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, 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).

Explore RhesusBase

Query Gene Page UCSC-mode Browser Molecular Evolution RhesusBase Quality Score Drug Discovery FUT BioMart
QueryGene PageUCSC-mode BrowserMolecular EvolutionRhesusBase Quality ScoreDrug Discovery Frequently-used FilesBioMart Data Portal

NGS Datasets Statistics

CategoriesDatasetsTotal Reads (million)
Genome-seq12,173
Exome-seq111,054
RNA-seq20210,679
Small RNA-seq1911,970
CLIP-seq734
Poly(A)-seq14206
ChIP-seq1,22628,660
ChIA-PET153,885
Sum1,66748,661

Functional Annotation Statistics

CategoriesRhesusBase v1.0RhesusBase v2.0
SNPs5,682,73820,327,025
mRNA Expression Profile1,330,8845,682,934
Polyadenylation Site01,184,140
Alternative Splicing0481,865
RNA Editing01,369,446
miRNA Expression Profile09,395
TFBSs174,80528,771,628
Chromatin Interactions0493,236
miRNA-targets15,909104,041
Sum7,204,33658,423,710

Citing RhesusBase