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Table 4 Enriched pathways

From: Genome-wide association meta-analysis for early age-related macular degeneration highlights novel loci and insights for advanced disease

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
  1. The table shows enriched pathways for highest prioritized genes (from Fritsche et al. 2016 without modifications) in the 25 late AMD loci with early AMD effects (35 genes) versus the 8 loci with no effect on early AMD (9 genes). Pathways with significant corrected P-value (Pcorr < 0.05) for each gene group from EnrichR querying human Reactome database 2016 are shown