Dataset Information

MepmiRDB: a medicinal plant microRNA database.

ABSTRACT: MicroRNAs (miRNAs) have been recognized as a key regulator in plant development and metabolism. Recent reports showed that the miRNAs of medicinal plants not only act as a critical modulator in secondary metabolism but also had a great potential of performing cross-kingdom gene regulation. Although several plant miRNA repositories have been publicly available, no miRNA database specific for medicinal plants has been reported to date. Here, we report the first version of MepmiRDB (medicinal plant microRNA database), which is freely accessible at http://mepmirdb.cn/mepmirdb/index.html. This database accommodates thousands of miRNA candidates belonging to 29 medicinal plant species. The miRNA information on sequences, expression patterns and regulatory networks has been included in the functional modules of the database. Specifically, the 'Sequence' module provides the sequences of the mature miRNAs and their precursors, and the structure information of the precursors. Moreover, the processing and small RNA accumulation signals on the miRNA precursors are also included in the 'Sequence' module. The organ/growth condition-specific expression information of the mature miRNAs has been stored in the 'Expression' module. The 'Interaction' module offers the information of the degradome-validated miRNA-target pairs of eight plant species. The 'Search' module enables users to search for the miRNAs by plant species and miRNA families, or by sequences. All data in this database are available for download. Taken together, the functional modules of MepmiRDB ensure its importance and timeliness for mechanistic and functional studies on the medicinal plant miRNAs.

SUBMITTER: Yu D

PROVIDER: S-EPMC6589547 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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MepmiRDB: a medicinal plant microRNA database.

Yu Dongliang D Lu Jiangjie J Shao Weishan W Ma Xiaoxia X Xie Tian T Ito Hidetaka H Wang Tingzhang T Xu Min M Wang Huizhong H Meng Yijun Y

Database : the journal of biological databases and curation 20190101

MicroRNAs (miRNAs) have been recognized as a key regulator in plant development and metabolism. Recent reports showed that the miRNAs of medicinal plants not only act as a critical modulator in secondary metabolism but also had a great potential of performing cross-kingdom gene regulation. Although several plant miRNA repositories have been publicly available, no miRNA database specific for medicinal plants has been reported to date. Here, we report the first version of MepmiRDB (medicinal plant ...[more]

PMID: 31231773

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Project description: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.

Dataset Information

MepmiRDB: a medicinal plant microRNA database.

Publications

MepmiRDB: a medicinal plant microRNA database.

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