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 38 genes and 8 molecular subtypes across 194 patients, 5 significant findings detected with P value < 0.05 and Q value < 0.25.

  • KRAS mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • ARID1A mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 38 genes and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 5 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		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
KRAS 11 (6%) 183 0.565
(1.00) 		4e-05
(0.012) 		8e-05
(0.024) 		0.00119
(0.352) 		0.00262
(0.773) 		0.00077
(0.229) 		0.036
(1.00) 		0.00019
(0.0568)
ARID1A 14 (7%) 180 0.00639
(1.00) 		0.00334
(0.982) 		0.0121
(1.00) 		0.00078
(0.232) 		0.103
(1.00) 		0.00445
(1.00) 		0.702
(1.00) 		0.00447
(1.00)
HLA-A 16 (8%) 178 0.26
(1.00) 		0.105
(1.00) 		0.0086
(1.00) 		0.128
(1.00) 		0.434
(1.00) 		0.00771
(1.00) 		0.696
(1.00) 		0.418
(1.00)
FBXW7 19 (10%) 175 0.494
(1.00) 		0.29
(1.00) 		1
(1.00) 		0.574
(1.00) 		0.4
(1.00) 		0.458
(1.00) 		0.226
(1.00) 		0.541
(1.00)
HLA-B 11 (6%) 183 0.519
(1.00) 		0.152
(1.00) 		0.0335
(1.00) 		0.0997
(1.00) 		0.0192
(1.00) 		0.135
(1.00) 		0.0128
(1.00) 		0.0484
(1.00)
PTEN 15 (8%) 179 0.567
(1.00) 		0.557
(1.00) 		0.0508
(1.00) 		0.221
(1.00) 		0.433
(1.00) 		0.192
(1.00) 		1
(1.00) 		0.418
(1.00)
MAPK1 9 (5%) 185 0.552
(1.00) 		0.257
(1.00) 		0.0302
(1.00) 		0.0634
(1.00) 		0.185
(1.00) 		0.0818
(1.00) 		0.0211
(1.00) 		0.0223
(1.00)
EP300 21 (11%) 173 1
(1.00) 		0.158
(1.00) 		0.0595
(1.00) 		0.0811
(1.00) 		0.84
(1.00) 		0.00893
(1.00) 		1
(1.00) 		0.247
(1.00)
PIK3CA 53 (27%) 141 0.0346
(1.00) 		0.195
(1.00) 		0.19
(1.00) 		0.0327
(1.00) 		0.328
(1.00) 		0.344
(1.00) 		0.48
(1.00) 		0.227
(1.00)
NFE2L2 12 (6%) 182 0.927
(1.00) 		0.0666
(1.00) 		0.134
(1.00) 		0.0666
(1.00) 		0.0351
(1.00) 		0.0182
(1.00) 		0.385
(1.00) 		0.0733
(1.00)
FAT2 11 (6%) 183 0.613
(1.00) 		0.3
(1.00) 		0.0856
(1.00) 		0.423
(1.00) 		0.583
(1.00) 		0.764
(1.00) 		0.0702
(1.00) 		0.0907
(1.00)
ZNF750 10 (5%) 184 0.085
(1.00) 		0.218
(1.00) 		0.653
(1.00) 		0.103
(1.00) 		0.182
(1.00) 		0.191
(1.00) 		0.47
(1.00) 		0.0723
(1.00)
BAP1 4 (2%) 190 0.139
(1.00) 		0.0852
(1.00) 		0.0853
(1.00) 		0.75
(1.00) 		0.69
(1.00) 		0.352
(1.00) 		0.26
(1.00) 		0.172
(1.00)
RAB35 4 (2%) 190 0.26
(1.00) 		0.141
(1.00) 		1
(1.00) 		0.751
(1.00) 		0.474
(1.00) 		0.107
(1.00) 		0.296
(1.00) 		0.0308
(1.00)
ERBB3 11 (6%) 183 0.0747
(1.00) 		0.604
(1.00) 		0.0152
(1.00) 		0.00923
(1.00) 		0.0798
(1.00) 		0.0287
(1.00) 		0.929
(1.00) 		0.335
(1.00)
SMAD4 7 (4%) 187 0.49
(1.00) 		0.25
(1.00) 		0.484
(1.00) 		0.87
(1.00) 		0.725
(1.00) 		0.599
(1.00) 		1
(1.00) 		0.946
(1.00)
TCTE1 5 (3%) 189 0.18
(1.00) 		0.378
(1.00) 		0.0155
(1.00) 		0.397
(1.00) 		0.0242
(1.00) 		0.101
(1.00) 		0.201
(1.00) 		0.338
(1.00)
NHS 12 (6%) 182 0.861
(1.00) 		0.863
(1.00) 		0.643
(1.00) 		0.264
(1.00) 		0.931
(1.00) 		0.834
(1.00) 		0.424
(1.00) 		0.436
(1.00)
LIN9 7 (4%) 187 0.158
(1.00) 		0.164
(1.00) 		0.894
(1.00) 		1
(1.00) 		0.886
(1.00) 		0.271
(1.00) 		0.3
(1.00) 		0.892
(1.00)
C12ORF43 4 (2%) 190 0.197
(1.00) 		0.802
(1.00) 		1
(1.00) 		0.75
(1.00) 		0.473
(1.00) 		0.206
(1.00) 		0.295
(1.00) 		0.161
(1.00)
MED1 11 (6%) 183 0.922
(1.00) 		0.0195
(1.00) 		0.0325
(1.00) 		0.0887
(1.00) 		0.188
(1.00) 		0.242
(1.00) 		0.507
(1.00) 		0.124
(1.00)
USP28 4 (2%) 190 0.198
(1.00) 		0.665
(1.00) 		0.453
(1.00) 		1
(1.00) 		0.392
(1.00) 		0.937
(1.00) 		0.201
(1.00) 		0.819
(1.00)
IDS 7 (4%) 187 0.188
(1.00) 		0.566
(1.00) 		0.792
(1.00) 		1
(1.00) 		0.495
(1.00) 		0.22
(1.00) 		0.439
(1.00) 		0.715
(1.00)
TRIM9 8 (4%) 186 0.33
(1.00) 		0.815
(1.00) 		0.0938
(1.00) 		0.565
(1.00) 		0.544
(1.00) 		0.0378
(1.00) 		0.567
(1.00) 		0.358
(1.00)
SEMA4B 7 (4%) 187 1
(1.00) 		0.911
(1.00) 		0.427
(1.00) 		0.12
(1.00) 		0.0607
(1.00) 		0.288
(1.00) 		0.39
(1.00) 		0.128
(1.00)
ARHGAP4 6 (3%) 188 1
(1.00) 		0.589
(1.00) 		0.327
(1.00) 		0.702
(1.00) 		0.509
(1.00) 		0.227
(1.00) 		0.692
(1.00) 		1
(1.00)
POU2F1 3 (2%) 191 0.453
(1.00) 		0.387
(1.00) 		0.461
(1.00) 		0.698
(1.00) 		0.63
(1.00) 		0.489
(1.00) 		0.293
(1.00) 		0.161
(1.00)
IFNGR1 6 (3%) 188 1
(1.00) 		0.4
(1.00) 		0.764
(1.00) 		1
(1.00) 		0.323
(1.00) 		0.033
(1.00) 		0.0529
(1.00) 		0.785
(1.00)
IGFN1 11 (6%) 183 0.215
(1.00) 		0.807
(1.00) 		0.727
(1.00) 		0.59
(1.00) 		0.356
(1.00) 		0.966
(1.00) 		0.331
(1.00) 		0.849
(1.00)
RPGR 9 (5%) 185 1
(1.00) 		0.872
(1.00) 		0.906
(1.00) 		0.876
(1.00) 		0.916
(1.00) 		0.952
(1.00) 		0.759
(1.00) 		0.8
(1.00)
CASP8 9 (5%) 185 0.674
(1.00) 		0.706
(1.00) 		0.308
(1.00) 		0.455
(1.00) 		0.571
(1.00) 		0.449
(1.00) 		0.124
(1.00) 		0.434
(1.00)
GAS6 4 (2%) 190 0.817
(1.00) 		0.137
(1.00) 		0.357
(1.00) 		0.75
(1.00) 		1
(1.00) 		0.392
(1.00) 		0.292
(1.00) 		0.755
(1.00)
ABCD1 7 (4%) 187 0.603
(1.00) 		0.863
(1.00) 		0.324
(1.00) 		0.135
(1.00) 		0.493
(1.00) 		0.52
(1.00) 		0.0568
(1.00) 		0.374
(1.00)
RPAP1 4 (2%) 190 0.682
(1.00) 		0.72
(1.00) 		0.453
(1.00) 		1
(1.00) 		1
(1.00) 		0.742
(1.00) 		1
(1.00) 		0.903
(1.00)
HIST1H4E 4 (2%) 190 0.199
(1.00) 		0.801
(1.00) 		0.357
(1.00) 		0.3
(1.00) 		0.473
(1.00) 		0.828
(1.00) 		0.401
(1.00) 		0.379
(1.00)
NLRC5 7 (4%) 187 0.68
(1.00) 		0.0993
(1.00) 		0.258
(1.00) 		0.156
(1.00) 		0.138
(1.00) 		0.275
(1.00) 		0.565
(1.00) 		0.159
(1.00)
DDX41 5 (3%) 189 0.0293
(1.00) 		0.123
(1.00) 		0.17
(1.00) 		0.4
(1.00) 		0.331
(1.00) 		0.784
(1.00) 		1
(1.00) 		0.546
(1.00)
MCM7 3 (2%) 191 0.0719
(1.00) 		1
(1.00) 		0.49
(1.00) 		0.0571
(1.00) 		0.163
(1.00)
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.565 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
KRAS MUTATED 7 1 3
KRAS WILD-TYPE 83 39 58
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.012

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
KRAS MUTATED 10 0 0 0 0 1
KRAS WILD-TYPE 38 34 37 35 28 11

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

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.024

Table S3.  Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
KRAS MUTATED 10 0 1
KRAS WILD-TYPE 56 80 44

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

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.35

Table S4.  Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
KRAS MUTATED 8 2 1
KRAS WILD-TYPE 40 118 22

Figure S3.  Get High-res Image Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00262 (Fisher's exact test), Q value = 0.77

Table S5.  Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
KRAS MUTATED 7 4 0
KRAS WILD-TYPE 52 52 79

Figure S4.  Get High-res Image Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.23

Table S6.  Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
KRAS MUTATED 8 0 2 1 0
KRAS WILD-TYPE 33 50 56 14 30

Figure S5.  Get High-res Image Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S7.  Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
KRAS MUTATED 6 5 0
KRAS WILD-TYPE 63 52 58

Figure S6.  Get High-res Image Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.057

Table S8.  Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
KRAS MUTATED 9 1 0 1
KRAS WILD-TYPE 33 31 28 81

Figure S7.  Get High-res Image Gene #1: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HLA-A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.26 (Fisher's exact test), Q value = 1

Table S9.  Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
HLA-A MUTATED 9 4 2
HLA-A WILD-TYPE 81 36 59
'HLA-A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.105 (Fisher's exact test), Q value = 1

Table S10.  Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
HLA-A MUTATED 1 3 5 6 1 0
HLA-A WILD-TYPE 47 31 32 29 27 12
'HLA-A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0086 (Fisher's exact test), Q value = 1

Table S11.  Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
HLA-A MUTATED 1 6 8
HLA-A WILD-TYPE 65 74 37

Figure S8.  Get High-res Image Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'HLA-A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.128 (Fisher's exact test), Q value = 1

Table S12.  Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
HLA-A MUTATED 1 11 3
HLA-A WILD-TYPE 47 109 20
'HLA-A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S13.  Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
HLA-A MUTATED 3 4 9
HLA-A WILD-TYPE 56 52 70
'HLA-A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00771 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
HLA-A MUTATED 0 4 3 3 6
HLA-A WILD-TYPE 41 46 55 12 24

Figure S9.  Get High-res Image Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S15.  Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
HLA-A MUTATED 4 4 6
HLA-A WILD-TYPE 65 53 52
'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.418 (Fisher's exact test), Q value = 1

Table S16.  Gene #2: 'HLA-A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
HLA-A MUTATED 1 2 2 9
HLA-A WILD-TYPE 41 30 26 73
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.494 (Fisher's exact test), Q value = 1

Table S17.  Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
FBXW7 MUTATED 11 3 4
FBXW7 WILD-TYPE 79 37 57
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.29 (Fisher's exact test), Q value = 1

Table S18.  Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
FBXW7 MUTATED 6 4 4 5 0 0
FBXW7 WILD-TYPE 42 30 33 30 28 12
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S19.  Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
FBXW7 MUTATED 6 8 4
FBXW7 WILD-TYPE 60 72 41
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.574 (Fisher's exact test), Q value = 1

Table S20.  Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
FBXW7 MUTATED 6 11 1
FBXW7 WILD-TYPE 42 109 22
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.4 (Fisher's exact test), Q value = 1

Table S21.  Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
FBXW7 MUTATED 6 3 10
FBXW7 WILD-TYPE 53 53 69
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.458 (Fisher's exact test), Q value = 1

Table S22.  Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
FBXW7 MUTATED 4 8 3 1 3
FBXW7 WILD-TYPE 37 42 55 14 27
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S23.  Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
FBXW7 MUTATED 10 3 6
FBXW7 WILD-TYPE 59 54 52
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.541 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
FBXW7 MUTATED 5 1 3 10
FBXW7 WILD-TYPE 37 31 25 72
'HLA-B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.519 (Fisher's exact test), Q value = 1

Table S25.  Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
HLA-B MUTATED 7 2 2
HLA-B WILD-TYPE 83 38 59
'HLA-B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.152 (Fisher's exact test), Q value = 1

Table S26.  Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
HLA-B MUTATED 0 4 3 2 1 1
HLA-B WILD-TYPE 48 30 34 33 27 11
'HLA-B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 1

Table S27.  Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
HLA-B MUTATED 1 4 6
HLA-B WILD-TYPE 65 76 39

Figure S10.  Get High-res Image Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'HLA-B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0997 (Fisher's exact test), Q value = 1

Table S28.  Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
HLA-B MUTATED 0 10 1
HLA-B WILD-TYPE 48 110 22
'HLA-B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 1

Table S29.  Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
HLA-B MUTATED 1 1 9
HLA-B WILD-TYPE 58 55 70

Figure S11.  Get High-res Image Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'HLA-B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.135 (Fisher's exact test), Q value = 1

Table S30.  Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
HLA-B MUTATED 0 5 2 1 3
HLA-B WILD-TYPE 41 45 56 14 27
'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 1

Table S31.  Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
HLA-B MUTATED 3 0 7
HLA-B WILD-TYPE 66 57 51

Figure S12.  Get High-res Image Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0484 (Fisher's exact test), Q value = 1

Table S32.  Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
HLA-B MUTATED 0 0 2 8
HLA-B WILD-TYPE 42 32 26 74

Figure S13.  Get High-res Image Gene #4: 'HLA-B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.567 (Fisher's exact test), Q value = 1

Table S33.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
PTEN MUTATED 9 3 3
PTEN WILD-TYPE 81 37 58
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.557 (Fisher's exact test), Q value = 1

Table S34.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
PTEN MUTATED 5 2 3 1 4 0
PTEN WILD-TYPE 43 32 34 34 24 12
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0508 (Fisher's exact test), Q value = 1

Table S35.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
PTEN MUTATED 6 9 0
PTEN WILD-TYPE 60 71 45
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.221 (Fisher's exact test), Q value = 1

Table S36.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
PTEN MUTATED 6 9 0
PTEN WILD-TYPE 42 111 23
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.433 (Fisher's exact test), Q value = 1

Table S37.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
PTEN MUTATED 7 3 5
PTEN WILD-TYPE 52 53 74
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.192 (Fisher's exact test), Q value = 1

Table S38.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
PTEN MUTATED 4 6 3 2 0
PTEN WILD-TYPE 37 44 55 13 30
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S39.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
PTEN MUTATED 6 4 5
PTEN WILD-TYPE 63 53 53
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.418 (Fisher's exact test), Q value = 1

Table S40.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
PTEN MUTATED 4 4 3 4
PTEN WILD-TYPE 38 28 25 78
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00639 (Fisher's exact test), Q value = 1

Table S41.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
ARID1A MUTATED 11 3 0
ARID1A WILD-TYPE 79 37 61

Figure S14.  Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00334 (Fisher's exact test), Q value = 0.98

Table S42.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
ARID1A MUTATED 10 2 2 0 0 0
ARID1A WILD-TYPE 38 32 35 35 28 12

Figure S15.  Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 1

Table S43.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
ARID1A MUTATED 10 2 2
ARID1A WILD-TYPE 56 78 43

Figure S16.  Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.23

Table S44.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
ARID1A MUTATED 10 4 0
ARID1A WILD-TYPE 38 116 23

Figure S17.  Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S45.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
ARID1A MUTATED 8 2 4
ARID1A WILD-TYPE 51 54 75
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00445 (Fisher's exact test), Q value = 1

Table S46.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
ARID1A MUTATED 7 1 1 3 2
ARID1A WILD-TYPE 34 49 57 12 28

Figure S18.  Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.702 (Fisher's exact test), Q value = 1

Table S47.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
ARID1A MUTATED 6 3 3
ARID1A WILD-TYPE 63 54 55
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00447 (Fisher's exact test), Q value = 1

Table S48.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
ARID1A MUTATED 7 0 3 2
ARID1A WILD-TYPE 35 32 25 80

Figure S19.  Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MAPK1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S49.  Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
MAPK1 MUTATED 6 1 2
MAPK1 WILD-TYPE 84 39 59
'MAPK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S50.  Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
MAPK1 MUTATED 0 2 3 1 2 1
MAPK1 WILD-TYPE 48 32 34 34 26 11
'MAPK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 1

Table S51.  Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
MAPK1 MUTATED 0 7 2
MAPK1 WILD-TYPE 66 73 43

Figure S20.  Get High-res Image Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'MAPK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0634 (Fisher's exact test), Q value = 1

Table S52.  Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
MAPK1 MUTATED 0 9 0
MAPK1 WILD-TYPE 48 111 23
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 1

Table S53.  Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
MAPK1 MUTATED 1 5 3
MAPK1 WILD-TYPE 58 51 76
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0818 (Fisher's exact test), Q value = 1

Table S54.  Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
MAPK1 MUTATED 0 2 6 1 0
MAPK1 WILD-TYPE 41 48 52 14 30
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 1

Table S55.  Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
MAPK1 MUTATED 0 5 4
MAPK1 WILD-TYPE 69 52 54

Figure S21.  Get High-res Image Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'MAPK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0223 (Fisher's exact test), Q value = 1

Table S56.  Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
MAPK1 MUTATED 0 5 1 3
MAPK1 WILD-TYPE 42 27 27 79

Figure S22.  Get High-res Image Gene #7: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'EP300 MUTATION STATUS' versus 'CN_CNMF'

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

Table S57.  Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
EP300 MUTATED 10 4 6
EP300 WILD-TYPE 80 36 55
'EP300 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S58.  Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
EP300 MUTATED 3 7 5 1 3 2
EP300 WILD-TYPE 45 27 32 34 25 10
'EP300 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0595 (Fisher's exact test), Q value = 1

Table S59.  Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
EP300 MUTATED 4 14 3
EP300 WILD-TYPE 62 66 42
'EP300 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0811 (Fisher's exact test), Q value = 1

Table S60.  Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
EP300 MUTATED 2 18 1
EP300 WILD-TYPE 46 102 22
'EP300 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.84 (Fisher's exact test), Q value = 1

Table S61.  Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
EP300 MUTATED 6 5 10
EP300 WILD-TYPE 53 51 69
'EP300 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00893 (Fisher's exact test), Q value = 1

Table S62.  Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
EP300 MUTATED 1 9 10 1 0
EP300 WILD-TYPE 40 41 48 14 30

Figure S23.  Get High-res Image Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S63.  Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
EP300 MUTATED 7 5 6
EP300 WILD-TYPE 62 52 52
'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.247 (Fisher's exact test), Q value = 1

Table S64.  Gene #8: 'EP300 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
EP300 MUTATED 2 3 1 12
EP300 WILD-TYPE 40 29 27 70
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 1

Table S65.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
PIK3CA MUTATED 33 7 13
PIK3CA WILD-TYPE 57 33 48

Figure S24.  Get High-res Image Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.195 (Fisher's exact test), Q value = 1

Table S66.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
PIK3CA MUTATED 17 10 11 5 9 1
PIK3CA WILD-TYPE 31 24 26 30 19 11
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S67.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
PIK3CA MUTATED 22 22 8
PIK3CA WILD-TYPE 44 58 37
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 1

Table S68.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
PIK3CA MUTATED 18 32 2
PIK3CA WILD-TYPE 30 88 21

Figure S25.  Get High-res Image Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.328 (Fisher's exact test), Q value = 1

Table S69.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
PIK3CA MUTATED 20 12 21
PIK3CA WILD-TYPE 39 44 58
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S70.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
PIK3CA MUTATED 14 17 13 4 5
PIK3CA WILD-TYPE 27 33 45 11 25
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S71.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
PIK3CA MUTATED 22 13 14
PIK3CA WILD-TYPE 47 44 44
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S72.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
PIK3CA MUTATED 16 9 7 17
PIK3CA WILD-TYPE 26 23 21 65
'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.927 (Fisher's exact test), Q value = 1

Table S73.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
NFE2L2 MUTATED 5 3 4
NFE2L2 WILD-TYPE 85 37 57
'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0666 (Fisher's exact test), Q value = 1

Table S74.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
NFE2L2 MUTATED 0 5 2 2 3 0
NFE2L2 WILD-TYPE 48 29 35 33 25 12
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S75.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
NFE2L2 MUTATED 1 7 4
NFE2L2 WILD-TYPE 65 73 41
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0666 (Fisher's exact test), Q value = 1

Table S76.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
NFE2L2 MUTATED 0 11 1
NFE2L2 WILD-TYPE 48 109 22
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0351 (Fisher's exact test), Q value = 1

Table S77.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
NFE2L2 MUTATED 0 5 7
NFE2L2 WILD-TYPE 59 51 72

Figure S26.  Get High-res Image Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0182 (Fisher's exact test), Q value = 1

Table S78.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
NFE2L2 MUTATED 0 1 6 3 2
NFE2L2 WILD-TYPE 41 49 52 12 28

Figure S27.  Get High-res Image Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S79.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
NFE2L2 MUTATED 2 4 5
NFE2L2 WILD-TYPE 67 53 53
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0733 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
NFE2L2 MUTATED 0 2 4 5
NFE2L2 WILD-TYPE 42 30 24 77
'FAT2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.613 (Fisher's exact test), Q value = 1

Table S81.  Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
FAT2 MUTATED 6 3 2
FAT2 WILD-TYPE 84 37 59
'FAT2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.3 (Fisher's exact test), Q value = 1

Table S82.  Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
FAT2 MUTATED 1 5 2 2 1 0
FAT2 WILD-TYPE 47 29 35 33 27 12
'FAT2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0856 (Fisher's exact test), Q value = 1

Table S83.  Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
FAT2 MUTATED 1 5 5
FAT2 WILD-TYPE 65 75 40
'FAT2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S84.  Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
FAT2 MUTATED 1 9 1
FAT2 WILD-TYPE 47 111 22
'FAT2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.583 (Fisher's exact test), Q value = 1

Table S85.  Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
FAT2 MUTATED 2 3 6
FAT2 WILD-TYPE 57 53 73
'FAT2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.764 (Fisher's exact test), Q value = 1

Table S86.  Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
FAT2 MUTATED 1 4 4 0 2
FAT2 WILD-TYPE 40 46 54 15 28
'FAT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0702 (Fisher's exact test), Q value = 1

Table S87.  Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
FAT2 MUTATED 3 1 7
FAT2 WILD-TYPE 66 56 51
'FAT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0907 (Fisher's exact test), Q value = 1

Table S88.  Gene #11: 'FAT2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
FAT2 MUTATED 1 0 1 9
FAT2 WILD-TYPE 41 32 27 73
'ZNF750 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.085 (Fisher's exact test), Q value = 1

Table S89.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
ZNF750 MUTATED 8 0 2
ZNF750 WILD-TYPE 82 40 59
'ZNF750 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S90.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
ZNF750 MUTATED 1 3 4 1 0 1
ZNF750 WILD-TYPE 47 31 33 34 28 11
'ZNF750 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.653 (Fisher's exact test), Q value = 1

Table S91.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
ZNF750 MUTATED 2 5 3
ZNF750 WILD-TYPE 64 75 42
'ZNF750 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S92.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
ZNF750 MUTATED 0 9 1
ZNF750 WILD-TYPE 48 111 22
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 1

Table S93.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
ZNF750 MUTATED 2 1 7
ZNF750 WILD-TYPE 57 55 72
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.191 (Fisher's exact test), Q value = 1

Table S94.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
ZNF750 MUTATED 0 5 2 1 2
ZNF750 WILD-TYPE 41 45 56 14 28
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S95.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
ZNF750 MUTATED 4 1 4
ZNF750 WILD-TYPE 65 56 54
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0723 (Fisher's exact test), Q value = 1

Table S96.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
ZNF750 MUTATED 0 0 2 7
ZNF750 WILD-TYPE 42 32 26 75
'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.139 (Fisher's exact test), Q value = 1

Table S97.  Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
BAP1 MUTATED 4 0 0
BAP1 WILD-TYPE 86 40 61
'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0852 (Fisher's exact test), Q value = 1

Table S98.  Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
BAP1 MUTATED 0 3 1 0 0 0
BAP1 WILD-TYPE 48 31 36 35 28 12
'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0853 (Fisher's exact test), Q value = 1

Table S99.  Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
BAP1 MUTATED 0 4 0
BAP1 WILD-TYPE 66 76 45
'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S100.  Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
BAP1 MUTATED 0 4 0
BAP1 WILD-TYPE 48 116 23
'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.69 (Fisher's exact test), Q value = 1

Table S101.  Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
BAP1 MUTATED 1 2 1
BAP1 WILD-TYPE 58 54 78
'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.352 (Fisher's exact test), Q value = 1

Table S102.  Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
BAP1 MUTATED 0 2 1 1 0
BAP1 WILD-TYPE 41 48 57 14 30
'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.26 (Fisher's exact test), Q value = 1

Table S103.  Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
BAP1 MUTATED 0 2 2
BAP1 WILD-TYPE 69 55 56
'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.172 (Fisher's exact test), Q value = 1

Table S104.  Gene #13: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
BAP1 MUTATED 0 2 1 1
BAP1 WILD-TYPE 42 30 27 81
'RAB35 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.26 (Fisher's exact test), Q value = 1

Table S105.  Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
RAB35 MUTATED 1 0 3
RAB35 WILD-TYPE 89 40 58
'RAB35 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 1

Table S106.  Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
RAB35 MUTATED 0 0 2 1 0 1
RAB35 WILD-TYPE 48 34 35 34 28 11
'RAB35 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S107.  Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
RAB35 MUTATED 1 2 1
RAB35 WILD-TYPE 65 78 44
'RAB35 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.751 (Fisher's exact test), Q value = 1

Table S108.  Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
RAB35 MUTATED 0 4 0
RAB35 WILD-TYPE 48 116 23
'RAB35 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S109.  Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
RAB35 MUTATED 0 2 2
RAB35 WILD-TYPE 59 54 77
'RAB35 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S110.  Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
RAB35 MUTATED 0 0 3 1 0
RAB35 WILD-TYPE 41 50 55 14 30
'RAB35 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S111.  Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
RAB35 MUTATED 0 1 2
RAB35 WILD-TYPE 69 56 56
'RAB35 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0308 (Fisher's exact test), Q value = 1

Table S112.  Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
RAB35 MUTATED 0 1 2 0
RAB35 WILD-TYPE 42 31 26 82

Figure S28.  Get High-res Image Gene #14: 'RAB35 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ERBB3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0747 (Fisher's exact test), Q value = 1

Table S113.  Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
ERBB3 MUTATED 5 5 1
ERBB3 WILD-TYPE 85 35 60
'ERBB3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.604 (Fisher's exact test), Q value = 1

Table S114.  Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
ERBB3 MUTATED 5 3 1 1 1 0
ERBB3 WILD-TYPE 43 31 36 34 27 12
'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 1

Table S115.  Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
ERBB3 MUTATED 8 1 2
ERBB3 WILD-TYPE 58 79 43

Figure S29.  Get High-res Image Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00923 (Fisher's exact test), Q value = 1

Table S116.  Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
ERBB3 MUTATED 7 3 1
ERBB3 WILD-TYPE 41 117 22

Figure S30.  Get High-res Image Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0798 (Fisher's exact test), Q value = 1

Table S117.  Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
ERBB3 MUTATED 5 5 1
ERBB3 WILD-TYPE 54 51 78
'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0287 (Fisher's exact test), Q value = 1

Table S118.  Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
ERBB3 MUTATED 7 2 1 0 1
ERBB3 WILD-TYPE 34 48 57 15 29

Figure S31.  Get High-res Image Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'ERBB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.929 (Fisher's exact test), Q value = 1

Table S119.  Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
ERBB3 MUTATED 4 4 3
ERBB3 WILD-TYPE 65 53 55
'ERBB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S120.  Gene #15: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
ERBB3 MUTATED 5 2 1 3
ERBB3 WILD-TYPE 37 30 27 79
'SMAD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.49 (Fisher's exact test), Q value = 1

Table S121.  Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
SMAD4 MUTATED 4 0 2
SMAD4 WILD-TYPE 86 40 59
'SMAD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.25 (Fisher's exact test), Q value = 1

Table S122.  Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
SMAD4 MUTATED 2 0 3 0 1 1
SMAD4 WILD-TYPE 46 34 34 35 27 11
'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.484 (Fisher's exact test), Q value = 1

Table S123.  Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
SMAD4 MUTATED 2 2 3
SMAD4 WILD-TYPE 64 78 42
'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.87 (Fisher's exact test), Q value = 1

Table S124.  Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
SMAD4 MUTATED 2 4 1
SMAD4 WILD-TYPE 46 116 22
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.725 (Fisher's exact test), Q value = 1

Table S125.  Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
SMAD4 MUTATED 2 1 4
SMAD4 WILD-TYPE 57 55 75
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.599 (Fisher's exact test), Q value = 1

Table S126.  Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
SMAD4 MUTATED 1 3 1 0 2
SMAD4 WILD-TYPE 40 47 57 15 28
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S127.  Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
SMAD4 MUTATED 3 2 2
SMAD4 WILD-TYPE 66 55 56
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S128.  Gene #16: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
SMAD4 MUTATED 1 1 1 4
SMAD4 WILD-TYPE 41 31 27 78
'TCTE1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S129.  Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
TCTE1 MUTATED 3 2 0
TCTE1 WILD-TYPE 87 38 61
'TCTE1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 1

Table S130.  Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
TCTE1 MUTATED 0 2 1 2 0 0
TCTE1 WILD-TYPE 48 32 36 33 28 12
'TCTE1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 1

Table S131.  Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
TCTE1 MUTATED 0 1 4
TCTE1 WILD-TYPE 66 79 41

Figure S32.  Get High-res Image Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'TCTE1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S132.  Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
TCTE1 MUTATED 0 4 1
TCTE1 WILD-TYPE 48 116 22
'TCTE1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 1

Table S133.  Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
TCTE1 MUTATED 0 0 5
TCTE1 WILD-TYPE 59 56 74

Figure S33.  Get High-res Image Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'TCTE1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.101 (Fisher's exact test), Q value = 1

Table S134.  Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
TCTE1 MUTATED 0 1 1 2 1
TCTE1 WILD-TYPE 41 49 57 13 29
'TCTE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.201 (Fisher's exact test), Q value = 1

Table S135.  Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
TCTE1 MUTATED 1 0 3
TCTE1 WILD-TYPE 68 57 55
'TCTE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S136.  Gene #17: 'TCTE1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
TCTE1 MUTATED 0 0 0 4
TCTE1 WILD-TYPE 42 32 28 78
'NHS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.861 (Fisher's exact test), Q value = 1

Table S137.  Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
NHS MUTATED 6 3 3
NHS WILD-TYPE 84 37 58
'NHS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.863 (Fisher's exact test), Q value = 1

Table S138.  Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
NHS MUTATED 4 3 1 2 2 0
NHS WILD-TYPE 44 31 36 33 26 12
'NHS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.643 (Fisher's exact test), Q value = 1

Table S139.  Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
NHS MUTATED 3 5 4
NHS WILD-TYPE 63 75 41
'NHS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.264 (Fisher's exact test), Q value = 1

Table S140.  Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
NHS MUTATED 3 6 3
NHS WILD-TYPE 45 114 20
'NHS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.931 (Fisher's exact test), Q value = 1

Table S141.  Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
NHS MUTATED 3 4 5
NHS WILD-TYPE 56 52 74
'NHS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.834 (Fisher's exact test), Q value = 1

Table S142.  Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
NHS MUTATED 3 3 3 0 3
NHS WILD-TYPE 38 47 55 15 27
'NHS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.424 (Fisher's exact test), Q value = 1

Table S143.  Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
NHS MUTATED 6 3 2
NHS WILD-TYPE 63 54 56
'NHS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.436 (Fisher's exact test), Q value = 1

Table S144.  Gene #18: 'NHS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
NHS MUTATED 3 1 0 7
NHS WILD-TYPE 39 31 28 75
'LIN9 MUTATION STATUS' versus 'CN_CNMF'

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

Table S145.  Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
LIN9 MUTATED 1 1 4
LIN9 WILD-TYPE 89 39 57
'LIN9 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S146.  Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
LIN9 MUTATED 1 1 2 0 1 2
LIN9 WILD-TYPE 47 33 35 35 27 10
'LIN9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.894 (Fisher's exact test), Q value = 1

Table S147.  Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
LIN9 MUTATED 3 3 1
LIN9 WILD-TYPE 63 77 44
'LIN9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S148.  Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
LIN9 MUTATED 2 5 0
LIN9 WILD-TYPE 46 115 23
'LIN9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.886 (Fisher's exact test), Q value = 1

Table S149.  Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
LIN9 MUTATED 3 2 2
LIN9 WILD-TYPE 56 54 77
'LIN9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S150.  Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
LIN9 MUTATED 0 2 4 1 0
LIN9 WILD-TYPE 41 48 54 14 30
'LIN9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.3 (Fisher's exact test), Q value = 1

Table S151.  Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
LIN9 MUTATED 1 2 4
LIN9 WILD-TYPE 68 55 54
'LIN9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.892 (Fisher's exact test), Q value = 1

Table S152.  Gene #19: 'LIN9 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
LIN9 MUTATED 1 2 1 3
LIN9 WILD-TYPE 41 30 27 79
'C12ORF43 MUTATION STATUS' versus 'CN_CNMF'

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

Table S153.  Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
C12ORF43 MUTATED 2 2 0
C12ORF43 WILD-TYPE 88 38 61
'C12ORF43 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.802 (Fisher's exact test), Q value = 1

Table S154.  Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
C12ORF43 MUTATED 0 1 1 1 1 0
C12ORF43 WILD-TYPE 48 33 36 34 27 12
'C12ORF43 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S155.  Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
C12ORF43 MUTATED 1 2 1
C12ORF43 WILD-TYPE 65 78 44
'C12ORF43 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S156.  Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
C12ORF43 MUTATED 0 4 0
C12ORF43 WILD-TYPE 48 116 23
'C12ORF43 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.473 (Fisher's exact test), Q value = 1

Table S157.  Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
C12ORF43 MUTATED 0 2 2
C12ORF43 WILD-TYPE 59 54 77
'C12ORF43 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S158.  Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
C12ORF43 MUTATED 0 0 2 1 1
C12ORF43 WILD-TYPE 41 50 56 14 29
'C12ORF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.295 (Fisher's exact test), Q value = 1

Table S159.  Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
C12ORF43 MUTATED 0 1 2
C12ORF43 WILD-TYPE 69 56 56
'C12ORF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S160.  Gene #20: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
C12ORF43 MUTATED 0 0 2 1
C12ORF43 WILD-TYPE 42 32 26 81
'MED1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.922 (Fisher's exact test), Q value = 1

Table S161.  Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
MED1 MUTATED 6 2 3
MED1 WILD-TYPE 84 38 58
'MED1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 1

Table S162.  Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
MED1 MUTATED 0 1 3 3 1 3
MED1 WILD-TYPE 48 33 34 32 27 9

Figure S34.  Get High-res Image Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'MED1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 1

Table S163.  Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
MED1 MUTATED 1 4 6
MED1 WILD-TYPE 65 76 39

Figure S35.  Get High-res Image Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'MED1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0887 (Fisher's exact test), Q value = 1

Table S164.  Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
MED1 MUTATED 0 9 2
MED1 WILD-TYPE 48 111 21
'MED1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.188 (Fisher's exact test), Q value = 1

Table S165.  Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
MED1 MUTATED 1 3 7
MED1 WILD-TYPE 58 53 72
'MED1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.242 (Fisher's exact test), Q value = 1

Table S166.  Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
MED1 MUTATED 0 4 4 0 3
MED1 WILD-TYPE 41 46 54 15 27
'MED1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S167.  Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
MED1 MUTATED 3 2 5
MED1 WILD-TYPE 66 55 53
'MED1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S168.  Gene #21: 'MED1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
MED1 MUTATED 0 1 3 6
MED1 WILD-TYPE 42 31 25 76
'USP28 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 1

Table S169.  Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
USP28 MUTATED 2 2 0
USP28 WILD-TYPE 88 38 61
'USP28 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S170.  Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
USP28 MUTATED 1 2 1 0 0 0
USP28 WILD-TYPE 47 32 36 35 28 12
'USP28 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.453 (Fisher's exact test), Q value = 1

Table S171.  Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
USP28 MUTATED 1 1 2
USP28 WILD-TYPE 65 79 43
'USP28 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S172.  Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
USP28 MUTATED 1 3 0
USP28 WILD-TYPE 47 117 23
'USP28 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.392 (Fisher's exact test), Q value = 1

Table S173.  Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
USP28 MUTATED 1 0 3
USP28 WILD-TYPE 58 56 76
'USP28 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.937 (Fisher's exact test), Q value = 1

Table S174.  Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
USP28 MUTATED 1 1 2 0 0
USP28 WILD-TYPE 40 49 56 15 30
'USP28 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.201 (Fisher's exact test), Q value = 1

Table S175.  Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
USP28 MUTATED 1 0 3
USP28 WILD-TYPE 68 57 55
'USP28 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.819 (Fisher's exact test), Q value = 1

Table S176.  Gene #22: 'USP28 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
USP28 MUTATED 1 0 0 3
USP28 WILD-TYPE 41 32 28 79
'IDS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.188 (Fisher's exact test), Q value = 1

Table S177.  Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
IDS MUTATED 4 2 0
IDS WILD-TYPE 86 38 61
'IDS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.566 (Fisher's exact test), Q value = 1

Table S178.  Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
IDS MUTATED 2 3 1 0 1 0
IDS WILD-TYPE 46 31 36 35 27 12
'IDS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.792 (Fisher's exact test), Q value = 1

Table S179.  Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
IDS MUTATED 2 4 1
IDS WILD-TYPE 64 76 44
'IDS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S180.  Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
IDS MUTATED 2 5 0
IDS WILD-TYPE 46 115 23
'IDS MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S181.  Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
IDS MUTATED 1 3 3
IDS WILD-TYPE 58 53 76
'IDS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.22 (Fisher's exact test), Q value = 1

Table S182.  Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
IDS MUTATED 1 1 3 2 0
IDS WILD-TYPE 40 49 55 13 30
'IDS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.439 (Fisher's exact test), Q value = 1

Table S183.  Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
IDS MUTATED 1 3 3
IDS WILD-TYPE 68 54 55
'IDS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S184.  Gene #23: 'IDS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
IDS MUTATED 2 2 0 3
IDS WILD-TYPE 40 30 28 79
'TRIM9 MUTATION STATUS' versus 'CN_CNMF'

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

Table S185.  Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
TRIM9 MUTATED 6 1 1
TRIM9 WILD-TYPE 84 39 60
'TRIM9 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.815 (Fisher's exact test), Q value = 1

Table S186.  Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
TRIM9 MUTATED 3 2 1 2 0 0
TRIM9 WILD-TYPE 45 32 36 33 28 12
'TRIM9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0938 (Fisher's exact test), Q value = 1

Table S187.  Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
TRIM9 MUTATED 3 1 4
TRIM9 WILD-TYPE 63 79 41
'TRIM9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.565 (Fisher's exact test), Q value = 1

Table S188.  Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
TRIM9 MUTATED 3 4 1
TRIM9 WILD-TYPE 45 116 22
'TRIM9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.544 (Fisher's exact test), Q value = 1

Table S189.  Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
TRIM9 MUTATED 2 1 5
TRIM9 WILD-TYPE 57 55 74
'TRIM9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0378 (Fisher's exact test), Q value = 1

Table S190.  Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
TRIM9 MUTATED 3 1 0 2 2
TRIM9 WILD-TYPE 38 49 58 13 28

Figure S36.  Get High-res Image Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'TRIM9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.567 (Fisher's exact test), Q value = 1

Table S191.  Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
TRIM9 MUTATED 4 1 2
TRIM9 WILD-TYPE 65 56 56
'TRIM9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S192.  Gene #24: 'TRIM9 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
TRIM9 MUTATED 3 0 0 4
TRIM9 WILD-TYPE 39 32 28 78
'SEMA4B MUTATION STATUS' versus 'CN_CNMF'

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

Table S193.  Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
SEMA4B MUTATED 4 1 2
SEMA4B WILD-TYPE 86 39 59
'SEMA4B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.911 (Fisher's exact test), Q value = 1

Table S194.  Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
SEMA4B MUTATED 1 2 1 2 1 0
SEMA4B WILD-TYPE 47 32 36 33 27 12
'SEMA4B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.427 (Fisher's exact test), Q value = 1

Table S195.  Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
SEMA4B MUTATED 1 3 3
SEMA4B WILD-TYPE 65 77 42
'SEMA4B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.12 (Fisher's exact test), Q value = 1

Table S196.  Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
SEMA4B MUTATED 0 5 2
SEMA4B WILD-TYPE 48 115 21
'SEMA4B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0607 (Fisher's exact test), Q value = 1

Table S197.  Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
SEMA4B MUTATED 1 0 6
SEMA4B WILD-TYPE 58 56 73
'SEMA4B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.288 (Fisher's exact test), Q value = 1

Table S198.  Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
SEMA4B MUTATED 0 2 2 0 3
SEMA4B WILD-TYPE 41 48 56 15 27
'SEMA4B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.39 (Fisher's exact test), Q value = 1

Table S199.  Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
SEMA4B MUTATED 2 1 4
SEMA4B WILD-TYPE 67 56 54
'SEMA4B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.128 (Fisher's exact test), Q value = 1

Table S200.  Gene #25: 'SEMA4B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
SEMA4B MUTATED 0 0 1 6
SEMA4B WILD-TYPE 42 32 27 76
'ARHGAP4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S201.  Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
ARHGAP4 MUTATED 3 1 2
ARHGAP4 WILD-TYPE 87 39 59
'ARHGAP4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.589 (Fisher's exact test), Q value = 1

Table S202.  Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
ARHGAP4 MUTATED 2 2 0 2 0 0
ARHGAP4 WILD-TYPE 46 32 37 33 28 12
'ARHGAP4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.327 (Fisher's exact test), Q value = 1

Table S203.  Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
ARHGAP4 MUTATED 1 2 3
ARHGAP4 WILD-TYPE 65 78 42
'ARHGAP4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.702 (Fisher's exact test), Q value = 1

Table S204.  Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
ARHGAP4 MUTATED 1 4 1
ARHGAP4 WILD-TYPE 47 116 22
'ARHGAP4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.509 (Fisher's exact test), Q value = 1

Table S205.  Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
ARHGAP4 MUTATED 1 1 4
ARHGAP4 WILD-TYPE 58 55 75
'ARHGAP4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S206.  Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
ARHGAP4 MUTATED 1 1 2 2 0
ARHGAP4 WILD-TYPE 40 49 56 13 30
'ARHGAP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.692 (Fisher's exact test), Q value = 1

Table S207.  Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
ARHGAP4 MUTATED 1 2 1
ARHGAP4 WILD-TYPE 68 55 57
'ARHGAP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S208.  Gene #26: 'ARHGAP4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
ARHGAP4 MUTATED 1 1 0 2
ARHGAP4 WILD-TYPE 41 31 28 80
'POU2F1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.453 (Fisher's exact test), Q value = 1

Table S209.  Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
POU2F1 MUTATED 2 1 0
POU2F1 WILD-TYPE 88 39 61
'POU2F1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S210.  Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
POU2F1 MUTATED 0 1 2 0 0 0
POU2F1 WILD-TYPE 48 33 35 35 28 12
'POU2F1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S211.  Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
POU2F1 MUTATED 0 2 1
POU2F1 WILD-TYPE 66 78 44
'POU2F1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.698 (Fisher's exact test), Q value = 1

Table S212.  Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
POU2F1 MUTATED 0 3 0
POU2F1 WILD-TYPE 48 117 23
'POU2F1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S213.  Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
POU2F1 MUTATED 0 1 2
POU2F1 WILD-TYPE 59 55 77
'POU2F1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.489 (Fisher's exact test), Q value = 1

Table S214.  Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
POU2F1 MUTATED 0 0 2 0 1
POU2F1 WILD-TYPE 41 50 56 15 29
'POU2F1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 1

Table S215.  Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
POU2F1 MUTATED 0 1 2
POU2F1 WILD-TYPE 69 56 56
'POU2F1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S216.  Gene #27: 'POU2F1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
POU2F1 MUTATED 0 0 2 1
POU2F1 WILD-TYPE 42 32 26 81
'IFNGR1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S217.  Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
IFNGR1 MUTATED 3 1 2
IFNGR1 WILD-TYPE 87 39 59
'IFNGR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.4 (Fisher's exact test), Q value = 1

Table S218.  Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
IFNGR1 MUTATED 2 2 0 1 0 1
IFNGR1 WILD-TYPE 46 32 37 34 28 11
'IFNGR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.764 (Fisher's exact test), Q value = 1

Table S219.  Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
IFNGR1 MUTATED 3 2 1
IFNGR1 WILD-TYPE 63 78 44
'IFNGR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S220.  Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
IFNGR1 MUTATED 2 4 0
IFNGR1 WILD-TYPE 46 116 23
'IFNGR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.323 (Fisher's exact test), Q value = 1

Table S221.  Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
IFNGR1 MUTATED 3 0 3
IFNGR1 WILD-TYPE 56 56 76
'IFNGR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.033 (Fisher's exact test), Q value = 1

Table S222.  Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
IFNGR1 MUTATED 1 3 0 2 0
IFNGR1 WILD-TYPE 40 47 58 13 30

Figure S37.  Get High-res Image Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'IFNGR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0529 (Fisher's exact test), Q value = 1

Table S223.  Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
IFNGR1 MUTATED 5 0 1
IFNGR1 WILD-TYPE 64 57 57
'IFNGR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.785 (Fisher's exact test), Q value = 1

Table S224.  Gene #28: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
IFNGR1 MUTATED 2 0 1 3
IFNGR1 WILD-TYPE 40 32 27 79
'IGFN1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.215 (Fisher's exact test), Q value = 1

Table S225.  Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
IGFN1 MUTATED 7 0 4
IGFN1 WILD-TYPE 83 40 57
'IGFN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.807 (Fisher's exact test), Q value = 1

Table S226.  Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
IGFN1 MUTATED 2 3 3 1 2 0
IGFN1 WILD-TYPE 46 31 34 34 26 12
'IGFN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.727 (Fisher's exact test), Q value = 1

Table S227.  Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
IGFN1 MUTATED 3 6 2
IGFN1 WILD-TYPE 63 74 43
'IGFN1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.59 (Fisher's exact test), Q value = 1

Table S228.  Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
IGFN1 MUTATED 3 8 0
IGFN1 WILD-TYPE 45 112 23
'IGFN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S229.  Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
IGFN1 MUTATED 4 1 6
IGFN1 WILD-TYPE 55 55 73
'IGFN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.966 (Fisher's exact test), Q value = 1

Table S230.  Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
IGFN1 MUTATED 3 3 3 1 1
IGFN1 WILD-TYPE 38 47 55 14 29
'IGFN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 1

Table S231.  Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
IGFN1 MUTATED 5 1 4
IGFN1 WILD-TYPE 64 56 54
'IGFN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S232.  Gene #29: 'IGFN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
IGFN1 MUTATED 2 1 1 6
IGFN1 WILD-TYPE 40 31 27 76
'RPGR MUTATION STATUS' versus 'CN_CNMF'

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

Table S233.  Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
RPGR MUTATED 4 2 3
RPGR WILD-TYPE 86 38 58
'RPGR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.872 (Fisher's exact test), Q value = 1

Table S234.  Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
RPGR MUTATED 3 2 1 1 1 1
RPGR WILD-TYPE 45 32 36 34 27 11
'RPGR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.906 (Fisher's exact test), Q value = 1

Table S235.  Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
RPGR MUTATED 4 3 2
RPGR WILD-TYPE 62 77 43
'RPGR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S236.  Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
RPGR MUTATED 3 5 1
RPGR WILD-TYPE 45 115 22
'RPGR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.916 (Fisher's exact test), Q value = 1

Table S237.  Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
RPGR MUTATED 3 3 3
RPGR WILD-TYPE 56 53 76
'RPGR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.952 (Fisher's exact test), Q value = 1

Table S238.  Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
RPGR MUTATED 2 2 4 0 1
RPGR WILD-TYPE 39 48 54 15 29
'RPGR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.759 (Fisher's exact test), Q value = 1

Table S239.  Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
RPGR MUTATED 3 2 4
RPGR WILD-TYPE 66 55 54
'RPGR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.8 (Fisher's exact test), Q value = 1

Table S240.  Gene #30: 'RPGR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
RPGR MUTATED 3 2 1 3
RPGR WILD-TYPE 39 30 27 79
'CASP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.674 (Fisher's exact test), Q value = 1

Table S241.  Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
CASP8 MUTATED 3 2 4
CASP8 WILD-TYPE 87 38 57
'CASP8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.706 (Fisher's exact test), Q value = 1

Table S242.  Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
CASP8 MUTATED 1 1 3 2 1 1
CASP8 WILD-TYPE 47 33 34 33 27 11
'CASP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.308 (Fisher's exact test), Q value = 1

Table S243.  Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
CASP8 MUTATED 1 5 3
CASP8 WILD-TYPE 65 75 42
'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S244.  Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
CASP8 MUTATED 1 6 2
CASP8 WILD-TYPE 47 114 21
'CASP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.571 (Fisher's exact test), Q value = 1

Table S245.  Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
CASP8 MUTATED 3 1 5
CASP8 WILD-TYPE 56 55 74
'CASP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.449 (Fisher's exact test), Q value = 1

Table S246.  Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
CASP8 MUTATED 0 3 3 1 2
CASP8 WILD-TYPE 41 47 55 14 28
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S247.  Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
CASP8 MUTATED 4 0 4
CASP8 WILD-TYPE 65 57 54
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S248.  Gene #31: 'CASP8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
CASP8 MUTATED 1 0 1 6
CASP8 WILD-TYPE 41 32 27 76
'GAS6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.817 (Fisher's exact test), Q value = 1

Table S249.  Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
GAS6 MUTATED 2 0 2
GAS6 WILD-TYPE 88 40 59
'GAS6 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S250.  Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
GAS6 MUTATED 0 0 3 1 0 0
GAS6 WILD-TYPE 48 34 34 34 28 12
'GAS6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S251.  Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
GAS6 MUTATED 0 3 1
GAS6 WILD-TYPE 66 77 44
'GAS6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S252.  Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
GAS6 MUTATED 0 4 0
GAS6 WILD-TYPE 48 116 23
'GAS6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S253.  Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
GAS6 MUTATED 1 1 2
GAS6 WILD-TYPE 58 55 77
'GAS6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.392 (Fisher's exact test), Q value = 1

Table S254.  Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
GAS6 MUTATED 0 3 1 0 0
GAS6 WILD-TYPE 41 47 57 15 30
'GAS6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.292 (Fisher's exact test), Q value = 1

Table S255.  Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
GAS6 MUTATED 0 1 2
GAS6 WILD-TYPE 69 56 56
'GAS6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.755 (Fisher's exact test), Q value = 1

Table S256.  Gene #32: 'GAS6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
GAS6 MUTATED 0 1 0 2
GAS6 WILD-TYPE 42 31 28 80
'ABCD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.603 (Fisher's exact test), Q value = 1

Table S257.  Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
ABCD1 MUTATED 2 2 1
ABCD1 WILD-TYPE 88 38 60
'ABCD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.863 (Fisher's exact test), Q value = 1

Table S258.  Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
ABCD1 MUTATED 1 1 1 2 2 0
ABCD1 WILD-TYPE 47 33 36 33 26 12
'ABCD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 1

Table S259.  Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
ABCD1 MUTATED 1 2 3
ABCD1 WILD-TYPE 65 78 42
'ABCD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.135 (Fisher's exact test), Q value = 1

Table S260.  Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
ABCD1 MUTATED 0 4 2
ABCD1 WILD-TYPE 48 116 21
'ABCD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S261.  Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
ABCD1 MUTATED 1 3 3
ABCD1 WILD-TYPE 58 53 76
'ABCD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S262.  Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
ABCD1 MUTATED 0 2 3 0 2
ABCD1 WILD-TYPE 41 48 55 15 28
'ABCD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0568 (Fisher's exact test), Q value = 1

Table S263.  Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
ABCD1 MUTATED 0 4 3
ABCD1 WILD-TYPE 69 53 55
'ABCD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.374 (Fisher's exact test), Q value = 1

Table S264.  Gene #33: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
ABCD1 MUTATED 0 1 2 4
ABCD1 WILD-TYPE 42 31 26 78
'RPAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.682 (Fisher's exact test), Q value = 1

Table S265.  Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
RPAP1 MUTATED 3 0 1
RPAP1 WILD-TYPE 87 40 60
'RPAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.72 (Fisher's exact test), Q value = 1

Table S266.  Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
RPAP1 MUTATED 1 1 2 0 0 0
RPAP1 WILD-TYPE 47 33 35 35 28 12
'RPAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.453 (Fisher's exact test), Q value = 1

Table S267.  Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
RPAP1 MUTATED 1 1 2
RPAP1 WILD-TYPE 65 79 43
'RPAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S268.  Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
RPAP1 MUTATED 1 3 0
RPAP1 WILD-TYPE 47 117 23
'RPAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S269.  Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
RPAP1 MUTATED 1 1 2
RPAP1 WILD-TYPE 58 55 77
'RPAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.742 (Fisher's exact test), Q value = 1

Table S270.  Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
RPAP1 MUTATED 0 2 1 0 1
RPAP1 WILD-TYPE 41 48 57 15 29
'RPAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S271.  Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
RPAP1 MUTATED 2 1 1
RPAP1 WILD-TYPE 67 56 57
'RPAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.903 (Fisher's exact test), Q value = 1

Table S272.  Gene #34: 'RPAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
RPAP1 MUTATED 1 0 1 2
RPAP1 WILD-TYPE 41 32 27 80
'HIST1H4E MUTATION STATUS' versus 'CN_CNMF'

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

Table S273.  Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
HIST1H4E MUTATED 2 2 0
HIST1H4E WILD-TYPE 88 38 61
'HIST1H4E MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.801 (Fisher's exact test), Q value = 1

Table S274.  Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
HIST1H4E MUTATED 0 1 1 1 1 0
HIST1H4E WILD-TYPE 48 33 36 34 27 12
'HIST1H4E MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S275.  Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
HIST1H4E MUTATED 0 3 1
HIST1H4E WILD-TYPE 66 77 44
'HIST1H4E MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.3 (Fisher's exact test), Q value = 1

Table S276.  Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
HIST1H4E MUTATED 0 3 1
HIST1H4E WILD-TYPE 48 117 22
'HIST1H4E MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.473 (Fisher's exact test), Q value = 1

Table S277.  Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
HIST1H4E MUTATED 0 2 2
HIST1H4E WILD-TYPE 59 54 77
'HIST1H4E MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.828 (Fisher's exact test), Q value = 1

Table S278.  Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
HIST1H4E MUTATED 0 1 2 0 1
HIST1H4E WILD-TYPE 41 49 56 15 29
'HIST1H4E MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S279.  Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
HIST1H4E MUTATED 1 2 0
HIST1H4E WILD-TYPE 68 55 58
'HIST1H4E MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.379 (Fisher's exact test), Q value = 1

Table S280.  Gene #35: 'HIST1H4E MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
HIST1H4E MUTATED 0 1 1 1
HIST1H4E WILD-TYPE 42 31 27 81
'NLRC5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S281.  Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
NLRC5 MUTATED 4 2 1
NLRC5 WILD-TYPE 86 38 60
'NLRC5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0993 (Fisher's exact test), Q value = 1

Table S282.  Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
NLRC5 MUTATED 4 2 0 0 0 1
NLRC5 WILD-TYPE 44 32 37 35 28 11
'NLRC5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S283.  Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
NLRC5 MUTATED 4 1 2
NLRC5 WILD-TYPE 62 79 43
'NLRC5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.156 (Fisher's exact test), Q value = 1

Table S284.  Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
NLRC5 MUTATED 4 3 0
NLRC5 WILD-TYPE 44 117 23
'NLRC5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.138 (Fisher's exact test), Q value = 1

Table S285.  Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
NLRC5 MUTATED 4 0 3
NLRC5 WILD-TYPE 55 56 76
'NLRC5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S286.  Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
NLRC5 MUTATED 3 0 2 1 1
NLRC5 WILD-TYPE 38 50 56 14 29
'NLRC5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.565 (Fisher's exact test), Q value = 1

Table S287.  Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
NLRC5 MUTATED 4 1 2
NLRC5 WILD-TYPE 65 56 56
'NLRC5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.159 (Fisher's exact test), Q value = 1

Table S288.  Gene #36: 'NLRC5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
NLRC5 MUTATED 4 0 1 2
NLRC5 WILD-TYPE 38 32 27 80
'DDX41 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 1

Table S289.  Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
DDX41 MUTATED 0 1 4
DDX41 WILD-TYPE 90 39 57

Figure S38.  Get High-res Image Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'DDX41 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.123 (Fisher's exact test), Q value = 1

Table S290.  Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
DDX41 MUTATED 0 3 0 1 1 0
DDX41 WILD-TYPE 48 31 37 34 27 12
'DDX41 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 1

Table S291.  Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 80 45
DDX41 MUTATED 0 4 1
DDX41 WILD-TYPE 66 76 44
'DDX41 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.4 (Fisher's exact test), Q value = 1

Table S292.  Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 120 23
DDX41 MUTATED 0 4 1
DDX41 WILD-TYPE 48 116 22
'DDX41 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 1

Table S293.  Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
DDX41 MUTATED 0 2 3
DDX41 WILD-TYPE 59 54 76
'DDX41 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.784 (Fisher's exact test), Q value = 1

Table S294.  Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
DDX41 MUTATED 0 2 2 0 1
DDX41 WILD-TYPE 41 48 56 15 29
'DDX41 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S295.  Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
DDX41 MUTATED 2 1 1
DDX41 WILD-TYPE 67 56 57
'DDX41 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S296.  Gene #37: 'DDX41 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
DDX41 MUTATED 0 1 0 3
DDX41 WILD-TYPE 42 31 28 79
'MCM7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0719 (Fisher's exact test), Q value = 1

Table S297.  Gene #38: 'MCM7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 48 34 37 35 28 12
MCM7 MUTATED 0 0 0 1 1 1
MCM7 WILD-TYPE 48 34 37 34 27 11
'MCM7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S298.  Gene #38: 'MCM7 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
MCM7 MUTATED 1 1 1
MCM7 WILD-TYPE 58 55 78
'MCM7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.49 (Fisher's exact test), Q value = 1

Table S299.  Gene #38: 'MCM7 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
MCM7 MUTATED 0 0 2 0 1
MCM7 WILD-TYPE 41 50 56 15 29
'MCM7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0571 (Fisher's exact test), Q value = 1

Table S300.  Gene #38: 'MCM7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
MCM7 MUTATED 0 0 3
MCM7 WILD-TYPE 69 57 55
'MCM7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.163 (Fisher's exact test), Q value = 1

Table S301.  Gene #38: 'MCM7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
MCM7 MUTATED 0 0 2 1
MCM7 WILD-TYPE 42 32 26 81
Methods & Data
Input

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

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

  • Number of patients = 194

  • Number of significantly mutated genes = 38

  • Number of Molecular subtypes = 8

  • 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)
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