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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...
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Nuclear magnetic resonance (NMR) spectroscopy is a very valuable analytical technique for researchers. It has been used for more than 50 years as an analytical tool. F. Bloch and E. Purcell formulated NMR in 1946 and won the 1952 Nobel Prize in Physics  for their work. Biological macromolecules such as proteins, nucleic acids, lipids, and organic molecules including pharmaceutical compounds, can be studied using this versatile tool that exploits the magnetic properties of certain nuclei.
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Related Experiment Video

Updated: Dec 20, 2025

mirMachine: A One-Stop Shop for Plant miRNA Annotation
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miRNet 2.0: network-based visual analytics for miRNA functional analysis and systems biology.

Le Chang1, Guangyan Zhou2, Othman Soufan2

  • 1Department of Human Genetics, McGill University, Montreal, Quebec, Canada.

Nucleic Acids Research
|June 3, 2020
PubMed
Summary

miRNet 2.0 enhances microRNA (miRNA) functional analysis by integrating transcription factors and SNPs into network visualizations. This updated platform offers expanded knowledgebases and improved usability for researchers studying complex gene regulation.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • MicroRNA (miRNA) research requires understanding their functions within broader biological networks.
  • Previous versions of miRNet focused primarily on miRNA-target gene interactions.
  • A comprehensive view of miRNA functions necessitates integrating additional regulatory elements.

Purpose of the Study:

  • To introduce miRNet version 2.0, an enhanced web-based platform for miRNA functional analysis.
  • To expand the platform's capabilities beyond miRNA-target interactions to include transcription factors (TFs) and single nucleotide polymorphisms (SNPs).
  • To improve data integration, network visualization, and analytical performance for researchers.

Main Methods:

  • Integration of TF and SNP data affecting miRNAs, miRNA-binding sites, and target genes.
  • Expansion of underlying knowledgebases for miRNAs, non-coding RNAs (ncRNAs), and disease associations (>5-fold increase).
  • Implementation of multipartite network creation, visual exploration, and in situ functional analysis tools.
  • Revamped web interface, optimized workflow, and introduction of microservices and API for real-time analysis.
  • Release of an accompanying R package for advanced data analysis.

Main Results:

  • miRNet 2.0 now supports the analysis of complex interactions involving miRNAs, TFs, and SNPs.
  • The knowledgebase has been significantly expanded, providing a more comprehensive resource.
  • New visualization and analysis functions enable deeper insights into miRNA functions.
  • Enhanced performance and usability through a revamped interface and microservices architecture.

Conclusions:

  • miRNet 2.0 provides a powerful and integrated platform for elucidating miRNA functions.
  • The inclusion of TFs and SNPs offers a more holistic approach to understanding gene regulation.
  • The platform's advanced features and expanded data support researchers in complex biological analyses.