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Table 2 Genetic and clinical features of all samples from TCGA and samples from TCGA belonging to each of the four methylation-based clusters

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

  CIMP-H (n = 59)
n (%)
CIMP-L (n = 104)
n (%)
Cluster 3 (n = 124)
n (%)
Cluster 4 (n = 94)
n (%)
ALL (n = 381)
n (%)
APC/WT 19/40 (32.2/67.8) 43/61 (41.3/58.7) 49/75 (39.5/60.5) 42/52 (44.7/55.3) 153/228 (40.2/59.8)
KRAS/WT 12/47 (20.3/79.7) 28/76 (26.9/73.1) 20/104 (16.1/83.9) 9/85 (9.6/90.4) 69/312 (18.1/81.9)
TP53/WT 15/44 (25.4/74.6) 23/81 (22.1/77.9) 43/81 (34.7/65.3) 37/57 (39.4/60.6) 118/263 (31.0/69.0)
BRAF/WT 21/38 (35.6/64.4) 5/99 (4.8/95.2) 4/120 (3.2/96.8) 0/94 (0.0/100.0) 30/351 (7.9/92.1)
MLH1 Methylated/Unmethylated 29/30 (49.2/50.8) 8/96 (7.7/92.3) 2/122 (1.6/98.4) 3/91 (3.2/96.8) 42/339 (11.0/89.0)
Gender Female/Male 30/29 (50.8/49.2) 46/58 (44.2/55.8) 51/73 (41.1/58.9) 47/47 (50.0/50.0) 174/207 (45.7/54.3)
Location
 Ascending colon 39 (73.6) 53 (52.5) 23 (18.7) 10 (11.0) 125 (34.2)
 Transverse colon 8 (15.1) 16 (15.8) 18 (14.6) 6 (6.6) 48 (13.2)
 Descending colon 2 (3.8) 5 (5.0) 2 (1.6) 5 (5.5) 14 (3.8)
 Sigmoid colon 3 (5.7) 13 (12.9) 34 (27.6) 36 (39.6) 86 (23.6)
 Rectum 1 (1.9) 14 (13.9) 46 (37.4) 31 (34.1) 92 (25.2)
 No data 6 3 1 3 16
T
 T1 2 (3.4) 2 (1.9) 4 (3.3) 3 (3.2) 11 (2.9)
 T2 12 (20.3) 18 (17.3) 7 (5.7) 15 (16.1) 52 (13.7)
 T3 37 (62.7) 71 (68.3) 91 (74.0) 67 (72.0) 266 (70.2)
 T4 7 (11.9) 13 (12.5) 21 (17.1) 8 (8.6) 49 (12.9)
 Tis 1 (1.7)     1 (0.3)
 No data    1 1 2
N
 N0 38 (64.4) 63 (60.6) 60 (48.8) 43 (46.2) 204 (53.8)
 N1 12 (20.3) 22 (21.2) 40 (32.5) 29 (31.2) 103 (27.2)
 N2 9 (15.3) 19 (18.3) 21 (17.1) 21 (22.6) 70 (18.5)
 Nx    2 (1.6)   2 (0.5)
 No data    1 1 2
M
 M0 46 (79.3) 71 (69.6) 83 (68.0) 58 (63.7) 258 (69.2)
 M1 3 (5.2) 11 (10.8) 23 (18.9) 16 (17.6) 53 (14.2)
 Mx 9 (15.5) 20 (19.2) 16 (13.1) 17 (18.7) 62 (16.6)
 No data 1 2 2 3 8
MSI
 MSI-H 28 (47.5) 12 (11.5) 6 (4.8) 7 (7.5) 53 (14.0)
 MSI-L 9 (15.3) 23 (22.1) 16 (12.9) 14 (15.1) 62 (16.4)
 MSS 22 (37.3) 68 (65.4) 102 (82.3) 72 (77.4) 264 (69.7)
 Indeterminate   1   1 2
Stage
 Stage I 14 (24.1) 17 (17.0) 6 (5.2) 15 (17.0) 52 (14.5)
 Stage II 24 (41.4) 43 (43.0) 48 (41.4) 23 (26.1) 138 (38.1)
 Stage III 17 (29.3) 29 (29.0) 40 (34.5) 32 (36.4) 118 (32.6)
 Stage IV 3 (5.2) 11 (11.0) 22 (19.0) 18 (20.5) 54 (14.9)
 No data 1 4 8 6 19
  1. CIMP the CpG island methylator phenotype, n number of samples, MUT mutation, WT wild-type, MSI microsatellite instability, MSS microsatellite stable, T tumor size, N lymph node infiltration, Nx lymph node infiltration not determined, M distant metastasis, Mx distant metastasis not determined