Table 2.
Enrichment of Gene Ontology (GO) terms and KEGG pathways associated with aging and AD-specific modules.
| Module (genes) | KEGG pathway | Biological process | Cellular components | Hub genes |
|---|---|---|---|---|
| M2 (2072) | Ribosome (1.7E-10), Spliceosome (1.2E-2), RNA transport (2.4E-4∗) | rRNA processing (2.4E-13), mRNA splicing (3.6E-5), mRNA processing (1.1E-4) | Nucleolus (1.6E-10), Ribosome (4.1E-6) | TFEB, PAN2, ARHGAP17 |
| M3 (675) | Fatty acid degradation (8.2E-3), Hippo signaling (2.7E-2), PPAR signaling (9.7E-4∗) | Cell adhesion (4.1E-2), Oxidation–reduction process (3.0E-4∗), Fatty acid beta-oxidation (8.5E-4∗) | Extracellular exosome (1.5E-2), Focal adhesion (3.9E-4∗), Extracellular space (8.9E-4∗) | CDC42EP4, EZR, ARHGEF26, TCF7L1, SOX9, ARHGEF6 |
| M4 (701) | Phagosome (4.3E-8), Toll-like receptor signaling (3.1E-6), Cytokine–cytokine receptor interaction (2.7E-4) | Inflammatory response (1.4E-18), Signal transduction (4.0E-12), Toll-like receptor signaling (7.6E-8) | MHC class II protein complex (1.8E-6), Integral component of membrane (2.6E-3), Phagocytic vesicle membrane (4.3E-3) | TYROBP, TREM2, ITGB2, MYO1F, C1Qs, TGFB1 |
| M5 (798) | TNF signaling (1.9E-6), Complement and coagulation cascades (5.6E-5), HIF-1 signaling (4.1E-4) | Inflammatory response (4.8E-16), Response to LPS (1.5E-8), Cellular response to TNF (2.2E-8) | Extracellular matrix (3.5E-7), Extracellular exosome (5.8E-7), MHC class 1 complex (1.4E-4) | TNFRSF1A, MSN, CLIC1, IFITM2 |
| M7 (333) | ECM-receptor interaction (6.4E-3∗), Focal adhesion (3.6E-2∗) | Outer dynein arm assembly (6.4E-12), Inner dynein arm assembly (3.8E-9), Cilium morphogenesis (9.0E-9) | Axoneme (1.3E-18), Motile cilium (5.5E-17) | ZMYND10, ARMC3, CFAP43 |
| M8 (695) | Axon guidance (5.9E-3), Oxytocin signaling (1.6E-3∗), Rap1 signaling (4.8E-3∗) | Calcium ion transport (8.1E-3∗), Potassium ion transport (9.9E-3∗), Dendritic spine morphogenesis (1.1E-2∗) | Cell junction (9.7E-9), Postsynaptic density (6.4E-8), Dendritic spine (9.1E-5) | ICAM5, PRKCG, JPH3, SPTBN2 |
| M9 (2377) | Synaptic vesicle (8.3E-10), Glutamatergic synapse (3.8E-5), Long term potentiation (4.2E-3) | Chemical synaptic transmission (2.3E-16), Neurotransmitter secretion (1.5E-6), Nervous system development (5.8E-5) | Neuron projection (2.5E-10), Dendrite (1.9E-10), Axon (4.9E-9) | UCHL1, STMN2, SYN1, SYT5, SNAP91, PAK3 |
| M10 (2660) | Oxidative phosphorylation (1.8E-19), Proteasome (6.6E-11), Spliceosome (7.5E-7), Protein processing in ER (3.8E-5) | Mitochondria electron transport (1.4E-12), Protein folding (9.3E-9) | Mitochondrion (2.4E-62), Mitochondrial matrix (2.4E-19), Proteasome complex (3.4E-9), Ribosome (2.5E-8) | NDUFAB1, VDAC3, ATP5G3, COPS4, RTCA, POP4 |
| M12 (584) | Retrograde endocannabinoid signaling (4.8E-4), Circadian entrainment (7.1E-3), Glutamatergic synapse (7.2E-3), GABAergic synapse (2.9E-2) | Peptidyl-serine phosphorylation (2.9E-4∗), Neuron cell–cell adhesion (2.1E-3∗) | Postsynaptic density (3.5E-2), Postsynaptic membrane (2.9E-2) | YWHAZ, GADP1, SYNJ1, MAPK9, G3BP2, ATP6AP2 |
Benjamini-Hochberg corrected p-values are given inside the bracket. ∗Represents uncorrected p-value.