Small non-coding RNAs (e.g. miRNAs) and long non-coding RNAs (e.g. lincRNAs and circRNAs) are emerging as key regulators of various cellular processes. However, only a very small fraction of these enigmatic RNAs have been well functionally characterized. In this study, we describe deepBase v2.0, an updated platform, to decode evolution, expression patterns and functions of diverse ncRNAs across 19 species. deepBase v2.0 has been updated to provide the most comprehensive collection of ncRNA-derived small RNAs generated from 588 sRNA-Seq datasets. Moreover, we developed a pipeline named lncSeeker to identify 176 680 high-confidence lncRNAs from 14 species. Temporal and spatial expression patterns of various ncRNAs were profiled. We identified approximately 24 280 primate-specific, 5193 rodent-specific lncRNAs, and 55 highly conserved lncRNA orthologs between human and zebrafish. We annotated 14 867 human circRNAs, 1260 of which are orthologous to mouse circRNAs. By combining expression profiles and functional genomic annotations, we developed lncFunction web-server to predict the function of lncRNAs based on protein-lncRNA co-expression networks. This study is expected to provide considerable resources to facilitate future experimental studies and to uncover ncRNA functions.
A system-level overview of the deepBase v2.0 core framework. A total of 558 small RNA datasets and 478 RNA-seq datasets were retrieved from NCBI GEO or SRA database. All the small and large noncoding RNAs were identified. The expression, evolution and functions of these ncRNAs were further analyzed. All the results generated by deepBase v2.0 were deposited in MySQL relational databases and displayed in the visual browser and web pages.
Availability – deepBase v2.0 is available at: http://biocenter.sysu.edu.cn/deepBase/
- Zheng LL, Li JH, Wu J, Sun WJ, Liu S, Wang ZL, Zhou H, Yang JH, Qu LH. (2015) deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data. Nucleic Acids Res [Epub ahead of print]. [article]