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

Abstract

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.

TOPK/PBK promotes cell migration via modulation of the PI3K/PTEN/AKT pathway and is associated with poor prognosis in lung cancer

“…Quantitative real-time PCR (Q-RT-PCR) was performed on 24 pairmatched lung adenocarcinoma tumors and adjacent non-tumor samples. Overexpression of TOPK was observed in 20 out of 24 lung patient tumors, showing a higher signal after normalization to DDX5, a novel internal control for lung adenocarcinoma (Su et al, 2007), for equal template loading. The average expression level of TOPK in lung adenocarcinoma was B5-fold higher than that in adjacent non-tumor lung tissue samples, as analyzed by boxplot ( Figure 1c).…”

“…As a result of our bioinformatic survey, we focused on the poorly characterized gene TOPK. First, we used a training microarray data set, namely samples from 27 patients with lung adenocarcinoma confirmed by histopathology, which were subjected to Affymetrix microarray profiling using HG-U133A (Su et al, 2007). Of many differentially expressed transcripts between the adjacent normal area and the tumor examined by Wilcoxon signed rank test (Po0.01) and tested using the Benjamini and Hochberg false discovery rate correlation (Po0.01), TOPK expression was upregulated, as shown by boxplot (Figure 1a, left).…”

“…First, a total of 66 samples from our previous study were used for microarray analysis via HG-U133A chip (Su et al, 2007). Second, 50 additional samples, corresponding to 25 pair-matched surgical samples from lung cancer patients, were subjected to microarray analysis via HG-U133 plus 2.0 chip.…”

MicroRNA-143 (miR-143) Regulates Cancer Glycolysis via Targeting Hexokinase 2 Gene

“…Two lung cancer gene expression microarray data sets, GSE7670 (27 lung cancers and 27 normals) (18) and GSE10072 (58 lung cancers and 49 normals) (19), were downloaded from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) (www.ncbi.nlm.nih.gov/ geo). Raw data were preprocessed with updated probe set definitions (20) using the robust multiarray average algorithm (17,21,22).…”

Tripartite Motif Containing 28 (Trim28) Can Regulate Cell Proliferation by Bridging HDAC1/E2F Interactions

“…With one exception (8), microarray studies in lung cancer that have included a significant number of normal tissue samples for comparison have demonstrated a statistically significant increase in the Trim28 mRNA in tumors relative to normal tissue (9 -11). Similar trends have been observed in breast cancer (see Trim28 in the Oncomine Database).…”