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 10 molecular subtypes across 283 patients, 46 significant findings detected with P value < 0.05 and Q value < 0.25.

  • TP53 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • RB1 mutation correlated to 'MRNA_CHIERARCHICAL' and 'METHLYATION_CNMF'.

  • PTEN mutation correlated to 'MIR_CNMF'.

  • NF1 mutation correlated to 'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'CN_CNMF', and 'RPPA_CHIERARCHICAL'.

  • IDH1 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • STAG2 mutation correlated to 'RPPA_CNMF'.

  • ATRX mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • BRAF mutation correlated to 'MIR_CHIERARCHICAL'.

  • EGFR mutation correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

  • PDGFRA mutation correlated to 'MRNA_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • TEX15 mutation correlated to 'MRNASEQ_CNMF'.

  • MUC17 mutation correlated to 'MRNA_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 38 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 46 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		MIR
CNMF 		MIR
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
IDH1 14 (5%) 269 7e-05
(0.00205) 		1e-05
(0.00076) 		3e-05
(0.00104) 		0.00299
(0.0406) 		3e-05
(0.00104) 		2e-05
(0.000844) 		0.00363
(0.0476) 		0.00126
(0.0228) 		0.0008
(0.016) 		1e-05
(0.00076)
ATRX 16 (6%) 267 0.00207
(0.0304) 		1e-05
(0.00076) 		0.00685
(0.0758) 		0.0181
(0.164) 		2e-05
(0.000844) 		2e-05
(0.000844) 		0.00649
(0.0747) 		0.0511
(0.366) 		0.00194
(0.0304) 		0.00023
(0.00583)
TP53 79 (28%) 204 0.00073
(0.0154) 		1e-05
(0.00076) 		0.00134
(0.0231) 		0.15
(0.668) 		2e-05
(0.000844) 		0.00099
(0.0188) 		0.0376
(0.297) 		0.00916
(0.0941) 		0.00208
(0.0304) 		0.0019
(0.0304)
EGFR 74 (26%) 209 0.00649
(0.0747) 		0.0567
(0.399) 		0.512
(1.00) 		0.138
(0.647) 		1e-05
(0.00076) 		0.00034
(0.00807) 		5e-05
(0.00158) 		0.00018
(0.00489) 		0.0418
(0.324) 		0.00613
(0.0747)
NF1 29 (10%) 254 0.0802
(0.484) 		0.00041
(0.00916) 		0.0252
(0.217) 		0.933
(1.00) 		0.00853
(0.09) 		0.0683
(0.448) 		0.231
(0.743) 		0.00578
(0.0732) 		0.567
(1.00) 		0.454
(1.00)
RB1 24 (8%) 259 0.0355
(0.287) 		0.0175
(0.163) 		0.134
(0.641) 		0.923
(1.00) 		0.106
(0.574) 		0.0111
(0.108) 		0.49
(1.00) 		0.226
(0.743) 		0.082
(0.487) 		0.578
(1.00)
PDGFRA 12 (4%) 271 0.0205
(0.181) 		0.135
(0.641) 		0.762
(1.00) 		0.0934
(0.53) 		0.19
(0.696) 		0.732
(1.00) 		0.769
(1.00) 		0.875
(1.00) 		0.0504
(0.366) 		0.0103
(0.103)
PTEN 87 (31%) 196 0.117
(0.601) 		0.0753
(0.469) 		0.0267
(0.225) 		0.64
(1.00) 		0.431
(0.98) 		0.222
(0.74) 		0.377
(0.917) 		0.142
(0.655) 		0.269
(0.783) 		0.643
(1.00)
STAG2 12 (4%) 271 0.392
(0.934) 		0.698
(1.00) 		0.715
(1.00) 		0.591
(1.00) 		0.75
(1.00) 		0.0434
(0.33) 		0.00698
(0.0758) 		0.392
(0.934) 		0.479
(1.00) 		0.103
(0.569)
BRAF 6 (2%) 277 0.767
(1.00) 		0.714
(1.00) 		0.319
(0.859) 		0.0289
(0.239) 		0.588
(1.00) 		1
(1.00) 		0.642
(1.00) 		0.79
(1.00) 		1
(1.00)
TEX15 8 (3%) 275 0.31
(0.841) 		0.242
(0.752) 		0.3
(0.832) 		0.722
(1.00) 		0.551
(1.00) 		0.824
(1.00) 		0.869
(1.00) 		0.272
(0.783) 		0.00294
(0.0406) 		0.824
(1.00)
MUC17 22 (8%) 261 0.0115
(0.11) 		0.192
(0.696) 		0.706
(1.00) 		0.702
(1.00) 		0.922
(1.00) 		0.841
(1.00) 		0.244
(0.752) 		0.326
(0.864) 		0.861
(1.00) 		1
(1.00)
PIK3R1 32 (11%) 251 0.752
(1.00) 		0.19
(0.696) 		0.198
(0.702) 		0.53
(1.00) 		0.637
(1.00) 		0.246
(0.752) 		0.988
(1.00) 		0.676
(1.00) 		0.406
(0.956) 		0.222
(0.74)
PIK3CA 29 (10%) 254 0.791
(1.00) 		0.164
(0.669) 		0.574
(1.00) 		1
(1.00) 		0.816
(1.00) 		0.821
(1.00) 		0.753
(1.00) 		0.31
(0.841) 		0.262
(0.775) 		0.237
(0.744)
SEMG2 11 (4%) 272 0.5
(1.00) 		0.421
(0.965) 		0.551
(1.00) 		0.921
(1.00) 		0.0616
(0.425) 		0.619
(1.00) 		0.228
(0.743) 		0.442
(0.999) 		0.816
(1.00) 		0.8
(1.00)
MAP3K1 6 (2%) 277 1
(1.00) 		0.73
(1.00) 		0.808
(1.00) 		0.648
(1.00) 		1
(1.00) 		0.571
(1.00) 		1
(1.00)
SLC26A3 7 (2%) 276 0.941
(1.00) 		0.767
(1.00) 		0.463
(1.00) 		0.363
(0.914) 		0.649
(1.00) 		0.183
(0.694) 		0.168
(0.669) 		0.154
(0.669) 		0.156
(0.669) 		0.163
(0.669)
TMPRSS6 6 (2%) 277 0.67
(1.00) 		0.701
(1.00) 		0.662
(1.00) 		0.263
(0.775) 		0.884
(1.00) 		0.348
(0.893) 		0.256
(0.771) 		0.328
(0.864) 		0.574
(1.00) 		1
(1.00)
SEMA3C 11 (4%) 272 0.482
(1.00) 		0.174
(0.669) 		0.122
(0.612) 		0.85
(1.00) 		0.542
(1.00) 		0.413
(0.957) 		0.338
(0.881) 		0.684
(1.00) 		0.102
(0.569) 		0.169
(0.669)
RPL5 7 (2%) 276 0.379
(0.917) 		0.51
(1.00) 		0.867
(1.00) 		0.467
(1.00) 		1
(1.00) 		0.843
(1.00) 		0.684
(1.00) 		0.466
(1.00) 		1
(1.00)
MMP13 5 (2%) 278 0.911
(1.00) 		0.221
(0.74) 		0.766
(1.00) 		0.0495
(0.366) 		0.151
(0.668)
REN 5 (2%) 278 0.476
(1.00) 		0.417
(0.961) 		0.0747
(0.469) 		0.511
(1.00) 		0.618
(1.00) 		1
(1.00) 		0.837
(1.00)
DSP 12 (4%) 271 0.488
(1.00) 		0.963
(1.00) 		0.569
(1.00) 		0.0735
(0.469) 		0.933
(1.00) 		0.529
(1.00) 		0.658
(1.00) 		0.705
(1.00)
CHD8 9 (3%) 274 0.702
(1.00) 		0.532
(1.00) 		0.135
(0.641) 		0.642
(1.00) 		0.191
(0.696) 		0.625
(1.00) 		0.759
(1.00) 		0.276
(0.788) 		0.613
(1.00)
KDR 8 (3%) 275 0.202
(0.709) 		0.655
(1.00) 		0.282
(0.794) 		0.51
(1.00) 		0.732
(1.00) 		0.345
(0.891) 		0.145
(0.655) 		0.527
(1.00)
ODF4 3 (1%) 280 0.879
(1.00) 		0.35
(0.893) 		1
(1.00) 		0.197
(0.702) 		0.634
(1.00)
TP63 6 (2%) 277 1
(1.00) 		0.729
(1.00) 		0.408
(0.956) 		0.644
(1.00) 		0.774
(1.00) 		0.0664
(0.443) 		0.206
(0.72) 		0.255
(0.771) 		0.109
(0.575)
PRKCD 3 (1%) 280 0.172
(0.669) 		0.0849
(0.497) 		0.162
(0.669) 		1
(1.00) 		0.376
(0.917)
ACSM2B 5 (2%) 278 0.079
(0.484) 		0.272
(0.783) 		0.59
(1.00) 		0.237
(0.744) 		0.393
(0.934) 		1
(1.00) 		0.174
(0.669) 		1
(1.00)
CLCN7 4 (1%) 279 0.111
(0.578) 		0.77
(1.00) 		0.697
(1.00) 		0.259
(0.775) 		0.235
(0.744) 		0.168
(0.669)
DDX5 4 (1%) 279 0.216
(0.739) 		1
(1.00) 		0.538
(1.00) 		0.444
(0.999) 		0.144
(0.655)
FBN3 11 (4%) 272 0.189
(0.696) 		0.306
(0.841) 		0.904
(1.00) 		0.922
(1.00) 		0.107
(0.574) 		1
(1.00) 		0.279
(0.792) 		0.375
(0.917) 		0.854
(1.00) 		1
(1.00)
CD1D 4 (1%) 279 0.879
(1.00) 		1
(1.00) 		0.645
(1.00) 		0.124
(0.612) 		0.825
(1.00) 		0.893
(1.00) 		1
(1.00)
KEL 15 (5%) 268 0.545
(1.00) 		0.213
(0.736) 		0.722
(1.00) 		0.888
(1.00) 		0.0911
(0.524) 		0.168
(0.669) 		0.377
(0.917) 		0.919
(1.00) 		0.41
(0.956) 		0.651
(1.00)
SLC6A14 5 (2%) 278 0.88
(1.00) 		0.482
(1.00) 		0.832
(1.00) 		1
(1.00) 		0.823
(1.00) 		0.231
(0.743) 		0.294
(0.821) 		0.643
(1.00)
LRRC55 6 (2%) 277 0.374
(0.917) 		0.536
(1.00) 		0.334
(0.874) 		0.87
(1.00) 		0.326
(0.864)
CD209 5 (2%) 278 0.912
(1.00) 		1
(1.00) 		0.0655
(0.443) 		0.608
(1.00) 		0.692
(1.00) 		0.491
(1.00) 		1
(1.00)
LZTR1 11 (4%) 272 1
(1.00) 		0.519
(1.00) 		0.355
(0.9) 		0.474
(1.00) 		0.788
(1.00) 		0.124
(0.612) 		0.66
(1.00) 		0.815
(1.00) 		0.174
(0.669) 		0.751
(1.00)
'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.015

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
TP53 MUTATED 16 19 11 22
TP53 WILD-TYPE 53 24 63 32

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

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00076

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
TP53 MUTATED 15 30 7 16
TP53 WILD-TYPE 48 20 41 63

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

'TP53 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.023

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
TP53 MUTATED 12 39 10 18
TP53 WILD-TYPE 65 54 35 42

Figure S3.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'TP53 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.15 (Fisher's exact test), Q value = 0.67

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
TP53 MUTATED 47 15 17
TP53 WILD-TYPE 91 46 59
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00084

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
TP53 MUTATED 35 14 29
TP53 WILD-TYPE 48 96 51

Figure S4.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.019

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
TP53 MUTATED 9 13 19
TP53 WILD-TYPE 34 39 13

Figure S5.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.3

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
TP53 MUTATED 12 17 4 10
TP53 WILD-TYPE 29 21 27 23

Figure S6.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00916 (Fisher's exact test), Q value = 0.094

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
TP53 MUTATED 15 22 6
TP53 WILD-TYPE 33 30 37

Figure S7.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00208 (Fisher's exact test), Q value = 0.03

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
TP53 MUTATED 23 13 8
TP53 WILD-TYPE 21 49 27

Figure S8.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0019 (Fisher's exact test), Q value = 0.03

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
TP53 MUTATED 18 21 5
TP53 WILD-TYPE 13 65 19

Figure S9.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'PIK3R1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S11.  Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
PIK3R1 MUTATED 7 2 8 5
PIK3R1 WILD-TYPE 62 41 66 49
'PIK3R1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.19 (Fisher's exact test), Q value = 0.7

Table S12.  Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
PIK3R1 MUTATED 7 6 6 3
PIK3R1 WILD-TYPE 56 44 42 76
'PIK3R1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 0.7

Table S13.  Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
PIK3R1 MUTATED 12 13 4 3
PIK3R1 WILD-TYPE 65 80 41 57
'PIK3R1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.53 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
PIK3R1 MUTATED 16 5 11
PIK3R1 WILD-TYPE 122 56 65
'PIK3R1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.637 (Fisher's exact test), Q value = 1

Table S15.  Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
PIK3R1 MUTATED 7 14 10
PIK3R1 WILD-TYPE 76 96 70
'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.246 (Fisher's exact test), Q value = 0.75

Table S16.  Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
PIK3R1 MUTATED 2 5 5
PIK3R1 WILD-TYPE 41 47 27
'PIK3R1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.988 (Fisher's exact test), Q value = 1

Table S17.  Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
PIK3R1 MUTATED 7 6 4 5
PIK3R1 WILD-TYPE 34 32 27 28
'PIK3R1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S18.  Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
PIK3R1 MUTATED 9 8 5
PIK3R1 WILD-TYPE 39 44 38
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.406 (Fisher's exact test), Q value = 0.96

Table S19.  Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
PIK3R1 MUTATED 5 6 1
PIK3R1 WILD-TYPE 39 56 34
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.222 (Fisher's exact test), Q value = 0.74

Table S20.  Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
PIK3R1 MUTATED 4 8 0
PIK3R1 WILD-TYPE 27 78 24
'RB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0355 (Fisher's exact test), Q value = 0.29

Table S21.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
RB1 MUTATED 11 2 3 2
RB1 WILD-TYPE 58 41 71 52

Figure S10.  Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'RB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 0.16

Table S22.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
RB1 MUTATED 5 2 0 11
RB1 WILD-TYPE 58 48 48 68

Figure S11.  Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 0.64

Table S23.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
RB1 MUTATED 11 4 3 6
RB1 WILD-TYPE 66 89 42 54
'RB1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.923 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
RB1 MUTATED 12 6 6
RB1 WILD-TYPE 126 55 70
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.106 (Fisher's exact test), Q value = 0.57

Table S25.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
RB1 MUTATED 9 5 10
RB1 WILD-TYPE 74 105 70
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.11

Table S26.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
RB1 MUTATED 9 2 1
RB1 WILD-TYPE 34 50 31

Figure S12.  Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S27.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
RB1 MUTATED 3 1 2 4
RB1 WILD-TYPE 38 37 29 29
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.226 (Fisher's exact test), Q value = 0.74

Table S28.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
RB1 MUTATED 6 2 2
RB1 WILD-TYPE 42 50 41
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.082 (Fisher's exact test), Q value = 0.49

Table S29.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
RB1 MUTATED 1 8 1
RB1 WILD-TYPE 43 54 34
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.578 (Fisher's exact test), Q value = 1

Table S30.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
RB1 MUTATED 1 8 1
RB1 WILD-TYPE 30 78 23
'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.117 (Fisher's exact test), Q value = 0.6

Table S31.  Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
PTEN MUTATED 25 10 18 22
PTEN WILD-TYPE 44 33 56 32
'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0753 (Fisher's exact test), Q value = 0.47

Table S32.  Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
PTEN MUTATED 18 16 9 32
PTEN WILD-TYPE 45 34 39 47
'PTEN MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.0267 (Fisher's exact test), Q value = 0.23

Table S33.  Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
PTEN MUTATED 30 19 18 20
PTEN WILD-TYPE 47 74 27 40

Figure S13.  Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'PTEN MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.64 (Fisher's exact test), Q value = 1

Table S34.  Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
PTEN MUTATED 45 21 21
PTEN WILD-TYPE 93 40 55
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.431 (Fisher's exact test), Q value = 0.98

Table S35.  Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
PTEN MUTATED 30 30 25
PTEN WILD-TYPE 53 80 55
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.222 (Fisher's exact test), Q value = 0.74

Table S36.  Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
PTEN MUTATED 17 12 11
PTEN WILD-TYPE 26 40 21
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.377 (Fisher's exact test), Q value = 0.92

Table S37.  Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
PTEN MUTATED 12 14 6 12
PTEN WILD-TYPE 29 24 25 21
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.142 (Fisher's exact test), Q value = 0.65

Table S38.  Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
PTEN MUTATED 20 13 11
PTEN WILD-TYPE 28 39 32
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.269 (Fisher's exact test), Q value = 0.78

Table S39.  Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
PTEN MUTATED 10 23 12
PTEN WILD-TYPE 34 39 23
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S40.  Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
PTEN MUTATED 8 28 9
PTEN WILD-TYPE 23 58 15
'NF1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0802 (Fisher's exact test), Q value = 0.48

Table S41.  Gene #5: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
NF1 MUTATED 11 4 4 2
NF1 WILD-TYPE 58 39 70 52
'NF1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0092

Table S42.  Gene #5: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
NF1 MUTATED 14 1 1 5
NF1 WILD-TYPE 49 49 47 74

Figure S14.  Get High-res Image Gene #5: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.0252 (Fisher's exact test), Q value = 0.22

Table S43.  Gene #5: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
NF1 MUTATED 12 3 5 8
NF1 WILD-TYPE 65 90 40 52

Figure S15.  Get High-res Image Gene #5: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'NF1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S44.  Gene #5: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
NF1 MUTATED 14 7 7
NF1 WILD-TYPE 124 54 69
'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00853 (Fisher's exact test), Q value = 0.09

Table S45.  Gene #5: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
NF1 MUTATED 5 8 16
NF1 WILD-TYPE 78 102 64

Figure S16.  Get High-res Image Gene #5: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0683 (Fisher's exact test), Q value = 0.45

Table S46.  Gene #5: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
NF1 MUTATED 8 2 3
NF1 WILD-TYPE 35 50 29
'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.231 (Fisher's exact test), Q value = 0.74

Table S47.  Gene #5: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
NF1 MUTATED 7 3 1 5
NF1 WILD-TYPE 34 35 30 28
'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00578 (Fisher's exact test), Q value = 0.073

Table S48.  Gene #5: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
NF1 MUTATED 11 4 1
NF1 WILD-TYPE 37 48 42

Figure S17.  Get High-res Image Gene #5: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S49.  Gene #5: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
NF1 MUTATED 2 5 4
NF1 WILD-TYPE 42 57 31
'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.454 (Fisher's exact test), Q value = 1

Table S50.  Gene #5: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
NF1 MUTATED 1 7 3
NF1 WILD-TYPE 30 79 21
'IDH1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.002

Table S51.  Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
IDH1 MUTATED 1 3 0 9
IDH1 WILD-TYPE 68 40 74 45

Figure S18.  Get High-res Image Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00076

Table S52.  Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
IDH1 MUTATED 0 13 0 0
IDH1 WILD-TYPE 63 37 48 79

Figure S19.  Get High-res Image Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.001

Table S53.  Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
IDH1 MUTATED 0 13 1 0
IDH1 WILD-TYPE 77 80 44 60

Figure S20.  Get High-res Image Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'IDH1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.00299 (Fisher's exact test), Q value = 0.041

Table S54.  Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
IDH1 MUTATED 13 0 1
IDH1 WILD-TYPE 125 61 75

Figure S21.  Get High-res Image Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.001

Table S55.  Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
IDH1 MUTATED 2 0 11
IDH1 WILD-TYPE 81 110 69

Figure S22.  Get High-res Image Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00084

Table S56.  Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
IDH1 MUTATED 0 0 9
IDH1 WILD-TYPE 43 52 23

Figure S23.  Get High-res Image Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'IDH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00363 (Fisher's exact test), Q value = 0.048

Table S57.  Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
IDH1 MUTATED 1 6 0 0
IDH1 WILD-TYPE 40 32 31 33

Figure S24.  Get High-res Image Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

'IDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.023

Table S58.  Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
IDH1 MUTATED 0 7 0
IDH1 WILD-TYPE 48 45 43

Figure S25.  Get High-res Image Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.016

Table S59.  Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
IDH1 MUTATED 7 0 1
IDH1 WILD-TYPE 37 62 34

Figure S26.  Get High-res Image Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00076

Table S60.  Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
IDH1 MUTATED 8 0 0
IDH1 WILD-TYPE 23 86 24

Figure S27.  Get High-res Image Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.791 (Fisher's exact test), Q value = 1

Table S61.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
PIK3CA MUTATED 6 6 9 5
PIK3CA WILD-TYPE 63 37 65 49
'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.164 (Fisher's exact test), Q value = 0.67

Table S62.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
PIK3CA MUTATED 8 6 8 4
PIK3CA WILD-TYPE 55 44 40 75
'PIK3CA MUTATION STATUS' versus 'MIR_CNMF'

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

Table S63.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
PIK3CA MUTATED 9 11 2 6
PIK3CA WILD-TYPE 68 82 43 54
'PIK3CA MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S64.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
PIK3CA MUTATED 14 6 8
PIK3CA WILD-TYPE 124 55 68
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.816 (Fisher's exact test), Q value = 1

Table S65.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
PIK3CA MUTATED 7 11 9
PIK3CA WILD-TYPE 76 99 71
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.821 (Fisher's exact test), Q value = 1

Table S66.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
PIK3CA MUTATED 4 7 3
PIK3CA WILD-TYPE 39 45 29
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.753 (Fisher's exact test), Q value = 1

Table S67.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
PIK3CA MUTATED 3 5 2 4
PIK3CA WILD-TYPE 38 33 29 29
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.31 (Fisher's exact test), Q value = 0.84

Table S68.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
PIK3CA MUTATED 7 5 2
PIK3CA WILD-TYPE 41 47 41
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 0.78

Table S69.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
PIK3CA MUTATED 6 3 2
PIK3CA WILD-TYPE 38 59 33
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.237 (Fisher's exact test), Q value = 0.74

Table S70.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
PIK3CA MUTATED 4 7 0
PIK3CA WILD-TYPE 27 79 24
'STAG2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.392 (Fisher's exact test), Q value = 0.93

Table S71.  Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
STAG2 MUTATED 4 3 1 2
STAG2 WILD-TYPE 65 40 73 52
'STAG2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S72.  Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
STAG2 MUTATED 2 1 3 4
STAG2 WILD-TYPE 61 49 45 75
'STAG2 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S73.  Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
STAG2 MUTATED 4 5 2 1
STAG2 WILD-TYPE 73 88 43 59
'STAG2 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.591 (Fisher's exact test), Q value = 1

Table S74.  Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
STAG2 MUTATED 5 2 5
STAG2 WILD-TYPE 133 59 71
'STAG2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S75.  Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
STAG2 MUTATED 5 4 3
STAG2 WILD-TYPE 78 106 77
'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 0.33

Table S76.  Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
STAG2 MUTATED 4 0 1
STAG2 WILD-TYPE 39 52 31

Figure S28.  Get High-res Image Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'STAG2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00698 (Fisher's exact test), Q value = 0.076

Table S77.  Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
STAG2 MUTATED 0 2 0 5
STAG2 WILD-TYPE 41 36 31 28

Figure S29.  Get High-res Image Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

'STAG2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.392 (Fisher's exact test), Q value = 0.93

Table S78.  Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
STAG2 MUTATED 4 2 1
STAG2 WILD-TYPE 44 50 42
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.479 (Fisher's exact test), Q value = 1

Table S79.  Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
STAG2 MUTATED 1 3 3
STAG2 WILD-TYPE 43 59 32
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.103 (Fisher's exact test), Q value = 0.57

Table S80.  Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
STAG2 MUTATED 0 4 3
STAG2 WILD-TYPE 31 82 21
'SEMG2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.5 (Fisher's exact test), Q value = 1

Table S81.  Gene #9: 'SEMG2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
SEMG2 MUTATED 2 1 6 2
SEMG2 WILD-TYPE 67 42 68 52
'SEMG2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.421 (Fisher's exact test), Q value = 0.96

Table S82.  Gene #9: 'SEMG2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
SEMG2 MUTATED 1 2 2 6
SEMG2 WILD-TYPE 62 48 46 73
'SEMG2 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.551 (Fisher's exact test), Q value = 1

Table S83.  Gene #9: 'SEMG2 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
SEMG2 MUTATED 3 6 1 1
SEMG2 WILD-TYPE 74 87 44 59
'SEMG2 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.921 (Fisher's exact test), Q value = 1

Table S84.  Gene #9: 'SEMG2 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
SEMG2 MUTATED 5 3 3
SEMG2 WILD-TYPE 133 58 73
'SEMG2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0616 (Fisher's exact test), Q value = 0.43

Table S85.  Gene #9: 'SEMG2 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
SEMG2 MUTATED 5 6 0
SEMG2 WILD-TYPE 78 104 80
'SEMG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S86.  Gene #9: 'SEMG2 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
SEMG2 MUTATED 2 1 2
SEMG2 WILD-TYPE 41 51 30
'SEMG2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.228 (Fisher's exact test), Q value = 0.74

Table S87.  Gene #9: 'SEMG2 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
SEMG2 MUTATED 1 1 3 0
SEMG2 WILD-TYPE 40 37 28 33
'SEMG2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.442 (Fisher's exact test), Q value = 1

Table S88.  Gene #9: 'SEMG2 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
SEMG2 MUTATED 1 1 3
SEMG2 WILD-TYPE 47 51 40
'SEMG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.816 (Fisher's exact test), Q value = 1

Table S89.  Gene #9: 'SEMG2 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
SEMG2 MUTATED 2 1 1
SEMG2 WILD-TYPE 42 61 34
'SEMG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S90.  Gene #9: 'SEMG2 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
SEMG2 MUTATED 1 2 1
SEMG2 WILD-TYPE 30 84 23
'MAP3K1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S91.  Gene #10: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
MAP3K1 MUTATED 1 1 2 1
MAP3K1 WILD-TYPE 68 42 72 53
'MAP3K1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.73 (Fisher's exact test), Q value = 1

Table S92.  Gene #10: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
MAP3K1 MUTATED 1 1 2 1
MAP3K1 WILD-TYPE 62 49 46 78
'MAP3K1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.808 (Fisher's exact test), Q value = 1

Table S93.  Gene #10: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
MAP3K1 MUTATED 2 2 0 2
MAP3K1 WILD-TYPE 75 91 45 58
'MAP3K1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.648 (Fisher's exact test), Q value = 1

Table S94.  Gene #10: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
MAP3K1 MUTATED 2 2 2
MAP3K1 WILD-TYPE 136 59 74
'MAP3K1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S95.  Gene #10: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
MAP3K1 MUTATED 2 2 2
MAP3K1 WILD-TYPE 81 108 78
'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S96.  Gene #10: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
MAP3K1 MUTATED 1 3 0
MAP3K1 WILD-TYPE 43 59 35
'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S97.  Gene #10: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
MAP3K1 MUTATED 1 3 0
MAP3K1 WILD-TYPE 30 83 24
'SLC26A3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.941 (Fisher's exact test), Q value = 1

Table S98.  Gene #11: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
SLC26A3 MUTATED 1 1 2 2
SLC26A3 WILD-TYPE 68 42 72 52
'SLC26A3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.767 (Fisher's exact test), Q value = 1

Table S99.  Gene #11: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
SLC26A3 MUTATED 2 1 2 1
SLC26A3 WILD-TYPE 61 49 46 78
'SLC26A3 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.463 (Fisher's exact test), Q value = 1

Table S100.  Gene #11: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
SLC26A3 MUTATED 1 4 0 2
SLC26A3 WILD-TYPE 76 89 45 58
'SLC26A3 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.363 (Fisher's exact test), Q value = 0.91

Table S101.  Gene #11: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
SLC26A3 MUTATED 4 0 3
SLC26A3 WILD-TYPE 134 61 73
'SLC26A3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.649 (Fisher's exact test), Q value = 1

Table S102.  Gene #11: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
SLC26A3 MUTATED 2 4 1
SLC26A3 WILD-TYPE 81 106 79
'SLC26A3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.183 (Fisher's exact test), Q value = 0.69

Table S103.  Gene #11: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
SLC26A3 MUTATED 0 3 0
SLC26A3 WILD-TYPE 43 49 32
'SLC26A3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.168 (Fisher's exact test), Q value = 0.67

Table S104.  Gene #11: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
SLC26A3 MUTATED 3 0 1 0
SLC26A3 WILD-TYPE 38 38 30 33
'SLC26A3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.154 (Fisher's exact test), Q value = 0.67

Table S105.  Gene #11: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
SLC26A3 MUTATED 3 0 1
SLC26A3 WILD-TYPE 45 52 42
'SLC26A3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.156 (Fisher's exact test), Q value = 0.67

Table S106.  Gene #11: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
SLC26A3 MUTATED 2 0 2
SLC26A3 WILD-TYPE 42 62 33
'SLC26A3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.163 (Fisher's exact test), Q value = 0.67

Table S107.  Gene #11: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
SLC26A3 MUTATED 2 1 1
SLC26A3 WILD-TYPE 29 85 23
'ATRX MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00207 (Fisher's exact test), Q value = 0.03

Table S108.  Gene #12: 'ATRX MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
ATRX MUTATED 2 4 0 7
ATRX WILD-TYPE 67 39 74 47

Figure S30.  Get High-res Image Gene #12: 'ATRX MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'ATRX MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00076

Table S109.  Gene #12: 'ATRX MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
ATRX MUTATED 0 11 0 2
ATRX WILD-TYPE 63 39 48 77

Figure S31.  Get High-res Image Gene #12: 'ATRX MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.00685 (Fisher's exact test), Q value = 0.076

Table S110.  Gene #12: 'ATRX MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
ATRX MUTATED 2 11 3 0
ATRX WILD-TYPE 75 82 42 60

Figure S32.  Get High-res Image Gene #12: 'ATRX MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'ATRX MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.16

Table S111.  Gene #12: 'ATRX MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
ATRX MUTATED 13 0 3
ATRX WILD-TYPE 125 61 73

Figure S33.  Get High-res Image Gene #12: 'ATRX MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00084

Table S112.  Gene #12: 'ATRX MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
ATRX MUTATED 1 1 13
ATRX WILD-TYPE 82 109 67

Figure S34.  Get High-res Image Gene #12: 'ATRX MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'ATRX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00084

Table S113.  Gene #12: 'ATRX MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
ATRX MUTATED 0 0 8
ATRX WILD-TYPE 43 52 24

Figure S35.  Get High-res Image Gene #12: 'ATRX MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'ATRX MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00649 (Fisher's exact test), Q value = 0.075

Table S114.  Gene #12: 'ATRX MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
ATRX MUTATED 0 6 0 2
ATRX WILD-TYPE 41 32 31 31

Figure S36.  Get High-res Image Gene #12: 'ATRX MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

'ATRX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0511 (Fisher's exact test), Q value = 0.37

Table S115.  Gene #12: 'ATRX MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
ATRX MUTATED 2 6 0
ATRX WILD-TYPE 46 46 43
'ATRX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00194 (Fisher's exact test), Q value = 0.03

Table S116.  Gene #12: 'ATRX MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
ATRX MUTATED 7 1 0
ATRX WILD-TYPE 37 61 35

Figure S37.  Get High-res Image Gene #12: 'ATRX MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'ATRX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.0058

Table S117.  Gene #12: 'ATRX MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
ATRX MUTATED 7 1 0
ATRX WILD-TYPE 24 85 24

Figure S38.  Get High-res Image Gene #12: 'ATRX MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.767 (Fisher's exact test), Q value = 1

Table S118.  Gene #13: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
BRAF MUTATED 1 1 2 0
BRAF WILD-TYPE 68 42 72 54
'BRAF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.714 (Fisher's exact test), Q value = 1

Table S119.  Gene #13: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
BRAF MUTATED 2 0 1 1
BRAF WILD-TYPE 61 50 47 78
'BRAF MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.319 (Fisher's exact test), Q value = 0.86

Table S120.  Gene #13: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
BRAF MUTATED 2 1 0 3
BRAF WILD-TYPE 75 92 45 57
'BRAF MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.0289 (Fisher's exact test), Q value = 0.24

Table S121.  Gene #13: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
BRAF MUTATED 2 4 0
BRAF WILD-TYPE 136 57 76

Figure S39.  Get High-res Image Gene #13: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'CN_CNMF'

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

Table S122.  Gene #13: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
BRAF MUTATED 1 2 3
BRAF WILD-TYPE 82 108 77
'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S123.  Gene #13: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
BRAF MUTATED 1 1 0 1
BRAF WILD-TYPE 40 37 31 32
'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.642 (Fisher's exact test), Q value = 1

Table S124.  Gene #13: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
BRAF MUTATED 2 1 0
BRAF WILD-TYPE 46 51 43
'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.79 (Fisher's exact test), Q value = 1

Table S125.  Gene #13: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
BRAF MUTATED 1 2 0
BRAF WILD-TYPE 43 60 35
'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S126.  Gene #13: 'BRAF MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
BRAF MUTATED 1 2 0
BRAF WILD-TYPE 30 84 24
'EGFR MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00649 (Fisher's exact test), Q value = 0.075

Table S127.  Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
EGFR MUTATED 20 7 31 10
EGFR WILD-TYPE 49 36 43 44

Figure S40.  Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'EGFR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0567 (Fisher's exact test), Q value = 0.4

Table S128.  Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
EGFR MUTATED 18 7 17 26
EGFR WILD-TYPE 45 43 31 53
'EGFR MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.512 (Fisher's exact test), Q value = 1

Table S129.  Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
EGFR MUTATED 22 27 8 17
EGFR WILD-TYPE 55 66 37 43
'EGFR MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.138 (Fisher's exact test), Q value = 0.65

Table S130.  Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
EGFR MUTATED 30 19 25
EGFR WILD-TYPE 108 42 51
'EGFR MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00076

Table S131.  Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
EGFR MUTATED 15 48 9
EGFR WILD-TYPE 68 62 71

Figure S41.  Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0081

Table S132.  Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
EGFR MUTATED 13 24 2
EGFR WILD-TYPE 30 28 30

Figure S42.  Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'EGFR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0016

Table S133.  Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
EGFR MUTATED 13 5 16 2
EGFR WILD-TYPE 28 33 15 31

Figure S43.  Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

'EGFR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.0049

Table S134.  Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
EGFR MUTATED 8 7 21
EGFR WILD-TYPE 40 45 22

Figure S44.  Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0418 (Fisher's exact test), Q value = 0.32

Table S135.  Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
EGFR MUTATED 8 22 15
EGFR WILD-TYPE 36 40 20

Figure S45.  Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'EGFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00613 (Fisher's exact test), Q value = 0.075

Table S136.  Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
EGFR MUTATED 3 32 10
EGFR WILD-TYPE 28 54 14

Figure S46.  Get High-res Image Gene #14: 'EGFR MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'TMPRSS6 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.67 (Fisher's exact test), Q value = 1

Table S137.  Gene #15: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
TMPRSS6 MUTATED 2 0 3 1
TMPRSS6 WILD-TYPE 67 43 71 53
'TMPRSS6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.701 (Fisher's exact test), Q value = 1

Table S138.  Gene #15: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
TMPRSS6 MUTATED 3 1 1 1
TMPRSS6 WILD-TYPE 60 49 47 78
'TMPRSS6 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.662 (Fisher's exact test), Q value = 1

Table S139.  Gene #15: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
TMPRSS6 MUTATED 3 1 1 1
TMPRSS6 WILD-TYPE 74 92 44 59
'TMPRSS6 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.263 (Fisher's exact test), Q value = 0.78

Table S140.  Gene #15: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
TMPRSS6 MUTATED 2 3 1
TMPRSS6 WILD-TYPE 136 58 75
'TMPRSS6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.884 (Fisher's exact test), Q value = 1

Table S141.  Gene #15: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
TMPRSS6 MUTATED 2 3 1
TMPRSS6 WILD-TYPE 81 107 79
'TMPRSS6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 0.89

Table S142.  Gene #15: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
TMPRSS6 MUTATED 2 0 1
TMPRSS6 WILD-TYPE 41 52 31
'TMPRSS6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.256 (Fisher's exact test), Q value = 0.77

Table S143.  Gene #15: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
TMPRSS6 MUTATED 2 0 2 0
TMPRSS6 WILD-TYPE 39 38 29 33
'TMPRSS6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.328 (Fisher's exact test), Q value = 0.86

Table S144.  Gene #15: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
TMPRSS6 MUTATED 2 0 2
TMPRSS6 WILD-TYPE 46 52 41
'TMPRSS6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S145.  Gene #15: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
TMPRSS6 MUTATED 1 4 1
TMPRSS6 WILD-TYPE 43 58 34
'TMPRSS6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S146.  Gene #15: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
TMPRSS6 MUTATED 1 4 1
TMPRSS6 WILD-TYPE 30 82 23
'SEMA3C MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S147.  Gene #16: 'SEMA3C MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
SEMA3C MUTATED 3 4 2 2
SEMA3C WILD-TYPE 66 39 72 52
'SEMA3C MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.174 (Fisher's exact test), Q value = 0.67

Table S148.  Gene #16: 'SEMA3C MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
SEMA3C MUTATED 1 5 1 4
SEMA3C WILD-TYPE 62 45 47 75
'SEMA3C MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.122 (Fisher's exact test), Q value = 0.61

Table S149.  Gene #16: 'SEMA3C MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
SEMA3C MUTATED 3 7 1 0
SEMA3C WILD-TYPE 74 86 44 60
'SEMA3C MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.85 (Fisher's exact test), Q value = 1

Table S150.  Gene #16: 'SEMA3C MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
SEMA3C MUTATED 5 2 4
SEMA3C WILD-TYPE 133 59 72
'SEMA3C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.542 (Fisher's exact test), Q value = 1

Table S151.  Gene #16: 'SEMA3C MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
SEMA3C MUTATED 5 4 2
SEMA3C WILD-TYPE 78 106 78
'SEMA3C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.413 (Fisher's exact test), Q value = 0.96

Table S152.  Gene #16: 'SEMA3C MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
SEMA3C MUTATED 1 4 3
SEMA3C WILD-TYPE 42 48 29
'SEMA3C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.338 (Fisher's exact test), Q value = 0.88

Table S153.  Gene #16: 'SEMA3C MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
SEMA3C MUTATED 2 2 0 0
SEMA3C WILD-TYPE 39 36 31 33
'SEMA3C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.684 (Fisher's exact test), Q value = 1

Table S154.  Gene #16: 'SEMA3C MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
SEMA3C MUTATED 1 1 2
SEMA3C WILD-TYPE 47 51 41
'SEMA3C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.57

Table S155.  Gene #16: 'SEMA3C MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
SEMA3C MUTATED 6 2 1
SEMA3C WILD-TYPE 38 60 34
'SEMA3C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.169 (Fisher's exact test), Q value = 0.67

Table S156.  Gene #16: 'SEMA3C MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
SEMA3C MUTATED 4 5 0
SEMA3C WILD-TYPE 27 81 24
'RPL5 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.379 (Fisher's exact test), Q value = 0.92

Table S157.  Gene #17: 'RPL5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
RPL5 MUTATED 1 2 3 0
RPL5 WILD-TYPE 68 41 71 54
'RPL5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.51 (Fisher's exact test), Q value = 1

Table S158.  Gene #17: 'RPL5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
RPL5 MUTATED 3 0 1 2
RPL5 WILD-TYPE 60 50 47 77
'RPL5 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S159.  Gene #17: 'RPL5 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
RPL5 MUTATED 1 3 1 2
RPL5 WILD-TYPE 76 90 44 58
'RPL5 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S160.  Gene #17: 'RPL5 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
RPL5 MUTATED 3 3 1
RPL5 WILD-TYPE 135 58 75
'RPL5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S161.  Gene #17: 'RPL5 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
RPL5 MUTATED 2 3 2
RPL5 WILD-TYPE 81 107 78
'RPL5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.843 (Fisher's exact test), Q value = 1

Table S162.  Gene #17: 'RPL5 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
RPL5 MUTATED 2 1 1 0
RPL5 WILD-TYPE 39 37 30 33
'RPL5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.684 (Fisher's exact test), Q value = 1

Table S163.  Gene #17: 'RPL5 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
RPL5 MUTATED 1 1 2
RPL5 WILD-TYPE 47 51 41
'RPL5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.466 (Fisher's exact test), Q value = 1

Table S164.  Gene #17: 'RPL5 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
RPL5 MUTATED 2 1 0
RPL5 WILD-TYPE 42 61 35
'RPL5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S165.  Gene #17: 'RPL5 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
RPL5 MUTATED 1 2 0
RPL5 WILD-TYPE 30 84 24
'PDGFRA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.18

Table S166.  Gene #18: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
PDGFRA MUTATED 1 6 3 1
PDGFRA WILD-TYPE 68 37 71 53

Figure S47.  Get High-res Image Gene #18: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'PDGFRA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.135 (Fisher's exact test), Q value = 0.64

Table S167.  Gene #18: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
PDGFRA MUTATED 1 5 3 2
PDGFRA WILD-TYPE 62 45 45 77
'PDGFRA MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.762 (Fisher's exact test), Q value = 1

Table S168.  Gene #18: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
PDGFRA MUTATED 5 3 2 2
PDGFRA WILD-TYPE 72 90 43 58
'PDGFRA MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.0934 (Fisher's exact test), Q value = 0.53

Table S169.  Gene #18: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
PDGFRA MUTATED 10 1 1
PDGFRA WILD-TYPE 128 60 75
'PDGFRA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.19 (Fisher's exact test), Q value = 0.7

Table S170.  Gene #18: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
PDGFRA MUTATED 2 3 6
PDGFRA WILD-TYPE 81 107 74
'PDGFRA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.732 (Fisher's exact test), Q value = 1

Table S171.  Gene #18: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
PDGFRA MUTATED 1 2 2
PDGFRA WILD-TYPE 42 50 30
'PDGFRA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.769 (Fisher's exact test), Q value = 1

Table S172.  Gene #18: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
PDGFRA MUTATED 3 1 1 1
PDGFRA WILD-TYPE 38 37 30 32
'PDGFRA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.875 (Fisher's exact test), Q value = 1

Table S173.  Gene #18: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
PDGFRA MUTATED 2 3 1
PDGFRA WILD-TYPE 46 49 42
'PDGFRA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0504 (Fisher's exact test), Q value = 0.37

Table S174.  Gene #18: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
PDGFRA MUTATED 5 2 0
PDGFRA WILD-TYPE 39 60 35
'PDGFRA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.1

Table S175.  Gene #18: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
PDGFRA MUTATED 5 2 0
PDGFRA WILD-TYPE 26 84 24

Figure S48.  Get High-res Image Gene #18: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'MMP13 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S176.  Gene #19: 'MMP13 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
MMP13 MUTATED 1 0 2 1
MMP13 WILD-TYPE 68 43 72 53
'MMP13 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.221 (Fisher's exact test), Q value = 0.74

Table S177.  Gene #19: 'MMP13 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
MMP13 MUTATED 1 1 2 0
MMP13 WILD-TYPE 62 49 46 79
'MMP13 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.766 (Fisher's exact test), Q value = 1

Table S178.  Gene #19: 'MMP13 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
MMP13 MUTATED 1 2 0 2
MMP13 WILD-TYPE 76 91 45 58
'MMP13 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.0495 (Fisher's exact test), Q value = 0.37

Table S179.  Gene #19: 'MMP13 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
MMP13 MUTATED 1 0 4
MMP13 WILD-TYPE 137 61 72

Figure S49.  Get High-res Image Gene #19: 'MMP13 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'MMP13 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.151 (Fisher's exact test), Q value = 0.67

Table S180.  Gene #19: 'MMP13 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
MMP13 MUTATED 0 4 1
MMP13 WILD-TYPE 83 106 79
'REN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.476 (Fisher's exact test), Q value = 1

Table S181.  Gene #20: 'REN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
REN MUTATED 0 0 2 1
REN WILD-TYPE 69 43 72 53
'REN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.417 (Fisher's exact test), Q value = 0.96

Table S182.  Gene #20: 'REN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
REN MUTATED 0 0 1 2
REN WILD-TYPE 63 50 47 77
'REN MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.0747 (Fisher's exact test), Q value = 0.47

Table S183.  Gene #20: 'REN MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
REN MUTATED 1 1 3 0
REN WILD-TYPE 76 92 42 60
'REN MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.511 (Fisher's exact test), Q value = 1

Table S184.  Gene #20: 'REN MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
REN MUTATED 4 0 1
REN WILD-TYPE 134 61 75
'REN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.618 (Fisher's exact test), Q value = 1

Table S185.  Gene #20: 'REN MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
REN MUTATED 2 1 2
REN WILD-TYPE 81 109 78
'REN MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S186.  Gene #20: 'REN MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
REN MUTATED 1 1 1 1
REN WILD-TYPE 40 37 30 32
'REN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.837 (Fisher's exact test), Q value = 1

Table S187.  Gene #20: 'REN MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
REN MUTATED 2 1 1
REN WILD-TYPE 46 51 42
'DSP MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.488 (Fisher's exact test), Q value = 1

Table S188.  Gene #21: 'DSP MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
DSP MUTATED 3 0 2 3
DSP WILD-TYPE 66 43 72 51
'DSP MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.963 (Fisher's exact test), Q value = 1

Table S189.  Gene #21: 'DSP MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
DSP MUTATED 2 1 2 3
DSP WILD-TYPE 61 49 46 76
'DSP MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.569 (Fisher's exact test), Q value = 1

Table S190.  Gene #21: 'DSP MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
DSP MUTATED 3 5 3 1
DSP WILD-TYPE 74 88 42 59
'DSP MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.0735 (Fisher's exact test), Q value = 0.47

Table S191.  Gene #21: 'DSP MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
DSP MUTATED 6 0 6
DSP WILD-TYPE 132 61 70
'DSP MUTATION STATUS' versus 'CN_CNMF'

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

Table S192.  Gene #21: 'DSP MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
DSP MUTATED 3 5 4
DSP WILD-TYPE 80 105 76
'DSP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.529 (Fisher's exact test), Q value = 1

Table S193.  Gene #21: 'DSP MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
DSP MUTATED 3 1 1
DSP WILD-TYPE 40 51 31
'DSP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.658 (Fisher's exact test), Q value = 1

Table S194.  Gene #21: 'DSP MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
DSP MUTATED 2 1 1 3
DSP WILD-TYPE 39 37 30 30
'DSP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.705 (Fisher's exact test), Q value = 1

Table S195.  Gene #21: 'DSP MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
DSP MUTATED 3 3 1
DSP WILD-TYPE 45 49 42
'CHD8 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S196.  Gene #22: 'CHD8 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
CHD8 MUTATED 3 2 1 2
CHD8 WILD-TYPE 66 41 73 52
'CHD8 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.532 (Fisher's exact test), Q value = 1

Table S197.  Gene #22: 'CHD8 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
CHD8 MUTATED 2 2 0 4
CHD8 WILD-TYPE 61 48 48 75
'CHD8 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.64

Table S198.  Gene #22: 'CHD8 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
CHD8 MUTATED 0 3 3 2
CHD8 WILD-TYPE 77 90 42 58
'CHD8 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.642 (Fisher's exact test), Q value = 1

Table S199.  Gene #22: 'CHD8 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
CHD8 MUTATED 5 2 1
CHD8 WILD-TYPE 133 59 75
'CHD8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.191 (Fisher's exact test), Q value = 0.7

Table S200.  Gene #22: 'CHD8 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
CHD8 MUTATED 1 3 5
CHD8 WILD-TYPE 82 107 75
'CHD8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.625 (Fisher's exact test), Q value = 1

Table S201.  Gene #22: 'CHD8 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
CHD8 MUTATED 2 4 2 1
CHD8 WILD-TYPE 39 34 29 32
'CHD8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S202.  Gene #22: 'CHD8 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
CHD8 MUTATED 2 4 3
CHD8 WILD-TYPE 46 48 40
'CHD8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.276 (Fisher's exact test), Q value = 0.79

Table S203.  Gene #22: 'CHD8 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
CHD8 MUTATED 2 1 3
CHD8 WILD-TYPE 42 61 32
'CHD8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S204.  Gene #22: 'CHD8 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
CHD8 MUTATED 2 4 0
CHD8 WILD-TYPE 29 82 24
'KDR MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.202 (Fisher's exact test), Q value = 0.71

Table S205.  Gene #23: 'KDR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
KDR MUTATED 1 2 1 4
KDR WILD-TYPE 68 41 73 50
'KDR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.655 (Fisher's exact test), Q value = 1

Table S206.  Gene #23: 'KDR MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
KDR MUTATED 1 3 1 3
KDR WILD-TYPE 62 47 47 76
'KDR MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.282 (Fisher's exact test), Q value = 0.79

Table S207.  Gene #23: 'KDR MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
KDR MUTATED 2 1 3 2
KDR WILD-TYPE 75 92 42 58
'KDR MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.51 (Fisher's exact test), Q value = 1

Table S208.  Gene #23: 'KDR MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
KDR MUTATED 6 1 1
KDR WILD-TYPE 132 60 75
'KDR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.732 (Fisher's exact test), Q value = 1

Table S209.  Gene #23: 'KDR MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
KDR MUTATED 3 2 3
KDR WILD-TYPE 80 108 77
'KDR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.345 (Fisher's exact test), Q value = 0.89

Table S210.  Gene #23: 'KDR MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
KDR MUTATED 2 0 1
KDR WILD-TYPE 41 52 31
'KDR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.145 (Fisher's exact test), Q value = 0.65

Table S211.  Gene #23: 'KDR MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
KDR MUTATED 3 0 0 2
KDR WILD-TYPE 38 38 31 31
'KDR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.527 (Fisher's exact test), Q value = 1

Table S212.  Gene #23: 'KDR MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
KDR MUTATED 3 1 1
KDR WILD-TYPE 45 51 42
'ODF4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.879 (Fisher's exact test), Q value = 1

Table S213.  Gene #24: 'ODF4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
ODF4 MUTATED 1 1 1 0
ODF4 WILD-TYPE 68 42 73 54
'ODF4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.35 (Fisher's exact test), Q value = 0.89

Table S214.  Gene #24: 'ODF4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
ODF4 MUTATED 2 1 0 0
ODF4 WILD-TYPE 61 49 48 79
'ODF4 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S215.  Gene #24: 'ODF4 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
ODF4 MUTATED 1 1 0 1
ODF4 WILD-TYPE 76 92 45 59
'ODF4 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.197 (Fisher's exact test), Q value = 0.7

Table S216.  Gene #24: 'ODF4 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
ODF4 MUTATED 1 2 0
ODF4 WILD-TYPE 137 59 76
'ODF4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.634 (Fisher's exact test), Q value = 1

Table S217.  Gene #24: 'ODF4 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
ODF4 MUTATED 0 2 1
ODF4 WILD-TYPE 83 108 79
'TP63 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S218.  Gene #25: 'TP63 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
TP63 MUTATED 1 1 2 1
TP63 WILD-TYPE 68 42 72 53
'TP63 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.729 (Fisher's exact test), Q value = 1

Table S219.  Gene #25: 'TP63 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
TP63 MUTATED 1 1 2 1
TP63 WILD-TYPE 62 49 46 78
'TP63 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.408 (Fisher's exact test), Q value = 0.96

Table S220.  Gene #25: 'TP63 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
TP63 MUTATED 1 1 1 3
TP63 WILD-TYPE 76 92 44 57
'TP63 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.644 (Fisher's exact test), Q value = 1

Table S221.  Gene #25: 'TP63 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
TP63 MUTATED 2 2 2
TP63 WILD-TYPE 136 59 74
'TP63 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.774 (Fisher's exact test), Q value = 1

Table S222.  Gene #25: 'TP63 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
TP63 MUTATED 1 3 2
TP63 WILD-TYPE 82 107 78
'TP63 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0664 (Fisher's exact test), Q value = 0.44

Table S223.  Gene #25: 'TP63 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
TP63 MUTATED 0 1 0 3
TP63 WILD-TYPE 41 37 31 30
'TP63 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.206 (Fisher's exact test), Q value = 0.72

Table S224.  Gene #25: 'TP63 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
TP63 MUTATED 3 1 0
TP63 WILD-TYPE 45 51 43
'TP63 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.255 (Fisher's exact test), Q value = 0.77

Table S225.  Gene #25: 'TP63 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
TP63 MUTATED 0 1 2
TP63 WILD-TYPE 44 61 33
'TP63 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.109 (Fisher's exact test), Q value = 0.57

Table S226.  Gene #25: 'TP63 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
TP63 MUTATED 0 1 2
TP63 WILD-TYPE 31 85 22
'PRKCD MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.172 (Fisher's exact test), Q value = 0.67

Table S227.  Gene #26: 'PRKCD MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
PRKCD MUTATED 0 2 1 0
PRKCD WILD-TYPE 69 41 73 54
'PRKCD MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0849 (Fisher's exact test), Q value = 0.5

Table S228.  Gene #26: 'PRKCD MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
PRKCD MUTATED 0 2 1 0
PRKCD WILD-TYPE 63 48 47 79
'PRKCD MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.162 (Fisher's exact test), Q value = 0.67

Table S229.  Gene #26: 'PRKCD MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
PRKCD MUTATED 0 3 0 0
PRKCD WILD-TYPE 77 90 45 60
'PRKCD MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S230.  Gene #26: 'PRKCD MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
PRKCD MUTATED 2 0 1
PRKCD WILD-TYPE 136 61 75
'PRKCD MUTATION STATUS' versus 'CN_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 0.92

Table S231.  Gene #26: 'PRKCD MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
PRKCD MUTATED 0 1 2
PRKCD WILD-TYPE 83 109 78
'ACSM2B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.079 (Fisher's exact test), Q value = 0.48

Table S232.  Gene #27: 'ACSM2B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
ACSM2B MUTATED 0 0 1 3
ACSM2B WILD-TYPE 69 43 73 51
'ACSM2B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.272 (Fisher's exact test), Q value = 0.78

Table S233.  Gene #27: 'ACSM2B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
ACSM2B MUTATED 0 2 0 2
ACSM2B WILD-TYPE 63 48 48 77
'ACSM2B MUTATION STATUS' versus 'MIR_CNMF'

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

Table S234.  Gene #27: 'ACSM2B MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
ACSM2B MUTATED 1 3 1 0
ACSM2B WILD-TYPE 76 90 44 60
'ACSM2B MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.237 (Fisher's exact test), Q value = 0.74

Table S235.  Gene #27: 'ACSM2B MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
ACSM2B MUTATED 2 0 3
ACSM2B WILD-TYPE 136 61 73
'ACSM2B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.393 (Fisher's exact test), Q value = 0.93

Table S236.  Gene #27: 'ACSM2B MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
ACSM2B MUTATED 2 3 0
ACSM2B WILD-TYPE 81 107 80
'ACSM2B MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S237.  Gene #27: 'ACSM2B MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
ACSM2B MUTATED 1 2 1
ACSM2B WILD-TYPE 42 50 31
'ACSM2B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.67

Table S238.  Gene #27: 'ACSM2B MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
ACSM2B MUTATED 2 0 1
ACSM2B WILD-TYPE 42 62 34
'ACSM2B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S239.  Gene #27: 'ACSM2B MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
ACSM2B MUTATED 1 2 0
ACSM2B WILD-TYPE 30 84 24
'CLCN7 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.111 (Fisher's exact test), Q value = 0.58

Table S240.  Gene #28: 'CLCN7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
CLCN7 MUTATED 3 1 0 0
CLCN7 WILD-TYPE 66 42 74 54
'CLCN7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.77 (Fisher's exact test), Q value = 1

Table S241.  Gene #28: 'CLCN7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
CLCN7 MUTATED 2 1 0 1
CLCN7 WILD-TYPE 61 49 48 78
'CLCN7 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.697 (Fisher's exact test), Q value = 1

Table S242.  Gene #28: 'CLCN7 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
CLCN7 MUTATED 1 1 0 2
CLCN7 WILD-TYPE 76 92 45 58
'CLCN7 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.259 (Fisher's exact test), Q value = 0.78

Table S243.  Gene #28: 'CLCN7 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
CLCN7 MUTATED 2 2 0
CLCN7 WILD-TYPE 136 59 76
'CLCN7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.235 (Fisher's exact test), Q value = 0.74

Table S244.  Gene #28: 'CLCN7 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
CLCN7 MUTATED 2 0 2
CLCN7 WILD-TYPE 81 110 78
'CLCN7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.168 (Fisher's exact test), Q value = 0.67

Table S245.  Gene #28: 'CLCN7 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
CLCN7 MUTATED 2 0 2
CLCN7 WILD-TYPE 41 52 30
'DDX5 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 0.74

Table S246.  Gene #29: 'DDX5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
DDX5 MUTATED 1 0 0 2
DDX5 WILD-TYPE 68 43 74 52
'DDX5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S247.  Gene #29: 'DDX5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
DDX5 MUTATED 1 1 0 1
DDX5 WILD-TYPE 62 49 48 78
'DDX5 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.538 (Fisher's exact test), Q value = 1

Table S248.  Gene #29: 'DDX5 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
DDX5 MUTATED 0 2 1 1
DDX5 WILD-TYPE 77 91 44 59
'DDX5 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.444 (Fisher's exact test), Q value = 1

Table S249.  Gene #29: 'DDX5 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
DDX5 MUTATED 1 1 2
DDX5 WILD-TYPE 137 60 74
'DDX5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.144 (Fisher's exact test), Q value = 0.65

Table S250.  Gene #29: 'DDX5 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
DDX5 MUTATED 0 1 3
DDX5 WILD-TYPE 83 109 77
'FBN3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.189 (Fisher's exact test), Q value = 0.7

Table S251.  Gene #30: 'FBN3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
FBN3 MUTATED 1 1 6 1
FBN3 WILD-TYPE 68 42 68 53
'FBN3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.306 (Fisher's exact test), Q value = 0.84

Table S252.  Gene #30: 'FBN3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
FBN3 MUTATED 1 2 4 2
FBN3 WILD-TYPE 62 48 44 77
'FBN3 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.904 (Fisher's exact test), Q value = 1

Table S253.  Gene #30: 'FBN3 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
FBN3 MUTATED 4 3 2 2
FBN3 WILD-TYPE 73 90 43 58
'FBN3 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S254.  Gene #30: 'FBN3 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
FBN3 MUTATED 5 3 3
FBN3 WILD-TYPE 133 58 73
'FBN3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 0.57

Table S255.  Gene #30: 'FBN3 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
FBN3 MUTATED 2 8 1
FBN3 WILD-TYPE 81 102 79
'FBN3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S256.  Gene #30: 'FBN3 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
FBN3 MUTATED 2 3 1
FBN3 WILD-TYPE 41 49 31
'FBN3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.279 (Fisher's exact test), Q value = 0.79

Table S257.  Gene #30: 'FBN3 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
FBN3 MUTATED 0 3 1 2
FBN3 WILD-TYPE 41 35 30 31
'FBN3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.375 (Fisher's exact test), Q value = 0.92

Table S258.  Gene #30: 'FBN3 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
FBN3 MUTATED 1 4 1
FBN3 WILD-TYPE 47 48 42
'FBN3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.854 (Fisher's exact test), Q value = 1

Table S259.  Gene #30: 'FBN3 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
FBN3 MUTATED 1 3 1
FBN3 WILD-TYPE 43 59 34
'FBN3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S260.  Gene #30: 'FBN3 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
FBN3 MUTATED 1 3 1
FBN3 WILD-TYPE 30 83 23
'CD1D MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.879 (Fisher's exact test), Q value = 1

Table S261.  Gene #31: 'CD1D MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
CD1D MUTATED 1 1 1 0
CD1D WILD-TYPE 68 42 73 54
'CD1D MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S262.  Gene #31: 'CD1D MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
CD1D MUTATED 1 1 0 1
CD1D WILD-TYPE 62 49 48 78
'CD1D MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.645 (Fisher's exact test), Q value = 1

Table S263.  Gene #31: 'CD1D MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
CD1D MUTATED 2 2 0 0
CD1D WILD-TYPE 75 91 45 60
'CD1D MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.124 (Fisher's exact test), Q value = 0.61

Table S264.  Gene #31: 'CD1D MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
CD1D MUTATED 1 0 3
CD1D WILD-TYPE 137 61 73
'CD1D MUTATION STATUS' versus 'CN_CNMF'

P value = 0.825 (Fisher's exact test), Q value = 1

Table S265.  Gene #31: 'CD1D MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
CD1D MUTATED 2 1 1
CD1D WILD-TYPE 81 109 79
'CD1D MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.893 (Fisher's exact test), Q value = 1

Table S266.  Gene #31: 'CD1D MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
CD1D MUTATED 1 1 1 0
CD1D WILD-TYPE 40 37 30 33
'CD1D MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S267.  Gene #31: 'CD1D MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
CD1D MUTATED 1 1 1
CD1D WILD-TYPE 47 51 42
'TEX15 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.31 (Fisher's exact test), Q value = 0.84

Table S268.  Gene #32: 'TEX15 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
TEX15 MUTATED 2 1 1 4
TEX15 WILD-TYPE 67 42 73 50
'TEX15 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.242 (Fisher's exact test), Q value = 0.75

Table S269.  Gene #32: 'TEX15 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
TEX15 MUTATED 1 2 0 5
TEX15 WILD-TYPE 62 48 48 74
'TEX15 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.3 (Fisher's exact test), Q value = 0.83

Table S270.  Gene #32: 'TEX15 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
TEX15 MUTATED 1 5 0 2
TEX15 WILD-TYPE 76 88 45 58
'TEX15 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S271.  Gene #32: 'TEX15 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
TEX15 MUTATED 3 2 3
TEX15 WILD-TYPE 135 59 73
'TEX15 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.551 (Fisher's exact test), Q value = 1

Table S272.  Gene #32: 'TEX15 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
TEX15 MUTATED 4 2 2
TEX15 WILD-TYPE 79 108 78
'TEX15 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.824 (Fisher's exact test), Q value = 1

Table S273.  Gene #32: 'TEX15 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
TEX15 MUTATED 2 1 1
TEX15 WILD-TYPE 41 51 31
'TEX15 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.869 (Fisher's exact test), Q value = 1

Table S274.  Gene #32: 'TEX15 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
TEX15 MUTATED 1 1 1 2
TEX15 WILD-TYPE 40 37 30 31
'TEX15 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.272 (Fisher's exact test), Q value = 0.78

Table S275.  Gene #32: 'TEX15 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
TEX15 MUTATED 0 3 2
TEX15 WILD-TYPE 48 49 41
'TEX15 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00294 (Fisher's exact test), Q value = 0.041

Table S276.  Gene #32: 'TEX15 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
TEX15 MUTATED 5 0 0
TEX15 WILD-TYPE 39 62 35

Figure S50.  Get High-res Image Gene #32: 'TEX15 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'TEX15 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.824 (Fisher's exact test), Q value = 1

Table S277.  Gene #32: 'TEX15 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
TEX15 MUTATED 1 4 0
TEX15 WILD-TYPE 30 82 24
'KEL MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.545 (Fisher's exact test), Q value = 1

Table S278.  Gene #33: 'KEL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
KEL MUTATED 3 3 7 2
KEL WILD-TYPE 66 40 67 52
'KEL MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.213 (Fisher's exact test), Q value = 0.74

Table S279.  Gene #33: 'KEL MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
KEL MUTATED 3 1 6 5
KEL WILD-TYPE 60 49 42 74
'KEL MUTATION STATUS' versus 'MIR_CNMF'

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

Table S280.  Gene #33: 'KEL MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
KEL MUTATED 3 5 2 5
KEL WILD-TYPE 74 88 43 55
'KEL MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.888 (Fisher's exact test), Q value = 1

Table S281.  Gene #33: 'KEL MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
KEL MUTATED 7 3 5
KEL WILD-TYPE 131 58 71
'KEL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0911 (Fisher's exact test), Q value = 0.52

Table S282.  Gene #33: 'KEL MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
KEL MUTATED 7 7 1
KEL WILD-TYPE 76 103 79
'KEL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.168 (Fisher's exact test), Q value = 0.67

Table S283.  Gene #33: 'KEL MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
KEL MUTATED 0 4 1
KEL WILD-TYPE 43 48 31
'KEL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.377 (Fisher's exact test), Q value = 0.92

Table S284.  Gene #33: 'KEL MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
KEL MUTATED 2 1 3 4
KEL WILD-TYPE 39 37 28 29
'KEL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.919 (Fisher's exact test), Q value = 1

Table S285.  Gene #33: 'KEL MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
KEL MUTATED 4 3 3
KEL WILD-TYPE 44 49 40
'KEL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.41 (Fisher's exact test), Q value = 0.96

Table S286.  Gene #33: 'KEL MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
KEL MUTATED 5 3 2
KEL WILD-TYPE 39 59 33
'KEL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.651 (Fisher's exact test), Q value = 1

Table S287.  Gene #33: 'KEL MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
KEL MUTATED 3 5 2
KEL WILD-TYPE 28 81 22
'MUC17 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.11

Table S288.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
MUC17 MUTATED 10 5 1 3
MUC17 WILD-TYPE 59 38 73 51

Figure S51.  Get High-res Image Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'MUC17 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.192 (Fisher's exact test), Q value = 0.7

Table S289.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
MUC17 MUTATED 8 1 3 7
MUC17 WILD-TYPE 55 49 45 72
'MUC17 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S290.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
MUC17 MUTATED 5 7 3 7
MUC17 WILD-TYPE 72 86 42 53
'MUC17 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S291.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
MUC17 MUTATED 10 4 8
MUC17 WILD-TYPE 128 57 68
'MUC17 MUTATION STATUS' versus 'CN_CNMF'

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

Table S292.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
MUC17 MUTATED 7 8 7
MUC17 WILD-TYPE 76 102 73
'MUC17 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.841 (Fisher's exact test), Q value = 1

Table S293.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
MUC17 MUTATED 3 5 2
MUC17 WILD-TYPE 40 47 30
'MUC17 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.244 (Fisher's exact test), Q value = 0.75

Table S294.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
MUC17 MUTATED 5 1 1 4
MUC17 WILD-TYPE 36 37 30 29
'MUC17 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.326 (Fisher's exact test), Q value = 0.86

Table S295.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
MUC17 MUTATED 6 3 2
MUC17 WILD-TYPE 42 49 41
'MUC17 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S296.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
MUC17 MUTATED 4 6 2
MUC17 WILD-TYPE 40 56 33
'MUC17 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S297.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
MUC17 MUTATED 2 8 2
MUC17 WILD-TYPE 29 78 22
'SLC6A14 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.88 (Fisher's exact test), Q value = 1

Table S298.  Gene #35: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
SLC6A14 MUTATED 1 1 1 0
SLC6A14 WILD-TYPE 68 42 73 54
'SLC6A14 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S299.  Gene #35: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
SLC6A14 MUTATED 1 1 1 0
SLC6A14 WILD-TYPE 62 49 47 79
'SLC6A14 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.832 (Fisher's exact test), Q value = 1

Table S300.  Gene #35: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
SLC6A14 MUTATED 2 1 0 1
SLC6A14 WILD-TYPE 75 92 45 59
'SLC6A14 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S301.  Gene #35: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
SLC6A14 MUTATED 2 1 1
SLC6A14 WILD-TYPE 136 60 75
'SLC6A14 MUTATION STATUS' versus 'CN_CNMF'

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

Table S302.  Gene #35: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
SLC6A14 MUTATED 2 1 1
SLC6A14 WILD-TYPE 81 109 79
'SLC6A14 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.231 (Fisher's exact test), Q value = 0.74

Table S303.  Gene #35: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
SLC6A14 MUTATED 3 1 0
SLC6A14 WILD-TYPE 40 51 32
'SLC6A14 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.294 (Fisher's exact test), Q value = 0.82

Table S304.  Gene #35: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
SLC6A14 MUTATED 1 0 0 2
SLC6A14 WILD-TYPE 40 38 31 31
'SLC6A14 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S305.  Gene #35: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
SLC6A14 MUTATED 2 1 0
SLC6A14 WILD-TYPE 46 51 43
'LRRC55 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.374 (Fisher's exact test), Q value = 0.92

Table S306.  Gene #36: 'LRRC55 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
LRRC55 MUTATED 0 1 3 1
LRRC55 WILD-TYPE 69 42 71 53
'LRRC55 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S307.  Gene #36: 'LRRC55 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
LRRC55 MUTATED 0 1 1 3
LRRC55 WILD-TYPE 63 49 47 76
'LRRC55 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.334 (Fisher's exact test), Q value = 0.87

Table S308.  Gene #36: 'LRRC55 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
LRRC55 MUTATED 3 3 0 0
LRRC55 WILD-TYPE 74 90 45 60
'LRRC55 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S309.  Gene #36: 'LRRC55 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
LRRC55 MUTATED 4 1 1
LRRC55 WILD-TYPE 134 60 75
'LRRC55 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.326 (Fisher's exact test), Q value = 0.86

Table S310.  Gene #36: 'LRRC55 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
LRRC55 MUTATED 3 3 0
LRRC55 WILD-TYPE 80 107 80
'CD209 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.912 (Fisher's exact test), Q value = 1

Table S311.  Gene #37: 'CD209 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
CD209 MUTATED 1 0 2 1
CD209 WILD-TYPE 68 43 72 53
'CD209 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S312.  Gene #37: 'CD209 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
CD209 MUTATED 1 1 1 1
CD209 WILD-TYPE 62 49 47 78
'CD209 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.0655 (Fisher's exact test), Q value = 0.44

Table S313.  Gene #37: 'CD209 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
CD209 MUTATED 2 0 0 3
CD209 WILD-TYPE 75 93 45 57
'CD209 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.608 (Fisher's exact test), Q value = 1

Table S314.  Gene #37: 'CD209 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
CD209 MUTATED 3 0 2
CD209 WILD-TYPE 135 61 74
'CD209 MUTATION STATUS' versus 'CN_CNMF'

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

Table S315.  Gene #37: 'CD209 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
CD209 MUTATED 1 1 2
CD209 WILD-TYPE 82 109 78
'CD209 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.491 (Fisher's exact test), Q value = 1

Table S316.  Gene #37: 'CD209 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
CD209 MUTATED 1 0 1 2
CD209 WILD-TYPE 40 38 30 31
'CD209 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S317.  Gene #37: 'CD209 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
CD209 MUTATED 1 2 1
CD209 WILD-TYPE 47 50 42
'LZTR1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S318.  Gene #38: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
LZTR1 MUTATED 2 1 2 2
LZTR1 WILD-TYPE 67 42 72 52
'LZTR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S319.  Gene #38: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
LZTR1 MUTATED 3 2 0 2
LZTR1 WILD-TYPE 60 48 48 77
'LZTR1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.355 (Fisher's exact test), Q value = 0.9

Table S320.  Gene #38: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
LZTR1 MUTATED 5 3 0 3
LZTR1 WILD-TYPE 72 90 45 57
'LZTR1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S321.  Gene #38: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
LZTR1 MUTATED 4 4 3
LZTR1 WILD-TYPE 134 57 73
'LZTR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.788 (Fisher's exact test), Q value = 1

Table S322.  Gene #38: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
LZTR1 MUTATED 4 4 2
LZTR1 WILD-TYPE 79 106 78
'LZTR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.124 (Fisher's exact test), Q value = 0.61

Table S323.  Gene #38: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
LZTR1 MUTATED 3 0 1
LZTR1 WILD-TYPE 40 52 31
'LZTR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.66 (Fisher's exact test), Q value = 1

Table S324.  Gene #38: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
LZTR1 MUTATED 1 2 2 3
LZTR1 WILD-TYPE 40 36 29 30
'LZTR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S325.  Gene #38: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 52 43
LZTR1 MUTATED 3 2 3
LZTR1 WILD-TYPE 45 50 40
'LZTR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.67

Table S326.  Gene #38: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
LZTR1 MUTATED 2 0 1
LZTR1 WILD-TYPE 42 62 34
'LZTR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S327.  Gene #38: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
LZTR1 MUTATED 0 3 0
LZTR1 WILD-TYPE 31 83 24
Methods & Data
Input

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/GBM-TP/15658344/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/GBM-TP/15125141/GBM-TP.transferedmergedcluster.txt

  • Number of patients = 283

  • Number of significantly mutated genes = 38

  • Number of Molecular subtypes = 10

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

Fisher's exact test

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

Q value calculation

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

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