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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

  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