title: deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data.
abstract: 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 (http://biocenter.sysu.edu.cn/deepBase/), 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.
authors.affiliation: RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P.R. China.
authors.forename: Ling-Ling
authors.initials: LL
authors.lastname: Zheng
authors.affiliation: RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P.R. China.
authors.forename: Jun-Hao
authors.initials: JH
authors.lastname: Li
authors.affiliation: RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P.R. China.
authors.forename: Jie
authors.initials: J
authors.lastname: Wu
authors.affiliation: RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P.R. China.
authors.forename: Wen-Ju
authors.initials: WJ
authors.lastname: Sun
authors.affiliation: RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P.R. China.
authors.forename: Shun
authors.initials: S
authors.lastname: Liu
authors.affiliation: RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P.R. China.
authors.forename: Ze-Lin
authors.initials: ZL
authors.lastname: Wang
authors.affiliation: RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P.R. China.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhou
authors.affiliation: RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P.R. China lssqlh@mail.sysu.edu.cn.
authors.forename: Jian-Hua
authors.initials: JH
authors.lastname: Yang
authors.affiliation: RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P.R. China lssqlh@mail.sysu.edu.cn.
authors.forename: Liang-Hu
authors.initials: LH
authors.lastname: Qu
mesh_terms: D000818:Animals; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D051379:Mice; D058977:Molecular Sequence Annotation; D012313:RNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D000079962:RNA, Circular; D062085:RNA, Long Noncoding / Q000737:chemistry / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D000079962:RNA, Circular; D062085:RNA, Long Noncoding; D058727:RNA, Small Untranslated; D012313:RNA