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Updated: Feb 16, 2026

mirMachine: A One-Stop Shop for Plant miRNA Annotation

mirMachine: A One-Stop Shop for Plant miRNA Annotation

Published on: May 1, 2021

DPMIND: degradome-based plant miRNA-target interaction and network database.

Yuhan Fei¹, Rui Wang¹, Haoyuan Li²

¹State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture.

Bioinformatics (Oxford, England)

|December 28, 2017

Summary

The Degradome-based Plant miRNA-target Interaction and Network Database (DPMIND) provides experimentally validated plant microRNA-target interactions and regulatory networks. This resource aids in understanding miRNA functions across various plant tissues and species.

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Area of Science:

Plant molecular biology
Bioinformatics
Genomics

Background:

MicroRNAs (miRNAs) regulate gene expression post-transcriptionally, impacting plant growth, development, and stress responses.
Existing miRNA-target prediction tools often lack experimental validation, limiting their reliability.
Degradome sequencing offers experimental validation for miRNA-target interactions (MTIs).

Purpose of the Study:

To develop a comprehensive database (DPMIND) for experimentally validated plant miRNA-target interactions (MTIs) and miRNA regulatory networks (MRNs).
To provide a platform for retrieving and analyzing MTIs and MRNs based on degradome sequencing data.
To facilitate the study of MTI conservation and specificity across plant tissues and species.

Main Methods:

Collected and curated publicly available plant degradome sequencing data.
Integrated data to identify and verify miRNA-target interactions (MTIs).
Developed a retrieval and analysis platform for MTIs and constructed degradome-based miRNA regulatory networks (MRNs).

Main Results:

DPMIND houses 3,794 miRNAs and 28,666 verified MTIs from 69 degradomes across 10 plant species.
The database enables retrieval of verified MTIs and construction of degradome-based MRNs.
Users can build MRNs using all or specific degradomes, allowing comparative analysis across tissues/treatments.

Conclusions:

DPMIND serves as a valuable resource for plant miRNA research, offering experimentally validated interactions and networks.
The database supports the investigation of miRNA-mediated gene regulation in plants.
DPMIND facilitates comparative studies of miRNA functions and regulatory networks in diverse plant contexts.