PMTED: a plant microRNA target expression database

doi:10.1186/1471-2105-14-174

	PMTED: a plant microRNA target expression database
	Sun, Xiuli 1; Dong, Boquan 1; Yin, Lingjie 2; Zhang, Rongzhi 2; Du, Wei 1; Liu, Dongfeng 2; Shi, Nan 2; Li, Aili 2; Liang, Yanchun 1; Mao, Long 2
刊名	BMC BIOINFORMATICS
	2013
卷号	14 页码:-
关键词	MiRNA Microarray Meta-analysis Stress response
ISSN号	1471-2105
DOI	10.1186/1471-2105-14-174
通讯作者	Sun, Xiuli
英文摘要	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.
学科主题	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology ; BIOCHEMICAL RESEARCH METHODS ; BIOTECHNOLOGY & APPLIED MICROBIOLOGY ; MATHEMATICAL & COMPUTATIONAL BIOLOGY
语种	英语
出版者	BIOMED CENTRAL LTD
WOS记录号	WOS:000320275800001
内容类型	期刊论文
源URL	[http://111.203.20.206/handle/2HMLN22E/5034]
专题	作物科学研究所_分子生物学系
作者单位	1.Jilin Univ, Coll Comp Sci & Technol, Minist Educ, Key Lab Symbol Computat & Knowledge Engn, Changchun 130012, Peoples R China 2.Chinese Acad Agr Sci, Inst Crop Sci, Beijing 100081, Peoples R China
推荐引用方式 GB/T 7714	Sun, Xiuli,Dong, Boquan,Yin, Lingjie,et al. PMTED: a plant microRNA target expression database[J]. BMC BIOINFORMATICS,2013,14:-.
APA	Sun, Xiuli.,Dong, Boquan.,Yin, Lingjie.,Zhang, Rongzhi.,Du, Wei.,...&Mao, Long.(2013).PMTED: a plant microRNA target expression database.BMC BIOINFORMATICS,14,-.
MLA	Sun, Xiuli,et al."PMTED: a plant microRNA target expression database".BMC BIOINFORMATICS 14(2013):-.