3.4.1. Analysis of Microarray Gene Expression Profiles via the Classification of Upregulated and Downregulated Genes
We characterized the genes that were upregulated or downregulated by PpIX treatment prior to X-ray irradiation. Accordingly, we first selected genes with altered expression in each treatment group with respect to the NT group based on their p-values (p < 0.01). Then, these genes were classified as upregulated or downregulated after each treatment. In the PpIX-XT group, 290 genes met the selection criteria for upregulation, and 203 genes met the selection criteria for downregulation. In the XT group, 196 genes were upregulated and 146 genes were downregulated. In the PpIXT group, 28 genes were upregulated and 39 genes were downregulated (Table 1). The number of differentially-expressed genes was highest in the PpIX-XT group, followed by the XT and PpIXT groups. We selected genes for the subsequent functional analysis based on their p-value. This selection method was mathematically proven to consider both the fold, as well as the differences.
microarrays-04-00025-t001_Table 1 Table 1  Summary of the microarray data with p-values < 0.01 in the PpIX treatment alone (PpIXT), 3 Gy X-ray irradiation alone (XT) and 3 Gy X-ray irradiation (PpIX-XT) groups, versus the non-treatment (NT) group.

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