Mid-jejunal mucosal gene expression analysis was performed using a homemade pig cDNA small intestinal microarray [34] . In two separate hybridization experiments, mRNA expression levels in an uninfected RNA pool (n = 3) were compared to expression levels in RNA pools prepared from 12-and 18-h infected piglets (both n = 2). For both comparisons, dye swaps were performed. Probes that hybridized differentially with a ratio (FC; infected over uninfected) of \0.28 or [3.6 in both slides of the dye-swap and that were identified with the lowest possible false-discovery rate (FDR; based on SAM, [43] ), i.e., 0.35% for the 18-h comparison and 4.6% for the 12-h comparison, were selected for further analysis. Raising of the FDR to a maximum of 10% did not identify additional probes with a FC \ 0.28 or [3.6 in either comparison. Selected probes were sequenced and annotated after blastn or blastx analysis (when not yet annotated). For each differential expressed probe, the mean FC calculated from the two dye-swap slides is presented in Table 2 . When Cy3-and Cy5-labeled cDNA was prepared from the same uninfected RNA pool and simultaneously hybridized on the array, none of the probes that hybridized differentially in the 12-and 18-h comparisons hybridized differentially (results not shown). Six out of the nine probes that hybridized with a FC of 3.6-fold or more in the 12-h comparison (panel ''higher in infected'') also hybridized significantly more strongly in the 18-h comparison. For three of these probes (R14-R16), the ratio of differential expression further increased with time. In contrast, only one probe (R1) hybridized significantly less strongly at both time points. Based on literature search and data mining, a tentative function was assigned for the genes identified by blast analysis (see Table 2 ). In addition, the FC (infected over uninfected) of genes which were also found to be regulated in a previous study by Cuadras et al. [13] , i.e., 16 h after infection of human intestinal epithelial Caco-2 cells with rotavirus live virus vaccine RVV, is provided in parentheses in Table 2 after the annotations. Probes coding for IFN-c, TNF-a, GM-CSF, and IL-2, 4, 6, 8, and 10 were spotted on the array. However, the fluorescence intensity was not higher than the background threshold for any of these probes, indicating that mRNA concentrations of these cytokines (including IFN-c) in infected and uninfected mucosal scrapings were too low to detect by microarray analysis, probably due to the relatively low percentage of cytokine-producing (immune) cells present in intestinal mucosa [6] . 