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Related Experiment Videos

Monitoring global messenger RNA changes in externally controlled microarray experiments.

Jeroen van de Peppel1, Patrick Kemmeren, Harm van Bakel

  • 1Genomics Laboratory, Department of Physiological Chemistry, University Medical Centre Utrecht, Postbus, Utrecht, The Netherlands.

EMBO Reports
|April 3, 2003
PubMed
Summary

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Accurate gene expression analysis requires accounting for global messenger RNA (mRNA) shifts. External RNA controls reveal widespread mRNA changes during yeast stationary phase and human heat shock, impacting differential expression results.

Area of Science:

  • Molecular biology
  • Genomics
  • Bioinformatics

Background:

  • Gene expression profiling is crucial for understanding biological processes.
  • Current microarray normalization methods often assume limited transcript variation.
  • This assumption can lead to inaccurate differential gene expression analysis.

Purpose of the Study:

  • To investigate the impact of global messenger RNA (mRNA) changes on gene expression profiling.
  • To assess the utility of external RNA controls for monitoring global mRNA shifts.
  • To determine if global mRNA changes are more frequent than currently assumed.

Main Methods:

  • Microarray experiments were designed to monitor global changes in transcript levels.
  • External RNA controls were incorporated into the experimental setup.

Related Experiment Videos

  • Analysis focused on identifying changes in mRNA levels during specific cellular conditions (yeast stationary phase, human heat shock).

    • Main Results:

    • External RNA controls revealed significant global changes in mRNA levels during yeast stationary phase and human heat shock.
    • Even minor global mRNA shifts substantially affected the identification of differentially expressed genes.
    • The findings challenge the assumption of limited transcript variation in normalization.

    Conclusions:

    • Global mRNA level changes are more common than previously recognized.
    • Monitoring global mRNA shifts using external controls is essential for accurate gene expression analysis.
    • Current normalization strategies may require adjustments to account for global transcriptomic variations.