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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...

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...

MicroRNAs

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Updated: Mar 21, 2026

Genome-wide Screen for miRNA Targets Using the MISSION Target ID Library

Genome-wide Screen for miRNA Targets Using the MISSION Target ID Library

Published on: April 6, 2012

Improving microRNA target prediction with gene expression profiles.

Cesaré Ovando-Vázquez¹, Daniel Lepe-Soltero¹, Cei Abreu-Goodger²

¹Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, 36821, México.

|May 19, 2016

Summary

This study introduces TargetExpress, a novel computational method that predicts microRNA targets by integrating expression profiles with machine learning. TargetExpress accurately identifies cell-specific microRNA functions, outperforming existing methods.

Keywords:

Biological context Gene expression profiles Support Vector Machine microRNA perturbation experiments microRNA target prediction

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Last Updated: Mar 21, 2026

Genome-wide Screen for miRNA Targets Using the MISSION Target ID Library

Genome-wide Screen for miRNA Targets Using the MISSION Target ID Library

Published on: April 6, 2012

Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay

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Published on: May 25, 2015

Biotin-based Pulldown Assay to Validate mRNA Targets of Cellular miRNAs

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Published on: June 12, 2018

Area of Science:

Genomics
Computational Biology
Molecular Biology

Background:

Mammalian genomes contain thousands of microRNAs (miRNAs) that regulate a vast number of protein-coding genes.
miRNAs are crucial in development and disease, necessitating accurate target prediction.
Current computational miRNA target prediction methods often overlook cell-specific expression, limiting functional insights.

Purpose of the Study:

To develop a novel computational method for predicting microRNA targets that accounts for cell-specific expression profiles.
To improve the accuracy and functional relevance of microRNA target predictions.

Main Methods:

Integrated popular miRNA target prediction algorithms with gene expression data using machine learning.
Developed a new predictor named TargetExpress.
Validated predictions using independent microarray and high-throughput sequencing data.

Main Results:

TargetExpress demonstrated superior performance compared to existing target prediction methods.
Predicted miRNA targets were enriched in functions consistent with expression profiles and literature.
The method successfully identified cell-specific miRNA target sets and functions.

Conclusions:

TargetExpress offers a more accurate and context-specific approach to miRNA target prediction.
The tool is valuable for researchers studying miRNA functions in specific cellular or tissue contexts.
TargetExpress is publicly available for use by the scientific community.