Selection of DDX5 as a novel internal control for Q-RT-PCR from microarray data using a block bootstrap re-sampling scheme

Li Jen Su, Ching Wei Chang, Yu Chung Wu, Kuang Chi Chen, Chien Ju Lin, Shu Ching Liang, Chi Hung Lin, Jacqueline Whang-Peng, Shih Lan Hsu, Chen Hsin Chen, Chi Ying F. Huang

研究成果: 雜誌貢獻文章同行評審

254 引文 斯高帕斯(Scopus)

摘要

Background: The development of microarrays permits us to monitor transcriptomes on a genome-wide scale. To validate microarray measurements, quantitative-real time-reverse transcription PCR (Q-RT-PCR) is one of the most robust and commonly used approaches. The new challenge in gene quantification analysis is how to explicitly incorporate statistical estimation in such studies. In the realm of statistical analysis, the various available methods of the probe level normalization for microarray analysis may result in distinctly different target selections and variation in the scores for the correlation between microarray and Q-RT-PCR. Moreover, it remains a major challenge to identify a proper internal control for Q-RT-PCR when confirming microarray measurements. Results: Sixty-six Affymetrix microarray slides using lung adenocarcinoma tissue RNAs were analyzed by a statistical re-sampling method in order to detect genes with minimal variation in gene expression. By this approach, we identified DDX5 as a novel internal control for Q-RT-PCR. Twenty-three genes, which were differentially expressed between adjacent normal and tumor samples, were selected and analyzed using 24 paired lung adenocarcinoma samples by Q-RT-PCR using two internal controls, DDX5 and GAPDH. The percentage correlation between Q-RT-PCR and microarray were 70% and 48% by using DDX5 and GAPDH as internal controls, respectively. Conclusion: Together, these quantification strategies for Q-RT-PCR data processing procedure, which focused on minimal variation, ought to significantly facilitate internal control evaluation and selection for Q-RT-PCR when corroborating microarray data.
原文英語
文章編號140
期刊BMC Genomics
8
DOIs
出版狀態已發佈 - 6月 1 2007
對外發佈

ASJC Scopus subject areas

  • 生物技術
  • 遺傳學

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