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Table 3 Cluster profiling: KEGG cellular pathways and Gene Ontology

From: Interleukin-8 is the single most up-regulated gene in whole genome profiling of H. pylori exposed gastric epithelial cells

Temporal profile over 24 h Cellular Pathway Impact Factor GO number GO name
MAPK signaling pathway 7.3 GO:0006916 anti-apoptosis
  Apoptosis 7.1 GO:0045063 T-helper 1 cell differentiation
    GO:0031665 negative regulation of LPS-mediated signaling pathway
    GO:0014912 negative regulation of smooth muscle cell migration
    GO:0043405 regulation of MAP kinase activity
Epithelial cell signaling in H. pylori infection 12.4 GO:0006935 chemotaxis
  Cytokine-cytokine receptor interaction 10.2 GO:0006954 inflammatory response
  Bladder cancer 6.8 GO:0006955 immune response
  Toll-like receptor signaling pathway 5.9 GO:0045091 regulation of retroviral genome replication
  Pathways in cancer 4.8 GO:0042119 neutrophil activation
    GO:0050930 induction of positive chemotaxis
    GO:0030593 neutrophil chemotaxis
    GO:0030155 regulation of cell adhesion
    GO:0019722 calcium-mediated signaling
Circadian rhythm 20.0 GO:0006915 apoptosis
  MAPK signaling pathway 10.7 GO:0006950 response to stress
  mTOR signaling pathway 7.5 GO:0007050 cell cycle arrest
  Tight junction 7.0 GO:0030216 keratinocyte differentiation
  Jak-STAT signaling pathway 6.7 GO:0006865 amino acid transport
  Cytokine-cytokine receptor interaction 6.5 GO:0031424 keratinization
  Regulation of autophagy 6.4 GO:0008652 amino acid biosynthetic process
  p53 signaling pathway 5.6 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 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 nucleic acid metabolic process
  Regulation of actin cytoskeleton 6.1 GO:0008299 isoprenoid biosynthetic process
    GO:0006601 creatine biosynthetic process
    GO:0009416 response to light stimulus
    GO:0043154 negative regulation of caspase activity
    GO:0007566 embryo implantation
  1. 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. Top 10 ontologies listed where number is exceeding 10