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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

From: Genes CEP55, FOXD3, FOXF2, GNAO1, GRIA4, and KCNA5 as potential diagnostic biomarkers in colorectal cancer

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%)
  1. 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