Table 5.
Top 20 pathway enrichments analysis of the common consensus subnetwork
| Pathway | Overlap | P-value | Adjusted P-value | Z-score | Combined Score | Genes |
|---|---|---|---|---|---|---|
| glioma | 4/62 | 7.19E-05 | 0.002277 | −2.14 | 13.00 | PDGFRB; PIK3R1;CALM1;TP53 |
| apoptosis | 4/81 | 1.94E-04 | 0.002277 | −1.85 | 11.28 | CASP8; CFLAR;PIK3R1;TP53 |
| huntingtons disease | 3/31 | 2.20E-04 | 0.002277 | −1.77 | 10.77 | CASP8;CALM1;TP53 |
| colorectal cancer | 4/84 | 2.22E-04 | 0.002277 | −1.84 | 11.18 | PDGFRB; GSK3B;PIK3R1;TP53 |
| prostate cancer | 4/86 | 2.42E-04 | 0.002277 | −1.80 | 10.97 | PDGFRB; GSK3B;PIK3R1;TP53 |
| endometrial cancer | 3/52 | 9.23E-04 | 0.007232 | −1.65 | 8.13 | GSK3B;PIK3R1;TP53 |
| renal cell carcinoma | 3/69 | 2.02E-03 | 0.01286 | −1.61 | 6.99 | GAB1;PIK3R1;HIF1A |
| melanoma | 3/71 | 2.19E-03 | 0.01286 | −1.49 | 6.50 | PDGFRB;PIK3R1;TP53 |
| erbb signaling pathway | 3/85 | 3.59E-03 | 0.018769 | −1.53 | 6.08 | GSK3B;GAB1;PIK3R1 |
| focal adhesion | 4/192 | 4.51E-03 | 0.02118 | −1.60 | 6.16 | PDGFRB; GSK3B;PIK3R1;RHOA |
| neurodegenerative diseases | 2/38 | 9.01E-03 | 0.038512 | −0.87 | 2.83 | NGFR;CASP8 |
| non small cell lung cancer | 2/53 | 1.66E-02 | 0.064347 | −1.21 | 3.32 | PIK3R1;TP53 |
| basal cell carcinoma | 2/55 | 1.78E-02 | 0.064347 | −0.92 | 2.53 | GSK3B;TP53 |
| b cell receptor signaling pathway | 2/62 | 2.22E-02 | 0.074377 | −0.91 | 2.37 | GSK3B;PIK3R1 |
| phosphatidylinositol signaling system | 2/72 | 2.91E-02 | 0.081711 | −1.00 | 2.50 | PIK3R1;CALM1 |
| pancreatic cancer | 2/73 | 2.98E-02 | 0.081711 | −0.99 | 2.49 | PIK3R1;TP53 |
| chronic myeloid leukemia | 2/75 | 3.13E-02 | 0.081711 | −0.93 | 2.33 | PIK3R1;TP53 |
| adherens junction | 2/75 | 3.13E-02 | 0.081711 | −0.78 | 1.96 | CSNK2A1;RHOA |
| regulation of actin cytoskeleton | 3/201 | 3.54E-02 | 0.087678 | −0.96 | 2.34 | PDGFRB; PIK3R1;RHOA |
| small cell lung cancer | 2/85 | 3.92E-02 | 0.092081 | −0.73 | 1.74 | PIK3R1;TP53 |
Pathway: The name of KEGG pathway
Overlap: The number of overlapping genes compared with the number of input genes
P-value: P-value was computed using the Fisher exact test
Adjusted P-value: Adjusted P-value was a corrected p-value to the Fisher exact test
Z-score: Computed by assessing the deviation from the expected rank
Combined score: Computed by taking the log of the p-value from the Fish exact test and multiplying that by the z-score of the deviation from the expected rank
Genes: The overlapping genes between the input and the pathway