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Selection of DDX5 as a novel internal control for Q-RT-PCR from microarray data using a block bootstrap re-sampling
Li-Jen Su1, Ching-Wei Chang, Yu-Chung Wu
1Institute of Cancer Research, National Health Research Institutes, Taipei, Taiwan. ljsu@vghtpe.gov.tw <ljsu@vghtpe.gov.tw>
BMC Genomics
|June 2, 2007
Summary
This study identified DDX5 as a novel internal control for quantitative-real time-reverse transcription PCR (Q-RT-PCR). Using DDX5 improved the correlation between Q-RT-PCR and microarray gene expression data in lung adenocarcinoma samples.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Microarrays enable genome-wide transcriptome monitoring.
- Quantitative-real time-reverse transcription PCR (Q-RT-PCR) is crucial for validating microarray data.
- Statistical normalization methods and internal control selection pose challenges in gene quantification.
Purpose of the Study:
- To identify a reliable internal control for Q-RT-PCR validation of microarray data.
- To improve the accuracy of gene expression analysis in lung adenocarcinoma.
Main Methods:
- Analyzed 66 Affymetrix microarray slides from lung adenocarcinoma tissues using a statistical re-sampling method.
- Identified DDX5 as a potential internal control based on minimal gene expression variation.
- Validated DDX5 and GAPDH as internal controls in Q-RT-PCR analysis of 23 differentially expressed genes in 24 paired tumor samples.
Main Results:
- DDX5 was identified as a novel internal control for Q-RT-PCR.
- Q-RT-PCR showed a 70% correlation with microarray data when using DDX5 as the internal control.
- Using GAPDH as the internal control resulted in only a 48% correlation.
Conclusions:
- The proposed quantification strategies focusing on minimal variation facilitate internal control selection for Q-RT-PCR.
- DDX5 is a more effective internal control than GAPDH for corroborating microarray data in lung adenocarcinoma studies.
- This approach enhances the reliability of gene expression validation in transcriptomic studies.
