Table I.
Pathway enrichment analysis of genes in the gene functional modules.
| A, Module 0 | ||
|---|---|---|
| Pathway enrichment | Protein from module | False discovery rate |
| Mitochondrial translation (R) | 34 | <5.000×10−4 |
| Ribosome (K) | 20 | <5.000×10−4 |
| B, Module 1 | ||
| Pathway enrichment | Protein from module | False discovery rate |
| The citric acid cycle and respiratory electron transport (R) | 16 | <1.667×10−4 |
| Parkinson's disease (K) | 16 | <1.667×10−4 |
| Alzheimer's disease (K) | 16 | <1.667×10−4 |
| Huntington's disease (K) | 16 | <1.667×10−4 |
| Non-alcoholic fatty liver disease (K) | 16 | <1.667×10−4 |
| C, Module 2 | ||
| Pathway enrichment | Protein from module | False discovery rate |
| Hedgehog ligand biogenesis (R) | 8 | <3.333×10−4 |
| Regulation of apoptosis (R) | 8 | <3.333×10−4 |
| Proteasome (K) | 8 | <3.333×10−4 |
| Degradation of beta-catenin by the destruction complex (R) | 8 | <2.500×10−4 |
| Metabolism of amino acids and derivatives (R) | 9 | <1.667×10−4 |
| D, Module 3 | ||
| Pathway enrichment | Protein from module | False discovery rate |
| Ribosome (K) | 7 | <1.000×10−3 |
| SRP-dependent co-translational protein targeting to membrane (R) | 6 | <5.000×10−4 |
| Eukaryotic translation termination (R) | 5 | <3.333×10−4 |
| Eukaryotic translation elongation (R) | 5 | <2.500×10−4 |
| Nonsense-mediated decay (R) | 5 | <2.000×10−4 |
| E, Module 5 | ||
| Pathway enrichment | Protein from module | False discovery rate |
| SRP-dependent co-translational protein targeting to membrane (R) | 7 | <1.000×10−3 |
| Eukaryotic translation termination (R) | 4 | <5.000×10−4 |
| Eukaryotic translation elongation (R) | 4 | <3.333×10−4 |
| Nonsense-mediated decay (R) | 4 | <2.500×10−4 |
| Eukaryotic translation initiation (R) | 4 | <2.000×10−4 |
| F, Module 6 | ||
| Pathway enrichment | Protein from module | False discovery rate |
| Processing of capped intron-containing Pre-mRNA (R) | 5 | <1.000×10−3 |
| RNA polymerase II transcription (R) | 3 | 4.000×10−3 |
| Processing of capped intron-less pre-mRNA (R) | 2 | 8.330×10−3 |
| Transcriptional regulation of pluripotent stem cells (R) | 2 | 1.230×10−2 |
| Regulatory RNA pathways (R) | 2 | 4.200×10−2 |
K indicates that the corresponding pathways were searched from the Kyoto Encyclopedia of Genes and Genomes database; R indicates that the corresponding pathways were searched from the Reactome database; SRP, signal recognition particle.