Abstract
BackgroundMicroRNAs (miRNAs) are identified in nearly all plants where they play important roles in development and stress responses by target mRNA cleavage or translation repression. MiRNAs exert their functions by sequence complementation with target genes and hence their targets can be predicted using bioinformatics algorithms. In the past two decades, microarray technology has been employed to study genes involved in important biological processes such as biotic response, abiotic response, and specific tissues and developmental stages, many of which are miRNA targets. Despite their value in assisting research work for plant biologists, miRNA target genes are difficult to access without pre-processing and assistance of necessary analytical and visualization tools because they are embedded in a large body of microarray data that are scattered around in public databases.DescriptionPlant MiRNA Target Expression Database (PMTED) is designed to retrieve and analyze expression profiles of miRNA targets represented in the plethora of existing microarray data that are manually curated. It provides a Basic Information query function for miRNAs and their target sequences, gene ontology, and differential expression profiles. It also provides searching and browsing functions for a global Meta-network among species, bioprocesses, conditions, and miRNAs, meta-terms curated from well annotated microarray experiments. Networks are displayed through a Cytoscape Web-based graphical interface. In addition to conserved miRNAs, PMTED provides a target prediction portal for user-defined novel miRNAs and corresponding target expression profile retrieval. Hypotheses that are suggested by miRNA-target networks should provide starting points for further experimental validation.ConclusionsPMTED exploits value-added microarray data to study the contextual significance of miRNA target genes and should assist functional investigation for both miRNAs and their targets. PMTED will be updated over time and is freely available for non-commercial use at http://pmted.agrinome.org.
Highlights
MicroRNAs are identified in most plants where they play important roles in development and stress responses by target mRNA cleavage or translation repression
Plant MiRNA Target Expression Database (PMTED) exploits value-added microarray data to study the contextual significance of miRNA target genes and should assist functional investigation for both miRNAs and their targets
PMTED will be updated over time and is freely available for non-commercial use at http://pmted.agrinome.org
Summary
PMTED is a database that comprises a number of querying, analytical, and visualization functionalities for miRNAs targets. It is designed to link miRNA target gene expression patterns from various microarray experiments and reveal contextual significance of miRNA-target gene regulatory networks. Competing interests The authors declare that they have no competing interests. XS, DL, BD, RZ, AL, WD, NS and LM analyzed the data, XS and LY developed the database. All authors read and approved the final manuscript. Funding China National High Tech ‘863’ Program No 2012AA10A308; NSFC Nos. 61073075, 61272207; Sci-Tech Development Project of Jilin Province No 20120730
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