PmiRExAt: plant miRNA expression atlas database and web applications

Area of Science:

• Plant Molecular Biology
• Bioinformatics
• Genomics

Background:

• High-throughput sequencing advances plant microRNA (miRNA) research.
• Data mining of small RNA (sRNA) data offers potential for crop improvement.
• Bioinformatics resources for cross-species miRNA meta-analysis are developing.

Purpose of the Study:

• To introduce PmiRExAt, a novel online database for plant miRNA expression atlas.
• To facilitate meta-analysis of miRNA expression across diverse plant species.
• To support crop improvement through enhanced understanding of miRNA regulatory networks.

Main Methods:

• Development of a web-based repository for plant miRNA expression profiles.
• Integration of query tools for wheat, rice, and maize miRNAs.
• Implementation of features for tissue-preferential, differential, and conserved miRNA expression analysis.
• Inclusion of custom expression analysis for novel miRNAs and sRNA dataset uploads.
• Provision of a SOAP web service API for programmatic access.

Main Results:

• PmiRExAt hosts expression profiles for 1859 wheat, 2330 rice, and 283 maize miRNAs.
• The database enables identification of tissue-specific and differentially expressed miRNAs.
• Cross-species conserved miRNA expression studies are supported.
• Custom analysis is available for 117 datasets, with support for 73 plant species.
• An API allows programmatic data retrieval and analysis.

Conclusions:

• PmiRExAt provides a valuable resource for plant miRNA research and crop improvement.
• The database facilitates exploration of miRNA regulatory networks.
• Accessible bioinformatics tools are crucial for advancing plant biotechnology.