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MicroRNAs

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...

MicroRNAs

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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...

MicroRNAs

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Updated: May 22, 2026

A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants

A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants

Published on: January 21, 2020

miRFANs: an integrated database for Arabidopsis thaliana microRNA function annotations.

Hui Liu¹, Ting Jin, Ruiqi Liao

¹Research Lab of Information Management, Changzhou University, Jiangsu, China.

BMC Plant Biology

|May 16, 2012

Summary

This study introduces miRFANs, an online database for Arabidopsis thaliana microRNA (miRNA) function annotations. It integrates diverse datasets and tools to aid in understanding plant miRNA regulatory networks and functions.

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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

Area of Science:

Plant molecular biology
Genomics
Bioinformatics

Background:

Plant microRNAs (miRNAs) regulate crucial developmental and stress-response pathways.
Understanding miRNA regulatory mechanisms and functions is limited by scarce validated targets and spatio-temporal specificity.
Current knowledge gaps hinder comprehensive analysis of plant miRNA roles.

Purpose of the Study:

To develop an integrated online database, miRFANs, for Arabidopsis thaliana miRNA function annotations.
To provide tools for analyzing miRNA-target interactions and regulatory networks.
To facilitate a deeper understanding of plant miRNA functions and mechanisms.

Main Methods:

Integrated diverse datasets: miRNA-target interactions, TF-target data, expression profiles, genomic annotations, and pathways.
Developed statistical and mining tools for data analysis.
Implemented a user-friendly web interface for database access and exploration.

Main Results:

Created a comprehensive collection of miRNA targets for Arabidopsis thaliana.
Extracted a miRNA-mediated genetic regulatory network from the integrated database.
Associated miRNA targets with gene ontology, pathway terms, and target site information.

Conclusions:

miRFANs offers valuable information for understanding plant miRNA functions.
The database facilitates the extraction of informative miRNA-mediated genetic regulatory networks.
Integrated tools and a user-friendly interface enhance the analysis of plant miRNA data.