogene
metasource: Fairsharing.orgversion: FAIRsharing.org: RhesusBase; RhesusBase; DOI: https://doi.org/10.25504/FAIRsharing.qkrmth; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
human and other vertebrate genomes
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
model organisms, comparative genomics
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
gene gene model annotation pseudogene human and other vertebrate genomes model organisms
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