6 GO:0006220 pyrimidine nucleotide metabolic process   Regulation of actin cytoskeleton 5.2       TGF-beta signaling pathway 5.2       Natural killer cell mediated cytotoxicity 4.7     Melanogenesis 8.3 GO:0030146 diuresis   GnRH signaling pathway 7.6 GO:0030147 natriuresis   ErbB signaling pathway 6.7 GO:0048661 positive regulation of smooth muscle cell proliferation   Pathways in cancer 6.4 GO:0002268 follicular dendritic cell differentiation   Epithelial cell signaling in H. pylori infection 5.7 GO:0031583 activation of phospholipase D activity by G-protein coupled receptor protein signaling       GO:0014826 vein smooth muscle contraction

      GO:0002467 germinal center formation       GO:0030578 PML body organization       GO:0030195 negative regulation of blood coagulation       GO:0043507 positive regulation of JUN kinase activity Antigen processing and presentation 13.7 GO:0006695 cholesterol SAHA solubility dmso biosynthetic process   MAPK signaling pathway 9.7 GO:0006986 response to unfolded protein   Bladder

cancer 6.2 GO:0006916 anti-apoptosis   Pathways in cancer 6.1 GO:0006139 nucleobase, -side, -tide and see more nucleic acid metabolic process   Regulation of actin cytoskeleton 6.1 GO:0008299 isoprenoid biosynthetic process       GO:0006601 creatine biosynthetic process       GO:0009416 www.selleckchem.com/products/PD-173074.html response to light stimulus       GO:0043154 negative regulation of caspase activity       GO:0007566 embryo implantation Temporal profiles of 5 main clusters identified by hiarchical clustering of the 245 most differentially expressed genes (p < 0.05) and associated gene ontologies (biological processes only) and KEGG cellular signaling pathways in each cluster in H. pylori exposed AGS cells. Data points are at 0.5, 1, 3, 6, 12 and 24 h of co-incubation. Error bars represent ± standard deviation of expression within the cluster. Branched chain aminotransferase Top 10 ontologies listed where number is exceeding 10 Cluster C comprised the largest cluster, and contained 150 genes that did not show any change until after 6-12 h. The GO terms apoptosis, cell cycle arrest and stress response

genes were markedly enriched, and many of these genes such as JUN, GADD45A, DDIT3, MKNK2, DUSP1, RPS6KA5, FLNC, and RASGRP were also involved in MAPK signaling. Furthermore, CSF2RA, IL24, IL20R and the oncogene PIM1 were involved in Jak-STAT signaling and cytokine-cytokine signaling. Cluster D showed a moderate increase peaking at 12 h, followed by a decrease towards 24 h. 13 genes were assigned to this cluster, including EDN1, one of the isoforms of the potent vasoconstrictor endothelin, which enriched virtually all of the listed GOs. NFKB2, one of two NF-κB subunits, HBEGF and ETS1 were also included in this cluster. Cluster E demonstrated 71 genes that showed down-regulation after 6-12 h and included FGFR3 and several heat shock protein genes that were involved in the MAPK signaling pathway and apoptosis inhibition. Also, several GO biosynthetic processes were enriched.