title: PceRBase: a database of plant competing endogenous RNA.
abstract: Competition for microRNA (miRNA) binding between RNA molecules has emerged as a novel mechanism for the regulation of eukaryotic gene expression. Competing endogenous RNA (ceRNA) can act as decoys for miRNA binding, thereby forming a ceRNA network by regulating the abundance of other RNA transcripts which share the same or similar microRNA response elements. Although this type of RNA cross talk was first described in Arabidopsis, and was subsequently shown to be active in animal models, there is no database collecting potential ceRNA data for plants. We have developed a Plant ceRNA database (PceRBase, http://bis.zju.edu.cn/pcernadb/index.jsp) which contains potential ceRNA target-target, and ceRNA target-mimic pairs from 26 plant species. For example, in Arabidopsis lyrata, 311 candidate ceRNAs are identified which could affect 2646 target-miRNA-target interactions. Predicted pairing structure between miRNAs and their target mRNA transcripts, expression levels of ceRNA pairs and associated GO annotations are also stored in the database. A web interface provides convenient browsing and searching for specific genes of interest. Tools are available for the visualization and enrichment analysis of genes in the ceRNA networks. Moreover, users can use PceRBase to predict novel competing mimic-target and target-target interactions from their own data.
authors.affiliation: Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
authors.forename: Chunhui
authors.initials: C
authors.lastname: Yuan
authors.affiliation: Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
authors.forename: Xianwen
authors.initials: X
authors.lastname: Meng
authors.affiliation: Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.|James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China.
authors.forename: Xue
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa.
authors.forename: Nicola
authors.initials: N
authors.lastname: Illing
authors.affiliation: Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Ingle
authors.affiliation: Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.|James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China.
authors.forename: Jingjing
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, College of Life Sciences, Zhejiang University, Hangzhou 310058, China mchen@zju.edu.cn.|James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China.
authors.forename: Ming
authors.initials: M
authors.lastname: Chen
mesh_terms: D019295:Computational Biology / Q000379:methods; D030561:Databases, Nucleic Acid; D018506:Gene Expression Regulation, Plant; D035683:MicroRNAs / Q000235:genetics; D010944:Plants / Q000235:genetics*; D034622:RNA Interference; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant; D057386:Search Engine; D012984:Software; D064878:Web Browser
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D018749:RNA, Plant