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 36 genes and 10 molecular subtypes across 283 patients, 44 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_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

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

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

  • PTEN mutation correlated to 'METHLYATION_CNMF'.

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

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

  • BRAF mutation correlated to 'MIR_CHIERARCHICAL'.

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

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

  • FBN3 mutation correlated to 'RPPA_CNMF'.

  • IL18RAP mutation correlated to 'MIR_CNMF'.

  • FAM126B mutation correlated to 'MRNA_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 36 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, 44 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 0.00022
(0.00609) 		1e-05
(0.000514) 		8e-05
(0.0024) 		0.00289
(0.0452) 		1e-05
(0.000514) 		3e-05
(0.00135) 		0.268
(0.813) 		0.00681
(0.0838) 		0.00099
(0.0178) 		1e-05
(0.000514)
ATRX 16 (6%) 267 0.00358
(0.0516) 		1e-05
(0.000514) 		0.0162
(0.167) 		0.0184
(0.18) 		1e-05
(0.000514) 		6e-05
(0.00196) 		0.554
(1.00) 		0.0135
(0.143) 		0.00255
(0.0417) 		0.00024
(0.00617)
TP53 80 (28%) 203 0.00075
(0.015) 		1e-05
(0.000514) 		0.0008
(0.0152) 		0.202
(0.769) 		0.00033
(0.00792) 		5e-05
(0.0018) 		0.00698
(0.0838) 		0.0475
(0.356) 		0.00124
(0.0213) 		0.00065
(0.0138)
EGFR 74 (26%) 209 0.0861
(0.477) 		0.0578
(0.4) 		0.278
(0.813) 		0.139
(0.654) 		4e-05
(0.0016) 		0.00355
(0.0516) 		0.256
(0.798) 		1e-05
(0.000514) 		0.0239
(0.215) 		0.00606
(0.0808)
NF1 29 (10%) 254 0.102
(0.523) 		0.00039
(0.00877) 		0.0332
(0.266) 		0.931
(1.00) 		0.00762
(0.0885) 		0.0593
(0.403) 		0.0529
(0.381) 		0.0121
(0.132) 		0.482
(0.993) 		0.45
(0.982)
PDGFRA 11 (4%) 272 0.00977
(0.11) 		0.148
(0.683) 		1
(1.00) 		0.14
(0.654) 		0.496
(0.998) 		0.214
(0.777) 		0.3
(0.849) 		0.732
(1.00) 		0.0269
(0.234) 		0.00491
(0.068)
RB1 24 (8%) 259 0.0841
(0.477) 		0.0177
(0.177) 		0.105
(0.524) 		0.922
(1.00) 		0.19
(0.762) 		0.0195
(0.182) 		0.816
(1.00) 		0.54
(1.00) 		0.0781
(0.461) 		0.577
(1.00)
PTEN 87 (31%) 196 0.151
(0.687) 		0.0753
(0.452) 		0.0447
(0.342) 		0.644
(1.00) 		0.1
(0.523) 		0.0273
(0.234) 		0.247
(0.78) 		0.382
(0.922) 		0.421
(0.953) 		0.646
(1.00)
BRAF 6 (2%) 277 0.598
(1.00) 		0.712
(1.00) 		0.317
(0.857) 		0.0285
(0.234) 		0.0967
(0.512) 		1
(1.00) 		0.78
(1.00) 		0.794
(1.00) 		1
(1.00)
FBN3 11 (4%) 272 0.348
(0.889) 		0.308
(0.854) 		1
(1.00) 		0.921
(1.00) 		0.088
(0.48) 		1
(1.00) 		0.0197
(0.182) 		0.664
(1.00) 		0.854
(1.00) 		1
(1.00)
IL18RAP 7 (2%) 276 0.072
(0.452) 		0.226
(0.777) 		0.0066
(0.0838) 		0.175
(0.738) 		0.485
(0.993) 		1
(1.00) 		0.366
(0.908) 		0.614
(1.00) 		0.685
(1.00) 		0.338
(0.875)
FAM126B 4 (1%) 279 0.24
(0.777) 		0.028
(0.234) 		0.587
(1.00) 		0.444
(0.982) 		0.55
(1.00) 		0.683
(1.00) 		1
(1.00) 		0.63
(1.00)
PIK3R1 32 (11%) 251 0.415
(0.951) 		0.191
(0.762) 		0.0618
(0.412) 		0.531
(1.00) 		0.0745
(0.452) 		0.417
(0.951) 		0.215
(0.777) 		0.0571
(0.4) 		0.469
(0.993) 		0.22
(0.777)
PIK3CA 27 (10%) 256 0.921
(1.00) 		0.288
(0.837) 		0.274
(0.813) 		0.861
(1.00) 		0.744
(1.00) 		0.381
(0.922) 		0.811
(1.00) 		0.405
(0.946) 		0.485
(0.993) 		0.232
(0.777)
STAG2 12 (4%) 271 0.492
(0.995) 		0.7
(1.00) 		0.527
(1.00) 		0.593
(1.00) 		0.488
(0.993) 		0.155
(0.691) 		0.277
(0.813) 		0.335
(0.875) 		0.427
(0.961) 		0.104
(0.524)
SLC26A3 7 (2%) 276 0.847
(1.00) 		0.767
(1.00) 		0.58
(1.00) 		0.365
(0.908) 		0.703
(1.00) 		0.235
(0.777) 		0.485
(0.993) 		0.31
(0.854) 		0.112
(0.547) 		0.164
(0.721)
SEMG1 8 (3%) 275 0.957
(1.00) 		0.176
(0.738) 		0.958
(1.00) 		1
(1.00) 		0.34
(0.875) 		0.271
(0.813) 		1
(1.00) 		0.337
(0.875)
KDR 8 (3%) 275 0.219
(0.777) 		0.655
(1.00) 		0.245
(0.779) 		0.512
(1.00) 		0.375
(0.918) 		0.34
(0.875) 		0.155
(0.691) 		0.737
(1.00)
RPL5 7 (2%) 276 0.399
(0.939) 		0.51
(1.00) 		0.907
(1.00) 		0.469
(0.993) 		0.797
(1.00) 		0.552
(1.00) 		0.69
(1.00) 		0.462
(0.993) 		1
(1.00)
MAP3K1 6 (2%) 277 0.93
(1.00) 		0.73
(1.00) 		0.76
(1.00) 		0.646
(1.00) 		0.654
(1.00) 		0.564
(1.00) 		1
(1.00)
TMPRSS6 6 (2%) 277 0.731
(1.00) 		0.703
(1.00) 		0.726
(1.00) 		0.263
(0.81) 		0.583
(1.00) 		1
(1.00) 		0.905
(1.00) 		0.469
(0.993) 		0.572
(1.00) 		1
(1.00)
PRKCD 3 (1%) 280 0.0817
(0.474) 		0.0851
(0.477) 		0.235
(0.777) 		1
(1.00) 		0.617
(1.00)
TP63 6 (2%) 277 0.93
(1.00) 		0.728
(1.00) 		0.316
(0.857) 		0.648
(1.00) 		0.763
(1.00) 		0.037
(0.29) 		0.388
(0.925) 		0.239
(0.777) 		0.109
(0.536)
CHD8 9 (3%) 274 0.775
(1.00) 		0.532
(1.00) 		0.172
(0.738) 		0.646
(1.00) 		0.233
(0.777) 		0.311
(0.854) 		0.915
(1.00) 		0.269
(0.813) 		0.612
(1.00)
IL4R 8 (3%) 275 0.846
(1.00) 		0.388
(0.925) 		0.744
(1.00) 		0.805
(1.00) 		0.53
(1.00) 		0.447
(0.982) 		0.227
(0.777) 		0.886
(1.00) 		0.45
(0.982) 		0.8
(1.00)
REN 5 (2%) 278 0.302
(0.849) 		0.414
(0.951) 		0.069
(0.444) 		0.513
(1.00) 		0.742
(1.00) 		0.553
(1.00) 		1
(1.00)
CD209 5 (2%) 278 0.832
(1.00) 		1
(1.00) 		0.328
(0.875) 		0.609
(1.00) 		0.838
(1.00) 		0.904
(1.00) 		1
(1.00)
MMP13 5 (2%) 278 0.832
(1.00) 		0.22
(0.777) 		0.762
(1.00) 		0.0493
(0.362) 		0.204
(0.769)
TCF12 4 (1%) 279 1
(1.00) 		0.481
(0.993) 		0.587
(1.00) 		0.257
(0.798) 		1
(1.00) 		0.0748
(0.452) 		1
(1.00)
LZTR1 10 (4%) 273 0.804
(1.00) 		0.516
(1.00) 		0.467
(0.993) 		0.702
(1.00) 		0.372
(0.917) 		0.336
(0.875) 		0.2
(0.769) 		0.563
(1.00) 		0.168
(0.728) 		0.751
(1.00)
ZDHHC4 3 (1%) 280 0.236
(0.777) 		1
(1.00) 		0.183
(0.754)
ODF4 3 (1%) 280 0.876
(1.00) 		0.35
(0.889) 		1
(1.00) 		0.195
(0.764) 		0.794
(1.00)
KEL 15 (5%) 268 0.293
(0.842) 		0.209
(0.777) 		0.835
(1.00) 		0.886
(1.00) 		0.115
(0.55) 		0.184
(0.754) 		0.675
(1.00) 		0.597
(1.00) 		0.485
(0.993) 		0.649
(1.00)
TESK1 3 (1%) 280 0.205
(0.769) 		0.698
(1.00) 		0.392
(0.929) 		0.602
(1.00) 		0.244
(0.779)
MUC17 22 (8%) 261 0.0629
(0.412) 		0.193
(0.762) 		0.802
(1.00) 		0.703
(1.00) 		0.296
(0.846) 		1
(1.00) 		0.553
(1.00) 		0.0909
(0.488) 		0.927
(1.00) 		1
(1.00)
DDX5 4 (1%) 279 0.411
(0.951) 		1
(1.00) 		0.646
(1.00) 		0.447
(0.982) 		0.361
(0.908)
'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00075 (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 78 41 64 57
TP53 MUTATED 17 18 10 24
TP53 WILD-TYPE 61 23 54 33

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 = 0.00051

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 16 30 7 16
TP53 WILD-TYPE 47 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 = 8e-04 (Fisher's exact test), Q value = 0.015

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
TP53 MUTATED 10 41 10 19
TP53 WILD-TYPE 60 57 34 44

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 = 0.202 (Fisher's exact test), Q value = 0.77

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 18
TP53 WILD-TYPE 91 46 58
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0079

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
TP53 MUTATED 36 37 6
TP53 WILD-TYPE 68 70 56

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 = 5e-05 (Fisher's exact test), Q value = 0.0018

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 19 42 33
TP53 MUTATED 8 2 10 21
TP53 WILD-TYPE 25 17 32 12

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 = 0.00698 (Fisher's exact test), Q value = 0.084

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
TP53 MUTATED 8 11 9 11 4
TP53 WILD-TYPE 23 24 15 8 31

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 = 0.0475 (Fisher's exact test), Q value = 0.36

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
TP53 MUTATED 18 18 7
TP53 WILD-TYPE 40 26 35

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 = 0.00124 (Fisher's exact test), Q value = 0.021

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
TP53 MUTATED 24 14 7
TP53 WILD-TYPE 21 49 26

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 = 0.00065 (Fisher's exact test), Q value = 0.014

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 19 21 5
TP53 WILD-TYPE 12 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 = 0.415 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
PIK3R1 MUTATED 8 1 7 6
PIK3R1 WILD-TYPE 70 40 57 51
'PIK3R1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.191 (Fisher's exact test), Q value = 0.76

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 = 0.0618 (Fisher's exact test), Q value = 0.41

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
PIK3R1 MUTATED 13 13 3 3
PIK3R1 WILD-TYPE 57 85 41 60
'PIK3R1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.531 (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 = 0.0745 (Fisher's exact test), Q value = 0.45

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
PIK3R1 MUTATED 13 7 11
PIK3R1 WILD-TYPE 91 100 51
'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.417 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 19 42 33
PIK3R1 MUTATED 1 2 4 5
PIK3R1 WILD-TYPE 32 17 38 28
'PIK3R1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.215 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
PIK3R1 MUTATED 9 4 3 1 5
PIK3R1 WILD-TYPE 22 31 21 18 30
'PIK3R1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0571 (Fisher's exact test), Q value = 0.4

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
PIK3R1 MUTATED 14 5 3
PIK3R1 WILD-TYPE 44 39 39
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.469 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
PIK3R1 MUTATED 5 6 1
PIK3R1 WILD-TYPE 40 57 32
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.22 (Fisher's exact test), Q value = 0.78

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 = 0.0841 (Fisher's exact test), Q value = 0.48

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
RB1 MUTATED 11 1 3 3
RB1 WILD-TYPE 67 40 61 54
'RB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0177 (Fisher's exact test), Q value = 0.18

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 S10.  Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.105 (Fisher's exact test), Q value = 0.52

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
RB1 MUTATED 10 4 3 7
RB1 WILD-TYPE 60 94 41 56
'RB1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.922 (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 = 0.19 (Fisher's exact test), Q value = 0.76

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
RB1 MUTATED 10 12 2
RB1 WILD-TYPE 94 95 60
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.18

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 19 42 33
RB1 MUTATED 8 1 2 1
RB1 WILD-TYPE 25 18 40 32

Figure S11.  Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.816 (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 CLUS_5
ALL 31 35 24 19 35
RB1 MUTATED 4 2 1 1 2
RB1 WILD-TYPE 27 33 23 18 33
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.54 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
RB1 MUTATED 6 2 2
RB1 WILD-TYPE 52 42 40
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0781 (Fisher's exact test), Q value = 0.46

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
RB1 MUTATED 1 8 1
RB1 WILD-TYPE 44 55 32
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.577 (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
'NF1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.52

Table S31.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
NF1 MUTATED 12 3 4 2
NF1 WILD-TYPE 66 38 60 55
'NF1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0088

Table S32.  Gene #4: '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 S12.  Get High-res Image Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.0332 (Fisher's exact test), Q value = 0.27

Table S33.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
NF1 MUTATED 12 4 4 8
NF1 WILD-TYPE 58 94 40 55

Figure S13.  Get High-res Image Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'NF1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S34.  Gene #4: '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 = 0.00762 (Fisher's exact test), Q value = 0.088

Table S35.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
NF1 MUTATED 19 6 4
NF1 WILD-TYPE 85 101 58

Figure S14.  Get High-res Image Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0593 (Fisher's exact test), Q value = 0.4

Table S36.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 19 42 33
NF1 MUTATED 7 2 1 3
NF1 WILD-TYPE 26 17 41 30
'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0529 (Fisher's exact test), Q value = 0.38

Table S37.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
NF1 MUTATED 8 3 3 1 1
NF1 WILD-TYPE 23 32 21 18 34
'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.13

Table S38.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
NF1 MUTATED 12 3 1
NF1 WILD-TYPE 46 41 41

Figure S15.  Get High-res Image Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.482 (Fisher's exact test), Q value = 0.99

Table S39.  Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
NF1 MUTATED 2 5 4
NF1 WILD-TYPE 43 58 29
'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.45 (Fisher's exact test), Q value = 0.98

Table S40.  Gene #4: '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
'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.151 (Fisher's exact test), Q value = 0.69

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
PTEN MUTATED 27 9 16 23
PTEN WILD-TYPE 51 32 48 34
'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0753 (Fisher's exact test), Q value = 0.45

Table S42.  Gene #5: '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 = 0.0447 (Fisher's exact test), Q value = 0.34

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
PTEN MUTATED 26 21 18 22
PTEN WILD-TYPE 44 77 26 41

Figure S16.  Get High-res Image Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'PTEN MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S44.  Gene #5: '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 = 0.1 (Fisher's exact test), Q value = 0.52

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
PTEN MUTATED 38 34 13
PTEN WILD-TYPE 66 73 49
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.23

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 19 42 33
PTEN MUTATED 15 2 10 13
PTEN WILD-TYPE 18 17 32 20

Figure S17.  Get High-res Image Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.247 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
PTEN MUTATED 12 8 11 6 8
PTEN WILD-TYPE 19 27 13 13 27
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.382 (Fisher's exact test), Q value = 0.92

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
PTEN MUTATED 22 12 11
PTEN WILD-TYPE 36 32 31
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.421 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
PTEN MUTATED 11 23 11
PTEN WILD-TYPE 34 40 22
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.646 (Fisher's exact test), Q value = 1

Table S50.  Gene #5: '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
'IDH1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0061

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
IDH1 MUTATED 1 3 0 9
IDH1 WILD-TYPE 77 38 64 48

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 = 0.00051

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 = 8e-05 (Fisher's exact test), Q value = 0.0024

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
IDH1 MUTATED 0 13 1 0
IDH1 WILD-TYPE 70 85 43 63

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 = 0.00289 (Fisher's exact test), Q value = 0.045

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 = 1e-05 (Fisher's exact test), Q value = 0.00051

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
IDH1 MUTATED 13 0 0
IDH1 WILD-TYPE 91 107 62

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 = 3e-05 (Fisher's exact test), Q value = 0.0013

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 19 42 33
IDH1 MUTATED 0 0 0 9
IDH1 WILD-TYPE 33 19 42 24

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 = 0.268 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
IDH1 MUTATED 0 2 3 1 1
IDH1 WILD-TYPE 31 33 21 18 34
'IDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00681 (Fisher's exact test), Q value = 0.084

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
IDH1 MUTATED 1 6 0
IDH1 WILD-TYPE 57 38 42

Figure S24.  Get High-res Image Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.018

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
IDH1 MUTATED 7 0 1
IDH1 WILD-TYPE 38 63 32

Figure S25.  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 = 0.00051

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 S26.  Get High-res Image Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.921 (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 78 41 64 57
PIK3CA MUTATED 7 5 7 5
PIK3CA WILD-TYPE 71 36 57 52
'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.288 (Fisher's exact test), Q value = 0.84

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 6 4
PIK3CA WILD-TYPE 55 44 42 75
'PIK3CA MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.274 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
PIK3CA MUTATED 9 10 1 6
PIK3CA WILD-TYPE 61 88 43 57
'PIK3CA MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.861 (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 12 6 8
PIK3CA WILD-TYPE 126 55 68
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.744 (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 104 107 62
PIK3CA MUTATED 11 8 6
PIK3CA WILD-TYPE 93 99 56
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 0.92

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 19 42 33
PIK3CA MUTATED 5 0 4 3
PIK3CA WILD-TYPE 28 19 38 30
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.811 (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 CLUS_5
ALL 31 35 24 19 35
PIK3CA MUTATED 2 3 3 3 3
PIK3CA WILD-TYPE 29 32 21 16 32
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.405 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
PIK3CA MUTATED 6 6 2
PIK3CA WILD-TYPE 52 38 40
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.485 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
PIK3CA MUTATED 5 3 2
PIK3CA WILD-TYPE 40 60 31
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.232 (Fisher's exact test), Q value = 0.78

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 6 0
PIK3CA WILD-TYPE 27 80 24
'STAG2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.492 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
STAG2 MUTATED 4 3 1 2
STAG2 WILD-TYPE 74 38 63 55
'STAG2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.7 (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 = 0.527 (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 70 98 44 63
STAG2 MUTATED 4 6 1 1
STAG2 WILD-TYPE 66 92 43 62
'STAG2 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.593 (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 = 0.488 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
STAG2 MUTATED 5 3 4
STAG2 WILD-TYPE 99 104 58
'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.155 (Fisher's exact test), Q value = 0.69

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 19 42 33
STAG2 MUTATED 3 1 0 1
STAG2 WILD-TYPE 30 18 42 32
'STAG2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.277 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
STAG2 MUTATED 3 0 2 1 1
STAG2 WILD-TYPE 28 35 22 18 34
'STAG2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.335 (Fisher's exact test), Q value = 0.88

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
STAG2 MUTATED 5 1 1
STAG2 WILD-TYPE 53 43 41
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.427 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
STAG2 MUTATED 1 3 3
STAG2 WILD-TYPE 44 60 30
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.104 (Fisher's exact test), Q value = 0.52

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
'SLC26A3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.847 (Fisher's exact test), Q value = 1

Table S81.  Gene #9: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
SLC26A3 MUTATED 1 1 2 2
SLC26A3 WILD-TYPE 77 40 62 55
'SLC26A3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S82.  Gene #9: '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 = 0.58 (Fisher's exact test), Q value = 1

Table S83.  Gene #9: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
SLC26A3 MUTATED 1 4 0 2
SLC26A3 WILD-TYPE 69 94 44 61
'SLC26A3 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.365 (Fisher's exact test), Q value = 0.91

Table S84.  Gene #9: '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 = 0.703 (Fisher's exact test), Q value = 1

Table S85.  Gene #9: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
SLC26A3 MUTATED 2 4 1
SLC26A3 WILD-TYPE 102 103 61
'SLC26A3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.235 (Fisher's exact test), Q value = 0.78

Table S86.  Gene #9: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 19 42 33
SLC26A3 MUTATED 0 1 2 0
SLC26A3 WILD-TYPE 33 18 40 33
'SLC26A3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.485 (Fisher's exact test), Q value = 0.99

Table S87.  Gene #9: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
SLC26A3 MUTATED 1 2 0 1 0
SLC26A3 WILD-TYPE 30 33 24 18 35
'SLC26A3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.31 (Fisher's exact test), Q value = 0.85

Table S88.  Gene #9: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
SLC26A3 MUTATED 3 0 1
SLC26A3 WILD-TYPE 55 44 41
'SLC26A3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 0.55

Table S89.  Gene #9: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
SLC26A3 MUTATED 2 0 2
SLC26A3 WILD-TYPE 43 63 31
'SLC26A3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.164 (Fisher's exact test), Q value = 0.72

Table S90.  Gene #9: '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
'SEMG1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.957 (Fisher's exact test), Q value = 1

Table S91.  Gene #10: 'SEMG1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
SEMG1 MUTATED 2 1 3 2
SEMG1 WILD-TYPE 76 40 61 55
'SEMG1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.176 (Fisher's exact test), Q value = 0.74

Table S92.  Gene #10: 'SEMG1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
SEMG1 MUTATED 0 2 1 5
SEMG1 WILD-TYPE 63 48 47 74
'SEMG1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.958 (Fisher's exact test), Q value = 1

Table S93.  Gene #10: 'SEMG1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
SEMG1 MUTATED 2 4 1 1
SEMG1 WILD-TYPE 68 94 43 62
'SEMG1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S94.  Gene #10: 'SEMG1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
SEMG1 MUTATED 4 2 2
SEMG1 WILD-TYPE 134 59 74
'SEMG1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.34 (Fisher's exact test), Q value = 0.88

Table S95.  Gene #10: 'SEMG1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
SEMG1 MUTATED 1 5 2
SEMG1 WILD-TYPE 103 102 60
'SEMG1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.271 (Fisher's exact test), Q value = 0.81

Table S96.  Gene #10: 'SEMG1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 19 42 33
SEMG1 MUTATED 2 0 0 2
SEMG1 WILD-TYPE 31 19 42 31
'SEMG1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S97.  Gene #10: 'SEMG1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
SEMG1 MUTATED 1 1 1
SEMG1 WILD-TYPE 44 62 32
'SEMG1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.337 (Fisher's exact test), Q value = 0.88

Table S98.  Gene #10: 'SEMG1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
SEMG1 MUTATED 1 1 1
SEMG1 WILD-TYPE 30 85 23
'KDR MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 0.78

Table S99.  Gene #11: 'KDR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
KDR MUTATED 1 2 1 4
KDR WILD-TYPE 77 39 63 53
'KDR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S100.  Gene #11: '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 = 0.245 (Fisher's exact test), Q value = 0.78

Table S101.  Gene #11: 'KDR MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
KDR MUTATED 2 1 3 2
KDR WILD-TYPE 68 97 41 61
'KDR MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S102.  Gene #11: '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 = 0.375 (Fisher's exact test), Q value = 0.92

Table S103.  Gene #11: 'KDR MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
KDR MUTATED 4 4 0
KDR WILD-TYPE 100 103 62
'KDR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.34 (Fisher's exact test), Q value = 0.88

Table S104.  Gene #11: 'KDR MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 19 42 33
KDR MUTATED 2 0 0 1
KDR WILD-TYPE 31 19 42 32
'KDR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.155 (Fisher's exact test), Q value = 0.69

Table S105.  Gene #11: 'KDR MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
KDR MUTATED 2 1 0 2 0
KDR WILD-TYPE 29 34 24 17 35
'KDR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.737 (Fisher's exact test), Q value = 1

Table S106.  Gene #11: 'KDR MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
KDR MUTATED 3 1 1
KDR WILD-TYPE 55 43 41
'RPL5 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.399 (Fisher's exact test), Q value = 0.94

Table S107.  Gene #12: 'RPL5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
RPL5 MUTATED 2 2 2 0
RPL5 WILD-TYPE 76 39 62 57
'RPL5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S108.  Gene #12: '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 = 0.907 (Fisher's exact test), Q value = 1

Table S109.  Gene #12: 'RPL5 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
RPL5 MUTATED 1 3 1 2
RPL5 WILD-TYPE 69 95 43 61
'RPL5 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.469 (Fisher's exact test), Q value = 0.99

Table S110.  Gene #12: '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 = 0.797 (Fisher's exact test), Q value = 1

Table S111.  Gene #12: 'RPL5 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
RPL5 MUTATED 3 2 2
RPL5 WILD-TYPE 101 105 60
'RPL5 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S112.  Gene #12: 'RPL5 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
RPL5 MUTATED 2 0 1 0 1
RPL5 WILD-TYPE 29 35 23 19 34
'RPL5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S113.  Gene #12: 'RPL5 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
RPL5 MUTATED 1 1 2
RPL5 WILD-TYPE 57 43 40
'RPL5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.462 (Fisher's exact test), Q value = 0.99

Table S114.  Gene #12: 'RPL5 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
RPL5 MUTATED 2 1 0
RPL5 WILD-TYPE 43 62 33
'RPL5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S115.  Gene #12: '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
'ATRX MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00358 (Fisher's exact test), Q value = 0.052

Table S116.  Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
ATRX MUTATED 2 4 0 7
ATRX WILD-TYPE 76 37 64 50

Figure S27.  Get High-res Image Gene #13: '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 = 0.00051

Table S117.  Gene #13: '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 S28.  Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.17

Table S118.  Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
ATRX MUTATED 3 11 2 0
ATRX WILD-TYPE 67 87 42 63

Figure S29.  Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'ATRX MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.0184 (Fisher's exact test), Q value = 0.18

Table S119.  Gene #13: '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 S30.  Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00051

Table S120.  Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
ATRX MUTATED 14 0 1
ATRX WILD-TYPE 90 107 61

Figure S31.  Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'ATRX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.002

Table S121.  Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 19 42 33
ATRX MUTATED 0 0 0 8
ATRX WILD-TYPE 33 19 42 25

Figure S32.  Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'ATRX MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.554 (Fisher's exact test), Q value = 1

Table S122.  Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
ATRX MUTATED 2 1 3 1 1
ATRX WILD-TYPE 29 34 21 18 34
'ATRX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.14

Table S123.  Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
ATRX MUTATED 2 6 0
ATRX WILD-TYPE 56 38 42

Figure S33.  Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00255 (Fisher's exact test), Q value = 0.042

Table S124.  Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
ATRX MUTATED 7 1 0
ATRX WILD-TYPE 38 62 33

Figure S34.  Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'ATRX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0062

Table S125.  Gene #13: '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 S35.  Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.93 (Fisher's exact test), Q value = 1

Table S126.  Gene #14: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
MAP3K1 MUTATED 1 1 2 1
MAP3K1 WILD-TYPE 77 40 62 56
'MAP3K1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S127.  Gene #14: '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 = 0.76 (Fisher's exact test), Q value = 1

Table S128.  Gene #14: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
MAP3K1 MUTATED 1 3 0 2
MAP3K1 WILD-TYPE 69 95 44 61
'MAP3K1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.646 (Fisher's exact test), Q value = 1

Table S129.  Gene #14: '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 = 0.654 (Fisher's exact test), Q value = 1

Table S130.  Gene #14: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
MAP3K1 MUTATED 1 3 2
MAP3K1 WILD-TYPE 103 104 60
'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.564 (Fisher's exact test), Q value = 1

Table S131.  Gene #14: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
MAP3K1 MUTATED 1 3 0
MAP3K1 WILD-TYPE 44 60 33
'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S132.  Gene #14: '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
'BRAF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.598 (Fisher's exact test), Q value = 1

Table S133.  Gene #15: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
BRAF MUTATED 1 1 2 0
BRAF WILD-TYPE 77 40 62 57
'BRAF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.712 (Fisher's exact test), Q value = 1

Table S134.  Gene #15: '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 = 0.317 (Fisher's exact test), Q value = 0.86

Table S135.  Gene #15: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
BRAF MUTATED 2 1 0 3
BRAF WILD-TYPE 68 97 44 60
'BRAF MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.0285 (Fisher's exact test), Q value = 0.23

Table S136.  Gene #15: '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 S36.  Get High-res Image Gene #15: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0967 (Fisher's exact test), Q value = 0.51

Table S137.  Gene #15: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
BRAF MUTATED 4 0 2
BRAF WILD-TYPE 100 107 60
'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S138.  Gene #15: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
BRAF MUTATED 1 1 0 0 1
BRAF WILD-TYPE 30 34 24 19 34
'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.78 (Fisher's exact test), Q value = 1

Table S139.  Gene #15: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
BRAF MUTATED 2 1 0
BRAF WILD-TYPE 56 43 42
'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.794 (Fisher's exact test), Q value = 1

Table S140.  Gene #15: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
BRAF MUTATED 1 2 0
BRAF WILD-TYPE 44 61 33
'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S141.  Gene #15: '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 = 0.0861 (Fisher's exact test), Q value = 0.48

Table S142.  Gene #16: 'EGFR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
EGFR MUTATED 26 8 23 11
EGFR WILD-TYPE 52 33 41 46
'EGFR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0578 (Fisher's exact test), Q value = 0.4

Table S143.  Gene #16: '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 = 0.278 (Fisher's exact test), Q value = 0.81

Table S144.  Gene #16: 'EGFR MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
EGFR MUTATED 19 31 7 17
EGFR WILD-TYPE 51 67 37 46
'EGFR MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.139 (Fisher's exact test), Q value = 0.65

Table S145.  Gene #16: '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 = 4e-05 (Fisher's exact test), Q value = 0.0016

Table S146.  Gene #16: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
EGFR MUTATED 13 33 26
EGFR WILD-TYPE 91 74 36

Figure S37.  Get High-res Image Gene #16: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00355 (Fisher's exact test), Q value = 0.052

Table S147.  Gene #16: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 19 42 33
EGFR MUTATED 9 8 19 3
EGFR WILD-TYPE 24 11 23 30

Figure S38.  Get High-res Image Gene #16: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'EGFR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.256 (Fisher's exact test), Q value = 0.8

Table S148.  Gene #16: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
EGFR MUTATED 6 13 4 3 11
EGFR WILD-TYPE 25 22 20 16 24
'EGFR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00051

Table S149.  Gene #16: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
EGFR MUTATED 11 4 22
EGFR WILD-TYPE 47 40 20

Figure S39.  Get High-res Image Gene #16: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.22

Table S150.  Gene #16: 'EGFR MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
EGFR MUTATED 8 22 15
EGFR WILD-TYPE 37 41 18

Figure S40.  Get High-res Image Gene #16: 'EGFR MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'EGFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00606 (Fisher's exact test), Q value = 0.081

Table S151.  Gene #16: '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 S41.  Get High-res Image Gene #16: 'EGFR MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'TMPRSS6 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.731 (Fisher's exact test), Q value = 1

Table S152.  Gene #17: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
TMPRSS6 MUTATED 3 0 2 1
TMPRSS6 WILD-TYPE 75 41 62 56
'TMPRSS6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.703 (Fisher's exact test), Q value = 1

Table S153.  Gene #17: '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 = 0.726 (Fisher's exact test), Q value = 1

Table S154.  Gene #17: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
TMPRSS6 MUTATED 2 1 1 2
TMPRSS6 WILD-TYPE 68 97 43 61
'TMPRSS6 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.263 (Fisher's exact test), Q value = 0.81

Table S155.  Gene #17: '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 = 0.583 (Fisher's exact test), Q value = 1

Table S156.  Gene #17: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
TMPRSS6 MUTATED 3 1 2
TMPRSS6 WILD-TYPE 101 106 60
'TMPRSS6 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S157.  Gene #17: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 19 42 33
TMPRSS6 MUTATED 1 0 1 1
TMPRSS6 WILD-TYPE 32 19 41 32
'TMPRSS6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.905 (Fisher's exact test), Q value = 1

Table S158.  Gene #17: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
TMPRSS6 MUTATED 1 1 0 0 2
TMPRSS6 WILD-TYPE 30 34 24 19 33
'TMPRSS6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.469 (Fisher's exact test), Q value = 0.99

Table S159.  Gene #17: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
TMPRSS6 MUTATED 2 0 2
TMPRSS6 WILD-TYPE 56 44 40
'TMPRSS6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S160.  Gene #17: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
TMPRSS6 MUTATED 1 4 1
TMPRSS6 WILD-TYPE 44 59 32
'TMPRSS6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S161.  Gene #17: '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
'PRKCD MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0817 (Fisher's exact test), Q value = 0.47

Table S162.  Gene #18: 'PRKCD MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
PRKCD MUTATED 0 2 1 0
PRKCD WILD-TYPE 78 39 63 57
'PRKCD MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0851 (Fisher's exact test), Q value = 0.48

Table S163.  Gene #18: '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 = 0.235 (Fisher's exact test), Q value = 0.78

Table S164.  Gene #18: 'PRKCD MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
PRKCD MUTATED 0 3 0 0
PRKCD WILD-TYPE 70 95 44 63
'PRKCD MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S165.  Gene #18: '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 = 0.617 (Fisher's exact test), Q value = 1

Table S166.  Gene #18: 'PRKCD MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
PRKCD MUTATED 2 1 0
PRKCD WILD-TYPE 102 106 62
'TP63 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.93 (Fisher's exact test), Q value = 1

Table S167.  Gene #19: 'TP63 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
TP63 MUTATED 1 1 2 1
TP63 WILD-TYPE 77 40 62 56
'TP63 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.728 (Fisher's exact test), Q value = 1

Table S168.  Gene #19: '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 = 0.316 (Fisher's exact test), Q value = 0.86

Table S169.  Gene #19: 'TP63 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
TP63 MUTATED 2 1 0 3
TP63 WILD-TYPE 68 97 44 60
'TP63 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S170.  Gene #19: '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 = 0.763 (Fisher's exact test), Q value = 1

Table S171.  Gene #19: 'TP63 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
TP63 MUTATED 2 2 2
TP63 WILD-TYPE 102 105 60
'TP63 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.29

Table S172.  Gene #19: 'TP63 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
TP63 MUTATED 2 0 0 2 0
TP63 WILD-TYPE 29 35 24 17 35

Figure S42.  Get High-res Image Gene #19: 'TP63 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

'TP63 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.388 (Fisher's exact test), Q value = 0.93

Table S173.  Gene #19: 'TP63 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
TP63 MUTATED 3 1 0
TP63 WILD-TYPE 55 43 42
'TP63 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.239 (Fisher's exact test), Q value = 0.78

Table S174.  Gene #19: 'TP63 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
TP63 MUTATED 0 1 2
TP63 WILD-TYPE 45 62 31
'TP63 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.109 (Fisher's exact test), Q value = 0.54

Table S175.  Gene #19: '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
'PDGFRA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00977 (Fisher's exact test), Q value = 0.11

Table S176.  Gene #20: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
PDGFRA MUTATED 2 6 1 1
PDGFRA WILD-TYPE 76 35 63 56

Figure S43.  Get High-res Image Gene #20: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'PDGFRA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.148 (Fisher's exact test), Q value = 0.68

Table S177.  Gene #20: '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 2 2
PDGFRA WILD-TYPE 62 45 46 77
'PDGFRA MUTATION STATUS' versus 'MIR_CNMF'

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

Table S178.  Gene #20: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
PDGFRA MUTATED 3 4 2 2
PDGFRA WILD-TYPE 67 94 42 61
'PDGFRA MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.14 (Fisher's exact test), Q value = 0.65

Table S179.  Gene #20: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
PDGFRA MUTATED 9 1 1
PDGFRA WILD-TYPE 129 60 75
'PDGFRA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.496 (Fisher's exact test), Q value = 1

Table S180.  Gene #20: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
PDGFRA MUTATED 4 6 1
PDGFRA WILD-TYPE 100 101 61
'PDGFRA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 0.78

Table S181.  Gene #20: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 19 42 33
PDGFRA MUTATED 0 2 1 2
PDGFRA WILD-TYPE 33 17 41 31
'PDGFRA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.3 (Fisher's exact test), Q value = 0.85

Table S182.  Gene #20: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
PDGFRA MUTATED 0 3 0 1 1
PDGFRA WILD-TYPE 31 32 24 18 34
'PDGFRA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S183.  Gene #20: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
PDGFRA MUTATED 3 1 1
PDGFRA WILD-TYPE 55 43 41
'PDGFRA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 0.23

Table S184.  Gene #20: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
PDGFRA MUTATED 5 1 0
PDGFRA WILD-TYPE 40 62 33

Figure S44.  Get High-res Image Gene #20: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'PDGFRA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00491 (Fisher's exact test), Q value = 0.068

Table S185.  Gene #20: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
PDGFRA MUTATED 5 1 0
PDGFRA WILD-TYPE 26 85 24

Figure S45.  Get High-res Image Gene #20: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'CHD8 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S186.  Gene #21: 'CHD8 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
CHD8 MUTATED 3 2 1 2
CHD8 WILD-TYPE 75 39 63 55
'CHD8 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S187.  Gene #21: '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 = 0.172 (Fisher's exact test), Q value = 0.74

Table S188.  Gene #21: 'CHD8 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
CHD8 MUTATED 0 3 3 2
CHD8 WILD-TYPE 70 95 41 61
'CHD8 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.646 (Fisher's exact test), Q value = 1

Table S189.  Gene #21: '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 = 0.233 (Fisher's exact test), Q value = 0.78

Table S190.  Gene #21: 'CHD8 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
CHD8 MUTATED 5 4 0
CHD8 WILD-TYPE 99 103 62
'CHD8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.311 (Fisher's exact test), Q value = 0.85

Table S191.  Gene #21: 'CHD8 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
CHD8 MUTATED 1 1 4 1 2
CHD8 WILD-TYPE 30 34 20 18 33
'CHD8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.915 (Fisher's exact test), Q value = 1

Table S192.  Gene #21: 'CHD8 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
CHD8 MUTATED 3 3 3
CHD8 WILD-TYPE 55 41 39
'CHD8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.269 (Fisher's exact test), Q value = 0.81

Table S193.  Gene #21: 'CHD8 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
CHD8 MUTATED 2 1 3
CHD8 WILD-TYPE 43 62 30
'CHD8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.612 (Fisher's exact test), Q value = 1

Table S194.  Gene #21: '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
'IL4R MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.846 (Fisher's exact test), Q value = 1

Table S195.  Gene #22: 'IL4R MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
IL4R MUTATED 1 1 2 2
IL4R WILD-TYPE 77 40 62 55
'IL4R MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.388 (Fisher's exact test), Q value = 0.93

Table S196.  Gene #22: 'IL4R MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
IL4R MUTATED 0 1 2 3
IL4R WILD-TYPE 63 49 46 76
'IL4R MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.744 (Fisher's exact test), Q value = 1

Table S197.  Gene #22: 'IL4R MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
IL4R MUTATED 1 3 2 2
IL4R WILD-TYPE 69 95 42 61
'IL4R MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.805 (Fisher's exact test), Q value = 1

Table S198.  Gene #22: 'IL4R MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
IL4R MUTATED 4 1 3
IL4R WILD-TYPE 134 60 73
'IL4R MUTATION STATUS' versus 'CN_CNMF'

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

Table S199.  Gene #22: 'IL4R MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
IL4R MUTATED 3 2 3
IL4R WILD-TYPE 101 105 59
'IL4R MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.447 (Fisher's exact test), Q value = 0.98

Table S200.  Gene #22: 'IL4R MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 19 42 33
IL4R MUTATED 0 1 3 1
IL4R WILD-TYPE 33 18 39 32
'IL4R MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.227 (Fisher's exact test), Q value = 0.78

Table S201.  Gene #22: 'IL4R MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
IL4R MUTATED 1 2 3 1 0
IL4R WILD-TYPE 30 33 21 18 35
'IL4R MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S202.  Gene #22: 'IL4R MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
IL4R MUTATED 2 3 2
IL4R WILD-TYPE 56 41 40
'IL4R MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.45 (Fisher's exact test), Q value = 0.98

Table S203.  Gene #22: 'IL4R MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
IL4R MUTATED 1 1 2
IL4R WILD-TYPE 44 62 31
'IL4R MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S204.  Gene #22: 'IL4R MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
IL4R MUTATED 1 2 1
IL4R WILD-TYPE 30 84 23
'REN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.302 (Fisher's exact test), Q value = 0.85

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
REN MUTATED 0 0 2 1
REN WILD-TYPE 78 41 62 56
'REN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.414 (Fisher's exact test), Q value = 0.95

Table S206.  Gene #23: '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 = 0.069 (Fisher's exact test), Q value = 0.44

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
REN MUTATED 1 1 3 0
REN WILD-TYPE 69 97 41 63
'REN MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S208.  Gene #23: '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 = 0.742 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
REN MUTATED 3 1 1
REN WILD-TYPE 101 106 61
'REN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.553 (Fisher's exact test), Q value = 1

Table S210.  Gene #23: 'REN MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
REN MUTATED 2 0 1 0 1
REN WILD-TYPE 29 35 23 19 34
'REN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S211.  Gene #23: 'REN MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
REN MUTATED 2 1 1
REN WILD-TYPE 56 43 41
'CD209 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.832 (Fisher's exact test), Q value = 1

Table S212.  Gene #24: 'CD209 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
CD209 MUTATED 1 0 2 1
CD209 WILD-TYPE 77 41 62 56
'CD209 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S213.  Gene #24: '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 = 0.328 (Fisher's exact test), Q value = 0.88

Table S214.  Gene #24: 'CD209 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
CD209 MUTATED 1 1 0 3
CD209 WILD-TYPE 69 97 44 60
'CD209 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.609 (Fisher's exact test), Q value = 1

Table S215.  Gene #24: '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 = 0.838 (Fisher's exact test), Q value = 1

Table S216.  Gene #24: 'CD209 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
CD209 MUTATED 2 1 1
CD209 WILD-TYPE 102 106 61
'CD209 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.904 (Fisher's exact test), Q value = 1

Table S217.  Gene #24: 'CD209 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
CD209 MUTATED 1 1 0 0 2
CD209 WILD-TYPE 30 34 24 19 33
'CD209 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S218.  Gene #24: 'CD209 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
CD209 MUTATED 2 1 1
CD209 WILD-TYPE 56 43 41
'FBN3 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S219.  Gene #25: 'FBN3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
FBN3 MUTATED 2 1 5 1
FBN3 WILD-TYPE 76 40 59 56
'FBN3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.308 (Fisher's exact test), Q value = 0.85

Table S220.  Gene #25: '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 = 1 (Fisher's exact test), Q value = 1

Table S221.  Gene #25: 'FBN3 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
FBN3 MUTATED 3 4 2 2
FBN3 WILD-TYPE 67 94 42 61
'FBN3 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S222.  Gene #25: '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 = 0.088 (Fisher's exact test), Q value = 0.48

Table S223.  Gene #25: 'FBN3 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
FBN3 MUTATED 1 7 3
FBN3 WILD-TYPE 103 100 59
'FBN3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S224.  Gene #25: 'FBN3 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 19 42 33
FBN3 MUTATED 1 1 2 2
FBN3 WILD-TYPE 32 18 40 31
'FBN3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.18

Table S225.  Gene #25: 'FBN3 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
FBN3 MUTATED 0 0 2 3 1
FBN3 WILD-TYPE 31 35 22 16 34

Figure S46.  Get High-res Image Gene #25: 'FBN3 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

'FBN3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.664 (Fisher's exact test), Q value = 1

Table S226.  Gene #25: 'FBN3 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
FBN3 MUTATED 2 3 1
FBN3 WILD-TYPE 56 41 41
'FBN3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.854 (Fisher's exact test), Q value = 1

Table S227.  Gene #25: 'FBN3 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
FBN3 MUTATED 1 3 1
FBN3 WILD-TYPE 44 60 32
'FBN3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S228.  Gene #25: '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
'MMP13 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.832 (Fisher's exact test), Q value = 1

Table S229.  Gene #26: 'MMP13 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
MMP13 MUTATED 1 0 2 1
MMP13 WILD-TYPE 77 41 62 56
'MMP13 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.22 (Fisher's exact test), Q value = 0.78

Table S230.  Gene #26: '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 = 0.762 (Fisher's exact test), Q value = 1

Table S231.  Gene #26: 'MMP13 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
MMP13 MUTATED 1 2 0 2
MMP13 WILD-TYPE 69 96 44 61
'MMP13 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.0493 (Fisher's exact test), Q value = 0.36

Table S232.  Gene #26: '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 S47.  Get High-res Image Gene #26: 'MMP13 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'MMP13 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.204 (Fisher's exact test), Q value = 0.77

Table S233.  Gene #26: 'MMP13 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
MMP13 MUTATED 1 1 3
MMP13 WILD-TYPE 103 106 59
'TCF12 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S234.  Gene #27: 'TCF12 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
TCF12 MUTATED 1 0 1 1
TCF12 WILD-TYPE 77 41 63 56
'TCF12 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.481 (Fisher's exact test), Q value = 0.99

Table S235.  Gene #27: 'TCF12 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
TCF12 MUTATED 1 1 1 0
TCF12 WILD-TYPE 62 49 47 79
'TCF12 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S236.  Gene #27: 'TCF12 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
TCF12 MUTATED 2 2 0 0
TCF12 WILD-TYPE 68 96 44 63
'TCF12 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.257 (Fisher's exact test), Q value = 0.8

Table S237.  Gene #27: 'TCF12 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
TCF12 MUTATED 2 2 0
TCF12 WILD-TYPE 136 59 76
'TCF12 MUTATION STATUS' versus 'CN_CNMF'

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

Table S238.  Gene #27: 'TCF12 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
TCF12 MUTATED 1 1 1
TCF12 WILD-TYPE 103 106 61
'TCF12 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0748 (Fisher's exact test), Q value = 0.45

Table S239.  Gene #27: 'TCF12 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
TCF12 MUTATED 0 3 0 1 0
TCF12 WILD-TYPE 31 32 24 18 35
'TCF12 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S240.  Gene #27: 'TCF12 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
TCF12 MUTATED 2 1 1
TCF12 WILD-TYPE 56 43 41
'LZTR1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S241.  Gene #28: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
LZTR1 MUTATED 2 2 1 2
LZTR1 WILD-TYPE 76 39 63 55
'LZTR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.516 (Fisher's exact test), Q value = 1

Table S242.  Gene #28: '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 = 0.467 (Fisher's exact test), Q value = 0.99

Table S243.  Gene #28: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
LZTR1 MUTATED 4 4 0 2
LZTR1 WILD-TYPE 66 94 44 61
'LZTR1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S244.  Gene #28: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
LZTR1 MUTATED 4 3 3
LZTR1 WILD-TYPE 134 58 73
'LZTR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.372 (Fisher's exact test), Q value = 0.92

Table S245.  Gene #28: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
LZTR1 MUTATED 2 6 1
LZTR1 WILD-TYPE 102 101 61
'LZTR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.336 (Fisher's exact test), Q value = 0.88

Table S246.  Gene #28: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 19 42 33
LZTR1 MUTATED 2 1 0 1
LZTR1 WILD-TYPE 31 18 42 32
'LZTR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.2 (Fisher's exact test), Q value = 0.77

Table S247.  Gene #28: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
LZTR1 MUTATED 3 0 1 2 1
LZTR1 WILD-TYPE 28 35 23 17 34
'LZTR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.563 (Fisher's exact test), Q value = 1

Table S248.  Gene #28: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
LZTR1 MUTATED 4 1 2
LZTR1 WILD-TYPE 54 43 40
'LZTR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.168 (Fisher's exact test), Q value = 0.73

Table S249.  Gene #28: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
LZTR1 MUTATED 2 0 1
LZTR1 WILD-TYPE 43 63 32
'LZTR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S250.  Gene #28: '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
'ZDHHC4 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.236 (Fisher's exact test), Q value = 0.78

Table S251.  Gene #29: 'ZDHHC4 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
ZDHHC4 MUTATED 0 3 0 0
ZDHHC4 WILD-TYPE 70 95 44 63
'ZDHHC4 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S252.  Gene #29: 'ZDHHC4 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
ZDHHC4 MUTATED 2 0 1
ZDHHC4 WILD-TYPE 136 61 75
'ZDHHC4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.183 (Fisher's exact test), Q value = 0.75

Table S253.  Gene #29: 'ZDHHC4 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
ZDHHC4 MUTATED 0 3 0
ZDHHC4 WILD-TYPE 104 104 62
'IL18RAP MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.072 (Fisher's exact test), Q value = 0.45

Table S254.  Gene #30: 'IL18RAP MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
IL18RAP MUTATED 0 3 2 1
IL18RAP WILD-TYPE 78 38 62 56
'IL18RAP MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.226 (Fisher's exact test), Q value = 0.78

Table S255.  Gene #30: 'IL18RAP MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
IL18RAP MUTATED 0 3 1 2
IL18RAP WILD-TYPE 63 47 47 77
'IL18RAP MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.0066 (Fisher's exact test), Q value = 0.084

Table S256.  Gene #30: 'IL18RAP MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
IL18RAP MUTATED 0 7 0 0
IL18RAP WILD-TYPE 70 91 44 63

Figure S48.  Get High-res Image Gene #30: 'IL18RAP MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'IL18RAP MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.175 (Fisher's exact test), Q value = 0.74

Table S257.  Gene #30: 'IL18RAP MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
IL18RAP MUTATED 3 0 4
IL18RAP WILD-TYPE 135 61 72
'IL18RAP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.485 (Fisher's exact test), Q value = 0.99

Table S258.  Gene #30: 'IL18RAP MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
IL18RAP MUTATED 1 4 2
IL18RAP WILD-TYPE 103 103 60
'IL18RAP MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S259.  Gene #30: 'IL18RAP MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 19 42 33
IL18RAP MUTATED 1 0 1 1
IL18RAP WILD-TYPE 32 19 41 32
'IL18RAP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.366 (Fisher's exact test), Q value = 0.91

Table S260.  Gene #30: 'IL18RAP MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
IL18RAP MUTATED 0 1 1 2 1
IL18RAP WILD-TYPE 31 34 23 17 34
'IL18RAP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S261.  Gene #30: 'IL18RAP MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
IL18RAP MUTATED 1 2 2
IL18RAP WILD-TYPE 57 42 40
'IL18RAP MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S262.  Gene #30: 'IL18RAP MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
IL18RAP MUTATED 2 2 0
IL18RAP WILD-TYPE 43 61 33
'IL18RAP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S263.  Gene #30: 'IL18RAP MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
IL18RAP MUTATED 2 2 0
IL18RAP WILD-TYPE 29 84 24
'ODF4 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S264.  Gene #31: 'ODF4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
ODF4 MUTATED 1 1 1 0
ODF4 WILD-TYPE 77 40 63 57
'ODF4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S265.  Gene #31: '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 S266.  Gene #31: 'ODF4 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
ODF4 MUTATED 1 1 0 1
ODF4 WILD-TYPE 69 97 44 62
'ODF4 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 0.76

Table S267.  Gene #31: '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 = 0.794 (Fisher's exact test), Q value = 1

Table S268.  Gene #31: 'ODF4 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
ODF4 MUTATED 1 2 0
ODF4 WILD-TYPE 103 105 62
'KEL MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 0.84

Table S269.  Gene #32: 'KEL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
KEL MUTATED 3 3 7 2
KEL WILD-TYPE 75 38 57 55
'KEL MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.209 (Fisher's exact test), Q value = 0.78

Table S270.  Gene #32: '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 = 0.835 (Fisher's exact test), Q value = 1

Table S271.  Gene #32: 'KEL MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
KEL MUTATED 3 5 2 5
KEL WILD-TYPE 67 93 42 58
'KEL MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S272.  Gene #32: '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 = 0.115 (Fisher's exact test), Q value = 0.55

Table S273.  Gene #32: 'KEL MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
KEL MUTATED 2 8 5
KEL WILD-TYPE 102 99 57
'KEL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.184 (Fisher's exact test), Q value = 0.75

Table S274.  Gene #32: 'KEL MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 19 42 33
KEL MUTATED 0 0 4 1
KEL WILD-TYPE 33 19 38 32
'KEL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.675 (Fisher's exact test), Q value = 1

Table S275.  Gene #32: 'KEL MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
KEL MUTATED 2 2 1 3 2
KEL WILD-TYPE 29 33 23 16 33
'KEL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.597 (Fisher's exact test), Q value = 1

Table S276.  Gene #32: 'KEL MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
KEL MUTATED 4 2 4
KEL WILD-TYPE 54 42 38
'KEL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.485 (Fisher's exact test), Q value = 0.99

Table S277.  Gene #32: 'KEL MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
KEL MUTATED 5 3 2
KEL WILD-TYPE 40 60 31
'KEL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S278.  Gene #32: '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
'TESK1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.205 (Fisher's exact test), Q value = 0.77

Table S279.  Gene #33: 'TESK1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
TESK1 MUTATED 0 1 2 0
TESK1 WILD-TYPE 78 40 62 57
'TESK1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S280.  Gene #33: 'TESK1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
TESK1 MUTATED 0 1 1 1
TESK1 WILD-TYPE 63 49 47 78
'TESK1 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S281.  Gene #33: 'TESK1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
TESK1 MUTATED 1 0 1 1
TESK1 WILD-TYPE 69 98 43 62
'TESK1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.602 (Fisher's exact test), Q value = 1

Table S282.  Gene #33: 'TESK1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
TESK1 MUTATED 2 1 0
TESK1 WILD-TYPE 136 60 76
'TESK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.244 (Fisher's exact test), Q value = 0.78

Table S283.  Gene #33: 'TESK1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
TESK1 MUTATED 0 1 2
TESK1 WILD-TYPE 104 106 60
'MUC17 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0629 (Fisher's exact test), Q value = 0.41

Table S284.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
MUC17 MUTATED 10 4 1 4
MUC17 WILD-TYPE 68 37 63 53
'MUC17 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.193 (Fisher's exact test), Q value = 0.76

Table S285.  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 = 0.802 (Fisher's exact test), Q value = 1

Table S286.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
MUC17 MUTATED 5 7 3 7
MUC17 WILD-TYPE 65 91 41 56
'MUC17 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.703 (Fisher's exact test), Q value = 1

Table S287.  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 = 0.296 (Fisher's exact test), Q value = 0.85

Table S288.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
MUC17 MUTATED 10 10 2
MUC17 WILD-TYPE 94 97 60
'MUC17 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S289.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 19 42 33
MUC17 MUTATED 3 1 3 3
MUC17 WILD-TYPE 30 18 39 30
'MUC17 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.553 (Fisher's exact test), Q value = 1

Table S290.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
MUC17 MUTATED 2 4 1 0 4
MUC17 WILD-TYPE 29 31 23 19 31
'MUC17 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0909 (Fisher's exact test), Q value = 0.49

Table S291.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
MUC17 MUTATED 8 1 2
MUC17 WILD-TYPE 50 43 40
'MUC17 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S292.  Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 63 33
MUC17 MUTATED 4 6 2
MUC17 WILD-TYPE 41 57 31
'MUC17 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S293.  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
'FAM126B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.24 (Fisher's exact test), Q value = 0.78

Table S294.  Gene #35: 'FAM126B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
FAM126B MUTATED 1 0 3 0
FAM126B WILD-TYPE 77 41 61 57
'FAM126B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.028 (Fisher's exact test), Q value = 0.23

Table S295.  Gene #35: 'FAM126B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 50 48 79
FAM126B MUTATED 1 0 3 0
FAM126B WILD-TYPE 62 50 45 79

Figure S49.  Get High-res Image Gene #35: 'FAM126B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'FAM126B MUTATION STATUS' versus 'MIR_CNMF'

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

Table S296.  Gene #35: 'FAM126B MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
FAM126B MUTATED 2 2 0 0
FAM126B WILD-TYPE 68 96 44 63
'FAM126B MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.444 (Fisher's exact test), Q value = 0.98

Table S297.  Gene #35: 'FAM126B MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 61 76
FAM126B MUTATED 1 1 2
FAM126B WILD-TYPE 137 60 74
'FAM126B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.55 (Fisher's exact test), Q value = 1

Table S298.  Gene #35: 'FAM126B MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
FAM126B MUTATED 1 1 2
FAM126B WILD-TYPE 103 106 60
'FAM126B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.683 (Fisher's exact test), Q value = 1

Table S299.  Gene #35: 'FAM126B MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 19 42 33
FAM126B MUTATED 1 1 2 0
FAM126B WILD-TYPE 32 18 40 33
'FAM126B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S300.  Gene #35: 'FAM126B MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 35 24 19 35
FAM126B MUTATED 1 1 0 0 1
FAM126B WILD-TYPE 30 34 24 19 34
'FAM126B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S301.  Gene #35: 'FAM126B MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 44 42
FAM126B MUTATED 2 0 1
FAM126B WILD-TYPE 56 44 41
'DDX5 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.411 (Fisher's exact test), Q value = 0.95

Table S302.  Gene #36: 'DDX5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 78 41 64 57
DDX5 MUTATED 1 0 0 2
DDX5 WILD-TYPE 77 41 64 55
'DDX5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S303.  Gene #36: '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 = 0.646 (Fisher's exact test), Q value = 1

Table S304.  Gene #36: 'DDX5 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 98 44 63
DDX5 MUTATED 0 2 1 1
DDX5 WILD-TYPE 70 96 43 62
'DDX5 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.447 (Fisher's exact test), Q value = 0.98

Table S305.  Gene #36: '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 = 0.361 (Fisher's exact test), Q value = 0.91

Table S306.  Gene #36: 'DDX5 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 104 107 62
DDX5 MUTATED 3 1 0
DDX5 WILD-TYPE 101 106 62
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/22811914/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/GBM-TP/22555065/GBM-TP.transferedmergedcluster.txt

  • Number of patients = 283

  • Number of significantly mutated genes = 36

  • 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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