Table 1.
Top 10 differentially promoter or gene body methylated mTOR pathway–related genes
| DataSet | GeneID | logFC | P value | Adj. P value | Contrast | GeneSymbol |
|---|---|---|---|---|---|---|
| Promoter | ENSG00000204060 | 1.75 | 1.61E‐05 | 0.05176 | Ctrl_vs_FCDIIa | FOXO6 |
| Promoter | ENSG00000156052 | 1.13 | 4.17E‐05 | 0.03882 | Ctrl_vs_FCDIIb | GNAQ |
| Promoter | ENSG00000204060 | 1.82 | 9.97E‐05 | 0.04797 | Ctrl_vs_FCDIIb | FOXO6 |
| Promoter | ENSG00000132024 | −0.26 | 0.00014 | 0.07459 | Ctrl_vs_FCDIa | CC2D1A |
| Promoter | ENSG00000204060 | 1.54 | 0.00033 | 0.10911 | Ctrl_vs_FCDIa | FOXO6 |
| Promoter | ENSG00000118689 | 0.72 | 0.00069 | 0.13200 | Ctrl_vs_FCDIa | FOXO3 |
| Promoter | ENSG00000167965 | −0.32 | 0.00140 | 0.52418 | FCDIa_vs_FCDIIb | MLST8 |
| Promoter | ENSG00000164327 | 0.37 | 0.00211 | 0.14265 | Ctrl_vs_FCDIIb | RICTOR |
| Promoter | ENSG00000040199 | −0.24 | 0.00310 | 0.16109 | Ctrl_vs_FCDIIb | PHLPP2 |
| Promoter | ENSG00000100150 | 0.28 | 0.00480 | 0.58119 | FCDIIb_vs_TLE | DEPDC5 |
| Genomic region | ||||||
| GeneBody | 18:60629433‐60629997 | 1.16 | 3.54E‐07 | 0.06283 | Ctrl_vs_FCDIa | PHLPP1 |
| GeneBody | 18:60629433‐60629997 | 0.97 | 2.62E‐05 | 0.21187 | Ctrl_vs_FCDIIb | PHLPP1 |
| GeneBody | 16:2629631‐2630231 | −1.11 | 2.70E‐05 | 0.26838 | Ctrl_vs_TLE | PDPK1 |
| GeneBody | 16:2110009‐2110609 | 0.63 | 2.81E‐05 | 0.23720 | FCDIa_vs_FCDIIb | TSC2 |
| GeneBody | 22:32220413‐32221013 | 1.32 | 5.38E‐05 | 0.37167 | FCDIIb_vs_TLE | DEPDC5 |
| GeneBody | 18:60629433‐60629997 | 0.82 | 6.32E‐05 | 0.41850 | Ctrl_vs_FCDIIa | PHLPP1 |
| GeneBody | 22:32220413‐32221013 | 1.12 | 7.01E‐05 | 0.55320 | FCDIIa_vs_TLE | DEPDC5 |
| GeneBody | 7:146547868‐146548468 | −1.11 | 8.22E‐05 | 0.55320 | FCDIIa_vs_TLE | CNTNAP2 |
| GeneBody | 17:78698196‐78698796 | −0.74 | 0.00017 | 0.40836 | Ctrl_vs_TLE | RPTOR |
| GeneBody | 22:32220413‐32221013 | −0.90 | 0.00017 | 0.34157 | Ctrl_vs_FCDIIb | DEPDC5 |
Table summarizes differential methylation of mTOR pathway–related genes. Differentials meeting our significance criteria (P < 1e‐4) were marked in bold.
Abbreviations: Ctrl, control; FCD, focal cortical dysplasia; TLE, temporal lobe epilepsy; logFC, log2‐fold change; CNTNAP2, contactin‐associated protein‐like 2; DEPDC5, DEP domain containing 5; FOXO6, forkhead box O6; GNAQ, G protein subunit alpha Q; PHLPP1, ph domain and leucine rich repeat protein phosphatase 1; PDPK1, 3‐phosphoinositide dependent protein kinase 1; TSC2, tuberous sclerosis complex 2.