Introduction
Rhesus Monkey is one of the important primate models widely used in the fields of disease mechanism study, pre-clinical test in drug discovery and molecular evolution. It is significant to study novel gene functions and disease mechanisms in the framework of well-annotated genomic contexts, which could provide state-of-the-art insights from the perspective of comparative genomics, gene regulation, expression patterns and evolutionary clues. However, currently the genomic annotation for rhesus monkey is limited and error-prone: the majority of rhesus gene annotations were putatively mapped from human genome, with only 1% supported by rhesus EST data. We propose that transcript structures in at least 28.7% rhesus macaque genes were mis-annotated by Ensembl annotation system, mainly due to incorrect exon-intron boundaries, incomplete UTRs and missed exons.
RhesusBase was thus developed to refine the Rhesus gene structures to facilitate functional genomics and disease mechanism analyses in multiple fields. As we generated and sequenced more than 1.2 billion 90-bp strand-specific mRNA fragments through RNA-Seq (~20,000-fold of all public Rhesus ESTs, statistics from dbEST, May 2012), we refined gene structures of 28.7% rhesus transcripts. We also integrated more than 60 public and in-house functional annotations for rhesus monkey, to make 'RhesusBase' one-stop resource in genomic medicine research.
Statistics
| Categories | Number |
|---|---|
| Biological Categories | 31 |
| RhesusBase Genes | 22,283 |
| RhesusBase Transcripts | 51,763 |
| Revised Events | 16,665 |
| Revised Transcripts | 12,303 (28.7%) |
| Genes Expression Level Estimated by RNA-Seq | 22,198 |
| Genes Covered by RNA-Seq | 16,462 |
| Total Records in RhesusBase | 5,587,587,788 |
Functions
Cite RhesusBase
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For Gene Page and Genome Browser:
Shi-Jian Zhang, Chu-Jun Liu, Mingming Shi, Lei Kong, Jia-Yu Chen, Wei-Zhen Zhou, Xiaotong Zhu, Peng Yu, Jue Wang, Xinzhuang Yang, Ning Hou, Zhiqiang Ye, Rongli Zhang, Ruiping Xiao, Xiuqin Zhang and Chuan-Yun Li, RhesusBase: a Knowledgebase for the Monkey Research Community, Nucleic Acids Research, 2012. [Abstract, Full text][PubMed] -
For RNA-Seq preparation:
Chen Xie, Yong E. Zhang, Jia-Yu Chen, Chu-Jun Liu, Wei-Zhen Zhou, Ying Li, Mao Zhang, Rongli Zhang, Liping Wei and Chuan-Yun Li, Hominoid-specific De Novo Protein-coding Genes Originating from Long Non-coding RNAs, PLoS Genetics, 2012. [Full text]
