Introduction
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 generated by 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 172 million functional annotation records derived from 1,761 NGS data sets. Especially, We developed Molecular Evolution Gateway, an NGS-oriented genomic framework to access and visualize macaque annotations in reference to human orthologous genes and the associated regulations, and PopGateway, the first genome-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 functional genes and regulatory regions in the primate evolution, and accelerate the pace of the human translational study.
RhesusBase News
More- [2017-10-12] (cover story) Molecular Biology and Evolution: Isoform Evolution in Primates through Independent Combination of Alternative RNA Processing
- [2016-03-21] RhesusBase PopGateway was featured by Molecular Biology and Evolution
- [2016-03-01] Molecular Biology and Evolution: The RhesusBase team release the population genetcis atlas in Rhesus Macaque
- [2015-09-03] The RhesusBase team reports the crosstalk between RNA editing regulation and piRNA biogenesis
- [2015-08-31] The RhesusBase team reports a new mechanism for the origination of functional human-specific proteins
- [2015-06-28] Population Genetics Gateway released!
- [2014-04-10] PLOS Genetics: The RhesusBase team release the RNA editome in Rhesus Macaque
Community News
More- [2016-10-28] Nature: A comprehensive transcriptional map of primate brain development
- [2016-10-24] Nature: Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior
- [2016-02-25] Science: Single Antibody Protects Rhesus Macaques from Ebola
- [2016-01-26] Nature: Autism-like behaviours and germline transmission in transgenic monkeys overexpressing MeCP2
Explore RhesusBase
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1000 Monkey Genomes | Gene Page | UCSC-mode Browser | Molecular Evolution | RhesusBase Quality Score | Drug Discovery | Frequently-used Files |
NGS Datasets Statistics
Categories | Datasets | Total Reads (million) |
---|---|---|
Genome-seq | 31 | 30,610 |
Exome-seq | 11 | 1,054 |
RNA-seq | 266 | 16,332 |
Small RNA-seq | 191 | 1,970 |
CLIP-seq | 7 | 34 |
Poly(A)-seq | 14 | 206 |
ChIP-seq | 1,226 | 28,660 |
ChIA-PET | 15 | 3,885 |
Sum | 1,761 | 82,751 |
Functional Annotation Statistics
Categories | RhesusBase 2013 | RhesusBase 2015 |
---|---|---|
SNPs | 5,682,738 | 66,716,227 |
mRNA Expression Profile | 1,330,884 | 7,183,606 |
Polyadenylation Site | 0 | 1,184,140 |
Alternative Splicing | 0 | 481,865 |
RNA Editing | 0 | 1,369,446 |
miRNA Expression Profile | 0 | 9,395 |
TFBSs | 174,805 | 28,771,628 |
Chromatin Interactions | 0 | 493,236 |
miRNA-targets | 15,909 | 104,041 |
Exon Usage | 0 | 9,884,834 |
Population Genetics Parameters | 0 | 56,057,621 |
Sum | 7,204,336 | 172,256,039 |
Citing RhesusBase
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For Gene Page, Genome Browser, Molecular Evolution Gateway and Population Genetics Gateway:
Xiaoming Zhong et al. RhesusBase PopGateway: Genome-wide Population Genetics Atlas in Rhesus Macaque. Molecular Biology and Evolution, 2016. [PubMed]
Shi-Jian Zhang et al. Evolutionary Interrogation of Human Biology in Well-annotated Genomic Framework of Rhesus Macaque. Molecular Biology and Evolution, 2014. [PubMed]
Shi-Jian Zhang et al. RhesusBase: a Knowledgebase for the Monkey Research Community. Nucleic Acids Research, 2013. [PubMed]
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For In-House NGS Data Preparation:
Xin-Zhuang Yang et al. Selectively Constrained RNA Editing Regulation Crosstalks with piRNA Biogenesis in Primates. Molecular Biology and Evolution, 2015. [PubMed]
Jia-Yu Chen et al. Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates. PLOS Genetics, 2015. [PubMed]
Jia-Yu Chen et al. RNA Editome in Rhesus Macaque Shaped by Purifying Selection. PLOS Genetics, 2014. [PubMed]
Chen Xie et al. Hominoid-specific De Novo Protein-coding Genes Originating from Long Non-coding RNAs. PLoS Genetics, 2012. [PubMed]