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A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants
06:34

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

Published on: January 21, 2020

The Usage of PmiREN (Plant miRNA ENcyclopedia)

Zhonglong Guo1, Zheng Kuang2, Xiaozeng Yang3

  • 1Co-Innovation Center for Sustainable Forestry in Southern China, School of Life Sciences, Nanjing Forestry University, Nanjing, China. guozhl@pku.edu.cn.

Methods in Molecular Biology (Clifton, N.J.)
|May 16, 2025
PubMed

Insights

The Plant miRNA Encyclopedia (PmiREN) database offers a comprehensive resource for plant microRNAs (miRNAs). It provides access to 38,186 miRNA loci across 179 species, aiding plant biology research.

Area of Science:

  • Plant Biology
  • Genomics
  • Bioinformatics

Background:

  • MicroRNAs (miRNAs) are crucial post-transcriptional gene regulators.
  • Increased research in plant miRNA identification, function, and evolution necessitates robust databases.
  • Existing resources require consolidation and uniform processing for broader accessibility.

Purpose of the Study:

  • To introduce and summarize the usage of the Plant miRNA Encyclopedia (PmiREN) database.
  • To provide a centralized, updated resource for plant miRNA research.
  • To support data mining and data-driven research in plant miRNA biology.

Main Methods:

  • Construction of a knowledge-based database (PmiREN).
  • Uniform processing of sequenced small RNA libraries using miRDeep-P2.
  • Inclusion of multiple data mining and analysis tools.

Main Results:

  • PmiREN contains 38,186 high-confidence miRNA loci.
  • The database covers 179 plant species.
  • PmiREN offers integrated tools for research.

Conclusions:

  • PmiREN serves as a valuable, updated resource for the plant miRNA research community.
  • The database facilitates efficient data mining and exploration of plant miRNA functions.
  • PmiREN aims to advance the understanding of plant gene regulation.
Keywords:
Plant miRNA, PmiREN, Database, Analysis tool, sRNA-seq

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