title: PmiRExAt: plant miRNA expression atlas database and web applications.
abstract: High-throughput small RNA (sRNA) sequencing technology enables an entirely new perspective for plant microRNA (miRNA) research and has immense potential to unravel regulatory networks. Novel insights gained through data mining in publically available rich resource of sRNA data will help in designing biotechnology-based approaches for crop improvement to enhance plant yield and nutritional value. Bioinformatics resources enabling meta-analysis of miRNA expression across multiple plant species are still evolving. Here, we report PmiRExAt, a new online database resource that caters plant miRNA expression atlas. The web-based repository comprises of miRNA expression profile and query tool for 1859 wheat, 2330 rice and 283 maize miRNA. The database interface offers open and easy access to miRNA expression profile and helps in identifying tissue preferential, differential and constitutively expressing miRNAs. A feature enabling expression study of conserved miRNA across multiple species is also implemented. Custom expression analysis feature enables expression analysis of novel miRNA in total 117 datasets. New sRNA dataset can also be uploaded for analysing miRNA expression profiles for 73 plant species. PmiRExAt application program interface, a simple object access protocol web service allows other programmers to remotely invoke the methods written for doing programmatic search operations on PmiRExAt database.Database URL:http://pmirexat.nabi.res.in.
authors.affiliation: Computational Biology Laboratory, National Agri Food Biotechnology Institute (NABI), Mohali, Punjab, India.
authors.forename: Anoop Kishor Singh
authors.initials: AK
authors.lastname: Gurjar
authors.affiliation: HPC-Tech, Center for Development of Advance Computing (C-DAC), Pune, Maharashtra, India.
authors.forename: Abhijeet Singh
authors.initials: AS
authors.lastname: Panwar
authors.affiliation: Computational Biology Laboratory, National Agri Food Biotechnology Institute (NABI), Mohali, Punjab, India.
authors.forename: Rajinder
authors.initials: R
authors.lastname: Gupta
authors.affiliation: Computational Biology Laboratory, National Agri Food Biotechnology Institute (NABI), Mohali, Punjab, India shrikant@nabi.res.in bioinfoman3@gmail.com.
authors.forename: Shrikant S
authors.initials: SS
authors.lastname: Mantri
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D003628:Database Management Systems; D030541:Databases, Genetic; D018506:Gene Expression Regulation, Plant; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D010944:Plants / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D012984:Software
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant