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, we release RhesusBase2 on June 28th 2013, an extensively improved version of RhesusBase, with 1,667 NGS datasets integrated (48.7 billion reads processed), 51.2 million new functional annotation records added, and multiple user-friendly interfaces developed to enhance the utilities of RhesusBase in NGS data visualization. Especially, we developed the Molecular Evolution Gateway, an NGS-oriented genomic framework to access and visualize macaque annotations in reference to human orthologous genes and the associated regulations (Zhang et al, Molecular Biology and Evolution, 2014).
- [2014-02-27] RhesusBase v2.0 is published on Molecular Biology and Evolution
- [2013-12-11] The ABrowse-mode Genome Browser is updated with UCSC-mode Genome Browser
- [2013-10-27] Molecular Evolution Gateway released!
- [2013-06-28] RhesusBase v2.0 released!
- [2013-05-31] RhesusBase releases a user-friendly interface -- UCSC-mode Browser
- [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
- [2012-09-13] Paper entitled 'Hominoid-Specific De Novo Protein-Coding Genes Originating from Long Non-Coding RNAs' is published
|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 v1.0||RhesusBase v2.0|
|mRNA Expression Profile||1,330,884||5,682,934|
|miRNA Expression Profile||0||9,395|
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. Accepted by PLOS Genetics, 2014.
Chen Xie et al. Hominoid-specific De Novo Protein-coding Genes Originating from Long Non-coding RNAs. PLoS Genetics, 2012. [PubMed]