Table 2.
Module genes enriched in biological pathways. The top five pathways are shown for each module.
| Module (# of Pathways Padj<0.10) | Term | P value | Adjusted P value | Odds Ratio | Module Genes / Pathway Genes | |
|---|---|---|---|---|---|---|
|
| ||||||
| RV-Response Pathways |
Black (4) Cell Proliferation |
Retinoblastoma Gene in Cancer | 4.63×10−05 | 2.18×10−02 | 2.96 | 17/87 |
| DNA Replication | 3.18×10−04 | 7.51×10−02 | 3.61 | 10/42 | ||
| Breast cancer pathway | 5.01×10−04 | 7.88×10−02 | 2.16 | 22/154 | ||
| EGF/EGFR Signaling Pathway | 1.00×10−03 | 9.45×10−02 | 2.06 | 22/162 | ||
| Signaling Pathways in Glioblastoma | 8.88×10−04 | 1.05×10−01 | 2.59 | 14/82 | ||
|
Red (67) Immune Response to Microbial Infection |
The human immune response to tuberculosis | 6.35×10−19 | 3.00×10−16 | 20.22 | 16/23 | |
| Type II interferon signaling (IFNG) | 3.5×10−17 | 8.27×10−15 | 14.14 | 18/37 | ||
| Retinoblastoma Gene in Cancer | 1.24×10−14 | 1.94×10−12 | 7.69 | 23/87 | ||
| DNA IR-damage and cellular response via ATR | 1.99×10−11 | 2.34×10−09 | 6.9 | 19/80 | ||
| Apoptosis | 2.34×10−08 | 2.21×10−06 | 5.54 | 16/84 | ||
|
Yellow (9) Lipid and Cholesterol Biosynthesis |
Genes related to primary cilium development | 8.29×10−13 | 3.91×10−10 | 3.45 | 39/103 | |
| Cholesterol Biosynthesis Pathway | 9.68×10−10 | 2.28×10−07 | 7.3 | 12/15 | ||
| Sterol Regulatory Element-Binding Proteins (SREBP) signaling | 5.83×10−07 | 9.17×10−05 | 3.04 | 23/69 | ||
| Ciliary landscape | 1.57×10−04 | 1.24×10−02 | 1.77 | 42/216 | ||
| Lipid Metabolism Pathway | 1.41×10−04 | 1.33×10−02 | 3.46 | 11/29 | ||
| CRS Gene Pathways |
Blue (10) Oxidative Phosphorylation |
Cytoplasmic Ribosomal Proteins | 1.31×10−39 | 6.21×10−37 | 12.93 | 45/89 |
| Electron Transport Chain (OXPHOS system in mitochondria) | 1.61×10−14 | 3.81×10−12 | 6.46 | 26/103 | ||
| Oxidative phosphorylation | 7.66×10−10 | 1.21×10−07 | 6.82 | 16/60 | ||
| Mitochondrial complex I assembly model OXPHOS system | 1.80×10−07 | 1.70×10−05 | 5.94 | 13/56 | ||
| Nonalcoholic fatty liver disease | 1.68×10−07 | 1.98×10−05 | 3.63 | 22/155 | ||
|
Turquoise (1) Leptin Signaling |
Leptin signaling pathway | 9.47×10−06 | 4.47×10−03 | 5.1 | 11/76 | |
| IL-5 Signaling Pathway | 8.62×10−04 | 1.02×10−01 | 5.28 | 6/40 | ||
| MET in type 1 papillary renal cell carcinoma | 1.36×10−03 | 1.07×10−01 | 4.18 | 7/59 | ||
| TNF alpha Signaling Pathway | 1.21×10−03 | 1.14×10−01 | 3.44 | 9/92 | ||
| Pathways Affected in Adenoid Cystic Carcinoma | 4.90×10−04 | 1.16×10−01 | 4.33 | 8/65 | ||