Correlation between gene mutation status and molecular subtypes
Colon Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C11R6NZN
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C11R6NZN
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.

Summary

Testing the association between mutation status of 16 genes and 9 molecular subtypes across 154 patients, 7 significant findings detected with P value < 0.05 and Q value < 0.25.

  • BRAF mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MRNASEQ_CNMF'.

  • KRAS mutation correlated to 'MRNA_CHIERARCHICAL'.

  • TP53 mutation correlated to 'CN_CNMF'.

  • FBXW7 mutation correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 16 genes and 9 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 7 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
BRAF 20 (13%) 134 4.96e-07
(6.65e-05) 		1.22e-07
(1.64e-05) 		0.000101
(0.0134) 		0.722
(1.00) 		0.926
(1.00) 		0.000866
(0.113) 		0.353
(1.00) 		0.462
(1.00) 		1
(1.00)
KRAS 58 (38%) 96 0.025
(1.00) 		0.000725
(0.0957) 		0.836
(1.00) 		0.704
(1.00) 		0.752
(1.00) 		0.513
(1.00) 		0.455
(1.00) 		0.626
(1.00) 		0.283
(1.00)
TP53 74 (48%) 80 0.00233
(0.3) 		0.0127
(1.00) 		2.17e-08
(2.95e-06) 		0.268
(1.00) 		0.38
(1.00) 		0.13
(1.00) 		1
(1.00) 		0.62
(1.00) 		1
(1.00)
FBXW7 29 (19%) 125 0.226
(1.00) 		0.093
(1.00) 		0.00183
(0.237) 		0.0038
(0.486) 		0.233
(1.00) 		1
(1.00) 		0.48
(1.00) 		1
(1.00) 		0.474
(1.00)
APC 103 (67%) 51 0.171
(1.00) 		0.0198
(1.00) 		0.0374
(1.00) 		0.218
(1.00) 		0.388
(1.00) 		0.498
(1.00) 		0.252
(1.00) 		0.601
(1.00) 		0.258
(1.00)
PIK3CA 26 (17%) 128 0.335
(1.00) 		0.321
(1.00) 		0.0338
(1.00) 		0.116
(1.00) 		0.332
(1.00) 		0.482
(1.00) 		1
(1.00) 		0.514
(1.00) 		0.416
(1.00)
NRAS 15 (10%) 139 0.0773
(1.00) 		0.38
(1.00) 		0.867
(1.00) 		0.465
(1.00) 		0.332
(1.00) 		0.845
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
SMAD4 18 (12%) 136 0.303
(1.00) 		0.587
(1.00) 		0.00721
(0.908) 		0.852
(1.00) 		0.495
(1.00) 		0.663
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
FAM123B 19 (12%) 135 0.21
(1.00) 		0.00698
(0.886) 		0.0249
(1.00) 		0.286
(1.00) 		0.422
(1.00) 		0.357
(1.00) 		1
(1.00) 		0.425
(1.00) 		0.338
(1.00)
SOX9 9 (6%) 145 0.235
(1.00) 		0.214
(1.00) 		0.398
(1.00) 		0.231
(1.00) 		0.461
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
ACVR2A 8 (5%) 146 0.045
(1.00) 		0.296
(1.00) 		0.0542
(1.00) 		0.199
(1.00) 		0.668
(1.00) 		0.171
(1.00) 		1
(1.00) 		1
(1.00) 		0.162
(1.00)
TNFRSF10C 6 (4%) 148 0.381
(1.00) 		0.676
(1.00) 		0.119
(1.00) 		0.68
(1.00) 		0.169
(1.00) 		0.248
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
ACOT4 3 (2%) 151 0.665
(1.00) 		0.391
(1.00) 		0.75
(1.00) 		0.225
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
SMAD2 10 (6%) 144 0.0995
(1.00) 		0.19
(1.00) 		0.0497
(1.00) 		1
(1.00) 		0.377
(1.00) 		0.818
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
PCBP1 4 (3%) 150 0.33
(1.00) 		0.552
(1.00) 		0.368
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
GGT1 3 (2%) 151 0.355
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
'APC MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.171 (Fisher's exact test), Q value = 1

Table S1.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 57 28 22
APC MUTATED 18 42 21 14
APC WILD-TYPE 16 15 7 8
'APC MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0198 (Fisher's exact test), Q value = 1

Table S2.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 42 46
APC MUTATED 40 21 34
APC WILD-TYPE 13 21 12

Figure S1.  Get High-res Image Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'APC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0374 (Fisher's exact test), Q value = 1

Table S3.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 67 20
APC MUTATED 49 37 15
APC WILD-TYPE 16 30 5

Figure S2.  Get High-res Image Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'APC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.218 (Fisher's exact test), Q value = 1

Table S4.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 47 18 16
APC MUTATED 19 28 12 9
APC WILD-TYPE 4 19 6 7
'APC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.388 (Fisher's exact test), Q value = 1

Table S5.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 8 10 79
APC MUTATED 4 5 9 50
APC WILD-TYPE 3 3 1 29
'APC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.498 (Fisher's exact test), Q value = 1

Table S6.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 11 125
APC MUTATED 10 6 84
APC WILD-TYPE 3 5 41
'APC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.252 (Fisher's exact test), Q value = 1

Table S7.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 1 2
APC MUTATED 99 0 1
APC WILD-TYPE 47 1 1
'APC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.601 (Fisher's exact test), Q value = 1

Table S8.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients CLUS_2 CLUS_3
ALL 4 137
APC MUTATED 2 92
APC WILD-TYPE 2 45
'APC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.258 (Fisher's exact test), Q value = 1

Table S9.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 138 1
APC MUTATED 1 93 0
APC WILD-TYPE 1 45 1
'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.335 (Fisher's exact test), Q value = 1

Table S10.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 57 28 22
PIK3CA MUTATED 6 5 6 4
PIK3CA WILD-TYPE 28 52 22 18
'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.321 (Fisher's exact test), Q value = 1

Table S11.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 42 46
PIK3CA MUTATED 9 8 4
PIK3CA WILD-TYPE 44 34 42
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 1

Table S12.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 67 20
PIK3CA MUTATED 6 17 2
PIK3CA WILD-TYPE 59 50 18

Figure S3.  Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.116 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 47 18 16
PIK3CA MUTATED 8 8 1 4
PIK3CA WILD-TYPE 15 39 17 12
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.332 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 8 10 79
PIK3CA MUTATED 1 2 4 14
PIK3CA WILD-TYPE 6 6 6 65
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.482 (Fisher's exact test), Q value = 1

Table S15.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 11 125
PIK3CA MUTATED 1 3 21
PIK3CA WILD-TYPE 12 8 104
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S16.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 1 2
PIK3CA MUTATED 25 0 0
PIK3CA WILD-TYPE 121 1 2
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.514 (Fisher's exact test), Q value = 1

Table S17.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients CLUS_2 CLUS_3
ALL 4 137
PIK3CA MUTATED 1 22
PIK3CA WILD-TYPE 3 115
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.416 (Fisher's exact test), Q value = 1

Table S18.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 138 1
PIK3CA MUTATED 1 22 0
PIK3CA WILD-TYPE 1 116 1
'BRAF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 4.96e-07 (Fisher's exact test), Q value = 6.6e-05

Table S19.  Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 57 28 22
BRAF MUTATED 14 1 3 0
BRAF WILD-TYPE 20 56 25 22

Figure S4.  Get High-res Image Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'BRAF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1.22e-07 (Fisher's exact test), Q value = 1.6e-05

Table S20.  Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 42 46
BRAF MUTATED 1 16 1
BRAF WILD-TYPE 52 26 45

Figure S5.  Get High-res Image Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.013

Table S21.  Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 67 20
BRAF MUTATED 1 17 2
BRAF WILD-TYPE 64 50 18

Figure S6.  Get High-res Image Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.722 (Fisher's exact test), Q value = 1

Table S22.  Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 47 18 16
BRAF MUTATED 3 4 3 1
BRAF WILD-TYPE 20 43 15 15
'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.926 (Fisher's exact test), Q value = 1

Table S23.  Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 8 10 79
BRAF MUTATED 1 1 1 8
BRAF WILD-TYPE 6 7 9 71
'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000866 (Fisher's exact test), Q value = 0.11

Table S24.  Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 11 125
BRAF MUTATED 0 6 14
BRAF WILD-TYPE 13 5 111

Figure S7.  Get High-res Image Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.353 (Fisher's exact test), Q value = 1

Table S25.  Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 1 2
BRAF MUTATED 19 0 1
BRAF WILD-TYPE 127 1 1
'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.462 (Fisher's exact test), Q value = 1

Table S26.  Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients CLUS_2 CLUS_3
ALL 4 137
BRAF MUTATED 1 19
BRAF WILD-TYPE 3 118
'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S27.  Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 138 1
BRAF MUTATED 0 20 0
BRAF WILD-TYPE 2 118 1
'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 1

Table S28.  Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 57 28 22
KRAS MUTATED 10 16 17 7
KRAS WILD-TYPE 24 41 11 15

Figure S8.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.000725 (Fisher's exact test), Q value = 0.096

Table S29.  Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 42 46
KRAS MUTATED 27 16 7
KRAS WILD-TYPE 26 26 39

Figure S9.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.836 (Fisher's exact test), Q value = 1

Table S30.  Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 67 20
KRAS MUTATED 23 27 7
KRAS WILD-TYPE 42 40 13
'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.704 (Fisher's exact test), Q value = 1

Table S31.  Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 47 18 16
KRAS MUTATED 9 22 6 8
KRAS WILD-TYPE 14 25 12 8
'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.752 (Fisher's exact test), Q value = 1

Table S32.  Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 8 10 79
KRAS MUTATED 3 2 5 35
KRAS WILD-TYPE 4 6 5 44
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.513 (Fisher's exact test), Q value = 1

Table S33.  Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 11 125
KRAS MUTATED 3 3 49
KRAS WILD-TYPE 10 8 76
'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.455 (Fisher's exact test), Q value = 1

Table S34.  Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 1 2
KRAS MUTATED 53 1 1
KRAS WILD-TYPE 93 0 1
'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.626 (Fisher's exact test), Q value = 1

Table S35.  Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients CLUS_2 CLUS_3
ALL 4 137
KRAS MUTATED 2 50
KRAS WILD-TYPE 2 87
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.283 (Fisher's exact test), Q value = 1

Table S36.  Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 138 1
KRAS MUTATED 0 51 1
KRAS WILD-TYPE 2 87 0
'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.3

Table S37.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 57 28 22
TP53 MUTATED 12 39 9 10
TP53 WILD-TYPE 22 18 19 12

Figure S10.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 1

Table S38.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 42 46
TP53 MUTATED 29 13 28
TP53 WILD-TYPE 24 29 18

Figure S11.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 2.17e-08 (Fisher's exact test), Q value = 2.9e-06

Table S39.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 67 20
TP53 MUTATED 47 15 11
TP53 WILD-TYPE 18 52 9

Figure S12.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.268 (Fisher's exact test), Q value = 1

Table S40.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 47 18 16
TP53 MUTATED 8 24 8 4
TP53 WILD-TYPE 15 23 10 12
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.38 (Fisher's exact test), Q value = 1

Table S41.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 8 10 79
TP53 MUTATED 3 1 4 36
TP53 WILD-TYPE 4 7 6 43
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 1

Table S42.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 11 125
TP53 MUTATED 7 2 62
TP53 WILD-TYPE 6 9 63
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S43.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 1 2
TP53 MUTATED 70 0 1
TP53 WILD-TYPE 76 1 1
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.62 (Fisher's exact test), Q value = 1

Table S44.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients CLUS_2 CLUS_3
ALL 4 137
TP53 MUTATED 1 68
TP53 WILD-TYPE 3 69
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S45.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 138 1
TP53 MUTATED 1 68 0
TP53 WILD-TYPE 1 70 1
'FBXW7 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.226 (Fisher's exact test), Q value = 1

Table S46.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 57 28 22
FBXW7 MUTATED 10 7 5 3
FBXW7 WILD-TYPE 24 50 23 19
'FBXW7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.093 (Fisher's exact test), Q value = 1

Table S47.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 42 46
FBXW7 MUTATED 8 12 5
FBXW7 WILD-TYPE 45 30 41
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.24

Table S48.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 67 20
FBXW7 MUTATED 5 21 3
FBXW7 WILD-TYPE 60 46 17

Figure S13.  Get High-res Image Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0038 (Fisher's exact test), Q value = 0.49

Table S49.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 47 18 16
FBXW7 MUTATED 4 8 1 9
FBXW7 WILD-TYPE 19 39 17 7

Figure S14.  Get High-res Image Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.233 (Fisher's exact test), Q value = 1

Table S50.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 8 10 79
FBXW7 MUTATED 1 4 2 15
FBXW7 WILD-TYPE 6 4 8 64
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S51.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 11 125
FBXW7 MUTATED 2 2 25
FBXW7 WILD-TYPE 11 9 100
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.48 (Fisher's exact test), Q value = 1

Table S52.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 1 2
FBXW7 MUTATED 28 0 1
FBXW7 WILD-TYPE 118 1 1
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S53.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients CLUS_2 CLUS_3
ALL 4 137
FBXW7 MUTATED 0 27
FBXW7 WILD-TYPE 4 110
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.474 (Fisher's exact test), Q value = 1

Table S54.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 138 1
FBXW7 MUTATED 1 26 0
FBXW7 WILD-TYPE 1 112 1
'NRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0773 (Fisher's exact test), Q value = 1

Table S55.  Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 57 28 22
NRAS MUTATED 0 8 4 2
NRAS WILD-TYPE 34 49 24 20
'NRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.38 (Fisher's exact test), Q value = 1

Table S56.  Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 42 46
NRAS MUTATED 7 2 5
NRAS WILD-TYPE 46 40 41
'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.867 (Fisher's exact test), Q value = 1

Table S57.  Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 67 20
NRAS MUTATED 7 7 1
NRAS WILD-TYPE 58 60 19
'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.465 (Fisher's exact test), Q value = 1

Table S58.  Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 47 18 16
NRAS MUTATED 1 8 1 2
NRAS WILD-TYPE 22 39 17 14
'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.332 (Fisher's exact test), Q value = 1

Table S59.  Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 8 10 79
NRAS MUTATED 0 2 0 10
NRAS WILD-TYPE 7 6 10 69
'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.845 (Fisher's exact test), Q value = 1

Table S60.  Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 11 125
NRAS MUTATED 1 0 13
NRAS WILD-TYPE 12 11 112
'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S61.  Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 1 2
NRAS MUTATED 14 0 0
NRAS WILD-TYPE 132 1 2
'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S62.  Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients CLUS_2 CLUS_3
ALL 4 137
NRAS MUTATED 0 13
NRAS WILD-TYPE 4 124
'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S63.  Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 138 1
NRAS MUTATED 0 13 0
NRAS WILD-TYPE 2 125 1
'SMAD4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.303 (Fisher's exact test), Q value = 1

Table S64.  Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 57 28 22
SMAD4 MUTATED 6 4 5 2
SMAD4 WILD-TYPE 28 53 23 20
'SMAD4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.587 (Fisher's exact test), Q value = 1

Table S65.  Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 42 46
SMAD4 MUTATED 5 7 5
SMAD4 WILD-TYPE 48 35 41
'SMAD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00721 (Fisher's exact test), Q value = 0.91

Table S66.  Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 67 20
SMAD4 MUTATED 2 12 4
SMAD4 WILD-TYPE 63 55 16

Figure S15.  Get High-res Image Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'SMAD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.852 (Fisher's exact test), Q value = 1

Table S67.  Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 47 18 16
SMAD4 MUTATED 3 8 2 1
SMAD4 WILD-TYPE 20 39 16 15
'SMAD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.495 (Fisher's exact test), Q value = 1

Table S68.  Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 8 10 79
SMAD4 MUTATED 2 0 1 11
SMAD4 WILD-TYPE 5 8 9 68
'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.663 (Fisher's exact test), Q value = 1

Table S69.  Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 11 125
SMAD4 MUTATED 1 0 16
SMAD4 WILD-TYPE 12 11 109
'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S70.  Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 1 2
SMAD4 MUTATED 17 0 0
SMAD4 WILD-TYPE 129 1 2
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S71.  Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients CLUS_2 CLUS_3
ALL 4 137
SMAD4 MUTATED 0 17
SMAD4 WILD-TYPE 4 120
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S72.  Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 138 1
SMAD4 MUTATED 0 17 0
SMAD4 WILD-TYPE 2 121 1
'FAM123B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.21 (Fisher's exact test), Q value = 1

Table S73.  Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 57 28 22
FAM123B MUTATED 8 6 4 1
FAM123B WILD-TYPE 26 51 24 21
'FAM123B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00698 (Fisher's exact test), Q value = 0.89

Table S74.  Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 42 46
FAM123B MUTATED 8 10 1
FAM123B WILD-TYPE 45 32 45

Figure S16.  Get High-res Image Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'FAM123B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 1

Table S75.  Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 67 20
FAM123B MUTATED 5 13 0
FAM123B WILD-TYPE 60 54 20

Figure S17.  Get High-res Image Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FAM123B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.286 (Fisher's exact test), Q value = 1

Table S76.  Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 47 18 16
FAM123B MUTATED 2 4 1 4
FAM123B WILD-TYPE 21 43 17 12
'FAM123B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.422 (Fisher's exact test), Q value = 1

Table S77.  Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 8 10 79
FAM123B MUTATED 0 2 1 8
FAM123B WILD-TYPE 7 6 9 71
'FAM123B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.357 (Fisher's exact test), Q value = 1

Table S78.  Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 11 125
FAM123B MUTATED 0 2 17
FAM123B WILD-TYPE 13 9 108
'FAM123B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S79.  Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 1 2
FAM123B MUTATED 19 0 0
FAM123B WILD-TYPE 127 1 2
'FAM123B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 1

Table S80.  Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients CLUS_2 CLUS_3
ALL 4 137
FAM123B MUTATED 1 17
FAM123B WILD-TYPE 3 120
'FAM123B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.338 (Fisher's exact test), Q value = 1

Table S81.  Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 138 1
FAM123B MUTATED 1 17 0
FAM123B WILD-TYPE 1 121 1
'SOX9 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.235 (Fisher's exact test), Q value = 1

Table S82.  Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 57 28 22
SOX9 MUTATED 2 3 0 3
SOX9 WILD-TYPE 32 54 28 19
'SOX9 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.214 (Fisher's exact test), Q value = 1

Table S83.  Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 42 46
SOX9 MUTATED 2 1 5
SOX9 WILD-TYPE 51 41 41
'SOX9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.398 (Fisher's exact test), Q value = 1

Table S84.  Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 67 20
SOX9 MUTATED 2 6 1
SOX9 WILD-TYPE 63 61 19
'SOX9 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.231 (Fisher's exact test), Q value = 1

Table S85.  Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 47 18 16
SOX9 MUTATED 0 3 0 2
SOX9 WILD-TYPE 23 44 18 14
'SOX9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.461 (Fisher's exact test), Q value = 1

Table S86.  Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 8 10 79
SOX9 MUTATED 1 0 0 4
SOX9 WILD-TYPE 6 8 10 75
'SOX9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S87.  Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 11 125
SOX9 MUTATED 0 0 9
SOX9 WILD-TYPE 13 11 116
'SOX9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S88.  Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 1 2
SOX9 MUTATED 9 0 0
SOX9 WILD-TYPE 137 1 2
'SOX9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S89.  Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients CLUS_2 CLUS_3
ALL 4 137
SOX9 MUTATED 0 9
SOX9 WILD-TYPE 4 128
'SOX9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S90.  Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 138 1
SOX9 MUTATED 0 9 0
SOX9 WILD-TYPE 2 129 1
'ACVR2A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.045 (Fisher's exact test), Q value = 1

Table S91.  Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 57 28 22
ACVR2A MUTATED 5 1 1 0
ACVR2A WILD-TYPE 29 56 27 22

Figure S18.  Get High-res Image Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'ACVR2A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.296 (Fisher's exact test), Q value = 1

Table S92.  Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 42 46
ACVR2A MUTATED 2 4 1
ACVR2A WILD-TYPE 51 38 45
'ACVR2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0542 (Fisher's exact test), Q value = 1

Table S93.  Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 67 20
ACVR2A MUTATED 1 7 0
ACVR2A WILD-TYPE 64 60 20
'ACVR2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 1

Table S94.  Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 47 18 16
ACVR2A MUTATED 0 4 0 2
ACVR2A WILD-TYPE 23 43 18 14
'ACVR2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.668 (Fisher's exact test), Q value = 1

Table S95.  Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 8 10 79
ACVR2A MUTATED 0 1 0 5
ACVR2A WILD-TYPE 7 7 10 74
'ACVR2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.171 (Fisher's exact test), Q value = 1

Table S96.  Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 11 125
ACVR2A MUTATED 0 2 6
ACVR2A WILD-TYPE 13 9 119
'ACVR2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S97.  Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 1 2
ACVR2A MUTATED 8 0 0
ACVR2A WILD-TYPE 138 1 2
'ACVR2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S98.  Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients CLUS_2 CLUS_3
ALL 4 137
ACVR2A MUTATED 0 8
ACVR2A WILD-TYPE 4 129
'ACVR2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.162 (Fisher's exact test), Q value = 1

Table S99.  Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 138 1
ACVR2A MUTATED 1 7 0
ACVR2A WILD-TYPE 1 131 1
'TNFRSF10C MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 1

Table S100.  Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 57 28 22
TNFRSF10C MUTATED 2 2 0 2
TNFRSF10C WILD-TYPE 32 55 28 20
'TNFRSF10C MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.676 (Fisher's exact test), Q value = 1

Table S101.  Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 42 46
TNFRSF10C MUTATED 2 1 3
TNFRSF10C WILD-TYPE 51 41 43
'TNFRSF10C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 1

Table S102.  Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 67 20
TNFRSF10C MUTATED 5 1 0
TNFRSF10C WILD-TYPE 60 66 20
'TNFRSF10C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.68 (Fisher's exact test), Q value = 1

Table S103.  Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 47 18 16
TNFRSF10C MUTATED 2 2 0 1
TNFRSF10C WILD-TYPE 21 45 18 15
'TNFRSF10C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.169 (Fisher's exact test), Q value = 1

Table S104.  Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 8 10 79
TNFRSF10C MUTATED 0 0 2 3
TNFRSF10C WILD-TYPE 7 8 8 76
'TNFRSF10C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.248 (Fisher's exact test), Q value = 1

Table S105.  Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 11 125
TNFRSF10C MUTATED 1 1 4
TNFRSF10C WILD-TYPE 12 10 121
'TNFRSF10C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S106.  Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 1 2
TNFRSF10C MUTATED 6 0 0
TNFRSF10C WILD-TYPE 140 1 2
'TNFRSF10C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S107.  Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients CLUS_2 CLUS_3
ALL 4 137
TNFRSF10C MUTATED 0 6
TNFRSF10C WILD-TYPE 4 131
'TNFRSF10C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S108.  Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 138 1
TNFRSF10C MUTATED 0 6 0
TNFRSF10C WILD-TYPE 2 132 1
'ACOT4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.665 (Fisher's exact test), Q value = 1

Table S109.  Gene #13: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 57 28 22
ACOT4 MUTATED 1 1 0 1
ACOT4 WILD-TYPE 33 56 28 21
'ACOT4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.391 (Fisher's exact test), Q value = 1

Table S110.  Gene #13: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 42 46
ACOT4 MUTATED 1 2 0
ACOT4 WILD-TYPE 52 40 46
'ACOT4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.75 (Fisher's exact test), Q value = 1

Table S111.  Gene #13: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 67 20
ACOT4 MUTATED 2 1 0
ACOT4 WILD-TYPE 63 66 20
'ACOT4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.225 (Fisher's exact test), Q value = 1

Table S112.  Gene #13: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 11 125
ACOT4 MUTATED 0 1 2
ACOT4 WILD-TYPE 13 10 123
'ACOT4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S113.  Gene #13: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 1 2
ACOT4 MUTATED 3 0 0
ACOT4 WILD-TYPE 143 1 2
'ACOT4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S114.  Gene #13: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients CLUS_2 CLUS_3
ALL 4 137
ACOT4 MUTATED 0 3
ACOT4 WILD-TYPE 4 134
'ACOT4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S115.  Gene #13: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 138 1
ACOT4 MUTATED 0 3 0
ACOT4 WILD-TYPE 2 135 1
'SMAD2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0995 (Fisher's exact test), Q value = 1

Table S116.  Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 57 28 22
SMAD2 MUTATED 3 1 4 1
SMAD2 WILD-TYPE 31 56 24 21
'SMAD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.19 (Fisher's exact test), Q value = 1

Table S117.  Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 42 46
SMAD2 MUTATED 3 5 1
SMAD2 WILD-TYPE 50 37 45
'SMAD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0497 (Fisher's exact test), Q value = 1

Table S118.  Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 67 20
SMAD2 MUTATED 1 8 1
SMAD2 WILD-TYPE 64 59 19

Figure S19.  Get High-res Image Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'SMAD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S119.  Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 47 18 16
SMAD2 MUTATED 2 3 1 1
SMAD2 WILD-TYPE 21 44 17 15
'SMAD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.377 (Fisher's exact test), Q value = 1

Table S120.  Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 8 10 79
SMAD2 MUTATED 1 1 0 5
SMAD2 WILD-TYPE 6 7 10 74
'SMAD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.818 (Fisher's exact test), Q value = 1

Table S121.  Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 11 125
SMAD2 MUTATED 0 0 10
SMAD2 WILD-TYPE 13 11 115
'SMAD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S122.  Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 1 2
SMAD2 MUTATED 10 0 0
SMAD2 WILD-TYPE 136 1 2
'SMAD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S123.  Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients CLUS_2 CLUS_3
ALL 4 137
SMAD2 MUTATED 0 9
SMAD2 WILD-TYPE 4 128
'SMAD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S124.  Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 138 1
SMAD2 MUTATED 0 9 0
SMAD2 WILD-TYPE 2 129 1
'PCBP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.33 (Fisher's exact test), Q value = 1

Table S125.  Gene #15: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 34 57 28 22
PCBP1 MUTATED 0 2 2 0
PCBP1 WILD-TYPE 34 55 26 22
'PCBP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.552 (Fisher's exact test), Q value = 1

Table S126.  Gene #15: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 42 46
PCBP1 MUTATED 2 0 2
PCBP1 WILD-TYPE 51 42 44
'PCBP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.368 (Fisher's exact test), Q value = 1

Table S127.  Gene #15: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 67 20
PCBP1 MUTATED 2 1 1
PCBP1 WILD-TYPE 63 66 19
'PCBP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S128.  Gene #15: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 11 125
PCBP1 MUTATED 0 0 4
PCBP1 WILD-TYPE 13 11 121
'PCBP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S129.  Gene #15: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 1 2
PCBP1 MUTATED 4 0 0
PCBP1 WILD-TYPE 142 1 2
'PCBP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S130.  Gene #15: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients CLUS_2 CLUS_3
ALL 4 137
PCBP1 MUTATED 0 3
PCBP1 WILD-TYPE 4 134
'PCBP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S131.  Gene #15: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 138 1
PCBP1 MUTATED 0 3 0
PCBP1 WILD-TYPE 2 135 1
'GGT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.355 (Fisher's exact test), Q value = 1

Table S132.  Gene #16: 'GGT1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 67 20
GGT1 MUTATED 0 3 0
GGT1 WILD-TYPE 65 64 20
'GGT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S133.  Gene #16: 'GGT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 11 125
GGT1 MUTATED 0 0 3
GGT1 WILD-TYPE 13 11 122
'GGT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S134.  Gene #16: 'GGT1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 146 1 2
GGT1 MUTATED 3 0 0
GGT1 WILD-TYPE 143 1 2
'GGT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S135.  Gene #16: 'GGT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients CLUS_2 CLUS_3
ALL 4 137
GGT1 MUTATED 0 3
GGT1 WILD-TYPE 4 134
'GGT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S136.  Gene #16: 'GGT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 138 1
GGT1 MUTATED 0 3 0
GGT1 WILD-TYPE 2 135 1
Methods & Data
Input

  • Mutation data file = transformed.cor.cli.txt

  • Molecular subtypes file = COAD-TP.transferedmergedcluster.txt

  • Number of patients = 154

  • Number of significantly mutated genes = 16

  • Number of Molecular subtypes = 9

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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