Skip to main content

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].