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.

Explore RhesusBase

1KMG Gene Page UCSC-mode Browser Molecular Evolution RhesusBase Quality Score Drug Discovery FUT
1000 Monkey GenomesGene PageUCSC-mode BrowserMolecular EvolutionRhesusBase Quality ScoreDrug Discovery Frequently-used Files

NGS Datasets Statistics

CategoriesDatasetsTotal Reads (million)
Genome-seq3130,610
Exome-seq111,054
RNA-seq26616,332
Small RNA-seq1911,970
CLIP-seq734
Poly(A)-seq14206
ChIP-seq1,22628,660
ChIA-PET153,885
Sum1,76182,751

Functional Annotation Statistics

CategoriesRhesusBase 2013RhesusBase 2015
SNPs5,682,73866,716,227
mRNA Expression Profile1,330,8847,183,606
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
Exon Usage09,884,834
Population Genetics Parameters056,057,621
Sum7,204,336172,256,039

Citing RhesusBase