Table 2 Upstream regulator analysis

From: Campylobacter jejuni impairs sodium transport and epithelial barrier function via cytokine release in human colon

Upstream regulator

Overlap p -value

Activation z -score

Number of genes that have expression direction consistent with activation of the cytokine

LPS

3.22E−66

11.94

343 (of 501 affected downstream targets)

IFNγ

3.95E−44

9.62

253 (of 370 affected downstream targets)

CSF2

2.58E−42

10.15

144 (of 182 affected downstream targets)

TNFα

3.23E−41

9.00

279 (of 462 affected downstream targets)

IL-6

1.18E−38

7.25

134 (of 236 affected downstream targets)

IL-13

1.39E−30

2.12

87 (of 145 affected downstream targets)

IL1β

1.54E−24

8.57

165 (of 236 affected downstream targets)

  1. Abbreviations: CSF2, granulocyte macrophage colony-stimulating factor; IFNγ, interferon-gamma; IL, interleukin; LPS, lipopolysaccharide; TNFα, tumor necrosis factor-alpha.
  2. Top upstream regulators, lipopolysaccharide (LPS) and proinflammatory cytokines with highly significant activation of their downstream targets in colon specimens from patients with campylobacteriosis (4 patients vs. 6 healthy controls). Column 1; gene name of the upstream regulator. Column 2; P-value of the overlap of the downstream target gene set and the pathway gene set. Column 3; Activation z-score. Column 4; number of genes with expression changes. The complete list of genes differentially expressed in patients with C. jejuni and controls, which are downstream targets of the upstream regulator is provided in the (Supplementary Table S2). For target gene names, see supplementary spreadsheet online (Supplementary Table S2 online). The overlap P-value measures whether there is a statistically significant overlap between the data set genes and the genes that are regulated by an upstream transcriptional regulator. It is calculated using Fisher’s exact test, and significance is generally attributed to P-values <0.01. A statistical approach defines a quantity (z-score) that determines whether an upstream transcription regulator has significantly more “activated” predictions than “inhibited” predictions (z>0) or vice versa (z<0).
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