title: PmiRKB: a plant microRNA knowledge base.
abstract: MicroRNAs (miRNAs), one type of small RNAs (sRNAs) in plants, play an essential role in gene regulation. Several miRNA databases were established; however, successively generated new datasets need to be collected, organized and analyzed. To this end, we have constructed a plant miRNA knowledge base (PmiRKB) that provides four major functional modules. In the 'SNP' module, single nucleotide polymorphism (SNP) data of seven Arabidopsis (Arabidopsis thaliana) accessions and 21 rice (Oryza sativa) subspecies were collected to inspect the SNPs within pre-miRNAs (precursor microRNAs) and miRNA-target RNA duplexes. Depending on their locations, SNPs can affect the secondary structures of pre-miRNAs, or interactions between miRNAs and their targets. A second module, 'Pri-miR', can be used to investigate the tissue-specific, transcriptional contexts of pre- and pri-miRNAs (primary microRNAs), based on massively parallel signature sequencing data. The third module, 'MiR-Tar', was designed to validate thousands of miRNA-target pairs by using parallel analysis of RNA end (PARE) data. Correspondingly, the fourth module, 'Self-reg', also used PARE data to investigate the metabolism of miRNA precursors, including precursor processing and miRNA- or miRNA*-mediated self-regulation effects on their host precursors. PmiRKB can be freely accessed at http://bis.zju.edu.cn/pmirkb/.
authors: Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry and Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China.
authors: Yijun
authors: Y
authors: Meng
authors: Lingfeng
authors: L
authors: Gou
authors: Dijun
authors: D
authors: Chen
authors: Chuanzao
authors: C
authors: Mao
authors: Yongfeng
authors: Y
authors: Jin
authors: Ping
authors: P
authors: Wu
authors: Ming
authors: M
authors: Chen
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D030561:Databases, Nucleic Acid; D005786:Gene Expression Regulation; D051188:Knowledge Bases; D035683:MicroRNAs / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012275:Oryza / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D012322:RNA Precursors / Q000737:chemistry / Q000378:metabolism; D018749:RNA, Plant; D017423:Sequence Analysis, RNA
chemical_list: D035683:MicroRNAs; D012322:RNA Precursors; D018749:RNA, Plant