Table 3.
Differentially methylated probes and differentially expressed genes from TCGA (p-values < 0.01), Δβ represents difference in methylation and logFC differential gene expression
| Gene | CpG | CIMP-H | CIMP-L | Cluster 3 | Cluster 4 | All | All | All | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Δβ | logFC | Δβ | logFC | Δβ | logFC | Δβ | logFC | Δβ | logFC | Changed Methylation (n = 381) | Changed Expression (n = 359) | ||
| CEP55 | cg25314624 | −0.36 | 1.62 | −0.38 | 1.38 | −0.38 | 1.24 | −0.35 | 1.18 | 0.37 | 1.32 | 376 (98.7%) | 341 up (95.0%) |
| FOXD3 | cg15617155 | 0.31 | −4.28 | 0.31 | −3.21 | 0.33 | −2.70 | 0.32 | −2.53 | 0.40 | − 3.05 | 373 (97.9%) | 353 down (98.3%) |
| FOXF2 | cg12221475 | 0.34 | −2.55 | 0.41 | −2.09 | 0.39 | −1.85 | 0.41 | −1.58 | 0.39 | −1.96 | 309 (81.1%) | 355 down (98.9%) |
| GNAO1 | cg00866976 | 0.35 | −4.04 | 0.39 | −3.18 | 0.37 | −2.69 | 0.41 | − 2.04 | 0.38 | − 2.88 | 304 (79.8%) | 352 down (98.1%) |
| cg10273340 | 0.40 | 0.44 | 0.42 | 0.46 | 0.43 | 306 (80.3%) | |||||||
| GRIA4 | cg00343633 | 0.52 | −3.12 | 0.55 | −2.59 | 0.55 | −2.19 | 0.51 | −2.03 | 0.54 | −2.41 | 375 (98.4%) | 352 down (98.1%) |
| cg03225817 | 0.44 | 0.49 | 0.49 | 0.45 | 0.47 | 367 (96.3%) | |||||||
| cg07972135 | 0.44 | 0.50 | 0.51 | 0.47 | 0.49 | 369 (96.9%) | |||||||
| cg23559689 | 0.43 | 0.48 | 0.47 | 0.46 | 0.46 | 375 (98.4%) | |||||||
| KCNA5 | cg16897114 | 0.34 | −2.81 | 0.35 | −2.24 | 0.35 | −1.97 | 0.34 | −1.32 | 0.35 | −2.02 | 358 (94.0%) | 354 down (98.6%) |
CIMP the CpG island methylator phenotype, logFC logarithm of fold change, Δβ difference in average beta value between tumor and normal mucosa samples, n number of samples