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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

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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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DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning
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A Simple Method for Optimization of Reference Gene Identification and Normalization in DNA Microarray Analysis.

Federico M Casares1

  • 1Department of Bioinformatics, Mitogenetics Research Institute, Farmingdale, NY, USA.

Medical Science Monitor Basic Research
|April 29, 2016
PubMed
Summary
This summary is machine-generated.

This study presents a method to identify stable reference genes from DNA microarray data for accurate gene expression normalization. The approach combines software and manual analysis to find reliable endogenous controls in Zucker diabetic fatty rats.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • DNA microarray analysis generates large gene expression datasets.
  • Stable reference genes are crucial for normalizing data in quantitative real-time reverse transcription-PCR (qRT-PCR) and relative RT-PCR.
  • Identifying reliable reference genes is less common in gene microarray analysis.

Purpose of the Study:

  • To develop a simple method for identifying reliable reference genes from DNA microarray data.
  • To utilize comparative statistical analysis of software-generated and manually calculated candidate genes.
  • To establish endogenous controls for accurate gene expression normalization.

Main Methods:

  • Used DNA microarray data from Zucker diabetic fatty (ZDF) rats (lean and diabetic obese).
  • Employed software-generated filtering for signal-to-noise ratios.
  • Applied 75th percentile signal manual normalization for reference gene selection.

Main Results:

  • Identified a group of 5 stably expressed endogenous control genes.
  • These genes are suitable for normalizing target gene expression in ZDF rat whole blood.
  • The combined normalization method proved effective.

Conclusions:

  • The developed method aids in selecting suitable endogenous control genes.
  • It helps correct potentially false results in gene expression analysis.
  • This approach is particularly useful for borderline results in software analysis.