Time-series gene expression profiles in AGS cells stimulated with Helicobacter pylori

Figure 1 Hierarchical cluster analysis of time-series gene expression alteration after infection of Helicobacter pylori at 5 time points. Genes that significantly changed during infection were included in hierarchical clustering analysis using average linkage and Euclidean dissimilarity methods. Significant clusters A and B show the details of genes including name of the gene down-regulated at 4 h and up-regulated at 6 h. Eighty of the most differentially expressed genes were clustered in C. Immunity and tumor related genes are labeled.

Figure 2 Short time-series expression miner (STEM) clustering of the differentially expressed genes. All profiles are ordered based on the P value significance of the number of genes assigned vs expected. A: Profile 123 (0, 0, 0, 0, -1, 0): 126.0 genes assigned, 37.8 genes expected, P-value = 5.4E-32 (significant); B: Profile 3 (0, -2, -2, -2, -4, -3): 11.0 genes assigned, 0.4 genes expected, P-value = 1.9E-12 (significant); C: Profile 144 (0, 0, 1, 0, 2, 3): 16.0 genes assigned, 2.5 genes expected, P-value = 8.5E-9 (significant); D: Profile 121 (0, 0, 0, 0, -2, -3): 21.0 genes assigned, 5.7 genes expected, P-value = 6.3E-7 (significant).

Figure 3 STEM clustering of all the 3577 differentially expressed genes labeled by accession number. All profiles were ordered based on the P value significance of the number of genes assigned vs expected. A: Profile 111 (0, 0, 0, -1, 1): 28.0 genes assigned, 4.2 genes expected, P-value = 1.2E-14 (significant); B: Profile 71 (0, -1, 0, 2, 2): 123.0 genes assigned, 19.0 genes expected, P-value = 4.4E-58 (significant); C: Profile 108 (0, 0, 0, -2, -3): 57.0 genes assigned, 16.2 genes expected, P-value = 1.5E-15 (significant); D: Profile 83 (0, -1, 1, 1, 3): 17.0 genes assigned, 2.7 genes expected, P-value = 4.3E-9 (significant).

Figure 4 A simplified gene network extracted from significant pathways using STRING database.