Table 1 shows the raw and the LY2835219 net expression signals of the 10 most up- and the 10 most down-regulated genes in AGS
cells infected with the different strains of H. Based on the direct analysis of the gene list, and those obtained from networks and pathways analysis, and very especially on the role of IL-8 in the induction of inflammatory responses, we focused our efforts on confirming the effects of the infection on IL-8 production. Figure 1 Differential gene expression profiles of AGS gastric epithelial cells infected with WT, rocF- and the rocF + complemented H. pylori strains. A. Representative portion of the Log10 ratio between the net expression values between the infected and the non-infected cells, as described in Materials and Methods. The analysis was done using four replicates of each treatment. The marked areas above the heat map show genes associated with different cellular functions. B. Venn diagram showing the number of genes affected (up- and down-regulated) by the infection of AGS cells with the WT, rocF-, Poziotinib cost or rocF + strains of H. pylori. The
green number (262) indicates the number of genes that are common to all treatments; the black numbers indicate unique genes in each treatment; the total shaded area represent 583 genes that are neither common nor unique (similar genes). Figure 2 Network interactions in AGS cells infected with H. pylori . A. Expanded central node of a network (RelA (p65), NFkB, c-IAP2, NFkBIA, and MUC1) generated using the net gene expression values of the different H. pylori infections of the AGS cells. Green arrow = positive regulation; green icons represent receptor ligands (IL-8, VEGFA); red icons represent transcription factors (NFKB1, STAT3); yellow icon represent generic enzyme (p300). Thicker arrows indicate stronger association. B. Heatmap showing the similarity of the different replicates, using the Log10 ratio of the expression values, as explained in Figure 1. Both Figures were generated using data from four replicate independent experiments. Table 1 Ten most up- and 10 most down-regulated
genes in AGS cells in response to the infection with the different strains Farnesyltransferase of H. pylori Raw Signal Net Signal* H. pyloristrain H. pyloristrain TargetID NS WT rocF- rocF + WT rocF- rocF + IL8 130.5 531.8 4021.7 1276.8 401.3 3891.2 1146.3 S100A3 143.6 298.2 1488.3 463 154.6 1344.7 319.4 KRT17 1115.3 2555.1 11710.4 7149.9 1439.8 10595.1 6034.6 LCP1 214.4 351.2 1585.8 568.8 136.8 1371.4 354.4 SERPINB2 116.2 129.1 547.4 235.8 12.9 431.2 119.6 RND1 113.6 171.3 576 195.7 57.7 462.4 82.1 ACTG2 402.8 417.7 1388.5 723.4 14.9 985.7 320.6 SPOCD1 170.4 250.4 748 321.4 80 577.6 151 RASD1 157.5 192.8 563.6 269.5 35.3 406.1 112 PLAUR 450.2 1714 4856.2 1649.2 1263.8 4406 1199 RPP40 2648 1581.3 591.7 2117.1 −1066.7 −2056.3 −530.9 RRS1 596.6 397.5 148.2 477.9 −199.1 −448.4 −118.7 CABC1 1038.4 698.2 254.1 652.8 −340.2 −784.3 −385.