Correlation between gene mutation status and molecular subtypes
Rectum Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1TX3DG6
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1TX3DG6
Overview
Introduction

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

Summary

Testing the association between mutation status of 39 genes and 12 molecular subtypes across 122 patients, 48 significant findings detected with P value < 0.05 and Q value < 0.25.

  • CRIPAK mutation correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • TP53 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • MUC4 mutation correlated to 'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • FMN2 mutation correlated to 'MRNASEQ_CNMF'.

  • SHROOM4 mutation correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • CDH1 mutation correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • RBM38 mutation correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • VCX2 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • ERBB2 mutation correlated to 'MRNASEQ_CNMF'.

  • HIST2H2AC mutation correlated to 'MIRSEQ_CNMF'.

  • CTNNB1 mutation correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • KIAA1804 mutation correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • KRAS mutation correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

  • ZNF354C mutation correlated to 'MRNASEQ_CNMF'.

  • BRAF mutation correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • PIK3CA mutation correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • RRP8 mutation correlated to 'RPPA_CNMF' and 'MIRSEQ_CNMF'.

  • RLIM mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 39 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, 48 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 Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
MUC4 25 (20%) 97 0.516
(0.983) 		0.0629
(0.342) 		0.233
(0.703) 		0.00306
(0.0682) 		1e-05
(0.000585) 		1e-05
(0.000585) 		1e-05
(0.000585) 		1e-05
(0.000585) 		0.48
(0.97) 		0.517
(0.983)
CRIPAK 11 (9%) 111 0.645
(1.00) 		0.361
(0.881) 		0.163
(0.601) 		0.0388
(0.284) 		0.00194
(0.0546) 		0.0021
(0.0546) 		0.00233
(0.0559) 		0.00131
(0.0438) 		0.266
(0.764) 		0.76
(1.00)
SHROOM4 7 (6%) 115 0.472
(0.969) 		0.555
(1.00) 		0.638
(1.00) 		0.0828
(0.399) 		0.0148
(0.173) 		0.00239
(0.0559) 		0.018
(0.196) 		0.00201
(0.0546) 		0.186
(0.628) 		0.128
(0.527)
CDH1 12 (10%) 110 0.759
(1.00) 		0.394
(0.901) 		1
(1.00) 		0.621
(1.00) 		0.0136
(0.172) 		0.00523
(0.0979) 		0.00389
(0.0792) 		0.00928
(0.131) 		0.479
(0.97) 		0.688
(1.00)
RBM38 8 (7%) 114 1
(1.00) 		1
(1.00) 		0.103
(0.462) 		0.487
(0.97) 		0.00181
(0.0546) 		0.00949
(0.131) 		0.00463
(0.0903) 		0.00895
(0.131) 		0.671
(1.00) 		0.359
(0.881)
CTNNB1 19 (16%) 103 0.0524
(0.319) 		0.177
(0.619) 		0.898
(1.00) 		0.753
(1.00) 		0.934
(1.00) 		0.0509
(0.319) 		0.0247
(0.246) 		0.00025
(0.0117) 		0.0165
(0.183) 		0.00022
(0.0114) 		1
(1.00) 		0.163
(0.601)
PIK3CA 37 (30%) 85 0.856
(1.00) 		0.988
(1.00) 		0.208
(0.664) 		0.942
(1.00) 		0.184
(0.628) 		0.0537
(0.322) 		1e-05
(0.000585) 		1e-05
(0.000585) 		1e-05
(0.000585) 		1e-05
(0.000585) 		0.114
(0.493) 		0.238
(0.714)
TP53 90 (74%) 32 0.00033
(0.014) 		0.0134
(0.172) 		0.0416
(0.29) 		0.753
(1.00) 		0.358
(0.881) 		0.369
(0.881) 		0.179
(0.622) 		0.0808
(0.398) 		0.146
(0.574) 		0.015
(0.173) 		0.265
(0.764) 		0.296
(0.796)
RLIM 3 (2%) 119 0.177
(0.619) 		0.019
(0.203) 		0.0199
(0.207) 		0.0149
(0.173) 		0.169
(0.608) 		0.194
(0.635)
KIAA1804 10 (8%) 112 0.512
(0.982) 		0.812
(1.00) 		0.0212
(0.215) 		0.745
(1.00) 		0.402
(0.902) 		0.509
(0.98) 		0.461
(0.959) 		0.0798
(0.398) 		0.00547
(0.0985)
KRAS 63 (52%) 59 0.192
(0.635) 		0.00684
(0.11) 		0.00606
(0.105) 		0.0267
(0.255) 		0.935
(1.00) 		0.851
(1.00) 		0.457
(0.958) 		0.158
(0.597) 		0.865
(1.00) 		0.0525
(0.319) 		0.685
(1.00) 		0.162
(0.601)
BRAF 12 (10%) 110 0.854
(1.00) 		0.313
(0.823) 		0.502
(0.978) 		0.125
(0.517) 		0.00674
(0.11) 		0.0935
(0.433) 		0.0578
(0.326) 		0.00913
(0.131) 		0.906
(1.00) 		0.0414
(0.29)
RRP8 5 (4%) 117 0.487
(0.97) 		1
(1.00) 		0.00336
(0.0715) 		0.0449
(0.3) 		0.339
(0.853) 		0.274
(0.769) 		0.00094
(0.0367) 		0.0388
(0.284) 		0.368
(0.881) 		0.421
(0.921)
FMN2 14 (11%) 108 0.28
(0.769) 		0.863
(1.00) 		0.0364
(0.279) 		0.506
(0.978) 		0.771
(1.00) 		0.153
(0.593) 		0.01
(0.134) 		0.108
(0.483) 		0.0352
(0.279) 		0.0298
(0.256) 		0.497
(0.973) 		1
(1.00)
VCX2 5 (4%) 117 0.737
(1.00) 		0.361
(0.881) 		0.818
(1.00) 		0.218
(0.681) 		0.0377
(0.284) 		0.124
(0.517) 		0.0422
(0.29) 		0.00948
(0.131) 		0.528
(0.992) 		0.321
(0.835)
ERBB2 8 (7%) 114 1
(1.00) 		1
(1.00) 		0.386
(0.899) 		0.205
(0.66) 		0.423
(0.921) 		0.766
(1.00) 		0.0256
(0.25) 		0.0722
(0.367) 		0.648
(1.00) 		0.338
(0.853) 		0.884
(1.00) 		0.58
(1.00)
HIST2H2AC 3 (2%) 119 0.212
(0.67) 		0.616
(1.00) 		0.0359
(0.279) 		0.0558
(0.323) 		0.0013
(0.0438) 		0.195
(0.635) 		0.0673
(0.358) 		0.374
(0.888)
ZNF354C 5 (4%) 117 0.681
(1.00) 		0.291
(0.788) 		1
(1.00) 		0.169
(0.608) 		0.0151
(0.173) 		0.206
(0.662) 		0.242
(0.72) 		0.193
(0.635) 		0.883
(1.00) 		0.145
(0.574)
APC 106 (87%) 16 0.804
(1.00) 		0.737
(1.00) 		0.875
(1.00) 		0.225
(0.692) 		0.527
(0.992) 		0.229
(0.699) 		0.0443
(0.3) 		0.03
(0.256) 		0.277
(0.769)
TCF7L2 13 (11%) 109 0.783
(1.00) 		0.173
(0.619) 		0.711
(1.00) 		0.75
(1.00) 		0.653
(1.00) 		0.887
(1.00) 		0.933
(1.00) 		0.536
(0.999) 		0.483
(0.97) 		0.845
(1.00) 		0.338
(0.853) 		0.833
(1.00)
RPTN 5 (4%) 117 0.742
(1.00) 		0.853
(1.00) 		0.299
(0.801) 		0.155
(0.593) 		0.0514
(0.319) 		0.0465
(0.306) 		0.0657
(0.354) 		0.0693
(0.364) 		1
(1.00) 		0.413
(0.911)
NRAS 11 (9%) 111 1
(1.00) 		0.887
(1.00) 		0.522
(0.988) 		1
(1.00) 		0.364
(0.881) 		0.799
(1.00) 		0.559
(1.00) 		0.573
(1.00) 		0.492
(0.973) 		0.254
(0.748) 		0.883
(1.00) 		0.057
(0.325)
ARID1A 11 (9%) 111 0.366
(0.881) 		0.393
(0.901) 		0.468
(0.965) 		0.354
(0.881) 		0.862
(1.00) 		0.11
(0.488) 		0.815
(1.00) 		0.829
(1.00) 		0.496
(0.973) 		0.603
(1.00) 		0.67
(1.00) 		0.167
(0.608)
SMAD2 7 (6%) 115 1
(1.00) 		0.433
(0.933) 		0.101
(0.458) 		1
(1.00) 		0.269
(0.768) 		0.125
(0.517) 		1
(1.00) 		0.927
(1.00) 		0.866
(1.00) 		0.391
(0.901)
RBM10 5 (4%) 117 1
(1.00) 		0.784
(1.00) 		0.924
(1.00) 		1
(1.00) 		0.942
(1.00) 		0.803
(1.00) 		0.789
(1.00) 		0.645
(1.00) 		0.711
(1.00)
PON3 4 (3%) 118 0.138
(0.553) 		0.816
(1.00) 		0.0349
(0.279) 		0.07
(0.364) 		0.0552
(0.323) 		0.0325
(0.268) 		0.187
(0.628) 		0.649
(1.00)
OXSM 4 (3%) 118 0.907
(1.00) 		0.481
(0.97) 		0.265
(0.764) 		0.31
(0.819) 		0.403
(0.902) 		0.0845
(0.399) 		0.467
(0.965) 		0.385
(0.899)
BCL9 5 (4%) 117 0.627
(1.00) 		0.882
(1.00) 		0.278
(0.769) 		0.304
(0.808) 		0.722
(1.00) 		0.619
(1.00) 		0.943
(1.00) 		0.0721
(0.367) 		0.245
(0.727)
SLC12A6 6 (5%) 116 0.45
(0.949) 		0.449
(0.949) 		1
(1.00) 		0.557
(1.00) 		0.0421
(0.29) 		0.151
(0.589) 		0.266
(0.764) 		0.327
(0.84)
GABRP 4 (3%) 118 0.673
(1.00) 		1
(1.00) 		0.344
(0.862) 		0.277
(0.769) 		0.182
(0.625) 		0.822
(1.00)
CEP290 6 (5%) 116 0.736
(1.00) 		0.0301
(0.256) 		0.449
(0.949) 		0.587
(1.00) 		0.137
(0.553) 		0.421
(0.921) 		0.176
(0.619) 		0.0622
(0.342) 		0.08
(0.398) 		0.531
(0.994)
LIG1 4 (3%) 118 0.82
(1.00) 		0.449
(0.949) 		0.781
(1.00) 		0.43
(0.932) 		0.0278
(0.256) 		0.123
(0.517) 		0.0835
(0.399) 		0.0326
(0.268)
PCBP1 4 (3%) 118 0.816
(1.00) 		0.617
(1.00) 		0.408
(0.906) 		0.4
(0.902) 		0.505
(0.978) 		0.382
(0.899)
ATP8B1 5 (4%) 117 0.495
(0.973) 		1
(1.00) 		0.794
(1.00) 		1
(1.00) 		0.281
(0.769) 		0.591
(1.00) 		0.096
(0.441) 		0.886
(1.00) 		0.711
(1.00)
FLT1 8 (7%) 114 0.837
(1.00) 		0.85
(1.00) 		0.405
(0.902) 		0.323
(0.835) 		0.0288
(0.256) 		0.223
(0.69) 		0.158
(0.597) 		0.384
(0.899) 		0.121
(0.517) 		0.578
(1.00)
OBSCN 13 (11%) 109 0.28
(0.769) 		0.693
(1.00) 		0.67
(1.00) 		0.486
(0.97) 		0.674
(1.00) 		0.33
(0.845) 		0.0844
(0.399) 		0.029
(0.256) 		0.0506
(0.319) 		0.132
(0.537) 		1
(1.00) 		0.214
(0.673)
VANGL1 3 (2%) 119 0.395
(0.901) 		1
(1.00) 		1
(1.00) 		0.0554
(0.323) 		0.23
(0.699) 		0.0514
(0.319) 		0.194
(0.635)
AGL 4 (3%) 118 0.442
(0.949) 		0.686
(1.00) 		0.459
(0.958) 		0.323
(0.835) 		0.694
(1.00) 		0.549
(1.00) 		0.825
(1.00)
STK32B 4 (3%) 118 1
(1.00) 		0.291
(0.788) 		0.112
(0.488) 		0.401
(0.902) 		0.0612
(0.341) 		0.0904
(0.423)
'APC MUTATION STATUS' versus 'MRNA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
APC MUTATED 19 16 16
APC WILD-TYPE 6 5 3
'APC MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
APC MUTATED 4 11 7 8 5 7 7 2
APC WILD-TYPE 2 2 5 1 1 2 1 0
'APC MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
APC MUTATED 45 17 17 25
APC WILD-TYPE 6 3 2 5
'APC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.225 (Fisher's exact test), Q value = 0.69

Table S4.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
APC MUTATED 22 25 37
APC WILD-TYPE 6 4 3
'APC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.527 (Fisher's exact test), Q value = 0.99

Table S5.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
APC MUTATED 18 15 22 3 18 8
APC WILD-TYPE 5 3 2 1 2 0
'APC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.229 (Fisher's exact test), Q value = 0.7

Table S6.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
APC MUTATED 14 13 20 13 46
APC WILD-TYPE 2 0 2 0 11
'APC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0443 (Fisher's exact test), Q value = 0.3

Table S7.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
APC MUTATED 11 23 6 12 26 15 13
APC WILD-TYPE 0 0 2 0 6 3 4

Figure S1.  Get High-res Image Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'APC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.03 (Fisher's exact test), Q value = 0.26

Table S8.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
APC MUTATED 11 28 14 6 46
APC WILD-TYPE 2 0 0 2 9

Figure S2.  Get High-res Image Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'APC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.277 (Fisher's exact test), Q value = 0.77

Table S9.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
APC MUTATED 19 41 45
APC WILD-TYPE 1 3 9
'CRIPAK MUTATION STATUS' versus 'CN_CNMF'

P value = 0.645 (Fisher's exact test), Q value = 1

Table S10.  Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
CRIPAK MUTATED 7 1 1 2
CRIPAK WILD-TYPE 44 19 18 28
'CRIPAK MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.361 (Fisher's exact test), Q value = 0.88

Table S11.  Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
CRIPAK MUTATED 5 4 2
CRIPAK WILD-TYPE 11 19 16
'CRIPAK MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.163 (Fisher's exact test), Q value = 0.6

Table S12.  Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
CRIPAK MUTATED 0 3 5
CRIPAK WILD-TYPE 28 26 35
'CRIPAK MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0388 (Fisher's exact test), Q value = 0.28

Table S13.  Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
CRIPAK MUTATED 0 0 2 1 3 2
CRIPAK WILD-TYPE 23 18 22 3 17 6

Figure S3.  Get High-res Image Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'CRIPAK MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00194 (Fisher's exact test), Q value = 0.055

Table S14.  Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
CRIPAK MUTATED 2 3 4 2 0
CRIPAK WILD-TYPE 14 10 18 11 57

Figure S4.  Get High-res Image Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CRIPAK MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0021 (Fisher's exact test), Q value = 0.055

Table S15.  Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
CRIPAK MUTATED 2 6 1 2 0 0 0
CRIPAK WILD-TYPE 9 17 7 10 32 18 17

Figure S5.  Get High-res Image Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CRIPAK MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.056

Table S16.  Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
CRIPAK MUTATED 2 5 3 1 0
CRIPAK WILD-TYPE 11 23 11 7 55

Figure S6.  Get High-res Image Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CRIPAK MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.044

Table S17.  Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
CRIPAK MUTATED 4 7 0
CRIPAK WILD-TYPE 16 37 54

Figure S7.  Get High-res Image Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CRIPAK MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.266 (Fisher's exact test), Q value = 0.76

Table S18.  Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
CRIPAK MUTATED 3 1 1 3
CRIPAK WILD-TYPE 5 6 12 5
'CRIPAK MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.76 (Fisher's exact test), Q value = 1

Table S19.  Gene #2: 'CRIPAK MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
CRIPAK MUTATED 2 1 3 1 1
CRIPAK WILD-TYPE 6 8 9 4 1
'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.014

Table S20.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
TP53 MUTATED 8 15 17
TP53 WILD-TYPE 17 6 2

Figure S8.  Get High-res Image Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.17

Table S21.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
TP53 MUTATED 2 9 4 9 5 6 5 0
TP53 WILD-TYPE 4 4 8 0 1 3 3 2

Figure S9.  Get High-res Image Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.29

Table S22.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
TP53 MUTATED 32 16 18 22
TP53 WILD-TYPE 19 4 1 8

Figure S10.  Get High-res Image Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S23.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
TP53 MUTATED 14 20 17
TP53 WILD-TYPE 2 3 1
'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.358 (Fisher's exact test), Q value = 0.88

Table S24.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
TP53 MUTATED 21 24 27
TP53 WILD-TYPE 7 5 13
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.369 (Fisher's exact test), Q value = 0.88

Table S25.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
TP53 MUTATED 15 15 16 3 15 8
TP53 WILD-TYPE 8 3 8 1 5 0
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.179 (Fisher's exact test), Q value = 0.62

Table S26.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
TP53 MUTATED 12 12 15 12 38
TP53 WILD-TYPE 4 1 7 1 19
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0808 (Fisher's exact test), Q value = 0.4

Table S27.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
TP53 MUTATED 11 19 7 10 21 10 11
TP53 WILD-TYPE 0 4 1 2 11 8 6
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.146 (Fisher's exact test), Q value = 0.57

Table S28.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
TP53 MUTATED 10 25 11 6 35
TP53 WILD-TYPE 3 3 3 2 20
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.17

Table S29.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
TP53 MUTATED 18 36 33
TP53 WILD-TYPE 2 8 21

Figure S11.  Get High-res Image Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.265 (Fisher's exact test), Q value = 0.76

Table S30.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
TP53 MUTATED 8 5 10 8
TP53 WILD-TYPE 0 2 3 0
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.296 (Fisher's exact test), Q value = 0.8

Table S31.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
TP53 MUTATED 8 7 10 5 1
TP53 WILD-TYPE 0 2 2 0 1
'MUC4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.516 (Fisher's exact test), Q value = 0.98

Table S32.  Gene #4: 'MUC4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
MUC4 MUTATED 12 3 2 8
MUC4 WILD-TYPE 39 17 17 22
'MUC4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0629 (Fisher's exact test), Q value = 0.34

Table S33.  Gene #4: 'MUC4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
MUC4 MUTATED 10 10 4
MUC4 WILD-TYPE 6 13 14
'MUC4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.233 (Fisher's exact test), Q value = 0.7

Table S34.  Gene #4: 'MUC4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
MUC4 MUTATED 3 8 10
MUC4 WILD-TYPE 25 21 30
'MUC4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00306 (Fisher's exact test), Q value = 0.068

Table S35.  Gene #4: 'MUC4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
MUC4 MUTATED 1 3 3 2 7 5
MUC4 WILD-TYPE 22 15 21 2 13 3

Figure S12.  Get High-res Image Gene #4: 'MUC4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'MUC4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00058

Table S36.  Gene #4: 'MUC4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
MUC4 MUTATED 8 5 8 4 0
MUC4 WILD-TYPE 8 8 14 9 57

Figure S13.  Get High-res Image Gene #4: 'MUC4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'MUC4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00058

Table S37.  Gene #4: 'MUC4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
MUC4 MUTATED 7 11 3 3 0 1 0
MUC4 WILD-TYPE 4 12 5 9 32 17 17

Figure S14.  Get High-res Image Gene #4: 'MUC4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'MUC4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00058

Table S38.  Gene #4: 'MUC4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
MUC4 MUTATED 5 13 5 1 1
MUC4 WILD-TYPE 8 15 9 7 54

Figure S15.  Get High-res Image Gene #4: 'MUC4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MUC4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00058

Table S39.  Gene #4: 'MUC4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
MUC4 MUTATED 8 16 1
MUC4 WILD-TYPE 12 28 53

Figure S16.  Get High-res Image Gene #4: 'MUC4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'MUC4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.48 (Fisher's exact test), Q value = 0.97

Table S40.  Gene #4: 'MUC4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
MUC4 MUTATED 5 3 7 2
MUC4 WILD-TYPE 3 4 6 6
'MUC4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.517 (Fisher's exact test), Q value = 0.98

Table S41.  Gene #4: 'MUC4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
MUC4 MUTATED 6 3 5 2 1
MUC4 WILD-TYPE 2 6 7 3 1
'TCF7L2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S42.  Gene #5: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
TCF7L2 MUTATED 2 2 3
TCF7L2 WILD-TYPE 23 19 16
'TCF7L2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.173 (Fisher's exact test), Q value = 0.62

Table S43.  Gene #5: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
TCF7L2 MUTATED 1 0 1 1 1 0 3 0
TCF7L2 WILD-TYPE 5 13 11 8 5 9 5 2
'TCF7L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.711 (Fisher's exact test), Q value = 1

Table S44.  Gene #5: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
TCF7L2 MUTATED 4 2 3 4
TCF7L2 WILD-TYPE 47 18 16 26
'TCF7L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S45.  Gene #5: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
TCF7L2 MUTATED 2 3 1
TCF7L2 WILD-TYPE 14 20 17
'TCF7L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.653 (Fisher's exact test), Q value = 1

Table S46.  Gene #5: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
TCF7L2 MUTATED 3 3 2
TCF7L2 WILD-TYPE 25 26 38
'TCF7L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.887 (Fisher's exact test), Q value = 1

Table S47.  Gene #5: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
TCF7L2 MUTATED 2 2 1 0 2 1
TCF7L2 WILD-TYPE 21 16 23 4 18 7
'TCF7L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S48.  Gene #5: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
TCF7L2 MUTATED 1 1 2 2 7
TCF7L2 WILD-TYPE 15 12 20 11 50
'TCF7L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.536 (Fisher's exact test), Q value = 1

Table S49.  Gene #5: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
TCF7L2 MUTATED 1 3 1 1 6 0 1
TCF7L2 WILD-TYPE 10 20 7 11 26 18 16
'TCF7L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 0.97

Table S50.  Gene #5: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
TCF7L2 MUTATED 1 5 0 0 6
TCF7L2 WILD-TYPE 12 23 14 8 49
'TCF7L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.845 (Fisher's exact test), Q value = 1

Table S51.  Gene #5: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
TCF7L2 MUTATED 1 5 6
TCF7L2 WILD-TYPE 19 39 48
'TCF7L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.338 (Fisher's exact test), Q value = 0.85

Table S52.  Gene #5: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
TCF7L2 MUTATED 0 1 4 1
TCF7L2 WILD-TYPE 8 6 9 7
'TCF7L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.833 (Fisher's exact test), Q value = 1

Table S53.  Gene #5: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
TCF7L2 MUTATED 1 2 3 0 0
TCF7L2 WILD-TYPE 7 7 9 5 2
'FMN2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.28 (Fisher's exact test), Q value = 0.77

Table S54.  Gene #6: 'FMN2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
FMN2 MUTATED 0 2 1
FMN2 WILD-TYPE 25 19 18
'FMN2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.863 (Fisher's exact test), Q value = 1

Table S55.  Gene #6: 'FMN2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
FMN2 MUTATED 0 1 0 1 0 0 1 0
FMN2 WILD-TYPE 6 12 12 8 6 9 7 2
'FMN2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.28

Table S56.  Gene #6: 'FMN2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
FMN2 MUTATED 4 0 5 5
FMN2 WILD-TYPE 47 20 14 25

Figure S17.  Get High-res Image Gene #6: 'FMN2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FMN2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.506 (Fisher's exact test), Q value = 0.98

Table S57.  Gene #6: 'FMN2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
FMN2 MUTATED 4 6 2
FMN2 WILD-TYPE 12 17 16
'FMN2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.771 (Fisher's exact test), Q value = 1

Table S58.  Gene #6: 'FMN2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
FMN2 MUTATED 2 4 4
FMN2 WILD-TYPE 26 25 36
'FMN2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.153 (Fisher's exact test), Q value = 0.59

Table S59.  Gene #6: 'FMN2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
FMN2 MUTATED 0 2 2 0 4 2
FMN2 WILD-TYPE 23 16 22 4 16 6
'FMN2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 0.13

Table S60.  Gene #6: 'FMN2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
FMN2 MUTATED 1 3 2 5 3
FMN2 WILD-TYPE 15 10 20 8 54

Figure S18.  Get High-res Image Gene #6: 'FMN2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'FMN2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.108 (Fisher's exact test), Q value = 0.48

Table S61.  Gene #6: 'FMN2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
FMN2 MUTATED 3 4 1 3 2 1 0
FMN2 WILD-TYPE 8 19 7 9 30 17 17
'FMN2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 0.28

Table S62.  Gene #6: 'FMN2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
FMN2 MUTATED 1 8 2 0 3
FMN2 WILD-TYPE 12 20 12 8 52

Figure S19.  Get High-res Image Gene #6: 'FMN2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'FMN2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0298 (Fisher's exact test), Q value = 0.26

Table S63.  Gene #6: 'FMN2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
FMN2 MUTATED 1 10 3
FMN2 WILD-TYPE 19 34 51

Figure S20.  Get High-res Image Gene #6: 'FMN2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'FMN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.497 (Fisher's exact test), Q value = 0.97

Table S64.  Gene #6: 'FMN2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
FMN2 MUTATED 1 0 4 2
FMN2 WILD-TYPE 7 7 9 6
'FMN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S65.  Gene #6: 'FMN2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
FMN2 MUTATED 2 2 2 1 0
FMN2 WILD-TYPE 6 7 10 4 2
'SHROOM4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.472 (Fisher's exact test), Q value = 0.97

Table S66.  Gene #7: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
SHROOM4 MUTATED 4 0 2 1
SHROOM4 WILD-TYPE 47 20 17 29
'SHROOM4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.555 (Fisher's exact test), Q value = 1

Table S67.  Gene #7: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
SHROOM4 MUTATED 1 4 1
SHROOM4 WILD-TYPE 15 19 17
'SHROOM4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.638 (Fisher's exact test), Q value = 1

Table S68.  Gene #7: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
SHROOM4 MUTATED 1 3 3
SHROOM4 WILD-TYPE 27 26 37
'SHROOM4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0828 (Fisher's exact test), Q value = 0.4

Table S69.  Gene #7: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
SHROOM4 MUTATED 0 0 2 0 3 2
SHROOM4 WILD-TYPE 23 18 22 4 17 6
'SHROOM4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.17

Table S70.  Gene #7: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
SHROOM4 MUTATED 1 1 3 2 0
SHROOM4 WILD-TYPE 15 12 19 11 57

Figure S21.  Get High-res Image Gene #7: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'SHROOM4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00239 (Fisher's exact test), Q value = 0.056

Table S71.  Gene #7: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
SHROOM4 MUTATED 1 2 0 4 0 0 0
SHROOM4 WILD-TYPE 10 21 8 8 32 18 17

Figure S22.  Get High-res Image Gene #7: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.2

Table S72.  Gene #7: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
SHROOM4 MUTATED 1 4 2 0 0
SHROOM4 WILD-TYPE 12 24 12 8 55

Figure S23.  Get High-res Image Gene #7: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00201 (Fisher's exact test), Q value = 0.055

Table S73.  Gene #7: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
SHROOM4 MUTATED 0 7 0
SHROOM4 WILD-TYPE 20 37 54

Figure S24.  Get High-res Image Gene #7: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.186 (Fisher's exact test), Q value = 0.63

Table S74.  Gene #7: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
SHROOM4 MUTATED 1 0 0 2
SHROOM4 WILD-TYPE 7 7 13 6
'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.128 (Fisher's exact test), Q value = 0.53

Table S75.  Gene #7: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
SHROOM4 MUTATED 0 0 1 2 0
SHROOM4 WILD-TYPE 8 9 11 3 2
'RPTN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.742 (Fisher's exact test), Q value = 1

Table S76.  Gene #8: 'RPTN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
RPTN MUTATED 1 1 1 1
RPTN WILD-TYPE 50 19 18 29
'RPTN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.853 (Fisher's exact test), Q value = 1

Table S77.  Gene #8: 'RPTN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
RPTN MUTATED 2 2 1
RPTN WILD-TYPE 14 21 17
'RPTN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.299 (Fisher's exact test), Q value = 0.8

Table S78.  Gene #8: 'RPTN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
RPTN MUTATED 1 0 3
RPTN WILD-TYPE 27 29 37
'RPTN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.155 (Fisher's exact test), Q value = 0.59

Table S79.  Gene #8: 'RPTN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
RPTN MUTATED 0 1 2 1 0 0
RPTN WILD-TYPE 23 17 22 3 20 8
'RPTN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0514 (Fisher's exact test), Q value = 0.32

Table S80.  Gene #8: 'RPTN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
RPTN MUTATED 2 1 1 1 0
RPTN WILD-TYPE 14 12 21 12 57
'RPTN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0465 (Fisher's exact test), Q value = 0.31

Table S81.  Gene #8: 'RPTN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
RPTN MUTATED 1 1 1 2 0 0 0
RPTN WILD-TYPE 10 22 7 10 32 18 17

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

'RPTN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0657 (Fisher's exact test), Q value = 0.35

Table S82.  Gene #8: 'RPTN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
RPTN MUTATED 1 2 1 1 0
RPTN WILD-TYPE 12 26 13 7 55
'RPTN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0693 (Fisher's exact test), Q value = 0.36

Table S83.  Gene #8: 'RPTN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
RPTN MUTATED 1 4 0
RPTN WILD-TYPE 19 40 54
'RPTN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S84.  Gene #8: 'RPTN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
RPTN MUTATED 1 1 1 1
RPTN WILD-TYPE 7 6 12 7
'RPTN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.413 (Fisher's exact test), Q value = 0.91

Table S85.  Gene #8: 'RPTN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
RPTN MUTATED 1 2 0 1 0
RPTN WILD-TYPE 7 7 12 4 2
'NRAS MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S86.  Gene #9: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
NRAS MUTATED 2 2 1
NRAS WILD-TYPE 23 19 18
'NRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.887 (Fisher's exact test), Q value = 1

Table S87.  Gene #9: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
NRAS MUTATED 1 2 1 1 0 0 0 0
NRAS WILD-TYPE 5 11 11 8 6 9 8 2
'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.522 (Fisher's exact test), Q value = 0.99

Table S88.  Gene #9: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
NRAS MUTATED 7 2 1 1
NRAS WILD-TYPE 44 18 18 29
'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S89.  Gene #9: 'NRAS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
NRAS MUTATED 2 2 2
NRAS WILD-TYPE 14 21 16
'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.364 (Fisher's exact test), Q value = 0.88

Table S90.  Gene #9: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
NRAS MUTATED 1 4 2
NRAS WILD-TYPE 27 25 38
'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S91.  Gene #9: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
NRAS MUTATED 1 1 2 0 3 0
NRAS WILD-TYPE 22 17 22 4 17 8
'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.559 (Fisher's exact test), Q value = 1

Table S92.  Gene #9: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
NRAS MUTATED 1 1 4 0 5
NRAS WILD-TYPE 15 12 18 13 52
'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.573 (Fisher's exact test), Q value = 1

Table S93.  Gene #9: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
NRAS MUTATED 1 5 0 1 2 1 1
NRAS WILD-TYPE 10 18 8 11 30 17 16
'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.492 (Fisher's exact test), Q value = 0.97

Table S94.  Gene #9: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
NRAS MUTATED 1 4 2 1 3
NRAS WILD-TYPE 12 24 12 7 52
'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.254 (Fisher's exact test), Q value = 0.75

Table S95.  Gene #9: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
NRAS MUTATED 0 6 5
NRAS WILD-TYPE 20 38 49
'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.883 (Fisher's exact test), Q value = 1

Table S96.  Gene #9: 'NRAS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
NRAS MUTATED 1 1 1 0
NRAS WILD-TYPE 7 6 12 8
'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.057 (Fisher's exact test), Q value = 0.33

Table S97.  Gene #9: 'NRAS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
NRAS MUTATED 1 0 0 1 1
NRAS WILD-TYPE 7 9 12 4 1
'CDH1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S98.  Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
CDH1 MUTATED 6 1 1 4
CDH1 WILD-TYPE 45 19 18 26
'CDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.394 (Fisher's exact test), Q value = 0.9

Table S99.  Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
CDH1 MUTATED 5 3 3
CDH1 WILD-TYPE 11 20 15
'CDH1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S100.  Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
CDH1 MUTATED 2 3 4
CDH1 WILD-TYPE 26 26 36
'CDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.621 (Fisher's exact test), Q value = 1

Table S101.  Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
CDH1 MUTATED 1 2 2 0 2 2
CDH1 WILD-TYPE 22 16 22 4 18 6
'CDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.17

Table S102.  Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
CDH1 MUTATED 3 3 3 2 1
CDH1 WILD-TYPE 13 10 19 11 56

Figure S26.  Get High-res Image Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00523 (Fisher's exact test), Q value = 0.098

Table S103.  Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
CDH1 MUTATED 1 6 1 3 0 1 0
CDH1 WILD-TYPE 10 17 7 9 32 17 17

Figure S27.  Get High-res Image Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00389 (Fisher's exact test), Q value = 0.079

Table S104.  Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
CDH1 MUTATED 1 6 4 0 1
CDH1 WILD-TYPE 12 22 10 8 54

Figure S28.  Get High-res Image Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00928 (Fisher's exact test), Q value = 0.13

Table S105.  Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
CDH1 MUTATED 4 7 1
CDH1 WILD-TYPE 16 37 53

Figure S29.  Get High-res Image Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.479 (Fisher's exact test), Q value = 0.97

Table S106.  Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
CDH1 MUTATED 3 1 2 3
CDH1 WILD-TYPE 5 6 11 5
'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S107.  Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
CDH1 MUTATED 2 1 4 1 1
CDH1 WILD-TYPE 6 8 8 4 1
'ARID1A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.366 (Fisher's exact test), Q value = 0.88

Table S108.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
ARID1A MUTATED 3 2 0
ARID1A WILD-TYPE 22 19 19
'ARID1A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.393 (Fisher's exact test), Q value = 0.9

Table S109.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
ARID1A MUTATED 1 1 1 0 0 1 0 1
ARID1A WILD-TYPE 5 12 11 9 6 8 8 1
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.468 (Fisher's exact test), Q value = 0.96

Table S110.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
ARID1A MUTATED 6 3 1 1
ARID1A WILD-TYPE 45 17 18 29
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.354 (Fisher's exact test), Q value = 0.88

Table S111.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
ARID1A MUTATED 3 1 2
ARID1A WILD-TYPE 13 22 16
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.862 (Fisher's exact test), Q value = 1

Table S112.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
ARID1A MUTATED 2 1 2
ARID1A WILD-TYPE 26 28 38
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.11 (Fisher's exact test), Q value = 0.49

Table S113.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
ARID1A MUTATED 2 0 0 1 1 1
ARID1A WILD-TYPE 21 18 24 3 19 7
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.815 (Fisher's exact test), Q value = 1

Table S114.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
ARID1A MUTATED 2 2 1 1 5
ARID1A WILD-TYPE 14 11 21 12 52
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.829 (Fisher's exact test), Q value = 1

Table S115.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
ARID1A MUTATED 2 3 0 1 2 1 2
ARID1A WILD-TYPE 9 20 8 11 30 17 15
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.496 (Fisher's exact test), Q value = 0.97

Table S116.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
ARID1A MUTATED 1 4 2 0 3
ARID1A WILD-TYPE 12 24 12 8 52
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.603 (Fisher's exact test), Q value = 1

Table S117.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
ARID1A MUTATED 2 5 3
ARID1A WILD-TYPE 18 39 51
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S118.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
ARID1A MUTATED 2 0 1 1
ARID1A WILD-TYPE 6 7 12 7
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.167 (Fisher's exact test), Q value = 0.61

Table S119.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
ARID1A MUTATED 3 0 1 0 0
ARID1A WILD-TYPE 5 9 11 5 2
'RBM38 MUTATION STATUS' versus 'CN_CNMF'

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

Table S120.  Gene #12: 'RBM38 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
RBM38 MUTATED 4 1 1 2
RBM38 WILD-TYPE 47 19 18 28
'RBM38 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S121.  Gene #12: 'RBM38 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
RBM38 MUTATED 2 3 3
RBM38 WILD-TYPE 14 20 15
'RBM38 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.103 (Fisher's exact test), Q value = 0.46

Table S122.  Gene #12: 'RBM38 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
RBM38 MUTATED 2 3 0
RBM38 WILD-TYPE 26 26 40
'RBM38 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.487 (Fisher's exact test), Q value = 0.97

Table S123.  Gene #12: 'RBM38 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
RBM38 MUTATED 0 1 1 0 2 1
RBM38 WILD-TYPE 23 17 23 4 18 7
'RBM38 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00181 (Fisher's exact test), Q value = 0.055

Table S124.  Gene #12: 'RBM38 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
RBM38 MUTATED 4 1 3 0 0
RBM38 WILD-TYPE 12 12 19 13 57

Figure S30.  Get High-res Image Gene #12: 'RBM38 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'RBM38 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00949 (Fisher's exact test), Q value = 0.13

Table S125.  Gene #12: 'RBM38 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
RBM38 MUTATED 3 3 1 1 0 0 0
RBM38 WILD-TYPE 8 20 7 11 32 18 17

Figure S31.  Get High-res Image Gene #12: 'RBM38 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'RBM38 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00463 (Fisher's exact test), Q value = 0.09

Table S126.  Gene #12: 'RBM38 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
RBM38 MUTATED 3 4 1 0 0
RBM38 WILD-TYPE 10 24 13 8 55

Figure S32.  Get High-res Image Gene #12: 'RBM38 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'RBM38 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00895 (Fisher's exact test), Q value = 0.13

Table S127.  Gene #12: 'RBM38 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
RBM38 MUTATED 3 5 0
RBM38 WILD-TYPE 17 39 54

Figure S33.  Get High-res Image Gene #12: 'RBM38 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'RBM38 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.671 (Fisher's exact test), Q value = 1

Table S128.  Gene #12: 'RBM38 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
RBM38 MUTATED 3 1 2 1
RBM38 WILD-TYPE 5 6 11 7
'RBM38 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.359 (Fisher's exact test), Q value = 0.88

Table S129.  Gene #12: 'RBM38 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
RBM38 MUTATED 3 1 2 0 1
RBM38 WILD-TYPE 5 8 10 5 1
'SMAD2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S130.  Gene #13: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
SMAD2 MUTATED 2 1 1
SMAD2 WILD-TYPE 23 20 18
'SMAD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.433 (Fisher's exact test), Q value = 0.93

Table S131.  Gene #13: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
SMAD2 MUTATED 0 0 1 0 0 2 1 0
SMAD2 WILD-TYPE 6 13 11 9 6 7 7 2
'SMAD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 0.46

Table S132.  Gene #13: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
SMAD2 MUTATED 6 0 1 0
SMAD2 WILD-TYPE 45 20 18 30
'SMAD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S133.  Gene #13: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
SMAD2 MUTATED 1 1 1
SMAD2 WILD-TYPE 15 22 17
'SMAD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.269 (Fisher's exact test), Q value = 0.77

Table S134.  Gene #13: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
SMAD2 MUTATED 0 3 2
SMAD2 WILD-TYPE 28 26 38
'SMAD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.125 (Fisher's exact test), Q value = 0.52

Table S135.  Gene #13: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
SMAD2 MUTATED 0 2 0 0 3 0
SMAD2 WILD-TYPE 23 16 24 4 17 8
'SMAD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S136.  Gene #13: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
SMAD2 MUTATED 1 1 1 0 4
SMAD2 WILD-TYPE 15 12 21 13 53
'SMAD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S137.  Gene #13: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
SMAD2 MUTATED 0 2 0 0 2 1 2
SMAD2 WILD-TYPE 11 21 8 12 30 17 15
'SMAD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.866 (Fisher's exact test), Q value = 1

Table S138.  Gene #13: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
SMAD2 MUTATED 0 1 1 0 5
SMAD2 WILD-TYPE 13 27 13 8 50
'SMAD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.391 (Fisher's exact test), Q value = 0.9

Table S139.  Gene #13: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
SMAD2 MUTATED 0 2 5
SMAD2 WILD-TYPE 20 42 49
'VCX2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S140.  Gene #14: 'VCX2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
VCX2 MUTATED 2 0 1 2
VCX2 WILD-TYPE 49 20 18 28
'VCX2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.361 (Fisher's exact test), Q value = 0.88

Table S141.  Gene #14: 'VCX2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
VCX2 MUTATED 3 1 1
VCX2 WILD-TYPE 13 22 17
'VCX2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S142.  Gene #14: 'VCX2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
VCX2 MUTATED 1 2 1
VCX2 WILD-TYPE 27 27 39
'VCX2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.218 (Fisher's exact test), Q value = 0.68

Table S143.  Gene #14: 'VCX2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
VCX2 MUTATED 0 1 0 0 2 1
VCX2 WILD-TYPE 23 17 24 4 18 7
'VCX2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.28

Table S144.  Gene #14: 'VCX2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
VCX2 MUTATED 1 1 1 2 0
VCX2 WILD-TYPE 15 12 21 11 57

Figure S34.  Get High-res Image Gene #14: 'VCX2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'VCX2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.124 (Fisher's exact test), Q value = 0.52

Table S145.  Gene #14: 'VCX2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
VCX2 MUTATED 1 2 1 1 0 0 0
VCX2 WILD-TYPE 10 21 7 11 32 18 17
'VCX2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.29

Table S146.  Gene #14: 'VCX2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
VCX2 MUTATED 2 2 1 0 0
VCX2 WILD-TYPE 11 26 13 8 55

Figure S35.  Get High-res Image Gene #14: 'VCX2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'VCX2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00948 (Fisher's exact test), Q value = 0.13

Table S147.  Gene #14: 'VCX2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
VCX2 MUTATED 3 2 0
VCX2 WILD-TYPE 17 42 54

Figure S36.  Get High-res Image Gene #14: 'VCX2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'VCX2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.528 (Fisher's exact test), Q value = 0.99

Table S148.  Gene #14: 'VCX2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
VCX2 MUTATED 0 1 2 2
VCX2 WILD-TYPE 8 6 11 6
'VCX2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.321 (Fisher's exact test), Q value = 0.84

Table S149.  Gene #14: 'VCX2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
VCX2 MUTATED 2 2 0 1 0
VCX2 WILD-TYPE 6 7 12 4 2
'ERBB2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S150.  Gene #15: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
ERBB2 MUTATED 1 1 1
ERBB2 WILD-TYPE 24 20 18
'ERBB2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S151.  Gene #15: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
ERBB2 MUTATED 0 1 1 1 0 0 0 0
ERBB2 WILD-TYPE 6 12 11 8 6 9 8 2
'ERBB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.386 (Fisher's exact test), Q value = 0.9

Table S152.  Gene #15: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
ERBB2 MUTATED 3 1 0 4
ERBB2 WILD-TYPE 48 19 19 26
'ERBB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.205 (Fisher's exact test), Q value = 0.66

Table S153.  Gene #15: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
ERBB2 MUTATED 0 4 1
ERBB2 WILD-TYPE 16 19 17
'ERBB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.423 (Fisher's exact test), Q value = 0.92

Table S154.  Gene #15: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
ERBB2 MUTATED 2 3 1
ERBB2 WILD-TYPE 26 26 39
'ERBB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S155.  Gene #15: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
ERBB2 MUTATED 1 1 1 0 3 0
ERBB2 WILD-TYPE 22 17 23 4 17 8
'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0256 (Fisher's exact test), Q value = 0.25

Table S156.  Gene #15: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
ERBB2 MUTATED 2 3 2 0 1
ERBB2 WILD-TYPE 14 10 20 13 56

Figure S37.  Get High-res Image Gene #15: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0722 (Fisher's exact test), Q value = 0.37

Table S157.  Gene #15: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
ERBB2 MUTATED 0 4 2 0 1 1 0
ERBB2 WILD-TYPE 11 19 6 12 31 17 17
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S158.  Gene #15: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
ERBB2 MUTATED 2 2 1 0 3
ERBB2 WILD-TYPE 11 26 13 8 52
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.338 (Fisher's exact test), Q value = 0.85

Table S159.  Gene #15: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
ERBB2 MUTATED 0 5 3
ERBB2 WILD-TYPE 20 39 51
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S160.  Gene #15: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
ERBB2 MUTATED 0 1 1 1
ERBB2 WILD-TYPE 8 6 12 7
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.58 (Fisher's exact test), Q value = 1

Table S161.  Gene #15: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
ERBB2 MUTATED 0 2 1 0 0
ERBB2 WILD-TYPE 8 7 11 5 2
'RBM10 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S162.  Gene #16: 'RBM10 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
RBM10 MUTATED 2 1 1
RBM10 WILD-TYPE 23 20 18
'RBM10 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.784 (Fisher's exact test), Q value = 1

Table S163.  Gene #16: 'RBM10 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
RBM10 MUTATED 1 1 0 1 0 1 0 0
RBM10 WILD-TYPE 5 12 12 8 6 8 8 2
'RBM10 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.924 (Fisher's exact test), Q value = 1

Table S164.  Gene #16: 'RBM10 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
RBM10 MUTATED 3 1 0 1
RBM10 WILD-TYPE 48 19 19 29
'RBM10 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S165.  Gene #16: 'RBM10 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
RBM10 MUTATED 1 1 2
RBM10 WILD-TYPE 27 28 38
'RBM10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.942 (Fisher's exact test), Q value = 1

Table S166.  Gene #16: 'RBM10 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
RBM10 MUTATED 1 0 2 0 1 0
RBM10 WILD-TYPE 22 18 22 4 19 8
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.803 (Fisher's exact test), Q value = 1

Table S167.  Gene #16: 'RBM10 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
RBM10 MUTATED 0 1 1 0 2
RBM10 WILD-TYPE 16 12 21 13 55
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.789 (Fisher's exact test), Q value = 1

Table S168.  Gene #16: 'RBM10 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
RBM10 MUTATED 0 2 0 0 2 0 0
RBM10 WILD-TYPE 11 21 8 12 30 18 17
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.645 (Fisher's exact test), Q value = 1

Table S169.  Gene #16: 'RBM10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
RBM10 MUTATED 0 1 0 1 3
RBM10 WILD-TYPE 13 27 14 7 52
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.711 (Fisher's exact test), Q value = 1

Table S170.  Gene #16: 'RBM10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
RBM10 MUTATED 1 1 3
RBM10 WILD-TYPE 19 43 51
'PON3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.138 (Fisher's exact test), Q value = 0.55

Table S171.  Gene #17: 'PON3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
PON3 MUTATED 1 1 2 0
PON3 WILD-TYPE 50 19 17 30
'PON3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S172.  Gene #17: 'PON3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
PON3 MUTATED 1 1 2
PON3 WILD-TYPE 15 22 16
'PON3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.28

Table S173.  Gene #17: 'PON3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
PON3 MUTATED 0 1 1 2 0
PON3 WILD-TYPE 16 12 21 11 57

Figure S38.  Get High-res Image Gene #17: 'PON3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PON3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.07 (Fisher's exact test), Q value = 0.36

Table S174.  Gene #17: 'PON3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
PON3 MUTATED 0 2 0 2 0 0 0
PON3 WILD-TYPE 11 21 8 10 32 18 17
'PON3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0552 (Fisher's exact test), Q value = 0.32

Table S175.  Gene #17: 'PON3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
PON3 MUTATED 0 2 2 0 0
PON3 WILD-TYPE 13 26 12 8 55
'PON3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0325 (Fisher's exact test), Q value = 0.27

Table S176.  Gene #17: 'PON3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
PON3 MUTATED 0 4 0
PON3 WILD-TYPE 20 40 54

Figure S39.  Get High-res Image Gene #17: 'PON3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PON3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.187 (Fisher's exact test), Q value = 0.63

Table S177.  Gene #17: 'PON3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
PON3 MUTATED 1 0 0 2
PON3 WILD-TYPE 7 7 13 6
'PON3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S178.  Gene #17: 'PON3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
PON3 MUTATED 1 0 1 1 0
PON3 WILD-TYPE 7 9 11 4 2
'HIST2H2AC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.212 (Fisher's exact test), Q value = 0.67

Table S179.  Gene #18: 'HIST2H2AC MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
HIST2H2AC MUTATED 1 2 0 0
HIST2H2AC WILD-TYPE 50 18 19 30
'HIST2H2AC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.616 (Fisher's exact test), Q value = 1

Table S180.  Gene #18: 'HIST2H2AC MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
HIST2H2AC MUTATED 1 2 0
HIST2H2AC WILD-TYPE 15 21 18
'HIST2H2AC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.28

Table S181.  Gene #18: 'HIST2H2AC MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
HIST2H2AC MUTATED 2 1 0 0 0
HIST2H2AC WILD-TYPE 14 12 22 13 57

Figure S40.  Get High-res Image Gene #18: 'HIST2H2AC MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'HIST2H2AC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0558 (Fisher's exact test), Q value = 0.32

Table S182.  Gene #18: 'HIST2H2AC MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
HIST2H2AC MUTATED 2 1 0 0 0 0 0
HIST2H2AC WILD-TYPE 9 22 8 12 32 18 17
'HIST2H2AC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.044

Table S183.  Gene #18: 'HIST2H2AC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
HIST2H2AC MUTATED 3 0 0 0 0
HIST2H2AC WILD-TYPE 10 28 14 8 55

Figure S41.  Get High-res Image Gene #18: 'HIST2H2AC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'HIST2H2AC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 0.63

Table S184.  Gene #18: 'HIST2H2AC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
HIST2H2AC MUTATED 1 2 0
HIST2H2AC WILD-TYPE 19 42 54
'HIST2H2AC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0673 (Fisher's exact test), Q value = 0.36

Table S185.  Gene #18: 'HIST2H2AC MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
HIST2H2AC MUTATED 1 2 0 0
HIST2H2AC WILD-TYPE 7 5 13 8
'HIST2H2AC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.374 (Fisher's exact test), Q value = 0.89

Table S186.  Gene #18: 'HIST2H2AC MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
HIST2H2AC MUTATED 1 2 0 0 0
HIST2H2AC WILD-TYPE 7 7 12 5 2
'CTNNB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0524 (Fisher's exact test), Q value = 0.32

Table S187.  Gene #19: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
CTNNB1 MUTATED 0 3 0
CTNNB1 WILD-TYPE 25 18 19
'CTNNB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.177 (Fisher's exact test), Q value = 0.62

Table S188.  Gene #19: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
CTNNB1 MUTATED 0 3 0 0 0 0 0 0
CTNNB1 WILD-TYPE 6 10 12 9 6 9 8 2
'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.898 (Fisher's exact test), Q value = 1

Table S189.  Gene #19: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
CTNNB1 MUTATED 7 3 3 6
CTNNB1 WILD-TYPE 44 17 16 24
'CTNNB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S190.  Gene #19: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
CTNNB1 MUTATED 4 8 4
CTNNB1 WILD-TYPE 12 15 14
'CTNNB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.934 (Fisher's exact test), Q value = 1

Table S191.  Gene #19: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
CTNNB1 MUTATED 4 5 5
CTNNB1 WILD-TYPE 24 24 35
'CTNNB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0509 (Fisher's exact test), Q value = 0.32

Table S192.  Gene #19: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
CTNNB1 MUTATED 0 4 3 1 3 3
CTNNB1 WILD-TYPE 23 14 21 3 17 5
'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.25

Table S193.  Gene #19: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
CTNNB1 MUTATED 6 3 3 3 4
CTNNB1 WILD-TYPE 10 10 19 10 53

Figure S42.  Get High-res Image Gene #19: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.012

Table S194.  Gene #19: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
CTNNB1 MUTATED 5 5 1 4 0 4 0
CTNNB1 WILD-TYPE 6 18 7 8 32 14 17

Figure S43.  Get High-res Image Gene #19: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.18

Table S195.  Gene #19: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
CTNNB1 MUTATED 2 9 4 0 4
CTNNB1 WILD-TYPE 11 19 10 8 51

Figure S44.  Get High-res Image Gene #19: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.011

Table S196.  Gene #19: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
CTNNB1 MUTATED 0 15 4
CTNNB1 WILD-TYPE 20 29 50

Figure S45.  Get High-res Image Gene #19: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S197.  Gene #19: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
CTNNB1 MUTATED 2 2 3 2
CTNNB1 WILD-TYPE 6 5 10 6
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.163 (Fisher's exact test), Q value = 0.6

Table S198.  Gene #19: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
CTNNB1 MUTATED 1 3 2 1 2
CTNNB1 WILD-TYPE 7 6 10 4 0
'KIAA1804 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.512 (Fisher's exact test), Q value = 0.98

Table S199.  Gene #20: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
KIAA1804 MUTATED 3 4 1
KIAA1804 WILD-TYPE 22 17 18
'KIAA1804 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.812 (Fisher's exact test), Q value = 1

Table S200.  Gene #20: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
KIAA1804 MUTATED 0 1 3 1 0 2 1 0
KIAA1804 WILD-TYPE 6 12 9 8 6 7 7 2
'KIAA1804 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.22

Table S201.  Gene #20: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
KIAA1804 MUTATED 9 0 0 1
KIAA1804 WILD-TYPE 42 20 19 29

Figure S46.  Get High-res Image Gene #20: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'KIAA1804 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.745 (Fisher's exact test), Q value = 1

Table S202.  Gene #20: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
KIAA1804 MUTATED 2 2 5
KIAA1804 WILD-TYPE 26 27 35
'KIAA1804 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.402 (Fisher's exact test), Q value = 0.9

Table S203.  Gene #20: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
KIAA1804 MUTATED 3 0 3 1 2 0
KIAA1804 WILD-TYPE 20 18 21 3 18 8
'KIAA1804 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.509 (Fisher's exact test), Q value = 0.98

Table S204.  Gene #20: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
KIAA1804 MUTATED 0 1 3 0 6
KIAA1804 WILD-TYPE 16 12 19 13 51
'KIAA1804 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.461 (Fisher's exact test), Q value = 0.96

Table S205.  Gene #20: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
KIAA1804 MUTATED 0 2 0 0 3 4 1
KIAA1804 WILD-TYPE 11 21 8 12 29 14 16
'KIAA1804 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0798 (Fisher's exact test), Q value = 0.4

Table S206.  Gene #20: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
KIAA1804 MUTATED 0 0 1 0 9
KIAA1804 WILD-TYPE 13 28 13 8 46
'KIAA1804 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00547 (Fisher's exact test), Q value = 0.098

Table S207.  Gene #20: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
KIAA1804 MUTATED 1 0 9
KIAA1804 WILD-TYPE 19 44 45

Figure S47.  Get High-res Image Gene #20: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'OXSM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.907 (Fisher's exact test), Q value = 1

Table S208.  Gene #21: 'OXSM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
OXSM MUTATED 2 0 1 1
OXSM WILD-TYPE 49 20 18 29
'OXSM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.481 (Fisher's exact test), Q value = 0.97

Table S209.  Gene #21: 'OXSM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
OXSM MUTATED 0 1 2
OXSM WILD-TYPE 16 22 16
'OXSM MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.265 (Fisher's exact test), Q value = 0.76

Table S210.  Gene #21: 'OXSM MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
OXSM MUTATED 1 2 0
OXSM WILD-TYPE 27 27 40
'OXSM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.31 (Fisher's exact test), Q value = 0.82

Table S211.  Gene #21: 'OXSM MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
OXSM MUTATED 0 1 0 0 2 0
OXSM WILD-TYPE 23 17 24 4 18 8
'OXSM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.403 (Fisher's exact test), Q value = 0.9

Table S212.  Gene #21: 'OXSM MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
OXSM MUTATED 1 0 1 1 1
OXSM WILD-TYPE 15 13 21 12 56
'OXSM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0845 (Fisher's exact test), Q value = 0.4

Table S213.  Gene #21: 'OXSM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
OXSM MUTATED 1 0 1 1 0 1 0
OXSM WILD-TYPE 10 23 7 11 32 17 17
'OXSM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 0.96

Table S214.  Gene #21: 'OXSM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
OXSM MUTATED 1 1 1 0 1
OXSM WILD-TYPE 12 27 13 8 54
'OXSM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.385 (Fisher's exact test), Q value = 0.9

Table S215.  Gene #21: 'OXSM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
OXSM MUTATED 0 3 1
OXSM WILD-TYPE 20 41 53
'BCL9 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.627 (Fisher's exact test), Q value = 1

Table S216.  Gene #22: 'BCL9 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
BCL9 MUTATED 2 0 1
BCL9 WILD-TYPE 23 21 18
'BCL9 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.882 (Fisher's exact test), Q value = 1

Table S217.  Gene #22: 'BCL9 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
BCL9 MUTATED 0 0 1 1 0 1 0 0
BCL9 WILD-TYPE 6 13 11 8 6 8 8 2
'BCL9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.278 (Fisher's exact test), Q value = 0.77

Table S218.  Gene #22: 'BCL9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
BCL9 MUTATED 2 1 2 0
BCL9 WILD-TYPE 49 19 17 30
'BCL9 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.304 (Fisher's exact test), Q value = 0.81

Table S219.  Gene #22: 'BCL9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
BCL9 MUTATED 1 0 3
BCL9 WILD-TYPE 27 29 37
'BCL9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.722 (Fisher's exact test), Q value = 1

Table S220.  Gene #22: 'BCL9 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
BCL9 MUTATED 1 0 1 0 1 1
BCL9 WILD-TYPE 22 18 23 4 19 7
'BCL9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S221.  Gene #22: 'BCL9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
BCL9 MUTATED 0 1 1 1 2
BCL9 WILD-TYPE 16 12 21 12 55
'BCL9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.943 (Fisher's exact test), Q value = 1

Table S222.  Gene #22: 'BCL9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
BCL9 MUTATED 0 1 0 1 2 1 0
BCL9 WILD-TYPE 11 22 8 11 30 17 17
'BCL9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0721 (Fisher's exact test), Q value = 0.37

Table S223.  Gene #22: 'BCL9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
BCL9 MUTATED 1 1 0 2 1
BCL9 WILD-TYPE 12 27 14 6 54
'BCL9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.245 (Fisher's exact test), Q value = 0.73

Table S224.  Gene #22: 'BCL9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
BCL9 MUTATED 2 2 1
BCL9 WILD-TYPE 18 42 53
'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.192 (Fisher's exact test), Q value = 0.63

Table S225.  Gene #23: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
KRAS MUTATED 17 10 8
KRAS WILD-TYPE 8 11 11
'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00684 (Fisher's exact test), Q value = 0.11

Table S226.  Gene #23: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
KRAS MUTATED 3 10 9 3 3 5 0 2
KRAS WILD-TYPE 3 3 3 6 3 4 8 0

Figure S48.  Get High-res Image Gene #23: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00606 (Fisher's exact test), Q value = 0.11

Table S227.  Gene #23: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
KRAS MUTATED 31 14 4 13
KRAS WILD-TYPE 20 6 15 17

Figure S49.  Get High-res Image Gene #23: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0267 (Fisher's exact test), Q value = 0.25

Table S228.  Gene #23: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
KRAS MUTATED 3 14 10
KRAS WILD-TYPE 13 9 8

Figure S50.  Get High-res Image Gene #23: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.935 (Fisher's exact test), Q value = 1

Table S229.  Gene #23: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
KRAS MUTATED 13 15 20
KRAS WILD-TYPE 15 14 20
'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.851 (Fisher's exact test), Q value = 1

Table S230.  Gene #23: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
KRAS MUTATED 12 9 14 2 8 3
KRAS WILD-TYPE 11 9 10 2 12 5
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.457 (Fisher's exact test), Q value = 0.96

Table S231.  Gene #23: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
KRAS MUTATED 8 6 15 5 28
KRAS WILD-TYPE 8 7 7 8 29
'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.158 (Fisher's exact test), Q value = 0.6

Table S232.  Gene #23: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
KRAS MUTATED 4 12 4 7 11 13 11
KRAS WILD-TYPE 7 11 4 5 21 5 6
'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S233.  Gene #23: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
KRAS MUTATED 6 14 6 3 30
KRAS WILD-TYPE 7 14 8 5 25
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0525 (Fisher's exact test), Q value = 0.32

Table S234.  Gene #23: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
KRAS MUTATED 5 24 30
KRAS WILD-TYPE 15 20 24
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S235.  Gene #23: 'KRAS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
KRAS MUTATED 2 4 6 3
KRAS WILD-TYPE 6 3 7 5
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.162 (Fisher's exact test), Q value = 0.6

Table S236.  Gene #23: 'KRAS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
KRAS MUTATED 4 4 7 0 0
KRAS WILD-TYPE 4 5 5 5 2
'SLC12A6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.45 (Fisher's exact test), Q value = 0.95

Table S237.  Gene #24: 'SLC12A6 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
SLC12A6 MUTATED 4 1 1 0
SLC12A6 WILD-TYPE 47 19 18 30
'SLC12A6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.449 (Fisher's exact test), Q value = 0.95

Table S238.  Gene #24: 'SLC12A6 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
SLC12A6 MUTATED 0 3 1
SLC12A6 WILD-TYPE 16 20 17
'SLC12A6 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S239.  Gene #24: 'SLC12A6 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
SLC12A6 MUTATED 1 1 1
SLC12A6 WILD-TYPE 27 28 39
'SLC12A6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.557 (Fisher's exact test), Q value = 1

Table S240.  Gene #24: 'SLC12A6 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
SLC12A6 MUTATED 0 0 1 0 2 0
SLC12A6 WILD-TYPE 23 18 23 4 18 8
'SLC12A6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0421 (Fisher's exact test), Q value = 0.29

Table S241.  Gene #24: 'SLC12A6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
SLC12A6 MUTATED 1 3 1 0 1
SLC12A6 WILD-TYPE 15 10 21 13 56

Figure S51.  Get High-res Image Gene #24: 'SLC12A6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'SLC12A6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.151 (Fisher's exact test), Q value = 0.59

Table S242.  Gene #24: 'SLC12A6 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
SLC12A6 MUTATED 0 3 0 1 0 2 0
SLC12A6 WILD-TYPE 11 20 8 11 32 16 17
'SLC12A6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.266 (Fisher's exact test), Q value = 0.76

Table S243.  Gene #24: 'SLC12A6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
SLC12A6 MUTATED 0 4 0 0 2
SLC12A6 WILD-TYPE 13 24 14 8 53
'SLC12A6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.327 (Fisher's exact test), Q value = 0.84

Table S244.  Gene #24: 'SLC12A6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
SLC12A6 MUTATED 0 4 2
SLC12A6 WILD-TYPE 20 40 52
'ZNF354C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.681 (Fisher's exact test), Q value = 1

Table S245.  Gene #25: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
ZNF354C MUTATED 3 0 0 2
ZNF354C WILD-TYPE 48 20 19 28
'ZNF354C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.291 (Fisher's exact test), Q value = 0.79

Table S246.  Gene #25: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
ZNF354C MUTATED 1 3 0
ZNF354C WILD-TYPE 15 20 18
'ZNF354C MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S247.  Gene #25: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
ZNF354C MUTATED 1 2 2
ZNF354C WILD-TYPE 27 27 38
'ZNF354C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.169 (Fisher's exact test), Q value = 0.61

Table S248.  Gene #25: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
ZNF354C MUTATED 0 0 1 0 3 1
ZNF354C WILD-TYPE 23 18 23 4 17 7
'ZNF354C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.17

Table S249.  Gene #25: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
ZNF354C MUTATED 2 0 3 0 0
ZNF354C WILD-TYPE 14 13 19 13 57

Figure S52.  Get High-res Image Gene #25: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'ZNF354C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.206 (Fisher's exact test), Q value = 0.66

Table S250.  Gene #25: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
ZNF354C MUTATED 1 2 1 0 0 1 0
ZNF354C WILD-TYPE 10 21 7 12 32 17 17
'ZNF354C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 0.72

Table S251.  Gene #25: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
ZNF354C MUTATED 1 1 1 1 1
ZNF354C WILD-TYPE 12 27 13 7 54
'ZNF354C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.193 (Fisher's exact test), Q value = 0.63

Table S252.  Gene #25: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
ZNF354C MUTATED 0 4 1
ZNF354C WILD-TYPE 20 40 53
'ZNF354C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.883 (Fisher's exact test), Q value = 1

Table S253.  Gene #25: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
ZNF354C MUTATED 0 1 1 1
ZNF354C WILD-TYPE 8 6 12 7
'ZNF354C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 0.57

Table S254.  Gene #25: 'ZNF354C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
ZNF354C MUTATED 0 0 2 0 1
ZNF354C WILD-TYPE 8 9 10 5 1
'GABRP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.673 (Fisher's exact test), Q value = 1

Table S255.  Gene #26: 'GABRP MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
GABRP MUTATED 2 0 0 2
GABRP WILD-TYPE 49 20 19 28
'GABRP MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S256.  Gene #26: 'GABRP MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
GABRP MUTATED 1 1 1
GABRP WILD-TYPE 15 22 17
'GABRP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.344 (Fisher's exact test), Q value = 0.86

Table S257.  Gene #26: 'GABRP MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
GABRP MUTATED 0 1 1 1 1
GABRP WILD-TYPE 16 12 21 12 56
'GABRP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.277 (Fisher's exact test), Q value = 0.77

Table S258.  Gene #26: 'GABRP MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
GABRP MUTATED 0 1 0 1 0 2 0
GABRP WILD-TYPE 11 22 8 11 32 16 17
'GABRP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 0.63

Table S259.  Gene #26: 'GABRP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
GABRP MUTATED 0 0 2 0 2
GABRP WILD-TYPE 13 28 12 8 53
'GABRP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.822 (Fisher's exact test), Q value = 1

Table S260.  Gene #26: 'GABRP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
GABRP MUTATED 1 1 2
GABRP WILD-TYPE 19 43 52
'BRAF MUTATION STATUS' versus 'CN_CNMF'

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

Table S261.  Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
BRAF MUTATED 5 1 2 4
BRAF WILD-TYPE 46 19 17 26
'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.313 (Fisher's exact test), Q value = 0.82

Table S262.  Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
BRAF MUTATED 3 2 5
BRAF WILD-TYPE 13 21 13
'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.502 (Fisher's exact test), Q value = 0.98

Table S263.  Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
BRAF MUTATED 5 2 5
BRAF WILD-TYPE 23 27 35
'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.125 (Fisher's exact test), Q value = 0.52

Table S264.  Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
BRAF MUTATED 1 3 2 2 2 2
BRAF WILD-TYPE 22 15 22 2 18 6
'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00674 (Fisher's exact test), Q value = 0.11

Table S265.  Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
BRAF MUTATED 4 1 3 3 1
BRAF WILD-TYPE 12 12 19 10 56

Figure S53.  Get High-res Image Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0935 (Fisher's exact test), Q value = 0.43

Table S266.  Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
BRAF MUTATED 2 4 2 2 1 1 0
BRAF WILD-TYPE 9 19 6 10 31 17 17
'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0578 (Fisher's exact test), Q value = 0.33

Table S267.  Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
BRAF MUTATED 3 5 2 0 2
BRAF WILD-TYPE 10 23 12 8 53
'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00913 (Fisher's exact test), Q value = 0.13

Table S268.  Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
BRAF MUTATED 4 7 1
BRAF WILD-TYPE 16 37 53

Figure S54.  Get High-res Image Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.906 (Fisher's exact test), Q value = 1

Table S269.  Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
BRAF MUTATED 2 1 1 1
BRAF WILD-TYPE 6 6 12 7
'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0414 (Fisher's exact test), Q value = 0.29

Table S270.  Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
BRAF MUTATED 0 3 0 1 1
BRAF WILD-TYPE 8 6 12 4 1

Figure S55.  Get High-res Image Gene #27: 'BRAF MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.856 (Fisher's exact test), Q value = 1

Table S271.  Gene #28: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
PIK3CA MUTATED 2 1 2
PIK3CA WILD-TYPE 23 20 17
'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S272.  Gene #28: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
PIK3CA MUTATED 0 2 1 1 0 1 0 0
PIK3CA WILD-TYPE 6 11 11 8 6 8 8 2
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.208 (Fisher's exact test), Q value = 0.66

Table S273.  Gene #28: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
PIK3CA MUTATED 13 4 9 11
PIK3CA WILD-TYPE 38 16 10 19
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.942 (Fisher's exact test), Q value = 1

Table S274.  Gene #28: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
PIK3CA MUTATED 9 12 11
PIK3CA WILD-TYPE 7 11 7
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.184 (Fisher's exact test), Q value = 0.63

Table S275.  Gene #28: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
PIK3CA MUTATED 7 13 10
PIK3CA WILD-TYPE 21 16 30
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0537 (Fisher's exact test), Q value = 0.32

Table S276.  Gene #28: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
PIK3CA MUTATED 3 5 8 0 9 5
PIK3CA WILD-TYPE 20 13 16 4 11 3
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00058

Table S277.  Gene #28: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
PIK3CA MUTATED 9 5 9 10 4
PIK3CA WILD-TYPE 7 8 13 3 53

Figure S56.  Get High-res Image Gene #28: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00058

Table S278.  Gene #28: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
PIK3CA MUTATED 8 10 5 7 2 4 1
PIK3CA WILD-TYPE 3 13 3 5 30 14 16

Figure S57.  Get High-res Image Gene #28: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00058

Table S279.  Gene #28: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
PIK3CA MUTATED 6 19 5 1 5
PIK3CA WILD-TYPE 7 9 9 7 50

Figure S58.  Get High-res Image Gene #28: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00058

Table S280.  Gene #28: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
PIK3CA MUTATED 7 25 4
PIK3CA WILD-TYPE 13 19 50

Figure S59.  Get High-res Image Gene #28: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.114 (Fisher's exact test), Q value = 0.49

Table S281.  Gene #28: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
PIK3CA MUTATED 6 1 7 5
PIK3CA WILD-TYPE 2 6 6 3
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.238 (Fisher's exact test), Q value = 0.71

Table S282.  Gene #28: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
PIK3CA MUTATED 5 2 7 4 1
PIK3CA WILD-TYPE 3 7 5 1 1
'CEP290 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.736 (Fisher's exact test), Q value = 1

Table S283.  Gene #29: 'CEP290 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
CEP290 MUTATED 2 0 1 2
CEP290 WILD-TYPE 49 20 18 28
'CEP290 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.26

Table S284.  Gene #29: 'CEP290 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
CEP290 MUTATED 4 1 0
CEP290 WILD-TYPE 12 22 18

Figure S60.  Get High-res Image Gene #29: 'CEP290 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CEP290 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.449 (Fisher's exact test), Q value = 0.95

Table S285.  Gene #29: 'CEP290 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
CEP290 MUTATED 0 2 3
CEP290 WILD-TYPE 28 27 37
'CEP290 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S286.  Gene #29: 'CEP290 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
CEP290 MUTATED 0 1 2 0 1 1
CEP290 WILD-TYPE 23 17 22 4 19 7
'CEP290 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.137 (Fisher's exact test), Q value = 0.55

Table S287.  Gene #29: 'CEP290 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
CEP290 MUTATED 1 0 3 1 1
CEP290 WILD-TYPE 15 13 19 12 56
'CEP290 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.421 (Fisher's exact test), Q value = 0.92

Table S288.  Gene #29: 'CEP290 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
CEP290 MUTATED 1 2 1 1 1 0 0
CEP290 WILD-TYPE 10 21 7 11 31 18 17
'CEP290 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.176 (Fisher's exact test), Q value = 0.62

Table S289.  Gene #29: 'CEP290 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
CEP290 MUTATED 0 3 1 1 1
CEP290 WILD-TYPE 13 25 13 7 54
'CEP290 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0622 (Fisher's exact test), Q value = 0.34

Table S290.  Gene #29: 'CEP290 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
CEP290 MUTATED 3 2 1
CEP290 WILD-TYPE 17 42 53
'CEP290 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.08 (Fisher's exact test), Q value = 0.4

Table S291.  Gene #29: 'CEP290 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
CEP290 MUTATED 0 0 4 0
CEP290 WILD-TYPE 8 7 9 8
'CEP290 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.531 (Fisher's exact test), Q value = 0.99

Table S292.  Gene #29: 'CEP290 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
CEP290 MUTATED 2 0 2 0 0
CEP290 WILD-TYPE 6 9 10 5 2
'LIG1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S293.  Gene #30: 'LIG1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
LIG1 MUTATED 3 0 0 1
LIG1 WILD-TYPE 48 20 19 29
'LIG1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.449 (Fisher's exact test), Q value = 0.95

Table S294.  Gene #30: 'LIG1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
LIG1 MUTATED 0 3 1
LIG1 WILD-TYPE 16 20 17
'LIG1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S295.  Gene #30: 'LIG1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
LIG1 MUTATED 0 1 2
LIG1 WILD-TYPE 28 28 38
'LIG1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.43 (Fisher's exact test), Q value = 0.93

Table S296.  Gene #30: 'LIG1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
LIG1 MUTATED 0 0 1 0 1 1
LIG1 WILD-TYPE 23 18 23 4 19 7
'LIG1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0278 (Fisher's exact test), Q value = 0.26

Table S297.  Gene #30: 'LIG1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
LIG1 MUTATED 0 1 3 0 0
LIG1 WILD-TYPE 16 12 19 13 57

Figure S61.  Get High-res Image Gene #30: 'LIG1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'LIG1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.123 (Fisher's exact test), Q value = 0.52

Table S298.  Gene #30: 'LIG1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
LIG1 MUTATED 0 2 1 1 0 0 0
LIG1 WILD-TYPE 11 21 7 11 32 18 17
'LIG1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0835 (Fisher's exact test), Q value = 0.4

Table S299.  Gene #30: 'LIG1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
LIG1 MUTATED 0 2 1 1 0
LIG1 WILD-TYPE 13 26 13 7 55
'LIG1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0326 (Fisher's exact test), Q value = 0.27

Table S300.  Gene #30: 'LIG1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
LIG1 MUTATED 0 4 0
LIG1 WILD-TYPE 20 40 54

Figure S62.  Get High-res Image Gene #30: 'LIG1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PCBP1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S301.  Gene #31: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
PCBP1 MUTATED 3 0 0 1
PCBP1 WILD-TYPE 48 20 19 29
'PCBP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.617 (Fisher's exact test), Q value = 1

Table S302.  Gene #31: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
PCBP1 MUTATED 1 2 0
PCBP1 WILD-TYPE 15 21 18
'PCBP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.408 (Fisher's exact test), Q value = 0.91

Table S303.  Gene #31: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
PCBP1 MUTATED 1 1 1 0 1
PCBP1 WILD-TYPE 15 12 21 13 56
'PCBP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.4 (Fisher's exact test), Q value = 0.9

Table S304.  Gene #31: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
PCBP1 MUTATED 0 3 0 0 1 0 0
PCBP1 WILD-TYPE 11 20 8 12 31 18 17
'PCBP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.505 (Fisher's exact test), Q value = 0.98

Table S305.  Gene #31: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
PCBP1 MUTATED 0 2 1 0 1
PCBP1 WILD-TYPE 13 26 13 8 54
'PCBP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.382 (Fisher's exact test), Q value = 0.9

Table S306.  Gene #31: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
PCBP1 MUTATED 0 3 1
PCBP1 WILD-TYPE 20 41 53
'ATP8B1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.495 (Fisher's exact test), Q value = 0.97

Table S307.  Gene #32: 'ATP8B1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
ATP8B1 MUTATED 1 2 0
ATP8B1 WILD-TYPE 24 19 19
'ATP8B1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S308.  Gene #32: 'ATP8B1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
ATP8B1 MUTATED 0 1 1 0 0 1 0 0
ATP8B1 WILD-TYPE 6 12 11 9 6 8 8 2
'ATP8B1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S309.  Gene #32: 'ATP8B1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
ATP8B1 MUTATED 2 1 0 2
ATP8B1 WILD-TYPE 49 19 19 28
'ATP8B1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S310.  Gene #32: 'ATP8B1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
ATP8B1 MUTATED 1 1 2
ATP8B1 WILD-TYPE 27 28 38
'ATP8B1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.281 (Fisher's exact test), Q value = 0.77

Table S311.  Gene #32: 'ATP8B1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
ATP8B1 MUTATED 1 0 0 0 2 1
ATP8B1 WILD-TYPE 22 18 24 4 18 7
'ATP8B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S312.  Gene #32: 'ATP8B1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
ATP8B1 MUTATED 1 0 2 0 2
ATP8B1 WILD-TYPE 15 13 20 13 55
'ATP8B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.096 (Fisher's exact test), Q value = 0.44

Table S313.  Gene #32: 'ATP8B1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
ATP8B1 MUTATED 1 0 1 0 0 2 1
ATP8B1 WILD-TYPE 10 23 7 12 32 16 16
'ATP8B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S314.  Gene #32: 'ATP8B1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
ATP8B1 MUTATED 1 1 0 0 3
ATP8B1 WILD-TYPE 12 27 14 8 52
'ATP8B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.711 (Fisher's exact test), Q value = 1

Table S315.  Gene #32: 'ATP8B1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
ATP8B1 MUTATED 1 1 3
ATP8B1 WILD-TYPE 19 43 51
'FLT1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S316.  Gene #33: 'FLT1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
FLT1 MUTATED 4 2 1 1
FLT1 WILD-TYPE 47 18 18 29
'FLT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S317.  Gene #33: 'FLT1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
FLT1 MUTATED 2 2 1
FLT1 WILD-TYPE 14 21 17
'FLT1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.405 (Fisher's exact test), Q value = 0.9

Table S318.  Gene #33: 'FLT1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
FLT1 MUTATED 1 1 5
FLT1 WILD-TYPE 27 28 35
'FLT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.323 (Fisher's exact test), Q value = 0.84

Table S319.  Gene #33: 'FLT1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
FLT1 MUTATED 1 0 2 0 2 2
FLT1 WILD-TYPE 22 18 22 4 18 6
'FLT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0288 (Fisher's exact test), Q value = 0.26

Table S320.  Gene #33: 'FLT1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
FLT1 MUTATED 0 2 3 2 1
FLT1 WILD-TYPE 16 11 19 11 56

Figure S63.  Get High-res Image Gene #33: 'FLT1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'FLT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.223 (Fisher's exact test), Q value = 0.69

Table S321.  Gene #33: 'FLT1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
FLT1 MUTATED 2 2 1 1 0 1 1
FLT1 WILD-TYPE 9 21 7 11 32 17 16
'FLT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.158 (Fisher's exact test), Q value = 0.6

Table S322.  Gene #33: 'FLT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
FLT1 MUTATED 2 1 2 1 2
FLT1 WILD-TYPE 11 27 12 7 53
'FLT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.384 (Fisher's exact test), Q value = 0.9

Table S323.  Gene #33: 'FLT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
FLT1 MUTATED 1 5 2
FLT1 WILD-TYPE 19 39 52
'FLT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.121 (Fisher's exact test), Q value = 0.52

Table S324.  Gene #33: 'FLT1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
FLT1 MUTATED 0 1 0 2
FLT1 WILD-TYPE 8 6 13 6
'FLT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S325.  Gene #33: 'FLT1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
FLT1 MUTATED 0 2 1 0 0
FLT1 WILD-TYPE 8 7 11 5 2
'OBSCN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.28 (Fisher's exact test), Q value = 0.77

Table S326.  Gene #34: 'OBSCN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 21 19
OBSCN MUTATED 0 2 1
OBSCN WILD-TYPE 25 19 18
'OBSCN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.693 (Fisher's exact test), Q value = 1

Table S327.  Gene #34: 'OBSCN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 6 13 12 9 6 9 8 2
OBSCN MUTATED 0 2 0 1 0 0 0 0
OBSCN WILD-TYPE 6 11 12 8 6 9 8 2
'OBSCN MUTATION STATUS' versus 'CN_CNMF'

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

Table S328.  Gene #34: 'OBSCN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
OBSCN MUTATED 7 1 1 4
OBSCN WILD-TYPE 44 19 18 26
'OBSCN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.486 (Fisher's exact test), Q value = 0.97

Table S329.  Gene #34: 'OBSCN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
OBSCN MUTATED 3 6 2
OBSCN WILD-TYPE 13 17 16
'OBSCN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.674 (Fisher's exact test), Q value = 1

Table S330.  Gene #34: 'OBSCN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
OBSCN MUTATED 2 4 3
OBSCN WILD-TYPE 26 25 37
'OBSCN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.33 (Fisher's exact test), Q value = 0.85

Table S331.  Gene #34: 'OBSCN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
OBSCN MUTATED 0 3 2 0 3 1
OBSCN WILD-TYPE 23 15 22 4 17 7
'OBSCN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0844 (Fisher's exact test), Q value = 0.4

Table S332.  Gene #34: 'OBSCN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
OBSCN MUTATED 1 3 5 1 3
OBSCN WILD-TYPE 15 10 17 12 54
'OBSCN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.26

Table S333.  Gene #34: 'OBSCN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
OBSCN MUTATED 0 5 2 3 1 2 0
OBSCN WILD-TYPE 11 18 6 9 31 16 17

Figure S64.  Get High-res Image Gene #34: 'OBSCN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'OBSCN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0506 (Fisher's exact test), Q value = 0.32

Table S334.  Gene #34: 'OBSCN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
OBSCN MUTATED 0 7 2 1 3
OBSCN WILD-TYPE 13 21 12 7 52
'OBSCN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.132 (Fisher's exact test), Q value = 0.54

Table S335.  Gene #34: 'OBSCN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
OBSCN MUTATED 2 8 3
OBSCN WILD-TYPE 18 36 51
'OBSCN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S336.  Gene #34: 'OBSCN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
OBSCN MUTATED 1 1 3 2
OBSCN WILD-TYPE 7 6 10 6
'OBSCN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.214 (Fisher's exact test), Q value = 0.67

Table S337.  Gene #34: 'OBSCN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
OBSCN MUTATED 1 0 4 1 1
OBSCN WILD-TYPE 7 9 8 4 1
'VANGL1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.395 (Fisher's exact test), Q value = 0.9

Table S338.  Gene #35: 'VANGL1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
VANGL1 MUTATED 3 0 0 0
VANGL1 WILD-TYPE 48 20 19 30
'VANGL1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S339.  Gene #35: 'VANGL1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
VANGL1 MUTATED 1 1 1
VANGL1 WILD-TYPE 27 28 39
'VANGL1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S340.  Gene #35: 'VANGL1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
VANGL1 MUTATED 1 0 1 0 1 0
VANGL1 WILD-TYPE 22 18 23 4 19 8
'VANGL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0554 (Fisher's exact test), Q value = 0.32

Table S341.  Gene #35: 'VANGL1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
VANGL1 MUTATED 2 0 1 0 0
VANGL1 WILD-TYPE 14 13 21 13 57
'VANGL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.23 (Fisher's exact test), Q value = 0.7

Table S342.  Gene #35: 'VANGL1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
VANGL1 MUTATED 0 2 0 1 0 0 0
VANGL1 WILD-TYPE 11 21 8 11 32 18 17
'VANGL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0514 (Fisher's exact test), Q value = 0.32

Table S343.  Gene #35: 'VANGL1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
VANGL1 MUTATED 0 1 2 0 0
VANGL1 WILD-TYPE 13 27 12 8 55
'VANGL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.194 (Fisher's exact test), Q value = 0.63

Table S344.  Gene #35: 'VANGL1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
VANGL1 MUTATED 1 2 0
VANGL1 WILD-TYPE 19 42 54
'RRP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.487 (Fisher's exact test), Q value = 0.97

Table S345.  Gene #36: 'RRP8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
RRP8 MUTATED 1 0 1 2
RRP8 WILD-TYPE 50 20 18 28
'RRP8 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S346.  Gene #36: 'RRP8 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
RRP8 MUTATED 1 2 2
RRP8 WILD-TYPE 15 21 16
'RRP8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00336 (Fisher's exact test), Q value = 0.071

Table S347.  Gene #36: 'RRP8 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
RRP8 MUTATED 0 5 0
RRP8 WILD-TYPE 28 24 40

Figure S65.  Get High-res Image Gene #36: 'RRP8 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'RRP8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0449 (Fisher's exact test), Q value = 0.3

Table S348.  Gene #36: 'RRP8 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
RRP8 MUTATED 0 1 0 0 4 0
RRP8 WILD-TYPE 23 17 24 4 16 8

Figure S66.  Get High-res Image Gene #36: 'RRP8 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'RRP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.339 (Fisher's exact test), Q value = 0.85

Table S349.  Gene #36: 'RRP8 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
RRP8 MUTATED 0 0 1 2 2
RRP8 WILD-TYPE 16 13 21 11 55
'RRP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.274 (Fisher's exact test), Q value = 0.77

Table S350.  Gene #36: 'RRP8 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
RRP8 MUTATED 1 0 1 1 2 0 0
RRP8 WILD-TYPE 10 23 7 11 30 18 17
'RRP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.037

Table S351.  Gene #36: 'RRP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
RRP8 MUTATED 0 1 1 3 0
RRP8 WILD-TYPE 13 27 13 5 55

Figure S67.  Get High-res Image Gene #36: 'RRP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'RRP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0388 (Fisher's exact test), Q value = 0.28

Table S352.  Gene #36: 'RRP8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
RRP8 MUTATED 2 3 0
RRP8 WILD-TYPE 18 41 54

Figure S68.  Get High-res Image Gene #36: 'RRP8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'RRP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.368 (Fisher's exact test), Q value = 0.88

Table S353.  Gene #36: 'RRP8 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 7 13 8
RRP8 MUTATED 0 0 1 2
RRP8 WILD-TYPE 8 7 12 6
'RRP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.421 (Fisher's exact test), Q value = 0.92

Table S354.  Gene #36: 'RRP8 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 9 12 5 2
RRP8 MUTATED 0 0 2 1 0
RRP8 WILD-TYPE 8 9 10 4 2
'AGL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.442 (Fisher's exact test), Q value = 0.95

Table S355.  Gene #37: 'AGL MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
AGL MUTATED 3 1 0 0
AGL WILD-TYPE 48 19 19 30
'AGL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 1

Table S356.  Gene #37: 'AGL MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 28 29 40
AGL MUTATED 2 1 1
AGL WILD-TYPE 26 28 39
'AGL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.459 (Fisher's exact test), Q value = 0.96

Table S357.  Gene #37: 'AGL MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 18 24 4 20 8
AGL MUTATED 2 0 0 0 2 0
AGL WILD-TYPE 21 18 24 4 18 8
'AGL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.323 (Fisher's exact test), Q value = 0.84

Table S358.  Gene #37: 'AGL MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
AGL MUTATED 1 0 2 0 1
AGL WILD-TYPE 15 13 20 13 56
'AGL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.694 (Fisher's exact test), Q value = 1

Table S359.  Gene #37: 'AGL MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
AGL MUTATED 0 1 1 0 1 1 0
AGL WILD-TYPE 11 22 7 12 31 17 17
'AGL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.549 (Fisher's exact test), Q value = 1

Table S360.  Gene #37: 'AGL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
AGL MUTATED 0 1 0 1 2
AGL WILD-TYPE 13 27 14 7 53
'AGL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.825 (Fisher's exact test), Q value = 1

Table S361.  Gene #37: 'AGL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
AGL MUTATED 1 1 2
AGL WILD-TYPE 19 43 52
'RLIM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.177 (Fisher's exact test), Q value = 0.62

Table S362.  Gene #38: 'RLIM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
RLIM MUTATED 1 0 2 0
RLIM WILD-TYPE 50 20 17 30
'RLIM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.2

Table S363.  Gene #38: 'RLIM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
RLIM MUTATED 3 0 0
RLIM WILD-TYPE 13 23 18

Figure S69.  Get High-res Image Gene #38: 'RLIM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'RLIM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.21

Table S364.  Gene #38: 'RLIM MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
RLIM MUTATED 1 0 0 2 0
RLIM WILD-TYPE 15 13 22 11 57

Figure S70.  Get High-res Image Gene #38: 'RLIM MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'RLIM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0149 (Fisher's exact test), Q value = 0.17

Table S365.  Gene #38: 'RLIM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
RLIM MUTATED 2 0 0 1 0 0 0
RLIM WILD-TYPE 9 23 8 11 32 18 17

Figure S71.  Get High-res Image Gene #38: 'RLIM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'RLIM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.169 (Fisher's exact test), Q value = 0.61

Table S366.  Gene #38: 'RLIM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
RLIM MUTATED 1 1 1 0 0
RLIM WILD-TYPE 12 27 13 8 55
'RLIM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.194 (Fisher's exact test), Q value = 0.63

Table S367.  Gene #38: 'RLIM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
RLIM MUTATED 1 2 0
RLIM WILD-TYPE 19 42 54
'STK32B MUTATION STATUS' versus 'CN_CNMF'

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

Table S368.  Gene #39: 'STK32B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 20 19 30
STK32B MUTATED 2 1 0 1
STK32B WILD-TYPE 49 19 19 29
'STK32B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.291 (Fisher's exact test), Q value = 0.79

Table S369.  Gene #39: 'STK32B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 23 18
STK32B MUTATED 1 3 0
STK32B WILD-TYPE 15 20 18
'STK32B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 0.49

Table S370.  Gene #39: 'STK32B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 16 13 22 13 57
STK32B MUTATED 1 2 0 0 1
STK32B WILD-TYPE 15 11 22 13 56
'STK32B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.401 (Fisher's exact test), Q value = 0.9

Table S371.  Gene #39: 'STK32B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 23 8 12 32 18 17
STK32B MUTATED 0 3 0 0 1 0 0
STK32B WILD-TYPE 11 20 8 12 31 18 17
'STK32B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0612 (Fisher's exact test), Q value = 0.34

Table S372.  Gene #39: 'STK32B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 13 28 14 8 55
STK32B MUTATED 1 2 0 1 0
STK32B WILD-TYPE 12 26 14 7 55
'STK32B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0904 (Fisher's exact test), Q value = 0.42

Table S373.  Gene #39: 'STK32B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 44 54
STK32B MUTATED 1 3 0
STK32B WILD-TYPE 19 41 54
Methods & Data
Input

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/READ-TP/15178178/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/READ-TP/15107799/READ-TP.transferedmergedcluster.txt

  • Number of patients = 122

  • Number of significantly mutated genes = 39

  • 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

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

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

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