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Real-time PCR was performed to verify the microarray expression pattern for a few selected OsARM genes, expressed significantly during three abiotic stresses and in various rice tissues/developmental stages.
The microarray expression pattern of Phlda2 was confirmed by real-time PCR.
Of the top 23 ranked genes in S. cerevisiae (according to our model), 19 had an expected microarray expression pattern for Met4 regulation.
Out of the 16 HrpL-regulated genes examined by qRT-PCR, only gene ASAP15704 (Bcr/CflA subfamily drug resistance transporter) exhibited a microarray expression pattern that did not correspond to the qRT-PCR value.
The F13a1 microarray expression pattern in the growth plate was confirmed at the protein level, with increased levels in the hypertrophic zone (Zone II) compared to the resting/proliferating zone (Zone I) and the maintenance of this expression in the mineralized area (Zone III), adding confidence to the results of the microarray data analysis (Figure 1C).
qRT-PCR validation of five of the selected candidates confirmed the microarray expression pattern.
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To further confirm the findings from the microarray results, 12 differentially expressed genes identified from microarray expression patterns in PBMC and 14 differentially expressed genes identified from microarray expression patterns in granulocytes were evaluated by quantitative real-time PCR on RNA obtained from the independent testing cohort.
Ten differentially expressed genes identified from microarray expression patterns of PBMC were evaluated.
Microarray expression patterns were visualized using TreeView [28].
Using a significance threshold (α = 0.005) and subsequent random permutations of our rank-lists, we identified 290 genes that were significantly differentially upregulated based on epigenetic screening and tissue microarray expression patterns (Table S2) [29].
Several genes were selected, including light-harvesting chlorophyll a/b binding protein (LOC_Os03g39610), starch and sucrose metabolism pathway related proteins such as glycogen/starch synthases (LOC_Os07g22930), 4-alpha-glucanotransferase (LOC_Os07g46790), and Glucan water dikinase (LOC_Os06g30310).The real-time RT-PCR results mostly matched the microarray expression patterns.
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