Table 3.
Top 20 GO terms showing significant enrichment for APOE ε4 vs. ε2-associated differentially methylated loci
| Ontology category | Term | Proportion* | P value | Genes |
|---|---|---|---|---|
| BP | Cholesterol metabolic process | 7/146 | 2.00 × 10−11 | DHCR24, APOC1, APOE, LDLR, SQLE, SREBF2, ABCG1 |
| BP | Secondary alcohol metabolic process | 7/156 | 3.59 × 10−11 | DHCR24, APOC1, APOE, LDLR, SQLE, SREBF2, ABCG1 |
| BP | Chylomicron remnant clearance | 4/9 | 4.29 × 10−11 | APOC1, APOC2, APOE, LDLR |
| BP | Triglyceride-rich lipoprotein particle clearance | 4/9 | 4.29 × 10−11 | APOC1, APOC2, APOE, LDLR |
| BP | Sterol metabolic process | 7/162 | 4.78 × 10−11 | DHCR24, APOC1, APOE, LDLR, SQLE, SREBF2, ABCG1 |
| BP | Cholesterol homeostasis | 6/94 | 7.57 × 10−11 | MYLIP, APOC2, APOE, LDLR, SREBF2, ABCG1 |
| BP | Sterol homeostasis | 6/94 | 7.57 × 10−11 | MYLIP, APOC2, APOE, LDLR, SREBF2, ABCG1 |
| BP | Cholesterol transport | 6/98 | 1.04 × 10−10 | APOC1, APOC2, APOE, LDLR, SREBF2, ABCG1 |
| BP | Regulation of plasma lipoprotein particle levels | 6/100 | 1.17 × 10−10 | MYLIP, APOC1, APOC2, APOE, LDLR, ABCG1 |
| BP | Phospholipid transport | 6/90 | 1.27 × 10−10 | APOC1, APOC2, APOE, KCNN4, LDLR, ABCG1 |
| BP | Regulation of lipid biosynthetic process | 7/190 | 1.50 × 10−10 | APOC1, APOC2, APOE, LDLR, SQLE, SREBF2, ABCG1 |
| BP | Phospholipid efflux | 4/12 | 1.50 × 10−10 | APOC1, APOC2, APOE, ABCG1 |
| BP | Sterol transport | 6/111 | 2.65 × 10−10 | APOC1, APOC2, APOE, LDLR, SREBF2, ABCG1 |
| BP | Cholesterol efflux | 5/56 | 4.60 × 10−10 | APOC1, APOC2, APOE, SREBF2, ABCG1 |
| BP | Organophosphate ester transport | 6/116 | 6.18 × 10−10 | APOC1, APOC2, APOE, KCNN4, LDLR, ABCG1 |
| BP | Regulation of cholesterol transport | 5/61 | 6.55 × 10−10 | APOC1, APOC2, APOE, SREBF2, ABCG1 |
| BP | Regulation of steroid metabolic process | 6/123 | 6.67 × 10−10 | APOC1, APOE, LDLR, SQLE, SREBF2, ABCG1 |
| BP | Regulation of sterol transport | 5/62 | 7.34 × 10−10 | APOC1, APOC2, APOE, SREBF2, ABCG1 |
| BP | Lipid localization | 8/407 | 7.54 × 10−10 | APOC1, APOC2, APOE, KCNN4, LDLR, SQLE, SREBF2, ABCG1 |
| BP | High-density lipoprotein particle remodeling | 4/18 | 1.14 × 10−9 | APOC1, APOC2, APOE, ABCG1 |
Abbreviations: BP biological process, GO gene ontology
*Number of significant target list-associated Entrez IDs associated with the gene ontology term/total number of Entrez IDs associated with the GO term. The target list comprised probes that met a nominal threshold for association with APOE ε4 vs. ε2 carrier status of P ≤ 1 × 10−5