Table 3 Gene enrichment test on the 1235 genes around the 1507 rsCpGs. Only protein classes with FDR smaller than 0.05 are listed
From: Genotype effects contribute to variation in longitudinal methylome patterns in older people
| Â | Reference genes (18607) | Test genes | Expected genes | Over/under | Fold enrichment | Raw P value | FDR |
|---|---|---|---|---|---|---|---|
PANTHER protein class | |||||||
 Homeodomain transcription factor (PC00119) | 101 | 27 | 5.5 | + | 4.9 | 3.7 × 10−11 | 3.9 × 10−8 |
 Basic helix-loop-helix transcription factor (PC00055) | 76 | 13 | 4.2 | + | 3.1 | 6.7 × 10−4 | 2.4 × 10−2 |
 Helix-turn-helix transcription factor (PC00116) | 176 | 36 | 9.7 | + | 3.7 | 3.1 × 10−10 | 6.6 × 10−8 |
 G-protein coupled receptor (PC00021) | 250 | 31 | 13.7 | + | 2.3 | 1.0 × 10−4 | 4.5 × 10−3 |
 Receptor (PC00197) | 644 | 71 | 35.3 | + | 2.0 | 1.7 × 10−7 | 1.2 × 10−5 |
 Transcription factor (PC00218) | 1073 | 95 | 58.8 | + | 1.6 | 1.2 × 10−5 | 6.6 × 10−4 |
PANTHER pathway | |||||||
 Cadherin signalling pathway (P00012) | 157 | 27 | 8.6 | + | 3.1 | 1.0 × 10−6 | 1.7 × 10−4 |
 Wnt signalling pathway (P00057) | 307 | 39 | 16.8 | + | 2.3 | 6.3 × 10−6 | 5.2 × 10−4 |
 Heterotrimeric G-protein signalling pathway-Gq alpha and Go alpha-mediated pathway (P00027) | 123 | 18 | 6.7 | + | 2.7 | 3.8 × 10−4 | 1.6 × 10−2 |