Table 4 Enriched pathways
Gene group | Reactome pathway | #Genes in gene set | #AMD loci in gene set | Raw P | Corrected P | Genes contributing to enrichment |
|---|---|---|---|---|---|---|
Effects on early and advanced AMD | Regulation of Complement cascade (R-HSA-977606) | 26 | 5 | 7.8 × 10−10 | 1.2 × 10−6 | C3;CFH;C9;CFI;CFB |
Lipoprotein metabolism (R-HSA-174824) | 34 | 4 | 3.5 × 10−7 | 1.8 × 10−4 | ABCA1;CETP;LIPC;APOE | |
Complement cascade (R-HSA-166658) | 80 | 5 | 2.7 × 10−7 | 2.0 × 10−4 | C3;CFH;C9;CFI;CFB | |
HDL-mediated lipid transport (R-HSA-194223) | 19 | 3 | 4.7 × 10− 6 | 1.8 × 10−3 | ABCA1;CETP;APOE | |
Lipid digestion, mobilization, and transport (R-HSA-73923) | 71 | 4 | 7.0 × 10− 6 | 2.2 × 10− 3 | ABCA1;CETP;LIPC;APOE | |
Activation of C3 and C5 (R-HSA-174577) | 6 | 2 | 4.4 × 10−5 | 0.011 | C3;CFB | |
no effects on early AMD | Assembly of collagen fibrils and other multimeric structures (R-HSA-2022090) | 54 | 3 | 1.5 × 10− 6 | 2.4 × 10−3 | COL15A1;COL8A1;MMP9 |
Collagen formation (R-HSA-1474290) | 85 | 3 | 6.1 × 10− 6 | 3.1 × 10− 3 | COL15A1;COL8A1;MMP9 | |
Extracellular matrix organization (R-HSA-1474244) | 283 | 4 | 4.7 × 10− 6 | 3.6 × 10− 3 | VTN;COL15A1;COL8A1;MMP9 |