Table 2.
Gene sets found to be highly associated with liver enzymes in KARE (P < 1E-03)
| Phenotype | Gene-set | KARE results | ||||||
|---|---|---|---|---|---|---|---|---|
| Maximum MAF | minimum MAC | P-value | ||||||
| GS. QTest1 | GS. QTest2 | GS. QTest3 | GS. SKAT | GS. SKATO | ||||
| ALT | PID_AURORA_A_PATHWAY | 0.05 | 2 | 5.0E-04 (4.2E-04)* | 1.2E-01 (1.5E-01) | 1.2E-03 (1.2E-03) | 1.8E-01 (1.9E-01) | 5.9E-03 (6.2E-03) |
| BIOCARTA_RELA_PATHWAY | 0.05 | 2 | 8.4E-04 (8.7E-04) | 2.2E-02 (2.7E-02) | 2.0E-03 (2.3E-03) | 2.4E-01 (2.2E-01) | 8.2E-02 (8.1E-02) | |
| KEGG_FOLATE_BIOSYNTHESIS | all | 2 | 4.6E-02 (4.5E-02) | 7.7E-04 (7.9E-04) | 2.7E-03 (2.8E-03) | 6.9E-01 (6.8E-01) | 7.0E-01 (6.8E-01) | |
| AST | REACTOME_SIGNALING_BY_NODAL | 0.05 | 2 | 9.9E-01 (9.9E-01) | 4.2E-05 (4.1E-05) | 3.4E-05 (3.4E-05) | 1.1E-03 (9.8E-04) | 2.3E-03 (2.2E-02) |
| REACTOME_GRB2_SOS_PROVIDES_LINKAGE_TO_MAPK_SIGNALING_FOR_INTERGRINS | 0.05 | 2 | 4.7E-04 (4.5E-04) | 4.3E-02 (4.3E-02) | 1.1E-03 (1.0E-03) | 1.3E-01 (1.4E-01). | 1.1E-02 (1.3E-02) | |
| REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES | 0.05 | 2 | 7.5E-01 (7.5E-01) | 7.5E-04 (7.8E-04) | 1.2E-03 (1.3E-03) | 9.3E-03 (9.5E-03) | 1.9E-02 (1.8E-02) | |
| PID_RETINOIC_ACID_PATHWAY | all | 2 | 9.7E-01 (9.6E-01) | 9.6E-04 (9.3E-04) | 1.2E-03 (1.0E-03) | 4.1E-02 (4.3E-01) | 8.3E-02 (8.3E-02) | |
| GGT | PID_ARF6_PATHWAY | 0.05 | 2 | 4.3E-04 (4.2E-04) | 6.9E-02 (6.9E-02) | 1.1E-04 (9.9E-05) | 1.5E-01 (1.7E-01) | 2.4E-03 (2.4E-03) |
| KEGG_BETA_ALANINE_METABOLISM | all | 2 | 2.1E-01 (1.9E-01) | 4.7E-06 (5.1E-06) | 1.1E-05 (1.3E-05) | 7.8E-02 (7.8E-02) | 8.6E-02 (8.6E-02) | |
| KEGG_LYSINE_DEGRADATION | all | 2 | 4.0E-02 (4.5E-02) | 4.5E-06 (4.7E-06) | 1.9E-05 (2.0E-05) | 3.0E-03 (2.8E-03) | 2.0E-03 (2.0E-03) | |
| KEGG_BUTANOATE_METABOLISM | all | 2 | 1.6E-01 (1.6E-01) | 6.8E-05 (6.6E-05) | 2.1E-04 (2.0E-04) | 3.8E-02 (3.7E-02) | 6.5E-02 (6.3E-02) | |
| REACTOME_ETHANOL_OXIDATION | all | 2 | 5.0E-04 (5.3E-04) | 6.1E-05 (6.1E-05) | 2.5E-04 (2.6E-04) | 1.7E-07 (1.6E-07) | 2.9E-07 (3.1E-07) | |
| KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION | all | 2 | 2.4E-01 (2.7E-01) | 8.5E-05 (8.3E-05) | 1.0E-03 (1.1E-03) | 8.8E-02 (8.6E-02) | 1.6E-01 (1.6E-01) | |
| REACTOME_IL_6_SIGNALING | all | 2 | 2.4E-04 (2.3E-04) | 1.8E-03 (1.8E-03) | 5.6E-04 (5.9E-04) | 4.1E-03 (4.5E-03) | 1.8E-03 (1.9E-03) | |
*Permutation P-values are given in parentheses.