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Open Access Highly Accessed Database

PMTED: a plant microRNA target expression database

Xiuli Sun1, Boquan Dong1, Lingjie Yin2, Rongzhi Zhang2, Wei Du1, Dongfeng Liu2, Nan Shi2, Aili Li2, Yanchun Liang1* and Long Mao2*

Author Affiliations

1 Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China

2 Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China

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BMC Bioinformatics 2013, 14:174  doi:10.1186/1471-2105-14-174

Published: 3 June 2013

Abstract

Background

MicroRNAs (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.

Description

Plant 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.

Conclusions

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 webcite.

Keywords:
MiRNA; Microarray; Meta-analysis; Stress response