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Table 1 Cancer types, sample sizes and probe-set cardinalities

From: Pan-cancer stratification of solid human epithelial tumors and cancer cell lines reveals commonalities and tissue-specific features of the CpG island methylator phenotype

Cancer type Variably methylated probes Differentially methylated probes Control Tumor CIMP- CIMPi CIMP+ CIMP− CIMP+
pan-cancer pan-cancer
BLCA (bladder urothelial carcinoma) 49,148 338 20 201 78 84 39 43 14
BRCA (breast invasive carcinoma) 46,722 1,311 96 676 270 244 162 76 47
COAD (colon adenocarcinoma) 46,168 2,656 38 274 96 92 86 71 60
HNSC (head and neck squamous cell carcinoma) 44,100 1,228 50 426 156 186 84 115 55
KIRC (kidney renal clear cell carcinoma) 26,148 196 160 296 126 94 76 97 65
KIRP (kidney renal papillary cell carcinoma) 28,083 40 45 147 60 59 28 NA NA
LIHC (liver hepatocellular carcinoma) 51,875 544 50 151 45 61 45 NA NA
LUAD (lung adenocarcinoma) 42,822 1,667 32 437 161 169 107 67 48
LUSC (lung squamous cell carcinoma) 40,606 1,430 42 359 140 142 77 32 11
PAAD (pancreatic adenocarcinoma) 27,899 1,602 9 65 16 33 16 NA NA
PRAD (prostate adenocarcinoma) 33,718 450 49 248 74 122 52 NA NA
READ (rectum adenocarcinoma) 40,496 1,255 7 96 31 39 26 22 22
STAD (stomach adenocarcinoma) 62,606 1,110 2 260 109 95 56 NA NA
THCA (thyroid carcinoma) 21,945 0 56 508 NA NA NA NA NA
UCEC (uterine corpus endometrioid carcinoma) 43,040 1,430 46 407 155 139 113 54 34
  1. Probe set cardinalities and sample sizes for the 15 cancer types that were included in our analysis. The last two columns show the number of CIMP+ and CIMP− samples from our genome-wide methylation study that also appear in the selected functional event data matrix from Ciriello et al. [27].