Correlation between gene mutation status and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between mutation status of 27 genes and 10 molecular subtypes across 306 patients, 17 significant findings detected with P value < 0.05 and Q value < 0.25.

  • TP53 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • CDKN2A mutation correlated to 'METHLYATION_CNMF'.

  • CASP8 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • MLL2 mutation correlated to 'CN_CNMF'.

  • NOTCH1 mutation correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CNMF'.

  • NFE2L2 mutation correlated to 'METHLYATION_CNMF'.

  • NSD1 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • HRAS mutation correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 27 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 17 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
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 Fisher's exact test
TP53 213 (70%) 93 1e-05
(0.0027) 		1e-05
(0.0027) 		0.0845
(1.00) 		0.89
(1.00) 		0.0088
(1.00) 		5e-05
(0.0131) 		0.00853
(1.00) 		1e-05
(0.0027) 		0.00444
(1.00) 		0.00316
(0.784)
CASP8 27 (9%) 279 2e-05
(0.00526) 		1e-05
(0.0027) 		0.0146
(1.00) 		0.384
(1.00) 		1e-05
(0.0027) 		0.00011
(0.0286) 		0.134
(1.00) 		0.933
(1.00) 		0.0943
(1.00) 		0.349
(1.00)
NSD1 33 (11%) 273 0.344
(1.00) 		1e-05
(0.0027) 		0.0955
(1.00) 		0.00668
(1.00) 		0.00034
(0.087) 		1e-05
(0.0027) 		0.0114
(1.00) 		0.00426
(1.00) 		0.00984
(1.00) 		0.00869
(1.00)
NOTCH1 57 (19%) 249 0.0222
(1.00) 		0.00152
(0.38) 		0.0554
(1.00) 		0.0691
(1.00) 		0.002
(0.498) 		0.00011
(0.0286) 		9e-05
(0.0235) 		0.348
(1.00) 		0.314
(1.00) 		0.0205
(1.00)
CDKN2A 65 (21%) 241 0.294
(1.00) 		0.00038
(0.0969) 		0.00106
(0.268) 		0.536
(1.00) 		0.186
(1.00) 		0.394
(1.00) 		0.507
(1.00) 		0.155
(1.00) 		0.231
(1.00) 		0.269
(1.00)
MLL2 53 (17%) 253 0.00087
(0.221) 		0.0483
(1.00) 		0.493
(1.00) 		0.346
(1.00) 		0.0823
(1.00) 		0.106
(1.00) 		0.107
(1.00) 		0.0244
(1.00) 		0.507
(1.00) 		0.0645
(1.00)
NFE2L2 17 (6%) 289 0.63
(1.00) 		0.00013
(0.0335) 		0.35
(1.00) 		0.685
(1.00) 		1
(1.00) 		0.434
(1.00) 		0.18
(1.00) 		0.738
(1.00) 		0.356
(1.00) 		0.92
(1.00)
HRAS 10 (3%) 296 0.00024
(0.0617) 		0.00509
(1.00) 		0.387
(1.00) 		0.343
(1.00) 		0.00139
(0.349) 		0.0145
(1.00) 		0.157
(1.00) 		0.272
(1.00) 		0.518
(1.00) 		0.851
(1.00)
FAT1 69 (23%) 237 0.124
(1.00) 		0.079
(1.00) 		0.917
(1.00) 		0.48
(1.00) 		0.106
(1.00) 		0.326
(1.00) 		0.338
(1.00) 		0.506
(1.00) 		0.289
(1.00) 		0.21
(1.00)
JUB 18 (6%) 288 0.257
(1.00) 		0.0805
(1.00) 		0.397
(1.00) 		0.746
(1.00) 		0.121
(1.00) 		0.423
(1.00) 		0.129
(1.00) 		1
(1.00) 		0.126
(1.00) 		0.849
(1.00)
ZNF750 13 (4%) 293 0.452
(1.00) 		0.137
(1.00) 		0.804
(1.00) 		0.33
(1.00) 		0.081
(1.00) 		0.07
(1.00) 		0.721
(1.00) 		0.938
(1.00) 		0.181
(1.00) 		1
(1.00)
RASA1 14 (5%) 292 0.252
(1.00) 		0.13
(1.00) 		0.376
(1.00) 		0.715
(1.00) 		0.348
(1.00) 		0.546
(1.00) 		0.471
(1.00) 		0.14
(1.00) 		0.273
(1.00) 		0.061
(1.00)
HLA-A 9 (3%) 297 0.0339
(1.00) 		0.317
(1.00) 		1
(1.00) 		0.639
(1.00) 		0.186
(1.00) 		0.0703
(1.00) 		0.346
(1.00) 		0.431
(1.00) 		0.673
(1.00) 		0.852
(1.00)
EPHA2 13 (4%) 293 0.306
(1.00) 		0.00135
(0.34) 		0.741
(1.00) 		0.932
(1.00) 		0.0638
(1.00) 		0.197
(1.00) 		0.485
(1.00) 		0.398
(1.00) 		0.0805
(1.00) 		0.248
(1.00)
RAC1 9 (3%) 297 0.31
(1.00) 		0.435
(1.00) 		1
(1.00) 		0.836
(1.00) 		0.19
(1.00) 		0.147
(1.00) 		0.262
(1.00) 		0.199
(1.00) 		0.256
(1.00) 		0.271
(1.00)
EP300 24 (8%) 282 0.339
(1.00) 		0.467
(1.00) 		0.572
(1.00) 		0.0881
(1.00) 		0.00481
(1.00) 		0.0584
(1.00) 		0.382
(1.00) 		0.212
(1.00) 		0.227
(1.00) 		1
(1.00)
TGFBR2 10 (3%) 296 0.376
(1.00) 		0.0113
(1.00) 		0.438
(1.00) 		0.901
(1.00) 		0.229
(1.00) 		0.0444
(1.00) 		0.775
(1.00) 		0.514
(1.00) 		0.933
(1.00) 		0.52
(1.00)
PIK3CA 64 (21%) 242 0.241
(1.00) 		0.0392
(1.00) 		0.696
(1.00) 		0.0483
(1.00) 		0.0965
(1.00) 		0.0535
(1.00) 		0.0057
(1.00) 		0.0644
(1.00) 		0.203
(1.00) 		0.23
(1.00)
FBXW7 15 (5%) 291 0.775
(1.00) 		0.47
(1.00) 		0.414
(1.00) 		0.112
(1.00) 		0.633
(1.00) 		0.876
(1.00) 		0.946
(1.00) 		0.206
(1.00) 		0.876
(1.00) 		0.272
(1.00)
RB1 10 (3%) 296 0.092
(1.00) 		0.385
(1.00) 		0.326
(1.00) 		0.275
(1.00) 		0.0562
(1.00) 		0.377
(1.00) 		0.103
(1.00) 		0.518
(1.00) 		0.44
(1.00) 		0.852
(1.00)
CTCF 11 (4%) 295 0.232
(1.00) 		0.036
(1.00) 		0.614
(1.00) 		0.469
(1.00) 		0.426
(1.00) 		0.526
(1.00) 		0.627
(1.00) 		0.462
(1.00) 		0.779
(1.00) 		1
(1.00)
KDM6A 8 (3%) 298 0.0175
(1.00) 		0.632
(1.00) 		0.158
(1.00) 		1
(1.00) 		0.908
(1.00) 		0.361
(1.00) 		0.382
(1.00) 		0.741
(1.00) 		0.145
(1.00) 		0.161
(1.00)
ELF4 5 (2%) 301 0.0361
(1.00) 		0.173
(1.00) 		0.358
(1.00) 		0.341
(1.00) 		0.619
(1.00) 		1
(1.00) 		0.297
(1.00) 		0.377
(1.00) 		0.588
(1.00) 		1
(1.00)
RHOA 4 (1%) 302 0.0151
(1.00) 		0.164
(1.00) 		0.137
(1.00) 		0.241
(1.00) 		0.823
(1.00) 		0.487
(1.00) 		0.167
(1.00) 		0.462
(1.00) 		0.396
(1.00) 		0.0375
(1.00)
HLA-B 8 (3%) 298 0.217
(1.00) 		0.401
(1.00) 		1
(1.00) 		0.0531
(1.00) 		0.00831
(1.00) 		0.147
(1.00) 		0.382
(1.00) 		0.0636
(1.00) 		0.561
(1.00) 		0.659
(1.00)
PRSS1 7 (2%) 299 0.494
(1.00) 		0.853
(1.00) 		0.872
(1.00) 		0.616
(1.00) 		0.721
(1.00) 		0.577
(1.00) 		1
(1.00) 		0.0131
(1.00) 		0.713
(1.00) 		0.429
(1.00)
GUCY2F 8 (3%) 298 0.884
(1.00) 		0.959
(1.00) 		0.832
(1.00) 		0.833
(1.00) 		0.666
(1.00) 		0.88
(1.00) 		0.154
(1.00) 		0.82
(1.00) 		0.0207
(1.00) 		0.658
(1.00)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0027

Table S1.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
TP53 MUTATED 80 77 47 7
TP53 WILD-TYPE 12 12 58 9

Figure S1.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0027

Table S2.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
TP53 MUTATED 35 35 50 53 4 26 10
TP53 WILD-TYPE 14 8 5 8 39 15 4

Figure S2.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0845 (Fisher's exact test), Q value = 1

Table S3.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
TP53 MUTATED 45 33 28 54
TP53 WILD-TYPE 10 19 7 12
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.89 (Fisher's exact test), Q value = 1

Table S4.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
TP53 MUTATED 61 64 35
TP53 WILD-TYPE 17 19 12
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0088 (Fisher's exact test), Q value = 1

Table S5.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
TP53 MUTATED 77 77 58
TP53 WILD-TYPE 47 18 27

Figure S3.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.013

Table S6.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
TP53 MUTATED 24 90 54 44
TP53 WILD-TYPE 7 19 24 42

Figure S4.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00853 (Fisher's exact test), Q value = 1

Table S7.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
TP53 MUTATED 82 44 86
TP53 WILD-TYPE 44 27 21

Figure S5.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0027

Table S8.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
TP53 MUTATED 98 63 51
TP53 WILD-TYPE 22 17 53

Figure S6.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00444 (Fisher's exact test), Q value = 1

Table S9.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
TP53 MUTATED 35 15 36 86 12
TP53 WILD-TYPE 8 13 18 25 13

Figure S7.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00316 (Fisher's exact test), Q value = 0.78

Table S10.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
TP53 MUTATED 88 85 11
TP53 WILD-TYPE 20 52 5

Figure S8.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CDKN2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.294 (Fisher's exact test), Q value = 1

Table S11.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
CDKN2A MUTATED 25 20 17 3
CDKN2A WILD-TYPE 67 69 88 13
'CDKN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.097

Table S12.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
CDKN2A MUTATED 11 5 17 19 1 11 1
CDKN2A WILD-TYPE 38 38 38 42 42 30 13

Figure S9.  Get High-res Image Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CDKN2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.27

Table S13.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
CDKN2A MUTATED 11 6 17 19
CDKN2A WILD-TYPE 44 46 18 47

Figure S10.  Get High-res Image Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CDKN2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.536 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
CDKN2A MUTATED 23 18 12
CDKN2A WILD-TYPE 55 65 35
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.186 (Fisher's exact test), Q value = 1

Table S15.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
CDKN2A MUTATED 22 19 24
CDKN2A WILD-TYPE 102 76 61
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.394 (Fisher's exact test), Q value = 1

Table S16.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
CDKN2A MUTATED 5 26 20 14
CDKN2A WILD-TYPE 26 83 58 72
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.507 (Fisher's exact test), Q value = 1

Table S17.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
CDKN2A MUTATED 23 15 26
CDKN2A WILD-TYPE 103 56 81
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.155 (Fisher's exact test), Q value = 1

Table S18.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
CDKN2A MUTATED 32 13 19
CDKN2A WILD-TYPE 88 67 85
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S19.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
CDKN2A MUTATED 8 5 11 31 2
CDKN2A WILD-TYPE 35 23 43 80 23
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.269 (Fisher's exact test), Q value = 1

Table S20.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
CDKN2A MUTATED 29 25 3
CDKN2A WILD-TYPE 79 112 13
'CASP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0053

Table S21.  Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
CASP8 MUTATED 4 0 21 1
CASP8 WILD-TYPE 88 89 84 15

Figure S11.  Get High-res Image Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CASP8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0027

Table S22.  Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
CASP8 MUTATED 6 1 3 0 0 16 1
CASP8 WILD-TYPE 43 42 52 61 43 25 13

Figure S12.  Get High-res Image Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CASP8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 1

Table S23.  Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
CASP8 MUTATED 5 1 8 8
CASP8 WILD-TYPE 50 51 27 58

Figure S13.  Get High-res Image Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CASP8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.384 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
CASP8 MUTATED 11 6 5
CASP8 WILD-TYPE 67 77 42
'CASP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0027

Table S25.  Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
CASP8 MUTATED 1 5 21
CASP8 WILD-TYPE 123 90 64

Figure S14.  Get High-res Image Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.029

Table S26.  Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
CASP8 MUTATED 1 8 17 1
CASP8 WILD-TYPE 30 101 61 85

Figure S15.  Get High-res Image Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CASP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 1

Table S27.  Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
CASP8 MUTATED 7 10 9
CASP8 WILD-TYPE 119 61 98
'CASP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.933 (Fisher's exact test), Q value = 1

Table S28.  Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
CASP8 MUTATED 11 7 8
CASP8 WILD-TYPE 109 73 96
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0943 (Fisher's exact test), Q value = 1

Table S29.  Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
CASP8 MUTATED 2 3 1 15 2
CASP8 WILD-TYPE 41 25 53 96 23
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.349 (Fisher's exact test), Q value = 1

Table S30.  Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
CASP8 MUTATED 12 9 2
CASP8 WILD-TYPE 96 128 14
'FAT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.124 (Fisher's exact test), Q value = 1

Table S31.  Gene #4: 'FAT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
FAT1 MUTATED 15 27 24 2
FAT1 WILD-TYPE 77 62 81 14
'FAT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.079 (Fisher's exact test), Q value = 1

Table S32.  Gene #4: 'FAT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
FAT1 MUTATED 11 10 11 17 3 14 3
FAT1 WILD-TYPE 38 33 44 44 40 27 11
'FAT1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.917 (Fisher's exact test), Q value = 1

Table S33.  Gene #4: 'FAT1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
FAT1 MUTATED 12 11 7 17
FAT1 WILD-TYPE 43 41 28 49
'FAT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S34.  Gene #4: 'FAT1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
FAT1 MUTATED 17 22 8
FAT1 WILD-TYPE 61 61 39
'FAT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.106 (Fisher's exact test), Q value = 1

Table S35.  Gene #4: 'FAT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
FAT1 MUTATED 21 27 21
FAT1 WILD-TYPE 103 68 64
'FAT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.326 (Fisher's exact test), Q value = 1

Table S36.  Gene #4: 'FAT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
FAT1 MUTATED 6 31 17 15
FAT1 WILD-TYPE 25 78 61 71
'FAT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S37.  Gene #4: 'FAT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
FAT1 MUTATED 26 13 29
FAT1 WILD-TYPE 100 58 78
'FAT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.506 (Fisher's exact test), Q value = 1

Table S38.  Gene #4: 'FAT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
FAT1 MUTATED 31 17 20
FAT1 WILD-TYPE 89 63 84
'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 1

Table S39.  Gene #4: 'FAT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
FAT1 MUTATED 11 9 12 27 2
FAT1 WILD-TYPE 32 19 42 84 23
'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S40.  Gene #4: 'FAT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
FAT1 MUTATED 31 28 2
FAT1 WILD-TYPE 77 109 14
'MLL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.22

Table S41.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
MLL2 MUTATED 11 28 11 3
MLL2 WILD-TYPE 81 61 94 13

Figure S16.  Get High-res Image Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0483 (Fisher's exact test), Q value = 1

Table S42.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
MLL2 MUTATED 5 10 8 17 9 4 0
MLL2 WILD-TYPE 44 33 47 44 34 37 14

Figure S17.  Get High-res Image Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'MLL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.493 (Fisher's exact test), Q value = 1

Table S43.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
MLL2 MUTATED 7 11 8 10
MLL2 WILD-TYPE 48 41 27 56
'MLL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.346 (Fisher's exact test), Q value = 1

Table S44.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
MLL2 MUTATED 14 17 5
MLL2 WILD-TYPE 64 66 42
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0823 (Fisher's exact test), Q value = 1

Table S45.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
MLL2 MUTATED 29 12 12
MLL2 WILD-TYPE 95 83 73
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.106 (Fisher's exact test), Q value = 1

Table S46.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
MLL2 MUTATED 7 13 12 21
MLL2 WILD-TYPE 24 96 66 65
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 1

Table S47.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
MLL2 MUTATED 27 13 12
MLL2 WILD-TYPE 99 58 95
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 1

Table S48.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
MLL2 MUTATED 12 18 22
MLL2 WILD-TYPE 108 62 82

Figure S18.  Get High-res Image Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.507 (Fisher's exact test), Q value = 1

Table S49.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
MLL2 MUTATED 5 3 13 19 4
MLL2 WILD-TYPE 38 25 41 92 21
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0645 (Fisher's exact test), Q value = 1

Table S50.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
MLL2 MUTATED 13 30 1
MLL2 WILD-TYPE 95 107 15
'JUB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.257 (Fisher's exact test), Q value = 1

Table S51.  Gene #6: 'JUB MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
JUB MUTATED 4 9 4 1
JUB WILD-TYPE 88 80 101 15
'JUB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0805 (Fisher's exact test), Q value = 1

Table S52.  Gene #6: 'JUB MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
JUB MUTATED 1 0 6 5 1 3 2
JUB WILD-TYPE 48 43 49 56 42 38 12
'JUB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 1

Table S53.  Gene #6: 'JUB MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
JUB MUTATED 5 2 3 2
JUB WILD-TYPE 50 50 32 64
'JUB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.746 (Fisher's exact test), Q value = 1

Table S54.  Gene #6: 'JUB MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
JUB MUTATED 6 4 2
JUB WILD-TYPE 72 79 45
'JUB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.121 (Fisher's exact test), Q value = 1

Table S55.  Gene #6: 'JUB MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
JUB MUTATED 5 4 9
JUB WILD-TYPE 119 91 76
'JUB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.423 (Fisher's exact test), Q value = 1

Table S56.  Gene #6: 'JUB MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
JUB MUTATED 0 8 6 4
JUB WILD-TYPE 31 101 72 82
'JUB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.129 (Fisher's exact test), Q value = 1

Table S57.  Gene #6: 'JUB MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
JUB MUTATED 8 7 3
JUB WILD-TYPE 118 64 104
'JUB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S58.  Gene #6: 'JUB MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
JUB MUTATED 7 5 6
JUB WILD-TYPE 113 75 98
'JUB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.126 (Fisher's exact test), Q value = 1

Table S59.  Gene #6: 'JUB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
JUB MUTATED 0 4 3 9 2
JUB WILD-TYPE 43 24 51 102 23
'JUB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.849 (Fisher's exact test), Q value = 1

Table S60.  Gene #6: 'JUB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
JUB MUTATED 6 11 1
JUB WILD-TYPE 102 126 15
'NOTCH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 1

Table S61.  Gene #7: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
NOTCH1 MUTATED 21 8 22 5
NOTCH1 WILD-TYPE 71 81 83 11

Figure S19.  Get High-res Image Gene #7: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NOTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00152 (Fisher's exact test), Q value = 0.38

Table S62.  Gene #7: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
NOTCH1 MUTATED 14 2 14 10 2 12 3
NOTCH1 WILD-TYPE 35 41 41 51 41 29 11

Figure S20.  Get High-res Image Gene #7: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NOTCH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0554 (Fisher's exact test), Q value = 1

Table S63.  Gene #7: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
NOTCH1 MUTATED 15 4 6 14
NOTCH1 WILD-TYPE 40 48 29 52
'NOTCH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0691 (Fisher's exact test), Q value = 1

Table S64.  Gene #7: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
NOTCH1 MUTATED 21 11 7
NOTCH1 WILD-TYPE 57 72 40
'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.5

Table S65.  Gene #7: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
NOTCH1 MUTATED 12 22 23
NOTCH1 WILD-TYPE 112 73 62

Figure S21.  Get High-res Image Gene #7: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.029

Table S66.  Gene #7: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
NOTCH1 MUTATED 2 24 25 6
NOTCH1 WILD-TYPE 29 85 53 80

Figure S22.  Get High-res Image Gene #7: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.023

Table S67.  Gene #7: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
NOTCH1 MUTATED 10 22 24
NOTCH1 WILD-TYPE 116 49 83

Figure S23.  Get High-res Image Gene #7: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.348 (Fisher's exact test), Q value = 1

Table S68.  Gene #7: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
NOTCH1 MUTATED 27 13 16
NOTCH1 WILD-TYPE 93 67 88
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.314 (Fisher's exact test), Q value = 1

Table S69.  Gene #7: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
NOTCH1 MUTATED 8 7 5 22 3
NOTCH1 WILD-TYPE 35 21 49 89 22
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 1

Table S70.  Gene #7: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
NOTCH1 MUTATED 27 16 2
NOTCH1 WILD-TYPE 81 121 14

Figure S24.  Get High-res Image Gene #7: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.63 (Fisher's exact test), Q value = 1

Table S71.  Gene #8: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
NFE2L2 MUTATED 3 6 7 1
NFE2L2 WILD-TYPE 89 83 98 15
'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.034

Table S72.  Gene #8: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
NFE2L2 MUTATED 2 0 0 10 0 5 0
NFE2L2 WILD-TYPE 47 43 55 51 43 36 14

Figure S25.  Get High-res Image Gene #8: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 1

Table S73.  Gene #8: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
NFE2L2 MUTATED 4 6 2 2
NFE2L2 WILD-TYPE 51 46 33 64
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.685 (Fisher's exact test), Q value = 1

Table S74.  Gene #8: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
NFE2L2 MUTATED 5 7 2
NFE2L2 WILD-TYPE 73 76 45
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S75.  Gene #8: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
NFE2L2 MUTATED 7 5 5
NFE2L2 WILD-TYPE 117 90 80
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.434 (Fisher's exact test), Q value = 1

Table S76.  Gene #8: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
NFE2L2 MUTATED 0 5 6 6
NFE2L2 WILD-TYPE 31 104 72 80
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.18 (Fisher's exact test), Q value = 1

Table S77.  Gene #8: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
NFE2L2 MUTATED 8 1 8
NFE2L2 WILD-TYPE 118 70 99
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.738 (Fisher's exact test), Q value = 1

Table S78.  Gene #8: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
NFE2L2 MUTATED 7 3 7
NFE2L2 WILD-TYPE 113 77 97
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.356 (Fisher's exact test), Q value = 1

Table S79.  Gene #8: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
NFE2L2 MUTATED 2 1 1 11 1
NFE2L2 WILD-TYPE 41 27 53 100 24
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.92 (Fisher's exact test), Q value = 1

Table S80.  Gene #8: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
NFE2L2 MUTATED 6 9 1
NFE2L2 WILD-TYPE 102 128 15
'NSD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.344 (Fisher's exact test), Q value = 1

Table S81.  Gene #9: 'NSD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
NSD1 MUTATED 10 14 8 1
NSD1 WILD-TYPE 82 75 97 15
'NSD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0027

Table S82.  Gene #9: 'NSD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
NSD1 MUTATED 1 25 1 0 3 3 0
NSD1 WILD-TYPE 48 18 54 61 40 38 14

Figure S26.  Get High-res Image Gene #9: 'NSD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NSD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0955 (Fisher's exact test), Q value = 1

Table S83.  Gene #9: 'NSD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
NSD1 MUTATED 7 7 5 2
NSD1 WILD-TYPE 48 45 30 64
'NSD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00668 (Fisher's exact test), Q value = 1

Table S84.  Gene #9: 'NSD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
NSD1 MUTATED 8 3 10
NSD1 WILD-TYPE 70 80 37

Figure S27.  Get High-res Image Gene #9: 'NSD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'NSD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.087

Table S85.  Gene #9: 'NSD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
NSD1 MUTATED 24 3 6
NSD1 WILD-TYPE 100 92 79

Figure S28.  Get High-res Image Gene #9: 'NSD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NSD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0027

Table S86.  Gene #9: 'NSD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
NSD1 MUTATED 22 5 4 2
NSD1 WILD-TYPE 9 104 74 84

Figure S29.  Get High-res Image Gene #9: 'NSD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NSD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 1

Table S87.  Gene #9: 'NSD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
NSD1 MUTATED 21 7 5
NSD1 WILD-TYPE 105 64 102

Figure S30.  Get High-res Image Gene #9: 'NSD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NSD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00426 (Fisher's exact test), Q value = 1

Table S88.  Gene #9: 'NSD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
NSD1 MUTATED 6 16 11
NSD1 WILD-TYPE 114 64 93

Figure S31.  Get High-res Image Gene #9: 'NSD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NSD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00984 (Fisher's exact test), Q value = 1

Table S89.  Gene #9: 'NSD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
NSD1 MUTATED 2 2 14 9 2
NSD1 WILD-TYPE 41 26 40 102 23

Figure S32.  Get High-res Image Gene #9: 'NSD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NSD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00869 (Fisher's exact test), Q value = 1

Table S90.  Gene #9: 'NSD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
NSD1 MUTATED 6 23 0
NSD1 WILD-TYPE 102 114 16

Figure S33.  Get High-res Image Gene #9: 'NSD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.062

Table S91.  Gene #10: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
HRAS MUTATED 0 0 10 0
HRAS WILD-TYPE 92 89 95 16

Figure S34.  Get High-res Image Gene #10: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00509 (Fisher's exact test), Q value = 1

Table S92.  Gene #10: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
HRAS MUTATED 2 1 1 0 0 6 0
HRAS WILD-TYPE 47 42 54 61 43 35 14

Figure S35.  Get High-res Image Gene #10: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.387 (Fisher's exact test), Q value = 1

Table S93.  Gene #10: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
HRAS MUTATED 1 1 3 2
HRAS WILD-TYPE 54 51 32 64
'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.343 (Fisher's exact test), Q value = 1

Table S94.  Gene #10: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
HRAS MUTATED 4 1 2
HRAS WILD-TYPE 74 82 45
'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.35

Table S95.  Gene #10: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
HRAS MUTATED 1 1 8
HRAS WILD-TYPE 123 94 77

Figure S36.  Get High-res Image Gene #10: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 1

Table S96.  Gene #10: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
HRAS MUTATED 1 1 7 1
HRAS WILD-TYPE 30 108 71 85

Figure S37.  Get High-res Image Gene #10: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.157 (Fisher's exact test), Q value = 1

Table S97.  Gene #10: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
HRAS MUTATED 3 5 2
HRAS WILD-TYPE 123 66 105
'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.272 (Fisher's exact test), Q value = 1

Table S98.  Gene #10: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
HRAS MUTATED 2 2 6
HRAS WILD-TYPE 118 78 98
'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.518 (Fisher's exact test), Q value = 1

Table S99.  Gene #10: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
HRAS MUTATED 0 1 1 6 1
HRAS WILD-TYPE 43 27 53 105 24
'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.851 (Fisher's exact test), Q value = 1

Table S100.  Gene #10: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
HRAS MUTATED 3 6 0
HRAS WILD-TYPE 105 131 16
'ZNF750 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.452 (Fisher's exact test), Q value = 1

Table S101.  Gene #11: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
ZNF750 MUTATED 2 6 5 0
ZNF750 WILD-TYPE 90 83 100 16
'ZNF750 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.137 (Fisher's exact test), Q value = 1

Table S102.  Gene #11: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
ZNF750 MUTATED 2 1 0 4 5 1 0
ZNF750 WILD-TYPE 47 42 55 57 38 40 14
'ZNF750 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.804 (Fisher's exact test), Q value = 1

Table S103.  Gene #11: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
ZNF750 MUTATED 2 2 0 2
ZNF750 WILD-TYPE 53 50 35 64
'ZNF750 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S104.  Gene #11: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
ZNF750 MUTATED 2 4 0
ZNF750 WILD-TYPE 76 79 47
'ZNF750 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.081 (Fisher's exact test), Q value = 1

Table S105.  Gene #11: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
ZNF750 MUTATED 9 3 1
ZNF750 WILD-TYPE 115 92 84
'ZNF750 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.07 (Fisher's exact test), Q value = 1

Table S106.  Gene #11: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
ZNF750 MUTATED 1 3 1 8
ZNF750 WILD-TYPE 30 106 77 78
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.721 (Fisher's exact test), Q value = 1

Table S107.  Gene #11: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
ZNF750 MUTATED 7 2 4
ZNF750 WILD-TYPE 119 69 103
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.938 (Fisher's exact test), Q value = 1

Table S108.  Gene #11: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
ZNF750 MUTATED 5 4 4
ZNF750 WILD-TYPE 115 76 100
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.181 (Fisher's exact test), Q value = 1

Table S109.  Gene #11: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
ZNF750 MUTATED 4 1 4 2 1
ZNF750 WILD-TYPE 39 27 50 109 24
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S110.  Gene #11: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
ZNF750 MUTATED 5 7 0
ZNF750 WILD-TYPE 103 130 16
'RASA1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S111.  Gene #12: 'RASA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
RASA1 MUTATED 7 4 2 0
RASA1 WILD-TYPE 85 85 103 16
'RASA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S112.  Gene #12: 'RASA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
RASA1 MUTATED 4 0 5 4 0 1 0
RASA1 WILD-TYPE 45 43 50 57 43 40 14
'RASA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 1

Table S113.  Gene #12: 'RASA1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
RASA1 MUTATED 5 1 1 3
RASA1 WILD-TYPE 50 51 34 63
'RASA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.715 (Fisher's exact test), Q value = 1

Table S114.  Gene #12: 'RASA1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
RASA1 MUTATED 5 3 2
RASA1 WILD-TYPE 73 80 45
'RASA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 1

Table S115.  Gene #12: 'RASA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
RASA1 MUTATED 4 7 3
RASA1 WILD-TYPE 120 88 82
'RASA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.546 (Fisher's exact test), Q value = 1

Table S116.  Gene #12: 'RASA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
RASA1 MUTATED 0 7 4 3
RASA1 WILD-TYPE 31 102 74 83
'RASA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.471 (Fisher's exact test), Q value = 1

Table S117.  Gene #12: 'RASA1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
RASA1 MUTATED 4 3 7
RASA1 WILD-TYPE 122 68 100
'RASA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.14 (Fisher's exact test), Q value = 1

Table S118.  Gene #12: 'RASA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
RASA1 MUTATED 9 3 2
RASA1 WILD-TYPE 111 77 102
'RASA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 1

Table S119.  Gene #12: 'RASA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
RASA1 MUTATED 4 2 3 3 0
RASA1 WILD-TYPE 39 26 51 108 25
'RASA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.061 (Fisher's exact test), Q value = 1

Table S120.  Gene #12: 'RASA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
RASA1 MUTATED 7 3 2
RASA1 WILD-TYPE 101 134 14
'HLA-A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0339 (Fisher's exact test), Q value = 1

Table S121.  Gene #13: 'HLA-A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
HLA-A MUTATED 3 0 4 2
HLA-A WILD-TYPE 89 89 101 14

Figure S38.  Get High-res Image Gene #13: 'HLA-A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HLA-A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.317 (Fisher's exact test), Q value = 1

Table S122.  Gene #13: 'HLA-A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
HLA-A MUTATED 1 0 1 2 1 4 0
HLA-A WILD-TYPE 48 43 54 59 42 37 14
'HLA-A MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S123.  Gene #13: 'HLA-A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
HLA-A MUTATED 1 1 1 2
HLA-A WILD-TYPE 54 51 34 64
'HLA-A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.639 (Fisher's exact test), Q value = 1

Table S124.  Gene #13: 'HLA-A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
HLA-A MUTATED 1 2 2
HLA-A WILD-TYPE 77 81 45
'HLA-A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.186 (Fisher's exact test), Q value = 1

Table S125.  Gene #13: 'HLA-A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
HLA-A MUTATED 3 1 5
HLA-A WILD-TYPE 121 94 80
'HLA-A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0703 (Fisher's exact test), Q value = 1

Table S126.  Gene #13: 'HLA-A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
HLA-A MUTATED 0 2 6 1
HLA-A WILD-TYPE 31 107 72 85
'HLA-A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.346 (Fisher's exact test), Q value = 1

Table S127.  Gene #13: 'HLA-A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
HLA-A MUTATED 3 4 2
HLA-A WILD-TYPE 123 67 105
'HLA-A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.431 (Fisher's exact test), Q value = 1

Table S128.  Gene #13: 'HLA-A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
HLA-A MUTATED 2 2 5
HLA-A WILD-TYPE 118 78 99
'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.673 (Fisher's exact test), Q value = 1

Table S129.  Gene #13: 'HLA-A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
HLA-A MUTATED 1 2 1 5 0
HLA-A WILD-TYPE 42 26 53 106 25
'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S130.  Gene #13: 'HLA-A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
HLA-A MUTATED 3 6 0
HLA-A WILD-TYPE 105 131 16
'EPHA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.306 (Fisher's exact test), Q value = 1

Table S131.  Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
EPHA2 MUTATED 5 1 5 1
EPHA2 WILD-TYPE 87 88 100 15
'EPHA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.34

Table S132.  Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
EPHA2 MUTATED 0 1 3 0 1 6 2
EPHA2 WILD-TYPE 49 42 52 61 42 35 12

Figure S39.  Get High-res Image Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EPHA2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.741 (Fisher's exact test), Q value = 1

Table S133.  Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
EPHA2 MUTATED 4 2 1 5
EPHA2 WILD-TYPE 51 50 34 61
'EPHA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.932 (Fisher's exact test), Q value = 1

Table S134.  Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
EPHA2 MUTATED 5 5 2
EPHA2 WILD-TYPE 73 78 45
'EPHA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0638 (Fisher's exact test), Q value = 1

Table S135.  Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
EPHA2 MUTATED 2 4 7
EPHA2 WILD-TYPE 122 91 78
'EPHA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.197 (Fisher's exact test), Q value = 1

Table S136.  Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
EPHA2 MUTATED 1 5 6 1
EPHA2 WILD-TYPE 30 104 72 85
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.485 (Fisher's exact test), Q value = 1

Table S137.  Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
EPHA2 MUTATED 3 4 5
EPHA2 WILD-TYPE 123 67 102
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S138.  Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
EPHA2 MUTATED 6 4 2
EPHA2 WILD-TYPE 114 76 102
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0805 (Fisher's exact test), Q value = 1

Table S139.  Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
EPHA2 MUTATED 0 2 0 7 0
EPHA2 WILD-TYPE 43 26 54 104 25
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S140.  Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
EPHA2 MUTATED 5 3 1
EPHA2 WILD-TYPE 103 134 15
'RAC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.31 (Fisher's exact test), Q value = 1

Table S141.  Gene #15: 'RAC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
RAC1 MUTATED 2 1 6 0
RAC1 WILD-TYPE 90 88 99 16
'RAC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.435 (Fisher's exact test), Q value = 1

Table S142.  Gene #15: 'RAC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
RAC1 MUTATED 3 0 1 1 1 2 1
RAC1 WILD-TYPE 46 43 54 60 42 39 13
'RAC1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S143.  Gene #15: 'RAC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
RAC1 MUTATED 1 1 1 1
RAC1 WILD-TYPE 54 51 34 65
'RAC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S144.  Gene #15: 'RAC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
RAC1 MUTATED 2 1 1
RAC1 WILD-TYPE 76 82 46
'RAC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S145.  Gene #15: 'RAC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
RAC1 MUTATED 3 1 5
RAC1 WILD-TYPE 121 94 80
'RAC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.147 (Fisher's exact test), Q value = 1

Table S146.  Gene #15: 'RAC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
RAC1 MUTATED 0 1 5 3
RAC1 WILD-TYPE 31 108 73 83
'RAC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 1

Table S147.  Gene #15: 'RAC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
RAC1 MUTATED 6 2 1
RAC1 WILD-TYPE 120 69 106
'RAC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S148.  Gene #15: 'RAC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
RAC1 MUTATED 1 3 5
RAC1 WILD-TYPE 119 77 99
'RAC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.256 (Fisher's exact test), Q value = 1

Table S149.  Gene #15: 'RAC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
RAC1 MUTATED 0 2 2 2 1
RAC1 WILD-TYPE 43 26 52 109 24
'RAC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.271 (Fisher's exact test), Q value = 1

Table S150.  Gene #15: 'RAC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
RAC1 MUTATED 1 6 0
RAC1 WILD-TYPE 107 131 16
'EP300 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.339 (Fisher's exact test), Q value = 1

Table S151.  Gene #16: 'EP300 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
EP300 MUTATED 7 4 12 1
EP300 WILD-TYPE 85 85 93 15
'EP300 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 1

Table S152.  Gene #16: 'EP300 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
EP300 MUTATED 4 2 2 4 5 6 1
EP300 WILD-TYPE 45 41 53 57 38 35 13
'EP300 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.572 (Fisher's exact test), Q value = 1

Table S153.  Gene #16: 'EP300 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
EP300 MUTATED 3 2 4 4
EP300 WILD-TYPE 52 50 31 62
'EP300 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0881 (Fisher's exact test), Q value = 1

Table S154.  Gene #16: 'EP300 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
EP300 MUTATED 7 6 0
EP300 WILD-TYPE 71 77 47
'EP300 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00481 (Fisher's exact test), Q value = 1

Table S155.  Gene #16: 'EP300 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
EP300 MUTATED 5 5 14
EP300 WILD-TYPE 119 90 71

Figure S40.  Get High-res Image Gene #16: 'EP300 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'EP300 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0584 (Fisher's exact test), Q value = 1

Table S156.  Gene #16: 'EP300 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
EP300 MUTATED 2 6 12 4
EP300 WILD-TYPE 29 103 66 82
'EP300 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 1

Table S157.  Gene #16: 'EP300 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
EP300 MUTATED 9 8 6
EP300 WILD-TYPE 117 63 101
'EP300 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.212 (Fisher's exact test), Q value = 1

Table S158.  Gene #16: 'EP300 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
EP300 MUTATED 7 4 12
EP300 WILD-TYPE 113 76 92
'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.227 (Fisher's exact test), Q value = 1

Table S159.  Gene #16: 'EP300 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
EP300 MUTATED 1 4 2 11 2
EP300 WILD-TYPE 42 24 52 100 23
'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S160.  Gene #16: 'EP300 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
EP300 MUTATED 8 11 1
EP300 WILD-TYPE 100 126 15
'TGFBR2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 1

Table S161.  Gene #17: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
TGFBR2 MUTATED 3 1 6 0
TGFBR2 WILD-TYPE 89 88 99 16
'TGFBR2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 1

Table S162.  Gene #17: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
TGFBR2 MUTATED 3 3 0 0 0 4 0
TGFBR2 WILD-TYPE 46 40 55 61 43 37 14

Figure S41.  Get High-res Image Gene #17: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TGFBR2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.438 (Fisher's exact test), Q value = 1

Table S163.  Gene #17: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
TGFBR2 MUTATED 3 1 0 4
TGFBR2 WILD-TYPE 52 51 35 62
'TGFBR2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.901 (Fisher's exact test), Q value = 1

Table S164.  Gene #17: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
TGFBR2 MUTATED 3 4 1
TGFBR2 WILD-TYPE 75 79 46
'TGFBR2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.229 (Fisher's exact test), Q value = 1

Table S165.  Gene #17: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
TGFBR2 MUTATED 2 3 5
TGFBR2 WILD-TYPE 122 92 80
'TGFBR2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0444 (Fisher's exact test), Q value = 1

Table S166.  Gene #17: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
TGFBR2 MUTATED 3 4 3 0
TGFBR2 WILD-TYPE 28 105 75 86

Figure S42.  Get High-res Image Gene #17: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.775 (Fisher's exact test), Q value = 1

Table S167.  Gene #17: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
TGFBR2 MUTATED 3 3 4
TGFBR2 WILD-TYPE 123 68 103
'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S168.  Gene #17: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
TGFBR2 MUTATED 4 4 2
TGFBR2 WILD-TYPE 116 76 102
'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.933 (Fisher's exact test), Q value = 1

Table S169.  Gene #17: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
TGFBR2 MUTATED 2 1 1 4 1
TGFBR2 WILD-TYPE 41 27 53 107 24
'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.52 (Fisher's exact test), Q value = 1

Table S170.  Gene #17: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
TGFBR2 MUTATED 4 4 1
TGFBR2 WILD-TYPE 104 133 15
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.241 (Fisher's exact test), Q value = 1

Table S171.  Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
PIK3CA MUTATED 13 19 27 3
PIK3CA WILD-TYPE 79 70 78 13
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0392 (Fisher's exact test), Q value = 1

Table S172.  Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
PIK3CA MUTATED 9 5 8 17 16 8 1
PIK3CA WILD-TYPE 40 38 47 44 27 33 13

Figure S43.  Get High-res Image Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.696 (Fisher's exact test), Q value = 1

Table S173.  Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
PIK3CA MUTATED 12 9 8 10
PIK3CA WILD-TYPE 43 43 27 56
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0483 (Fisher's exact test), Q value = 1

Table S174.  Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
PIK3CA MUTATED 15 10 14
PIK3CA WILD-TYPE 63 73 33

Figure S44.  Get High-res Image Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0965 (Fisher's exact test), Q value = 1

Table S175.  Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
PIK3CA MUTATED 31 13 20
PIK3CA WILD-TYPE 93 82 65
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0535 (Fisher's exact test), Q value = 1

Table S176.  Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
PIK3CA MUTATED 3 17 21 23
PIK3CA WILD-TYPE 28 92 57 63
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0057 (Fisher's exact test), Q value = 1

Table S177.  Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
PIK3CA MUTATED 33 19 12
PIK3CA WILD-TYPE 93 52 95

Figure S45.  Get High-res Image Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0644 (Fisher's exact test), Q value = 1

Table S178.  Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
PIK3CA MUTATED 21 13 30
PIK3CA WILD-TYPE 99 67 74
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.203 (Fisher's exact test), Q value = 1

Table S179.  Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
PIK3CA MUTATED 9 5 17 23 2
PIK3CA WILD-TYPE 34 23 37 88 23
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.23 (Fisher's exact test), Q value = 1

Table S180.  Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
PIK3CA MUTATED 18 35 3
PIK3CA WILD-TYPE 90 102 13
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.775 (Fisher's exact test), Q value = 1

Table S181.  Gene #19: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
FBXW7 MUTATED 6 5 4 0
FBXW7 WILD-TYPE 86 84 101 16
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.47 (Fisher's exact test), Q value = 1

Table S182.  Gene #19: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
FBXW7 MUTATED 1 3 1 5 1 3 1
FBXW7 WILD-TYPE 48 40 54 56 42 38 13
'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.414 (Fisher's exact test), Q value = 1

Table S183.  Gene #19: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
FBXW7 MUTATED 1 4 1 5
FBXW7 WILD-TYPE 54 48 34 61
'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.112 (Fisher's exact test), Q value = 1

Table S184.  Gene #19: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
FBXW7 MUTATED 2 8 1
FBXW7 WILD-TYPE 76 75 46
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.633 (Fisher's exact test), Q value = 1

Table S185.  Gene #19: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
FBXW7 MUTATED 7 3 5
FBXW7 WILD-TYPE 117 92 80
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.876 (Fisher's exact test), Q value = 1

Table S186.  Gene #19: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
FBXW7 MUTATED 2 5 3 5
FBXW7 WILD-TYPE 29 104 75 81
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.946 (Fisher's exact test), Q value = 1

Table S187.  Gene #19: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
FBXW7 MUTATED 6 4 5
FBXW7 WILD-TYPE 120 67 102
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.206 (Fisher's exact test), Q value = 1

Table S188.  Gene #19: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
FBXW7 MUTATED 5 7 3
FBXW7 WILD-TYPE 115 73 101
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.876 (Fisher's exact test), Q value = 1

Table S189.  Gene #19: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
FBXW7 MUTATED 1 1 4 5 1
FBXW7 WILD-TYPE 42 27 50 106 24
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.272 (Fisher's exact test), Q value = 1

Table S190.  Gene #19: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
FBXW7 MUTATED 4 6 2
FBXW7 WILD-TYPE 104 131 14
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.092 (Fisher's exact test), Q value = 1

Table S191.  Gene #20: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
RB1 MUTATED 0 5 5 0
RB1 WILD-TYPE 92 84 100 16
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 1

Table S192.  Gene #20: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
RB1 MUTATED 1 3 0 2 3 1 0
RB1 WILD-TYPE 48 40 55 59 40 40 14
'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.326 (Fisher's exact test), Q value = 1

Table S193.  Gene #20: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
RB1 MUTATED 0 1 0 3
RB1 WILD-TYPE 55 51 35 63
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 1

Table S194.  Gene #20: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
RB1 MUTATED 0 3 1
RB1 WILD-TYPE 78 80 46
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0562 (Fisher's exact test), Q value = 1

Table S195.  Gene #20: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
RB1 MUTATED 8 1 1
RB1 WILD-TYPE 116 94 84
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S196.  Gene #20: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
RB1 MUTATED 2 3 1 4
RB1 WILD-TYPE 29 106 77 82
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.103 (Fisher's exact test), Q value = 1

Table S197.  Gene #20: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
RB1 MUTATED 7 0 3
RB1 WILD-TYPE 119 71 104
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.518 (Fisher's exact test), Q value = 1

Table S198.  Gene #20: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
RB1 MUTATED 4 4 2
RB1 WILD-TYPE 116 76 102
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 1

Table S199.  Gene #20: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
RB1 MUTATED 1 0 3 3 2
RB1 WILD-TYPE 42 28 51 108 23
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S200.  Gene #20: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
RB1 MUTATED 3 6 0
RB1 WILD-TYPE 105 131 16
'CTCF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.232 (Fisher's exact test), Q value = 1

Table S201.  Gene #21: 'CTCF MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
CTCF MUTATED 3 1 7 0
CTCF WILD-TYPE 89 88 98 16
'CTCF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 1

Table S202.  Gene #21: 'CTCF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
CTCF MUTATED 1 3 1 0 1 5 0
CTCF WILD-TYPE 48 40 54 61 42 36 14

Figure S46.  Get High-res Image Gene #21: 'CTCF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CTCF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.614 (Fisher's exact test), Q value = 1

Table S203.  Gene #21: 'CTCF MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
CTCF MUTATED 2 2 0 4
CTCF WILD-TYPE 53 50 35 62
'CTCF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.469 (Fisher's exact test), Q value = 1

Table S204.  Gene #21: 'CTCF MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
CTCF MUTATED 2 5 1
CTCF WILD-TYPE 76 78 46
'CTCF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.426 (Fisher's exact test), Q value = 1

Table S205.  Gene #21: 'CTCF MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
CTCF MUTATED 4 2 5
CTCF WILD-TYPE 120 93 80
'CTCF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.526 (Fisher's exact test), Q value = 1

Table S206.  Gene #21: 'CTCF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
CTCF MUTATED 2 3 4 2
CTCF WILD-TYPE 29 106 74 84
'CTCF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.627 (Fisher's exact test), Q value = 1

Table S207.  Gene #21: 'CTCF MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
CTCF MUTATED 4 4 3
CTCF WILD-TYPE 122 67 104
'CTCF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S208.  Gene #21: 'CTCF MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
CTCF MUTATED 5 1 5
CTCF WILD-TYPE 115 79 99
'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.779 (Fisher's exact test), Q value = 1

Table S209.  Gene #21: 'CTCF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
CTCF MUTATED 1 2 2 4 0
CTCF WILD-TYPE 42 26 52 107 25
'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S210.  Gene #21: 'CTCF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
CTCF MUTATED 4 5 0
CTCF WILD-TYPE 104 132 16
'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 1

Table S211.  Gene #22: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
KDM6A MUTATED 3 3 0 2
KDM6A WILD-TYPE 89 86 105 14

Figure S47.  Get High-res Image Gene #22: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.632 (Fisher's exact test), Q value = 1

Table S212.  Gene #22: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
KDM6A MUTATED 0 2 1 2 1 1 1
KDM6A WILD-TYPE 49 41 54 59 42 40 13
'KDM6A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.158 (Fisher's exact test), Q value = 1

Table S213.  Gene #22: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
KDM6A MUTATED 1 3 1 0
KDM6A WILD-TYPE 54 49 34 66
'KDM6A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S214.  Gene #22: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
KDM6A MUTATED 2 2 1
KDM6A WILD-TYPE 76 81 46
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.908 (Fisher's exact test), Q value = 1

Table S215.  Gene #22: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
KDM6A MUTATED 4 2 2
KDM6A WILD-TYPE 120 93 83
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.361 (Fisher's exact test), Q value = 1

Table S216.  Gene #22: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
KDM6A MUTATED 2 2 1 3
KDM6A WILD-TYPE 29 107 77 83
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 1

Table S217.  Gene #22: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
KDM6A MUTATED 4 3 1
KDM6A WILD-TYPE 122 68 106
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.741 (Fisher's exact test), Q value = 1

Table S218.  Gene #22: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
KDM6A MUTATED 4 1 3
KDM6A WILD-TYPE 116 79 101
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.145 (Fisher's exact test), Q value = 1

Table S219.  Gene #22: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
KDM6A MUTATED 0 2 0 5 0
KDM6A WILD-TYPE 43 26 54 106 25
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.161 (Fisher's exact test), Q value = 1

Table S220.  Gene #22: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
KDM6A MUTATED 1 5 1
KDM6A WILD-TYPE 107 132 15
'ELF4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0361 (Fisher's exact test), Q value = 1

Table S221.  Gene #23: 'ELF4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
ELF4 MUTATED 0 0 5 0
ELF4 WILD-TYPE 92 89 100 16

Figure S48.  Get High-res Image Gene #23: 'ELF4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ELF4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.173 (Fisher's exact test), Q value = 1

Table S222.  Gene #23: 'ELF4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
ELF4 MUTATED 1 0 0 0 2 2 0
ELF4 WILD-TYPE 48 43 55 61 41 39 14
'ELF4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.358 (Fisher's exact test), Q value = 1

Table S223.  Gene #23: 'ELF4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
ELF4 MUTATED 2 1 0 0
ELF4 WILD-TYPE 53 51 35 66
'ELF4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.341 (Fisher's exact test), Q value = 1

Table S224.  Gene #23: 'ELF4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
ELF4 MUTATED 2 0 1
ELF4 WILD-TYPE 76 83 46
'ELF4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.619 (Fisher's exact test), Q value = 1

Table S225.  Gene #23: 'ELF4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
ELF4 MUTATED 1 2 2
ELF4 WILD-TYPE 123 93 83
'ELF4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S226.  Gene #23: 'ELF4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
ELF4 MUTATED 0 2 1 2
ELF4 WILD-TYPE 31 107 77 84
'ELF4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 1

Table S227.  Gene #23: 'ELF4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
ELF4 MUTATED 4 0 1
ELF4 WILD-TYPE 122 71 106
'ELF4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S228.  Gene #23: 'ELF4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
ELF4 MUTATED 2 0 3
ELF4 WILD-TYPE 118 80 101
'ELF4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.588 (Fisher's exact test), Q value = 1

Table S229.  Gene #23: 'ELF4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
ELF4 MUTATED 1 0 0 3 1
ELF4 WILD-TYPE 42 28 54 108 24
'ELF4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S230.  Gene #23: 'ELF4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
ELF4 MUTATED 2 3 0
ELF4 WILD-TYPE 106 134 16
'RHOA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 1

Table S231.  Gene #24: 'RHOA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
RHOA MUTATED 1 0 1 2
RHOA WILD-TYPE 91 89 104 14

Figure S49.  Get High-res Image Gene #24: 'RHOA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RHOA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 1

Table S232.  Gene #24: 'RHOA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
RHOA MUTATED 1 0 3 0 0 0 0
RHOA WILD-TYPE 48 43 52 61 43 41 14
'RHOA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.137 (Fisher's exact test), Q value = 1

Table S233.  Gene #24: 'RHOA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
RHOA MUTATED 0 0 0 3
RHOA WILD-TYPE 55 52 35 63
'RHOA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.241 (Fisher's exact test), Q value = 1

Table S234.  Gene #24: 'RHOA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
RHOA MUTATED 0 3 0
RHOA WILD-TYPE 78 80 47
'RHOA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.823 (Fisher's exact test), Q value = 1

Table S235.  Gene #24: 'RHOA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
RHOA MUTATED 1 2 1
RHOA WILD-TYPE 123 93 84
'RHOA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.487 (Fisher's exact test), Q value = 1

Table S236.  Gene #24: 'RHOA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
RHOA MUTATED 0 3 1 0
RHOA WILD-TYPE 31 106 77 86
'RHOA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.167 (Fisher's exact test), Q value = 1

Table S237.  Gene #24: 'RHOA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
RHOA MUTATED 0 2 2
RHOA WILD-TYPE 126 69 105
'RHOA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S238.  Gene #24: 'RHOA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
RHOA MUTATED 3 0 1
RHOA WILD-TYPE 117 80 103
'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.396 (Fisher's exact test), Q value = 1

Table S239.  Gene #24: 'RHOA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
RHOA MUTATED 2 0 0 2 0
RHOA WILD-TYPE 41 28 54 109 25
'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0375 (Fisher's exact test), Q value = 1

Table S240.  Gene #24: 'RHOA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
RHOA MUTATED 3 0 1
RHOA WILD-TYPE 105 137 15

Figure S50.  Get High-res Image Gene #24: 'RHOA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HLA-B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.217 (Fisher's exact test), Q value = 1

Table S241.  Gene #25: 'HLA-B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
HLA-B MUTATED 4 0 4 0
HLA-B WILD-TYPE 88 89 101 16
'HLA-B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.401 (Fisher's exact test), Q value = 1

Table S242.  Gene #25: 'HLA-B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
HLA-B MUTATED 0 0 2 2 1 3 0
HLA-B WILD-TYPE 49 43 53 59 42 38 14
'HLA-B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S243.  Gene #25: 'HLA-B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
HLA-B MUTATED 2 1 1 2
HLA-B WILD-TYPE 53 51 34 64
'HLA-B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0531 (Fisher's exact test), Q value = 1

Table S244.  Gene #25: 'HLA-B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
HLA-B MUTATED 3 0 3
HLA-B WILD-TYPE 75 83 44
'HLA-B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00831 (Fisher's exact test), Q value = 1

Table S245.  Gene #25: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
HLA-B MUTATED 2 0 6
HLA-B WILD-TYPE 122 95 79

Figure S51.  Get High-res Image Gene #25: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HLA-B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.147 (Fisher's exact test), Q value = 1

Table S246.  Gene #25: 'HLA-B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
HLA-B MUTATED 0 1 5 2
HLA-B WILD-TYPE 31 108 73 84
'HLA-B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 1

Table S247.  Gene #25: 'HLA-B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
HLA-B MUTATED 4 3 1
HLA-B WILD-TYPE 122 68 106
'HLA-B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0636 (Fisher's exact test), Q value = 1

Table S248.  Gene #25: 'HLA-B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
HLA-B MUTATED 1 1 6
HLA-B WILD-TYPE 119 79 98
'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.561 (Fisher's exact test), Q value = 1

Table S249.  Gene #25: 'HLA-B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
HLA-B MUTATED 0 0 1 5 1
HLA-B WILD-TYPE 43 28 53 106 24
'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.659 (Fisher's exact test), Q value = 1

Table S250.  Gene #25: 'HLA-B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
HLA-B MUTATED 2 5 0
HLA-B WILD-TYPE 106 132 16
'PRSS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.494 (Fisher's exact test), Q value = 1

Table S251.  Gene #26: 'PRSS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
PRSS1 MUTATED 4 2 1 0
PRSS1 WILD-TYPE 88 87 104 16
'PRSS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.853 (Fisher's exact test), Q value = 1

Table S252.  Gene #26: 'PRSS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
PRSS1 MUTATED 1 1 2 1 0 2 0
PRSS1 WILD-TYPE 48 42 53 60 43 39 14
'PRSS1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.872 (Fisher's exact test), Q value = 1

Table S253.  Gene #26: 'PRSS1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
PRSS1 MUTATED 1 0 1 1
PRSS1 WILD-TYPE 54 52 34 65
'PRSS1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.616 (Fisher's exact test), Q value = 1

Table S254.  Gene #26: 'PRSS1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
PRSS1 MUTATED 2 1 0
PRSS1 WILD-TYPE 76 82 47
'PRSS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.721 (Fisher's exact test), Q value = 1

Table S255.  Gene #26: 'PRSS1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
PRSS1 MUTATED 4 2 1
PRSS1 WILD-TYPE 120 93 84
'PRSS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.577 (Fisher's exact test), Q value = 1

Table S256.  Gene #26: 'PRSS1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
PRSS1 MUTATED 1 2 3 1
PRSS1 WILD-TYPE 30 107 75 85
'PRSS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S257.  Gene #26: 'PRSS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
PRSS1 MUTATED 3 2 2
PRSS1 WILD-TYPE 123 69 105
'PRSS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 1

Table S258.  Gene #26: 'PRSS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
PRSS1 MUTATED 2 5 0
PRSS1 WILD-TYPE 118 75 104

Figure S52.  Get High-res Image Gene #26: 'PRSS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PRSS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.713 (Fisher's exact test), Q value = 1

Table S259.  Gene #26: 'PRSS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
PRSS1 MUTATED 0 1 1 4 1
PRSS1 WILD-TYPE 43 27 53 107 24
'PRSS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.429 (Fisher's exact test), Q value = 1

Table S260.  Gene #26: 'PRSS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
PRSS1 MUTATED 2 4 1
PRSS1 WILD-TYPE 106 133 15
'GUCY2F MUTATION STATUS' versus 'CN_CNMF'

P value = 0.884 (Fisher's exact test), Q value = 1

Table S261.  Gene #27: 'GUCY2F MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 92 89 105 16
GUCY2F MUTATED 2 2 4 0
GUCY2F WILD-TYPE 90 87 101 16
'GUCY2F MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.959 (Fisher's exact test), Q value = 1

Table S262.  Gene #27: 'GUCY2F MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 49 43 55 61 43 41 14
GUCY2F MUTATED 1 1 2 1 1 2 0
GUCY2F WILD-TYPE 48 42 53 60 42 39 14
'GUCY2F MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.832 (Fisher's exact test), Q value = 1

Table S263.  Gene #27: 'GUCY2F MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 66
GUCY2F MUTATED 2 1 0 1
GUCY2F WILD-TYPE 53 51 35 65
'GUCY2F MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.833 (Fisher's exact test), Q value = 1

Table S264.  Gene #27: 'GUCY2F MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 83 47
GUCY2F MUTATED 2 1 1
GUCY2F WILD-TYPE 76 82 46
'GUCY2F MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.666 (Fisher's exact test), Q value = 1

Table S265.  Gene #27: 'GUCY2F MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 95 85
GUCY2F MUTATED 2 3 3
GUCY2F WILD-TYPE 122 92 82
'GUCY2F MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.88 (Fisher's exact test), Q value = 1

Table S266.  Gene #27: 'GUCY2F MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 109 78 86
GUCY2F MUTATED 0 3 3 2
GUCY2F WILD-TYPE 31 106 75 84
'GUCY2F MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.154 (Fisher's exact test), Q value = 1

Table S267.  Gene #27: 'GUCY2F MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 126 71 107
GUCY2F MUTATED 3 4 1
GUCY2F WILD-TYPE 123 67 106
'GUCY2F MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.82 (Fisher's exact test), Q value = 1

Table S268.  Gene #27: 'GUCY2F MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 80 104
GUCY2F MUTATED 3 3 2
GUCY2F WILD-TYPE 117 77 102
'GUCY2F MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 1

Table S269.  Gene #27: 'GUCY2F MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 28 54 111 25
GUCY2F MUTATED 0 4 1 2 0
GUCY2F WILD-TYPE 43 24 53 109 25

Figure S53.  Get High-res Image Gene #27: 'GUCY2F MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'GUCY2F MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.658 (Fisher's exact test), Q value = 1

Table S270.  Gene #27: 'GUCY2F MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 108 137 16
GUCY2F MUTATED 2 5 0
GUCY2F WILD-TYPE 106 132 16
Methods & Data
Input

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

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

  • Number of patients = 306

  • Number of significantly mutated genes = 27

  • Number of Molecular subtypes = 10

  • 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.

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)
Made with Nozzle