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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

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...

DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Updated: May 11, 2026

MicroRNA Amplification and Recognition through Locked-nucleic-acid In situ Hybridization as a Novel Detection and Quantification Method

MicroRNA Amplification and Recognition through Locked-nucleic-acid In situ Hybridization as a Novel Detection and Quantification Method

Published on: October 7, 2025

The use of miRNA microarrays for the analysis of cancer samples with global miRNA decrease.

Di Wu¹, Yifang Hu, Stephen Tong

¹Centre for Cancer Research, Monash Institute of Medical Research, Monash University, Clayton, Victoria 3168, Australia.

RNA (New York, N.Y.)

|May 28, 2013

Summary

This summary is machine-generated.

MicroRNA (miRNA) profiling using microarrays can be biased. A new normalization method using cyclic loess improves detection of decreased miRNA expression in cancer, enhancing accuracy in cancer research.

Keywords:

Dicer1 miRNA microarray microRNA normalization

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Area of Science:

Molecular Biology
Genomics
Cancer Research

Background:

Decreased microRNA (miRNA) expression is common in cancers and linked to poor prognosis.
The accuracy of miRNA microarrays in detecting these global decreases is uncertain.
Standard normalization methods may introduce bias, misidentifying downregulated miRNAs as upregulated.

Purpose of the Study:

To evaluate the suitability of miRNA microarrays for detecting global miRNA decreases in cancer.
To identify improved preprocessing and normalization methods for accurate miRNA profiling.
To validate findings in prostate cancer patient samples.

Main Methods:

Analysis of miRNA profiles from samples with induced Dicer1 deletion (global miRNA decrease).
Comparison of five probe-level preprocessing steps for Affymetrix miRNA microarrays.
Validation using prostate cancer patient samples with optimized normalization: robust normal-exponential background correction, cyclic loess, and array weights.

Main Results:

Standard normalization (RMA) incorrectly identified up to a third of deregulated miRNAs as upregulated.
Cyclic loess normalization, utilizing non-miRNA small RNAs, significantly improved detection sensitivity and specificity.
The optimized method correctly identified the most decreased miRNAs and minimized false positives in prostate cancer samples.

Conclusions:

miRNA microarray normalization is critical for accurately detecting differential miRNA expression in cancer.
Cyclic loess normalization based on non-miRNA small RNAs enhances sensitivity and specificity.
This improved approach is valuable for miRNA profiling in cancer samples exhibiting global miRNA downregulation.