Correlation between gene mutation status and molecular subtypes
Breast Invasive Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
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/C1MK6C1S
Overview
Introduction

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

Summary

Testing the association between mutation status of 79 genes and 12 molecular subtypes across 977 patients, 95 significant findings detected with P value < 0.05 and Q value < 0.25.

  • PIK3CA mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • TP53 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • GATA3 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • MAP3K1 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • CDH1 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • CBFB mutation correlated to 'METHLYATION_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • RUNX1 mutation correlated to 'MRNA_CNMF',  'CN_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • CDKN1B mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • MAP2K4 mutation correlated to 'MRNA_CHIERARCHICAL',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • FOXA1 mutation correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • CTCF mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • SPEN mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • ERBB2 mutation correlated to 'METHLYATION_CNMF'.

  • RAB42 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • MYB mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • MUC6 mutation correlated to 'MRNA_CNMF'.

  • EYS mutation correlated to 'MRNASEQ_CNMF'.

  • ZFP36L1 mutation correlated to 'CN_CNMF'.

  • FBXW7 mutation correlated to 'METHLYATION_CNMF'.

  • RHBG mutation correlated to 'MRNASEQ_CNMF'.

  • PHACTR1 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • DLG1 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • GPRASP2 mutation correlated to 'MRNA_CNMF' and 'MRNA_CHIERARCHICAL'.

  • CCDC82 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • CCDC27 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • OR8D1 mutation correlated to 'MRNA_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 79 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, 95 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
PIK3CA 316 (32%) 661 1e-05
(0.000249)
1e-05
(0.000249)
1e-05
(0.000249)
1e-05
(0.000249)
0.00144
(0.0244)
1e-05
(0.000249)
1e-05
(0.000249)
1e-05
(0.000249)
1e-05
(0.000249)
1e-05
(0.000249)
1e-05
(0.000249)
1e-05
(0.000249)
TP53 296 (30%) 681 1e-05
(0.000249)
1e-05
(0.000249)
1e-05
(0.000249)
1e-05
(0.000249)
1e-05
(0.000249)
1e-05
(0.000249)
1e-05
(0.000249)
1e-05
(0.000249)
1e-05
(0.000249)
1e-05
(0.000249)
1e-05
(0.000249)
1e-05
(0.000249)
CDH1 107 (11%) 870 3e-05
(0.000729)
0.00371
(0.0541)
1e-05
(0.000249)
1e-05
(0.000249)
0.0101
(0.127)
0.0136
(0.155)
1e-05
(0.000249)
1e-05
(0.000249)
1e-05
(0.000249)
1e-05
(0.000249)
1e-05
(0.000249)
1e-05
(0.000249)
GATA3 97 (10%) 880 1e-05
(0.000249)
1e-05
(0.000249)
0.00091
(0.0169)
0.00083
(0.0157)
0.0147
(0.163)
0.00083
(0.0157)
1e-05
(0.000249)
1e-05
(0.000249)
0.00214
(0.035)
1e-05
(0.000249)
1e-05
(0.000249)
0.113
(0.542)
MAP3K1 71 (7%) 906 4e-05
(0.000948)
0.00018
(0.00416)
0.00176
(0.0293)
0.00347
(0.0522)
0.00053
(0.0107)
1e-05
(0.000249)
0.00052
(0.0107)
0.00026
(0.00573)
0.00035
(0.00754)
0.00103
(0.0188)
0.11
(0.541)
0.13
(0.577)
MAP2K4 32 (3%) 945 0.0581
(0.405)
0.00437
(0.0618)
0.0631
(0.421)
0.00742
(0.102)
0.00308
(0.0471)
0.211
(0.723)
0.00274
(0.0426)
0.00365
(0.0541)
0.0125
(0.145)
0.00037
(0.00779)
0.0118
(0.14)
0.0122
(0.143)
RUNX1 29 (3%) 948 0.0153
(0.164)
0.0864
(0.472)
0.00864
(0.115)
0.111
(0.541)
0.343
(0.85)
0.329
(0.837)
0.0649
(0.425)
0.0115
(0.138)
0.0223
(0.233)
0.404
(0.879)
0.313
(0.826)
0.454
(0.909)
CBFB 22 (2%) 955 0.163
(0.64)
0.307
(0.826)
0.0834
(0.47)
0.00077
(0.0152)
0.142
(0.609)
0.279
(0.826)
0.0714
(0.442)
0.611
(0.981)
0.0288
(0.263)
0.00019
(0.00429)
0.0477
(0.374)
0.00112
(0.02)
CTCF 16 (2%) 961 0.0589
(0.408)
0.0443
(0.359)
0.023
(0.235)
0.0147
(0.163)
0.0483
(0.375)
0.115
(0.546)
0.119
(0.556)
0.486
(0.917)
0.0849
(0.471)
0.0102
(0.127)
0.945
(1.00)
0.576
(0.967)
FOXA1 23 (2%) 954 0.37
(0.865)
0.538
(0.952)
0.334
(0.841)
0.0753
(0.452)
0.801
(1.00)
0.749
(1.00)
0.0578
(0.405)
0.16
(0.631)
0.0235
(0.237)
0.0248
(0.247)
0.184
(0.69)
0.524
(0.946)
GPRASP2 10 (1%) 967 0.0137
(0.155)
0.0107
(0.132)
0.2
(0.713)
0.482
(0.915)
0.168
(0.649)
0.538
(0.952)
0.642
(0.988)
0.253
(0.784)
0.722
(1.00)
0.627
(0.986)
0.606
(0.981)
0.672
(0.991)
CDKN1B 10 (1%) 967 0.639
(0.988)
0.739
(1.00)
0.0694
(0.436)
0.228
(0.747)
0.743
(1.00)
0.198
(0.712)
0.1
(0.513)
0.459
(0.909)
0.448
(0.902)
0.166
(0.643)
0.391
(0.879)
0.0151
(0.164)
SPEN 32 (3%) 945 0.666
(0.991)
0.788
(1.00)
0.483
(0.915)
0.464
(0.909)
0.791
(1.00)
0.0271
(0.259)
0.207
(0.718)
0.119
(0.557)
0.213
(0.728)
0.00913
(0.119)
0.0943
(0.499)
0.658
(0.991)
ERBB2 20 (2%) 957 0.575
(0.967)
0.465
(0.909)
0.0271
(0.259)
0.00238
(0.0382)
0.309
(0.826)
0.955
(1.00)
0.217
(0.731)
0.134
(0.582)
0.217
(0.731)
0.106
(0.532)
0.319
(0.835)
0.603
(0.981)
RAB42 4 (0%) 973 0.408
(0.879)
0.0679
(0.435)
0.0413
(0.343)
0.515
(0.941)
0.388
(0.879)
0.117
(0.552)
0.156
(0.629)
0.232
(0.749)
0.00999
(0.127)
MYB 12 (1%) 965 0.736
(1.00)
0.0285
(0.262)
0.226
(0.745)
0.323
(0.837)
0.869
(1.00)
0.696
(1.00)
1
(1.00)
0.901
(1.00)
0.0972
(0.506)
0.125
(0.564)
0.283
(0.826)
0.00127
(0.0223)
MUC6 14 (1%) 963 0.0206
(0.22)
0.608
(0.981)
0.506
(0.934)
0.674
(0.991)
0.479
(0.915)
0.941
(1.00)
0.0613
(0.418)
0.204
(0.713)
0.625
(0.986)
0.112
(0.541)
0.283
(0.826)
0.0513
(0.389)
EYS 21 (2%) 956 0.262
(0.794)
0.285
(0.826)
0.0325
(0.286)
0.0651
(0.425)
0.223
(0.742)
0.383
(0.879)
0.022
(0.231)
0.202
(0.713)
0.1
(0.513)
0.0324
(0.286)
0.371
(0.865)
0.126
(0.566)
ZFP36L1 8 (1%) 969 0.401
(0.879)
0.897
(1.00)
0.00136
(0.0234)
0.78
(1.00)
0.0613
(0.418)
0.0489
(0.377)
0.184
(0.69)
0.731
(1.00)
0.895
(1.00)
0.854
(1.00)
0.949
(1.00)
0.823
(1.00)
FBXW7 15 (2%) 962 0.815
(1.00)
0.531
(0.946)
0.157
(0.629)
0.00732
(0.102)
0.644
(0.988)
0.94
(1.00)
0.23
(0.748)
0.145
(0.609)
0.355
(0.85)
0.101
(0.513)
0.0629
(0.421)
0.899
(1.00)
RHBG 4 (0%) 973 0.895
(1.00)
0.0077
(0.104)
0.106
(0.532)
0.524
(0.946)
0.265
(0.796)
PHACTR1 7 (1%) 970 0.416
(0.879)
0.43
(0.887)
0.815
(1.00)
0.341
(0.85)
0.166
(0.643)
0.937
(1.00)
0.201
(0.713)
0.0795
(0.457)
0.412
(0.879)
0.0228
(0.235)
1
(1.00)
1
(1.00)
DLG1 13 (1%) 964 0.343
(0.85)
0.32
(0.835)
0.427
(0.883)
0.572
(0.967)
0.445
(0.899)
0.114
(0.544)
0.125
(0.564)
0.186
(0.691)
0.673
(0.991)
0.0038
(0.0546)
0.67
(0.991)
0.805
(1.00)
CCDC82 6 (1%) 971 0.461
(0.909)
0.0577
(0.405)
0.303
(0.826)
0.0365
(0.312)
0.724
(1.00)
0.349
(0.85)
0.00243
(0.0384)
0.309
(0.826)
0.9
(1.00)
1
(1.00)
1
(1.00)
CCDC27 7 (1%) 970 0.088
(0.477)
0.13
(0.577)
0.0458
(0.365)
0.0449
(0.36)
0.11
(0.541)
0.941
(1.00)
0.0329
(0.286)
0.264
(0.794)
0.522
(0.946)
0.0111
(0.135)
0.0542
(0.4)
1
(1.00)
OR8D1 5 (1%) 972 0.639
(0.988)
0.00909
(0.119)
0.646
(0.988)
0.873
(1.00)
0.692
(1.00)
0.793
(1.00)
0.338
(0.847)
0.182
(0.687)
0.774
(1.00)
0.593
(0.981)
PTEN 35 (4%) 942 0.31
(0.826)
0.904
(1.00)
0.17
(0.654)
0.284
(0.826)
0.855
(1.00)
0.475
(0.915)
1
(1.00)
0.575
(0.967)
0.135
(0.583)
0.663
(0.991)
0.652
(0.991)
0.826
(1.00)
MLL3 70 (7%) 907 0.624
(0.986)
0.0699
(0.436)
0.684
(0.994)
0.245
(0.771)
0.604
(0.981)
0.559
(0.964)
0.196
(0.707)
0.412
(0.879)
0.192
(0.707)
0.124
(0.564)
0.407
(0.879)
0.312
(0.826)
ARID1A 27 (3%) 950 0.303
(0.826)
0.941
(1.00)
0.0383
(0.321)
0.0848
(0.471)
1
(1.00)
0.195
(0.707)
0.346
(0.85)
0.644
(0.988)
0.665
(0.991)
0.398
(0.879)
0.164
(0.64)
0.565
(0.965)
GPS2 10 (1%) 967 0.0679
(0.435)
0.0976
(0.506)
0.0369
(0.312)
0.417
(0.879)
0.202
(0.713)
0.631
(0.988)
0.583
(0.973)
0.0672
(0.435)
0.11
(0.541)
0.436
(0.893)
0.481
(0.915)
0.418
(0.879)
TBX3 27 (3%) 950 0.578
(0.968)
0.626
(0.986)
0.325
(0.837)
0.288
(0.826)
0.164
(0.64)
0.967
(1.00)
0.0439
(0.359)
0.133
(0.578)
0.0579
(0.405)
0.125
(0.564)
0.603
(0.981)
0.722
(1.00)
RB1 19 (2%) 958 0.879
(1.00)
0.305
(0.826)
0.159
(0.631)
0.153
(0.628)
0.371
(0.865)
0.607
(0.981)
0.0272
(0.259)
0.26
(0.794)
0.057
(0.405)
0.0275
(0.259)
0.0936
(0.499)
0.209
(0.72)
RBMX 13 (1%) 964 0.385
(0.879)
0.105
(0.532)
0.0646
(0.425)
0.53
(0.946)
0.476
(0.915)
0.848
(1.00)
0.0686
(0.435)
0.0285
(0.262)
0.242
(0.769)
0.573
(0.967)
0.0688
(0.435)
1
(1.00)
HRNR 31 (3%) 946 0.988
(1.00)
0.783
(1.00)
0.353
(0.85)
0.994
(1.00)
0.655
(0.991)
0.568
(0.965)
0.494
(0.927)
0.682
(0.994)
0.596
(0.981)
0.195
(0.707)
0.148
(0.614)
0.786
(1.00)
ZMYM3 15 (2%) 962 0.499
(0.927)
0.441
(0.898)
0.751
(1.00)
0.671
(0.991)
0.114
(0.544)
0.654
(0.991)
0.123
(0.564)
0.486
(0.917)
0.443
(0.899)
0.97
(1.00)
0.23
(0.748)
0.856
(1.00)
NCOR1 40 (4%) 937 0.848
(1.00)
0.903
(1.00)
0.923
(1.00)
0.615
(0.981)
0.298
(0.826)
0.614
(0.981)
0.826
(1.00)
0.53
(0.946)
0.811
(1.00)
0.122
(0.563)
0.716
(1.00)
0.783
(1.00)
GPRIN2 11 (1%) 966 0.604
(0.981)
0.624
(0.986)
0.98
(1.00)
0.67
(0.991)
0.777
(1.00)
0.144
(0.609)
0.467
(0.91)
0.42
(0.881)
0.371
(0.865)
0.0628
(0.421)
0.401
(0.879)
0.666
(0.991)
NF1 28 (3%) 949 0.57
(0.965)
0.805
(1.00)
0.567
(0.965)
0.224
(0.742)
0.549
(0.96)
0.233
(0.75)
0.385
(0.879)
0.417
(0.879)
0.329
(0.837)
0.677
(0.991)
0.943
(1.00)
0.542
(0.954)
TCP11 6 (1%) 971 0.785
(1.00)
0.512
(0.938)
0.456
(0.909)
1
(1.00)
0.61
(0.981)
0.745
(1.00)
0.374
(0.872)
0.946
(1.00)
0.761
(1.00)
SF3B1 16 (2%) 961 0.846
(1.00)
0.845
(1.00)
0.539
(0.952)
0.0765
(0.452)
0.0776
(0.452)
0.0788
(0.456)
0.288
(0.826)
0.356
(0.851)
0.262
(0.794)
0.387
(0.879)
0.353
(0.85)
0.247
(0.772)
CDC42EP1 5 (1%) 972 0.522
(0.946)
0.462
(0.909)
0.381
(0.879)
0.327
(0.837)
0.558
(0.964)
0.473
(0.915)
0.845
(1.00)
0.561
(0.965)
0.728
(1.00)
0.306
(0.826)
KDM6A 15 (2%) 962 0.74
(1.00)
0.345
(0.85)
0.535
(0.952)
0.176
(0.671)
0.508
(0.934)
0.965
(1.00)
0.304
(0.826)
0.408
(0.879)
0.675
(0.991)
0.647
(0.988)
0.759
(1.00)
0.449
(0.902)
AQP12A 6 (1%) 971 0.627
(0.986)
0.726
(1.00)
0.346
(0.85)
0.543
(0.954)
0.296
(0.826)
0.435
(0.892)
1
(1.00)
1
(1.00)
0.945
(1.00)
0.497
(0.927)
0.385
(0.879)
1
(1.00)
KRAS 6 (1%) 971 0.539
(0.952)
0.632
(0.988)
0.325
(0.837)
0.506
(0.934)
0.296
(0.826)
0.512
(0.938)
0.746
(1.00)
0.0842
(0.471)
0.852
(1.00)
0.958
(1.00)
0.922
(1.00)
0.126
(0.564)
NBPF9 5 (1%) 972 0.614
(0.981)
0.626
(0.986)
0.804
(1.00)
1
(1.00)
0.641
(0.988)
0.603
(0.981)
0.155
(0.629)
0.143
(0.609)
0.301
(0.826)
ZNF362 5 (1%) 972 0.879
(1.00)
0.87
(1.00)
0.091
(0.49)
0.0761
(0.452)
0.662
(0.991)
0.41
(0.879)
0.91
(1.00)
0.0857
(0.472)
0.415
(0.879)
TBL1XR1 9 (1%) 968 0.158
(0.629)
0.0812
(0.461)
0.0506
(0.387)
0.354
(0.85)
0.155
(0.629)
0.544
(0.954)
0.566
(0.965)
0.478
(0.915)
0.553
(0.963)
1
(1.00)
0.0747
(0.452)
SP3 7 (1%) 970 0.882
(1.00)
0.553
(0.963)
0.558
(0.964)
0.907
(1.00)
0.879
(1.00)
0.441
(0.898)
0.398
(0.879)
0.409
(0.879)
0.319
(0.835)
1
(1.00)
FGFR2 11 (1%) 966 0.917
(1.00)
0.876
(1.00)
0.329
(0.837)
0.094
(0.499)
0.868
(1.00)
0.796
(1.00)
0.79
(1.00)
0.431
(0.887)
0.226
(0.745)
0.498
(0.927)
0.608
(0.981)
0.673
(0.991)
ZBTB7C 5 (1%) 972 0.496
(0.927)
0.307
(0.826)
0.497
(0.927)
0.678
(0.991)
0.685
(0.994)
0.921
(1.00)
NCDN 4 (0%) 973 1
(1.00)
0.791
(1.00)
1
(1.00)
0.403
(0.879)
0.483
(0.915)
0.82
(1.00)
0.913
(1.00)
0.841
(1.00)
0.0519
(0.39)
TGS1 13 (1%) 964 0.637
(0.988)
0.666
(0.991)
0.421
(0.881)
0.236
(0.757)
0.205
(0.713)
0.558
(0.964)
1
(1.00)
0.245
(0.771)
0.27
(0.808)
0.46
(0.909)
0.248
(0.773)
0.354
(0.85)
TFE3 7 (1%) 970 0.676
(0.991)
0.903
(1.00)
0.741
(1.00)
0.322
(0.837)
1
(1.00)
0.941
(1.00)
0.786
(1.00)
0.647
(0.988)
0.751
(1.00)
0.425
(0.881)
0.856
(1.00)
0.301
(0.826)
IRS4 11 (1%) 966 0.146
(0.609)
0.782
(1.00)
0.223
(0.742)
0.683
(0.994)
0.869
(1.00)
0.847
(1.00)
0.217
(0.731)
0.47
(0.912)
1
(1.00)
0.174
(0.666)
0.949
(1.00)
0.824
(1.00)
NLGN3 11 (1%) 966 0.544
(0.954)
0.562
(0.965)
0.244
(0.771)
0.153
(0.628)
0.0546
(0.4)
0.255
(0.788)
0.789
(1.00)
0.0812
(0.461)
0.953
(1.00)
0.747
(1.00)
0.608
(0.981)
0.673
(0.991)
IL1RAP 9 (1%) 968 0.15
(0.622)
0.301
(0.826)
0.289
(0.826)
0.644
(0.988)
0.615
(0.981)
0.897
(1.00)
0.587
(0.976)
0.686
(0.994)
USP36 8 (1%) 969 0.835
(1.00)
0.182
(0.687)
0.968
(1.00)
0.73
(1.00)
0.642
(0.988)
0.744
(1.00)
0.457
(0.909)
0.077
(0.452)
0.676
(0.991)
0.344
(0.85)
CASZ1 14 (1%) 963 0.936
(1.00)
0.854
(1.00)
0.903
(1.00)
0.813
(1.00)
0.204
(0.713)
0.933
(1.00)
0.822
(1.00)
0.733
(1.00)
0.518
(0.945)
0.735
(1.00)
0.425
(0.881)
0.326
(0.837)
KCNN3 9 (1%) 968 0.144
(0.609)
0.507
(0.934)
0.252
(0.782)
0.122
(0.563)
0.391
(0.879)
0.768
(1.00)
0.287
(0.826)
0.397
(0.879)
0.304
(0.826)
0.713
(1.00)
0.58
(0.969)
0.409
(0.879)
ICOSLG 5 (1%) 972 0.772
(1.00)
0.133
(0.578)
0.0434
(0.358)
0.833
(1.00)
0.599
(0.981)
0.968
(1.00)
0.772
(1.00)
0.467
(0.91)
ACTL6B 10 (1%) 967 0.353
(0.85)
0.291
(0.826)
0.0294
(0.266)
0.353
(0.85)
1
(1.00)
0.194
(0.707)
0.837
(1.00)
0.194
(0.707)
0.739
(1.00)
0.714
(1.00)
0.423
(0.881)
0.714
(1.00)
MYH9 18 (2%) 959 0.396
(0.879)
0.424
(0.881)
0.366
(0.864)
0.402
(0.879)
0.821
(1.00)
0.0538
(0.4)
0.663
(0.991)
0.146
(0.609)
0.736
(1.00)
0.402
(0.879)
0.508
(0.934)
0.261
(0.794)
FRMPD2 13 (1%) 964 0.529
(0.946)
0.978
(1.00)
0.465
(0.909)
0.444
(0.899)
0.558
(0.964)
0.933
(1.00)
1
(1.00)
0.0548
(0.4)
0.216
(0.731)
0.73
(1.00)
0.187
(0.691)
0.756
(1.00)
ZFP36L2 7 (1%) 970 0.392
(0.879)
1
(1.00)
0.0276
(0.259)
0.779
(1.00)
1
(1.00)
0.883
(1.00)
0.526
(0.946)
0.567
(0.965)
0.785
(1.00)
0.903
(1.00)
0.361
(0.857)
0.858
(1.00)
TPP2 8 (1%) 969 0.0866
(0.472)
0.945
(1.00)
0.637
(0.988)
0.465
(0.909)
0.363
(0.859)
0.917
(1.00)
0.53
(0.946)
0.88
(1.00)
0.875
(1.00)
0.594
(0.981)
C17ORF95 5 (1%) 972 0.866
(1.00)
0.858
(1.00)
1
(1.00)
0.842
(1.00)
0.968
(1.00)
0.727
(1.00)
0.751
(1.00)
RUFY1 6 (1%) 971 0.387
(0.879)
0.727
(1.00)
0.313
(0.826)
0.291
(0.826)
0.653
(0.991)
0.24
(0.765)
0.851
(1.00)
0.132
(0.578)
0.899
(1.00)
0.411
(0.879)
MED23 14 (1%) 963 0.0974
(0.506)
0.283
(0.826)
0.355
(0.85)
0.0766
(0.452)
0.0753
(0.452)
0.222
(0.742)
0.047
(0.372)
0.0731
(0.45)
0.353
(0.85)
0.389
(0.879)
0.283
(0.826)
0.414
(0.879)
PAX2 4 (0%) 973 0.946
(1.00)
0.335
(0.841)
0.298
(0.826)
0.204
(0.713)
0.0567
(0.405)
0.316
(0.832)
0.287
(0.826)
0.776
(1.00)
0.477
(0.915)
MED12 21 (2%) 956 0.84
(1.00)
0.78
(1.00)
0.398
(0.879)
0.678
(0.991)
0.263
(0.794)
0.0777
(0.452)
0.644
(0.988)
0.41
(0.879)
0.952
(1.00)
0.88
(1.00)
0.35
(0.85)
0.481
(0.915)
CHD4 19 (2%) 958 0.233
(0.75)
0.359
(0.855)
0.845
(1.00)
0.631
(0.988)
0.292
(0.826)
0.393
(0.879)
0.554
(0.963)
0.272
(0.809)
0.299
(0.826)
0.437
(0.893)
0.75
(1.00)
0.312
(0.826)
PFKP 6 (1%) 971 0.481
(0.915)
0.0255
(0.252)
0.186
(0.691)
0.392
(0.879)
0.794
(1.00)
0.418
(0.879)
0.302
(0.826)
0.309
(0.826)
0.205
(0.713)
PSIP1 8 (1%) 969 0.69
(0.998)
0.719
(1.00)
0.57
(0.965)
0.756
(1.00)
0.833
(1.00)
0.965
(1.00)
0.362
(0.858)
0.936
(1.00)
0.21
(0.72)
0.455
(0.909)
0.859
(1.00)
0.133
(0.578)
LRIG2 7 (1%) 970 0.565
(0.965)
0.0316
(0.282)
0.247
(0.772)
0.111
(0.541)
0.157
(0.629)
0.722
(1.00)
0.461
(0.909)
0.886
(1.00)
0.621
(0.986)
0.608
(0.981)
0.857
(1.00)
1
(1.00)
RIBC1 4 (0%) 973 0.59
(0.979)
0.383
(0.879)
0.757
(1.00)
0.506
(0.934)
0.527
(0.946)
0.606
(0.981)
0.447
(0.902)
0.327
(0.837)
PLK2 9 (1%) 968 0.297
(0.826)
0.924
(1.00)
0.975
(1.00)
0.892
(1.00)
0.911
(1.00)
0.798
(1.00)
0.97
(1.00)
0.524
(0.946)
0.82
(1.00)
0.673
(0.991)
ANKRD20A4 7 (1%) 970 0.193
(0.707)
0.0962
(0.506)
0.715
(1.00)
0.708
(1.00)
0.645
(0.988)
1
(1.00)
0.231
(0.748)
0.331
(0.839)
0.881
(1.00)
0.967
(1.00)
0.48
(0.915)
0.0365
(0.312)
RHOA 6 (1%) 971 0.906
(1.00)
0.587
(0.976)
0.781
(1.00)
0.938
(1.00)
0.112
(0.541)
0.603
(0.981)
0.415
(0.879)
0.259
(0.794)
1
(1.00)
0.796
(1.00)
MAMLD1 10 (1%) 967 0.919
(1.00)
0.433
(0.891)
0.624
(0.986)
0.731
(1.00)
0.332
(0.84)
0.937
(1.00)
0.702
(1.00)
0.653
(0.991)
0.495
(0.927)
0.157
(0.629)
0.256
(0.789)
1
(1.00)
'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S1.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
PIK3CA MUTATED 7 13 23 8 61 23 8 21
PIK3CA WILD-TYPE 14 25 91 89 47 50 11 18

Figure S1.  Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S2.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
PIK3CA MUTATED 19 70 39 5 31
PIK3CA WILD-TYPE 77 82 77 84 25

Figure S2.  Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S3.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
PIK3CA MUTATED 61 147 48 49 9
PIK3CA WILD-TYPE 186 216 38 182 27

Figure S3.  Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S4.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
PIK3CA MUTATED 30 32 94 33 7 20
PIK3CA WILD-TYPE 90 52 95 68 109 34

Figure S4.  Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.024

Table S5.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
PIK3CA MUTATED 30 48 44
PIK3CA WILD-TYPE 118 76 78

Figure S5.  Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S6.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
PIK3CA MUTATED 30 24 12 23 27 6
PIK3CA WILD-TYPE 29 24 78 30 86 25

Figure S6.  Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S7.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
PIK3CA MUTATED 187 44 85
PIK3CA WILD-TYPE 318 235 105

Figure S7.  Get High-res Image Gene #1: '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 = 0.00025

Table S8.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
PIK3CA MUTATED 79 55 34 125 7 16
PIK3CA WILD-TYPE 184 96 45 136 161 36

Figure S8.  Get High-res Image Gene #1: '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 = 0.00025

Table S9.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
PIK3CA MUTATED 43 70 97 104
PIK3CA WILD-TYPE 229 107 136 172

Figure S9.  Get High-res Image Gene #1: '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 = 0.00025

Table S10.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
PIK3CA MUTATED 99 32 89 73 15 6
PIK3CA WILD-TYPE 176 104 117 61 72 114

Figure S10.  Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S11.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
PIK3CA MUTATED 57 14 27 34 50
PIK3CA WILD-TYPE 121 106 39 58 62

Figure S11.  Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S12.  Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
PIK3CA MUTATED 52 75 55
PIK3CA WILD-TYPE 227 106 53

Figure S12.  Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S13.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
TP53 MUTATED 7 6 18 74 6 41 7 6
TP53 WILD-TYPE 14 32 96 23 102 32 12 33

Figure S13.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S14.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
TP53 MUTATED 12 17 65 69 2
TP53 WILD-TYPE 84 135 51 20 54

Figure S14.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S15.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
TP53 MUTATED 59 52 8 166 8
TP53 WILD-TYPE 188 311 78 65 28

Figure S15.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S16.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
TP53 MUTATED 31 25 13 34 87 7
TP53 WILD-TYPE 89 59 176 67 29 47

Figure S16.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S17.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
TP53 MUTATED 97 33 8
TP53 WILD-TYPE 51 91 114

Figure S17.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S18.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
TP53 MUTATED 4 7 68 10 31 18
TP53 WILD-TYPE 55 41 22 43 82 13

Figure S18.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S19.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
TP53 MUTATED 77 201 17
TP53 WILD-TYPE 428 78 173

Figure S19.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S20.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
TP53 MUTATED 25 64 3 37 126 40
TP53 WILD-TYPE 238 87 76 224 42 12

Figure S20.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S21.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
TP53 MUTATED 172 27 26 64
TP53 WILD-TYPE 100 150 207 212

Figure S21.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S22.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
TP53 MUTATED 71 86 23 15 4 90
TP53 WILD-TYPE 204 50 183 119 83 30

Figure S22.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S23.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
TP53 MUTATED 30 91 9 18 24
TP53 WILD-TYPE 148 29 57 74 88

Figure S23.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S24.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
TP53 MUTATED 121 35 16
TP53 WILD-TYPE 158 146 92

Figure S24.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S25.  Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
GATA3 MUTATED 1 6 27 2 18 4 2 0
GATA3 WILD-TYPE 20 32 87 95 90 69 17 39

Figure S25.  Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'GATA3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S26.  Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
GATA3 MUTATED 28 22 5 1 4
GATA3 WILD-TYPE 68 130 111 88 52

Figure S26.  Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.017

Table S27.  Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
GATA3 MUTATED 33 44 9 9 1
GATA3 WILD-TYPE 214 319 77 222 35

Figure S27.  Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'GATA3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.016

Table S28.  Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
GATA3 MUTATED 14 11 21 5 1 7
GATA3 WILD-TYPE 106 73 168 96 115 47

Figure S28.  Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'GATA3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.16

Table S29.  Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
GATA3 MUTATED 12 11 23
GATA3 WILD-TYPE 136 113 99

Figure S29.  Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'GATA3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00083 (Fisher's exact test), Q value = 0.016

Table S30.  Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
GATA3 MUTATED 12 4 2 4 21 3
GATA3 WILD-TYPE 47 44 88 49 92 28

Figure S30.  Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S31.  Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
GATA3 MUTATED 77 3 16
GATA3 WILD-TYPE 428 276 174

Figure S31.  Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'GATA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S32.  Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
GATA3 MUTATED 46 14 3 33 0 0
GATA3 WILD-TYPE 217 137 76 228 168 52

Figure S32.  Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.035

Table S33.  Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
GATA3 MUTATED 14 14 28 39
GATA3 WILD-TYPE 258 163 205 237

Figure S33.  Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S34.  Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
GATA3 MUTATED 34 7 11 24 19 0
GATA3 WILD-TYPE 241 129 195 110 68 120

Figure S34.  Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S35.  Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
GATA3 MUTATED 33 0 5 10 9
GATA3 WILD-TYPE 145 120 61 82 103

Figure S35.  Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.113 (Fisher's exact test), Q value = 0.54

Table S36.  Gene #3: 'GATA3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
GATA3 MUTATED 30 12 15
GATA3 WILD-TYPE 249 169 93
'MAP3K1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00095

Table S37.  Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
MAP3K1 MUTATED 5 1 12 1 16 1 0 4
MAP3K1 WILD-TYPE 16 37 102 96 92 72 19 35

Figure S36.  Get High-res Image Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.0042

Table S38.  Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
MAP3K1 MUTATED 9 14 4 1 12
MAP3K1 WILD-TYPE 87 138 112 88 44

Figure S37.  Get High-res Image Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00176 (Fisher's exact test), Q value = 0.029

Table S39.  Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
MAP3K1 MUTATED 15 40 7 6 3
MAP3K1 WILD-TYPE 232 323 79 225 33

Figure S38.  Get High-res Image Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'MAP3K1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00347 (Fisher's exact test), Q value = 0.052

Table S40.  Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
MAP3K1 MUTATED 5 1 21 7 2 4
MAP3K1 WILD-TYPE 115 83 168 94 114 50

Figure S39.  Get High-res Image Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MAP3K1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.011

Table S41.  Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
MAP3K1 MUTATED 4 14 19
MAP3K1 WILD-TYPE 144 110 103

Figure S40.  Get High-res Image Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'MAP3K1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S42.  Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
MAP3K1 MUTATED 16 8 1 7 5 0
MAP3K1 WILD-TYPE 43 40 89 46 108 31

Figure S41.  Get High-res Image Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.011

Table S43.  Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
MAP3K1 MUTATED 47 7 17
MAP3K1 WILD-TYPE 458 272 173

Figure S42.  Get High-res Image Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0057

Table S44.  Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
MAP3K1 MUTATED 31 8 7 22 3 0
MAP3K1 WILD-TYPE 232 143 72 239 165 52

Figure S43.  Get High-res Image Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0075

Table S45.  Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
MAP3K1 MUTATED 6 17 23 25
MAP3K1 WILD-TYPE 266 160 210 251

Figure S44.  Get High-res Image Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.019

Table S46.  Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
MAP3K1 MUTATED 19 4 24 11 11 2
MAP3K1 WILD-TYPE 256 132 182 123 76 118

Figure S45.  Get High-res Image Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 0.54

Table S47.  Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
MAP3K1 MUTATED 15 3 3 10 7
MAP3K1 WILD-TYPE 163 117 63 82 105
'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.13 (Fisher's exact test), Q value = 0.58

Table S48.  Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
MAP3K1 MUTATED 15 11 12
MAP3K1 WILD-TYPE 264 170 96
'CDH1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00073

Table S49.  Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
CDH1 MUTATED 0 6 1 1 10 7 1 7
CDH1 WILD-TYPE 21 32 113 96 98 66 18 32

Figure S46.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00371 (Fisher's exact test), Q value = 0.054

Table S50.  Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
CDH1 MUTATED 3 19 8 1 2
CDH1 WILD-TYPE 93 133 108 88 54

Figure S47.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S51.  Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
CDH1 MUTATED 13 60 24 3 5
CDH1 WILD-TYPE 234 303 62 228 31

Figure S48.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S52.  Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
CDH1 MUTATED 4 17 39 20 0 8
CDH1 WILD-TYPE 116 67 150 81 116 46

Figure S49.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CDH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.13

Table S53.  Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
CDH1 MUTATED 4 14 5
CDH1 WILD-TYPE 144 110 117

Figure S50.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'CDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.16

Table S54.  Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
CDH1 MUTATED 1 7 1 5 7 2
CDH1 WILD-TYPE 58 41 89 48 106 29

Figure S51.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S55.  Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
CDH1 MUTATED 50 7 50
CDH1 WILD-TYPE 455 272 140

Figure S52.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S56.  Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
CDH1 MUTATED 12 11 29 51 1 3
CDH1 WILD-TYPE 251 140 50 210 167 49

Figure S53.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S57.  Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
CDH1 MUTATED 4 49 40 12
CDH1 WILD-TYPE 268 128 193 264

Figure S54.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S58.  Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
CDH1 MUTATED 13 3 68 19 2 0
CDH1 WILD-TYPE 262 133 138 115 85 120

Figure S55.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S59.  Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
CDH1 MUTATED 9 1 20 12 33
CDH1 WILD-TYPE 169 119 46 80 79

Figure S56.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00025

Table S60.  Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
CDH1 MUTATED 9 56 10
CDH1 WILD-TYPE 270 125 98

Figure S57.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CBFB MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.163 (Fisher's exact test), Q value = 0.64

Table S61.  Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
CBFB MUTATED 1 1 0 1 5 2 0 0
CBFB WILD-TYPE 20 37 114 96 103 71 19 39
'CBFB MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.307 (Fisher's exact test), Q value = 0.83

Table S62.  Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
CBFB MUTATED 0 5 2 1 2
CBFB WILD-TYPE 96 147 114 88 54
'CBFB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0834 (Fisher's exact test), Q value = 0.47

Table S63.  Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
CBFB MUTATED 6 11 4 1 0
CBFB WILD-TYPE 241 352 82 230 36
'CBFB MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S64.  Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
CBFB MUTATED 0 2 12 1 0 0
CBFB WILD-TYPE 120 82 177 100 116 54

Figure S58.  Get High-res Image Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CBFB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 0.61

Table S65.  Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
CBFB MUTATED 1 3 5
CBFB WILD-TYPE 147 121 117
'CBFB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.279 (Fisher's exact test), Q value = 0.83

Table S66.  Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
CBFB MUTATED 4 1 2 1 1 0
CBFB WILD-TYPE 55 47 88 52 112 31
'CBFB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0714 (Fisher's exact test), Q value = 0.44

Table S67.  Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
CBFB MUTATED 16 2 4
CBFB WILD-TYPE 489 277 186
'CBFB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.611 (Fisher's exact test), Q value = 0.98

Table S68.  Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
CBFB MUTATED 7 3 2 8 1 1
CBFB WILD-TYPE 256 148 77 253 167 51
'CBFB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0288 (Fisher's exact test), Q value = 0.26

Table S69.  Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
CBFB MUTATED 1 5 9 6
CBFB WILD-TYPE 271 172 224 270

Figure S59.  Get High-res Image Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CBFB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.0043

Table S70.  Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
CBFB MUTATED 6 0 3 11 1 0
CBFB WILD-TYPE 269 136 203 123 86 120

Figure S60.  Get High-res Image Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CBFB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0477 (Fisher's exact test), Q value = 0.37

Table S71.  Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
CBFB MUTATED 6 0 1 5 1
CBFB WILD-TYPE 172 120 65 87 111

Figure S61.  Get High-res Image Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'CBFB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.02

Table S72.  Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
CBFB MUTATED 4 1 8
CBFB WILD-TYPE 275 180 100

Figure S62.  Get High-res Image Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.31 (Fisher's exact test), Q value = 0.83

Table S73.  Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
PTEN MUTATED 2 2 3 1 4 1 0 0
PTEN WILD-TYPE 19 36 111 96 104 72 19 39
'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S74.  Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
PTEN MUTATED 3 5 3 1 1
PTEN WILD-TYPE 93 147 113 88 55
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 0.65

Table S75.  Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
PTEN MUTATED 6 14 7 8 0
PTEN WILD-TYPE 241 349 79 223 36
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.284 (Fisher's exact test), Q value = 0.83

Table S76.  Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
PTEN MUTATED 4 6 7 7 5 0
PTEN WILD-TYPE 116 78 182 94 111 54
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.855 (Fisher's exact test), Q value = 1

Table S77.  Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
PTEN MUTATED 3 3 4
PTEN WILD-TYPE 145 121 118
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.475 (Fisher's exact test), Q value = 0.91

Table S78.  Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
PTEN MUTATED 2 3 2 0 3 0
PTEN WILD-TYPE 57 45 88 53 110 31
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S79.  Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
PTEN MUTATED 18 10 7
PTEN WILD-TYPE 487 269 183
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.575 (Fisher's exact test), Q value = 0.97

Table S80.  Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
PTEN MUTATED 7 6 5 9 5 3
PTEN WILD-TYPE 256 145 74 252 163 49
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.58

Table S81.  Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
PTEN MUTATED 7 12 7 9
PTEN WILD-TYPE 265 165 226 267
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.663 (Fisher's exact test), Q value = 0.99

Table S82.  Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
PTEN MUTATED 12 5 10 3 1 4
PTEN WILD-TYPE 263 131 196 131 86 116
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.652 (Fisher's exact test), Q value = 0.99

Table S83.  Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
PTEN MUTATED 7 3 3 5 7
PTEN WILD-TYPE 171 117 63 87 105
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.826 (Fisher's exact test), Q value = 1

Table S84.  Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
PTEN MUTATED 11 9 5
PTEN WILD-TYPE 268 172 103
'RUNX1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.16

Table S85.  Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
RUNX1 MUTATED 3 1 3 0 5 2 0 4
RUNX1 WILD-TYPE 18 37 111 97 103 71 19 35

Figure S63.  Get High-res Image Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'RUNX1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0864 (Fisher's exact test), Q value = 0.47

Table S86.  Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
RUNX1 MUTATED 3 10 3 0 2
RUNX1 WILD-TYPE 93 142 113 89 54
'RUNX1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00864 (Fisher's exact test), Q value = 0.12

Table S87.  Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
RUNX1 MUTATED 4 16 6 2 0
RUNX1 WILD-TYPE 243 347 80 229 36

Figure S64.  Get High-res Image Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'RUNX1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.111 (Fisher's exact test), Q value = 0.54

Table S88.  Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
RUNX1 MUTATED 0 4 6 5 2 2
RUNX1 WILD-TYPE 120 80 183 96 114 52
'RUNX1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.343 (Fisher's exact test), Q value = 0.85

Table S89.  Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
RUNX1 MUTATED 5 4 1
RUNX1 WILD-TYPE 143 120 121
'RUNX1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.329 (Fisher's exact test), Q value = 0.84

Table S90.  Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
RUNX1 MUTATED 1 2 0 2 4 1
RUNX1 WILD-TYPE 58 46 90 51 109 30
'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0649 (Fisher's exact test), Q value = 0.43

Table S91.  Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
RUNX1 MUTATED 15 4 10
RUNX1 WILD-TYPE 490 275 180
'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.14

Table S92.  Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
RUNX1 MUTATED 4 9 4 11 1 0
RUNX1 WILD-TYPE 259 142 75 250 167 52

Figure S65.  Get High-res Image Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.23

Table S93.  Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
RUNX1 MUTATED 2 9 7 11
RUNX1 WILD-TYPE 270 168 226 265

Figure S66.  Get High-res Image Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.404 (Fisher's exact test), Q value = 0.88

Table S94.  Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
RUNX1 MUTATED 11 2 7 6 2 1
RUNX1 WILD-TYPE 264 134 199 128 85 119
'RUNX1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.313 (Fisher's exact test), Q value = 0.83

Table S95.  Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
RUNX1 MUTATED 5 2 1 6 5
RUNX1 WILD-TYPE 173 118 65 86 107
'RUNX1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.454 (Fisher's exact test), Q value = 0.91

Table S96.  Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
RUNX1 MUTATED 7 8 4
RUNX1 WILD-TYPE 272 173 104
'MLL3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.624 (Fisher's exact test), Q value = 0.99

Table S97.  Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
MLL3 MUTATED 2 1 8 5 12 4 1 4
MLL3 WILD-TYPE 19 37 106 92 96 69 18 35
'MLL3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0699 (Fisher's exact test), Q value = 0.44

Table S98.  Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
MLL3 MUTATED 6 10 6 5 10
MLL3 WILD-TYPE 90 142 110 84 46
'MLL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.684 (Fisher's exact test), Q value = 0.99

Table S99.  Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
MLL3 MUTATED 17 30 7 12 2
MLL3 WILD-TYPE 230 333 79 219 34
'MLL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.245 (Fisher's exact test), Q value = 0.77

Table S100.  Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
MLL3 MUTATED 9 9 18 5 4 5
MLL3 WILD-TYPE 111 75 171 96 112 49
'MLL3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.604 (Fisher's exact test), Q value = 0.98

Table S101.  Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
MLL3 MUTATED 10 10 6
MLL3 WILD-TYPE 138 114 116
'MLL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.559 (Fisher's exact test), Q value = 0.96

Table S102.  Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
MLL3 MUTATED 6 4 7 3 4 2
MLL3 WILD-TYPE 53 44 83 50 109 29
'MLL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.196 (Fisher's exact test), Q value = 0.71

Table S103.  Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
MLL3 MUTATED 43 14 13
MLL3 WILD-TYPE 462 265 177
'MLL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.412 (Fisher's exact test), Q value = 0.88

Table S104.  Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
MLL3 MUTATED 22 15 3 19 8 3
MLL3 WILD-TYPE 241 136 76 242 160 49
'MLL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.192 (Fisher's exact test), Q value = 0.71

Table S105.  Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
MLL3 MUTATED 12 12 19 24
MLL3 WILD-TYPE 260 165 214 252
'MLL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.124 (Fisher's exact test), Q value = 0.56

Table S106.  Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
MLL3 MUTATED 18 7 14 16 8 4
MLL3 WILD-TYPE 257 129 192 118 79 116
'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.407 (Fisher's exact test), Q value = 0.88

Table S107.  Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
MLL3 MUTATED 16 4 4 5 8
MLL3 WILD-TYPE 162 116 62 87 104
'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.312 (Fisher's exact test), Q value = 0.83

Table S108.  Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
MLL3 MUTATED 14 14 9
MLL3 WILD-TYPE 265 167 99
'CDKN1B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.639 (Fisher's exact test), Q value = 0.99

Table S109.  Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
CDKN1B MUTATED 0 0 1 0 3 1 0 1
CDKN1B WILD-TYPE 21 38 113 97 105 72 19 38
'CDKN1B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.739 (Fisher's exact test), Q value = 1

Table S110.  Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
CDKN1B MUTATED 1 3 1 0 1
CDKN1B WILD-TYPE 95 149 115 89 55
'CDKN1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0694 (Fisher's exact test), Q value = 0.44

Table S111.  Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
CDKN1B MUTATED 0 5 3 2 0
CDKN1B WILD-TYPE 247 358 83 229 36
'CDKN1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.228 (Fisher's exact test), Q value = 0.75

Table S112.  Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
CDKN1B MUTATED 0 0 4 2 0 0
CDKN1B WILD-TYPE 120 84 185 99 116 54
'CDKN1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.743 (Fisher's exact test), Q value = 1

Table S113.  Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
CDKN1B MUTATED 1 2 2
CDKN1B WILD-TYPE 147 122 120
'CDKN1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.198 (Fisher's exact test), Q value = 0.71

Table S114.  Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
CDKN1B MUTATED 2 0 0 2 1 0
CDKN1B WILD-TYPE 57 48 90 51 112 31
'CDKN1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.1 (Fisher's exact test), Q value = 0.51

Table S115.  Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
CDKN1B MUTATED 7 0 3
CDKN1B WILD-TYPE 498 279 187
'CDKN1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.459 (Fisher's exact test), Q value = 0.91

Table S116.  Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
CDKN1B MUTATED 2 2 1 5 0 0
CDKN1B WILD-TYPE 261 149 78 256 168 52
'CDKN1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.448 (Fisher's exact test), Q value = 0.9

Table S117.  Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
CDKN1B MUTATED 1 3 2 4
CDKN1B WILD-TYPE 271 174 231 272
'CDKN1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.166 (Fisher's exact test), Q value = 0.64

Table S118.  Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
CDKN1B MUTATED 3 0 3 4 0 0
CDKN1B WILD-TYPE 272 136 203 130 87 120
'CDKN1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.391 (Fisher's exact test), Q value = 0.88

Table S119.  Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
CDKN1B MUTATED 1 0 1 2 1
CDKN1B WILD-TYPE 177 120 65 90 111
'CDKN1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.16

Table S120.  Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
CDKN1B MUTATED 0 2 3
CDKN1B WILD-TYPE 279 179 105

Figure S67.  Get High-res Image Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MAP2K4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0581 (Fisher's exact test), Q value = 0.41

Table S121.  Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
MAP2K4 MUTATED 0 3 3 0 8 2 1 2
MAP2K4 WILD-TYPE 21 35 111 97 100 71 18 37
'MAP2K4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00437 (Fisher's exact test), Q value = 0.062

Table S122.  Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
MAP2K4 MUTATED 2 9 2 0 6
MAP2K4 WILD-TYPE 94 143 114 89 50

Figure S68.  Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'MAP2K4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0631 (Fisher's exact test), Q value = 0.42

Table S123.  Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
MAP2K4 MUTATED 7 14 5 3 3
MAP2K4 WILD-TYPE 240 349 81 228 33
'MAP2K4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00742 (Fisher's exact test), Q value = 0.1

Table S124.  Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
MAP2K4 MUTATED 9 2 11 1 0 2
MAP2K4 WILD-TYPE 111 82 178 100 116 52

Figure S69.  Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MAP2K4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00308 (Fisher's exact test), Q value = 0.047

Table S125.  Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
MAP2K4 MUTATED 0 8 5
MAP2K4 WILD-TYPE 148 116 117

Figure S70.  Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'MAP2K4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.211 (Fisher's exact test), Q value = 0.72

Table S126.  Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
MAP2K4 MUTATED 2 4 1 3 3 0
MAP2K4 WILD-TYPE 57 44 89 50 110 31
'MAP2K4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00274 (Fisher's exact test), Q value = 0.043

Table S127.  Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
MAP2K4 MUTATED 25 2 5
MAP2K4 WILD-TYPE 480 277 185

Figure S71.  Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'MAP2K4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00365 (Fisher's exact test), Q value = 0.054

Table S128.  Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
MAP2K4 MUTATED 17 4 2 9 0 0
MAP2K4 WILD-TYPE 246 147 77 252 168 52

Figure S72.  Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.14

Table S129.  Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
MAP2K4 MUTATED 3 5 7 17
MAP2K4 WILD-TYPE 269 172 226 259

Figure S73.  Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0078

Table S130.  Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
MAP2K4 MUTATED 12 1 3 10 6 0
MAP2K4 WILD-TYPE 263 135 203 124 81 120

Figure S74.  Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.14

Table S131.  Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
MAP2K4 MUTATED 11 0 0 3 3
MAP2K4 WILD-TYPE 167 120 66 89 109

Figure S75.  Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0122 (Fisher's exact test), Q value = 0.14

Table S132.  Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
MAP2K4 MUTATED 7 2 8
MAP2K4 WILD-TYPE 272 179 100

Figure S76.  Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.303 (Fisher's exact test), Q value = 0.83

Table S133.  Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
ARID1A MUTATED 3 1 4 2 3 1 0 1
ARID1A WILD-TYPE 18 37 110 95 105 72 19 38
'ARID1A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.941 (Fisher's exact test), Q value = 1

Table S134.  Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
ARID1A MUTATED 4 5 3 2 1
ARID1A WILD-TYPE 92 147 113 87 55
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.32

Table S135.  Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
ARID1A MUTATED 12 9 0 3 2
ARID1A WILD-TYPE 235 354 86 228 34

Figure S77.  Get High-res Image Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0848 (Fisher's exact test), Q value = 0.47

Table S136.  Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
ARID1A MUTATED 8 1 5 1 1 2
ARID1A WILD-TYPE 112 83 184 100 115 52
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S137.  Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
ARID1A MUTATED 4 3 3
ARID1A WILD-TYPE 144 121 119
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 0.71

Table S138.  Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
ARID1A MUTATED 2 0 1 0 5 2
ARID1A WILD-TYPE 57 48 89 53 108 29
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.346 (Fisher's exact test), Q value = 0.85

Table S139.  Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
ARID1A MUTATED 18 5 4
ARID1A WILD-TYPE 487 274 186
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.644 (Fisher's exact test), Q value = 0.99

Table S140.  Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
ARID1A MUTATED 8 5 1 10 2 1
ARID1A WILD-TYPE 255 146 78 251 166 51
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.665 (Fisher's exact test), Q value = 0.99

Table S141.  Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
ARID1A MUTATED 5 5 8 9
ARID1A WILD-TYPE 267 172 225 267
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.398 (Fisher's exact test), Q value = 0.88

Table S142.  Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
ARID1A MUTATED 8 5 3 4 5 2
ARID1A WILD-TYPE 267 131 203 130 82 118
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.64

Table S143.  Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
ARID1A MUTATED 5 0 3 1 2
ARID1A WILD-TYPE 173 120 63 91 110
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.565 (Fisher's exact test), Q value = 0.97

Table S144.  Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
ARID1A MUTATED 4 5 2
ARID1A WILD-TYPE 275 176 106
'FOXA1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.37 (Fisher's exact test), Q value = 0.87

Table S145.  Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
FOXA1 MUTATED 0 0 3 0 1 2 0 2
FOXA1 WILD-TYPE 21 38 111 97 107 71 19 37
'FOXA1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.538 (Fisher's exact test), Q value = 0.95

Table S146.  Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
FOXA1 MUTATED 3 2 2 0 1
FOXA1 WILD-TYPE 93 150 114 89 55
'FOXA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.334 (Fisher's exact test), Q value = 0.84

Table S147.  Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
FOXA1 MUTATED 6 11 3 2 1
FOXA1 WILD-TYPE 241 352 83 229 35
'FOXA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S148.  Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
FOXA1 MUTATED 3 6 5 3 0 1
FOXA1 WILD-TYPE 117 78 184 98 116 53
'FOXA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.801 (Fisher's exact test), Q value = 1

Table S149.  Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
FOXA1 MUTATED 2 2 3
FOXA1 WILD-TYPE 146 122 119
'FOXA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.749 (Fisher's exact test), Q value = 1

Table S150.  Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
FOXA1 MUTATED 1 1 1 0 4 0
FOXA1 WILD-TYPE 58 47 89 53 109 31
'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0578 (Fisher's exact test), Q value = 0.41

Table S151.  Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
FOXA1 MUTATED 14 2 7
FOXA1 WILD-TYPE 491 277 183
'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.16 (Fisher's exact test), Q value = 0.63

Table S152.  Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
FOXA1 MUTATED 5 5 1 11 1 0
FOXA1 WILD-TYPE 258 146 78 250 167 52
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.24

Table S153.  Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
FOXA1 MUTATED 3 7 10 3
FOXA1 WILD-TYPE 269 170 223 273

Figure S78.  Get High-res Image Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0248 (Fisher's exact test), Q value = 0.25

Table S154.  Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
FOXA1 MUTATED 3 2 6 9 2 1
FOXA1 WILD-TYPE 272 134 200 125 85 119

Figure S79.  Get High-res Image Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.184 (Fisher's exact test), Q value = 0.69

Table S155.  Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
FOXA1 MUTATED 6 0 3 2 3
FOXA1 WILD-TYPE 172 120 63 90 109
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.524 (Fisher's exact test), Q value = 0.95

Table S156.  Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
FOXA1 MUTATED 5 6 3
FOXA1 WILD-TYPE 274 175 105
'GPS2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0679 (Fisher's exact test), Q value = 0.43

Table S157.  Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
GPS2 MUTATED 0 3 2 0 1 0 0 1
GPS2 WILD-TYPE 21 35 112 97 107 73 19 38
'GPS2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0976 (Fisher's exact test), Q value = 0.51

Table S158.  Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
GPS2 MUTATED 2 5 0 0 0
GPS2 WILD-TYPE 94 147 116 89 56
'GPS2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 0.31

Table S159.  Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
GPS2 MUTATED 1 9 0 0 0
GPS2 WILD-TYPE 246 354 86 231 36

Figure S80.  Get High-res Image Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'GPS2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.417 (Fisher's exact test), Q value = 0.88

Table S160.  Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
GPS2 MUTATED 1 2 1 0 2 1
GPS2 WILD-TYPE 119 82 188 101 114 53
'GPS2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.202 (Fisher's exact test), Q value = 0.71

Table S161.  Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
GPS2 MUTATED 0 1 2
GPS2 WILD-TYPE 148 123 120
'GPS2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.631 (Fisher's exact test), Q value = 0.99

Table S162.  Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
GPS2 MUTATED 1 1 0 0 1 0
GPS2 WILD-TYPE 58 47 90 53 112 31
'GPS2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.583 (Fisher's exact test), Q value = 0.97

Table S163.  Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
GPS2 MUTATED 5 2 3
GPS2 WILD-TYPE 500 277 187
'GPS2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0672 (Fisher's exact test), Q value = 0.43

Table S164.  Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
GPS2 MUTATED 2 0 1 5 0 2
GPS2 WILD-TYPE 261 151 78 256 168 50
'GPS2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 0.54

Table S165.  Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
GPS2 MUTATED 2 1 6 1
GPS2 WILD-TYPE 270 176 227 275
'GPS2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.436 (Fisher's exact test), Q value = 0.89

Table S166.  Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
GPS2 MUTATED 4 3 1 2 0 0
GPS2 WILD-TYPE 271 133 205 132 87 120
'GPS2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.481 (Fisher's exact test), Q value = 0.91

Table S167.  Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
GPS2 MUTATED 1 0 1 1 2
GPS2 WILD-TYPE 177 120 65 91 110
'GPS2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.418 (Fisher's exact test), Q value = 0.88

Table S168.  Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
GPS2 MUTATED 2 3 0
GPS2 WILD-TYPE 277 178 108
'TBX3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.578 (Fisher's exact test), Q value = 0.97

Table S169.  Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
TBX3 MUTATED 0 1 3 2 7 1 0 2
TBX3 WILD-TYPE 21 37 111 95 101 72 19 37
'TBX3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.626 (Fisher's exact test), Q value = 0.99

Table S170.  Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
TBX3 MUTATED 3 6 3 1 3
TBX3 WILD-TYPE 93 146 113 88 53
'TBX3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.325 (Fisher's exact test), Q value = 0.84

Table S171.  Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
TBX3 MUTATED 6 13 4 3 1
TBX3 WILD-TYPE 241 350 82 228 35
'TBX3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.288 (Fisher's exact test), Q value = 0.83

Table S172.  Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
TBX3 MUTATED 1 2 9 2 1 1
TBX3 WILD-TYPE 119 82 180 99 115 53
'TBX3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.64

Table S173.  Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
TBX3 MUTATED 1 5 4
TBX3 WILD-TYPE 147 119 118
'TBX3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.967 (Fisher's exact test), Q value = 1

Table S174.  Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
TBX3 MUTATED 2 1 2 1 4 0
TBX3 WILD-TYPE 57 47 88 52 109 31
'TBX3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0439 (Fisher's exact test), Q value = 0.36

Table S175.  Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
TBX3 MUTATED 15 3 9
TBX3 WILD-TYPE 490 276 181

Figure S81.  Get High-res Image Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TBX3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.133 (Fisher's exact test), Q value = 0.58

Table S176.  Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
TBX3 MUTATED 6 2 5 11 2 1
TBX3 WILD-TYPE 257 149 74 250 166 51
'TBX3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0579 (Fisher's exact test), Q value = 0.41

Table S177.  Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
TBX3 MUTATED 5 4 13 5
TBX3 WILD-TYPE 267 173 220 271
'TBX3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.125 (Fisher's exact test), Q value = 0.56

Table S178.  Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
TBX3 MUTATED 5 2 8 6 5 1
TBX3 WILD-TYPE 270 134 198 128 82 119
'TBX3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.603 (Fisher's exact test), Q value = 0.98

Table S179.  Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
TBX3 MUTATED 3 2 3 2 4
TBX3 WILD-TYPE 175 118 63 90 108
'TBX3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S180.  Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
TBX3 MUTATED 6 6 2
TBX3 WILD-TYPE 273 175 106
'RB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.879 (Fisher's exact test), Q value = 1

Table S181.  Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
RB1 MUTATED 0 0 2 4 2 2 0 0
RB1 WILD-TYPE 21 38 112 93 106 71 19 39
'RB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.305 (Fisher's exact test), Q value = 0.83

Table S182.  Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
RB1 MUTATED 2 1 4 3 0
RB1 WILD-TYPE 94 151 112 86 56
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.159 (Fisher's exact test), Q value = 0.63

Table S183.  Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
RB1 MUTATED 4 4 4 7 0
RB1 WILD-TYPE 243 359 82 224 36
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.153 (Fisher's exact test), Q value = 0.63

Table S184.  Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
RB1 MUTATED 1 2 2 0 5 1
RB1 WILD-TYPE 119 82 187 101 111 53
'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.371 (Fisher's exact test), Q value = 0.87

Table S185.  Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
RB1 MUTATED 5 1 3
RB1 WILD-TYPE 143 123 119
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.607 (Fisher's exact test), Q value = 0.98

Table S186.  Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
RB1 MUTATED 1 0 4 2 2 0
RB1 WILD-TYPE 58 48 86 51 111 31
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0272 (Fisher's exact test), Q value = 0.26

Table S187.  Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
RB1 MUTATED 10 9 0
RB1 WILD-TYPE 495 270 190

Figure S82.  Get High-res Image Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.26 (Fisher's exact test), Q value = 0.79

Table S188.  Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
RB1 MUTATED 4 5 0 3 6 1
RB1 WILD-TYPE 259 146 79 258 162 51
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.057 (Fisher's exact test), Q value = 0.41

Table S189.  Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
RB1 MUTATED 8 0 2 6
RB1 WILD-TYPE 264 177 231 270
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0275 (Fisher's exact test), Q value = 0.26

Table S190.  Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
RB1 MUTATED 5 6 0 3 0 2
RB1 WILD-TYPE 270 130 206 131 87 118

Figure S83.  Get High-res Image Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0936 (Fisher's exact test), Q value = 0.5

Table S191.  Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
RB1 MUTATED 2 6 0 3 1
RB1 WILD-TYPE 176 114 66 89 111
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.209 (Fisher's exact test), Q value = 0.72

Table S192.  Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
RB1 MUTATED 8 1 3
RB1 WILD-TYPE 271 180 105
'CTCF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0589 (Fisher's exact test), Q value = 0.41

Table S193.  Gene #17: 'CTCF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
CTCF MUTATED 1 0 2 1 8 0 0 1
CTCF WILD-TYPE 20 38 112 96 100 73 19 38
'CTCF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0443 (Fisher's exact test), Q value = 0.36

Table S194.  Gene #17: 'CTCF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
CTCF MUTATED 3 3 1 1 5
CTCF WILD-TYPE 93 149 115 88 51

Figure S84.  Get High-res Image Gene #17: 'CTCF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'CTCF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.23

Table S195.  Gene #17: 'CTCF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
CTCF MUTATED 2 13 0 1 0
CTCF WILD-TYPE 245 350 86 230 36

Figure S85.  Get High-res Image Gene #17: 'CTCF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CTCF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.16

Table S196.  Gene #17: 'CTCF MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
CTCF MUTATED 0 0 8 1 0 1
CTCF WILD-TYPE 120 84 181 100 116 53

Figure S86.  Get High-res Image Gene #17: 'CTCF MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CTCF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0483 (Fisher's exact test), Q value = 0.38

Table S197.  Gene #17: 'CTCF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
CTCF MUTATED 1 3 7
CTCF WILD-TYPE 147 121 115

Figure S87.  Get High-res Image Gene #17: 'CTCF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'CTCF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.115 (Fisher's exact test), Q value = 0.55

Table S198.  Gene #17: 'CTCF MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
CTCF MUTATED 5 0 1 1 4 0
CTCF WILD-TYPE 54 48 89 52 109 31
'CTCF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 0.56

Table S199.  Gene #17: 'CTCF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
CTCF MUTATED 11 1 4
CTCF WILD-TYPE 494 278 186
'CTCF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.486 (Fisher's exact test), Q value = 0.92

Table S200.  Gene #17: 'CTCF MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
CTCF MUTATED 7 1 1 6 1 0
CTCF WILD-TYPE 256 150 78 255 167 52
'CTCF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0849 (Fisher's exact test), Q value = 0.47

Table S201.  Gene #17: 'CTCF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
CTCF MUTATED 1 2 7 6
CTCF WILD-TYPE 271 175 226 270
'CTCF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.13

Table S202.  Gene #17: 'CTCF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
CTCF MUTATED 2 2 4 2 6 0
CTCF WILD-TYPE 273 134 202 132 81 120

Figure S88.  Get High-res Image Gene #17: 'CTCF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.945 (Fisher's exact test), Q value = 1

Table S203.  Gene #17: 'CTCF MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
CTCF MUTATED 3 1 0 1 1
CTCF WILD-TYPE 175 119 66 91 111
'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.576 (Fisher's exact test), Q value = 0.97

Table S204.  Gene #17: 'CTCF MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
CTCF MUTATED 3 1 2
CTCF WILD-TYPE 276 180 106
'RBMX MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 0.88

Table S205.  Gene #18: 'RBMX MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
RBMX MUTATED 0 0 0 3 2 0 0 1
RBMX WILD-TYPE 21 38 114 94 106 73 19 38
'RBMX MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.105 (Fisher's exact test), Q value = 0.53

Table S206.  Gene #18: 'RBMX MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
RBMX MUTATED 0 3 0 3 0
RBMX WILD-TYPE 96 149 116 86 56
'RBMX MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0646 (Fisher's exact test), Q value = 0.43

Table S207.  Gene #18: 'RBMX MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
RBMX MUTATED 0 5 1 6 1
RBMX WILD-TYPE 247 358 85 225 35
'RBMX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.53 (Fisher's exact test), Q value = 0.95

Table S208.  Gene #18: 'RBMX MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
RBMX MUTATED 1 2 1 2 3 1
RBMX WILD-TYPE 119 82 188 99 113 53
'RBMX MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.476 (Fisher's exact test), Q value = 0.91

Table S209.  Gene #18: 'RBMX MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
RBMX MUTATED 2 0 2
RBMX WILD-TYPE 146 124 120
'RBMX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.848 (Fisher's exact test), Q value = 1

Table S210.  Gene #18: 'RBMX MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
RBMX MUTATED 1 0 2 0 1 0
RBMX WILD-TYPE 58 48 88 53 112 31
'RBMX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0686 (Fisher's exact test), Q value = 0.43

Table S211.  Gene #18: 'RBMX MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
RBMX MUTATED 3 7 3
RBMX WILD-TYPE 502 272 187
'RBMX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0285 (Fisher's exact test), Q value = 0.26

Table S212.  Gene #18: 'RBMX MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
RBMX MUTATED 0 1 0 6 5 1
RBMX WILD-TYPE 263 150 79 255 163 51

Figure S89.  Get High-res Image Gene #18: 'RBMX MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'RBMX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 0.77

Table S213.  Gene #18: 'RBMX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
RBMX MUTATED 6 3 3 1
RBMX WILD-TYPE 266 174 230 275
'RBMX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.573 (Fisher's exact test), Q value = 0.97

Table S214.  Gene #18: 'RBMX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
RBMX MUTATED 3 4 2 2 0 2
RBMX WILD-TYPE 272 132 204 132 87 118
'RBMX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0688 (Fisher's exact test), Q value = 0.43

Table S215.  Gene #18: 'RBMX MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
RBMX MUTATED 0 4 0 1 2
RBMX WILD-TYPE 178 116 66 91 110
'RBMX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S216.  Gene #18: 'RBMX MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
RBMX MUTATED 4 2 1
RBMX WILD-TYPE 275 179 107
'HRNR MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.988 (Fisher's exact test), Q value = 1

Table S217.  Gene #19: 'HRNR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
HRNR MUTATED 0 1 5 5 4 4 0 1
HRNR WILD-TYPE 21 37 109 92 104 69 19 38
'HRNR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S218.  Gene #19: 'HRNR MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
HRNR MUTATED 2 7 4 5 2
HRNR WILD-TYPE 94 145 112 84 54
'HRNR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.353 (Fisher's exact test), Q value = 0.85

Table S219.  Gene #19: 'HRNR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
HRNR MUTATED 5 12 5 7 2
HRNR WILD-TYPE 242 351 81 224 34
'HRNR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.994 (Fisher's exact test), Q value = 1

Table S220.  Gene #19: 'HRNR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
HRNR MUTATED 3 2 6 3 4 2
HRNR WILD-TYPE 117 82 183 98 112 52
'HRNR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.655 (Fisher's exact test), Q value = 0.99

Table S221.  Gene #19: 'HRNR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
HRNR MUTATED 5 7 4
HRNR WILD-TYPE 143 117 118
'HRNR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.568 (Fisher's exact test), Q value = 0.97

Table S222.  Gene #19: 'HRNR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
HRNR MUTATED 2 0 3 3 6 2
HRNR WILD-TYPE 57 48 87 50 107 29
'HRNR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.494 (Fisher's exact test), Q value = 0.93

Table S223.  Gene #19: 'HRNR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
HRNR MUTATED 13 11 7
HRNR WILD-TYPE 492 268 183
'HRNR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.682 (Fisher's exact test), Q value = 0.99

Table S224.  Gene #19: 'HRNR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
HRNR MUTATED 8 3 3 7 7 3
HRNR WILD-TYPE 255 148 76 254 161 49
'HRNR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.596 (Fisher's exact test), Q value = 0.98

Table S225.  Gene #19: 'HRNR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
HRNR MUTATED 11 3 7 9
HRNR WILD-TYPE 261 174 226 267
'HRNR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 0.71

Table S226.  Gene #19: 'HRNR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
HRNR MUTATED 6 7 4 6 5 2
HRNR WILD-TYPE 269 129 202 128 82 118
'HRNR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.148 (Fisher's exact test), Q value = 0.61

Table S227.  Gene #19: 'HRNR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
HRNR MUTATED 6 4 0 0 5
HRNR WILD-TYPE 172 116 66 92 107
'HRNR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.786 (Fisher's exact test), Q value = 1

Table S228.  Gene #19: 'HRNR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
HRNR MUTATED 9 4 2
HRNR WILD-TYPE 270 177 106
'ZMYM3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.499 (Fisher's exact test), Q value = 0.93

Table S229.  Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
ZMYM3 MUTATED 1 0 1 4 4 1 0 0
ZMYM3 WILD-TYPE 20 38 113 93 104 72 19 39
'ZMYM3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.441 (Fisher's exact test), Q value = 0.9

Table S230.  Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
ZMYM3 MUTATED 1 4 1 4 1
ZMYM3 WILD-TYPE 95 148 115 85 55
'ZMYM3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S231.  Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
ZMYM3 MUTATED 2 8 1 4 0
ZMYM3 WILD-TYPE 245 355 85 227 36
'ZMYM3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.671 (Fisher's exact test), Q value = 0.99

Table S232.  Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
ZMYM3 MUTATED 2 1 1 1 3 0
ZMYM3 WILD-TYPE 118 83 188 100 113 54
'ZMYM3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.114 (Fisher's exact test), Q value = 0.54

Table S233.  Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
ZMYM3 MUTATED 5 0 2
ZMYM3 WILD-TYPE 143 124 120
'ZMYM3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.654 (Fisher's exact test), Q value = 0.99

Table S234.  Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
ZMYM3 MUTATED 1 0 3 0 2 1
ZMYM3 WILD-TYPE 58 48 87 53 111 30
'ZMYM3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.123 (Fisher's exact test), Q value = 0.56

Table S235.  Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
ZMYM3 MUTATED 10 5 0
ZMYM3 WILD-TYPE 495 274 190
'ZMYM3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.486 (Fisher's exact test), Q value = 0.92

Table S236.  Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
ZMYM3 MUTATED 2 3 0 6 4 0
ZMYM3 WILD-TYPE 261 148 79 255 164 52
'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.443 (Fisher's exact test), Q value = 0.9

Table S237.  Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
ZMYM3 MUTATED 6 1 5 3
ZMYM3 WILD-TYPE 266 176 228 273
'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.97 (Fisher's exact test), Q value = 1

Table S238.  Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
ZMYM3 MUTATED 6 2 3 1 1 2
ZMYM3 WILD-TYPE 269 134 203 133 86 118
'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.23 (Fisher's exact test), Q value = 0.75

Table S239.  Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
ZMYM3 MUTATED 2 0 2 0 1
ZMYM3 WILD-TYPE 176 120 64 92 111
'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.856 (Fisher's exact test), Q value = 1

Table S240.  Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
ZMYM3 MUTATED 2 2 1
ZMYM3 WILD-TYPE 277 179 107
'NCOR1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.848 (Fisher's exact test), Q value = 1

Table S241.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
NCOR1 MUTATED 0 2 4 3 6 3 0 0
NCOR1 WILD-TYPE 21 36 110 94 102 70 19 39
'NCOR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.903 (Fisher's exact test), Q value = 1

Table S242.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
NCOR1 MUTATED 3 6 3 3 3
NCOR1 WILD-TYPE 93 146 113 86 53
'NCOR1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S243.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
NCOR1 MUTATED 10 17 2 8 1
NCOR1 WILD-TYPE 237 346 84 223 35
'NCOR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.615 (Fisher's exact test), Q value = 0.98

Table S244.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
NCOR1 MUTATED 4 7 8 4 4 3
NCOR1 WILD-TYPE 116 77 181 97 112 51
'NCOR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.298 (Fisher's exact test), Q value = 0.83

Table S245.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
NCOR1 MUTATED 5 5 1
NCOR1 WILD-TYPE 143 119 121
'NCOR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.614 (Fisher's exact test), Q value = 0.98

Table S246.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
NCOR1 MUTATED 1 2 2 2 2 2
NCOR1 WILD-TYPE 58 46 88 51 111 29
'NCOR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.826 (Fisher's exact test), Q value = 1

Table S247.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
NCOR1 MUTATED 23 10 7
NCOR1 WILD-TYPE 482 269 183
'NCOR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.53 (Fisher's exact test), Q value = 0.95

Table S248.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
NCOR1 MUTATED 7 10 3 12 6 2
NCOR1 WILD-TYPE 256 141 76 249 162 50
'NCOR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.811 (Fisher's exact test), Q value = 1

Table S249.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
NCOR1 MUTATED 10 9 11 10
NCOR1 WILD-TYPE 262 168 222 266
'NCOR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.122 (Fisher's exact test), Q value = 0.56

Table S250.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
NCOR1 MUTATED 18 5 7 6 0 4
NCOR1 WILD-TYPE 257 131 199 128 87 116
'NCOR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S251.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
NCOR1 MUTATED 7 4 3 1 4
NCOR1 WILD-TYPE 171 116 63 91 108
'NCOR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S252.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
NCOR1 MUTATED 8 7 4
NCOR1 WILD-TYPE 271 174 104
'GPRIN2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.604 (Fisher's exact test), Q value = 0.98

Table S253.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
GPRIN2 MUTATED 0 1 0 2 3 1 0 0
GPRIN2 WILD-TYPE 21 37 114 95 105 72 19 39
'GPRIN2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.624 (Fisher's exact test), Q value = 0.99

Table S254.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
GPRIN2 MUTATED 0 3 1 2 1
GPRIN2 WILD-TYPE 96 149 115 87 55
'GPRIN2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.98 (Fisher's exact test), Q value = 1

Table S255.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
GPRIN2 MUTATED 3 5 1 2 0
GPRIN2 WILD-TYPE 244 358 85 229 36
'GPRIN2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.67 (Fisher's exact test), Q value = 0.99

Table S256.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
GPRIN2 MUTATED 1 2 2 0 2 0
GPRIN2 WILD-TYPE 119 82 187 101 114 54
'GPRIN2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.777 (Fisher's exact test), Q value = 1

Table S257.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
GPRIN2 MUTATED 3 1 2
GPRIN2 WILD-TYPE 145 123 120
'GPRIN2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.144 (Fisher's exact test), Q value = 0.61

Table S258.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
GPRIN2 MUTATED 2 0 1 0 1 2
GPRIN2 WILD-TYPE 57 48 89 53 112 29
'GPRIN2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 0.91

Table S259.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
GPRIN2 MUTATED 5 5 1
GPRIN2 WILD-TYPE 500 274 189
'GPRIN2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.42 (Fisher's exact test), Q value = 0.88

Table S260.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
GPRIN2 MUTATED 1 2 0 4 4 0
GPRIN2 WILD-TYPE 262 149 79 257 164 52
'GPRIN2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.371 (Fisher's exact test), Q value = 0.87

Table S261.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
GPRIN2 MUTATED 4 1 4 1
GPRIN2 WILD-TYPE 268 176 229 275
'GPRIN2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0628 (Fisher's exact test), Q value = 0.42

Table S262.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
GPRIN2 MUTATED 2 0 1 3 0 4
GPRIN2 WILD-TYPE 273 136 205 131 87 116
'GPRIN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.401 (Fisher's exact test), Q value = 0.88

Table S263.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
GPRIN2 MUTATED 1 3 1 0 1
GPRIN2 WILD-TYPE 177 117 65 92 111
'GPRIN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.666 (Fisher's exact test), Q value = 0.99

Table S264.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
GPRIN2 MUTATED 4 2 0
GPRIN2 WILD-TYPE 275 179 108
'SPEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.666 (Fisher's exact test), Q value = 0.99

Table S265.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
SPEN MUTATED 0 1 4 2 8 3 1 1
SPEN WILD-TYPE 21 37 110 95 100 70 18 38
'SPEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.788 (Fisher's exact test), Q value = 1

Table S266.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
SPEN MUTATED 4 8 5 2 1
SPEN WILD-TYPE 92 144 111 87 55
'SPEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 0.91

Table S267.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
SPEN MUTATED 6 15 2 5 2
SPEN WILD-TYPE 241 348 84 226 34
'SPEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.464 (Fisher's exact test), Q value = 0.91

Table S268.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
SPEN MUTATED 5 3 9 5 1 1
SPEN WILD-TYPE 115 81 180 96 115 53
'SPEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.791 (Fisher's exact test), Q value = 1

Table S269.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
SPEN MUTATED 6 5 3
SPEN WILD-TYPE 142 119 119
'SPEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0271 (Fisher's exact test), Q value = 0.26

Table S270.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
SPEN MUTATED 1 5 2 0 3 3
SPEN WILD-TYPE 58 43 88 53 110 28

Figure S90.  Get High-res Image Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'SPEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.207 (Fisher's exact test), Q value = 0.72

Table S271.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
SPEN MUTATED 21 5 6
SPEN WILD-TYPE 484 274 184
'SPEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.119 (Fisher's exact test), Q value = 0.56

Table S272.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
SPEN MUTATED 6 7 1 14 2 2
SPEN WILD-TYPE 257 144 78 247 166 50
'SPEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.213 (Fisher's exact test), Q value = 0.73

Table S273.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
SPEN MUTATED 5 5 8 14
SPEN WILD-TYPE 267 172 225 262
'SPEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00913 (Fisher's exact test), Q value = 0.12

Table S274.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
SPEN MUTATED 15 0 4 8 3 2
SPEN WILD-TYPE 260 136 202 126 84 118

Figure S91.  Get High-res Image Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'SPEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0943 (Fisher's exact test), Q value = 0.5

Table S275.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
SPEN MUTATED 5 1 4 0 3
SPEN WILD-TYPE 173 119 62 92 109
'SPEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.658 (Fisher's exact test), Q value = 0.99

Table S276.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
SPEN MUTATED 7 5 1
SPEN WILD-TYPE 272 176 107
'NF1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 0.97

Table S277.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
NF1 MUTATED 1 0 2 3 4 2 0 3
NF1 WILD-TYPE 20 38 112 94 104 71 19 36
'NF1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S278.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
NF1 MUTATED 2 4 3 3 3
NF1 WILD-TYPE 94 148 113 86 53
'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.567 (Fisher's exact test), Q value = 0.97

Table S279.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
NF1 MUTATED 4 13 3 7 0
NF1 WILD-TYPE 243 350 83 224 36
'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.224 (Fisher's exact test), Q value = 0.74

Table S280.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
NF1 MUTATED 3 4 3 6 3 0
NF1 WILD-TYPE 117 80 186 95 113 54
'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.549 (Fisher's exact test), Q value = 0.96

Table S281.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
NF1 MUTATED 4 4 6
NF1 WILD-TYPE 144 120 116
'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.233 (Fisher's exact test), Q value = 0.75

Table S282.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
NF1 MUTATED 0 3 2 3 6 0
NF1 WILD-TYPE 59 45 88 50 107 31
'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 0.88

Table S283.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
NF1 MUTATED 12 11 4
NF1 WILD-TYPE 493 268 186
'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.417 (Fisher's exact test), Q value = 0.88

Table S284.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
NF1 MUTATED 4 7 3 6 6 1
NF1 WILD-TYPE 259 144 76 255 162 51
'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.329 (Fisher's exact test), Q value = 0.84

Table S285.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
NF1 MUTATED 6 8 4 9
NF1 WILD-TYPE 266 169 229 267
'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.677 (Fisher's exact test), Q value = 0.99

Table S286.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
NF1 MUTATED 9 5 4 2 4 3
NF1 WILD-TYPE 266 131 202 132 83 117
'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S287.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
NF1 MUTATED 4 4 1 3 3
NF1 WILD-TYPE 174 116 65 89 109
'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.542 (Fisher's exact test), Q value = 0.95

Table S288.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
NF1 MUTATED 9 5 1
NF1 WILD-TYPE 270 176 107
'TCP11 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.785 (Fisher's exact test), Q value = 1

Table S289.  Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
TCP11 MUTATED 0 1 2 1 1 0 0 1
TCP11 WILD-TYPE 21 37 112 96 107 73 19 38
'TCP11 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.512 (Fisher's exact test), Q value = 0.94

Table S290.  Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
TCP11 MUTATED 2 3 0 1 0
TCP11 WILD-TYPE 94 149 116 88 56
'TCP11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.456 (Fisher's exact test), Q value = 0.91

Table S291.  Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
TCP11 MUTATED 1 3 0 1 1
TCP11 WILD-TYPE 246 360 86 230 35
'TCP11 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S292.  Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
TCP11 MUTATED 2 2 1
TCP11 WILD-TYPE 146 122 121
'TCP11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.61 (Fisher's exact test), Q value = 0.98

Table S293.  Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
TCP11 MUTATED 0 0 1 2 2 0
TCP11 WILD-TYPE 59 48 89 51 111 31
'TCP11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S294.  Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
TCP11 MUTATED 3 1 2
TCP11 WILD-TYPE 502 278 188
'TCP11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.374 (Fisher's exact test), Q value = 0.87

Table S295.  Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
TCP11 MUTATED 1 1 2 1 1 0
TCP11 WILD-TYPE 262 150 77 260 167 52
'TCP11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.946 (Fisher's exact test), Q value = 1

Table S296.  Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
TCP11 MUTATED 1 1 2 2
TCP11 WILD-TYPE 271 176 231 274
'TCP11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.761 (Fisher's exact test), Q value = 1

Table S297.  Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
TCP11 MUTATED 2 0 2 0 1 1
TCP11 WILD-TYPE 273 136 204 134 86 119
'SF3B1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S298.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
SF3B1 MUTATED 0 0 1 1 3 2 0 1
SF3B1 WILD-TYPE 21 38 113 96 105 71 19 38
'SF3B1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S299.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
SF3B1 MUTATED 1 4 2 1 0
SF3B1 WILD-TYPE 95 148 114 88 56
'SF3B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.539 (Fisher's exact test), Q value = 0.95

Table S300.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
SF3B1 MUTATED 7 6 1 2 0
SF3B1 WILD-TYPE 240 357 85 229 36
'SF3B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0765 (Fisher's exact test), Q value = 0.45

Table S301.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
SF3B1 MUTATED 3 2 8 0 0 1
SF3B1 WILD-TYPE 117 82 181 101 116 53
'SF3B1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0776 (Fisher's exact test), Q value = 0.45

Table S302.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
SF3B1 MUTATED 1 4 0
SF3B1 WILD-TYPE 147 120 122
'SF3B1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0788 (Fisher's exact test), Q value = 0.46

Table S303.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
SF3B1 MUTATED 0 2 1 2 0 0
SF3B1 WILD-TYPE 59 46 89 51 113 31
'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.288 (Fisher's exact test), Q value = 0.83

Table S304.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
SF3B1 MUTATED 11 2 3
SF3B1 WILD-TYPE 494 277 187
'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.356 (Fisher's exact test), Q value = 0.85

Table S305.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
SF3B1 MUTATED 5 4 3 3 1 0
SF3B1 WILD-TYPE 258 147 76 258 167 52
'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 0.79

Table S306.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
SF3B1 MUTATED 2 3 7 4
SF3B1 WILD-TYPE 270 174 226 272
'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.387 (Fisher's exact test), Q value = 0.88

Table S307.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
SF3B1 MUTATED 2 2 5 3 3 1
SF3B1 WILD-TYPE 273 134 201 131 84 119
'SF3B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.353 (Fisher's exact test), Q value = 0.85

Table S308.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
SF3B1 MUTATED 1 0 1 2 2
SF3B1 WILD-TYPE 177 120 65 90 110
'SF3B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.247 (Fisher's exact test), Q value = 0.77

Table S309.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
SF3B1 MUTATED 1 3 2
SF3B1 WILD-TYPE 278 178 106
'ERBB2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.575 (Fisher's exact test), Q value = 0.97

Table S310.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
ERBB2 MUTATED 1 1 1 1 3 3 0 1
ERBB2 WILD-TYPE 20 37 113 96 105 70 19 38
'ERBB2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.465 (Fisher's exact test), Q value = 0.91

Table S311.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
ERBB2 MUTATED 1 6 3 1 0
ERBB2 WILD-TYPE 95 146 113 88 56
'ERBB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0271 (Fisher's exact test), Q value = 0.26

Table S312.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
ERBB2 MUTATED 3 10 5 1 0
ERBB2 WILD-TYPE 244 353 81 230 36

Figure S92.  Get High-res Image Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ERBB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00238 (Fisher's exact test), Q value = 0.038

Table S313.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
ERBB2 MUTATED 0 4 1 3 1 4
ERBB2 WILD-TYPE 120 80 188 98 115 50

Figure S93.  Get High-res Image Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'ERBB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.309 (Fisher's exact test), Q value = 0.83

Table S314.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
ERBB2 MUTATED 1 4 2
ERBB2 WILD-TYPE 147 120 120
'ERBB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.955 (Fisher's exact test), Q value = 1

Table S315.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
ERBB2 MUTATED 1 1 1 1 2 1
ERBB2 WILD-TYPE 58 47 89 52 111 30
'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S316.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
ERBB2 MUTATED 9 4 7
ERBB2 WILD-TYPE 496 275 183
'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.134 (Fisher's exact test), Q value = 0.58

Table S317.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
ERBB2 MUTATED 3 3 2 8 1 3
ERBB2 WILD-TYPE 260 148 77 253 167 49
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S318.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
ERBB2 MUTATED 2 5 7 6
ERBB2 WILD-TYPE 270 172 226 270
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.106 (Fisher's exact test), Q value = 0.53

Table S319.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
ERBB2 MUTATED 4 2 7 6 1 0
ERBB2 WILD-TYPE 271 134 199 128 86 120
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.319 (Fisher's exact test), Q value = 0.84

Table S320.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
ERBB2 MUTATED 1 1 1 3 3
ERBB2 WILD-TYPE 177 119 65 89 109
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.603 (Fisher's exact test), Q value = 0.98

Table S321.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
ERBB2 MUTATED 3 4 2
ERBB2 WILD-TYPE 276 177 106
'RAB42 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.408 (Fisher's exact test), Q value = 0.88

Table S322.  Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
RAB42 MUTATED 0 0 0 3 1 0 0 0
RAB42 WILD-TYPE 21 38 114 94 107 73 19 39
'RAB42 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0679 (Fisher's exact test), Q value = 0.43

Table S323.  Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
RAB42 MUTATED 0 1 0 3 0
RAB42 WILD-TYPE 96 151 116 86 56
'RAB42 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0413 (Fisher's exact test), Q value = 0.34

Table S324.  Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
RAB42 MUTATED 0 0 1 3 0
RAB42 WILD-TYPE 247 363 85 228 36

Figure S94.  Get High-res Image Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'RAB42 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.515 (Fisher's exact test), Q value = 0.94

Table S325.  Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
RAB42 MUTATED 1 2 0
RAB42 WILD-TYPE 147 122 122
'RAB42 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.388 (Fisher's exact test), Q value = 0.88

Table S326.  Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
RAB42 MUTATED 0 0 2 1 0 0
RAB42 WILD-TYPE 59 48 88 52 113 31
'RAB42 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.117 (Fisher's exact test), Q value = 0.55

Table S327.  Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
RAB42 MUTATED 1 3 0
RAB42 WILD-TYPE 504 276 190
'RAB42 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.156 (Fisher's exact test), Q value = 0.63

Table S328.  Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
RAB42 MUTATED 0 0 0 1 3 0
RAB42 WILD-TYPE 263 151 79 260 165 52
'RAB42 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.232 (Fisher's exact test), Q value = 0.75

Table S329.  Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
RAB42 MUTATED 3 0 0 1
RAB42 WILD-TYPE 269 177 233 275
'RAB42 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00999 (Fisher's exact test), Q value = 0.13

Table S330.  Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
RAB42 MUTATED 0 0 0 1 0 3
RAB42 WILD-TYPE 275 136 206 133 87 117

Figure S95.  Get High-res Image Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CDC42EP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.522 (Fisher's exact test), Q value = 0.95

Table S331.  Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
CDC42EP1 MUTATED 0 0 1 2 0 0 0 1
CDC42EP1 WILD-TYPE 21 38 113 95 108 73 19 38
'CDC42EP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.462 (Fisher's exact test), Q value = 0.91

Table S332.  Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
CDC42EP1 MUTATED 1 1 0 2 0
CDC42EP1 WILD-TYPE 95 151 116 87 56
'CDC42EP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 0.88

Table S333.  Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
CDC42EP1 MUTATED 0 2 1 2 0
CDC42EP1 WILD-TYPE 247 361 85 229 36
'CDC42EP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S334.  Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
CDC42EP1 MUTATED 0 0 1 2 0 0
CDC42EP1 WILD-TYPE 120 84 188 99 116 54
'CDC42EP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.558 (Fisher's exact test), Q value = 0.96

Table S335.  Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
CDC42EP1 MUTATED 2 2 0
CDC42EP1 WILD-TYPE 146 122 122
'CDC42EP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.473 (Fisher's exact test), Q value = 0.91

Table S336.  Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
CDC42EP1 MUTATED 1 0 2 1 0 0
CDC42EP1 WILD-TYPE 58 48 88 52 113 31
'CDC42EP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S337.  Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
CDC42EP1 MUTATED 2 2 1
CDC42EP1 WILD-TYPE 503 277 189
'CDC42EP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.561 (Fisher's exact test), Q value = 0.97

Table S338.  Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
CDC42EP1 MUTATED 1 0 1 1 2 0
CDC42EP1 WILD-TYPE 262 151 78 260 166 52
'CDC42EP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S339.  Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
CDC42EP1 MUTATED 2 0 2 1
CDC42EP1 WILD-TYPE 270 177 231 275
'CDC42EP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.306 (Fisher's exact test), Q value = 0.83

Table S340.  Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
CDC42EP1 MUTATED 0 2 1 1 0 1
CDC42EP1 WILD-TYPE 275 134 205 133 87 119
'KDM6A MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S341.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
KDM6A MUTATED 0 1 1 2 3 0 0 1
KDM6A WILD-TYPE 21 37 113 95 105 73 19 38
'KDM6A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.345 (Fisher's exact test), Q value = 0.85

Table S342.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
KDM6A MUTATED 2 4 0 2 0
KDM6A WILD-TYPE 94 148 116 87 56
'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.535 (Fisher's exact test), Q value = 0.95

Table S343.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
KDM6A MUTATED 5 5 2 2 1
KDM6A WILD-TYPE 242 358 84 229 35
'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.176 (Fisher's exact test), Q value = 0.67

Table S344.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
KDM6A MUTATED 3 1 1 0 3 2
KDM6A WILD-TYPE 117 83 188 101 113 52
'KDM6A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.508 (Fisher's exact test), Q value = 0.93

Table S345.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
KDM6A MUTATED 4 1 2
KDM6A WILD-TYPE 144 123 120
'KDM6A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.965 (Fisher's exact test), Q value = 1

Table S346.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
KDM6A MUTATED 1 1 2 0 3 0
KDM6A WILD-TYPE 58 47 88 53 110 31
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.304 (Fisher's exact test), Q value = 0.83

Table S347.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
KDM6A MUTATED 5 6 4
KDM6A WILD-TYPE 500 273 186
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.408 (Fisher's exact test), Q value = 0.88

Table S348.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
KDM6A MUTATED 2 3 0 5 5 0
KDM6A WILD-TYPE 261 148 79 256 163 52
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.675 (Fisher's exact test), Q value = 0.99

Table S349.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
KDM6A MUTATED 5 4 2 4
KDM6A WILD-TYPE 267 173 231 272
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.647 (Fisher's exact test), Q value = 0.99

Table S350.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
KDM6A MUTATED 4 2 3 2 0 4
KDM6A WILD-TYPE 271 134 203 132 87 116
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S351.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
KDM6A MUTATED 4 3 0 1 1
KDM6A WILD-TYPE 174 117 66 91 111
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.449 (Fisher's exact test), Q value = 0.9

Table S352.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
KDM6A MUTATED 6 1 2
KDM6A WILD-TYPE 273 180 106
'AQP12A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.627 (Fisher's exact test), Q value = 0.99

Table S353.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
AQP12A MUTATED 0 1 1 0 1 0 0 0
AQP12A WILD-TYPE 21 37 113 97 107 73 19 39
'AQP12A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.726 (Fisher's exact test), Q value = 1

Table S354.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
AQP12A MUTATED 1 2 0 0 0
AQP12A WILD-TYPE 95 150 116 89 56
'AQP12A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.346 (Fisher's exact test), Q value = 0.85

Table S355.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
AQP12A MUTATED 4 1 0 1 0
AQP12A WILD-TYPE 243 362 86 230 36
'AQP12A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.543 (Fisher's exact test), Q value = 0.95

Table S356.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
AQP12A MUTATED 1 2 1 0 1 0
AQP12A WILD-TYPE 119 82 188 101 115 54
'AQP12A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.296 (Fisher's exact test), Q value = 0.83

Table S357.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
AQP12A MUTATED 0 2 1
AQP12A WILD-TYPE 148 122 121
'AQP12A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.435 (Fisher's exact test), Q value = 0.89

Table S358.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
AQP12A MUTATED 0 0 0 0 3 0
AQP12A WILD-TYPE 59 48 90 53 110 31
'AQP12A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S359.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
AQP12A MUTATED 3 2 1
AQP12A WILD-TYPE 502 277 189
'AQP12A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S360.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
AQP12A MUTATED 2 1 0 2 1 0
AQP12A WILD-TYPE 261 150 79 259 167 52
'AQP12A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.945 (Fisher's exact test), Q value = 1

Table S361.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
AQP12A MUTATED 1 1 2 2
AQP12A WILD-TYPE 271 176 231 274
'AQP12A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.497 (Fisher's exact test), Q value = 0.93

Table S362.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
AQP12A MUTATED 1 0 1 2 1 1
AQP12A WILD-TYPE 274 136 205 132 86 119
'AQP12A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 0.88

Table S363.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
AQP12A MUTATED 2 0 1 0 0
AQP12A WILD-TYPE 176 120 65 92 112
'AQP12A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S364.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
AQP12A MUTATED 2 1 0
AQP12A WILD-TYPE 277 180 108
'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.539 (Fisher's exact test), Q value = 0.95

Table S365.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
KRAS MUTATED 0 0 0 1 2 0 0 1
KRAS WILD-TYPE 21 38 114 96 106 73 19 38
'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.632 (Fisher's exact test), Q value = 0.99

Table S366.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
KRAS MUTATED 0 2 1 0 1
KRAS WILD-TYPE 96 150 115 89 55
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.325 (Fisher's exact test), Q value = 0.84

Table S367.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
KRAS MUTATED 0 5 0 1 0
KRAS WILD-TYPE 247 358 86 230 36
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.506 (Fisher's exact test), Q value = 0.93

Table S368.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
KRAS MUTATED 0 0 3 1 0 0
KRAS WILD-TYPE 120 84 186 100 116 54
'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.296 (Fisher's exact test), Q value = 0.83

Table S369.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
KRAS MUTATED 0 2 1
KRAS WILD-TYPE 148 122 121
'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.512 (Fisher's exact test), Q value = 0.94

Table S370.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
KRAS MUTATED 1 0 1 1 0 0
KRAS WILD-TYPE 58 48 89 52 113 31
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.746 (Fisher's exact test), Q value = 1

Table S371.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
KRAS MUTATED 3 1 2
KRAS WILD-TYPE 502 278 188
'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0842 (Fisher's exact test), Q value = 0.47

Table S372.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
KRAS MUTATED 2 0 2 1 0 1
KRAS WILD-TYPE 261 151 77 260 168 51
'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.852 (Fisher's exact test), Q value = 1

Table S373.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
KRAS MUTATED 1 1 1 3
KRAS WILD-TYPE 271 176 232 273
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S374.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
KRAS MUTATED 3 1 1 1 0 0
KRAS WILD-TYPE 272 135 205 133 87 120
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.922 (Fisher's exact test), Q value = 1

Table S375.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
KRAS MUTATED 1 1 0 1 0
KRAS WILD-TYPE 177 119 66 91 112
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.126 (Fisher's exact test), Q value = 0.56

Table S376.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
KRAS MUTATED 1 0 2
KRAS WILD-TYPE 278 181 106
'NBPF9 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.614 (Fisher's exact test), Q value = 0.98

Table S377.  Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
NBPF9 MUTATED 1 0 1 1 2 0 0 0
NBPF9 WILD-TYPE 20 38 113 96 106 73 19 39
'NBPF9 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.626 (Fisher's exact test), Q value = 0.99

Table S378.  Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
NBPF9 MUTATED 0 1 2 1 1
NBPF9 WILD-TYPE 96 151 114 88 55
'NBPF9 MUTATION STATUS' versus 'CN_CNMF'

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

Table S379.  Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
NBPF9 MUTATED 1 2 1 1 0
NBPF9 WILD-TYPE 246 361 85 230 36
'NBPF9 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S380.  Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
NBPF9 MUTATED 2 2 1
NBPF9 WILD-TYPE 146 122 121
'NBPF9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.641 (Fisher's exact test), Q value = 0.99

Table S381.  Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
NBPF9 MUTATED 1 0 1 2 1 0
NBPF9 WILD-TYPE 58 48 89 51 112 31
'NBPF9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.603 (Fisher's exact test), Q value = 0.98

Table S382.  Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
NBPF9 MUTATED 4 1 0
NBPF9 WILD-TYPE 501 278 190
'NBPF9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.155 (Fisher's exact test), Q value = 0.63

Table S383.  Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
NBPF9 MUTATED 1 3 0 0 1 0
NBPF9 WILD-TYPE 262 148 79 261 167 52
'NBPF9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.143 (Fisher's exact test), Q value = 0.61

Table S384.  Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
NBPF9 MUTATED 2 0 3 0
NBPF9 WILD-TYPE 270 177 230 276
'NBPF9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.301 (Fisher's exact test), Q value = 0.83

Table S385.  Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
NBPF9 MUTATED 2 2 0 0 1 0
NBPF9 WILD-TYPE 273 134 206 134 86 120
'MYB MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.736 (Fisher's exact test), Q value = 1

Table S386.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
MYB MUTATED 0 0 2 2 4 0 0 1
MYB WILD-TYPE 21 38 112 95 104 73 19 38
'MYB MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0285 (Fisher's exact test), Q value = 0.26

Table S387.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
MYB MUTATED 0 2 1 2 4
MYB WILD-TYPE 96 150 115 87 52

Figure S96.  Get High-res Image Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'MYB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.226 (Fisher's exact test), Q value = 0.75

Table S388.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
MYB MUTATED 1 6 3 2 0
MYB WILD-TYPE 246 357 83 229 36
'MYB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.323 (Fisher's exact test), Q value = 0.84

Table S389.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
MYB MUTATED 0 1 1 0 2 1
MYB WILD-TYPE 120 83 188 101 114 53
'MYB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.869 (Fisher's exact test), Q value = 1

Table S390.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
MYB MUTATED 2 1 2
MYB WILD-TYPE 146 123 120
'MYB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.696 (Fisher's exact test), Q value = 1

Table S391.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
MYB MUTATED 2 0 1 1 1 0
MYB WILD-TYPE 57 48 89 52 112 31
'MYB MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S392.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
MYB MUTATED 7 3 2
MYB WILD-TYPE 498 276 188
'MYB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.901 (Fisher's exact test), Q value = 1

Table S393.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
MYB MUTATED 4 1 0 4 3 0
MYB WILD-TYPE 259 150 79 257 165 52
'MYB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0972 (Fisher's exact test), Q value = 0.51

Table S394.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
MYB MUTATED 2 1 7 2
MYB WILD-TYPE 270 176 226 274
'MYB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.125 (Fisher's exact test), Q value = 0.56

Table S395.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
MYB MUTATED 3 2 0 4 2 1
MYB WILD-TYPE 272 134 206 130 85 119
'MYB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.283 (Fisher's exact test), Q value = 0.83

Table S396.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
MYB MUTATED 2 0 0 2 0
MYB WILD-TYPE 176 120 66 90 112
'MYB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.022

Table S397.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
MYB MUTATED 0 0 4
MYB WILD-TYPE 279 181 104

Figure S97.  Get High-res Image Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ZNF362 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.879 (Fisher's exact test), Q value = 1

Table S398.  Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
ZNF362 MUTATED 0 0 2 0 2 1 0 0
ZNF362 WILD-TYPE 21 38 112 97 106 72 19 39
'ZNF362 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.87 (Fisher's exact test), Q value = 1

Table S399.  Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
ZNF362 MUTATED 1 2 1 0 1
ZNF362 WILD-TYPE 95 150 115 89 55
'ZNF362 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.091 (Fisher's exact test), Q value = 0.49

Table S400.  Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
ZNF362 MUTATED 0 1 1 1 1
ZNF362 WILD-TYPE 247 362 85 230 35
'ZNF362 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0761 (Fisher's exact test), Q value = 0.45

Table S401.  Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
ZNF362 MUTATED 0 1 3
ZNF362 WILD-TYPE 148 123 119
'ZNF362 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.662 (Fisher's exact test), Q value = 0.99

Table S402.  Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
ZNF362 MUTATED 1 1 0 0 2 0
ZNF362 WILD-TYPE 58 47 90 53 111 31
'ZNF362 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.41 (Fisher's exact test), Q value = 0.88

Table S403.  Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
ZNF362 MUTATED 4 0 1
ZNF362 WILD-TYPE 501 279 189
'ZNF362 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.91 (Fisher's exact test), Q value = 1

Table S404.  Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
ZNF362 MUTATED 2 1 0 2 0 0
ZNF362 WILD-TYPE 261 150 79 259 168 52
'ZNF362 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0857 (Fisher's exact test), Q value = 0.47

Table S405.  Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
ZNF362 MUTATED 0 0 1 4
ZNF362 WILD-TYPE 272 177 232 272
'ZNF362 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.415 (Fisher's exact test), Q value = 0.88

Table S406.  Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
ZNF362 MUTATED 1 0 1 2 1 0
ZNF362 WILD-TYPE 274 136 205 132 86 120
'TBL1XR1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.158 (Fisher's exact test), Q value = 0.63

Table S407.  Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
TBL1XR1 MUTATED 1 0 1 0 5 1 0 0
TBL1XR1 WILD-TYPE 20 38 113 97 103 72 19 39
'TBL1XR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S408.  Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
TBL1XR1 MUTATED 0 3 2 0 3
TBL1XR1 WILD-TYPE 96 149 114 89 53
'TBL1XR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0506 (Fisher's exact test), Q value = 0.39

Table S409.  Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
TBL1XR1 MUTATED 1 5 3 0 0
TBL1XR1 WILD-TYPE 246 358 83 231 36
'TBL1XR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.354 (Fisher's exact test), Q value = 0.85

Table S410.  Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
TBL1XR1 MUTATED 2 1 4
TBL1XR1 WILD-TYPE 146 123 118
'TBL1XR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.155 (Fisher's exact test), Q value = 0.63

Table S411.  Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
TBL1XR1 MUTATED 3 1 0 1 1 1
TBL1XR1 WILD-TYPE 56 47 90 52 112 30
'TBL1XR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.544 (Fisher's exact test), Q value = 0.95

Table S412.  Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
TBL1XR1 MUTATED 6 1 2
TBL1XR1 WILD-TYPE 499 278 188
'TBL1XR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.566 (Fisher's exact test), Q value = 0.97

Table S413.  Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
TBL1XR1 MUTATED 4 1 0 4 0 0
TBL1XR1 WILD-TYPE 259 150 79 257 168 52
'TBL1XR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.478 (Fisher's exact test), Q value = 0.91

Table S414.  Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
TBL1XR1 MUTATED 1 1 4 3
TBL1XR1 WILD-TYPE 271 176 229 273
'TBL1XR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.553 (Fisher's exact test), Q value = 0.96

Table S415.  Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
TBL1XR1 MUTATED 3 1 1 3 1 0
TBL1XR1 WILD-TYPE 272 135 205 131 86 120
'TBL1XR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S416.  Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
TBL1XR1 MUTATED 2 1 0 1 1
TBL1XR1 WILD-TYPE 176 119 66 91 111
'TBL1XR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0747 (Fisher's exact test), Q value = 0.45

Table S417.  Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
TBL1XR1 MUTATED 1 1 3
TBL1XR1 WILD-TYPE 278 180 105
'SP3 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S418.  Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
SP3 MUTATED 0 0 1 0 2 1 0 0
SP3 WILD-TYPE 21 38 113 97 106 72 19 39
'SP3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.553 (Fisher's exact test), Q value = 0.96

Table S419.  Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
SP3 MUTATED 0 3 1 0 0
SP3 WILD-TYPE 96 149 115 89 56
'SP3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.558 (Fisher's exact test), Q value = 0.96

Table S420.  Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
SP3 MUTATED 2 3 1 0 0
SP3 WILD-TYPE 245 360 85 231 36
'SP3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S421.  Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
SP3 MUTATED 1 0 2 1 0 0
SP3 WILD-TYPE 119 84 187 100 116 54
'SP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.879 (Fisher's exact test), Q value = 1

Table S422.  Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
SP3 MUTATED 3 2 2
SP3 WILD-TYPE 502 277 188
'SP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.441 (Fisher's exact test), Q value = 0.9

Table S423.  Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
SP3 MUTATED 1 2 0 4 0 0
SP3 WILD-TYPE 262 149 79 257 168 52
'SP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.398 (Fisher's exact test), Q value = 0.88

Table S424.  Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
SP3 MUTATED 1 0 3 3
SP3 WILD-TYPE 271 177 230 273
'SP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.409 (Fisher's exact test), Q value = 0.88

Table S425.  Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
SP3 MUTATED 3 2 0 1 1 0
SP3 WILD-TYPE 272 134 206 133 86 120
'SP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.319 (Fisher's exact test), Q value = 0.84

Table S426.  Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
SP3 MUTATED 1 0 1 0 2
SP3 WILD-TYPE 177 120 65 92 110
'SP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S427.  Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
SP3 MUTATED 2 1 1
SP3 WILD-TYPE 277 180 107
'FGFR2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.917 (Fisher's exact test), Q value = 1

Table S428.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
FGFR2 MUTATED 0 0 1 1 2 2 0 0
FGFR2 WILD-TYPE 21 38 113 96 106 71 19 39
'FGFR2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S429.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
FGFR2 MUTATED 1 1 2 1 1
FGFR2 WILD-TYPE 95 151 114 88 55
'FGFR2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.329 (Fisher's exact test), Q value = 0.84

Table S430.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
FGFR2 MUTATED 2 3 3 3 0
FGFR2 WILD-TYPE 245 360 83 228 36
'FGFR2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.094 (Fisher's exact test), Q value = 0.5

Table S431.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
FGFR2 MUTATED 3 1 0 1 0 1
FGFR2 WILD-TYPE 117 83 189 100 116 53
'FGFR2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.868 (Fisher's exact test), Q value = 1

Table S432.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
FGFR2 MUTATED 2 1 2
FGFR2 WILD-TYPE 146 123 120
'FGFR2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S433.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
FGFR2 MUTATED 0 0 1 1 3 0
FGFR2 WILD-TYPE 59 48 89 52 110 31
'FGFR2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.79 (Fisher's exact test), Q value = 1

Table S434.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
FGFR2 MUTATED 7 3 1
FGFR2 WILD-TYPE 498 276 189
'FGFR2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.431 (Fisher's exact test), Q value = 0.89

Table S435.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
FGFR2 MUTATED 2 4 0 3 1 1
FGFR2 WILD-TYPE 261 147 79 258 167 51
'FGFR2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.226 (Fisher's exact test), Q value = 0.75

Table S436.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
FGFR2 MUTATED 5 0 4 2
FGFR2 WILD-TYPE 267 177 229 274
'FGFR2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.498 (Fisher's exact test), Q value = 0.93

Table S437.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
FGFR2 MUTATED 6 1 3 0 0 1
FGFR2 WILD-TYPE 269 135 203 134 87 119
'FGFR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.608 (Fisher's exact test), Q value = 0.98

Table S438.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
FGFR2 MUTATED 2 0 1 0 1
FGFR2 WILD-TYPE 176 120 65 92 111
'FGFR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.673 (Fisher's exact test), Q value = 0.99

Table S439.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
FGFR2 MUTATED 2 2 0
FGFR2 WILD-TYPE 277 179 108
'ZBTB7C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.496 (Fisher's exact test), Q value = 0.93

Table S440.  Gene #39: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
ZBTB7C MUTATED 1 2 1 0 0
ZBTB7C WILD-TYPE 246 361 85 231 36
'ZBTB7C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.307 (Fisher's exact test), Q value = 0.83

Table S441.  Gene #39: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
ZBTB7C MUTATED 0 1 1 0 0 1
ZBTB7C WILD-TYPE 120 83 188 101 116 53
'ZBTB7C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.497 (Fisher's exact test), Q value = 0.93

Table S442.  Gene #39: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
ZBTB7C MUTATED 2 1 2
ZBTB7C WILD-TYPE 503 278 188
'ZBTB7C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.678 (Fisher's exact test), Q value = 0.99

Table S443.  Gene #39: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
ZBTB7C MUTATED 1 1 1 2 0 0
ZBTB7C WILD-TYPE 262 150 78 259 168 52
'ZBTB7C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.685 (Fisher's exact test), Q value = 0.99

Table S444.  Gene #39: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
ZBTB7C MUTATED 1 2 1 1
ZBTB7C WILD-TYPE 271 175 232 275
'ZBTB7C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S445.  Gene #39: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
ZBTB7C MUTATED 2 1 2 0 0 0
ZBTB7C WILD-TYPE 273 135 204 134 87 120
'NCDN MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S446.  Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
NCDN MUTATED 0 0 1 1 1 0 0 0
NCDN WILD-TYPE 21 38 113 96 107 73 19 39
'NCDN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.791 (Fisher's exact test), Q value = 1

Table S447.  Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
NCDN MUTATED 1 1 0 1 0
NCDN WILD-TYPE 95 151 116 88 56
'NCDN MUTATION STATUS' versus 'CN_CNMF'

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

Table S448.  Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
NCDN MUTATED 1 2 0 1 0
NCDN WILD-TYPE 246 361 86 230 36
'NCDN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.403 (Fisher's exact test), Q value = 0.88

Table S449.  Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
NCDN MUTATED 1 0 2
NCDN WILD-TYPE 147 124 120
'NCDN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.483 (Fisher's exact test), Q value = 0.91

Table S450.  Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
NCDN MUTATED 1 1 1 0 0 0
NCDN WILD-TYPE 58 47 89 53 113 31
'NCDN MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S451.  Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
NCDN MUTATED 3 1 0
NCDN WILD-TYPE 502 278 190
'NCDN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.913 (Fisher's exact test), Q value = 1

Table S452.  Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
NCDN MUTATED 1 0 0 2 1 0
NCDN WILD-TYPE 262 151 79 259 167 52
'NCDN MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S453.  Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
NCDN MUTATED 2 0 1 1
NCDN WILD-TYPE 270 177 232 275
'NCDN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0519 (Fisher's exact test), Q value = 0.39

Table S454.  Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
NCDN MUTATED 0 0 0 2 1 1
NCDN WILD-TYPE 275 136 206 132 86 119
'MUC6 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.22

Table S455.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
MUC6 MUTATED 2 2 0 3 1 0 0 1
MUC6 WILD-TYPE 19 36 114 94 107 73 19 38

Figure S98.  Get High-res Image Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'MUC6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.608 (Fisher's exact test), Q value = 0.98

Table S456.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
MUC6 MUTATED 0 3 3 2 1
MUC6 WILD-TYPE 96 149 113 87 55
'MUC6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.506 (Fisher's exact test), Q value = 0.93

Table S457.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
MUC6 MUTATED 4 4 0 6 0
MUC6 WILD-TYPE 243 359 86 225 36
'MUC6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.674 (Fisher's exact test), Q value = 0.99

Table S458.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
MUC6 MUTATED 2 1 1 2 3 1
MUC6 WILD-TYPE 118 83 188 99 113 53
'MUC6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.479 (Fisher's exact test), Q value = 0.91

Table S459.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
MUC6 MUTATED 4 4 1
MUC6 WILD-TYPE 144 120 121
'MUC6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.941 (Fisher's exact test), Q value = 1

Table S460.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
MUC6 MUTATED 1 1 2 2 2 1
MUC6 WILD-TYPE 58 47 88 51 111 30
'MUC6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0613 (Fisher's exact test), Q value = 0.42

Table S461.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
MUC6 MUTATED 4 8 2
MUC6 WILD-TYPE 501 271 188
'MUC6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.204 (Fisher's exact test), Q value = 0.71

Table S462.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
MUC6 MUTATED 1 3 0 4 5 1
MUC6 WILD-TYPE 262 148 79 257 163 51
'MUC6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.625 (Fisher's exact test), Q value = 0.99

Table S463.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
MUC6 MUTATED 6 1 3 4
MUC6 WILD-TYPE 266 176 230 272
'MUC6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.112 (Fisher's exact test), Q value = 0.54

Table S464.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
MUC6 MUTATED 6 1 0 2 1 4
MUC6 WILD-TYPE 269 135 206 132 86 116
'MUC6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.283 (Fisher's exact test), Q value = 0.83

Table S465.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
MUC6 MUTATED 3 3 0 0 0
MUC6 WILD-TYPE 175 117 66 92 112
'MUC6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0513 (Fisher's exact test), Q value = 0.39

Table S466.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
MUC6 MUTATED 6 0 0
MUC6 WILD-TYPE 273 181 108
'TGS1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.637 (Fisher's exact test), Q value = 0.99

Table S467.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
TGS1 MUTATED 1 0 1 1 1 2 0 0
TGS1 WILD-TYPE 20 38 113 96 107 71 19 39
'TGS1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.666 (Fisher's exact test), Q value = 0.99

Table S468.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
TGS1 MUTATED 1 1 3 1 0
TGS1 WILD-TYPE 95 151 113 88 56
'TGS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.421 (Fisher's exact test), Q value = 0.88

Table S469.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
TGS1 MUTATED 2 7 0 2 1
TGS1 WILD-TYPE 245 356 86 229 35
'TGS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.236 (Fisher's exact test), Q value = 0.76

Table S470.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
TGS1 MUTATED 1 3 4 3 0 0
TGS1 WILD-TYPE 119 81 185 98 116 54
'TGS1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.205 (Fisher's exact test), Q value = 0.71

Table S471.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
TGS1 MUTATED 1 3 0
TGS1 WILD-TYPE 147 121 122
'TGS1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.558 (Fisher's exact test), Q value = 0.96

Table S472.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
TGS1 MUTATED 0 1 1 0 1 1
TGS1 WILD-TYPE 59 47 89 53 112 30
'TGS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S473.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
TGS1 MUTATED 7 4 2
TGS1 WILD-TYPE 498 275 188
'TGS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.245 (Fisher's exact test), Q value = 0.77

Table S474.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
TGS1 MUTATED 2 5 0 4 1 1
TGS1 WILD-TYPE 261 146 79 257 167 51
'TGS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.27 (Fisher's exact test), Q value = 0.81

Table S475.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
TGS1 MUTATED 1 2 4 6
TGS1 WILD-TYPE 271 175 229 270
'TGS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.46 (Fisher's exact test), Q value = 0.91

Table S476.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
TGS1 MUTATED 5 1 5 2 0 0
TGS1 WILD-TYPE 270 135 201 132 87 120
'TGS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.248 (Fisher's exact test), Q value = 0.77

Table S477.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
TGS1 MUTATED 3 0 2 0 2
TGS1 WILD-TYPE 175 120 64 92 110
'TGS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.354 (Fisher's exact test), Q value = 0.85

Table S478.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
TGS1 MUTATED 2 4 1
TGS1 WILD-TYPE 277 177 107
'TFE3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.676 (Fisher's exact test), Q value = 0.99

Table S479.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
TFE3 MUTATED 1 1 1 2 1 1 0 0
TFE3 WILD-TYPE 20 37 113 95 107 72 19 39
'TFE3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.903 (Fisher's exact test), Q value = 1

Table S480.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
TFE3 MUTATED 1 2 2 2 0
TFE3 WILD-TYPE 95 150 114 87 56
'TFE3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.741 (Fisher's exact test), Q value = 1

Table S481.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
TFE3 MUTATED 2 2 0 3 0
TFE3 WILD-TYPE 245 361 86 228 36
'TFE3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.322 (Fisher's exact test), Q value = 0.84

Table S482.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
TFE3 MUTATED 1 0 0 1 1 1
TFE3 WILD-TYPE 119 84 189 100 115 53
'TFE3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S483.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
TFE3 MUTATED 1 1 1
TFE3 WILD-TYPE 147 123 121
'TFE3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.941 (Fisher's exact test), Q value = 1

Table S484.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
TFE3 MUTATED 0 0 1 0 2 0
TFE3 WILD-TYPE 59 48 89 53 111 31
'TFE3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.786 (Fisher's exact test), Q value = 1

Table S485.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
TFE3 MUTATED 3 3 1
TFE3 WILD-TYPE 502 276 189
'TFE3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.647 (Fisher's exact test), Q value = 0.99

Table S486.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
TFE3 MUTATED 2 1 0 1 2 1
TFE3 WILD-TYPE 261 150 79 260 166 51
'TFE3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S487.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
TFE3 MUTATED 2 2 2 1
TFE3 WILD-TYPE 270 175 231 275
'TFE3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.425 (Fisher's exact test), Q value = 0.88

Table S488.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
TFE3 MUTATED 1 3 1 1 0 1
TFE3 WILD-TYPE 274 133 205 133 87 119
'TFE3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.856 (Fisher's exact test), Q value = 1

Table S489.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
TFE3 MUTATED 2 1 0 0 0
TFE3 WILD-TYPE 176 119 66 92 112
'TFE3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.301 (Fisher's exact test), Q value = 0.83

Table S490.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
TFE3 MUTATED 3 0 0
TFE3 WILD-TYPE 276 181 108
'IRS4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.146 (Fisher's exact test), Q value = 0.61

Table S491.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
IRS4 MUTATED 1 2 1 1 0 1 0 1
IRS4 WILD-TYPE 20 36 113 96 108 72 19 38
'IRS4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.782 (Fisher's exact test), Q value = 1

Table S492.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
IRS4 MUTATED 1 4 1 1 0
IRS4 WILD-TYPE 95 148 115 88 56
'IRS4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.223 (Fisher's exact test), Q value = 0.74

Table S493.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
IRS4 MUTATED 3 2 0 6 0
IRS4 WILD-TYPE 244 361 86 225 36
'IRS4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.683 (Fisher's exact test), Q value = 0.99

Table S494.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
IRS4 MUTATED 2 1 1 1 3 1
IRS4 WILD-TYPE 118 83 188 100 113 53
'IRS4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.869 (Fisher's exact test), Q value = 1

Table S495.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
IRS4 MUTATED 2 1 2
IRS4 WILD-TYPE 146 123 120
'IRS4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S496.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
IRS4 MUTATED 1 0 1 0 3 0
IRS4 WILD-TYPE 58 48 89 53 110 31
'IRS4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S497.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
IRS4 MUTATED 3 5 3
IRS4 WILD-TYPE 502 274 187
'IRS4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.47 (Fisher's exact test), Q value = 0.91

Table S498.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
IRS4 MUTATED 2 0 1 4 3 1
IRS4 WILD-TYPE 261 151 78 257 165 51
'IRS4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S499.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
IRS4 MUTATED 3 2 2 3
IRS4 WILD-TYPE 269 175 231 273
'IRS4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.174 (Fisher's exact test), Q value = 0.67

Table S500.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
IRS4 MUTATED 3 3 0 3 0 1
IRS4 WILD-TYPE 272 133 206 131 87 119
'IRS4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.949 (Fisher's exact test), Q value = 1

Table S501.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
IRS4 MUTATED 2 1 0 0 1
IRS4 WILD-TYPE 176 119 66 92 111
'IRS4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.824 (Fisher's exact test), Q value = 1

Table S502.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
IRS4 MUTATED 3 1 0
IRS4 WILD-TYPE 276 180 108
'NLGN3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.544 (Fisher's exact test), Q value = 0.95

Table S503.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
NLGN3 MUTATED 0 0 3 1 3 0 1 0
NLGN3 WILD-TYPE 21 38 111 96 105 73 18 39
'NLGN3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.562 (Fisher's exact test), Q value = 0.97

Table S504.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
NLGN3 MUTATED 2 1 2 1 2
NLGN3 WILD-TYPE 94 151 114 88 54
'NLGN3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.244 (Fisher's exact test), Q value = 0.77

Table S505.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
NLGN3 MUTATED 1 8 1 1 0
NLGN3 WILD-TYPE 246 355 85 230 36
'NLGN3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.153 (Fisher's exact test), Q value = 0.63

Table S506.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
NLGN3 MUTATED 3 0 1 0 0 1
NLGN3 WILD-TYPE 117 84 188 101 116 53
'NLGN3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0546 (Fisher's exact test), Q value = 0.4

Table S507.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
NLGN3 MUTATED 5 0 1
NLGN3 WILD-TYPE 143 124 121
'NLGN3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.255 (Fisher's exact test), Q value = 0.79

Table S508.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
NLGN3 MUTATED 0 0 1 0 5 0
NLGN3 WILD-TYPE 59 48 89 53 108 31
'NLGN3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S509.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
NLGN3 MUTATED 7 3 1
NLGN3 WILD-TYPE 498 276 189
'NLGN3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S510.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
NLGN3 MUTATED 4 4 1 0 1 1
NLGN3 WILD-TYPE 259 147 78 261 167 51
'NLGN3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.953 (Fisher's exact test), Q value = 1

Table S511.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
NLGN3 MUTATED 4 2 2 3
NLGN3 WILD-TYPE 268 175 231 273
'NLGN3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.747 (Fisher's exact test), Q value = 1

Table S512.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
NLGN3 MUTATED 5 2 2 0 1 1
NLGN3 WILD-TYPE 270 134 204 134 86 119
'NLGN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.608 (Fisher's exact test), Q value = 0.98

Table S513.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
NLGN3 MUTATED 2 0 1 0 1
NLGN3 WILD-TYPE 176 120 65 92 111
'NLGN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.673 (Fisher's exact test), Q value = 0.99

Table S514.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
NLGN3 MUTATED 2 2 0
NLGN3 WILD-TYPE 277 179 108
'IL1RAP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.15 (Fisher's exact test), Q value = 0.62

Table S515.  Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
IL1RAP MUTATED 2 1 1 4 1
IL1RAP WILD-TYPE 245 362 85 227 35
'IL1RAP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.301 (Fisher's exact test), Q value = 0.83

Table S516.  Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
IL1RAP MUTATED 0 1 2 0 3 1
IL1RAP WILD-TYPE 120 83 187 101 113 53
'IL1RAP MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S517.  Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
IL1RAP MUTATED 5 4 0
IL1RAP WILD-TYPE 500 275 190
'IL1RAP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.644 (Fisher's exact test), Q value = 0.99

Table S518.  Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
IL1RAP MUTATED 1 2 0 3 2 1
IL1RAP WILD-TYPE 262 149 79 258 166 51
'IL1RAP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.615 (Fisher's exact test), Q value = 0.98

Table S519.  Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
IL1RAP MUTATED 3 0 2 3
IL1RAP WILD-TYPE 269 177 231 273
'IL1RAP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.897 (Fisher's exact test), Q value = 1

Table S520.  Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
IL1RAP MUTATED 3 1 1 1 0 2
IL1RAP WILD-TYPE 272 135 205 133 87 118
'IL1RAP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.587 (Fisher's exact test), Q value = 0.98

Table S521.  Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
IL1RAP MUTATED 3 3 0 0 1
IL1RAP WILD-TYPE 175 117 66 92 111
'IL1RAP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.686 (Fisher's exact test), Q value = 0.99

Table S522.  Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
IL1RAP MUTATED 5 1 1
IL1RAP WILD-TYPE 274 180 107
'USP36 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.835 (Fisher's exact test), Q value = 1

Table S523.  Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
USP36 MUTATED 0 0 2 3 2 0 0 0
USP36 WILD-TYPE 21 38 112 94 106 73 19 39
'USP36 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.182 (Fisher's exact test), Q value = 0.69

Table S524.  Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
USP36 MUTATED 2 1 0 3 1
USP36 WILD-TYPE 94 151 116 86 55
'USP36 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.968 (Fisher's exact test), Q value = 1

Table S525.  Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
USP36 MUTATED 2 3 1 2 0
USP36 WILD-TYPE 245 360 85 229 36
'USP36 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S526.  Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
USP36 MUTATED 0 1 1 0 1 0
USP36 WILD-TYPE 120 83 188 101 115 54
'USP36 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 0.99

Table S527.  Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
USP36 MUTATED 3 1 3
USP36 WILD-TYPE 145 123 119
'USP36 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S528.  Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
USP36 MUTATED 1 0 3 0 3 0
USP36 WILD-TYPE 58 48 87 53 110 31
'USP36 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.457 (Fisher's exact test), Q value = 0.91

Table S529.  Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
USP36 MUTATED 5 3 0
USP36 WILD-TYPE 500 276 190
'USP36 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.077 (Fisher's exact test), Q value = 0.45

Table S530.  Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
USP36 MUTATED 5 0 0 0 3 0
USP36 WILD-TYPE 258 151 79 261 165 52
'USP36 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.676 (Fisher's exact test), Q value = 0.99

Table S531.  Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
USP36 MUTATED 3 1 3 1
USP36 WILD-TYPE 269 176 230 275
'USP36 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.344 (Fisher's exact test), Q value = 0.85

Table S532.  Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
USP36 MUTATED 2 0 1 1 1 3
USP36 WILD-TYPE 273 136 205 133 86 117
'CASZ1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.936 (Fisher's exact test), Q value = 1

Table S533.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
CASZ1 MUTATED 0 1 1 2 2 1 0 0
CASZ1 WILD-TYPE 21 37 113 95 106 72 19 39
'CASZ1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S534.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
CASZ1 MUTATED 1 3 1 2 0
CASZ1 WILD-TYPE 95 149 115 87 56
'CASZ1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.903 (Fisher's exact test), Q value = 1

Table S535.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
CASZ1 MUTATED 5 4 1 3 0
CASZ1 WILD-TYPE 242 359 85 228 36
'CASZ1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.813 (Fisher's exact test), Q value = 1

Table S536.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
CASZ1 MUTATED 2 2 2 1 3 0
CASZ1 WILD-TYPE 118 82 187 100 113 54
'CASZ1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.204 (Fisher's exact test), Q value = 0.71

Table S537.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
CASZ1 MUTATED 1 3 0
CASZ1 WILD-TYPE 147 121 122
'CASZ1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S538.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
CASZ1 MUTATED 0 0 1 1 2 0
CASZ1 WILD-TYPE 59 48 89 52 111 31
'CASZ1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.822 (Fisher's exact test), Q value = 1

Table S539.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
CASZ1 MUTATED 7 5 2
CASZ1 WILD-TYPE 498 274 188
'CASZ1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S540.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
CASZ1 MUTATED 2 2 1 5 4 0
CASZ1 WILD-TYPE 261 149 78 256 164 52
'CASZ1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.518 (Fisher's exact test), Q value = 0.95

Table S541.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
CASZ1 MUTATED 2 3 5 3
CASZ1 WILD-TYPE 270 174 228 273
'CASZ1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.735 (Fisher's exact test), Q value = 1

Table S542.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
CASZ1 MUTATED 5 1 3 1 0 3
CASZ1 WILD-TYPE 270 135 203 133 87 117
'CASZ1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 0.88

Table S543.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
CASZ1 MUTATED 4 1 0 0 3
CASZ1 WILD-TYPE 174 119 66 92 109
'CASZ1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.326 (Fisher's exact test), Q value = 0.84

Table S544.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
CASZ1 MUTATED 6 2 0
CASZ1 WILD-TYPE 273 179 108
'EYS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 0.79

Table S545.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
EYS MUTATED 1 0 2 3 1 2 2 1
EYS WILD-TYPE 20 38 112 94 107 71 17 38
'EYS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.285 (Fisher's exact test), Q value = 0.83

Table S546.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
EYS MUTATED 1 3 6 2 0
EYS WILD-TYPE 95 149 110 87 56
'EYS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 0.29

Table S547.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
EYS MUTATED 6 4 0 11 0
EYS WILD-TYPE 241 359 86 220 36

Figure S99.  Get High-res Image Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'EYS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0651 (Fisher's exact test), Q value = 0.43

Table S548.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
EYS MUTATED 5 1 0 2 3 1
EYS WILD-TYPE 115 83 189 99 113 53
'EYS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.223 (Fisher's exact test), Q value = 0.74

Table S549.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
EYS MUTATED 6 2 1
EYS WILD-TYPE 142 122 121
'EYS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.383 (Fisher's exact test), Q value = 0.88

Table S550.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
EYS MUTATED 1 0 3 0 3 2
EYS WILD-TYPE 58 48 87 53 110 29
'EYS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.23

Table S551.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
EYS MUTATED 7 12 2
EYS WILD-TYPE 498 267 188

Figure S100.  Get High-res Image Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'EYS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.202 (Fisher's exact test), Q value = 0.71

Table S552.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
EYS MUTATED 2 4 1 7 4 3
EYS WILD-TYPE 261 147 78 254 164 49
'EYS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.1 (Fisher's exact test), Q value = 0.51

Table S553.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
EYS MUTATED 11 2 5 3
EYS WILD-TYPE 261 175 228 273
'EYS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0324 (Fisher's exact test), Q value = 0.29

Table S554.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
EYS MUTATED 7 8 2 1 0 3
EYS WILD-TYPE 268 128 204 133 87 117

Figure S101.  Get High-res Image Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'EYS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.371 (Fisher's exact test), Q value = 0.87

Table S555.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
EYS MUTATED 5 5 1 0 3
EYS WILD-TYPE 173 115 65 92 109
'EYS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.126 (Fisher's exact test), Q value = 0.57

Table S556.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
EYS MUTATED 10 4 0
EYS WILD-TYPE 269 177 108
'KCNN3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.144 (Fisher's exact test), Q value = 0.61

Table S557.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
KCNN3 MUTATED 1 0 0 2 0 1 0 1
KCNN3 WILD-TYPE 20 38 114 95 108 72 19 38
'KCNN3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.507 (Fisher's exact test), Q value = 0.93

Table S558.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
KCNN3 MUTATED 0 1 2 2 0
KCNN3 WILD-TYPE 96 151 114 87 56
'KCNN3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.252 (Fisher's exact test), Q value = 0.78

Table S559.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
KCNN3 MUTATED 4 1 0 4 0
KCNN3 WILD-TYPE 243 362 86 227 36
'KCNN3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.122 (Fisher's exact test), Q value = 0.56

Table S560.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
KCNN3 MUTATED 2 0 0 0 2 1
KCNN3 WILD-TYPE 118 84 189 101 114 53
'KCNN3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.391 (Fisher's exact test), Q value = 0.88

Table S561.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
KCNN3 MUTATED 3 1 0
KCNN3 WILD-TYPE 145 123 122
'KCNN3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.768 (Fisher's exact test), Q value = 1

Table S562.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
KCNN3 MUTATED 0 0 2 1 1 0
KCNN3 WILD-TYPE 59 48 88 52 112 31
'KCNN3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.287 (Fisher's exact test), Q value = 0.83

Table S563.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
KCNN3 MUTATED 5 4 0
KCNN3 WILD-TYPE 500 275 190
'KCNN3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.397 (Fisher's exact test), Q value = 0.88

Table S564.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
KCNN3 MUTATED 1 3 0 2 2 1
KCNN3 WILD-TYPE 262 148 79 259 166 51
'KCNN3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.304 (Fisher's exact test), Q value = 0.83

Table S565.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
KCNN3 MUTATED 4 0 1 4
KCNN3 WILD-TYPE 268 177 232 272
'KCNN3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.713 (Fisher's exact test), Q value = 1

Table S566.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
KCNN3 MUTATED 3 3 1 1 0 1
KCNN3 WILD-TYPE 272 133 205 133 87 119
'KCNN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.58 (Fisher's exact test), Q value = 0.97

Table S567.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
KCNN3 MUTATED 2 2 0 0 0
KCNN3 WILD-TYPE 176 118 66 92 112
'KCNN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.409 (Fisher's exact test), Q value = 0.88

Table S568.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
KCNN3 MUTATED 3 0 1
KCNN3 WILD-TYPE 276 181 107
'ZFP36L1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.401 (Fisher's exact test), Q value = 0.88

Table S569.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
ZFP36L1 MUTATED 1 0 1 0 1 1 0 1
ZFP36L1 WILD-TYPE 20 38 113 97 107 72 19 38
'ZFP36L1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.897 (Fisher's exact test), Q value = 1

Table S570.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
ZFP36L1 MUTATED 1 2 2 0 0
ZFP36L1 WILD-TYPE 95 150 114 89 56
'ZFP36L1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00136 (Fisher's exact test), Q value = 0.023

Table S571.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
ZFP36L1 MUTATED 4 0 3 0 1
ZFP36L1 WILD-TYPE 243 363 83 231 35

Figure S102.  Get High-res Image Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ZFP36L1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S572.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
ZFP36L1 MUTATED 2 1 1 0 1 0
ZFP36L1 WILD-TYPE 118 83 188 101 115 54
'ZFP36L1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0613 (Fisher's exact test), Q value = 0.42

Table S573.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
ZFP36L1 MUTATED 0 3 0
ZFP36L1 WILD-TYPE 148 121 122
'ZFP36L1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0489 (Fisher's exact test), Q value = 0.38

Table S574.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
ZFP36L1 MUTATED 0 1 0 2 0 0
ZFP36L1 WILD-TYPE 59 47 90 51 113 31

Figure S103.  Get High-res Image Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'ZFP36L1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.184 (Fisher's exact test), Q value = 0.69

Table S575.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
ZFP36L1 MUTATED 7 1 0
ZFP36L1 WILD-TYPE 498 278 190
'ZFP36L1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S576.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
ZFP36L1 MUTATED 4 2 0 1 1 0
ZFP36L1 WILD-TYPE 259 149 79 260 167 52
'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.895 (Fisher's exact test), Q value = 1

Table S577.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
ZFP36L1 MUTATED 2 1 3 2
ZFP36L1 WILD-TYPE 270 176 230 274
'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S578.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
ZFP36L1 MUTATED 4 1 2 0 0 1
ZFP36L1 WILD-TYPE 271 135 204 134 87 119
'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.949 (Fisher's exact test), Q value = 1

Table S579.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
ZFP36L1 MUTATED 2 1 0 0 1
ZFP36L1 WILD-TYPE 176 119 66 92 111
'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.823 (Fisher's exact test), Q value = 1

Table S580.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
ZFP36L1 MUTATED 3 1 0
ZFP36L1 WILD-TYPE 276 180 108
'ICOSLG MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.772 (Fisher's exact test), Q value = 1

Table S581.  Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
ICOSLG MUTATED 0 0 2 1 0 0 0 0
ICOSLG WILD-TYPE 21 38 112 96 108 73 19 39
'ICOSLG MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.133 (Fisher's exact test), Q value = 0.58

Table S582.  Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
ICOSLG MUTATED 2 0 0 1 0
ICOSLG WILD-TYPE 94 152 116 88 56
'ICOSLG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 0.36

Table S583.  Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
ICOSLG MUTATED 1 0 1 2 1
ICOSLG WILD-TYPE 246 363 85 229 35

Figure S104.  Get High-res Image Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ICOSLG MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S584.  Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
ICOSLG MUTATED 0 1 1 1 1 0
ICOSLG WILD-TYPE 120 83 188 100 115 54
'ICOSLG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.599 (Fisher's exact test), Q value = 0.98

Table S585.  Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
ICOSLG MUTATED 4 1 0
ICOSLG WILD-TYPE 501 278 190
'ICOSLG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.968 (Fisher's exact test), Q value = 1

Table S586.  Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
ICOSLG MUTATED 1 1 0 2 1 0
ICOSLG WILD-TYPE 262 150 79 259 167 52
'ICOSLG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.772 (Fisher's exact test), Q value = 1

Table S587.  Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
ICOSLG MUTATED 1 0 2 2
ICOSLG WILD-TYPE 271 177 231 274
'ICOSLG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.467 (Fisher's exact test), Q value = 0.91

Table S588.  Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
ICOSLG MUTATED 1 1 0 1 1 1
ICOSLG WILD-TYPE 274 135 206 133 86 119
'ACTL6B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.353 (Fisher's exact test), Q value = 0.85

Table S589.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
ACTL6B MUTATED 1 0 1 2 0 2 0 0
ACTL6B WILD-TYPE 20 38 113 95 108 71 19 39
'ACTL6B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S590.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
ACTL6B MUTATED 1 0 2 2 1
ACTL6B WILD-TYPE 95 152 114 87 55
'ACTL6B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.27

Table S591.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
ACTL6B MUTATED 1 2 0 5 2
ACTL6B WILD-TYPE 246 361 86 226 34

Figure S105.  Get High-res Image Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ACTL6B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.353 (Fisher's exact test), Q value = 0.85

Table S592.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
ACTL6B MUTATED 0 1 3 0 3 0
ACTL6B WILD-TYPE 120 83 186 101 113 54
'ACTL6B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S593.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
ACTL6B MUTATED 2 2 1
ACTL6B WILD-TYPE 146 122 121
'ACTL6B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.194 (Fisher's exact test), Q value = 0.71

Table S594.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
ACTL6B MUTATED 0 1 2 2 0 0
ACTL6B WILD-TYPE 59 47 88 51 113 31
'ACTL6B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.837 (Fisher's exact test), Q value = 1

Table S595.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
ACTL6B MUTATED 6 3 1
ACTL6B WILD-TYPE 499 276 189
'ACTL6B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.194 (Fisher's exact test), Q value = 0.71

Table S596.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
ACTL6B MUTATED 3 3 1 0 3 0
ACTL6B WILD-TYPE 260 148 78 261 165 52
'ACTL6B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.739 (Fisher's exact test), Q value = 1

Table S597.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
ACTL6B MUTATED 3 2 1 4
ACTL6B WILD-TYPE 269 175 232 272
'ACTL6B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.714 (Fisher's exact test), Q value = 1

Table S598.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
ACTL6B MUTATED 3 1 1 1 2 2
ACTL6B WILD-TYPE 272 135 205 133 85 118
'ACTL6B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.423 (Fisher's exact test), Q value = 0.88

Table S599.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
ACTL6B MUTATED 3 0 0 0 2
ACTL6B WILD-TYPE 175 120 66 92 110
'ACTL6B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.714 (Fisher's exact test), Q value = 1

Table S600.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
ACTL6B MUTATED 3 2 0
ACTL6B WILD-TYPE 276 179 108
'MYH9 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.396 (Fisher's exact test), Q value = 0.88

Table S601.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
MYH9 MUTATED 0 1 0 2 2 1 1 1
MYH9 WILD-TYPE 21 37 114 95 106 72 18 38
'MYH9 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.424 (Fisher's exact test), Q value = 0.88

Table S602.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
MYH9 MUTATED 0 4 3 1 0
MYH9 WILD-TYPE 96 148 113 88 56
'MYH9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.366 (Fisher's exact test), Q value = 0.86

Table S603.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
MYH9 MUTATED 4 10 0 2 0
MYH9 WILD-TYPE 243 353 86 229 36
'MYH9 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.402 (Fisher's exact test), Q value = 0.88

Table S604.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
MYH9 MUTATED 1 3 7 1 2 0
MYH9 WILD-TYPE 119 81 182 100 114 54
'MYH9 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.821 (Fisher's exact test), Q value = 1

Table S605.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
MYH9 MUTATED 4 2 2
MYH9 WILD-TYPE 144 122 120
'MYH9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0538 (Fisher's exact test), Q value = 0.4

Table S606.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
MYH9 MUTATED 1 0 1 2 1 3
MYH9 WILD-TYPE 58 48 89 51 112 28
'MYH9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.663 (Fisher's exact test), Q value = 0.99

Table S607.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
MYH9 MUTATED 8 7 3
MYH9 WILD-TYPE 497 272 187
'MYH9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 0.61

Table S608.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
MYH9 MUTATED 1 3 1 8 3 2
MYH9 WILD-TYPE 262 148 78 253 165 50
'MYH9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.736 (Fisher's exact test), Q value = 1

Table S609.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
MYH9 MUTATED 4 4 6 4
MYH9 WILD-TYPE 268 173 227 272
'MYH9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.402 (Fisher's exact test), Q value = 0.88

Table S610.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
MYH9 MUTATED 3 3 7 3 0 2
MYH9 WILD-TYPE 272 133 199 131 87 118
'MYH9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.508 (Fisher's exact test), Q value = 0.93

Table S611.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
MYH9 MUTATED 3 3 2 0 3
MYH9 WILD-TYPE 175 117 64 92 109
'MYH9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 0.79

Table S612.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
MYH9 MUTATED 6 5 0
MYH9 WILD-TYPE 273 176 108
'FBXW7 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S613.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
FBXW7 MUTATED 0 1 1 2 2 0 0 0
FBXW7 WILD-TYPE 21 37 113 95 106 73 19 39
'FBXW7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.531 (Fisher's exact test), Q value = 0.95

Table S614.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
FBXW7 MUTATED 1 2 0 2 1
FBXW7 WILD-TYPE 95 150 116 87 55
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.157 (Fisher's exact test), Q value = 0.63

Table S615.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
FBXW7 MUTATED 2 5 0 8 0
FBXW7 WILD-TYPE 245 358 86 223 36
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00732 (Fisher's exact test), Q value = 0.1

Table S616.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
FBXW7 MUTATED 0 0 2 1 7 1
FBXW7 WILD-TYPE 120 84 187 100 109 53

Figure S106.  Get High-res Image Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.644 (Fisher's exact test), Q value = 0.99

Table S617.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
FBXW7 MUTATED 2 0 1
FBXW7 WILD-TYPE 146 124 121
'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.94 (Fisher's exact test), Q value = 1

Table S618.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
FBXW7 MUTATED 0 0 1 0 2 0
FBXW7 WILD-TYPE 59 48 89 53 111 31
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.23 (Fisher's exact test), Q value = 0.75

Table S619.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
FBXW7 MUTATED 7 7 1
FBXW7 WILD-TYPE 498 272 189
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 0.61

Table S620.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
FBXW7 MUTATED 3 1 0 4 7 0
FBXW7 WILD-TYPE 260 150 79 257 161 52
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.355 (Fisher's exact test), Q value = 0.85

Table S621.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
FBXW7 MUTATED 7 3 3 2
FBXW7 WILD-TYPE 265 174 230 274
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.101 (Fisher's exact test), Q value = 0.51

Table S622.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
FBXW7 MUTATED 3 1 3 2 0 6
FBXW7 WILD-TYPE 272 135 203 132 87 114
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0629 (Fisher's exact test), Q value = 0.42

Table S623.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
FBXW7 MUTATED 1 5 0 0 2
FBXW7 WILD-TYPE 177 115 66 92 110
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.899 (Fisher's exact test), Q value = 1

Table S624.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
FBXW7 MUTATED 5 2 1
FBXW7 WILD-TYPE 274 179 107
'FRMPD2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.529 (Fisher's exact test), Q value = 0.95

Table S625.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
FRMPD2 MUTATED 0 2 1 1 1 2 0 0
FRMPD2 WILD-TYPE 21 36 113 96 107 71 19 39
'FRMPD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.978 (Fisher's exact test), Q value = 1

Table S626.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
FRMPD2 MUTATED 1 3 2 1 0
FRMPD2 WILD-TYPE 95 149 114 88 56
'FRMPD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.465 (Fisher's exact test), Q value = 0.91

Table S627.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
FRMPD2 MUTATED 3 4 0 5 1
FRMPD2 WILD-TYPE 244 359 86 226 35
'FRMPD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 0.9

Table S628.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
FRMPD2 MUTATED 2 1 1 1 4 1
FRMPD2 WILD-TYPE 118 83 188 100 112 53
'FRMPD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.558 (Fisher's exact test), Q value = 0.96

Table S629.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
FRMPD2 MUTATED 2 2 0
FRMPD2 WILD-TYPE 146 122 122
'FRMPD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S630.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
FRMPD2 MUTATED 0 0 1 1 2 0
FRMPD2 WILD-TYPE 59 48 89 52 111 31
'FRMPD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S631.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
FRMPD2 MUTATED 7 4 2
FRMPD2 WILD-TYPE 498 275 188
'FRMPD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0548 (Fisher's exact test), Q value = 0.4

Table S632.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
FRMPD2 MUTATED 0 4 0 5 4 0
FRMPD2 WILD-TYPE 263 147 79 256 164 52
'FRMPD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 0.73

Table S633.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
FRMPD2 MUTATED 4 5 1 3
FRMPD2 WILD-TYPE 268 172 232 273
'FRMPD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S634.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
FRMPD2 MUTATED 5 1 2 2 0 3
FRMPD2 WILD-TYPE 270 135 204 132 87 117
'FRMPD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.187 (Fisher's exact test), Q value = 0.69

Table S635.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 178 120 66 92 112
FRMPD2 MUTATED 0 2 0 2 2
FRMPD2 WILD-TYPE 178 118 66 90 110
'FRMPD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.756 (Fisher's exact test), Q value = 1

Table S636.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 279 181 108
FRMPD2 MUTATED 2 3 1
FRMPD2 WILD-TYPE 277 178 107
'ZFP36L2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.392 (Fisher's exact test), Q value = 0.88

Table S637.  Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 21 38 114 97 108 73 19 39
ZFP36L2 MUTATED 0 0 1 1 0 1 1 0
ZFP36L2 WILD-TYPE 21 38 113 96 108 72 18 39
'ZFP36L2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S638.  Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 96 152 116 89 56
ZFP36L2 MUTATED 1 1 1 1 0
ZFP36L2 WILD-TYPE 95 151 115 88 56
'ZFP36L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 0.26

Table S639.  Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 247 363 86 231 36
ZFP36L2 MUTATED 2 2 1 0 2
ZFP36L2 WILD-TYPE 245 361 85 231 34

Figure S107.  Get High-res Image Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ZFP36L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.779 (Fisher's exact test), Q value = 1

Table S640.  Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 120 84 189 101 116 54
ZFP36L2 MUTATED 2 1 1 0 1 0
ZFP36L2 WILD-TYPE 118 83 188 101 115 54
'ZFP36L2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S641.  Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 148 124 122
ZFP36L2 MUTATED 1 1 1
ZFP36L2 WILD-TYPE 147 123 121
'ZFP36L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S642.  Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 59 48 90 53 113 31
ZFP36L2 MUTATED 0 0 1 1 1 0
ZFP36L2 WILD-TYPE 59 48 89 52 112 31
'ZFP36L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.526 (Fisher's exact test), Q value = 0.95

Table S643.  Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 505 279 190
ZFP36L2 MUTATED 5 2 0
ZFP36L2 WILD-TYPE 500 277 190
'ZFP36L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.567 (Fisher's exact test), Q value = 0.97

Table S644.  Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
ZFP36L2 MUTATED 2 3 0 1 1 0
ZFP36L2 WILD-TYPE 261 148 79 260 167 52
'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.785 (Fisher's exact test), Q value = 1

Table S645.  Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 272 177 233 276
ZFP36L2 MUTATED 1 2 2 2
ZFP36L2 WILD-TYPE 271 175 231 274
'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.903 (Fisher's exact test), Q value = 1

Table S646.  Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 275 136 206 134 87 120
ZFP36L2 MUTATED 2 0