Correlation between gene mutation status and molecular subtypes
Brain Lower Grade Glioma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C12B8WPW
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C12B8WPW
Overview
Introduction

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

Summary

Testing the association between mutation status of 23 genes and 12 molecular subtypes across 289 patients, 52 significant findings detected with P value < 0.05 and Q value < 0.25.

  • NOTCH1 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • PIK3CA mutation correlated to 'METHLYATION_CNMF'.

  • IDH2 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • IDH1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • TP53 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • CIC mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • ATRX mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • FUBP1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

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

  • PTEN mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • NF1 mutation correlated to 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 23 genes and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 52 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Chi-square test Fisher's exact test Chi-square test Fisher's exact test
PTEN 13 (4%) 276 4.87e-09
(1.06e-06) 		2.64e-12
(6.05e-10) 		0.000505
(0.101) 		0.00543
(1.00) 		2.06e-08
(4.47e-06) 		0.000666
(0.132) 		1.59e-05
(0.00327) 		0.000823
(0.162) 		5.97e-08
(1.28e-05) 		0.257
(1.00)
TP53 146 (51%) 143 0.0627
(1.00) 		0.00754
(1.00) 		4.02e-26
(9.7e-24) 		9.23e-53
(2.27e-50) 		0.0296
(1.00) 		0.656
(1.00) 		2.53e-26
(6.12e-24) 		1.06e-17
(2.5e-15) 		7.68e-11
(1.73e-08) 		0.0171
(1.00) 		3.23e-16
(7.47e-14) 		0.00104
(0.203)
CIC 54 (19%) 235 0.0428
(1.00) 		0.00303
(0.585) 		2.92e-17
(6.8e-15) 		4.06e-32
(9.86e-30) 		7.25e-05
(0.0147) 		0.192
(1.00) 		9.12e-24
(2.18e-21) 		4.82e-24
(1.16e-21) 		7.81e-13
(1.8e-10) 		0.00995
(1.00) 		1.85e-11
(4.2e-09) 		0.405
(1.00)
IDH1 220 (76%) 69 0.272
(1.00) 		0.523
(1.00) 		1.97e-16
(4.58e-14) 		2.57e-37
(6.28e-35) 		3.15e-07
(6.7e-05) 		0.0308
(1.00) 		6.91e-23
(1.65e-20) 		0.0127
(1.00) 		2.69e-08
(5.82e-06) 		0.0228
(1.00) 		4.02e-19
(9.54e-17) 		0.475
(1.00)
ATRX 114 (39%) 175 0.0185
(1.00) 		0.0572
(1.00) 		1.52e-17
(3.55e-15) 		1.83e-37
(4.49e-35) 		0.273
(1.00) 		0.838
(1.00) 		2.31e-18
(5.45e-16) 		8.6e-11
(1.93e-08) 		4.09e-06
(0.000859) 		0.0799
(1.00) 		6.41e-10
(1.43e-07) 		0.0664
(1.00)
FUBP1 26 (9%) 263 0.0248
(1.00) 		0.00595
(1.00) 		2.22e-09
(4.91e-07) 		2.29e-11
(5.17e-09) 		0.0188
(1.00) 		0.168
(1.00) 		2.26e-09
(4.97e-07) 		3.81e-09
(8.34e-07) 		5.19e-05
(0.0106) 		0.245
(1.00) 		2.04e-06
(0.00043) 		1
(1.00)
NOTCH1 29 (10%) 260 0.463
(1.00) 		0.223
(1.00) 		0.00784
(1.00) 		5.24e-08
(1.13e-05) 		0.875
(1.00) 		0.231
(1.00) 		7.96e-05
(0.0161) 		4.19e-06
(0.000876) 		0.00339
(0.648) 		0.000876
(0.172) 		0.000393
(0.0786) 		0.00786
(1.00)
EGFR 17 (6%) 272 8.91e-10
(1.98e-07) 		1.03e-11
(2.35e-09) 		0.00754
(1.00) 		0.121
(1.00) 		4.4e-07
(9.33e-05) 		0.0737
(1.00) 		0.0107
(1.00) 		0.132
(1.00) 		2.75e-05
(0.00564) 		0.778
(1.00)
PIK3CA 25 (9%) 264 0.00215
(0.417) 		4.69e-06
(0.000972) 		0.566
(1.00) 		0.107
(1.00) 		0.0431
(1.00) 		0.00683
(1.00) 		0.0518
(1.00) 		0.637
(1.00) 		0.0064
(1.00) 		0.82
(1.00)
IDH2 12 (4%) 277 0.0328
(1.00) 		0.0258
(1.00) 		0.517
(1.00) 		1
(1.00) 		0.0154
(1.00) 		0.000162
(0.0326) 		0.0281
(1.00) 		0.0619
(1.00) 		0.0465
(1.00) 		0.0927
(1.00)
NF1 19 (7%) 270 0.0169
(1.00) 		4.67e-06
(0.000972) 		0.0318
(1.00) 		0.305
(1.00) 		0.0084
(1.00) 		0.857
(1.00) 		0.388
(1.00) 		0.23
(1.00) 		0.291
(1.00) 		0.585
(1.00)
STK19 8 (3%) 281 0.427
(1.00) 		0.147
(1.00) 		0.0183
(1.00) 		0.0121
(1.00) 		0.695
(1.00) 		0.781
(1.00) 		0.567
(1.00) 		0.648
(1.00) 		0.651
(1.00) 		1
(1.00)
PIK3R1 13 (4%) 276 0.602
(1.00) 		0.865
(1.00) 		0.108
(1.00) 		0.146
(1.00) 		0.89
(1.00) 		1
(1.00) 		0.826
(1.00) 		0.451
(1.00) 		0.743
(1.00) 		0.684
(1.00) 		0.61
(1.00) 		0.679
(1.00)
PCDHAC2 17 (6%) 272 0.00336
(0.646) 		0.513
(1.00) 		1
(1.00) 		0.453
(1.00) 		0.542
(1.00) 		0.54
(1.00) 		0.808
(1.00) 		0.179
(1.00) 		0.357
(1.00) 		0.36
(1.00)
CREBZF 5 (2%) 284 0.206
(1.00) 		0.0369
(1.00) 		0.0857
(1.00) 		0.047
(1.00) 		0.679
(1.00) 		0.176
(1.00) 		0.786
(1.00) 		0.36
(1.00) 		0.591
(1.00) 		0.235
(1.00)
EIF1AX 4 (1%) 285 0.818
(1.00) 		0.307
(1.00) 		0.378
(1.00) 		1
(1.00) 		0.859
(1.00) 		0.808
(1.00) 		0.185
(1.00) 		0.697
(1.00) 		0.211
(1.00) 		0.177
(1.00)
HTRA2 4 (1%) 285 0.818
(1.00) 		1
(1.00) 		0.414
(1.00) 		1
(1.00) 		0.991
(1.00) 		0.62
(1.00) 		0.423
(1.00) 		1
(1.00) 		0.791
(1.00) 		1
(1.00)
VAV3 8 (3%) 281 0.427
(1.00) 		0.838
(1.00) 		0.962
(1.00) 		0.605
(1.00) 		0.0678
(1.00) 		0.781
(1.00) 		0.701
(1.00) 		0.138
(1.00) 		0.952
(1.00) 		0.531
(1.00)
TMEM216 3 (1%) 286 0.167
(1.00) 		1
(1.00) 		0.794
(1.00) 		0.646
(1.00) 		0.926
(1.00) 		0.538
(1.00) 		0.492
(1.00) 		0.217
(1.00) 		0.96
(1.00) 		0.608
(1.00)
SPANXE 4 (1%) 285 0.571
(1.00) 		0.8
(1.00) 		0.344
(1.00) 		1
(1.00) 		0.822
(1.00) 		0.62
(1.00) 		0.829
(1.00) 		1
(1.00) 		0.848
(1.00) 		1
(1.00)
TCF12 8 (3%) 281 0.728
(1.00) 		0.458
(1.00) 		0.198
(1.00) 		0.168
(1.00) 		0.181
(1.00) 		0.478
(1.00) 		0.499
(1.00) 		0.138
(1.00) 		0.165
(1.00) 		1
(1.00)
SMARCA4 13 (4%) 276 0.172
(1.00) 		0.143
(1.00) 		0.317
(1.00) 		1
(1.00) 		0.33
(1.00) 		0.574
(1.00) 		0.557
(1.00) 		0.74
(1.00) 		0.585
(1.00) 		0.36
(1.00)
BCOR 9 (3%) 280 1
(1.00) 		1
(1.00) 		0.383
(1.00) 		0.797
(1.00) 		0.916
(1.00) 		0.773
(1.00) 		0.876
(1.00) 		0.102
(1.00) 		0.518
(1.00) 		0.56
(1.00) 		0.738
(1.00) 		0.768
(1.00)
'NOTCH1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S1.  Gene #1: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 7
NOTCH1 MUTATED 0 2 1
NOTCH1 WILD-TYPE 9 8 6
'NOTCH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.223 (Fisher's exact test), Q value = 1

Table S2.  Gene #1: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 5 10 4
NOTCH1 MUTATED 2 1 0 0
NOTCH1 WILD-TYPE 5 4 10 4
'NOTCH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00784 (Fisher's exact test), Q value = 1

Table S3.  Gene #1: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
NOTCH1 MUTATED 4 4 21
NOTCH1 WILD-TYPE 86 64 107

Figure S1.  Get High-res Image Gene #1: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'NOTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 5.24e-08 (Fisher's exact test), Q value = 1.1e-05

Table S4.  Gene #1: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
NOTCH1 MUTATED 6 0 0 22
NOTCH1 WILD-TYPE 122 36 43 56

Figure S2.  Get High-res Image Gene #1: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'NOTCH1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S5.  Gene #1: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
NOTCH1 MUTATED 4 6 7 9
NOTCH1 WILD-TYPE 48 55 58 64
'NOTCH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S6.  Gene #1: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
NOTCH1 MUTATED 2 11 13
NOTCH1 WILD-TYPE 6 115 104
'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 7.96e-05 (Chi-square test), Q value = 0.016

Table S7.  Gene #1: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
NOTCH1 MUTATED 2 1 12 14 0 0
NOTCH1 WILD-TYPE 73 57 36 74 6 13

Figure S3.  Get High-res Image Gene #1: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.19e-06 (Fisher's exact test), Q value = 0.00088

Table S8.  Gene #1: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
NOTCH1 MUTATED 3 7 19
NOTCH1 WILD-TYPE 145 33 81

Figure S4.  Get High-res Image Gene #1: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00339 (Chi-square test), Q value = 0.65

Table S9.  Gene #1: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
NOTCH1 MUTATED 0 1 1 4 16 7 0
NOTCH1 WILD-TYPE 40 52 15 16 69 56 12

Figure S5.  Get High-res Image Gene #1: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000876 (Fisher's exact test), Q value = 0.17

Table S10.  Gene #1: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
NOTCH1 MUTATED 22 0 7
NOTCH1 WILD-TYPE 102 14 144

Figure S6.  Get High-res Image Gene #1: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000393 (Chi-square test), Q value = 0.079

Table S11.  Gene #1: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
NOTCH1 MUTATED 1 1 7 15 4 1 0
NOTCH1 WILD-TYPE 58 57 20 66 35 9 15

Figure S7.  Get High-res Image Gene #1: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00786 (Fisher's exact test), Q value = 1

Table S12.  Gene #1: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
NOTCH1 MUTATED 0 21 8
NOTCH1 WILD-TYPE 4 108 148

Figure S8.  Get High-res Image Gene #1: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00215 (Fisher's exact test), Q value = 0.42

Table S13.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
PIK3CA MUTATED 1 7 17
PIK3CA WILD-TYPE 89 61 111

Figure S9.  Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4.69e-06 (Fisher's exact test), Q value = 0.00097

Table S14.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
PIK3CA MUTATED 1 5 3 16
PIK3CA WILD-TYPE 127 31 40 62

Figure S10.  Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S15.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
PIK3CA MUTATED 3 7 4 8
PIK3CA WILD-TYPE 49 54 61 65
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S16.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
PIK3CA MUTATED 2 8 12
PIK3CA WILD-TYPE 6 118 105
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0431 (Chi-square test), Q value = 1

Table S17.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
PIK3CA MUTATED 1 5 7 9 0 3
PIK3CA WILD-TYPE 74 53 41 79 6 10

Figure S11.  Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00683 (Fisher's exact test), Q value = 1

Table S18.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
PIK3CA MUTATED 6 7 12
PIK3CA WILD-TYPE 142 33 88

Figure S12.  Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0518 (Chi-square test), Q value = 1

Table S19.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
PIK3CA MUTATED 1 6 0 4 8 3 3
PIK3CA WILD-TYPE 39 47 16 16 77 60 9
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S20.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
PIK3CA MUTATED 10 2 13
PIK3CA WILD-TYPE 114 12 138
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0064 (Chi-square test), Q value = 1

Table S21.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
PIK3CA MUTATED 0 6 6 9 1 0 3
PIK3CA WILD-TYPE 59 52 21 72 38 10 12

Figure S13.  Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.82 (Fisher's exact test), Q value = 1

Table S22.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
PIK3CA MUTATED 0 12 13
PIK3CA WILD-TYPE 4 117 143
'IDH2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0328 (Fisher's exact test), Q value = 1

Table S23.  Gene #3: 'IDH2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
IDH2 MUTATED 1 1 10
IDH2 WILD-TYPE 89 67 118

Figure S14.  Get High-res Image Gene #3: 'IDH2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'IDH2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0258 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'IDH2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
IDH2 MUTATED 2 0 3 7
IDH2 WILD-TYPE 126 36 40 71

Figure S15.  Get High-res Image Gene #3: 'IDH2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'IDH2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.517 (Fisher's exact test), Q value = 1

Table S25.  Gene #3: 'IDH2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
IDH2 MUTATED 1 4 2 5
IDH2 WILD-TYPE 51 57 63 68
'IDH2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S26.  Gene #3: 'IDH2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
IDH2 MUTATED 0 6 6
IDH2 WILD-TYPE 8 120 111
'IDH2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0154 (Chi-square test), Q value = 1

Table S27.  Gene #3: 'IDH2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
IDH2 MUTATED 0 0 4 8 0 0
IDH2 WILD-TYPE 75 58 44 80 6 13

Figure S16.  Get High-res Image Gene #3: 'IDH2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'IDH2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000162 (Fisher's exact test), Q value = 0.033

Table S28.  Gene #3: 'IDH2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
IDH2 MUTATED 0 4 8
IDH2 WILD-TYPE 148 36 92

Figure S17.  Get High-res Image Gene #3: 'IDH2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'IDH2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0281 (Chi-square test), Q value = 1

Table S29.  Gene #3: 'IDH2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
IDH2 MUTATED 0 1 0 3 7 1 0
IDH2 WILD-TYPE 40 52 16 17 78 62 12

Figure S18.  Get High-res Image Gene #3: 'IDH2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'IDH2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0619 (Fisher's exact test), Q value = 1

Table S30.  Gene #3: 'IDH2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
IDH2 MUTATED 9 0 3
IDH2 WILD-TYPE 115 14 148
'IDH2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0465 (Chi-square test), Q value = 1

Table S31.  Gene #3: 'IDH2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
IDH2 MUTATED 0 2 3 7 0 0 0
IDH2 WILD-TYPE 59 56 24 74 39 10 15

Figure S19.  Get High-res Image Gene #3: 'IDH2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'IDH2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0927 (Fisher's exact test), Q value = 1

Table S32.  Gene #3: 'IDH2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
IDH2 MUTATED 0 9 3
IDH2 WILD-TYPE 4 120 153
'IDH1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S33.  Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 7
IDH1 MUTATED 9 7 6
IDH1 WILD-TYPE 0 3 1
'IDH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.523 (Fisher's exact test), Q value = 1

Table S34.  Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 5 10 4
IDH1 MUTATED 5 5 9 3
IDH1 WILD-TYPE 2 0 1 1
'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1.97e-16 (Fisher's exact test), Q value = 4.6e-14

Table S35.  Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
IDH1 MUTATED 84 25 109
IDH1 WILD-TYPE 6 43 19

Figure S20.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2.57e-37 (Fisher's exact test), Q value = 6.3e-35

Table S36.  Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
IDH1 MUTATED 125 0 21 71
IDH1 WILD-TYPE 3 36 22 7

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

'IDH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 3.15e-07 (Fisher's exact test), Q value = 6.7e-05

Table S37.  Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
IDH1 MUTATED 42 31 61 57
IDH1 WILD-TYPE 10 30 4 16

Figure S22.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'IDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S38.  Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
IDH1 MUTATED 8 88 95
IDH1 WILD-TYPE 0 38 22

Figure S23.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 6.91e-23 (Chi-square test), Q value = 1.6e-20

Table S39.  Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
IDH1 MUTATED 74 15 44 67 6 13
IDH1 WILD-TYPE 1 43 4 21 0 0

Figure S24.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 1

Table S40.  Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
IDH1 MUTATED 103 36 80
IDH1 WILD-TYPE 45 4 20

Figure S25.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2.69e-08 (Chi-square test), Q value = 5.8e-06

Table S41.  Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
IDH1 MUTATED 40 24 11 17 65 51 12
IDH1 WILD-TYPE 0 29 5 3 20 12 0

Figure S26.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0228 (Fisher's exact test), Q value = 1

Table S42.  Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
IDH1 MUTATED 103 12 105
IDH1 WILD-TYPE 21 2 46

Figure S27.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.02e-19 (Chi-square test), Q value = 9.5e-17

Table S43.  Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
IDH1 MUTATED 59 17 24 62 36 8 14
IDH1 WILD-TYPE 0 41 3 19 3 2 1

Figure S28.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.475 (Fisher's exact test), Q value = 1

Table S44.  Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
IDH1 MUTATED 4 101 115
IDH1 WILD-TYPE 0 28 41
'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0627 (Fisher's exact test), Q value = 1

Table S45.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 7
TP53 MUTATED 8 4 3
TP53 WILD-TYPE 1 6 4
'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00754 (Fisher's exact test), Q value = 1

Table S46.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 5 10 4
TP53 MUTATED 1 2 8 4
TP53 WILD-TYPE 6 3 2 0

Figure S29.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 4.02e-26 (Fisher's exact test), Q value = 9.7e-24

Table S47.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
TP53 MUTATED 85 27 34
TP53 WILD-TYPE 5 41 94

Figure S30.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 9.23e-53 (Fisher's exact test), Q value = 2.3e-50

Table S48.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
TP53 MUTATED 124 7 12 3
TP53 WILD-TYPE 4 29 31 75

Figure S31.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 1

Table S49.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
TP53 MUTATED 33 30 39 29
TP53 WILD-TYPE 19 31 26 44

Figure S32.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.656 (Fisher's exact test), Q value = 1

Table S50.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
TP53 MUTATED 5 68 58
TP53 WILD-TYPE 3 58 59
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 2.53e-26 (Chi-square test), Q value = 6.1e-24

Table S51.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
TP53 MUTATED 75 20 2 36 6 7
TP53 WILD-TYPE 0 38 46 52 0 6

Figure S33.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.06e-17 (Fisher's exact test), Q value = 2.5e-15

Table S52.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
TP53 MUTATED 106 1 39
TP53 WILD-TYPE 42 39 61

Figure S34.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 7.68e-11 (Chi-square test), Q value = 1.7e-08

Table S53.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
TP53 MUTATED 38 25 13 2 33 32 3
TP53 WILD-TYPE 2 28 3 18 52 31 9

Figure S35.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 1

Table S54.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
TP53 MUTATED 51 7 88
TP53 WILD-TYPE 73 7 63

Figure S36.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.23e-16 (Chi-square test), Q value = 7.5e-14

Table S55.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
TP53 MUTATED 56 19 4 30 24 9 4
TP53 WILD-TYPE 3 39 23 51 15 1 11

Figure S37.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00104 (Fisher's exact test), Q value = 0.2

Table S56.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
TP53 MUTATED 4 52 90
TP53 WILD-TYPE 0 77 66

Figure S38.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'STK19 MUTATION STATUS' versus 'CN_CNMF'

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

Table S57.  Gene #6: 'STK19 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
STK19 MUTATED 3 3 2
STK19 WILD-TYPE 87 65 126
'STK19 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S58.  Gene #6: 'STK19 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
STK19 MUTATED 4 2 2 0
STK19 WILD-TYPE 124 34 41 78
'STK19 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 1

Table S59.  Gene #6: 'STK19 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
STK19 MUTATED 4 0 0 2
STK19 WILD-TYPE 48 61 65 71

Figure S39.  Get High-res Image Gene #6: 'STK19 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'STK19 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S60.  Gene #6: 'STK19 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
STK19 MUTATED 1 0 5
STK19 WILD-TYPE 7 126 112

Figure S40.  Get High-res Image Gene #6: 'STK19 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'STK19 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.695 (Chi-square test), Q value = 1

Table S61.  Gene #6: 'STK19 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
STK19 MUTATED 2 2 0 4 0 0
STK19 WILD-TYPE 73 56 48 84 6 13
'STK19 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.781 (Fisher's exact test), Q value = 1

Table S62.  Gene #6: 'STK19 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
STK19 MUTATED 5 0 3
STK19 WILD-TYPE 143 40 97
'STK19 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.567 (Chi-square test), Q value = 1

Table S63.  Gene #6: 'STK19 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
STK19 MUTATED 1 2 1 0 4 0 0
STK19 WILD-TYPE 39 51 15 20 81 63 12
'STK19 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S64.  Gene #6: 'STK19 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
STK19 MUTATED 5 0 3
STK19 WILD-TYPE 119 14 148
'STK19 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.651 (Chi-square test), Q value = 1

Table S65.  Gene #6: 'STK19 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
STK19 MUTATED 2 2 0 4 0 0 0
STK19 WILD-TYPE 57 56 27 77 39 10 15
'STK19 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S66.  Gene #6: 'STK19 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
STK19 MUTATED 0 4 4
STK19 WILD-TYPE 4 125 152
'CIC MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0428 (Fisher's exact test), Q value = 1

Table S67.  Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 7
CIC MUTATED 0 5 2
CIC WILD-TYPE 9 5 5

Figure S41.  Get High-res Image Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CIC MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00303 (Fisher's exact test), Q value = 0.59

Table S68.  Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 5 10 4
CIC MUTATED 5 2 0 0
CIC WILD-TYPE 2 3 10 4

Figure S42.  Get High-res Image Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'CN_CNMF'

P value = 2.92e-17 (Fisher's exact test), Q value = 6.8e-15

Table S69.  Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
CIC MUTATED 0 3 51
CIC WILD-TYPE 90 65 77

Figure S43.  Get High-res Image Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CIC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4.06e-32 (Fisher's exact test), Q value = 9.9e-30

Table S70.  Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
CIC MUTATED 0 0 2 51
CIC WILD-TYPE 128 36 41 27

Figure S44.  Get High-res Image Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CIC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 7.25e-05 (Fisher's exact test), Q value = 0.015

Table S71.  Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
CIC MUTATED 1 6 20 15
CIC WILD-TYPE 51 55 45 58

Figure S45.  Get High-res Image Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'CIC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S72.  Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
CIC MUTATED 3 22 17
CIC WILD-TYPE 5 104 100
'CIC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 9.12e-24 (Chi-square test), Q value = 2.2e-21

Table S73.  Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
CIC MUTATED 0 0 34 18 0 2
CIC WILD-TYPE 75 58 14 70 6 11

Figure S46.  Get High-res Image Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CIC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.82e-24 (Fisher's exact test), Q value = 1.2e-21

Table S74.  Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
CIC MUTATED 1 29 24
CIC WILD-TYPE 147 11 76

Figure S47.  Get High-res Image Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 7.81e-13 (Chi-square test), Q value = 1.8e-10

Table S75.  Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
CIC MUTATED 0 3 0 15 18 12 6
CIC WILD-TYPE 40 50 16 5 67 51 6

Figure S48.  Get High-res Image Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CIC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00995 (Fisher's exact test), Q value = 1

Table S76.  Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
CIC MUTATED 33 1 20
CIC WILD-TYPE 91 13 131

Figure S49.  Get High-res Image Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.85e-11 (Chi-square test), Q value = 4.2e-09

Table S77.  Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
CIC MUTATED 1 5 18 19 6 0 5
CIC WILD-TYPE 58 53 9 62 33 10 10

Figure S50.  Get High-res Image Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'CIC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.405 (Fisher's exact test), Q value = 1

Table S78.  Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
CIC MUTATED 0 28 26
CIC WILD-TYPE 4 101 130
'ATRX MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 1

Table S79.  Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 7
ATRX MUTATED 8 3 2
ATRX WILD-TYPE 1 7 5

Figure S51.  Get High-res Image Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'ATRX MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0572 (Fisher's exact test), Q value = 1

Table S80.  Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 5 10 4
ATRX MUTATED 1 2 8 2
ATRX WILD-TYPE 6 3 2 2
'ATRX MUTATION STATUS' versus 'CN_CNMF'

P value = 1.52e-17 (Fisher's exact test), Q value = 3.5e-15

Table S81.  Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
ATRX MUTATED 69 20 25
ATRX WILD-TYPE 21 48 103

Figure S52.  Get High-res Image Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ATRX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.83e-37 (Fisher's exact test), Q value = 4.5e-35

Table S82.  Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
ATRX MUTATED 101 1 10 2
ATRX WILD-TYPE 27 35 33 76

Figure S53.  Get High-res Image Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'ATRX MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S83.  Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
ATRX MUTATED 25 23 31 25
ATRX WILD-TYPE 27 38 34 48
'ATRX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.838 (Fisher's exact test), Q value = 1

Table S84.  Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
ATRX MUTATED 4 51 49
ATRX WILD-TYPE 4 75 68
'ATRX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 2.31e-18 (Chi-square test), Q value = 5.4e-16

Table S85.  Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
ATRX MUTATED 61 12 1 32 3 5
ATRX WILD-TYPE 14 46 47 56 3 8

Figure S54.  Get High-res Image Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'ATRX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.6e-11 (Fisher's exact test), Q value = 1.9e-08

Table S86.  Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
ATRX MUTATED 81 1 32
ATRX WILD-TYPE 67 39 68

Figure S55.  Get High-res Image Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 4.09e-06 (Chi-square test), Q value = 0.00086

Table S87.  Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
ATRX MUTATED 29 17 11 2 28 24 3
ATRX WILD-TYPE 11 36 5 18 57 39 9

Figure S56.  Get High-res Image Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'ATRX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0799 (Fisher's exact test), Q value = 1

Table S88.  Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
ATRX MUTATED 43 3 68
ATRX WILD-TYPE 81 11 83
'ATRX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.41e-10 (Chi-square test), Q value = 1.4e-07

Table S89.  Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
ATRX MUTATED 43 13 2 25 19 7 5
ATRX WILD-TYPE 16 45 25 56 20 3 10

Figure S57.  Get High-res Image Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'ATRX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0664 (Fisher's exact test), Q value = 1

Table S90.  Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
ATRX MUTATED 3 43 68
ATRX WILD-TYPE 1 86 88
'FUBP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0248 (Fisher's exact test), Q value = 1

Table S91.  Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 7
FUBP1 MUTATED 0 4 0
FUBP1 WILD-TYPE 9 6 7

Figure S58.  Get High-res Image Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'FUBP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00595 (Fisher's exact test), Q value = 1

Table S92.  Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 5 10 4
FUBP1 MUTATED 4 0 0 0
FUBP1 WILD-TYPE 3 5 10 4

Figure S59.  Get High-res Image Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'FUBP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 2.22e-09 (Fisher's exact test), Q value = 4.9e-07

Table S93.  Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
FUBP1 MUTATED 0 0 26
FUBP1 WILD-TYPE 90 68 102

Figure S60.  Get High-res Image Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FUBP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2.29e-11 (Fisher's exact test), Q value = 5.2e-09

Table S94.  Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
FUBP1 MUTATED 0 0 1 22
FUBP1 WILD-TYPE 128 36 42 56

Figure S61.  Get High-res Image Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'FUBP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 1

Table S95.  Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
FUBP1 MUTATED 1 2 9 10
FUBP1 WILD-TYPE 51 59 56 63

Figure S62.  Get High-res Image Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'FUBP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.168 (Fisher's exact test), Q value = 1

Table S96.  Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
FUBP1 MUTATED 2 9 11
FUBP1 WILD-TYPE 6 117 106
'FUBP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 2.26e-09 (Chi-square test), Q value = 5e-07

Table S97.  Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
FUBP1 MUTATED 0 0 16 8 0 2
FUBP1 WILD-TYPE 75 58 32 80 6 11

Figure S63.  Get High-res Image Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'FUBP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.81e-09 (Fisher's exact test), Q value = 8.3e-07

Table S98.  Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
FUBP1 MUTATED 1 13 12
FUBP1 WILD-TYPE 147 27 88

Figure S64.  Get High-res Image Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'FUBP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 5.19e-05 (Chi-square test), Q value = 0.011

Table S99.  Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
FUBP1 MUTATED 0 1 0 7 9 6 3
FUBP1 WILD-TYPE 40 52 16 13 76 57 9

Figure S65.  Get High-res Image Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'FUBP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.245 (Fisher's exact test), Q value = 1

Table S100.  Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
FUBP1 MUTATED 14 2 10
FUBP1 WILD-TYPE 110 12 141
'FUBP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.04e-06 (Chi-square test), Q value = 0.00043

Table S101.  Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
FUBP1 MUTATED 1 1 10 10 2 0 2
FUBP1 WILD-TYPE 58 57 17 71 37 10 13

Figure S66.  Get High-res Image Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'FUBP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S102.  Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
FUBP1 MUTATED 0 12 14
FUBP1 WILD-TYPE 4 117 142
'EGFR MUTATION STATUS' versus 'CN_CNMF'

P value = 8.91e-10 (Fisher's exact test), Q value = 2e-07

Table S103.  Gene #10: 'EGFR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
EGFR MUTATED 0 16 1
EGFR WILD-TYPE 90 52 127

Figure S67.  Get High-res Image Gene #10: 'EGFR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.03e-11 (Fisher's exact test), Q value = 2.4e-09

Table S104.  Gene #10: 'EGFR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
EGFR MUTATED 0 14 2 1
EGFR WILD-TYPE 128 22 41 77

Figure S68.  Get High-res Image Gene #10: 'EGFR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'EGFR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00754 (Fisher's exact test), Q value = 1

Table S105.  Gene #10: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
EGFR MUTATED 1 9 1 3
EGFR WILD-TYPE 51 52 64 70

Figure S69.  Get High-res Image Gene #10: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'EGFR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S106.  Gene #10: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
EGFR MUTATED 0 11 3
EGFR WILD-TYPE 8 115 114
'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 4.4e-07 (Chi-square test), Q value = 9.3e-05

Table S107.  Gene #10: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
EGFR MUTATED 0 13 0 4 0 0
EGFR WILD-TYPE 75 45 48 84 6 13

Figure S70.  Get High-res Image Gene #10: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'EGFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0737 (Fisher's exact test), Q value = 1

Table S108.  Gene #10: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
EGFR MUTATED 13 0 4
EGFR WILD-TYPE 135 40 96
'EGFR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0107 (Chi-square test), Q value = 1

Table S109.  Gene #10: 'EGFR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
EGFR MUTATED 0 9 1 0 4 3 0
EGFR WILD-TYPE 40 44 15 20 81 60 12

Figure S71.  Get High-res Image Gene #10: 'EGFR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'EGFR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.132 (Fisher's exact test), Q value = 1

Table S110.  Gene #10: 'EGFR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
EGFR MUTATED 4 0 13
EGFR WILD-TYPE 120 14 138
'EGFR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.75e-05 (Chi-square test), Q value = 0.0056

Table S111.  Gene #10: 'EGFR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
EGFR MUTATED 0 12 0 4 1 0 0
EGFR WILD-TYPE 59 46 27 77 38 10 15

Figure S72.  Get High-res Image Gene #10: 'EGFR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'EGFR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.778 (Fisher's exact test), Q value = 1

Table S112.  Gene #10: 'EGFR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
EGFR MUTATED 0 7 10
EGFR WILD-TYPE 4 122 146
'PIK3R1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S113.  Gene #11: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 7
PIK3R1 MUTATED 2 1 0
PIK3R1 WILD-TYPE 7 9 7
'PIK3R1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.865 (Fisher's exact test), Q value = 1

Table S114.  Gene #11: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 5 10 4
PIK3R1 MUTATED 1 0 2 0
PIK3R1 WILD-TYPE 6 5 8 4
'PIK3R1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.108 (Fisher's exact test), Q value = 1

Table S115.  Gene #11: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
PIK3R1 MUTATED 1 3 9
PIK3R1 WILD-TYPE 89 65 119
'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.146 (Fisher's exact test), Q value = 1

Table S116.  Gene #11: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
PIK3R1 MUTATED 3 1 1 7
PIK3R1 WILD-TYPE 125 35 42 71
'PIK3R1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S117.  Gene #11: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
PIK3R1 MUTATED 3 2 4 4
PIK3R1 WILD-TYPE 49 59 61 69
'PIK3R1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S118.  Gene #11: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
PIK3R1 MUTATED 0 7 6
PIK3R1 WILD-TYPE 8 119 111
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.826 (Chi-square test), Q value = 1

Table S119.  Gene #11: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
PIK3R1 MUTATED 2 3 3 5 0 0
PIK3R1 WILD-TYPE 73 55 45 83 6 13
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S120.  Gene #11: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
PIK3R1 MUTATED 5 3 5
PIK3R1 WILD-TYPE 143 37 95
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.743 (Chi-square test), Q value = 1

Table S121.  Gene #11: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
PIK3R1 MUTATED 2 2 0 2 3 4 0
PIK3R1 WILD-TYPE 38 51 16 18 82 59 12
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S122.  Gene #11: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
PIK3R1 MUTATED 5 1 7
PIK3R1 WILD-TYPE 119 13 144
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.61 (Chi-square test), Q value = 1

Table S123.  Gene #11: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
PIK3R1 MUTATED 3 2 3 4 1 0 0
PIK3R1 WILD-TYPE 56 56 24 77 38 10 15
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.679 (Fisher's exact test), Q value = 1

Table S124.  Gene #11: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
PIK3R1 MUTATED 0 5 8
PIK3R1 WILD-TYPE 4 124 148
'PCDHAC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00336 (Fisher's exact test), Q value = 0.65

Table S125.  Gene #12: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
PCDHAC2 MUTATED 6 9 2
PCDHAC2 WILD-TYPE 84 59 126

Figure S73.  Get High-res Image Gene #12: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PCDHAC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S126.  Gene #12: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
PCDHAC2 MUTATED 8 4 2 3
PCDHAC2 WILD-TYPE 120 32 41 75
'PCDHAC2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S127.  Gene #12: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
PCDHAC2 MUTATED 2 3 3 4
PCDHAC2 WILD-TYPE 50 58 62 69
'PCDHAC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S128.  Gene #12: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
PCDHAC2 MUTATED 1 6 5
PCDHAC2 WILD-TYPE 7 120 112
'PCDHAC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.542 (Chi-square test), Q value = 1

Table S129.  Gene #12: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
PCDHAC2 MUTATED 4 4 2 4 1 2
PCDHAC2 WILD-TYPE 71 54 46 84 5 11
'PCDHAC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S130.  Gene #12: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
PCDHAC2 MUTATED 11 2 4
PCDHAC2 WILD-TYPE 137 38 96
'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.808 (Chi-square test), Q value = 1

Table S131.  Gene #12: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
PCDHAC2 MUTATED 4 4 0 1 4 3 1
PCDHAC2 WILD-TYPE 36 49 16 19 81 60 11
'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.179 (Fisher's exact test), Q value = 1

Table S132.  Gene #12: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
PCDHAC2 MUTATED 5 2 10
PCDHAC2 WILD-TYPE 119 12 141
'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.357 (Chi-square test), Q value = 1

Table S133.  Gene #12: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
PCDHAC2 MUTATED 6 3 1 4 0 1 2
PCDHAC2 WILD-TYPE 53 55 26 77 39 9 13
'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.36 (Fisher's exact test), Q value = 1

Table S134.  Gene #12: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
PCDHAC2 MUTATED 0 5 12
PCDHAC2 WILD-TYPE 4 124 144
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 4.87e-09 (Fisher's exact test), Q value = 1.1e-06

Table S135.  Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
PTEN MUTATED 0 13 0
PTEN WILD-TYPE 90 55 128

Figure S74.  Get High-res Image Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2.64e-12 (Fisher's exact test), Q value = 6e-10

Table S136.  Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
PTEN MUTATED 0 12 0 0
PTEN WILD-TYPE 128 24 43 78

Figure S75.  Get High-res Image Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.000505 (Fisher's exact test), Q value = 0.1

Table S137.  Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
PTEN MUTATED 1 8 1 0
PTEN WILD-TYPE 51 53 64 73

Figure S76.  Get High-res Image Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00543 (Fisher's exact test), Q value = 1

Table S138.  Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
PTEN MUTATED 0 10 0
PTEN WILD-TYPE 8 116 117

Figure S77.  Get High-res Image Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 2.06e-08 (Chi-square test), Q value = 4.5e-06

Table S139.  Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
PTEN MUTATED 0 12 0 1 0 0
PTEN WILD-TYPE 75 46 48 87 6 13

Figure S78.  Get High-res Image Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000666 (Fisher's exact test), Q value = 0.13

Table S140.  Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
PTEN MUTATED 13 0 0
PTEN WILD-TYPE 135 40 100

Figure S79.  Get High-res Image Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.59e-05 (Chi-square test), Q value = 0.0033

Table S141.  Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
PTEN MUTATED 0 10 0 0 1 2 0
PTEN WILD-TYPE 40 43 16 20 84 61 12

Figure S80.  Get High-res Image Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000823 (Fisher's exact test), Q value = 0.16

Table S142.  Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
PTEN MUTATED 0 0 13
PTEN WILD-TYPE 124 14 138

Figure S81.  Get High-res Image Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.97e-08 (Chi-square test), Q value = 1.3e-05

Table S143.  Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
PTEN MUTATED 0 12 0 1 0 0 0
PTEN WILD-TYPE 59 46 27 80 39 10 15

Figure S82.  Get High-res Image Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S144.  Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
PTEN MUTATED 0 3 10
PTEN WILD-TYPE 4 126 146
'CREBZF MUTATION STATUS' versus 'CN_CNMF'

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

Table S145.  Gene #14: 'CREBZF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
CREBZF MUTATED 0 1 4
CREBZF WILD-TYPE 90 67 124
'CREBZF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 1

Table S146.  Gene #14: 'CREBZF MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
CREBZF MUTATED 0 0 1 4
CREBZF WILD-TYPE 128 36 42 74

Figure S83.  Get High-res Image Gene #14: 'CREBZF MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CREBZF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0857 (Fisher's exact test), Q value = 1

Table S147.  Gene #14: 'CREBZF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
CREBZF MUTATED 0 1 0 4
CREBZF WILD-TYPE 52 60 65 69
'CREBZF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.047 (Fisher's exact test), Q value = 1

Table S148.  Gene #14: 'CREBZF MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
CREBZF MUTATED 0 0 5
CREBZF WILD-TYPE 8 126 112

Figure S84.  Get High-res Image Gene #14: 'CREBZF MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'CREBZF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.679 (Chi-square test), Q value = 1

Table S149.  Gene #14: 'CREBZF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
CREBZF MUTATED 0 1 1 3 0 0
CREBZF WILD-TYPE 75 57 47 85 6 13
'CREBZF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.176 (Fisher's exact test), Q value = 1

Table S150.  Gene #14: 'CREBZF MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
CREBZF MUTATED 1 0 4
CREBZF WILD-TYPE 147 40 96
'CREBZF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.786 (Chi-square test), Q value = 1

Table S151.  Gene #14: 'CREBZF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
CREBZF MUTATED 0 1 0 0 3 1 0
CREBZF WILD-TYPE 40 52 16 20 82 62 12
'CREBZF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.36 (Fisher's exact test), Q value = 1

Table S152.  Gene #14: 'CREBZF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
CREBZF MUTATED 4 0 1
CREBZF WILD-TYPE 120 14 150
'CREBZF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.591 (Chi-square test), Q value = 1

Table S153.  Gene #14: 'CREBZF MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
CREBZF MUTATED 0 1 1 3 0 0 0
CREBZF WILD-TYPE 59 57 26 78 39 10 15
'CREBZF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.235 (Fisher's exact test), Q value = 1

Table S154.  Gene #14: 'CREBZF MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
CREBZF MUTATED 0 4 1
CREBZF WILD-TYPE 4 125 155
'EIF1AX MUTATION STATUS' versus 'CN_CNMF'

P value = 0.818 (Fisher's exact test), Q value = 1

Table S155.  Gene #15: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
EIF1AX MUTATED 2 1 1
EIF1AX WILD-TYPE 88 67 127
'EIF1AX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.307 (Fisher's exact test), Q value = 1

Table S156.  Gene #15: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
EIF1AX MUTATED 4 0 0 0
EIF1AX WILD-TYPE 124 36 43 78
'EIF1AX MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S157.  Gene #15: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
EIF1AX MUTATED 0 0 2 2
EIF1AX WILD-TYPE 52 61 63 71
'EIF1AX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S158.  Gene #15: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
EIF1AX MUTATED 0 2 2
EIF1AX WILD-TYPE 8 124 115
'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.859 (Chi-square test), Q value = 1

Table S159.  Gene #15: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
EIF1AX MUTATED 2 1 0 1 0 0
EIF1AX WILD-TYPE 73 57 48 87 6 13
'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S160.  Gene #15: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
EIF1AX MUTATED 3 0 1
EIF1AX WILD-TYPE 145 40 99
'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.185 (Chi-square test), Q value = 1

Table S161.  Gene #15: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
EIF1AX MUTATED 2 2 0 0 0 0 0
EIF1AX WILD-TYPE 38 51 16 20 85 63 12
'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S162.  Gene #15: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
EIF1AX MUTATED 1 0 3
EIF1AX WILD-TYPE 123 14 148
'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.211 (Chi-square test), Q value = 1

Table S163.  Gene #15: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
EIF1AX MUTATED 3 1 0 0 0 0 0
EIF1AX WILD-TYPE 56 57 27 81 39 10 15
'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.177 (Fisher's exact test), Q value = 1

Table S164.  Gene #15: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
EIF1AX MUTATED 0 0 4
EIF1AX WILD-TYPE 4 129 152
'HTRA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.818 (Fisher's exact test), Q value = 1

Table S165.  Gene #16: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
HTRA2 MUTATED 2 1 1
HTRA2 WILD-TYPE 88 67 127
'HTRA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S166.  Gene #16: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
HTRA2 MUTATED 2 0 1 1
HTRA2 WILD-TYPE 126 36 42 77
'HTRA2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S167.  Gene #16: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
HTRA2 MUTATED 2 1 0 1
HTRA2 WILD-TYPE 50 60 65 72
'HTRA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S168.  Gene #16: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
HTRA2 MUTATED 0 2 2
HTRA2 WILD-TYPE 8 124 115
'HTRA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.991 (Chi-square test), Q value = 1

Table S169.  Gene #16: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
HTRA2 MUTATED 1 1 1 1 0 0
HTRA2 WILD-TYPE 74 57 47 87 6 13
'HTRA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.62 (Fisher's exact test), Q value = 1

Table S170.  Gene #16: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
HTRA2 MUTATED 2 1 1
HTRA2 WILD-TYPE 146 39 99
'HTRA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.423 (Chi-square test), Q value = 1

Table S171.  Gene #16: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
HTRA2 MUTATED 0 2 0 1 1 0 0
HTRA2 WILD-TYPE 40 51 16 19 84 63 12
'HTRA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S172.  Gene #16: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
HTRA2 MUTATED 2 0 2
HTRA2 WILD-TYPE 122 14 149
'HTRA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.791 (Chi-square test), Q value = 1

Table S173.  Gene #16: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
HTRA2 MUTATED 1 2 0 1 0 0 0
HTRA2 WILD-TYPE 58 56 27 80 39 10 15
'HTRA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S174.  Gene #16: 'HTRA2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
HTRA2 MUTATED 0 2 2
HTRA2 WILD-TYPE 4 127 154
'VAV3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S175.  Gene #17: 'VAV3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
VAV3 MUTATED 3 3 2
VAV3 WILD-TYPE 87 65 126
'VAV3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.838 (Fisher's exact test), Q value = 1

Table S176.  Gene #17: 'VAV3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
VAV3 MUTATED 3 1 2 2
VAV3 WILD-TYPE 125 35 41 76
'VAV3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.962 (Fisher's exact test), Q value = 1

Table S177.  Gene #17: 'VAV3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
VAV3 MUTATED 1 2 2 3
VAV3 WILD-TYPE 51 59 63 70
'VAV3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.605 (Fisher's exact test), Q value = 1

Table S178.  Gene #17: 'VAV3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
VAV3 MUTATED 0 3 5
VAV3 WILD-TYPE 8 123 112
'VAV3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0678 (Chi-square test), Q value = 1

Table S179.  Gene #17: 'VAV3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
VAV3 MUTATED 0 2 1 3 0 2
VAV3 WILD-TYPE 75 56 47 85 6 11
'VAV3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.781 (Fisher's exact test), Q value = 1

Table S180.  Gene #17: 'VAV3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
VAV3 MUTATED 5 0 3
VAV3 WILD-TYPE 143 40 97
'VAV3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.701 (Chi-square test), Q value = 1

Table S181.  Gene #17: 'VAV3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
VAV3 MUTATED 0 2 0 0 3 3 0
VAV3 WILD-TYPE 40 51 16 20 82 60 12
'VAV3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.138 (Fisher's exact test), Q value = 1

Table S182.  Gene #17: 'VAV3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
VAV3 MUTATED 5 1 2
VAV3 WILD-TYPE 119 13 149
'VAV3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.952 (Chi-square test), Q value = 1

Table S183.  Gene #17: 'VAV3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
VAV3 MUTATED 1 2 1 2 1 0 1
VAV3 WILD-TYPE 58 56 26 79 38 10 14
'VAV3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.531 (Fisher's exact test), Q value = 1

Table S184.  Gene #17: 'VAV3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
VAV3 MUTATED 0 5 3
VAV3 WILD-TYPE 4 124 153
'TMEM216 MUTATION STATUS' versus 'CN_CNMF'

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

Table S185.  Gene #18: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
TMEM216 MUTATED 2 1 0
TMEM216 WILD-TYPE 88 67 128
'TMEM216 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S186.  Gene #18: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
TMEM216 MUTATED 2 0 0 1
TMEM216 WILD-TYPE 126 36 43 77
'TMEM216 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S187.  Gene #18: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
TMEM216 MUTATED 1 1 0 1
TMEM216 WILD-TYPE 51 60 65 72
'TMEM216 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S188.  Gene #18: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
TMEM216 MUTATED 0 1 2
TMEM216 WILD-TYPE 8 125 115
'TMEM216 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.926 (Chi-square test), Q value = 1

Table S189.  Gene #18: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
TMEM216 MUTATED 1 0 1 1 0 0
TMEM216 WILD-TYPE 74 58 47 87 6 13
'TMEM216 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.538 (Fisher's exact test), Q value = 1

Table S190.  Gene #18: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
TMEM216 MUTATED 1 1 1
TMEM216 WILD-TYPE 147 39 99
'TMEM216 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.492 (Chi-square test), Q value = 1

Table S191.  Gene #18: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
TMEM216 MUTATED 1 0 0 1 1 0 0
TMEM216 WILD-TYPE 39 53 16 19 84 63 12
'TMEM216 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S192.  Gene #18: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
TMEM216 MUTATED 3 0 0
TMEM216 WILD-TYPE 121 14 151
'TMEM216 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.96 (Chi-square test), Q value = 1

Table S193.  Gene #18: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
TMEM216 MUTATED 1 1 0 1 0 0 0
TMEM216 WILD-TYPE 58 57 27 80 39 10 15
'TMEM216 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.608 (Fisher's exact test), Q value = 1

Table S194.  Gene #18: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
TMEM216 MUTATED 0 2 1
TMEM216 WILD-TYPE 4 127 155
'SPANXE MUTATION STATUS' versus 'CN_CNMF'

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

Table S195.  Gene #19: 'SPANXE MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
SPANXE MUTATED 1 0 3
SPANXE WILD-TYPE 89 68 125
'SPANXE MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S196.  Gene #19: 'SPANXE MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
SPANXE MUTATED 2 0 0 2
SPANXE WILD-TYPE 126 36 43 76
'SPANXE MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S197.  Gene #19: 'SPANXE MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
SPANXE MUTATED 2 1 1 0
SPANXE WILD-TYPE 50 60 64 73
'SPANXE MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S198.  Gene #19: 'SPANXE MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
SPANXE MUTATED 0 2 2
SPANXE WILD-TYPE 8 124 115
'SPANXE MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.822 (Chi-square test), Q value = 1

Table S199.  Gene #19: 'SPANXE MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
SPANXE MUTATED 2 0 1 1 0 0
SPANXE WILD-TYPE 73 58 47 87 6 13
'SPANXE MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.62 (Fisher's exact test), Q value = 1

Table S200.  Gene #19: 'SPANXE MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
SPANXE MUTATED 2 1 1
SPANXE WILD-TYPE 146 39 99
'SPANXE MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.829 (Chi-square test), Q value = 1

Table S201.  Gene #19: 'SPANXE MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
SPANXE MUTATED 0 1 0 0 1 2 0
SPANXE WILD-TYPE 40 52 16 20 84 61 12
'SPANXE MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S202.  Gene #19: 'SPANXE MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
SPANXE MUTATED 2 0 2
SPANXE WILD-TYPE 122 14 149
'SPANXE MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.848 (Chi-square test), Q value = 1

Table S203.  Gene #19: 'SPANXE MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
SPANXE MUTATED 1 0 0 2 1 0 0
SPANXE WILD-TYPE 58 58 27 79 38 10 15
'SPANXE MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S204.  Gene #19: 'SPANXE MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
SPANXE MUTATED 0 2 2
SPANXE WILD-TYPE 4 127 154
'TCF12 MUTATION STATUS' versus 'CN_CNMF'

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

Table S205.  Gene #20: 'TCF12 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
TCF12 MUTATED 2 1 5
TCF12 WILD-TYPE 88 67 123
'TCF12 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S206.  Gene #20: 'TCF12 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
TCF12 MUTATED 2 1 1 4
TCF12 WILD-TYPE 126 35 42 74
'TCF12 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S207.  Gene #20: 'TCF12 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
TCF12 MUTATED 1 1 5 1
TCF12 WILD-TYPE 51 60 60 72
'TCF12 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.168 (Fisher's exact test), Q value = 1

Table S208.  Gene #20: 'TCF12 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
TCF12 MUTATED 1 5 2
TCF12 WILD-TYPE 7 121 115
'TCF12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.181 (Chi-square test), Q value = 1

Table S209.  Gene #20: 'TCF12 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
TCF12 MUTATED 1 2 4 1 0 0
TCF12 WILD-TYPE 74 56 44 87 6 13
'TCF12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S210.  Gene #20: 'TCF12 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
TCF12 MUTATED 3 2 3
TCF12 WILD-TYPE 145 38 97
'TCF12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.499 (Chi-square test), Q value = 1

Table S211.  Gene #20: 'TCF12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
TCF12 MUTATED 1 1 0 2 3 1 0
TCF12 WILD-TYPE 39 52 16 18 82 62 12
'TCF12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.138 (Fisher's exact test), Q value = 1

Table S212.  Gene #20: 'TCF12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
TCF12 MUTATED 5 1 2
TCF12 WILD-TYPE 119 13 149
'TCF12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.165 (Chi-square test), Q value = 1

Table S213.  Gene #20: 'TCF12 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
TCF12 MUTATED 2 1 3 2 0 0 0
TCF12 WILD-TYPE 57 57 24 79 39 10 15
'TCF12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S214.  Gene #20: 'TCF12 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
TCF12 MUTATED 0 4 4
TCF12 WILD-TYPE 4 125 152
'SMARCA4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S215.  Gene #21: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
SMARCA4 MUTATED 7 1 5
SMARCA4 WILD-TYPE 83 67 123
'SMARCA4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.143 (Fisher's exact test), Q value = 1

Table S216.  Gene #21: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
SMARCA4 MUTATED 9 0 0 4
SMARCA4 WILD-TYPE 119 36 43 74
'SMARCA4 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S217.  Gene #21: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
SMARCA4 MUTATED 0 3 4 4
SMARCA4 WILD-TYPE 52 58 61 69
'SMARCA4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S218.  Gene #21: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
SMARCA4 MUTATED 0 6 5
SMARCA4 WILD-TYPE 8 120 112
'SMARCA4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.33 (Chi-square test), Q value = 1

Table S219.  Gene #21: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
SMARCA4 MUTATED 3 0 3 5 1 1
SMARCA4 WILD-TYPE 72 58 45 83 5 12
'SMARCA4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S220.  Gene #21: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
SMARCA4 MUTATED 6 3 4
SMARCA4 WILD-TYPE 142 37 96
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.557 (Chi-square test), Q value = 1

Table S221.  Gene #21: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
SMARCA4 MUTATED 3 0 0 1 5 3 1
SMARCA4 WILD-TYPE 37 53 16 19 80 60 11
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.74 (Fisher's exact test), Q value = 1

Table S222.  Gene #21: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
SMARCA4 MUTATED 7 0 6
SMARCA4 WILD-TYPE 117 14 145
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.585 (Chi-square test), Q value = 1

Table S223.  Gene #21: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
SMARCA4 MUTATED 4 0 1 5 2 0 1
SMARCA4 WILD-TYPE 55 58 26 76 37 10 14
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.36 (Fisher's exact test), Q value = 1

Table S224.  Gene #21: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
SMARCA4 MUTATED 0 8 5
SMARCA4 WILD-TYPE 4 121 151
'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 1

Table S225.  Gene #22: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
NF1 MUTATED 3 10 6
NF1 WILD-TYPE 87 58 122

Figure S85.  Get High-res Image Gene #22: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4.67e-06 (Fisher's exact test), Q value = 0.00097

Table S226.  Gene #22: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
NF1 MUTATED 1 7 6 1
NF1 WILD-TYPE 127 29 37 77

Figure S86.  Get High-res Image Gene #22: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0318 (Fisher's exact test), Q value = 1

Table S227.  Gene #22: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
NF1 MUTATED 1 9 2 4
NF1 WILD-TYPE 51 52 63 69

Figure S87.  Get High-res Image Gene #22: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.305 (Fisher's exact test), Q value = 1

Table S228.  Gene #22: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
NF1 MUTATED 0 11 5
NF1 WILD-TYPE 8 115 112
'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0084 (Chi-square test), Q value = 1

Table S229.  Gene #22: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
NF1 MUTATED 1 10 3 5 0 0
NF1 WILD-TYPE 74 48 45 83 6 13

Figure S88.  Get High-res Image Gene #22: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.857 (Fisher's exact test), Q value = 1

Table S230.  Gene #22: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
NF1 MUTATED 11 2 6
NF1 WILD-TYPE 137 38 94
'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.388 (Chi-square test), Q value = 1

Table S231.  Gene #22: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
NF1 MUTATED 0 5 2 1 5 6 0
NF1 WILD-TYPE 40 48 14 19 80 57 12
'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S232.  Gene #22: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
NF1 MUTATED 5 1 13
NF1 WILD-TYPE 119 13 138
'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.291 (Chi-square test), Q value = 1

Table S233.  Gene #22: 'NF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
NF1 MUTATED 2 8 2 3 2 1 1
NF1 WILD-TYPE 57 50 25 78 37 9 14
'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.585 (Fisher's exact test), Q value = 1

Table S234.  Gene #22: 'NF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
NF1 MUTATED 0 7 12
NF1 WILD-TYPE 4 122 144
'BCOR MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S235.  Gene #23: 'BCOR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 10 7
BCOR MUTATED 1 1 1
BCOR WILD-TYPE 8 9 6
'BCOR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S236.  Gene #23: 'BCOR MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 5 10 4
BCOR MUTATED 1 1 1 0
BCOR WILD-TYPE 6 4 9 4
'BCOR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.383 (Fisher's exact test), Q value = 1

Table S237.  Gene #23: 'BCOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 68 128
BCOR MUTATED 1 2 6
BCOR WILD-TYPE 89 66 122
'BCOR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S238.  Gene #23: 'BCOR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 128 36 43 78
BCOR MUTATED 3 1 1 4
BCOR WILD-TYPE 125 35 42 74
'BCOR MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S239.  Gene #23: 'BCOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 52 61 65 73
BCOR MUTATED 2 2 1 2
BCOR WILD-TYPE 50 59 64 71
'BCOR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.773 (Fisher's exact test), Q value = 1

Table S240.  Gene #23: 'BCOR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 126 117
BCOR MUTATED 0 3 4
BCOR WILD-TYPE 8 123 113
'BCOR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.876 (Chi-square test), Q value = 1

Table S241.  Gene #23: 'BCOR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 75 58 48 88 6 13
BCOR MUTATED 2 1 2 4 0 0
BCOR WILD-TYPE 73 57 46 84 6 13
'BCOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.102 (Fisher's exact test), Q value = 1

Table S242.  Gene #23: 'BCOR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 40 100
BCOR MUTATED 2 1 6
BCOR WILD-TYPE 146 39 94
'BCOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.518 (Chi-square test), Q value = 1

Table S243.  Gene #23: 'BCOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 40 53 16 20 85 63 12
BCOR MUTATED 1 1 0 0 5 1 1
BCOR WILD-TYPE 39 52 16 20 80 62 11
'BCOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.56 (Fisher's exact test), Q value = 1

Table S244.  Gene #23: 'BCOR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 14 151
BCOR MUTATED 4 1 4
BCOR WILD-TYPE 120 13 147
'BCOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.738 (Chi-square test), Q value = 1

Table S245.  Gene #23: 'BCOR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 59 58 27 81 39 10 15
BCOR MUTATED 1 2 1 4 0 0 1
BCOR WILD-TYPE 58 56 26 77 39 10 14
'BCOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.768 (Fisher's exact test), Q value = 1

Table S246.  Gene #23: 'BCOR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 129 156
BCOR MUTATED 0 5 4
BCOR WILD-TYPE 4 124 152
Methods & Data
Input

  • Mutation data file = transformed.cor.cli.txt

  • Molecular subtypes file = LGG-TP.transferedmergedcluster.txt

  • Number of patients = 289

  • Number of significantly mutated genes = 23

  • Number of Molecular subtypes = 12

  • 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] 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)
Copyright © 2014 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle