In addition, we used real-time reverse transcription PCR (RT-PCR) to validate the microarray results for five selected genes, and found concordance for the direction of differential expression in each case, including a non-differentially expressed transcript (Fig. 2).
Candidate DBRs with an FDR corrected P-value of < 0.01 were called as differentially enriched between castes, and the direction of differential binding enrichment was determined from the MAnorm-produced normalized between-comparison ChIP enrichment M-value (log2 ratio).
Overlap analysis is inconclusive: Table S8 counts genes in common between the sets of differentially expressed genes, classified by tissue, sex, and F1 genotype, and whether the direction of differential expression is the same.
Overall, 28 of the 106 interacted with PREs, with the direction of differential expression often matching the pattern of motif enrichment.
The direction of differential expression correlated with copy number aberration for 39/64 genes (61%; p<0.05) (Tables 9 and 10).
An independent evaluation [13] of SPIA amplification from picograms of RNA observed thousands of probe sets to measure the opposite direction of differential expression compared to the standard protocol recommended by the microarray manufacturer.
For the axis corresponding to PC4MN and PC2RC, there are 656 transcript probes in common at p<10−5, each of which shows the same direction of differential expression in the two studies (291 down and 365 up).
Metabolic (KEGG Ids: 00520, 00240) and signaling (KEGG Id: 04115) pathways were significantly modulated in VC- mice, with heterogeneity regarding direction of differential expression within the same pathway (Tables S4, S5, S6, Figures S5, S6, S7).
Beyond the diagnostic potential of this PBMC differential expression profile, the normal functions and direction of differential expression of each of the genes, especially the 65 that were ≥1.5 fold differentially expressed, hints at potential pathophysiologic mechanisms.
Unlike genes annotated to inflammation/immune response pathways, the direction of differential gene expression for cholesterol/lipid metabolism and cell cycle genes was very clear (Figs. 2 and 4; Supporting Information, Tables S4 and S5).
Specific gene nodes on each pathway were 'painted' according to the direction of differential expression of that gene on day 7 of DSS treatment: red if up-regulated, green if down-regulated.
