Table 2.
Top 5 enriched pathways per database (Reactome Pathways, WikiPathways, and KEGG Pathways). The column “Gene” is the number of genes in the network associated with each pathway term. The column “Proportion” is the ratio between the number of genes with that term divided by the total number of genes in the network (n = 3718).
| Database | Pathway | Genes | FDR Value | Proportion |
|---|---|---|---|---|
| Reactome Pathways | Metabolism of proteins | 660 | 5.03 × 10−52 | 17.75% |
| Reactome Pathways | Gene expression (Transcription) | 536 | 1.6 × 10−51 | 14.42% |
| Reactome Pathways | Cellular responses to stress | 278 | 1.73 × 10−44 | 7.48% |
| Reactome Pathways | Disease | 525 | 3.89 × 10−42 | 14.12% |
| Reactome Pathways | Metabolism of RNA | 299 | 1.99 × 10−40 | 8.04% |
| WikiPathways | VEGFA-VEGFR2 signaling pathway | 205 | 4.44 × 10−29 | 5.51% |
| WikiPathways | Alzheimer’s disease and miRNA effects | 129 | 3.6 × 10−19 | 3.47% |
| WikiPathways | DNA IR-damage and cellular response via ATR | 64 | 8.38 × 10−17 | 1.72% |
| WikiPathways | Integrated breast cancer pathway | 89 | 1.39 × 10−16 | 2.39% |
| WikiPathways | Androgen receptor signaling pathway | 65 | 1.94 × 10−15 | 1.75% |
| KEGG Pathways | Shigellosis | 122 | 3.57 × 10−21 | 3.28% |
| KEGG Pathways | Amyotrophic lateral sclerosis | 148 | 4.07 × 10−17 | 3.98% |
| KEGG Pathways | Viral carcinogenesis | 99 | 6.45 × 10−17 | 2.66% |
| KEGG Pathways | Parkinson disease | 110 | 9.04 × 10−15 | 2.96% |
| KEGG Pathways | Huntington disease | 125 | 1.41 × 10−14 | 3.36% |