Fourth, our method produces sufficient amplified sense RNA for multiple microarray analyses after a single round of amplification from as little as 1 μg of total RNA.
The only pro-apoptotic gene consistently upregulated across multiple microarray analyses is the BH3-only BCL-2 family member BIM, and it has been shown that BIM has a critical role in glucocorticoid sensitivity and resistance [ 37], although in this current study BIM was only induced 1.3 fold.
In this setting, 130-fold amplification produces more than enough RNA for multiple downstream microarray analyses and confers the benefit of reduced bias inherent in a single-round amplification protocol.
The results obtained here confirm results from our multiple microarray co-expression analyses indicating that WRKY28 and WRKY46 are transcriptional activators of ICS1 and PBS3, respectively, and support this in silico screening as a powerful tool for identifying new components of stress signaling pathways.
Recently, multiple microarray or RNA-Seq analyses of purified meiocytes have been reported [ 5, 41, 42, 71].
In multiple adult cell types microarray analyses found a correlation between HOX gene expression and anatomic site of origin [ 6, 7].
Our motivation in this study was to determine when stable predictive biomarkers can be identified from multiple microarray studies or meta-analyses.
Analyses of multiple microarray datasets derived from human colorectal cancer indicated that correlation levels of FoxM1 and pituitary tumor transforming gene (PTTG1) are highly concordant (R = 0.68 ~ 0.89, p = 2.1E-226 ~ 9.6E-86 9.6E-86
By combining gene expression analyses across multiple microarray studies and with the qPCR validation of putative genes, we can provide greater confidence in the scientific findings, which include potential genes and biological pathways in psychiatric disorders, as compared to the result obtained from a single study.
Multiple testing methods normally used in microarray analyses to correct for false positives include FDR (false discovery rate) and Q-value [51] [53].
Indeed present/absent calls, expression thresholds and, most popularly, variance filters [ 38] are frequently used in downstream microarray analyses to reduce multiple testing and improve power for discovery (as compared in [ 39]).
