Table 1.
Pathway level analysis of genes differentially expressed following stimulation with BCG.
| BCG stimulation | PPD stimulation | |||||||||
| Pathway Name | Rank | aImpact Factor | b#Genes in Pathway | cp-value | dgamma p-value | Rank | aImpact Factor | b#Genes in Pathway | cp-value | dgamma p-value |
| Cell adhesion molecules (CAMs) | 1 | 45.4 | 4/133 | 0.153 | 9.00E-19 | - | - | - | - | - |
| Cytokine-cytokine receptor interaction | 2 | 34.6 | 34/259 | 1.31E-12 | 3.51E-14 | 15 | 7.2 | 27/259 | -5.50E-14 | 0.006 |
| Hematopoietic cell lineage | 3 | 30.6 | 14/88 | 8.34E-11 | 1.57E-12 | 1 | 27.3 | 12/88 | 2.68E-10 | 3.86E-11 |
| Toll-like receptor signaling pathway | 4 | 26.4 | 14/102 | 6.39E-10 | 9.56E-11 | 4 | 18.3 | 9/102 | 2.11E-06 | 2.14E-07 |
| Fc epsilon RI signaling pathway | 5 | 21.6 | 2/77 | 0.336 | 9.24E-09 | 11 | 10.2 | 2/77 | 0.211 | 4.24E-04 |
| Jak-STAT signaling pathway | 6 | 21.3 | 13/153 | 8.33E-07 | 1.22E-08 | 6 | 14.0 | 8/153 | 3.24E-04 | 1.21E-05 |
| Graft-versus-host disease | 7 | 20.1 | 5/42 | 4.65E-04 | 4.03E-08 | 3 | 18.6 | 5/42 | 9.93E-05 | 1.67E-07 |
| MAPK signaling pathway | 8 | 17.0 | 13/265 | 2.78E-04 | 7.67E-07 | 5 | 16.0 | 9/265 | 0.003 | 1.98E-06 |
| TGF-beta signaling pathway | 9 | 16.9 | 1/89 | 0.752 | 8.29E-07 | 10 | 10.6 | 3/89 | 0.079 | 3.01E-04 |
| GnRH signaling pathway | 10 | 15.8 | 1/97 | 0.781 | 2.29E-06 | 2 | 26.2 | 1/97 | 0.662 | 1.15E-10 |
| Apoptosis | 11 | 14.1 | 6/84 | 0.002 | 1.13E-05 | 7 | 13.4 | 4/84 | 0.014 | 2.24E-05 |
| Type I diabetes mellitus | 12 | 13.9 | 6/44 | 5.76E-05 | 1.33E-05 | 8 | 12.9 | 5/44 | 1.25E-04 | 3.43E-05 |
| T cell receptor signaling pathway | 13 | 13.1 | 6/93 | 0.003 | 2.84E-05 | 13 | 8.8 | 3/93 | 0.085 | 0.001 |
| PPAR signaling pathway | 14 | 12.5 | 8/69 | 1.14E-05 | 5.14E-05 | 9 | 12.0 | 7/69 | 1.16E-05 | 8.11E-05 |
| Natural killer cell mediated cytotoxicity | 15 | 11.4 | 5/131 | 0.054 | 1.34E-04 | 14 | 7.9 | 3/131 | 0.179 | 0.003 |
| Type II diabetes mellitus | 16 | 9.0 | 3/44 | 0.031 | 0.001 | 17 | 6.6 | 1/44 | 0.388 | 0.009 |
| Adipocytokine signaling pathway | 17 | 9.0 | 4/72 | 0.026 | 0.001 | - | - | - | - | - |
| Epithelial cell signaling in Helicobacter pylori infection | 18 | 8.6 | 4/69 | 0.022 | 0.002 | 12 | 9.5 | 3/69 | 0.041 | 7.85E-04 |
| Complement and coagulation cascades | 19 | 7.6 | 6/69 | 7.06E-04 | 0.004 | - | - | - | - | - |
| Bladder cancer | 20 | 6.9 | 3/42 | 0.027 | 0.008 | 16 | 6.9 | 3/42 | 0.011 | 0.008 |
| Acute myeloid leukemia | 21 | 6.8 | 5/57 | 0.002 | 0.008 | - | - | - | - | - |
a calculated on basis of proportion of differentially expressed genes in a pathway and gene perturbation factors of all genes in the pathway
b number of genes in a particular pathway
c P value for pathways that contain a proportion of differentially expressed genes that is significantly different from what is expected by chance
d This perturbation factor takes into consideration the (i) normalized fold change of the gene and (ii) the number of genes upstream of its position on a pathway