Table 3

Cluster profiling: KEGG cellular pathways and Gene Ontology

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


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

Eftang et al. BMC Microbiology 2012 12:9   doi:10.1186/1471-2180-12-9

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