Table 3.
Pathway analysis for significant genes identified in gene differential expression analysis in both smoker and nonsmoker group
| Top canonical pathway | p value | Top upstream regulators | p value | Disease and disorders | p value | # molecul |
|---|---|---|---|---|---|---|
| Significant genes with FDR<0.05 and |logFC|>1 in nonsmoking group |
||||||
| Bladder cancer signaling (N) | 2.27E-03 | Estrogen receptor | 5.50E-07 | Cancer | 1.05E-02–1.66E-07 | 197 |
| Granulocyte adhesion and diapedesis (U) | 2.76E-03 | Tetrachlorodibenzodioxin | 7.55E-07 | Organismal injury and abnormalities |
1.05E-02–1.66E-07 | 197 |
| Sertoli cell-Sertoli cell junction signaling (U) | 2.85E-03 | NFkB (complex) | 1.53E-06 | Infectious disease | 3.85E-03–1.61E-06 | 27 |
| IL-12 signaling and production in macrophages (D) | 3.10E-03 | Growth hormone | 4.93E-06 | Inflammatory response | 1.05E-02–3.87E-06 | 58 |
| Role of macrophages, fibroblasts, and endothelial cells in rheumatoid arthritis (D) |
4.46E-03 | EGFR | 6.57E-06 | Dermatological diseases and conditions |
1.05E-02–7.98E-06 | 106 |
| Significant genes with FDR<0.05 and |logFC|>1 in smoking group |
||||||
| MSP-RON signaling pathway (D) | 8.10E-05 | lipopolysaccharide | 1.14E-15 | Cancer | 3.41E-04–4.63E-23 | 764 |
| Axonal guidance signaling (U) | 9.00E-05 | TGFB1 | 8.15E-15 | Organismal injury and abnormalities |
3.58E-04–4.63E-23 | 765 |
| Molecular mechanisms of cancer (N) | 2.10E-04 | Dexamethasone | 9.28E-15 | Gastrointestinal disease | 3.10E-04–2.09E-16 | 581 |
| EL-12 signaling and production in macrophages (D) | 1.18E-03 | dihydrotestosterone | 1.05E-12 | Dermatological diseases and conditions |
6.18E-05–5.52E-16 | 379 |
| FXR/RXR activation (D) | 1.97E-03 | Beta-estradiol | 3.46E-11 | Reproductive system disease | 3.58E-04–3.32E-11 | 395 |
| Significant genes common to both the nonsmoker and smoker groups |
||||||
| Granulocyte adhesion and diapedesis (D) | 3.80E-09 | TGFB1 | 2.92E-52 | Cancer | 6.08E-08–4.85E-69 | 1521 |
| Agranulocyte adhesion and diapedesis (D) | 8.19E-09 | Vegf | 8.12E-41 | Organismal injury and abnormalities |
6.08E-08–4.85E-69 | 1545 |
| Atherosclerosis signaling (N) | 9.42E-08 | Progesterone | 7.53E-40 | Reproductive system disease | 6.08E-08–4.85E-69 | 877 |
| Hepatic fibrosis/hepatic stellate cell activation (N) | 9.74E-08 | ERBB2 | 5.44E-39 | Neurological disease | 3.55E-08–8.67E-40 | 1160 |
| Eicosanoid signaling (D) | 1.48E-06 | Dexamethasone | 7.77E-34 | Cardiovascular disease | 6.70E-09–11.23E-28 | 757 |
The canonical pathway is labeled with U if most of the involved genes are upregulated and D if most genes are downregulated. Ef comparable of genes are upregulated and downregulated, then labeled with N