Real time qRT-PCR analysis of the CD40, IL1B, IL6 and TNF genes following infection with M. avium subsp. paratuberculosis . Log2 fold-changes in expression in the M. avium subsp. paratuberculosis-infected MDM (MPTb) relative to the non-infected control MDM at all three time points are shown. All data presented is based on the conventionally-prepared cDNA template. For comparison, the expression profiles for these genes as per the microarray data are also shown. The significance of the fold-changes in expression for each gene based on the real time qRT-PCR analysis only are denoted by asterisks in the figure (*P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001). In addition, the log2 fold-change in expression for the non-infected control MDM at each time point relative to the 0 hour non-infected control MDM are also shown for both the microarray and real time qRT-PCR data; no significant differences in gene expression between the non-infected control MDM relative to the 0 h non-infected control was observed at each time point (P ≥ 0.05).