Correlation between gene mutation status and molecular subtypes
Brain Lower Grade Glioma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1QC021N
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/C1QC021N
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, 51 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • PIK3CA mutation correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • IDH2 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

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

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

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

  • 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_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 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, 51 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
TP53 146 (51%) 143 0.0627
(1.00) 		0.00754
(1.00) 		1.13e-22
(2.71e-20) 		1.44e-52
(3.55e-50) 		0.0296
(1.00) 		0.656
(1.00) 		3.68e-25
(8.9e-23) 		1.99e-17
(4.68e-15) 		0.000184
(0.0374) 		0.00035
(0.0696) 		3.16e-13
(7.31e-11) 		5.07e-05
(0.0106)
CIC 54 (19%) 235 0.0428
(1.00) 		0.00303
(0.579) 		1.16e-23
(2.8e-21) 		5.4e-32
(1.31e-29) 		7.25e-05
(0.0151) 		0.192
(1.00) 		1.18e-23
(2.83e-21) 		1.19e-22
(2.83e-20) 		1.62e-05
(0.00341) 		0.0148
(1.00) 		1.02e-09
(2.26e-07) 		0.00435
(0.822)
PTEN 13 (4%) 276 6.65e-09
(1.46e-06) 		1.64e-10
(3.71e-08) 		0.000505
(0.0995) 		0.00543
(1.00) 		2.06e-08
(4.52e-06) 		0.000379
(0.075) 		0.00236
(0.455) 		0.117
(1.00) 		1.85e-10
(4.17e-08) 		0.000695
(0.136)
NOTCH1 29 (10%) 260 0.463
(1.00) 		0.223
(1.00) 		0.000167
(0.0341) 		3.02e-08
(6.59e-06) 		0.875
(1.00) 		0.231
(1.00) 		0.000128
(0.0263) 		8.06e-06
(0.00172) 		0.00242
(0.464) 		0.00016
(0.0329) 		0.0072
(1.00) 		0.000115
(0.0238)
IDH1 220 (76%) 69 0.272
(1.00) 		0.523
(1.00) 		2.32e-16
(5.44e-14) 		9.6e-40
(2.35e-37) 		3.15e-07
(6.83e-05) 		0.0308
(1.00) 		3.06e-21
(7.26e-19) 		0.00498
(0.937) 		0.0332
(1.00) 		0.555
(1.00) 		6.7e-16
(1.55e-13) 		1.27e-05
(0.00268)
ATRX 114 (39%) 175 0.0185
(1.00) 		0.0572
(1.00) 		6.52e-16
(1.52e-13) 		7.44e-38
(1.82e-35) 		0.273
(1.00) 		0.838
(1.00) 		9.8e-18
(2.31e-15) 		8.3e-10
(1.84e-07) 		0.00881
(1.00) 		0.0113
(1.00) 		1e-06
(0.000215) 		0.0067
(1.00)
FUBP1 26 (9%) 263 0.0248
(1.00) 		0.00595
(1.00) 		3.21e-12
(7.38e-10) 		5.37e-11
(1.22e-08) 		0.0188
(1.00) 		0.168
(1.00) 		6.55e-10
(1.47e-07) 		3.98e-11
(9.07e-09) 		0.00155
(0.3) 		0.419
(1.00) 		0.0296
(1.00) 		0.0992
(1.00)
EGFR 17 (6%) 272 7.79e-10
(1.74e-07) 		2.38e-11
(5.46e-09) 		0.00754
(1.00) 		0.121
(1.00) 		4.55e-07
(9.83e-05) 		0.0904
(1.00) 		0.427
(1.00) 		1
(1.00) 		0.000259
(0.0523) 		0.00898
(1.00)
PIK3CA 25 (9%) 264 0.000281
(0.0565) 		8.22e-06
(0.00174) 		0.566
(1.00) 		0.107
(1.00) 		0.0383
(1.00) 		0.0337
(1.00) 		0.112
(1.00) 		0.714
(1.00) 		0.0298
(1.00) 		0.71
(1.00)
IDH2 12 (4%) 277 0.111
(1.00) 		0.00549
(1.00) 		0.517
(1.00) 		1
(1.00) 		0.0156
(1.00) 		0.000284
(0.0569) 		0.0162
(1.00) 		0.11
(1.00) 		0.176
(1.00) 		0.0808
(1.00)
NF1 19 (7%) 270 0.0144
(1.00) 		1.4e-06
(0.000299) 		0.0318
(1.00) 		0.305
(1.00) 		0.00829
(1.00) 		1
(1.00) 		0.766
(1.00) 		0.573
(1.00) 		0.00129
(0.252) 		0.00349
(0.663)
STK19 8 (3%) 281 0.38
(1.00) 		0.159
(1.00) 		0.0183
(1.00) 		0.0121
(1.00) 		0.714
(1.00) 		0.556
(1.00) 		0.356
(1.00) 		0.75
(1.00) 		0.469
(1.00) 		0.789
(1.00)
PIK3R1 13 (4%) 276 0.602
(1.00) 		0.865
(1.00) 		0.0407
(1.00) 		0.119
(1.00) 		0.89
(1.00) 		1
(1.00) 		0.817
(1.00) 		0.517
(1.00) 		0.329
(1.00) 		0.391
(1.00) 		0.132
(1.00) 		0.824
(1.00)
PCDHAC2 17 (6%) 272 0.02
(1.00) 		0.417
(1.00) 		1
(1.00) 		0.453
(1.00) 		0.598
(1.00) 		1
(1.00) 		0.465
(1.00) 		0.304
(1.00) 		0.596
(1.00) 		0.184
(1.00)
CREBZF 5 (2%) 284 0.0632
(1.00) 		0.0225
(1.00) 		0.0857
(1.00) 		0.047
(1.00) 		0.691
(1.00) 		0.352
(1.00) 		0.623
(1.00) 		0.203
(1.00) 		0.67
(1.00) 		0.291
(1.00)
EIF1AX 4 (1%) 285 0.17
(1.00) 		0.303
(1.00) 		0.378
(1.00) 		1
(1.00) 		0.855
(1.00) 		0.81
(1.00) 		0.721
(1.00) 		0.156
(1.00) 		0.585
(1.00) 		0.241
(1.00)
HTRA2 4 (1%) 285 0.286
(1.00) 		0.698
(1.00) 		0.414
(1.00) 		1
(1.00) 		0.989
(1.00) 		0.635
(1.00) 		0.227
(1.00) 		1
(1.00) 		0.961
(1.00) 		1
(1.00)
VAV3 8 (3%) 281 0.475
(1.00) 		0.618
(1.00) 		0.962
(1.00) 		0.605
(1.00) 		0.0309
(1.00) 		0.0874
(1.00) 		0.396
(1.00) 		0.502
(1.00) 		0.8
(1.00) 		0.177
(1.00)
TMEM216 3 (1%) 286 1
(1.00) 		1
(1.00) 		0.794
(1.00) 		0.646
(1.00) 		0.917
(1.00) 		0.544
(1.00) 		0.185
(1.00) 		0.594
(1.00) 		0.273
(1.00) 		0.617
(1.00)
SPANXE 4 (1%) 285 0.361
(1.00) 		0.788
(1.00) 		0.344
(1.00) 		1
(1.00) 		0.808
(1.00) 		0.635
(1.00) 		0.863
(1.00) 		1
(1.00) 		0.00818
(1.00) 		1
(1.00)
TCF12 8 (3%) 281 0.419
(1.00) 		0.526
(1.00) 		0.198
(1.00) 		0.168
(1.00) 		0.591
(1.00) 		0.486
(1.00) 		0.0935
(1.00) 		0.75
(1.00) 		0.656
(1.00) 		0.789
(1.00)
SMARCA4 13 (4%) 276 0.117
(1.00) 		0.152
(1.00) 		0.317
(1.00) 		1
(1.00) 		0.381
(1.00) 		0.517
(1.00) 		0.147
(1.00) 		0.271
(1.00) 		0.115
(1.00) 		0.326
(1.00)
BCOR 9 (3%) 280 1
(1.00) 		1
(1.00) 		0.466
(1.00) 		0.666
(1.00) 		0.916
(1.00) 		0.773
(1.00) 		0.31
(1.00) 		0.472
(1.00) 		0.811
(1.00) 		0.24
(1.00) 		0.419
(1.00) 		0.252
(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 = 0.000167 (Fisher's exact test), Q value = 0.034

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 67 103
NOTCH1 MUTATED 5 3 21
NOTCH1 WILD-TYPE 111 64 82

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 = 3.02e-08 (Fisher's exact test), Q value = 6.6e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 45 76 33
NOTCH1 MUTATED 6 0 22 0
NOTCH1 WILD-TYPE 125 45 54 33

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 = 0.000128 (Chi-square test), Q value = 0.026

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 74 58 46 90 7 13
NOTCH1 MUTATED 2 1 11 15 0 0
NOTCH1 WILD-TYPE 72 57 35 75 7 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 = 8.06e-06 (Fisher's exact test), Q value = 0.0017

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 143 103
NOTCH1 MUTATED 9 3 17
NOTCH1 WILD-TYPE 33 140 86

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 = 0.00242 (Chi-square test), Q value = 0.46

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 56 97 15 49
NOTCH1 MUTATED 1 2 17 3 6
NOTCH1 WILD-TYPE 71 54 80 12 43

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 = 0.00016 (Fisher's exact test), Q value = 0.033

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 160 127
NOTCH1 MUTATED 0 6 23
NOTCH1 WILD-TYPE 2 154 104

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 = 0.0072 (Chi-square test), Q value = 1

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 CLUS_8
ALL 48 46 37 79 29 32 4 14
NOTCH1 MUTATED 1 0 6 13 6 3 0 0
NOTCH1 WILD-TYPE 47 46 31 66 23 29 4 14

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 = 0.000115 (Fisher's exact test), Q value = 0.024

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 160 120
NOTCH1 MUTATED 0 6 23
NOTCH1 WILD-TYPE 9 154 97

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 = 0.000281 (Fisher's exact test), Q value = 0.056

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 67 103
PIK3CA MUTATED 2 6 17
PIK3CA WILD-TYPE 114 61 86

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 = 8.22e-06 (Fisher's exact test), Q value = 0.0017

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 45 76 33
PIK3CA MUTATED 1 5 15 4
PIK3CA WILD-TYPE 130 40 61 29

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 = 0.0383 (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 74 58 46 90 7 13
PIK3CA MUTATED 1 5 7 9 0 3
PIK3CA WILD-TYPE 73 53 39 81 7 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 = 0.0337 (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 42 143 103
PIK3CA MUTATED 7 7 11
PIK3CA WILD-TYPE 35 136 92

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 = 0.112 (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
ALL 72 56 97 15 49
PIK3CA MUTATED 4 5 9 4 3
PIK3CA WILD-TYPE 68 51 88 11 46
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.714 (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 2 160 127
PIK3CA MUTATED 0 15 10
PIK3CA WILD-TYPE 2 145 117
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0298 (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 CLUS_8
ALL 48 46 37 79 29 32 4 14
PIK3CA MUTATED 0 5 1 8 6 2 0 3
PIK3CA WILD-TYPE 48 41 36 71 23 30 4 11

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 = 0.71 (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 9 160 120
PIK3CA MUTATED 0 13 12
PIK3CA WILD-TYPE 9 147 108
'IDH2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.111 (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 116 67 103
IDH2 MUTATED 3 1 8
IDH2 WILD-TYPE 113 66 95
'IDH2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00549 (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 131 45 76 33
IDH2 MUTATED 2 0 6 4
IDH2 WILD-TYPE 129 45 70 29

Figure S14.  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 = 0.0156 (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 74 58 46 90 7 13
IDH2 MUTATED 0 0 4 8 0 0
IDH2 WILD-TYPE 74 58 42 82 7 13

Figure S15.  Get High-res Image Gene #3: 'IDH2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'IDH2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000284 (Fisher's exact test), Q value = 0.057

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 143 103
IDH2 MUTATED 4 0 8
IDH2 WILD-TYPE 38 143 95

Figure S16.  Get High-res Image Gene #3: 'IDH2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'IDH2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0162 (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
ALL 72 56 97 15 49
IDH2 MUTATED 2 0 8 2 0
IDH2 WILD-TYPE 70 56 89 13 49

Figure S17.  Get High-res Image Gene #3: 'IDH2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'IDH2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.11 (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 2 160 127
IDH2 MUTATED 0 3 9
IDH2 WILD-TYPE 2 157 118
'IDH2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.176 (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 CLUS_8
ALL 48 46 37 79 29 32 4 14
IDH2 MUTATED 0 0 2 6 3 1 0 0
IDH2 WILD-TYPE 48 46 35 73 26 31 4 14
'IDH2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0808 (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 9 160 120
IDH2 MUTATED 0 3 9
IDH2 WILD-TYPE 9 157 111
'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 = 2.32e-16 (Fisher's exact test), Q value = 5.4e-14

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 67 103
IDH1 MUTATED 100 24 94
IDH1 WILD-TYPE 16 43 9

Figure S18.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 9.6e-40 (Fisher's exact test), Q value = 2.4e-37

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 45 76 33
IDH1 MUTATED 128 1 70 18
IDH1 WILD-TYPE 3 44 6 15

Figure S19.  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 = 6.8e-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 S20.  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 S21.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3.06e-21 (Chi-square test), Q value = 7.3e-19

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 74 58 46 90 7 13
IDH1 MUTATED 73 16 42 69 6 13
IDH1 WILD-TYPE 1 42 4 21 1 0

Figure S22.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00498 (Fisher's exact test), Q value = 0.94

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 143 103
IDH1 MUTATED 38 98 83
IDH1 WILD-TYPE 4 45 20

Figure S23.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0332 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 56 97 15 49
IDH1 MUTATED 47 40 77 13 43
IDH1 WILD-TYPE 25 16 20 2 6

Figure S24.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.555 (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 2 160 127
IDH1 MUTATED 2 118 100
IDH1 WILD-TYPE 0 42 27
'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.7e-16 (Chi-square test), Q value = 1.6e-13

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 CLUS_8
ALL 48 46 37 79 29 32 4 14
IDH1 MUTATED 48 13 34 61 26 21 4 13
IDH1 WILD-TYPE 0 33 3 18 3 11 0 1

Figure S25.  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 = 1.27e-05 (Fisher's exact test), Q value = 0.0027

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 160 120
IDH1 MUTATED 1 118 101
IDH1 WILD-TYPE 8 42 19

Figure S26.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'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 S27.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1.13e-22 (Fisher's exact test), Q value = 2.7e-20

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 67 103
TP53 MUTATED 98 27 21
TP53 WILD-TYPE 18 40 82

Figure S28.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.44e-52 (Fisher's exact test), Q value = 3.6e-50

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 45 76 33
TP53 MUTATED 126 8 3 9
TP53 WILD-TYPE 5 37 73 24

Figure S29.  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 S30.  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 = 3.68e-25 (Chi-square test), Q value = 8.9e-23

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 74 58 46 90 7 13
TP53 MUTATED 74 20 2 37 6 7
TP53 WILD-TYPE 0 38 44 53 1 6

Figure S31.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.99e-17 (Fisher's exact test), Q value = 4.7e-15

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 143 103
TP53 MUTATED 1 102 43
TP53 WILD-TYPE 41 41 60

Figure S32.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.000184 (Chi-square test), Q value = 0.037

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 56 97 15 49
TP53 MUTATED 40 40 37 3 26
TP53 WILD-TYPE 32 16 60 12 23

Figure S33.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.07

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 160 127
TP53 MUTATED 2 95 49
TP53 WILD-TYPE 0 65 78

Figure S34.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.16e-13 (Chi-square test), Q value = 7.3e-11

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 CLUS_8
ALL 48 46 37 79 29 32 4 14
TP53 MUTATED 47 15 25 31 7 13 4 4
TP53 WILD-TYPE 1 31 12 48 22 19 0 10

Figure S35.  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 = 5.07e-05 (Fisher's exact test), Q value = 0.011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 160 120
TP53 MUTATED 3 99 44
TP53 WILD-TYPE 6 61 76

Figure S36.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'STK19 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.38 (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 116 67 103
STK19 MUTATED 5 2 1
STK19 WILD-TYPE 111 65 102
'STK19 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.159 (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 131 45 76 33
STK19 MUTATED 4 2 0 2
STK19 WILD-TYPE 127 43 76 31
'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 S37.  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 S38.  Get High-res Image Gene #6: 'STK19 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'STK19 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.714 (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 74 58 46 90 7 13
STK19 MUTATED 2 2 0 4 0 0
STK19 WILD-TYPE 72 56 46 86 7 13
'STK19 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.556 (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 42 143 103
STK19 MUTATED 0 4 4
STK19 WILD-TYPE 42 139 99
'STK19 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.356 (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
ALL 72 56 97 15 49
STK19 MUTATED 1 3 4 0 0
STK19 WILD-TYPE 71 53 93 15 49
'STK19 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.75 (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 2 160 127
STK19 MUTATED 0 4 4
STK19 WILD-TYPE 2 156 123
'STK19 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.469 (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 CLUS_8
ALL 48 46 37 79 29 32 4 14
STK19 MUTATED 1 1 3 3 0 0 0 0
STK19 WILD-TYPE 47 45 34 76 29 32 4 14
'STK19 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.789 (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 9 160 120
STK19 MUTATED 0 4 4
STK19 WILD-TYPE 9 156 116
'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 S39.  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 = 0.58

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 S40.  Get High-res Image Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'CN_CNMF'

P value = 1.16e-23 (Fisher's exact test), Q value = 2.8e-21

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 67 103
CIC MUTATED 0 3 51
CIC WILD-TYPE 116 64 52

Figure S41.  Get High-res Image Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CIC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 5.4e-32 (Fisher's exact test), Q value = 1.3e-29

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 45 76 33
CIC MUTATED 0 0 50 3
CIC WILD-TYPE 131 45 26 30

Figure S42.  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 S43.  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 = 1.18e-23 (Chi-square test), Q value = 2.8e-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 74 58 46 90 7 13
CIC MUTATED 0 0 33 19 0 2
CIC WILD-TYPE 74 58 13 71 7 11

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

'CIC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.19e-22 (Fisher's exact test), Q value = 2.8e-20

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 143 103
CIC MUTATED 29 1 24
CIC WILD-TYPE 13 142 79

Figure S45.  Get High-res Image Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.62e-05 (Chi-square test), Q value = 0.0034

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 56 97 15 49
CIC MUTATED 11 2 23 9 9
CIC WILD-TYPE 61 54 74 6 40

Figure S46.  Get High-res Image Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CIC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0148 (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 2 160 127
CIC MUTATED 0 21 33
CIC WILD-TYPE 2 139 94

Figure S47.  Get High-res Image Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.02e-09 (Chi-square test), Q value = 2.3e-07

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 CLUS_8
ALL 48 46 37 79 29 32 4 14
CIC MUTATED 0 2 8 17 18 5 0 4
CIC WILD-TYPE 48 44 29 62 11 27 4 10

Figure S48.  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 = 0.00435 (Fisher's exact test), Q value = 0.82

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 160 120
CIC MUTATED 0 21 33
CIC WILD-TYPE 9 139 87

Figure S49.  Get High-res Image Gene #7: 'CIC MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'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 S50.  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 = 6.52e-16 (Fisher's exact test), Q value = 1.5e-13

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 67 103
ATRX MUTATED 79 19 16
ATRX WILD-TYPE 37 48 87

Figure S51.  Get High-res Image Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ATRX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 7.44e-38 (Fisher's exact test), Q value = 1.8e-35

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 45 76 33
ATRX MUTATED 103 2 2 7
ATRX WILD-TYPE 28 43 74 26

Figure S52.  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 = 9.8e-18 (Chi-square test), Q value = 2.3e-15

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 74 58 46 90 7 13
ATRX MUTATED 60 12 1 33 3 5
ATRX WILD-TYPE 14 46 45 57 4 8

Figure S53.  Get High-res Image Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'ATRX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.3e-10 (Fisher's exact test), Q value = 1.8e-07

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 143 103
ATRX MUTATED 1 75 38
ATRX WILD-TYPE 41 68 65

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

'ATRX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00881 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 56 97 15 49
ATRX MUTATED 28 33 31 3 19
ATRX WILD-TYPE 44 23 66 12 30

Figure S55.  Get High-res Image Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'ATRX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0113 (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 2 160 127
ATRX MUTATED 1 74 39
ATRX WILD-TYPE 1 86 88

Figure S56.  Get High-res Image Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-06 (Chi-square test), Q value = 0.00022

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 CLUS_8
ALL 48 46 37 79 29 32 4 14
ATRX MUTATED 35 10 20 24 7 10 3 5
ATRX WILD-TYPE 13 36 17 55 22 22 1 9

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 = 0.0067 (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 9 160 120
ATRX MUTATED 1 75 38
ATRX WILD-TYPE 8 85 82

Figure S58.  Get High-res Image Gene #8: 'ATRX MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'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 S59.  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 S60.  Get High-res Image Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'FUBP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 3.21e-12 (Fisher's exact test), Q value = 7.4e-10

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 67 103
FUBP1 MUTATED 0 0 26
FUBP1 WILD-TYPE 116 67 77

Figure S61.  Get High-res Image Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FUBP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 5.37e-11 (Fisher's exact test), Q value = 1.2e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 45 76 33
FUBP1 MUTATED 0 0 21 2
FUBP1 WILD-TYPE 131 45 55 31

Figure S62.  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 S63.  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 = 6.55e-10 (Chi-square test), Q value = 1.5e-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 74 58 46 90 7 13
FUBP1 MUTATED 0 0 16 8 0 2
FUBP1 WILD-TYPE 74 58 30 82 7 11

Figure S64.  Get High-res Image Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'FUBP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.98e-11 (Fisher's exact test), Q value = 9.1e-09

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 143 103
FUBP1 MUTATED 15 0 11
FUBP1 WILD-TYPE 27 143 92

Figure S65.  Get High-res Image Gene #9: 'FUBP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'FUBP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00155 (Chi-square test), Q value = 0.3

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 56 97 15 49
FUBP1 MUTATED 5 0 11 5 5
FUBP1 WILD-TYPE 67 56 86 10 44

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

'FUBP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.419 (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 2 160 127
FUBP1 MUTATED 0 12 14
FUBP1 WILD-TYPE 2 148 113
'FUBP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0296 (Chi-square test), Q value = 1

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 CLUS_8
ALL 48 46 37 79 29 32 4 14
FUBP1 MUTATED 0 2 3 9 7 3 0 2
FUBP1 WILD-TYPE 48 44 34 70 22 29 4 12

Figure S67.  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 = 0.0992 (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 9 160 120
FUBP1 MUTATED 0 10 16
FUBP1 WILD-TYPE 9 150 104
'EGFR MUTATION STATUS' versus 'CN_CNMF'

P value = 7.79e-10 (Fisher's exact test), Q value = 1.7e-07

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 67 103
EGFR MUTATED 1 16 0
EGFR WILD-TYPE 115 51 103

Figure S68.  Get High-res Image Gene #10: 'EGFR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2.38e-11 (Fisher's exact test), Q value = 5.5e-09

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 45 76 33
EGFR MUTATED 0 15 1 1
EGFR WILD-TYPE 131 30 75 32

Figure S69.  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 S70.  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 = 4.55e-07 (Chi-square test), Q value = 9.8e-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 74 58 46 90 7 13
EGFR MUTATED 0 13 0 4 0 0
EGFR WILD-TYPE 74 45 46 86 7 13

Figure S71.  Get High-res Image Gene #10: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'EGFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0904 (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 42 143 103
EGFR MUTATED 1 13 3
EGFR WILD-TYPE 41 130 100
'EGFR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.427 (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
ALL 72 56 97 15 49
EGFR MUTATED 7 4 4 0 2
EGFR WILD-TYPE 65 52 93 15 47
'EGFR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (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 2 160 127
EGFR MUTATED 0 10 7
EGFR WILD-TYPE 2 150 120
'EGFR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000259 (Chi-square test), Q value = 0.052

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 CLUS_8
ALL 48 46 37 79 29 32 4 14
EGFR MUTATED 0 10 1 4 0 2 0 0
EGFR WILD-TYPE 48 36 36 75 29 30 4 14

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 = 0.00898 (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 9 160 120
EGFR MUTATED 3 10 4
EGFR WILD-TYPE 6 150 116

Figure S73.  Get High-res Image Gene #10: 'EGFR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'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 = 0.0407 (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 116 67 103
PIK3R1 MUTATED 2 2 9
PIK3R1 WILD-TYPE 114 65 94

Figure S74.  Get High-res Image Gene #11: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.119 (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 131 45 76 33
PIK3R1 MUTATED 4 1 7 0
PIK3R1 WILD-TYPE 127 44 69 33
'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 = 0.817 (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 74 58 46 90 7 13
PIK3R1 MUTATED 2 3 3 5 0 0
PIK3R1 WILD-TYPE 72 55 43 85 7 13
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.517 (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 42 143 103
PIK3R1 MUTATED 3 5 5
PIK3R1 WILD-TYPE 39 138 98
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.329 (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
ALL 72 56 97 15 49
PIK3R1 MUTATED 4 1 3 2 3
PIK3R1 WILD-TYPE 68 55 94 13 46
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.391 (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 2 160 127
PIK3R1 MUTATED 0 9 4
PIK3R1 WILD-TYPE 2 151 123
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.132 (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 CLUS_8
ALL 48 46 37 79 29 32 4 14
PIK3R1 MUTATED 1 2 1 3 1 5 0 0
PIK3R1 WILD-TYPE 47 44 36 76 28 27 4 14
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.824 (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 9 160 120
PIK3R1 MUTATED 0 8 5
PIK3R1 WILD-TYPE 9 152 115
'PCDHAC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 67 103
PCDHAC2 MUTATED 5 9 3
PCDHAC2 WILD-TYPE 111 58 100

Figure S75.  Get High-res Image Gene #12: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PCDHAC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.417 (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 131 45 76 33
PCDHAC2 MUTATED 8 5 3 1
PCDHAC2 WILD-TYPE 123 40 73 32
'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 = 0.598 (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 74 58 46 90 7 13
PCDHAC2 MUTATED 4 4 2 4 1 2
PCDHAC2 WILD-TYPE 70 54 44 86 6 11
'PCDHAC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (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 42 143 103
PCDHAC2 MUTATED 2 9 6
PCDHAC2 WILD-TYPE 40 134 97
'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.465 (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
ALL 72 56 97 15 49
PCDHAC2 MUTATED 6 5 4 1 1
PCDHAC2 WILD-TYPE 66 51 93 14 48
'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.304 (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 2 160 127
PCDHAC2 MUTATED 0 12 5
PCDHAC2 WILD-TYPE 2 148 122
'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.596 (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 CLUS_8
ALL 48 46 37 79 29 32 4 14
PCDHAC2 MUTATED 4 1 4 4 1 3 0 0
PCDHAC2 WILD-TYPE 44 45 33 75 28 29 4 14
'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.184 (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 9 160 120
PCDHAC2 MUTATED 1 12 4
PCDHAC2 WILD-TYPE 8 148 116
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 6.65e-09 (Fisher's exact test), Q value = 1.5e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 67 103
PTEN MUTATED 0 13 0
PTEN WILD-TYPE 116 54 103

Figure S76.  Get High-res Image Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.64e-10 (Fisher's exact test), Q value = 3.7e-08

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 45 76 33
PTEN MUTATED 0 12 0 0
PTEN WILD-TYPE 131 33 76 33

Figure S77.  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 S78.  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 S79.  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 74 58 46 90 7 13
PTEN MUTATED 0 12 0 1 0 0
PTEN WILD-TYPE 74 46 46 89 7 13

Figure S80.  Get High-res Image Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000379 (Fisher's exact test), Q value = 0.075

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 143 103
PTEN MUTATED 0 13 0
PTEN WILD-TYPE 42 130 103

Figure S81.  Get High-res Image Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00236 (Chi-square test), Q value = 0.45

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 72 56 97 15 49
PTEN MUTATED 9 3 1 0 0
PTEN WILD-TYPE 63 53 96 15 49

Figure S82.  Get High-res Image Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.117 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 160 127
PTEN MUTATED 0 11 2
PTEN WILD-TYPE 2 149 125
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.85e-10 (Chi-square test), Q value = 4.2e-08

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 CLUS_8
ALL 48 46 37 79 29 32 4 14
PTEN MUTATED 0 12 0 1 0 0 0 0
PTEN WILD-TYPE 48 34 37 78 29 32 4 14

Figure S83.  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 = 0.000695 (Fisher's exact test), Q value = 0.14

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 160 120
PTEN MUTATED 2 11 0
PTEN WILD-TYPE 7 149 120

Figure S84.  Get High-res Image Gene #13: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CREBZF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0632 (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 116 67 103
CREBZF MUTATED 0 1 4
CREBZF WILD-TYPE 116 66 99
'CREBZF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0225 (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 131 45 76 33
CREBZF MUTATED 0 0 4 1
CREBZF WILD-TYPE 131 45 72 32

Figure S85.  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 S86.  Get High-res Image Gene #14: 'CREBZF MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'CREBZF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.691 (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 74 58 46 90 7 13
CREBZF MUTATED 0 1 1 3 0 0
CREBZF WILD-TYPE 74 57 45 87 7 13
'CREBZF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.352 (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 42 143 103
CREBZF MUTATED 1 1 3
CREBZF WILD-TYPE 41 142 100
'CREBZF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.623 (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
ALL 72 56 97 15 49
CREBZF MUTATED 0 1 3 0 1
CREBZF WILD-TYPE 72 55 94 15 48
'CREBZF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.203 (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 2 160 127
CREBZF MUTATED 0 1 4
CREBZF WILD-TYPE 2 159 123
'CREBZF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.67 (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 CLUS_8
ALL 48 46 37 79 29 32 4 14
CREBZF MUTATED 0 1 0 3 1 0 0 0
CREBZF WILD-TYPE 48 45 37 76 28 32 4 14
'CREBZF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.291 (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 9 160 120
CREBZF MUTATED 0 1 4
CREBZF WILD-TYPE 9 159 116
'EIF1AX MUTATION STATUS' versus 'CN_CNMF'

P value = 0.17 (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 116 67 103
EIF1AX MUTATED 0 1 3
EIF1AX WILD-TYPE 116 66 100
'EIF1AX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.303 (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 131 45 76 33
EIF1AX MUTATED 4 0 0 0
EIF1AX WILD-TYPE 127 45 76 33
'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 = 0.855 (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 74 58 46 90 7 13
EIF1AX MUTATED 2 1 0 1 0 0
EIF1AX WILD-TYPE 72 57 46 89 7 13
'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.81 (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 42 143 103
EIF1AX MUTATED 0 3 1
EIF1AX WILD-TYPE 42 140 102
'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.721 (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
ALL 72 56 97 15 49
EIF1AX MUTATED 2 1 1 0 0
EIF1AX WILD-TYPE 70 55 96 15 49
'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.156 (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 2 160 127
EIF1AX MUTATED 0 4 0
EIF1AX WILD-TYPE 2 156 127
'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.585 (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 CLUS_8
ALL 48 46 37 79 29 32 4 14
EIF1AX MUTATED 2 1 1 0 0 0 0 0
EIF1AX WILD-TYPE 46 45 36 79 29 32 4 14
'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.241 (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 9 160 120
EIF1AX MUTATED 0 4 0
EIF1AX WILD-TYPE 9 156 120
'HTRA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.286 (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 116 67 103
HTRA2 MUTATED 3 1 0
HTRA2 WILD-TYPE 113 66 103
'HTRA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.698 (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 131 45 76 33
HTRA2 MUTATED 2 0 1 1
HTRA2 WILD-TYPE 129 45 75 32
'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 = 0.989 (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 74 58 46 90 7 13
HTRA2 MUTATED 1 1 1 1 0 0
HTRA2 WILD-TYPE 73 57 45 89 7 13
'HTRA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.635 (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 42 143 103
HTRA2 MUTATED 1 2 1
HTRA2 WILD-TYPE 41 141 102
'HTRA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.227 (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
ALL 72 56 97 15 49
HTRA2 MUTATED 2 0 1 1 0
HTRA2 WILD-TYPE 70 56 96 14 49
'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 2 160 127
HTRA2 MUTATED 0 2 2
HTRA2 WILD-TYPE 2 158 125
'HTRA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.961 (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 CLUS_8
ALL 48 46 37 79 29 32 4 14
HTRA2 MUTATED 1 1 1 1 0 0 0 0
HTRA2 WILD-TYPE 47 45 36 78 29 32 4 14
'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 9 160 120
HTRA2 MUTATED 0 2 2
HTRA2 WILD-TYPE 9 158 118
'VAV3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.475 (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 116 67 103
VAV3 MUTATED 5 1 2
VAV3 WILD-TYPE 111 66 101
'VAV3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.618 (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 131 45 76 33
VAV3 MUTATED 3 1 2 2
VAV3 WILD-TYPE 128 44 74 31
'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 = 0.0309 (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 74 58 46 90 7 13
VAV3 MUTATED 0 2 0 4 0 2
VAV3 WILD-TYPE 74 56 46 86 7 11

Figure S87.  Get High-res Image Gene #17: 'VAV3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'VAV3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0874 (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 42 143 103
VAV3 MUTATED 0 2 6
VAV3 WILD-TYPE 42 141 97
'VAV3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.396 (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
ALL 72 56 97 15 49
VAV3 MUTATED 2 1 5 0 0
VAV3 WILD-TYPE 70 55 92 15 49
'VAV3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.502 (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 2 160 127
VAV3 MUTATED 0 3 5
VAV3 WILD-TYPE 2 157 122
'VAV3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.8 (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 CLUS_8
ALL 48 46 37 79 29 32 4 14
VAV3 MUTATED 1 2 0 3 0 1 0 1
VAV3 WILD-TYPE 47 44 37 76 29 31 4 13
'VAV3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.177 (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 9 160 120
VAV3 MUTATED 1 3 4
VAV3 WILD-TYPE 8 157 116
'TMEM216 MUTATION STATUS' versus 'CN_CNMF'

P value = 1 (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 116 67 103
TMEM216 MUTATED 1 1 1
TMEM216 WILD-TYPE 115 66 102
'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 131 45 76 33
TMEM216 MUTATED 2 0 1 0
TMEM216 WILD-TYPE 129 45 75 33
'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 = 0.917 (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 74 58 46 90 7 13
TMEM216 MUTATED 1 0 1 1 0 0
TMEM216 WILD-TYPE 73 58 45 89 7 13
'TMEM216 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.544 (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 42 143 103
TMEM216 MUTATED 1 1 1
TMEM216 WILD-TYPE 41 142 102
'TMEM216 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.185 (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
ALL 72 56 97 15 49
TMEM216 MUTATED 0 1 1 1 0
TMEM216 WILD-TYPE 72 55 96 14 49
'TMEM216 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.594 (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 2 160 127
TMEM216 MUTATED 0 1 2
TMEM216 WILD-TYPE 2 159 125
'TMEM216 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.273 (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 CLUS_8
ALL 48 46 37 79 29 32 4 14
TMEM216 MUTATED 0 0 2 1 0 0 0 0
TMEM216 WILD-TYPE 48 46 35 78 29 32 4 14
'TMEM216 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.617 (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 9 160 120
TMEM216 MUTATED 0 1 2
TMEM216 WILD-TYPE 9 159 118
'SPANXE MUTATION STATUS' versus 'CN_CNMF'

P value = 0.361 (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 116 67 103
SPANXE MUTATED 1 0 3
SPANXE WILD-TYPE 115 67 100
'SPANXE MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.788 (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 131 45 76 33
SPANXE MUTATED 2 0 2 0
SPANXE WILD-TYPE 129 45 74 33
'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 = 0.808 (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 74 58 46 90 7 13
SPANXE MUTATED 2 0 1 1 0 0
SPANXE WILD-TYPE 72 58 45 89 7 13
'SPANXE MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.635 (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 42 143 103
SPANXE MUTATED 1 2 1
SPANXE WILD-TYPE 41 141 102
'SPANXE MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.863 (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
ALL 72 56 97 15 49
SPANXE MUTATED 1 1 2 0 0
SPANXE WILD-TYPE 71 55 95 15 49
'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 2 160 127
SPANXE MUTATED 0 2 2
SPANXE WILD-TYPE 2 158 125
'SPANXE MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00818 (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 CLUS_8
ALL 48 46 37 79 29 32 4 14
SPANXE MUTATED 1 0 0 1 0 1 1 0
SPANXE WILD-TYPE 47 46 37 78 29 31 3 14

Figure S88.  Get High-res Image Gene #19: 'SPANXE MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'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 9 160 120
SPANXE MUTATED 0 2 2
SPANXE WILD-TYPE 9 158 118
'TCF12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.419 (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 116 67 103
TCF12 MUTATED 2 1 5
TCF12 WILD-TYPE 114 66 98
'TCF12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.526 (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 131 45 76 33
TCF12 MUTATED 3 1 4 0
TCF12 WILD-TYPE 128 44 72 33
'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 = 0.591 (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 74 58 46 90 7 13
TCF12 MUTATED 1 2 3 2 0 0
TCF12 WILD-TYPE 73 56 43 88 7 13
'TCF12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.486 (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 42 143 103
TCF12 MUTATED 2 3 3
TCF12 WILD-TYPE 40 140 100
'TCF12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0935 (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
ALL 72 56 97 15 49
TCF12 MUTATED 2 0 3 2 1
TCF12 WILD-TYPE 70 56 94 13 48
'TCF12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.75 (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 2 160 127
TCF12 MUTATED 0 4 4
TCF12 WILD-TYPE 2 156 123
'TCF12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.656 (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 CLUS_8
ALL 48 46 37 79 29 32 4 14
TCF12 MUTATED 2 1 0 3 2 0 0 0
TCF12 WILD-TYPE 46 45 37 76 27 32 4 14
'TCF12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.789 (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 9 160 120
TCF12 MUTATED 0 4 4
TCF12 WILD-TYPE 9 156 116
'SMARCA4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.117 (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 116 67 103
SMARCA4 MUTATED 9 1 3
SMARCA4 WILD-TYPE 107 66 100
'SMARCA4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.152 (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 131 45 76 33
SMARCA4 MUTATED 9 0 4 0
SMARCA4 WILD-TYPE 122 45 72 33
'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 = 0.381 (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 74 58 46 90 7 13
SMARCA4 MUTATED 3 0 3 5 1 1
SMARCA4 WILD-TYPE 71 58 43 85 6 12
'SMARCA4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.517 (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 42 143 103
SMARCA4 MUTATED 3 5 5
SMARCA4 WILD-TYPE 39 138 98
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.147 (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
ALL 72 56 97 15 49
SMARCA4 MUTATED 2 0 6 2 3
SMARCA4 WILD-TYPE 70 56 91 13 46
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.271 (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 2 160 127
SMARCA4 MUTATED 0 5 8
SMARCA4 WILD-TYPE 2 155 119
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.115 (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 CLUS_8
ALL 48 46 37 79 29 32 4 14
SMARCA4 MUTATED 3 0 1 5 4 0 0 0
SMARCA4 WILD-TYPE 45 46 36 74 25 32 4 14
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.326 (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 9 160 120
SMARCA4 MUTATED 0 5 8
SMARCA4 WILD-TYPE 9 155 112
'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0144 (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 116 67 103
NF1 MUTATED 4 10 5
NF1 WILD-TYPE 112 57 98

Figure S89.  Get High-res Image Gene #22: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.4e-06 (Fisher's exact test), Q value = 3e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 131 45 76 33
NF1 MUTATED 1 10 1 3
NF1 WILD-TYPE 130 35 75 30

Figure S90.  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 S91.  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 = 0.00829 (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 74 58 46 90 7 13
NF1 MUTATED 1 10 3 5 0 0
NF1 WILD-TYPE 73 48 43 85 7 13

Figure S92.  Get High-res Image Gene #22: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (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 42 143 103
NF1 MUTATED 2 10 7
NF1 WILD-TYPE 40 133 96
'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.766 (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
ALL 72 56 97 15 49
NF1 MUTATED 6 5 4 1 3
NF1 WILD-TYPE 66 51 93 14 46
'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.573 (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 2 160 127
NF1 MUTATED 0 12 7
NF1 WILD-TYPE 2 148 120
'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00129 (Chi-square test), Q value = 0.25

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 CLUS_8
ALL 48 46 37 79 29 32 4 14
NF1 MUTATED 1 9 1 3 0 5 0 0
NF1 WILD-TYPE 47 37 36 76 29 27 4 14

Figure S93.  Get High-res Image Gene #22: 'NF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00349 (Fisher's exact test), Q value = 0.66

Table S234.  Gene #22: 'NF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 9 160 120
NF1 MUTATED 3 13 3
NF1 WILD-TYPE 6 147 117

Figure S94.  Get High-res Image Gene #22: 'NF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'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 = 0.466 (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 116 67 103
BCOR MUTATED 2 3 4
BCOR WILD-TYPE 114 64 99
'BCOR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.666 (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 131 45 76 33
BCOR MUTATED 3 1 4 1
BCOR WILD-TYPE 128 44 72 32
'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 = 0.31 (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 74 58 46 90 7 13
BCOR MUTATED 2 0 2 4 1 0
BCOR WILD-TYPE 72 58 44 86 6 13
'BCOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.472 (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 42 143 103
BCOR MUTATED 2 3 4
BCOR WILD-TYPE 40 140 99
'BCOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.811 (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
ALL 72 56 97 15 49
BCOR MUTATED 3 1 4 0 1
BCOR WILD-TYPE 69 55 93 15 48
'BCOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.24 (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 2 160 127
BCOR MUTATED 0 3 6
BCOR WILD-TYPE 2 157 121
'BCOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.419 (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 CLUS_8
ALL 48 46 37 79 29 32 4 14
BCOR MUTATED 0 0 3 3 1 1 0 1
BCOR WILD-TYPE 48 46 34 76 28 31 4 13
'BCOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.252 (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 9 160 120
BCOR MUTATED 1 4 4
BCOR WILD-TYPE 8 156 116
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)
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