title: PMTED: a plant microRNA target expression database.
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.
  
  
  METHODS
  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.
authors.affiliation: Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China.
authors.forename: Xiuli
authors.initials: X
authors.lastname: Sun
authors.forename: Boquan
authors.initials: B
authors.lastname: Dong
authors.forename: Lingjie
authors.initials: L
authors.lastname: Yin
authors.forename: Rongzhi
authors.initials: R
authors.lastname: Zhang
authors.forename: Wei
authors.initials: W
authors.lastname: Du
authors.forename: Dongfeng
authors.initials: D
authors.lastname: Liu
authors.forename: Nan
authors.initials: N
authors.lastname: Shi
authors.forename: Aili
authors.initials: A
authors.lastname: Li
authors.forename: Yanchun
authors.initials: Y
authors.lastname: Liang
authors.forename: Long
authors.initials: L
authors.lastname: Mao
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D035683:MicroRNAs / Q000737:chemistry / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis
chemical_list: D035683:MicroRNAs