Correlation between gene mutation status and molecular subtypes
Glioblastoma Multiforme (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1SQ8ZKP
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1SQ8ZKP
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, 47 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',  'MIR_CNMF',  'CN_CNMF', and 'RPPA_CHIERARCHICAL'.

  • PTEN mutation correlated to 'MIR_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 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

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

  • IL4R mutation correlated to 'METHLYATION_CNMF'.

  • FBN3 mutation correlated to 'RPPA_CNMF'.

  • IL18RAP mutation correlated to 'MIR_CNMF'.

  • MUC17 mutation correlated to 'MRNA_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, 47 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 0.00014
(0.00388) 		1e-05
(0.00045) 		4e-05
(0.00131) 		0.00283
(0.0408) 		7e-05
(0.0021) 		1e-05
(0.00045) 		0.266
(0.798) 		0.00734
(0.0826) 		0.00077
(0.0146) 		1e-05
(0.00045)
ATRX 16 (6%) 267 0.00213
(0.0322) 		1e-05
(0.00045) 		0.00613
(0.0761) 		0.0181
(0.163) 		2e-05
(0.00072) 		1e-05
(0.00045) 		0.556
(1.00) 		0.0141
(0.134) 		0.00215
(0.0322) 		0.00018
(0.00463)
TP53 80 (28%) 203 0.001
(0.0164) 		1e-05
(0.00045) 		0.00082
(0.0148) 		0.203
(0.703) 		2e-05
(0.00072) 		0.00087
(0.0149) 		0.00732
(0.0826) 		0.0462
(0.32) 		0.00076
(0.0146) 		0.00054
(0.0114)
EGFR 74 (26%) 209 0.00696
(0.0826) 		0.0567
(0.364) 		0.507
(1.00) 		0.137
(0.641) 		1e-05
(0.00045) 		0.00033
(0.00742) 		0.257
(0.789) 		1e-05
(0.00045) 		0.0419
(0.301) 		0.00608
(0.0761)
NF1 29 (10%) 254 0.0812
(0.457) 		0.00027
(0.00648) 		0.0253
(0.212) 		0.932
(1.00) 		0.00839
(0.0915) 		0.0684
(0.417) 		0.0519
(0.34) 		0.012
(0.123) 		0.565
(1.00) 		0.451
(1.00)
PDGFRA 11 (4%) 272 0.0128
(0.125) 		0.146
(0.658) 		0.902
(1.00) 		0.141
(0.653) 		0.192
(0.7) 		0.728
(1.00) 		0.296
(0.84) 		0.732
(1.00) 		0.0253
(0.212) 		0.00489
(0.0652)
RB1 24 (8%) 259 0.034
(0.255) 		0.0169
(0.156) 		0.133
(0.635) 		0.923
(1.00) 		0.107
(0.553) 		0.0108
(0.114) 		0.817
(1.00) 		0.537
(1.00) 		0.0796
(0.455) 		0.579
(1.00)
PTEN 87 (31%) 196 0.116
(0.581) 		0.075
(0.437) 		0.0263
(0.215) 		0.647
(1.00) 		0.429
(0.996) 		0.223
(0.729) 		0.249
(0.781) 		0.382
(0.955) 		0.271
(0.805) 		0.645
(1.00)
BRAF 6 (2%) 277 0.768
(1.00) 		0.713
(1.00) 		0.318
(0.874) 		0.0291
(0.223) 		0.591
(1.00) 		1
(1.00) 		0.782
(1.00) 		0.793
(1.00) 		1
(1.00)
IL4R 8 (3%) 275 0.94
(1.00) 		0.387
(0.955) 		0.719
(1.00) 		0.807
(1.00) 		0.909
(1.00) 		0.0278
(0.222) 		0.226
(0.729) 		0.886
(1.00) 		0.467
(1.00) 		0.799
(1.00)
FBN3 11 (4%) 272 0.192
(0.7) 		0.308
(0.856) 		0.904
(1.00) 		0.92
(1.00) 		0.106
(0.553) 		1
(1.00) 		0.019
(0.167) 		0.662
(1.00) 		0.855
(1.00) 		1
(1.00)
IL18RAP 7 (2%) 276 0.129
(0.627) 		0.227
(0.729) 		0.00351
(0.0486) 		0.178
(0.688) 		1
(1.00) 		0.469
(1.00) 		0.366
(0.935) 		0.614
(1.00) 		0.688
(1.00) 		0.339
(0.912)
MUC17 22 (8%) 261 0.0124
(0.124) 		0.191
(0.7) 		0.704
(1.00) 		0.704
(1.00) 		0.923
(1.00) 		0.841
(1.00) 		0.551
(1.00) 		0.0915
(0.492) 		0.859
(1.00) 		1
(1.00)
FAM126B 4 (1%) 279 0.395
(0.96) 		0.0289
(0.223) 		0.641
(1.00) 		0.443
(1.00) 		0.476
(1.00) 		0.454
(1.00) 		1
(1.00) 		0.63
(1.00)
PIK3R1 32 (11%) 251 0.753
(1.00) 		0.187
(0.7) 		0.2
(0.703) 		0.527
(1.00) 		0.637
(1.00) 		0.249
(0.781) 		0.217
(0.729) 		0.0586
(0.37) 		0.405
(0.964) 		0.222
(0.729)
PIK3CA 27 (10%) 256 0.954
(1.00) 		0.289
(0.832) 		0.291
(0.832) 		0.861
(1.00) 		0.671
(1.00) 		0.867
(1.00) 		0.811
(1.00) 		0.405
(0.964) 		0.407
(0.964) 		0.232
(0.738)
STAG2 12 (4%) 271 0.392
(0.959) 		0.697
(1.00) 		0.716
(1.00) 		0.59
(1.00) 		0.754
(1.00) 		0.0432
(0.305) 		0.275
(0.805) 		0.335
(0.912) 		0.478
(1.00) 		0.105
(0.553)
SLC26A3 7 (2%) 276 0.942
(1.00) 		0.767
(1.00) 		0.465
(1.00) 		0.366
(0.935) 		0.648
(1.00) 		0.182
(0.697) 		0.48
(1.00) 		0.309
(0.856) 		0.156
(0.679) 		0.163
(0.68)
SEMG1 8 (3%) 275 0.679
(1.00) 		0.177
(0.688) 		0.888
(1.00) 		1
(1.00) 		0.164
(0.68) 		0.168
(0.688) 		1
(1.00) 		0.339
(0.912)
KDR 8 (3%) 275 0.203
(0.703) 		0.658
(1.00) 		0.282
(0.817) 		0.511
(1.00) 		0.733
(1.00) 		0.346
(0.917) 		0.157
(0.679) 		0.733
(1.00)
RPL5 7 (2%) 276 0.382
(0.955) 		0.509
(1.00) 		0.868
(1.00) 		0.467
(1.00) 		1
(1.00) 		0.551
(1.00) 		0.688
(1.00) 		0.463
(1.00) 		1
(1.00)
MAP3K1 6 (2%) 277 1
(1.00) 		0.73
(1.00) 		0.808
(1.00) 		0.646
(1.00) 		1
(1.00) 		0.571
(1.00) 		1
(1.00)
TMPRSS6 6 (2%) 277 0.665
(1.00) 		0.699
(1.00) 		0.663
(1.00) 		0.264
(0.798) 		0.882
(1.00) 		0.346
(0.917) 		0.904
(1.00) 		0.471
(1.00) 		0.576
(1.00) 		1
(1.00)
PRKCD 3 (1%) 280 0.173
(0.688) 		0.0855
(0.474) 		0.164
(0.68) 		1
(1.00) 		0.377
(0.955)
TP63 6 (2%) 277 1
(1.00) 		0.73
(1.00) 		0.41
(0.965) 		0.645
(1.00) 		0.774
(1.00) 		0.0367
(0.269) 		0.385
(0.955) 		0.253
(0.784) 		0.112
(0.567)
CHD8 9 (3%) 274 0.702
(1.00) 		0.534
(1.00) 		0.134
(0.635) 		0.643
(1.00) 		0.191
(0.7) 		0.309
(0.856) 		0.915
(1.00) 		0.275
(0.805) 		0.611
(1.00)
REN 5 (2%) 278 0.481
(1.00) 		0.416
(0.973) 		0.0735
(0.437) 		0.514
(1.00) 		0.618
(1.00) 		0.552
(1.00) 		1
(1.00)
CD209 5 (2%) 278 0.912
(1.00) 		1
(1.00) 		0.0668
(0.414) 		0.607
(1.00) 		0.693
(1.00) 		0.906
(1.00) 		1
(1.00)
MMP13 5 (2%) 278 0.912
(1.00) 		0.219
(0.729) 		0.761
(1.00) 		0.05
(0.339) 		0.153
(0.679)
TCF12 4 (1%) 279 1
(1.00) 		0.482
(1.00) 		0.64
(1.00) 		0.259
(0.789) 		0.49
(1.00) 		0.0752
(0.437) 		1
(1.00)
LZTR1 10 (4%) 273 1
(1.00) 		0.516
(1.00) 		0.36
(0.933) 		0.704
(1.00) 		0.441
(1.00) 		0.125
(0.615) 		0.2
(0.703) 		0.563
(1.00) 		0.174
(0.688) 		0.754
(1.00)
ZDHHC4 3 (1%) 280 0.163
(0.68) 		1
(1.00) 		0.0509
(0.339)
ODF4 3 (1%) 280 0.878
(1.00) 		0.352
(0.926) 		1
(1.00) 		0.196
(0.703) 		0.633
(1.00)
KEL 15 (5%) 268 0.547
(1.00) 		0.212
(0.727) 		0.722
(1.00) 		0.886
(1.00) 		0.0907
(0.492) 		0.171
(0.688) 		0.671
(1.00) 		0.596
(1.00) 		0.407
(0.964) 		0.649
(1.00)
TESK1 3 (1%) 280 0.359
(0.933) 		0.697
(1.00) 		0.457
(1.00) 		0.604
(1.00) 		0.783
(1.00)
DDX5 4 (1%) 279 0.216
(0.729) 		1
(1.00) 		0.536
(1.00) 		0.443
(1.00) 		0.144
(0.656)
'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
TP53 MUTATED 17 19 11 22
TP53 WILD-TYPE 52 24 63 32

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

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00045

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 = 0.00082 (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 77 93 45 60
TP53 MUTATED 12 40 10 18
TP53 WILD-TYPE 65 53 35 42

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

'TP53 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.203 (Fisher's exact test), Q value = 0.7

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 = 2e-05 (Fisher's exact test), Q value = 0.00072

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
TP53 MUTATED 36 14 29
TP53 WILD-TYPE 47 96 51

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

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.015

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

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

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

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00732 (Fisher's exact test), Q value = 0.083

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 = 0.0462 (Fisher's exact test), Q value = 0.32

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 = 0.00076 (Fisher's exact test), Q value = 0.015

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
TP53 MUTATED 24 13 8
TP53 WILD-TYPE 20 49 27

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

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.011

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

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

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

P value = 0.187 (Fisher's exact test), Q value = 0.7

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

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

P value = 0.2 (Fisher's exact test), Q value = 0.7

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

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

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

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

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

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

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

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

P value = 0.249 (Fisher's exact test), Q value = 0.78

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

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

P value = 0.217 (Fisher's exact test), Q value = 0.73

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 = 0.0586 (Fisher's exact test), Q value = 0.37

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 = 0.405 (Fisher's exact test), Q value = 0.96

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

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

P value = 0.222 (Fisher's exact test), Q value = 0.73

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 = 0.034 (Fisher's exact test), Q value = 0.25

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

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

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

'RB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0169 (Fisher's exact test), Q value = 0.16

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

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

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

'RB1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.133 (Fisher's exact test), Q value = 0.64

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

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

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

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

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

P value = 0.107 (Fisher's exact test), Q value = 0.55

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

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

P value = 0.0108 (Fisher's exact test), Q value = 0.11

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

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

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

'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.817 (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 = 0.537 (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 = 0.0796 (Fisher's exact test), Q value = 0.45

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

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

P value = 0.579 (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 = 0.0812 (Fisher's exact test), Q value = 0.46

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

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

P value = 0.00027 (Fisher's exact test), Q value = 0.0065

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 S13.  Get High-res Image Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 0.21

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

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

Figure S14.  Get High-res Image Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'NF1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.932 (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 = 0.00839 (Fisher's exact test), Q value = 0.092

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

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

Figure S15.  Get High-res Image Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0684 (Fisher's exact test), Q value = 0.42

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

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

P value = 0.0519 (Fisher's exact test), Q value = 0.34

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 = 0.012 (Fisher's exact test), Q value = 0.12

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 S16.  Get High-res Image Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

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

P value = 0.451 (Fisher's exact test), Q value = 1

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 = 0.116 (Fisher's exact test), Q value = 0.58

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

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

P value = 0.075 (Fisher's exact test), Q value = 0.44

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 = 0.0263 (Fisher's exact test), Q value = 0.21

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

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

Figure S17.  Get High-res Image Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'PTEN MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.647 (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 = 0.429 (Fisher's exact test), Q value = 1

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

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

P value = 0.223 (Fisher's exact test), Q value = 0.73

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

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

P value = 0.249 (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 = 0.96

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 = 0.271 (Fisher's exact test), Q value = 0.8

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

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

P value = 0.645 (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 = 0.00014 (Fisher's exact test), Q value = 0.0039

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

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

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

'IDH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00045

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 = 4e-05 (Fisher's exact test), Q value = 0.0013

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

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

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

'IDH1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.00283 (Fisher's exact test), Q value = 0.041

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

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

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

'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0021

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

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

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

'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00045

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

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

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

'IDH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.266 (Fisher's exact test), Q value = 0.8

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 = 0.00734 (Fisher's exact test), Q value = 0.083

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 = 0.00077 (Fisher's exact test), Q value = 0.015

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

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

Figure 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 = 0.00045

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 = 0.954 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
PIK3CA MUTATED 6 5 8 5
PIK3CA WILD-TYPE 63 38 66 49
'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.289 (Fisher's exact test), Q value = 0.83

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 = 0.291 (Fisher's exact test), Q value = 0.83

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
PIK3CA MUTATED 9 10 1 6
PIK3CA WILD-TYPE 68 83 44 54
'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 = 0.671 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
PIK3CA MUTATED 6 10 9
PIK3CA WILD-TYPE 77 100 71
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
PIK3CA MUTATED 4 6 2
PIK3CA WILD-TYPE 39 46 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 = 0.96

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 = 0.407 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
PIK3CA MUTATED 5 3 2
PIK3CA WILD-TYPE 39 59 33
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.232 (Fisher's exact test), Q value = 0.74

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 86 24
PIK3CA MUTATED 4 6 0
PIK3CA WILD-TYPE 27 80 24
'STAG2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.392 (Fisher's exact test), Q value = 0.96

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

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

P value = 0.697 (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 = 0.716 (Fisher's exact test), Q value = 1

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

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

P value = 0.59 (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 = 0.754 (Fisher's exact test), Q value = 1

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

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

P value = 0.0432 (Fisher's exact test), Q value = 0.31

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

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

Figure S27.  Get High-res Image Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'STAG2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.275 (Fisher's exact test), Q value = 0.8

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 = 0.91

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 = 0.478 (Fisher's exact test), Q value = 1

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

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

P value = 0.105 (Fisher's exact test), Q value = 0.55

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 = 0.942 (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 69 43 74 54
SLC26A3 MUTATED 1 1 2 2
SLC26A3 WILD-TYPE 68 42 72 52
'SLC26A3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table 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 = 0.465 (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 77 93 45 60
SLC26A3 MUTATED 1 4 0 2
SLC26A3 WILD-TYPE 76 89 45 58
'SLC26A3 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.366 (Fisher's exact test), Q value = 0.94

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 = 0.648 (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 83 110 80
SLC26A3 MUTATED 2 4 1
SLC26A3 WILD-TYPE 81 106 79
'SLC26A3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 0.7

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

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

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

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 = 0.309 (Fisher's exact test), Q value = 0.86

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 = 0.156 (Fisher's exact test), Q value = 0.68

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

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

P value = 0.163 (Fisher's exact test), Q value = 0.68

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 = 0.679 (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 69 43 74 54
SEMG1 MUTATED 1 1 4 2
SEMG1 WILD-TYPE 68 42 70 52
'SEMG1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.177 (Fisher's exact test), Q value = 0.69

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 = 0.888 (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 77 93 45 60
SEMG1 MUTATED 2 4 1 1
SEMG1 WILD-TYPE 75 89 44 59
'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 = 0.164 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
SEMG1 MUTATED 3 5 0
SEMG1 WILD-TYPE 80 105 80
'SEMG1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.168 (Fisher's exact test), Q value = 0.69

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
SEMG1 MUTATED 2 0 2
SEMG1 WILD-TYPE 41 52 30
'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 44 62 35
SEMG1 MUTATED 1 1 1
SEMG1 WILD-TYPE 43 61 34
'SEMG1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.339 (Fisher's exact test), Q value = 0.91

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 = 0.203 (Fisher's exact test), Q value = 0.7

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

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

P value = 0.658 (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 = 0.282 (Fisher's exact test), Q value = 0.82

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

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

P value = 0.511 (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 = 0.733 (Fisher's exact test), Q value = 1

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

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

P value = 0.346 (Fisher's exact test), Q value = 0.92

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

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

P value = 0.157 (Fisher's exact test), Q value = 0.68

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 = 0.733 (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 = 0.382 (Fisher's exact test), Q value = 0.96

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

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

P value = 0.509 (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 = 0.868 (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 77 93 45 60
RPL5 MUTATED 1 3 1 2
RPL5 WILD-TYPE 76 90 44 58
'RPL5 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table 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 = 1 (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 83 110 80
RPL5 MUTATED 2 3 2
RPL5 WILD-TYPE 81 107 78
'RPL5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.551 (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 = 0.688 (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 = 0.463 (Fisher's exact test), Q value = 1

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

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

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

Table 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 = 0.00213 (Fisher's exact test), Q value = 0.032

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

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

Figure S28.  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 = 0.00045

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 S29.  Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.00613 (Fisher's exact test), Q value = 0.076

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

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

Figure S30.  Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'ATRX MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table 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 S31.  Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00072

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

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

Figure S32.  Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'ATRX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00045

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

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

Figure S33.  Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'ATRX MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.556 (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 = 0.0141 (Fisher's exact test), Q value = 0.13

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 S34.  Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00215 (Fisher's exact test), Q value = 0.032

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

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

Figure S35.  Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'ATRX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.0046

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 S36.  Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 1 (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 69 43 74 54
MAP3K1 MUTATED 1 1 2 1
MAP3K1 WILD-TYPE 68 42 72 53
'MAP3K1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table 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 = 0.808 (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 77 93 45 60
MAP3K1 MUTATED 2 2 0 2
MAP3K1 WILD-TYPE 75 91 45 58
'MAP3K1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.646 (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 = 1 (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 83 110 80
MAP3K1 MUTATED 2 2 2
MAP3K1 WILD-TYPE 81 108 78
'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

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

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

Table 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 = 0.768 (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 69 43 74 54
BRAF MUTATED 1 1 2 0
BRAF WILD-TYPE 68 42 72 54
'BRAF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.713 (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 = 0.318 (Fisher's exact test), Q value = 0.87

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

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

P value = 0.0291 (Fisher's exact test), Q value = 0.22

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 S37.  Get High-res Image Gene #15: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'CN_CNMF'

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

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

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

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

Table 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 = 0.782 (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 = 0.793 (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 44 62 35
BRAF MUTATED 1 2 0
BRAF WILD-TYPE 43 60 35
'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table 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 = 0.00696 (Fisher's exact test), Q value = 0.083

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

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

Figure S38.  Get High-res Image Gene #16: 'EGFR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'EGFR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0567 (Fisher's exact test), Q value = 0.36

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

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

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

P value = 0.137 (Fisher's exact test), Q value = 0.64

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 = 1e-05 (Fisher's exact test), Q value = 0.00045

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

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

Figure S39.  Get High-res Image Gene #16: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0074

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

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

Figure S40.  Get High-res Image Gene #16: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'EGFR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.257 (Fisher's exact test), Q value = 0.79

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 = 0.00045

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 S41.  Get High-res Image Gene #16: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0419 (Fisher's exact test), Q value = 0.3

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

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

Figure S42.  Get High-res Image Gene #16: 'EGFR MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'EGFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00608 (Fisher's exact test), Q value = 0.076

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 S43.  Get High-res Image Gene #16: 'EGFR MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'TMPRSS6 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.665 (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 69 43 74 54
TMPRSS6 MUTATED 2 0 3 1
TMPRSS6 WILD-TYPE 67 43 71 53
'TMPRSS6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.699 (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 = 0.663 (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 77 93 45 60
TMPRSS6 MUTATED 3 1 1 1
TMPRSS6 WILD-TYPE 74 92 44 59
'TMPRSS6 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.264 (Fisher's exact test), Q value = 0.8

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 = 0.882 (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 83 110 80
TMPRSS6 MUTATED 2 3 1
TMPRSS6 WILD-TYPE 81 107 79
'TMPRSS6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.346 (Fisher's exact test), Q value = 0.92

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

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

P value = 0.904 (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 = 0.471 (Fisher's exact test), Q value = 1

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 = 0.576 (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 44 62 35
TMPRSS6 MUTATED 1 4 1
TMPRSS6 WILD-TYPE 43 58 34
'TMPRSS6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table 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 = 0.173 (Fisher's exact test), Q value = 0.69

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

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

P value = 0.0855 (Fisher's exact test), Q value = 0.47

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 = 0.164 (Fisher's exact test), Q value = 0.68

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

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

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

Table 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 = 0.377 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
PRKCD MUTATED 0 1 2
PRKCD WILD-TYPE 83 109 78
'TP63 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 1 (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 69 43 74 54
TP63 MUTATED 1 1 2 1
TP63 WILD-TYPE 68 42 72 53
'TP63 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.73 (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 = 0.41 (Fisher's exact test), Q value = 0.97

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

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

P value = 0.645 (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 = 0.774 (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 83 110 80
TP63 MUTATED 1 3 2
TP63 WILD-TYPE 82 107 78
'TP63 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0367 (Fisher's exact test), Q value = 0.27

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 S44.  Get High-res Image Gene #19: 'TP63 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

'TP63 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.385 (Fisher's exact test), Q value = 0.96

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 = 0.253 (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 44 62 35
TP63 MUTATED 0 1 2
TP63 WILD-TYPE 44 61 33
'TP63 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.112 (Fisher's exact test), Q value = 0.57

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 = 0.0128 (Fisher's exact test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
PDGFRA MUTATED 1 6 2 1
PDGFRA WILD-TYPE 68 37 72 53

Figure S45.  Get High-res Image Gene #20: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'PDGFRA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 0.66

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 = 0.902 (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 77 93 45 60
PDGFRA MUTATED 4 3 2 2
PDGFRA WILD-TYPE 73 90 43 58
'PDGFRA MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.141 (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 = 0.192 (Fisher's exact test), Q value = 0.7

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

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

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

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

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

P value = 0.296 (Fisher's exact test), Q value = 0.84

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 = 0.0253 (Fisher's exact test), Q value = 0.21

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
PDGFRA MUTATED 5 1 0
PDGFRA WILD-TYPE 39 61 35

Figure S46.  Get High-res Image Gene #20: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'PDGFRA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00489 (Fisher's exact test), Q value = 0.065

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 S47.  Get High-res Image Gene #20: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'CHD8 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.702 (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 69 43 74 54
CHD8 MUTATED 3 2 1 2
CHD8 WILD-TYPE 66 41 73 52
'CHD8 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.534 (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 = 0.134 (Fisher's exact test), Q value = 0.64

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

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

P value = 0.643 (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 = 0.191 (Fisher's exact test), Q value = 0.7

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

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

P value = 0.309 (Fisher's exact test), Q value = 0.86

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 = 0.275 (Fisher's exact test), Q value = 0.8

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

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

P value = 0.611 (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 = 0.94 (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 69 43 74 54
IL4R MUTATED 1 1 2 2
IL4R WILD-TYPE 68 42 72 52
'IL4R MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.387 (Fisher's exact test), Q value = 0.96

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 = 0.719 (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 77 93 45 60
IL4R MUTATED 1 3 2 2
IL4R WILD-TYPE 76 90 43 58
'IL4R MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.807 (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 = 0.909 (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 83 110 80
IL4R MUTATED 2 4 2
IL4R WILD-TYPE 81 106 78
'IL4R MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0278 (Fisher's exact test), Q value = 0.22

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
IL4R MUTATED 0 5 0
IL4R WILD-TYPE 43 47 32

Figure S48.  Get High-res Image Gene #22: 'IL4R MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'IL4R MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.226 (Fisher's exact test), Q value = 0.73

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
IL4R MUTATED 1 1 2
IL4R WILD-TYPE 43 61 33
'IL4R MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.799 (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 = 0.481 (Fisher's exact test), Q value = 1

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

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

P value = 0.416 (Fisher's exact test), Q value = 0.97

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 = 0.0735 (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 77 93 45 60
REN MUTATED 1 1 3 0
REN WILD-TYPE 76 92 42 60
'REN MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.514 (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 = 0.618 (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 83 110 80
REN MUTATED 2 1 2
REN WILD-TYPE 81 109 78
'REN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.552 (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 = 0.912 (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 69 43 74 54
CD209 MUTATED 1 0 2 1
CD209 WILD-TYPE 68 43 72 53
'CD209 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table 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 = 0.0668 (Fisher's exact test), Q value = 0.41

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
CD209 MUTATED 2 0 0 3
CD209 WILD-TYPE 75 93 45 57
'CD209 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.607 (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 = 0.693 (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 83 110 80
CD209 MUTATED 1 1 2
CD209 WILD-TYPE 82 109 78
'CD209 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.906 (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 = 0.192 (Fisher's exact test), Q value = 0.7

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
FBN3 MUTATED 1 1 6 1
FBN3 WILD-TYPE 68 42 68 53
'FBN3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.308 (Fisher's exact test), Q value = 0.86

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 = 0.904 (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 77 93 45 60
FBN3 MUTATED 4 3 2 2
FBN3 WILD-TYPE 73 90 43 58
'FBN3 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.92 (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 = 0.106 (Fisher's exact test), Q value = 0.55

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
FBN3 MUTATED 2 8 1
FBN3 WILD-TYPE 81 102 79
'FBN3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
FBN3 MUTATED 2 3 1
FBN3 WILD-TYPE 41 49 31
'FBN3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.17

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 S49.  Get High-res Image Gene #25: 'FBN3 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

'FBN3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.662 (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 = 0.855 (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 44 62 35
FBN3 MUTATED 1 3 1
FBN3 WILD-TYPE 43 59 34
'FBN3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table 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 = 0.912 (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 69 43 74 54
MMP13 MUTATED 1 0 2 1
MMP13 WILD-TYPE 68 43 72 53
'MMP13 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.219 (Fisher's exact test), Q value = 0.73

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 = 0.761 (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 77 93 45 60
MMP13 MUTATED 1 2 0 2
MMP13 WILD-TYPE 76 91 45 58
'MMP13 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.05 (Fisher's exact test), Q value = 0.34

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 S50.  Get High-res Image Gene #26: 'MMP13 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'MMP13 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.153 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
MMP13 MUTATED 0 4 1
MMP13 WILD-TYPE 83 106 79
'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 69 43 74 54
TCF12 MUTATED 1 0 1 1
TCF12 WILD-TYPE 68 43 73 53
'TCF12 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

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 = 0.64 (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 77 93 45 60
TCF12 MUTATED 2 2 0 0
TCF12 WILD-TYPE 75 91 45 60
'TCF12 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.259 (Fisher's exact test), Q value = 0.79

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 = 0.49 (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 83 110 80
TCF12 MUTATED 2 1 0
TCF12 WILD-TYPE 81 109 80
'TCF12 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0752 (Fisher's exact test), Q value = 0.44

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 = 1 (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 69 43 74 54
LZTR1 MUTATED 2 1 2 2
LZTR1 WILD-TYPE 67 42 72 52
'LZTR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.516 (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 = 0.36 (Fisher's exact test), Q value = 0.93

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
LZTR1 MUTATED 5 3 0 2
LZTR1 WILD-TYPE 72 90 45 58
'LZTR1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.704 (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 = 0.441 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
LZTR1 MUTATED 4 4 1
LZTR1 WILD-TYPE 79 106 79
'LZTR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 0.62

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
LZTR1 MUTATED 3 0 1
LZTR1 WILD-TYPE 40 52 31
'LZTR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.2 (Fisher's exact test), Q value = 0.7

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 = 0.174 (Fisher's exact test), Q value = 0.69

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
LZTR1 MUTATED 2 0 1
LZTR1 WILD-TYPE 42 62 34
'LZTR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.754 (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 = 0.163 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
ZDHHC4 MUTATED 0 3 0 0
ZDHHC4 WILD-TYPE 77 90 45 60
'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 = 0.0509 (Fisher's exact test), Q value = 0.34

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
ZDHHC4 MUTATED 3 0 0
ZDHHC4 WILD-TYPE 80 110 80
'IL18RAP MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.129 (Fisher's exact test), Q value = 0.63

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
IL18RAP MUTATED 0 3 2 1
IL18RAP WILD-TYPE 69 40 72 53
'IL18RAP MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.227 (Fisher's exact test), Q value = 0.73

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 = 0.00351 (Fisher's exact test), Q value = 0.049

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
IL18RAP MUTATED 0 7 0 0
IL18RAP WILD-TYPE 77 86 45 60

Figure S51.  Get High-res Image Gene #30: 'IL18RAP MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'IL18RAP MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.178 (Fisher's exact test), Q value = 0.69

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
IL18RAP MUTATED 2 3 2
IL18RAP WILD-TYPE 81 107 78
'IL18RAP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.469 (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
ALL 43 52 32
IL18RAP MUTATED 0 2 1
IL18RAP WILD-TYPE 43 50 31
'IL18RAP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.366 (Fisher's exact test), Q value = 0.94

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 = 0.688 (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 44 62 35
IL18RAP MUTATED 2 2 0
IL18RAP WILD-TYPE 42 60 35
'IL18RAP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.339 (Fisher's exact test), Q value = 0.91

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 = 0.878 (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 69 43 74 54
ODF4 MUTATED 1 1 1 0
ODF4 WILD-TYPE 68 42 73 54
'ODF4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.352 (Fisher's exact test), Q value = 0.93

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 77 93 45 60
ODF4 MUTATED 1 1 0 1
ODF4 WILD-TYPE 76 92 45 59
'ODF4 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.196 (Fisher's exact test), Q value = 0.7

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 = 0.633 (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 83 110 80
ODF4 MUTATED 0 2 1
ODF4 WILD-TYPE 83 108 79
'KEL MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.547 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
KEL MUTATED 3 3 7 2
KEL WILD-TYPE 66 40 67 52
'KEL MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.212 (Fisher's exact test), Q value = 0.73

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 = 0.722 (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 77 93 45 60
KEL MUTATED 3 5 2 5
KEL WILD-TYPE 74 88 43 55
'KEL MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.886 (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 = 0.0907 (Fisher's exact test), Q value = 0.49

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
KEL MUTATED 7 7 1
KEL WILD-TYPE 76 103 79
'KEL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.171 (Fisher's exact test), Q value = 0.69

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
KEL MUTATED 0 4 1
KEL WILD-TYPE 43 48 31
'KEL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.671 (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 = 0.596 (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 = 0.407 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
KEL MUTATED 5 3 2
KEL WILD-TYPE 39 59 33
'KEL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.649 (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 = 0.359 (Fisher's exact test), Q value = 0.93

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
TESK1 MUTATED 0 1 2 0
TESK1 WILD-TYPE 69 42 72 54
'TESK1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.697 (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 = 0.457 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
TESK1 MUTATED 1 0 1 1
TESK1 WILD-TYPE 76 93 44 59
'TESK1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.604 (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 = 0.783 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
TESK1 MUTATED 1 2 0
TESK1 WILD-TYPE 82 108 80
'MUC17 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
MUC17 MUTATED 10 5 1 3
MUC17 WILD-TYPE 59 38 73 51

Figure S52.  Get High-res Image Gene #34: 'MUC17 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'MUC17 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

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 = 0.704 (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 77 93 45 60
MUC17 MUTATED 5 7 3 7
MUC17 WILD-TYPE 72 86 42 53
'MUC17 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.704 (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 = 0.923 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
MUC17 MUTATED 7 8 7
MUC17 WILD-TYPE 76 102 73
'MUC17 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.841 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 52 32
MUC17 MUTATED 3 5 2
MUC17 WILD-TYPE 40 47 30
'MUC17 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.551 (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 = 0.0915 (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 = 0.859 (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 44 62 35
MUC17 MUTATED 4 6 2
MUC17 WILD-TYPE 40 56 33
'MUC17 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table 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 = 0.395 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
FAM126B MUTATED 1 0 3 0
FAM126B WILD-TYPE 68 43 71 54
'FAM126B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0289 (Fisher's exact test), Q value = 0.22

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 S53.  Get High-res Image Gene #35: 'FAM126B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'FAM126B MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.641 (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 77 93 45 60
FAM126B MUTATED 2 2 0 0
FAM126B WILD-TYPE 75 91 45 60
'FAM126B MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.443 (Fisher's exact test), Q value = 1

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 = 0.476 (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 83 110 80
FAM126B MUTATED 0 2 2
FAM126B WILD-TYPE 83 108 78
'FAM126B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.454 (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
ALL 43 52 32
FAM126B MUTATED 1 3 0
FAM126B WILD-TYPE 42 49 32
'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 = 0.216 (Fisher's exact test), Q value = 0.73

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

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

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

Table 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 = 0.536 (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 77 93 45 60
DDX5 MUTATED 0 2 1 1
DDX5 WILD-TYPE 77 91 44 59
'DDX5 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.443 (Fisher's exact test), Q value = 1

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 = 0.144 (Fisher's exact test), Q value = 0.66

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 83 110 80
DDX5 MUTATED 0 1 3
DDX5 WILD-TYPE 83 109 77
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/20063478/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/GBM-TP/20125497/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.

Download Results

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

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