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 PopGateway, the first genome-wide effort to identify and visualize the population genetics profile in rhesus monkey, which 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.
- [2015-06-28] Population Genetics Gateway released!
- [2014-04-10] PLOS Genetics: The RhesusBase team release the RNA editome in Rhesus Macaque
- [2014-02-27] Molecular Biology and Evolution: The RhesusBase team identified a catalog of 9,295 human-biased regulatory events
- [2013-12-11] The ABrowse-mode Genome Browser is updated with UCSC-mode Genome Browser
- [2013-10-27] Molecular Evolution Gateway released!
- [2014-10-02] Cell Stem Cell: Generation of Naive Induced Pluripotent Stem Cells from Rhesus Monkey Fibroblasts
- [2014-02-13] TALEN-Mediated Gene Mutagenesis in Rhesus and Cynomolgus Monkeys
- [2014-01-30] Generation of Gene-Modified Cynomolgus Monkey via Cas9/RNA-Mediated Gene Targeting
- [2013-04-18] NIH developed rhesus macaque model to study novel coronavirus infection
|Query||Gene Page||UCSC-mode Browser||Molecular Evolution||RhesusBase Quality Score||Drug Discovery||Frequently-used Files||BioMart Data Portal|
NGS Datasets Statistics
|Categories||Datasets||Total Reads (million)|
Functional Annotation Statistics
|Categories||RhesusBase 2013||RhesusBase 2015|
|mRNA Expression Profile||1,330,884||7,183,606|
|miRNA Expression Profile||0||9,395|
|Population Genetics Parameters||0||56,057,621|
For Gene Page, Genome Browser and Molecular Evolution Gateway:
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]
For In-House NGS Data Preparation:
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]