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Table 2 Time course: 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

Time KEGG cellular pathway name IF GO up-regulated genes GO down-regulated genes
0.5 No significant genes   No significant genes No significant genes
1 Epithelial cell signaling in Helicobacter pylori infection 16.6 No significant GO No significant genes
  Cytokine-cytokine receptor interaction 8.1   
  Bladder cancer 7.5   
  Toll-like receptor signaling pathway 6.6   
  Base excision repair 6.0   
  Primary immunodeficiency 5.9   
  Pathways in cancer 5.4   
3 Epithelial cell signaling in Helicobacter pylori infection 17.8 anti-apoptosis No significant GO
  Pathways in cancer 16.9 regulation of retroviral genome  
  Small cell lung cancer 14.2 replication  
  MAPK signaling pathway 14.2 T-helper 1 cell differentiation  
  Apoptosis 12.5 negative regulation of LPS-mediated signaling pathway  
  Adipocytokine signaling pathway 12.3 negative regulation of smooth muscle cell migration  
  Prostate cancer 11.4 regulation of MAP kinase activity chemotaxis  
  Toll-like receptor signaling pathway 11.1 protein amino acid dephosphorylation  
  T cell receptor signaling pathway 10.5 neutrophil activation  
  B cell receptor signaling pathway 9.9 entrainment of circadian clock  
6 Phosphatidylinositol signaling system 32.2 anti-apoptosis No significant GO
  Epithelial cell signaling in Helicobacter pylori infection 15.5 regulation of retroviral genome  
  Small cell lung cancer 14.2 replication  
  Pathways in cancer 12.4 T-helper 1 cell differentiation  
  Apoptosis 11.6 neutrophil activation  
  Adipocytokine signaling pathway 10.1 negative regulation of I-kappaB  
  Toll-like receptor signaling pathway 8.9 kinase/NF-kB cascade  
  MAPK signaling pathway 8.7 induction of positive chemotaxis  
  Bladder cancer 8.5 myeloid dendritic cell differentiation  
  B cell receptor signaling pathway 8.3   
12 Leukocyte transendothelial migration 309.7 cell cycle arrest response to unfolded protein
  Cell adhesion molecules (CAMs) 75.4 amino acid transport S-adenosylmethionine biosynthetic process
  DNA replication 25.0 positive regulation of transcription  
  Cell cycle 20.0 response to stress  
  Pathways in cancer 19.4 regulation of MAP kinase activity  
  p53 signaling pathway 17.0   
  Antigen processing and presentation 15.7   
  MAPK signaling pathway 13.2   
  Small cell lung cancer 12.2   
  Circadian rhythm 11.9   
24 Leukocyte transendothelial migration 80.3 keratinocyte differentiation cholesterol biosynthetic process
  Cell cycle 24.4 amino acid transport response to unfolded protein
  p53 signaling pathway 20.9 keratinization isoprenoid biosynthetic process
  Circadian rhythm 18.6 angiogenesis creatine biosynthetic process
  DNA replication 18.0 apoptosis response to oxidative stress
  Adherens junction 16.1 response to stress  
  Pathways in cancer 14.9 cell cycle arrest  
  Nucleotide excision repair 14.3 pyrimidine nucleotide metabolic  
  Ubiquitin mediated proteolysis 14.2 process  
  Phosphatidylinositol signaling system 13.7 induction of positive chemotaxis  
  1. Significantly impacted KEGG cellular pathways and enriched Gene Ontology terms (biological processes only) (p < 0.05) at different time points following co-culture of H. pylori and AGS cells. Top 10 pathways/ontologies included where number exceeds 10. IF = impact factor