Correlation between gene mutation status and molecular subtypes
Breast Invasive Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1FQ9V6S
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1FQ9V6S
Overview
Introduction

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

Summary

Testing the association between mutation status of 73 genes and 12 molecular subtypes across 975 patients, 53 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'.

  • CBFB mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

  • GATA3 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • MAP3K1 mutation correlated to 'MRNA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • 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'.

  • MAP2K4 mutation correlated to 'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • FBXO17 mutation correlated to 'MIRSEQ_CNMF'.

  • CCL13 mutation correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 73 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, 53 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 Chi-square test Fisher's exact test Chi-square test Chi-square test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test
PIK3CA 316 (32%) 659 7.32e-13
(5.87e-10) 		3.48e-10
(2.78e-07) 		3.25e-13
(2.61e-10) 		4.27e-12
(3.42e-09) 		0.00017
(0.132) 		5.38e-06
(0.00424) 		9.78e-29
(7.97e-26) 		1.66e-19
(1.34e-16) 		1.32e-07
(0.000104) 		2.46e-13
(1.98e-10) 		1.26e-07
(9.97e-05) 		2.62e-12
(2.1e-09)
TP53 295 (30%) 680 2.35e-31
(1.92e-28) 		2.14e-29
(1.75e-26) 		4.49e-56
(3.69e-53) 		1.26e-32
(1.03e-29) 		4.63e-23
(3.76e-20) 		2.58e-23
(2.09e-20) 		5.53e-71
(4.56e-68) 		1.89e-63
(1.55e-60) 		2.23e-43
(1.83e-40) 		7.04e-58
(5.79e-55) 		1.87e-41
(1.54e-38) 		2.35e-35
(1.92e-32)
CDH1 105 (11%) 870 0.000174
(0.135) 		0.00336
(1.00) 		3.71e-15
(2.99e-12) 		2.58e-08
(2.05e-05) 		0.00404
(1.00) 		0.0106
(1.00) 		1.04e-17
(8.37e-15) 		8.89e-18
(7.18e-15) 		2.5e-17
(2.01e-14) 		2.62e-25
(2.13e-22) 		2.21e-21
(1.79e-18) 		2.03e-19
(1.64e-16)
GATA3 97 (10%) 878 6.02e-06
(0.00474) 		1.91e-07
(0.000151) 		0.00139
(1.00) 		0.00251
(1.00) 		0.0184
(1.00) 		0.000929
(0.715) 		1.79e-08
(1.42e-05) 		1.11e-12
(8.87e-10) 		0.00178
(1.00) 		3.98e-10
(3.17e-07) 		1.2e-08
(9.52e-06) 		5.63e-11
(4.49e-08)
MAP3K1 70 (7%) 905 9.82e-05
(0.0769) 		0.000689
(0.532) 		0.0029
(1.00) 		0.034
(1.00) 		0.00069
(0.532) 		3.81e-05
(0.0299) 		0.000166
(0.13) 		0.000178
(0.138) 		0.0083
(1.00) 		0.00014
(0.11) 		0.000214
(0.166) 		0.00905
(1.00)
MAP2K4 32 (3%) 943 0.123
(1.00) 		0.00395
(1.00) 		0.189
(1.00) 		0.0204
(1.00) 		0.00262
(1.00) 		0.0298
(1.00) 		0.00977
(1.00) 		0.000198
(0.154) 		0.00448
(1.00) 		0.000294
(0.228) 		2.58e-05
(0.0202) 		0.00129
(0.988)
CBFB 23 (2%) 952 0.134
(1.00) 		0.925
(1.00) 		0.0228
(1.00) 		9.16e-05
(0.0718) 		0.124
(1.00) 		0.513
(1.00) 		9.44e-06
(0.00743) 		0.045
(1.00) 		0.541
(1.00) 		0.00367
(1.00) 		0.00358
(1.00) 		0.00427
(1.00)
FBXO17 5 (1%) 970 0.82
(1.00) 		0.399
(1.00) 		0.579
(1.00) 		0.38
(1.00) 		0.000298
(0.23) 		1
(1.00) 		1
(1.00) 		1
(1.00)
CCL13 4 (0%) 971 0.000182
(0.141) 		0.36
(1.00) 		0.778
(1.00) 		0.568
(1.00) 		0.16
(1.00) 		0.532
(1.00)
RUNX1 29 (3%) 946 0.0149
(1.00) 		0.0452
(1.00) 		0.0018
(1.00) 		0.0766
(1.00) 		1
(1.00) 		0.285
(1.00) 		0.0185
(1.00) 		0.0984
(1.00) 		0.0389
(1.00) 		0.257
(1.00) 		0.157
(1.00) 		0.0369
(1.00)
FOXA1 23 (2%) 952 0.356
(1.00) 		0.238
(1.00) 		0.289
(1.00) 		0.0393
(1.00) 		0.894
(1.00) 		0.309
(1.00) 		0.127
(1.00) 		0.053
(1.00) 		0.319
(1.00) 		0.0882
(1.00) 		0.0673
(1.00) 		0.551
(1.00)
SF3B1 16 (2%) 959 0.815
(1.00) 		0.298
(1.00) 		0.376
(1.00) 		0.172
(1.00) 		0.45
(1.00) 		0.0246
(1.00) 		0.655
(1.00) 		0.243
(1.00) 		0.885
(1.00) 		0.704
(1.00) 		0.612
(1.00) 		0.323
(1.00)
PTEN 35 (4%) 940 0.28
(1.00) 		0.658
(1.00) 		0.29
(1.00) 		0.419
(1.00) 		0.922
(1.00) 		0.667
(1.00) 		0.474
(1.00) 		0.665
(1.00) 		0.118
(1.00) 		0.648
(1.00) 		0.486
(1.00) 		0.744
(1.00)
TBX3 27 (3%) 948 0.428
(1.00) 		0.307
(1.00) 		0.435
(1.00) 		0.108
(1.00) 		0.083
(1.00) 		0.609
(1.00) 		0.0604
(1.00) 		0.0409
(1.00) 		0.137
(1.00) 		0.0401
(1.00) 		0.279
(1.00) 		0.391
(1.00)
MLL3 69 (7%) 906 0.598
(1.00) 		0.688
(1.00) 		0.605
(1.00) 		0.157
(1.00) 		0.597
(1.00) 		0.865
(1.00) 		0.182
(1.00) 		0.234
(1.00) 		0.0613
(1.00) 		0.0886
(1.00) 		0.32
(1.00) 		0.75
(1.00)
RB1 19 (2%) 956 0.666
(1.00) 		0.403
(1.00) 		0.0798
(1.00) 		0.0615
(1.00) 		0.482
(1.00) 		0.763
(1.00) 		0.149
(1.00) 		0.0564
(1.00) 		0.272
(1.00) 		0.00282
(1.00) 		0.013
(1.00) 		0.318
(1.00)
NCOR1 41 (4%) 934 0.571
(1.00) 		0.954
(1.00) 		0.71
(1.00) 		0.944
(1.00) 		0.435
(1.00) 		0.167
(1.00) 		0.398
(1.00) 		0.77
(1.00) 		0.64
(1.00) 		0.572
(1.00) 		1
(1.00) 		0.554
(1.00)
CTCF 17 (2%) 958 0.0331
(1.00) 		0.322
(1.00) 		0.0412
(1.00) 		0.00932
(1.00) 		0.0685
(1.00) 		0.297
(1.00) 		0.577
(1.00) 		0.191
(1.00) 		0.13
(1.00) 		0.0475
(1.00) 		0.642
(1.00) 		0.443
(1.00)
GPS2 11 (1%) 964 0.00133
(1.00) 		0.00592
(1.00) 		0.12
(1.00) 		0.38
(1.00) 		0.268
(1.00) 		0.315
(1.00) 		0.0534
(1.00) 		0.0946
(1.00) 		0.137
(1.00) 		1
(1.00) 		0.867
(1.00) 		0.721
(1.00)
THEM5 11 (1%) 964 0.231
(1.00) 		0.441
(1.00) 		0.529
(1.00) 		0.28
(1.00) 		0.209
(1.00) 		0.0398
(1.00) 		0.701
(1.00) 		0.562
(1.00) 		0.939
(1.00) 		1
(1.00) 		0.337
(1.00) 		0.137
(1.00)
RPGR 18 (2%) 957 0.99
(1.00) 		0.664
(1.00) 		0.869
(1.00) 		0.601
(1.00) 		0.767
(1.00) 		0.695
(1.00) 		0.948
(1.00) 		0.669
(1.00) 		0.783
(1.00) 		1
(1.00) 		0.909
(1.00) 		0.452
(1.00)
DNAH12 17 (2%) 958 0.973
(1.00) 		0.158
(1.00) 		0.473
(1.00) 		0.707
(1.00) 		0.45
(1.00) 		0.627
(1.00) 		0.00224
(1.00) 		0.382
(1.00) 		0.61
(1.00) 		0.28
(1.00) 		0.4
(1.00) 		0.178
(1.00)
CDKN1B 10 (1%) 965 0.634
(1.00) 		0.178
(1.00) 		0.142
(1.00) 		0.108
(1.00) 		0.741
(1.00) 		0.28
(1.00) 		0.232
(1.00) 		0.0943
(1.00) 		0.252
(1.00) 		0.111
(1.00) 		0.295
(1.00) 		0.557
(1.00)
ZFP36L1 9 (1%) 966 0.57
(1.00) 		0.441
(1.00) 		0.0232
(1.00) 		0.758
(1.00) 		0.0266
(1.00) 		0.0233
(1.00) 		0.119
(1.00) 		0.294
(1.00) 		0.23
(1.00) 		0.906
(1.00) 		0.867
(1.00) 		0.721
(1.00)
ASB10 8 (1%) 967 0.869
(1.00) 		0.811
(1.00) 		0.981
(1.00) 		0.787
(1.00) 		0.561
(1.00) 		0.386
(1.00) 		0.624
(1.00) 		0.799
(1.00) 		0.867
(1.00) 		1
(1.00)
HIST1H3B 11 (1%) 964 0.638
(1.00) 		1
(1.00) 		0.923
(1.00) 		0.677
(1.00) 		0.631
(1.00) 		1
(1.00) 		0.324
(1.00) 		0.137
(1.00) 		0.476
(1.00) 		0.918
(1.00) 		0.778
(1.00) 		0.871
(1.00)
FAM86B1 8 (1%) 967 0.734
(1.00) 		0.87
(1.00) 		0.4
(1.00) 		0.538
(1.00) 		0.394
(1.00) 		0.00543
(1.00) 		0.893
(1.00) 		0.593
(1.00)
PIK3R1 15 (2%) 960 0.0266
(1.00) 		0.722
(1.00) 		0.873
(1.00) 		0.0774
(1.00) 		0.631
(1.00) 		0.452
(1.00) 		0.511
(1.00) 		0.484
(1.00) 		0.0307
(1.00) 		0.135
(1.00) 		0.141
(1.00) 		0.566
(1.00)
MYH9 19 (2%) 956 0.711
(1.00) 		0.182
(1.00) 		0.123
(1.00) 		0.465
(1.00) 		0.822
(1.00) 		0.606
(1.00) 		0.869
(1.00) 		0.286
(1.00) 		0.354
(1.00) 		0.192
(1.00) 		0.66
(1.00) 		0.134
(1.00)
CASP8 12 (1%) 963 0.423
(1.00) 		0.358
(1.00) 		0.0663
(1.00) 		0.436
(1.00) 		0.531
(1.00) 		0.739
(1.00) 		0.0633
(1.00) 		1
(1.00) 		0.436
(1.00) 		0.424
(1.00) 		0.741
(1.00) 		0.452
(1.00)
COL6A5 25 (3%) 950 0.144
(1.00) 		0.44
(1.00) 		0.791
(1.00) 		0.204
(1.00) 		0.075
(1.00) 		0.076
(1.00) 		0.208
(1.00) 		0.342
(1.00) 		0.578
(1.00) 		0.0383
(1.00) 		0.0502
(1.00) 		0.0577
(1.00)
TBL1XR1 10 (1%) 965 0.123
(1.00) 		0.238
(1.00) 		0.0497
(1.00) 		0.492
(1.00) 		0.451
(1.00) 		0.568
(1.00) 		0.0228
(1.00) 		0.145
(1.00) 		0.475
(1.00) 		0.042
(1.00) 		0.575
(1.00) 		0.242
(1.00)
ASXL2 16 (2%) 959 0.403
(1.00) 		0.0975
(1.00) 		0.861
(1.00) 		0.971
(1.00) 		0.281
(1.00) 		0.00505
(1.00) 		0.512
(1.00) 		0.4
(1.00) 		0.803
(1.00) 		0.187
(1.00) 		0.741
(1.00) 		0.26
(1.00)
ARID1A 27 (3%) 948 0.135
(1.00) 		0.943
(1.00) 		0.152
(1.00) 		0.0615
(1.00) 		1
(1.00) 		0.475
(1.00) 		0.0924
(1.00) 		0.272
(1.00) 		0.443
(1.00) 		0.0936
(1.00) 		0.837
(1.00) 		0.0456
(1.00)
AQP12A 6 (1%) 969 0.715
(1.00) 		0.203
(1.00) 		0.207
(1.00) 		0.0247
(1.00) 		0.201
(1.00) 		0.115
(1.00) 		0.69
(1.00) 		1
(1.00) 		0.689
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
EPDR1 5 (1%) 970 0.379
(1.00) 		1
(1.00) 		0.79
(1.00) 		0.557
(1.00) 		0.468
(1.00) 		0.191
(1.00) 		1
(1.00) 		0.599
(1.00) 		1
(1.00) 		0.293
(1.00) 		1
(1.00)
ERBB2 21 (2%) 954 0.886
(1.00) 		0.349
(1.00) 		0.0254
(1.00) 		0.0101
(1.00) 		0.549
(1.00) 		0.906
(1.00) 		0.296
(1.00) 		0.658
(1.00) 		0.112
(1.00) 		0.183
(1.00) 		0.584
(1.00) 		0.503
(1.00)
MYB 12 (1%) 963 0.631
(1.00) 		1
(1.00) 		0.23
(1.00) 		0.514
(1.00) 		1
(1.00) 		0.862
(1.00) 		0.764
(1.00) 		0.657
(1.00) 		0.0344
(1.00) 		0.172
(1.00) 		0.0683
(1.00) 		0.489
(1.00)
TMEM151B 6 (1%) 969 0.915
(1.00) 		0.297
(1.00) 		0.115
(1.00) 		0.576
(1.00) 		0.0266
(1.00) 		0.195
(1.00) 		0.514
(1.00) 		0.0313
(1.00) 		0.272
(1.00) 		0.716
(1.00) 		0.397
(1.00) 		0.191
(1.00)
GALNTL6 5 (1%) 970 0.921
(1.00) 		1
(1.00) 		0.225
(1.00) 		0.0124
(1.00) 		0.427
(1.00) 		0.132
(1.00) 		0.11
(1.00) 		0.654
(1.00) 		0.397
(1.00) 		0.191
(1.00)
AKD1 18 (2%) 957 0.44
(1.00) 		0.598
(1.00) 		0.361
(1.00) 		0.532
(1.00) 		0.235
(1.00) 		0.124
(1.00) 		0.242
(1.00) 		0.0808
(1.00) 		0.896
(1.00) 		0.474
(1.00) 		0.0812
(1.00) 		0.431
(1.00)
AARS 9 (1%) 966 0.403
(1.00) 		0.0107
(1.00) 		0.738
(1.00) 		0.424
(1.00) 		0.836
(1.00) 		0.563
(1.00) 		0.00241
(1.00) 		0.472
(1.00) 		0.746
(1.00) 		0.319
(1.00) 		0.0573
(1.00) 		0.072
(1.00)
HLA-C 9 (1%) 966 0.316
(1.00) 		0.203
(1.00) 		0.58
(1.00) 		0.106
(1.00) 		0.399
(1.00) 		0.634
(1.00) 		0.27
(1.00) 		0.236
(1.00) 		0.181
(1.00) 		0.0717
(1.00) 		0.199
(1.00) 		0.0267
(1.00)
GPRIN2 11 (1%) 964 0.655
(1.00) 		0.465
(1.00) 		0.698
(1.00) 		0.655
(1.00) 		0.877
(1.00) 		0.33
(1.00) 		0.845
(1.00) 		0.433
(1.00) 		0.406
(1.00) 		0.578
(1.00) 		0.7
(1.00) 		0.324
(1.00)
TRPM5 11 (1%) 964 0.237
(1.00) 		0.615
(1.00) 		0.786
(1.00) 		0.251
(1.00) 		0.778
(1.00) 		0.782
(1.00) 		0.288
(1.00) 		0.0629
(1.00) 		0.288
(1.00) 		0.105
(1.00) 		0.0222
(1.00) 		0.0171
(1.00)
ANKRD12 18 (2%) 957 0.178
(1.00) 		0.115
(1.00) 		0.66
(1.00) 		0.863
(1.00) 		0.385
(1.00) 		0.518
(1.00) 		0.42
(1.00) 		0.1
(1.00) 		0.537
(1.00) 		0.64
(1.00) 		1
(1.00) 		0.399
(1.00)
FBXW7 15 (2%) 960 0.818
(1.00) 		0.64
(1.00) 		0.0841
(1.00) 		0.0025
(1.00) 		0.778
(1.00) 		0.782
(1.00) 		0.0582
(1.00) 		0.135
(1.00) 		0.426
(1.00) 		0.256
(1.00) 		0.48
(1.00) 		0.125
(1.00)
PRICKLE3 11 (1%) 964 0.335
(1.00) 		0.282
(1.00) 		0.951
(1.00) 		0.609
(1.00) 		0.509
(1.00) 		0.891
(1.00) 		0.327
(1.00) 		0.126
(1.00) 		0.491
(1.00) 		0.13
(1.00) 		0.598
(1.00) 		0.261
(1.00)
WDR52 16 (2%) 959 0.768
(1.00) 		0.0565
(1.00) 		0.22
(1.00) 		0.165
(1.00) 		0.00424
(1.00) 		0.137
(1.00) 		0.0134
(1.00) 		0.4
(1.00) 		0.303
(1.00) 		0.477
(1.00) 		0.0455
(1.00) 		0.547
(1.00)
CDC42EP1 5 (1%) 970 0.579
(1.00) 		0.452
(1.00) 		0.638
(1.00) 		0.242
(1.00) 		0.836
(1.00) 		0.829
(1.00) 		0.276
(1.00) 		0.536
(1.00) 		0.707
(1.00) 		0.124
(1.00)
ERBB3 18 (2%) 957 0.412
(1.00) 		0.225
(1.00) 		0.867
(1.00) 		0.522
(1.00) 		0.335
(1.00) 		0.298
(1.00) 		0.031
(1.00) 		0.211
(1.00) 		0.143
(1.00) 		0.81
(1.00) 		1
(1.00) 		0.817
(1.00)
FHOD3 13 (1%) 962 0.0431
(1.00) 		0.0205
(1.00) 		0.162
(1.00) 		0.0262
(1.00) 		0.385
(1.00) 		0.0261
(1.00) 		0.129
(1.00) 		0.00296
(1.00) 		0.17
(1.00) 		0.02
(1.00) 		0.7
(1.00) 		0.0408
(1.00)
PTHLH 7 (1%) 968 0.442
(1.00) 		0.358
(1.00) 		0.00881
(1.00) 		0.0533
(1.00) 		0.69
(1.00) 		0.392
(1.00) 		0.721
(1.00) 		0.341
(1.00) 		0.231
(1.00) 		0.29
(1.00)
SHISA4 5 (1%) 970 0.0213
(1.00) 		0.203
(1.00) 		0.218
(1.00) 		0.266
(1.00) 		0.272
(1.00) 		0.454
(1.00) 		0.342
(1.00) 		1
(1.00)
KCNN3 9 (1%) 966 0.321
(1.00) 		0.839
(1.00) 		0.212
(1.00) 		0.27
(1.00) 		0.328
(1.00) 		0.144
(1.00) 		0.326
(1.00) 		0.236
(1.00) 		0.409
(1.00) 		0.906
(1.00) 		0.165
(1.00) 		0.613
(1.00)
FGFR2 11 (1%) 964 0.841
(1.00) 		0.876
(1.00) 		0.829
(1.00) 		0.208
(1.00) 		1
(1.00) 		1
(1.00) 		0.443
(1.00) 		0.796
(1.00) 		0.666
(1.00) 		1
(1.00) 		0.803
(1.00) 		0.593
(1.00)
HLA-DRB5 6 (1%) 969 0.00723
(1.00) 		0.0135
(1.00) 		0.248
(1.00) 		0.876
(1.00) 		0.253
(1.00) 		0.77
(1.00) 		0.224
(1.00) 		1
(1.00) 		0.78
(1.00) 		1
(1.00)
ICOSLG 6 (1%) 969 0.693
(1.00) 		1
(1.00) 		0.0103
(1.00) 		0.623
(1.00) 		0.107
(1.00) 		1
(1.00) 		0.156
(1.00) 		1
(1.00) 		1
(1.00) 		0.607
(1.00)
GYG2 8 (1%) 967 0.703
(1.00) 		1
(1.00) 		0.165
(1.00) 		0.714
(1.00) 		0.156
(1.00) 		0.0398
(1.00) 		0.885
(1.00) 		0.907
(1.00) 		0.44
(1.00) 		1
(1.00) 		0.397
(1.00) 		0.191
(1.00)
PPEF1 11 (1%) 964 0.84
(1.00) 		1
(1.00) 		0.306
(1.00) 		0.575
(1.00) 		1
(1.00) 		1
(1.00) 		0.823
(1.00) 		0.634
(1.00) 		0.259
(1.00) 		0.33
(1.00) 		0.803
(1.00) 		0.785
(1.00)
MAP4K1 10 (1%) 965 0.828
(1.00) 		0.452
(1.00) 		0.358
(1.00) 		0.577
(1.00) 		1
(1.00) 		0.782
(1.00) 		0.434
(1.00) 		0.849
(1.00) 		0.963
(1.00) 		0.326
(1.00) 		0.239
(1.00) 		0.207
(1.00)
ZNF41 11 (1%) 964 0.81
(1.00) 		0.465
(1.00) 		0.656
(1.00) 		0.207
(1.00) 		0.877
(1.00) 		0.291
(1.00) 		0.693
(1.00) 		0.471
(1.00) 		0.0401
(1.00) 		0.848
(1.00) 		0.0924
(1.00) 		0.645
(1.00)
HRNR 31 (3%) 944 0.892
(1.00) 		0.46
(1.00) 		0.0636
(1.00) 		0.975
(1.00) 		0.587
(1.00) 		0.588
(1.00) 		0.931
(1.00) 		0.482
(1.00) 		0.516
(1.00) 		0.878
(1.00) 		0.938
(1.00) 		0.763
(1.00)
STAG2 13 (1%) 962 0.357
(1.00) 		1
(1.00) 		0.226
(1.00) 		0.337
(1.00) 		0.877
(1.00) 		0.676
(1.00) 		0.323
(1.00) 		0.727
(1.00) 		0.307
(1.00) 		0.453
(1.00) 		0.508
(1.00) 		0.687
(1.00)
CEP57 6 (1%) 969 0.324
(1.00) 		1
(1.00) 		0.112
(1.00) 		0.129
(1.00) 		0.154
(1.00) 		1
(1.00) 		0.388
(1.00) 		0.0622
(1.00) 		0.293
(1.00) 		0.0267
(1.00)
SPRR2B 3 (0%) 972 0.734
(1.00) 		0.505
(1.00) 		0.795
(1.00) 		0.909
(1.00) 		0.43
(1.00)
ZFP36L2 7 (1%) 968 0.437
(1.00) 		1
(1.00) 		0.00951
(1.00) 		0.206
(1.00) 		1
(1.00) 		1
(1.00) 		0.499
(1.00) 		0.798
(1.00) 		0.66
(1.00) 		0.781
(1.00) 		1
(1.00) 		0.836
(1.00)
DMXL2 19 (2%) 956 0.697
(1.00) 		0.182
(1.00) 		0.0502
(1.00) 		0.158
(1.00) 		0.107
(1.00) 		0.0727
(1.00) 		0.00947
(1.00) 		0.0697
(1.00) 		0.0505
(1.00) 		0.221
(1.00) 		0.085
(1.00) 		0.137
(1.00)
ZBTB7C 5 (1%) 970 0.682
(1.00) 		0.746
(1.00) 		0.811
(1.00) 		0.38
(1.00) 		0.675
(1.00) 		0.498
(1.00) 		0.78
(1.00) 		1
(1.00)
MUC5B 33 (3%) 942 0.694
(1.00) 		0.879
(1.00) 		0.414
(1.00) 		0.285
(1.00) 		0.915
(1.00) 		0.695
(1.00) 		0.371
(1.00) 		0.759
(1.00) 		0.779
(1.00) 		0.21
(1.00) 		0.746
(1.00) 		0.83
(1.00)
XBP1 4 (0%) 971 0.0164
(1.00) 		0.36
(1.00) 		0.347
(1.00) 		1
(1.00) 		0.394
(1.00) 		0.532
(1.00) 		0.393
(1.00) 		0.812
(1.00)
FXYD5 5 (1%) 970 0.693
(1.00) 		0.615
(1.00) 		0.335
(1.00) 		0.643
(1.00) 		1
(1.00) 		0.31
(1.00) 		0.454
(1.00) 		0.756
(1.00) 		0.498
(1.00)
ATXN2 15 (2%) 960 0.837
(1.00) 		0.366
(1.00) 		0.392
(1.00) 		0.642
(1.00) 		0.234
(1.00) 		0.0766
(1.00) 		0.757
(1.00) 		0.364
(1.00) 		0.538
(1.00) 		0.342
(1.00) 		0.793
(1.00) 		0.916
(1.00)
'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 7.32e-13 (Chi-square test), Q value = 5.9e-10

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 = 3.48e-10 (Fisher's exact test), Q value = 2.8e-07

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
PIK3CA MUTATED 62 16 86
PIK3CA WILD-TYPE 60 110 175

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 = 3.25e-13 (Chi-square test), Q value = 2.6e-10

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 353 239 94 233 42
PIK3CA MUTATED 142 56 56 49 11
PIK3CA WILD-TYPE 211 183 38 184 31

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 = 4.27e-12 (Chi-square test), Q value = 3.4e-09

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 111 163 95 121 54 103
PIK3CA MUTATED 6 79 39 32 20 32
PIK3CA WILD-TYPE 105 84 56 89 34 71

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 = 0.00017 (Fisher's exact test), Q value = 0.13

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
PIK3CA MUTATED 27 49 46
PIK3CA WILD-TYPE 118 81 72

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 = 5.38e-06 (Fisher's exact test), Q value = 0.0042

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
PIK3CA MUTATED 52 50 20
PIK3CA WILD-TYPE 102 63 106

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 = 9.78e-29 (Chi-square test), Q value = 8e-26

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
PIK3CA MUTATED 10 35 138 61 53 19
PIK3CA WILD-TYPE 171 59 106 101 190 28

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 = 1.66e-19 (Fisher's exact test), Q value = 1.3e-16

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
PIK3CA MUTATED 154 134 28
PIK3CA WILD-TYPE 166 283 206

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 = 1.32e-07 (Chi-square test), Q value = 1e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
PIK3CA MUTATED 82 55 84 42 37 14
PIK3CA WILD-TYPE 114 101 123 192 95 17

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 = 2.46e-13 (Fisher's exact test), Q value = 2e-10

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
PIK3CA MUTATED 192 38 84
PIK3CA WILD-TYPE 319 217 106

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 = 1.26e-07 (Fisher's exact test), Q value = 1e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
PIK3CA MUTATED 94 83 34
PIK3CA WILD-TYPE 153 124 163

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 = 2.62e-12 (Fisher's exact test), Q value = 2.1e-09

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
PIK3CA MUTATED 16 121 74
PIK3CA WILD-TYPE 134 220 86

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

'CBFB MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.134 (Chi-square test), Q value = 1

Table S13.  Gene #2: '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 6 2 0 0
CBFB WILD-TYPE 20 37 114 96 102 71 19 39
'CBFB MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.925 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
CBFB MUTATED 3 2 6
CBFB WILD-TYPE 119 124 255
'CBFB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0228 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
CBFB MUTATED 13 4 5 1 0
CBFB WILD-TYPE 340 235 89 232 42

Figure S13.  Get High-res Image Gene #2: 'CBFB MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CBFB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 9.16e-05 (Chi-square test), Q value = 0.072

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
CBFB MUTATED 0 12 2 0 0 1
CBFB WILD-TYPE 111 151 93 121 54 102

Figure S14.  Get High-res Image Gene #2: 'CBFB MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CBFB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.124 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
CBFB MUTATED 1 6 3
CBFB WILD-TYPE 144 124 115
'CBFB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
CBFB MUTATED 6 2 2
CBFB WILD-TYPE 148 111 124
'CBFB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 9.44e-06 (Chi-square test), Q value = 0.0074

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
CBFB MUTATED 1 2 17 2 1 0
CBFB WILD-TYPE 180 92 227 160 242 47

Figure S15.  Get High-res Image Gene #2: 'CBFB MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CBFB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.045 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
CBFB MUTATED 13 8 2
CBFB WILD-TYPE 307 409 232

Figure S16.  Get High-res Image Gene #2: 'CBFB MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CBFB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.541 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
CBFB MUTATED 6 5 6 2 2 1
CBFB WILD-TYPE 190 151 201 232 130 30
'CBFB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00367 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
CBFB MUTATED 16 0 6
CBFB WILD-TYPE 495 255 184

Figure S17.  Get High-res Image Gene #2: 'CBFB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CBFB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00358 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
CBFB MUTATED 11 4 0
CBFB WILD-TYPE 236 203 197

Figure S18.  Get High-res Image Gene #2: 'CBFB MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'CBFB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00427 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
CBFB MUTATED 0 14 1
CBFB WILD-TYPE 150 327 159

Figure S19.  Get High-res Image Gene #2: 'CBFB MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RUNX1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0149 (Chi-square test), Q value = 1

Table S25.  Gene #3: '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 S20.  Get High-res Image Gene #3: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'RUNX1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0452 (Fisher's exact test), Q value = 1

Table S26.  Gene #3: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
RUNX1 MUTATED 8 1 9
RUNX1 WILD-TYPE 114 125 252

Figure S21.  Get High-res Image Gene #3: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'RUNX1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0018 (Chi-square test), Q value = 1

Table S27.  Gene #3: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
RUNX1 MUTATED 16 3 7 2 0
RUNX1 WILD-TYPE 337 236 87 231 42

Figure S22.  Get High-res Image Gene #3: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'RUNX1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0766 (Chi-square test), Q value = 1

Table S28.  Gene #3: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
RUNX1 MUTATED 2 4 4 0 4 5
RUNX1 WILD-TYPE 109 159 91 121 50 98
'RUNX1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S29.  Gene #3: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
RUNX1 MUTATED 4 3 3
RUNX1 WILD-TYPE 141 127 115
'RUNX1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.285 (Fisher's exact test), Q value = 1

Table S30.  Gene #3: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
RUNX1 MUTATED 5 4 1
RUNX1 WILD-TYPE 149 109 125
'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0185 (Chi-square test), Q value = 1

Table S31.  Gene #3: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
RUNX1 MUTATED 1 4 14 6 3 1
RUNX1 WILD-TYPE 180 90 230 156 240 46

Figure S23.  Get High-res Image Gene #3: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0984 (Fisher's exact test), Q value = 1

Table S32.  Gene #3: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
RUNX1 MUTATED 15 10 4
RUNX1 WILD-TYPE 305 407 230
'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0389 (Chi-square test), Q value = 1

Table S33.  Gene #3: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
RUNX1 MUTATED 10 7 4 1 5 2
RUNX1 WILD-TYPE 186 149 203 233 127 29

Figure S24.  Get High-res Image Gene #3: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S34.  Gene #3: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
RUNX1 MUTATED 18 4 7
RUNX1 WILD-TYPE 493 251 183
'RUNX1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.157 (Fisher's exact test), Q value = 1

Table S35.  Gene #3: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
RUNX1 MUTATED 7 10 3
RUNX1 WILD-TYPE 240 197 194
'RUNX1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S36.  Gene #3: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
RUNX1 MUTATED 1 10 9
RUNX1 WILD-TYPE 149 331 151

Figure S25.  Get High-res Image Gene #3: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 6.02e-06 (Chi-square test), Q value = 0.0047

Table S37.  Gene #4: '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 S26.  Get High-res Image Gene #4: 'GATA3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'GATA3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1.91e-07 (Fisher's exact test), Q value = 0.00015

Table S38.  Gene #4: 'GATA3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
GATA3 MUTATED 12 1 47
GATA3 WILD-TYPE 110 125 214

Figure S27.  Get High-res Image Gene #4: 'GATA3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00139 (Chi-square test), Q value = 1

Table S39.  Gene #4: 'GATA3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
GATA3 MUTATED 42 32 12 9 1
GATA3 WILD-TYPE 311 207 82 224 41

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

'GATA3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00251 (Chi-square test), Q value = 1

Table S40.  Gene #4: 'GATA3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
GATA3 MUTATED 0 20 11 14 7 5
GATA3 WILD-TYPE 111 143 84 107 47 98

Figure S29.  Get High-res Image Gene #4: 'GATA3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'GATA3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 1

Table S41.  Gene #4: 'GATA3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
GATA3 MUTATED 12 24 10
GATA3 WILD-TYPE 133 106 108

Figure S30.  Get High-res Image Gene #4: 'GATA3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'GATA3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.000929 (Fisher's exact test), Q value = 0.72

Table S42.  Gene #4: 'GATA3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
GATA3 MUTATED 29 11 6
GATA3 WILD-TYPE 125 102 120

Figure S31.  Get High-res Image Gene #4: 'GATA3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.79e-08 (Chi-square test), Q value = 1.4e-05

Table S43.  Gene #4: 'GATA3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
GATA3 MUTATED 1 8 35 7 42 3
GATA3 WILD-TYPE 180 86 209 155 201 44

Figure S32.  Get High-res Image Gene #4: 'GATA3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'GATA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.11e-12 (Fisher's exact test), Q value = 8.9e-10

Table S44.  Gene #4: 'GATA3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
GATA3 MUTATED 34 62 0
GATA3 WILD-TYPE 286 355 234

Figure S33.  Get High-res Image Gene #4: 'GATA3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00178 (Chi-square test), Q value = 1

Table S45.  Gene #4: 'GATA3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
GATA3 MUTATED 27 11 22 10 19 6
GATA3 WILD-TYPE 169 145 185 224 113 25

Figure S34.  Get High-res Image Gene #4: 'GATA3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.98e-10 (Fisher's exact test), Q value = 3.2e-07

Table S46.  Gene #4: 'GATA3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
GATA3 MUTATED 77 4 14
GATA3 WILD-TYPE 434 251 176

Figure S35.  Get High-res Image Gene #4: 'GATA3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.2e-08 (Fisher's exact test), Q value = 9.5e-06

Table S47.  Gene #4: 'GATA3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
GATA3 MUTATED 46 17 4
GATA3 WILD-TYPE 201 190 193

Figure S36.  Get High-res Image Gene #4: 'GATA3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'GATA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.63e-11 (Fisher's exact test), Q value = 4.5e-08

Table S48.  Gene #4: 'GATA3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
GATA3 MUTATED 0 58 9
GATA3 WILD-TYPE 150 283 151

Figure S37.  Get High-res Image Gene #4: 'GATA3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'FOXA1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.356 (Chi-square test), Q value = 1

Table S49.  Gene #5: '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 = 0.238 (Fisher's exact test), Q value = 1

Table S50.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
FOXA1 MUTATED 2 0 6
FOXA1 WILD-TYPE 120 126 255
'FOXA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.289 (Chi-square test), Q value = 1

Table S51.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
FOXA1 MUTATED 13 5 2 2 1
FOXA1 WILD-TYPE 340 234 92 231 41
'FOXA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0393 (Chi-square test), Q value = 1

Table S52.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
FOXA1 MUTATED 0 4 7 3 1 2
FOXA1 WILD-TYPE 111 159 88 118 53 101

Figure S38.  Get High-res Image Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'FOXA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.894 (Fisher's exact test), Q value = 1

Table S53.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
FOXA1 MUTATED 2 3 2
FOXA1 WILD-TYPE 143 127 116
'FOXA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.309 (Fisher's exact test), Q value = 1

Table S54.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
FOXA1 MUTATED 5 1 1
FOXA1 WILD-TYPE 149 112 125
'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.127 (Chi-square test), Q value = 1

Table S55.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
FOXA1 MUTATED 1 1 9 3 6 3
FOXA1 WILD-TYPE 180 93 235 159 237 44
'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.053 (Fisher's exact test), Q value = 1

Table S56.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
FOXA1 MUTATED 10 12 1
FOXA1 WILD-TYPE 310 405 233
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.319 (Chi-square test), Q value = 1

Table S57.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
FOXA1 MUTATED 4 6 6 4 1 2
FOXA1 WILD-TYPE 192 150 201 230 131 29
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0882 (Fisher's exact test), Q value = 1

Table S58.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
FOXA1 MUTATED 14 2 7
FOXA1 WILD-TYPE 497 253 183
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0673 (Fisher's exact test), Q value = 1

Table S59.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
FOXA1 MUTATED 9 7 1
FOXA1 WILD-TYPE 238 200 196
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S60.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
FOXA1 MUTATED 2 11 4
FOXA1 WILD-TYPE 148 330 156
'SF3B1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.815 (Chi-square test), Q value = 1

Table S61.  Gene #6: '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 = 0.298 (Fisher's exact test), Q value = 1

Table S62.  Gene #6: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
SF3B1 MUTATED 4 1 3
SF3B1 WILD-TYPE 118 125 258
'SF3B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.376 (Chi-square test), Q value = 1

Table S63.  Gene #6: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
SF3B1 MUTATED 5 7 2 2 0
SF3B1 WILD-TYPE 348 232 92 231 42
'SF3B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.172 (Chi-square test), Q value = 1

Table S64.  Gene #6: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
SF3B1 MUTATED 0 6 3 4 1 0
SF3B1 WILD-TYPE 111 157 92 117 53 103
'SF3B1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.45 (Fisher's exact test), Q value = 1

Table S65.  Gene #6: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
SF3B1 MUTATED 1 1 3
SF3B1 WILD-TYPE 144 129 115
'SF3B1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0246 (Fisher's exact test), Q value = 1

Table S66.  Gene #6: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
SF3B1 MUTATED 0 4 1
SF3B1 WILD-TYPE 154 109 125

Figure S39.  Get High-res Image Gene #6: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.655 (Chi-square test), Q value = 1

Table S67.  Gene #6: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
SF3B1 MUTATED 1 2 6 3 4 0
SF3B1 WILD-TYPE 180 92 238 159 239 47
'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.243 (Fisher's exact test), Q value = 1

Table S68.  Gene #6: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
SF3B1 MUTATED 6 9 1
SF3B1 WILD-TYPE 314 408 233
'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.885 (Chi-square test), Q value = 1

Table S69.  Gene #6: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
SF3B1 MUTATED 4 3 4 2 2 1
SF3B1 WILD-TYPE 192 153 203 232 130 30
'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S70.  Gene #6: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
SF3B1 MUTATED 9 3 4
SF3B1 WILD-TYPE 502 252 186
'SF3B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.612 (Fisher's exact test), Q value = 1

Table S71.  Gene #6: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
SF3B1 MUTATED 4 3 1
SF3B1 WILD-TYPE 243 204 196
'SF3B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.323 (Fisher's exact test), Q value = 1

Table S72.  Gene #6: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
SF3B1 MUTATED 0 5 3
SF3B1 WILD-TYPE 150 336 157
'MAP3K1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 9.82e-05 (Chi-square test), Q value = 0.077

Table S73.  Gene #7: '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 3
MAP3K1 WILD-TYPE 16 37 102 96 92 72 19 36

Figure S40.  Get High-res Image Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.000689 (Fisher's exact test), Q value = 0.53

Table S74.  Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
MAP3K1 MUTATED 12 1 26
MAP3K1 WILD-TYPE 110 125 235

Figure S41.  Get High-res Image Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0029 (Chi-square test), Q value = 1

Table S75.  Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
MAP3K1 MUTATED 39 14 7 6 4
MAP3K1 WILD-TYPE 314 225 87 227 38

Figure S42.  Get High-res Image Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'MAP3K1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.034 (Chi-square test), Q value = 1

Table S76.  Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
MAP3K1 MUTATED 2 17 2 7 3 7
MAP3K1 WILD-TYPE 109 146 93 114 51 96

Figure S43.  Get High-res Image Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MAP3K1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.53

Table S77.  Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
MAP3K1 MUTATED 4 20 12
MAP3K1 WILD-TYPE 141 110 106

Figure S44.  Get High-res Image Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'MAP3K1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 3.81e-05 (Fisher's exact test), Q value = 0.03

Table S78.  Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
MAP3K1 MUTATED 20 15 1
MAP3K1 WILD-TYPE 134 98 125

Figure S45.  Get High-res Image Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000166 (Chi-square test), Q value = 0.13

Table S79.  Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
MAP3K1 MUTATED 4 6 31 4 22 3
MAP3K1 WILD-TYPE 177 88 213 158 221 44

Figure S46.  Get High-res Image Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000178 (Fisher's exact test), Q value = 0.14

Table S80.  Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
MAP3K1 MUTATED 28 38 4
MAP3K1 WILD-TYPE 292 379 230

Figure S47.  Get High-res Image Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0083 (Chi-square test), Q value = 1

Table S81.  Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
MAP3K1 MUTATED 14 13 24 5 11 3
MAP3K1 WILD-TYPE 182 143 183 229 121 28

Figure S48.  Get High-res Image Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.11

Table S82.  Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
MAP3K1 MUTATED 41 6 23
MAP3K1 WILD-TYPE 470 249 167

Figure S49.  Get High-res Image Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000214 (Fisher's exact test), Q value = 0.17

Table S83.  Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
MAP3K1 MUTATED 25 19 3
MAP3K1 WILD-TYPE 222 188 194

Figure S50.  Get High-res Image Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00905 (Fisher's exact test), Q value = 1

Table S84.  Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
MAP3K1 MUTATED 3 31 13
MAP3K1 WILD-TYPE 147 310 147

Figure S51.  Get High-res Image Gene #7: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 2.35e-31 (Chi-square test), Q value = 1.9e-28

Table S85.  Gene #8: '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 73 6 41 7 6
TP53 WILD-TYPE 14 32 96 24 102 32 12 33

Figure S52.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 2.14e-29 (Fisher's exact test), Q value = 1.7e-26

Table S86.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
TP53 MUTATED 15 93 56
TP53 WILD-TYPE 107 33 205

Figure S53.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 4.49e-56 (Chi-square test), Q value = 3.7e-53

Table S87.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
TP53 MUTATED 47 58 9 168 10
TP53 WILD-TYPE 306 181 85 65 32

Figure S54.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.26e-32 (Chi-square test), Q value = 1e-29

Table S88.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
TP53 MUTATED 83 10 28 30 8 31
TP53 WILD-TYPE 28 153 67 91 46 72

Figure S55.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 4.63e-23 (Fisher's exact test), Q value = 3.8e-20

Table S89.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
TP53 MUTATED 93 11 33
TP53 WILD-TYPE 52 119 85

Figure S56.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 2.58e-23 (Fisher's exact test), Q value = 2.1e-20

Table S90.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
TP53 MUTATED 30 18 89
TP53 WILD-TYPE 124 95 37

Figure S57.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 5.53e-71 (Chi-square test), Q value = 4.6e-68

Table S91.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
TP53 MUTATED 133 11 18 94 29 8
TP53 WILD-TYPE 48 83 226 68 214 39

Figure S58.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.89e-63 (Fisher's exact test), Q value = 1.6e-60

Table S92.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
TP53 MUTATED 31 88 174
TP53 WILD-TYPE 289 329 60

Figure S59.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2.23e-43 (Chi-square test), Q value = 1.8e-40

Table S93.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
TP53 MUTATED 45 24 17 153 44 5
TP53 WILD-TYPE 151 132 190 81 88 26

Figure S60.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.04e-58 (Fisher's exact test), Q value = 5.8e-55

Table S94.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
TP53 MUTATED 88 180 20
TP53 WILD-TYPE 423 75 170

Figure S61.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.87e-41 (Fisher's exact test), Q value = 1.5e-38

Table S95.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
TP53 MUTATED 43 20 133
TP53 WILD-TYPE 204 187 64

Figure S62.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.35e-35 (Fisher's exact test), Q value = 1.9e-32

Table S96.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
TP53 MUTATED 108 70 18
TP53 WILD-TYPE 42 271 142

Figure S63.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MAP2K4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.123 (Chi-square test), Q value = 1

Table S97.  Gene #9: '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 = 0.00395 (Fisher's exact test), Q value = 1

Table S98.  Gene #9: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
MAP2K4 MUTATED 9 0 10
MAP2K4 WILD-TYPE 113 126 251

Figure S64.  Get High-res Image Gene #9: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'MAP2K4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.189 (Chi-square test), Q value = 1

Table S99.  Gene #9: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
MAP2K4 MUTATED 13 8 6 3 2
MAP2K4 WILD-TYPE 340 231 88 230 40
'MAP2K4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0204 (Chi-square test), Q value = 1

Table S100.  Gene #9: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
MAP2K4 MUTATED 0 10 3 9 2 1
MAP2K4 WILD-TYPE 111 153 92 112 52 102

Figure S65.  Get High-res Image Gene #9: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MAP2K4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00262 (Fisher's exact test), Q value = 1

Table S101.  Gene #9: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
MAP2K4 MUTATED 0 5 8
MAP2K4 WILD-TYPE 145 125 110

Figure S66.  Get High-res Image Gene #9: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'MAP2K4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0298 (Fisher's exact test), Q value = 1

Table S102.  Gene #9: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
MAP2K4 MUTATED 4 8 1
MAP2K4 WILD-TYPE 150 105 125

Figure S67.  Get High-res Image Gene #9: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'MAP2K4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00977 (Chi-square test), Q value = 1

Table S103.  Gene #9: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
MAP2K4 MUTATED 0 2 14 4 12 0
MAP2K4 WILD-TYPE 181 92 230 158 231 47

Figure S68.  Get High-res Image Gene #9: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'MAP2K4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000198 (Fisher's exact test), Q value = 0.15

Table S104.  Gene #9: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
MAP2K4 MUTATED 10 22 0
MAP2K4 WILD-TYPE 310 395 234

Figure S69.  Get High-res Image Gene #9: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00448 (Chi-square test), Q value = 1

Table S105.  Gene #9: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
MAP2K4 MUTATED 14 3 8 1 4 2
MAP2K4 WILD-TYPE 182 153 199 233 128 29

Figure S70.  Get High-res Image Gene #9: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000294 (Fisher's exact test), Q value = 0.23

Table S106.  Gene #9: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
MAP2K4 MUTATED 28 2 2
MAP2K4 WILD-TYPE 483 253 188

Figure S71.  Get High-res Image Gene #9: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.58e-05 (Fisher's exact test), Q value = 0.02

Table S107.  Gene #9: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
MAP2K4 MUTATED 17 3 0
MAP2K4 WILD-TYPE 230 204 197

Figure S72.  Get High-res Image Gene #9: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00129 (Fisher's exact test), Q value = 0.99

Table S108.  Gene #9: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
MAP2K4 MUTATED 0 18 2
MAP2K4 WILD-TYPE 150 323 158

Figure S73.  Get High-res Image Gene #9: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.28 (Chi-square test), Q value = 1

Table S109.  Gene #10: '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 = 0.658 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
PTEN MUTATED 4 2 7
PTEN WILD-TYPE 118 124 254
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.29 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
PTEN MUTATED 13 6 7 8 1
PTEN WILD-TYPE 340 233 87 225 41
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.419 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
PTEN MUTATED 5 7 6 4 0 7
PTEN WILD-TYPE 106 156 89 117 54 96
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.922 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
PTEN MUTATED 3 4 3
PTEN WILD-TYPE 142 126 115
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.667 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
PTEN MUTATED 5 3 2
PTEN WILD-TYPE 149 110 124
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.474 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
PTEN MUTATED 4 5 9 9 6 2
PTEN WILD-TYPE 177 89 235 153 237 45
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.665 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
PTEN MUTATED 14 13 8
PTEN WILD-TYPE 306 404 226
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.118 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
PTEN MUTATED 9 11 6 5 4 0
PTEN WILD-TYPE 187 145 201 229 128 31
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
PTEN MUTATED 17 9 9
PTEN WILD-TYPE 494 246 181
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.486 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
PTEN MUTATED 7 10 9
PTEN WILD-TYPE 240 197 188
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.744 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
PTEN MUTATED 7 12 7
PTEN WILD-TYPE 143 329 153
'CDH1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.000174 (Chi-square test), Q value = 0.14

Table S121.  Gene #11: '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 6 1 7
CDH1 WILD-TYPE 21 32 113 96 98 67 18 32

Figure S74.  Get High-res Image Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00336 (Fisher's exact test), Q value = 1

Table S122.  Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
CDH1 MUTATED 16 4 12
CDH1 WILD-TYPE 106 122 249

Figure S75.  Get High-res Image Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 3.71e-15 (Chi-square test), Q value = 3e-12

Table S123.  Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
CDH1 MUTATED 61 11 25 2 4
CDH1 WILD-TYPE 292 228 69 231 38

Figure S76.  Get High-res Image Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2.58e-08 (Chi-square test), Q value = 2e-05

Table S124.  Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
CDH1 MUTATED 0 31 19 3 8 21
CDH1 WILD-TYPE 111 132 76 118 46 82

Figure S77.  Get High-res Image Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CDH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00404 (Fisher's exact test), Q value = 1

Table S125.  Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
CDH1 MUTATED 4 4 14
CDH1 WILD-TYPE 141 126 104

Figure S78.  Get High-res Image Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'CDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 1

Table S126.  Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
CDH1 MUTATED 5 13 4
CDH1 WILD-TYPE 149 100 122

Figure S79.  Get High-res Image Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.04e-17 (Chi-square test), Q value = 8.4e-15

Table S127.  Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
CDH1 MUTATED 1 24 44 9 12 15
CDH1 WILD-TYPE 180 70 200 153 231 32

Figure S80.  Get High-res Image Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.89e-18 (Fisher's exact test), Q value = 7.2e-15

Table S128.  Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
CDH1 MUTATED 75 25 5
CDH1 WILD-TYPE 245 392 229

Figure S81.  Get High-res Image Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2.5e-17 (Chi-square test), Q value = 2e-14

Table S129.  Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
CDH1 MUTATED 13 44 34 2 8 2
CDH1 WILD-TYPE 183 112 173 232 124 29

Figure S82.  Get High-res Image Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.62e-25 (Fisher's exact test), Q value = 2.1e-22

Table S130.  Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
CDH1 MUTATED 37 3 63
CDH1 WILD-TYPE 474 252 127

Figure S83.  Get High-res Image Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.21e-21 (Fisher's exact test), Q value = 1.8e-18

Table S131.  Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
CDH1 MUTATED 13 64 3
CDH1 WILD-TYPE 234 143 194

Figure S84.  Get High-res Image Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.03e-19 (Fisher's exact test), Q value = 1.6e-16

Table S132.  Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
CDH1 MUTATED 3 22 55
CDH1 WILD-TYPE 147 319 105

Figure S85.  Get High-res Image Gene #11: 'CDH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TBX3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.428 (Chi-square test), Q value = 1

Table S133.  Gene #12: '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 = 0.307 (Fisher's exact test), Q value = 1

Table S134.  Gene #12: 'TBX3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
TBX3 MUTATED 6 2 8
TBX3 WILD-TYPE 116 124 253
'TBX3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.435 (Chi-square test), Q value = 1

Table S135.  Gene #12: 'TBX3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
TBX3 MUTATED 13 6 4 3 1
TBX3 WILD-TYPE 340 233 90 230 41
'TBX3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.108 (Chi-square test), Q value = 1

Table S136.  Gene #12: 'TBX3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
TBX3 MUTATED 1 9 2 1 1 2
TBX3 WILD-TYPE 110 154 93 120 53 101
'TBX3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.083 (Fisher's exact test), Q value = 1

Table S137.  Gene #12: 'TBX3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
TBX3 MUTATED 1 3 6
TBX3 WILD-TYPE 144 127 112
'TBX3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.609 (Fisher's exact test), Q value = 1

Table S138.  Gene #12: 'TBX3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
TBX3 MUTATED 4 4 2
TBX3 WILD-TYPE 150 109 124
'TBX3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0604 (Chi-square test), Q value = 1

Table S139.  Gene #12: 'TBX3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
TBX3 MUTATED 3 6 10 1 5 2
TBX3 WILD-TYPE 178 88 234 161 238 45
'TBX3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0409 (Fisher's exact test), Q value = 1

Table S140.  Gene #12: 'TBX3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
TBX3 MUTATED 15 9 3
TBX3 WILD-TYPE 305 408 231

Figure S86.  Get High-res Image Gene #12: 'TBX3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TBX3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.137 (Chi-square test), Q value = 1

Table S141.  Gene #12: 'TBX3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
TBX3 MUTATED 3 6 11 4 2 1
TBX3 WILD-TYPE 193 150 196 230 130 30
'TBX3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0401 (Fisher's exact test), Q value = 1

Table S142.  Gene #12: 'TBX3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
TBX3 MUTATED 14 3 10
TBX3 WILD-TYPE 497 252 180

Figure S87.  Get High-res Image Gene #12: 'TBX3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TBX3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.279 (Fisher's exact test), Q value = 1

Table S143.  Gene #12: 'TBX3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
TBX3 MUTATED 6 7 2
TBX3 WILD-TYPE 241 200 195
'TBX3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.391 (Fisher's exact test), Q value = 1

Table S144.  Gene #12: 'TBX3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
TBX3 MUTATED 2 7 6
TBX3 WILD-TYPE 148 334 154
'MLL3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.598 (Chi-square test), Q value = 1

Table S145.  Gene #13: '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 1 1 8 5 12 4 1 4
MLL3 WILD-TYPE 20 37 106 92 96 69 18 35
'MLL3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S146.  Gene #13: 'MLL3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
MLL3 MUTATED 8 7 21
MLL3 WILD-TYPE 114 119 240
'MLL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.605 (Chi-square test), Q value = 1

Table S147.  Gene #13: 'MLL3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
MLL3 MUTATED 29 16 8 12 2
MLL3 WILD-TYPE 324 223 86 221 40
'MLL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.157 (Chi-square test), Q value = 1

Table S148.  Gene #13: 'MLL3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
MLL3 MUTATED 4 16 11 10 5 4
MLL3 WILD-TYPE 107 147 84 111 49 99
'MLL3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.597 (Fisher's exact test), Q value = 1

Table S149.  Gene #13: 'MLL3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
MLL3 MUTATED 10 6 9
MLL3 WILD-TYPE 135 124 109
'MLL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S150.  Gene #13: 'MLL3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
MLL3 MUTATED 10 6 9
MLL3 WILD-TYPE 144 107 117
'MLL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.182 (Chi-square test), Q value = 1

Table S151.  Gene #13: 'MLL3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
MLL3 MUTATED 8 4 23 13 20 1
MLL3 WILD-TYPE 173 90 221 149 223 46
'MLL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.234 (Fisher's exact test), Q value = 1

Table S152.  Gene #13: 'MLL3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
MLL3 MUTATED 21 36 12
MLL3 WILD-TYPE 299 381 222
'MLL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0613 (Chi-square test), Q value = 1

Table S153.  Gene #13: 'MLL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
MLL3 MUTATED 21 8 17 8 9 3
MLL3 WILD-TYPE 175 148 190 226 123 28
'MLL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0886 (Fisher's exact test), Q value = 1

Table S154.  Gene #13: 'MLL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
MLL3 MUTATED 44 12 10
MLL3 WILD-TYPE 467 243 180
'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.32 (Fisher's exact test), Q value = 1

Table S155.  Gene #13: 'MLL3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
MLL3 MUTATED 20 12 9
MLL3 WILD-TYPE 227 195 188
'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S156.  Gene #13: 'MLL3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
MLL3 MUTATED 8 24 9
MLL3 WILD-TYPE 142 317 151
'RB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.666 (Chi-square test), Q value = 1

Table S157.  Gene #14: '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 = 0.403 (Fisher's exact test), Q value = 1

Table S158.  Gene #14: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
RB1 MUTATED 1 4 5
RB1 WILD-TYPE 121 122 256
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0798 (Chi-square test), Q value = 1

Table S159.  Gene #14: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
RB1 MUTATED 3 4 4 8 0
RB1 WILD-TYPE 350 235 90 225 42
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0615 (Chi-square test), Q value = 1

Table S160.  Gene #14: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
RB1 MUTATED 5 2 3 0 1 0
RB1 WILD-TYPE 106 161 92 121 53 103
'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S161.  Gene #14: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
RB1 MUTATED 4 4 1
RB1 WILD-TYPE 141 126 117
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.763 (Fisher's exact test), Q value = 1

Table S162.  Gene #14: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
RB1 MUTATED 3 2 4
RB1 WILD-TYPE 151 111 122
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.149 (Chi-square test), Q value = 1

Table S163.  Gene #14: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
RB1 MUTATED 7 0 4 5 3 0
RB1 WILD-TYPE 174 94 240 157 240 47
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0564 (Fisher's exact test), Q value = 1

Table S164.  Gene #14: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
RB1 MUTATED 3 7 9
RB1 WILD-TYPE 317 410 225
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.272 (Chi-square test), Q value = 1

Table S165.  Gene #14: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
RB1 MUTATED 3 0 2 6 4 1
RB1 WILD-TYPE 193 156 205 228 128 30
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00282 (Fisher's exact test), Q value = 1

Table S166.  Gene #14: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
RB1 MUTATED 6 10 0
RB1 WILD-TYPE 505 245 190

Figure S88.  Get High-res Image Gene #14: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 1

Table S167.  Gene #14: 'RB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
RB1 MUTATED 5 0 7
RB1 WILD-TYPE 242 207 190

Figure S89.  Get High-res Image Gene #14: 'RB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.318 (Fisher's exact test), Q value = 1

Table S168.  Gene #14: 'RB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
RB1 MUTATED 5 5 2
RB1 WILD-TYPE 145 336 158
'NCOR1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.571 (Chi-square test), Q value = 1

Table S169.  Gene #15: '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 7 3 0 0
NCOR1 WILD-TYPE 21 36 110 94 101 70 19 39
'NCOR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S170.  Gene #15: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
NCOR1 MUTATED 5 4 10
NCOR1 WILD-TYPE 117 122 251
'NCOR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.71 (Chi-square test), Q value = 1

Table S171.  Gene #15: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
NCOR1 MUTATED 17 11 2 8 1
NCOR1 WILD-TYPE 336 228 92 225 41
'NCOR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.944 (Chi-square test), Q value = 1

Table S172.  Gene #15: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
NCOR1 MUTATED 4 8 6 5 3 4
NCOR1 WILD-TYPE 107 155 89 116 51 99
'NCOR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.435 (Fisher's exact test), Q value = 1

Table S173.  Gene #15: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
NCOR1 MUTATED 5 2 5
NCOR1 WILD-TYPE 140 128 113
'NCOR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S174.  Gene #15: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
NCOR1 MUTATED 2 6 4
NCOR1 WILD-TYPE 152 107 122
'NCOR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.398 (Chi-square test), Q value = 1

Table S175.  Gene #15: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
NCOR1 MUTATED 6 4 12 11 6 2
NCOR1 WILD-TYPE 175 90 232 151 237 45
'NCOR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.77 (Fisher's exact test), Q value = 1

Table S176.  Gene #15: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
NCOR1 MUTATED 15 18 8
NCOR1 WILD-TYPE 305 399 226
'NCOR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.64 (Chi-square test), Q value = 1

Table S177.  Gene #15: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
NCOR1 MUTATED 11 6 7 12 3 2
NCOR1 WILD-TYPE 185 150 200 222 129 29
'NCOR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.572 (Fisher's exact test), Q value = 1

Table S178.  Gene #15: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
NCOR1 MUTATED 24 8 9
NCOR1 WILD-TYPE 487 247 181
'NCOR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S179.  Gene #15: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
NCOR1 MUTATED 9 8 7
NCOR1 WILD-TYPE 238 199 190
'NCOR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.554 (Fisher's exact test), Q value = 1

Table S180.  Gene #15: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
NCOR1 MUTATED 4 12 8
NCOR1 WILD-TYPE 146 329 152
'CTCF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0331 (Chi-square test), Q value = 1

Table S181.  Gene #16: '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

Figure S90.  Get High-res Image Gene #16: 'CTCF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CTCF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.322 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
CTCF MUTATED 3 1 9
CTCF WILD-TYPE 119 125 252
'CTCF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0412 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
CTCF MUTATED 12 3 0 1 1
CTCF WILD-TYPE 341 236 94 232 41

Figure S91.  Get High-res Image Gene #16: 'CTCF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CTCF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00932 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
CTCF MUTATED 0 8 1 0 0 2
CTCF WILD-TYPE 111 155 94 121 54 101

Figure S92.  Get High-res Image Gene #16: 'CTCF MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CTCF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0685 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
CTCF MUTATED 1 7 3
CTCF WILD-TYPE 144 123 115
'CTCF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.297 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
CTCF MUTATED 7 2 2
CTCF WILD-TYPE 147 111 124
'CTCF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.577 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
CTCF MUTATED 1 2 5 2 5 2
CTCF WILD-TYPE 180 92 239 160 238 45
'CTCF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.191 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
CTCF MUTATED 7 9 1
CTCF WILD-TYPE 313 408 233
'CTCF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.13 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
CTCF MUTATED 4 2 8 1 2 0
CTCF WILD-TYPE 192 154 199 233 130 31
'CTCF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0475 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
CTCF MUTATED 14 1 2
CTCF WILD-TYPE 497 254 188

Figure S93.  Get High-res Image Gene #16: 'CTCF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
CTCF MUTATED 5 2 2
CTCF WILD-TYPE 242 205 195
'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
CTCF MUTATED 1 7 1
CTCF WILD-TYPE 149 334 159
'GPS2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00133 (Chi-square test), Q value = 1

Table S193.  Gene #17: '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 4 2 0 1 0 0 1
GPS2 WILD-TYPE 21 34 112 97 107 73 19 38

Figure S94.  Get High-res Image Gene #17: 'GPS2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'GPS2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00592 (Fisher's exact test), Q value = 1

Table S194.  Gene #17: 'GPS2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
GPS2 MUTATED 6 0 2
GPS2 WILD-TYPE 116 126 259

Figure S95.  Get High-res Image Gene #17: 'GPS2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'GPS2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.12 (Chi-square test), Q value = 1

Table S195.  Gene #17: 'GPS2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
GPS2 MUTATED 8 2 1 0 0
GPS2 WILD-TYPE 345 237 93 233 42
'GPS2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.38 (Chi-square test), Q value = 1

Table S196.  Gene #17: 'GPS2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
GPS2 MUTATED 2 1 3 1 1 0
GPS2 WILD-TYPE 109 162 92 120 53 103
'GPS2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.268 (Fisher's exact test), Q value = 1

Table S197.  Gene #17: 'GPS2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
GPS2 MUTATED 0 2 2
GPS2 WILD-TYPE 145 128 116
'GPS2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.315 (Fisher's exact test), Q value = 1

Table S198.  Gene #17: 'GPS2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
GPS2 MUTATED 3 1 0
GPS2 WILD-TYPE 151 112 126
'GPS2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0534 (Chi-square test), Q value = 1

Table S199.  Gene #17: 'GPS2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
GPS2 MUTATED 0 3 1 2 3 2
GPS2 WILD-TYPE 181 91 243 160 240 45
'GPS2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0946 (Fisher's exact test), Q value = 1

Table S200.  Gene #17: 'GPS2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
GPS2 MUTATED 7 2 2
GPS2 WILD-TYPE 313 415 232
'GPS2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.137 (Chi-square test), Q value = 1

Table S201.  Gene #17: 'GPS2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
GPS2 MUTATED 1 2 6 2 0 0
GPS2 WILD-TYPE 195 154 201 232 132 31
'GPS2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S202.  Gene #17: 'GPS2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
GPS2 MUTATED 6 3 2
GPS2 WILD-TYPE 505 252 188
'GPS2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S203.  Gene #17: 'GPS2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
GPS2 MUTATED 2 1 2
GPS2 WILD-TYPE 245 206 195
'GPS2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.721 (Fisher's exact test), Q value = 1

Table S204.  Gene #17: 'GPS2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
GPS2 MUTATED 2 2 1
GPS2 WILD-TYPE 148 339 159
'THEM5 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.231 (Chi-square test), Q value = 1

Table S205.  Gene #18: 'THEM5 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
THEM5 MUTATED 1 0 1 0 3 0 0 0
THEM5 WILD-TYPE 20 38 113 97 105 73 19 39
'THEM5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S206.  Gene #18: 'THEM5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
THEM5 MUTATED 1 0 4
THEM5 WILD-TYPE 121 126 257
'THEM5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.529 (Chi-square test), Q value = 1

Table S207.  Gene #18: 'THEM5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
THEM5 MUTATED 2 4 2 2 1
THEM5 WILD-TYPE 351 235 92 231 41
'THEM5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.28 (Chi-square test), Q value = 1

Table S208.  Gene #18: 'THEM5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
THEM5 MUTATED 0 3 0 2 0 3
THEM5 WILD-TYPE 111 160 95 119 54 100
'THEM5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.209 (Fisher's exact test), Q value = 1

Table S209.  Gene #18: 'THEM5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
THEM5 MUTATED 1 3 0
THEM5 WILD-TYPE 144 127 118
'THEM5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0398 (Fisher's exact test), Q value = 1

Table S210.  Gene #18: 'THEM5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
THEM5 MUTATED 4 0 0
THEM5 WILD-TYPE 150 113 126

Figure S96.  Get High-res Image Gene #18: 'THEM5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'THEM5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S211.  Gene #18: 'THEM5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
THEM5 MUTATED 1 0 4 2 2 1
THEM5 WILD-TYPE 180 94 240 160 241 46
'THEM5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.562 (Fisher's exact test), Q value = 1

Table S212.  Gene #18: 'THEM5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
THEM5 MUTATED 3 6 1
THEM5 WILD-TYPE 317 411 233
'THEM5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.939 (Chi-square test), Q value = 1

Table S213.  Gene #18: 'THEM5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
THEM5 MUTATED 2 1 3 2 2 0
THEM5 WILD-TYPE 194 155 204 232 130 31
'THEM5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S214.  Gene #18: 'THEM5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
THEM5 MUTATED 6 2 2
THEM5 WILD-TYPE 505 253 188
'THEM5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.337 (Fisher's exact test), Q value = 1

Table S215.  Gene #18: 'THEM5 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
THEM5 MUTATED 2 5 2
THEM5 WILD-TYPE 245 202 195
'THEM5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.137 (Fisher's exact test), Q value = 1

Table S216.  Gene #18: 'THEM5 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
THEM5 MUTATED 1 3 5
THEM5 WILD-TYPE 149 338 155
'RPGR MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.99 (Chi-square test), Q value = 1

Table S217.  Gene #19: 'RPGR 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
RPGR MUTATED 0 1 3 2 2 2 0 1
RPGR WILD-TYPE 21 37 111 95 106 71 19 38
'RPGR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.664 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
RPGR MUTATED 4 2 5
RPGR WILD-TYPE 118 124 256
'RPGR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.869 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
RPGR MUTATED 7 4 2 3 0
RPGR WILD-TYPE 346 235 92 230 42
'RPGR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.601 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
RPGR MUTATED 3 2 1 5 1 2
RPGR WILD-TYPE 108 161 94 116 53 101
'RPGR MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
RPGR MUTATED 3 4 2
RPGR WILD-TYPE 142 126 116
'RPGR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.695 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
RPGR MUTATED 5 2 2
RPGR WILD-TYPE 149 111 124
'RPGR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.948 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
RPGR MUTATED 4 2 4 3 5 0
RPGR WILD-TYPE 177 92 240 159 238 47
'RPGR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.669 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
RPGR MUTATED 7 6 5
RPGR WILD-TYPE 313 411 229
'RPGR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.783 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
RPGR MUTATED 2 2 4 4 4 1
RPGR WILD-TYPE 194 154 203 230 128 30
'RPGR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
RPGR MUTATED 10 4 3
RPGR WILD-TYPE 501 251 187
'RPGR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.909 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
RPGR MUTATED 3 2 3
RPGR WILD-TYPE 244 205 194
'RPGR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.452 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
RPGR MUTATED 3 3 2
RPGR WILD-TYPE 147 338 158
'DNAH12 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.973 (Chi-square test), Q value = 1

Table S229.  Gene #20: 'DNAH12 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
DNAH12 MUTATED 0 0 2 2 2 1 0 1
DNAH12 WILD-TYPE 21 38 112 95 106 72 19 38
'DNAH12 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.158 (Fisher's exact test), Q value = 1

Table S230.  Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
DNAH12 MUTATED 4 2 2
DNAH12 WILD-TYPE 118 124 259
'DNAH12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.473 (Chi-square test), Q value = 1

Table S231.  Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
DNAH12 MUTATED 9 4 1 2 0
DNAH12 WILD-TYPE 344 235 93 231 42
'DNAH12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.707 (Chi-square test), Q value = 1

Table S232.  Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
DNAH12 MUTATED 1 5 2 2 0 2
DNAH12 WILD-TYPE 110 158 93 119 54 101
'DNAH12 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.45 (Fisher's exact test), Q value = 1

Table S233.  Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
DNAH12 MUTATED 1 1 3
DNAH12 WILD-TYPE 144 129 115
'DNAH12 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S234.  Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
DNAH12 MUTATED 1 2 2
DNAH12 WILD-TYPE 153 111 124
'DNAH12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00224 (Chi-square test), Q value = 1

Table S235.  Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
DNAH12 MUTATED 5 0 3 0 5 4
DNAH12 WILD-TYPE 176 94 241 162 238 43

Figure S97.  Get High-res Image Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'DNAH12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.382 (Fisher's exact test), Q value = 1

Table S236.  Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
DNAH12 MUTATED 8 5 4
DNAH12 WILD-TYPE 312 412 230
'DNAH12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S237.  Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
DNAH12 MUTATED 1 4 5 4 3 0
DNAH12 WILD-TYPE 195 152 202 230 129 31
'DNAH12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.28 (Fisher's exact test), Q value = 1

Table S238.  Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
DNAH12 MUTATED 7 4 6
DNAH12 WILD-TYPE 504 251 184
'DNAH12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.4 (Fisher's exact test), Q value = 1

Table S239.  Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
DNAH12 MUTATED 2 5 4
DNAH12 WILD-TYPE 245 202 193
'DNAH12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.178 (Fisher's exact test), Q value = 1

Table S240.  Gene #20: 'DNAH12 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
DNAH12 MUTATED 3 3 5
DNAH12 WILD-TYPE 147 338 155
'CDKN1B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.634 (Chi-square test), Q value = 1

Table S241.  Gene #21: '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 = 0.178 (Fisher's exact test), Q value = 1

Table S242.  Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
CDKN1B MUTATED 3 0 3
CDKN1B WILD-TYPE 119 126 258
'CDKN1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.142 (Chi-square test), Q value = 1

Table S243.  Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
CDKN1B MUTATED 5 1 3 1 0
CDKN1B WILD-TYPE 348 238 91 232 42
'CDKN1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.108 (Chi-square test), Q value = 1

Table S244.  Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
CDKN1B MUTATED 0 4 0 0 0 1
CDKN1B WILD-TYPE 111 159 95 121 54 102
'CDKN1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.741 (Fisher's exact test), Q value = 1

Table S245.  Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
CDKN1B MUTATED 1 2 2
CDKN1B WILD-TYPE 144 128 116
'CDKN1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.28 (Fisher's exact test), Q value = 1

Table S246.  Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
CDKN1B MUTATED 3 2 0
CDKN1B WILD-TYPE 151 111 126
'CDKN1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.232 (Chi-square test), Q value = 1

Table S247.  Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
CDKN1B MUTATED 0 1 5 3 1 0
CDKN1B WILD-TYPE 181 93 239 159 242 47
'CDKN1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0943 (Fisher's exact test), Q value = 1

Table S248.  Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
CDKN1B MUTATED 6 4 0
CDKN1B WILD-TYPE 314 413 234
'CDKN1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.252 (Chi-square test), Q value = 1

Table S249.  Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
CDKN1B MUTATED 4 1 4 0 1 0
CDKN1B WILD-TYPE 192 155 203 234 131 31
'CDKN1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.111 (Fisher's exact test), Q value = 1

Table S250.  Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
CDKN1B MUTATED 7 0 3
CDKN1B WILD-TYPE 504 255 187
'CDKN1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.295 (Fisher's exact test), Q value = 1

Table S251.  Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
CDKN1B MUTATED 3 3 0
CDKN1B WILD-TYPE 244 204 197
'CDKN1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S252.  Gene #21: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
CDKN1B MUTATED 0 4 2
CDKN1B WILD-TYPE 150 337 158
'ZFP36L1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.57 (Chi-square test), Q value = 1

Table S253.  Gene #22: '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 = 0.441 (Fisher's exact test), Q value = 1

Table S254.  Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
ZFP36L1 MUTATED 1 0 4
ZFP36L1 WILD-TYPE 121 126 257
'ZFP36L1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0232 (Chi-square test), Q value = 1

Table S255.  Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
ZFP36L1 MUTATED 1 4 3 0 1
ZFP36L1 WILD-TYPE 352 235 91 233 41

Figure S98.  Get High-res Image Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ZFP36L1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.758 (Chi-square test), Q value = 1

Table S256.  Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
ZFP36L1 MUTATED 1 1 1 2 0 0
ZFP36L1 WILD-TYPE 110 162 94 119 54 103
'ZFP36L1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 1

Table S257.  Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
ZFP36L1 MUTATED 0 0 3
ZFP36L1 WILD-TYPE 145 130 115

Figure S99.  Get High-res Image Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'ZFP36L1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0233 (Fisher's exact test), Q value = 1

Table S258.  Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
ZFP36L1 MUTATED 0 3 0
ZFP36L1 WILD-TYPE 154 110 126

Figure S100.  Get High-res Image Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'ZFP36L1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.119 (Chi-square test), Q value = 1

Table S259.  Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
ZFP36L1 MUTATED 1 0 0 3 5 0
ZFP36L1 WILD-TYPE 180 94 244 159 238 47
'ZFP36L1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.294 (Fisher's exact test), Q value = 1

Table S260.  Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
ZFP36L1 MUTATED 1 6 2
ZFP36L1 WILD-TYPE 319 411 232
'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.23 (Chi-square test), Q value = 1

Table S261.  Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
ZFP36L1 MUTATED 1 0 1 3 3 1
ZFP36L1 WILD-TYPE 195 156 206 231 129 30
'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.906 (Fisher's exact test), Q value = 1

Table S262.  Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
ZFP36L1 MUTATED 5 3 1
ZFP36L1 WILD-TYPE 506 252 189
'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S263.  Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
ZFP36L1 MUTATED 2 1 2
ZFP36L1 WILD-TYPE 245 206 195
'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.721 (Fisher's exact test), Q value = 1

Table S264.  Gene #22: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
ZFP36L1 MUTATED 2 2 1
ZFP36L1 WILD-TYPE 148 339 159
'ASB10 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.869 (Chi-square test), Q value = 1

Table S265.  Gene #23: 'ASB10 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
ASB10 MUTATED 0 0 1 1 2 0 0 0
ASB10 WILD-TYPE 21 38 113 96 106 73 19 39
'ASB10 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.811 (Fisher's exact test), Q value = 1

Table S266.  Gene #23: 'ASB10 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
ASB10 MUTATED 0 1 3
ASB10 WILD-TYPE 122 125 258
'ASB10 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.981 (Chi-square test), Q value = 1

Table S267.  Gene #23: 'ASB10 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
ASB10 MUTATED 3 2 1 2 0
ASB10 WILD-TYPE 350 237 93 231 42
'ASB10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.787 (Chi-square test), Q value = 1

Table S268.  Gene #23: 'ASB10 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
ASB10 MUTATED 2 3 1 1 1 0
ASB10 WILD-TYPE 109 160 94 120 53 103
'ASB10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.561 (Chi-square test), Q value = 1

Table S269.  Gene #23: 'ASB10 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
ASB10 MUTATED 2 0 4 1 1 0
ASB10 WILD-TYPE 179 94 240 161 242 47
'ASB10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.386 (Fisher's exact test), Q value = 1

Table S270.  Gene #23: 'ASB10 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
ASB10 MUTATED 1 4 3
ASB10 WILD-TYPE 319 413 231
'ASB10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.624 (Chi-square test), Q value = 1

Table S271.  Gene #23: 'ASB10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
ASB10 MUTATED 1 0 3 2 2 0
ASB10 WILD-TYPE 195 156 204 232 130 31
'ASB10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S272.  Gene #23: 'ASB10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
ASB10 MUTATED 4 3 1
ASB10 WILD-TYPE 507 252 189
'ASB10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S273.  Gene #23: 'ASB10 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
ASB10 MUTATED 2 1 2
ASB10 WILD-TYPE 245 206 195
'ASB10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S274.  Gene #23: 'ASB10 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
ASB10 MUTATED 1 3 1
ASB10 WILD-TYPE 149 338 159
'HIST1H3B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.638 (Chi-square test), Q value = 1

Table S275.  Gene #24: 'HIST1H3B 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
HIST1H3B MUTATED 0 0 1 1 0 2 0 1
HIST1H3B WILD-TYPE 21 38 113 96 108 71 19 38
'HIST1H3B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S276.  Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
HIST1H3B MUTATED 1 1 3
HIST1H3B WILD-TYPE 121 125 258
'HIST1H3B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.923 (Chi-square test), Q value = 1

Table S277.  Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
HIST1H3B MUTATED 3 3 1 3 1
HIST1H3B WILD-TYPE 350 236 93 230 41
'HIST1H3B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.677 (Chi-square test), Q value = 1

Table S278.  Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
HIST1H3B MUTATED 2 1 2 3 0 1
HIST1H3B WILD-TYPE 109 162 93 118 54 102
'HIST1H3B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 1

Table S279.  Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
HIST1H3B MUTATED 3 1 1
HIST1H3B WILD-TYPE 142 129 117
'HIST1H3B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S280.  Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
HIST1H3B MUTATED 2 1 2
HIST1H3B WILD-TYPE 152 112 124
'HIST1H3B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.324 (Chi-square test), Q value = 1

Table S281.  Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
HIST1H3B MUTATED 2 1 0 4 3 1
HIST1H3B WILD-TYPE 179 93 244 158 240 46
'HIST1H3B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.137 (Fisher's exact test), Q value = 1

Table S282.  Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
HIST1H3B MUTATED 1 8 2
HIST1H3B WILD-TYPE 319 409 232
'HIST1H3B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.476 (Chi-square test), Q value = 1

Table S283.  Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
HIST1H3B MUTATED 4 1 2 3 0 1
HIST1H3B WILD-TYPE 192 155 205 231 132 30
'HIST1H3B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.918 (Fisher's exact test), Q value = 1

Table S284.  Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
HIST1H3B MUTATED 7 2 2
HIST1H3B WILD-TYPE 504 253 188
'HIST1H3B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S285.  Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
HIST1H3B MUTATED 3 1 2
HIST1H3B WILD-TYPE 244 206 195
'HIST1H3B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.871 (Fisher's exact test), Q value = 1

Table S286.  Gene #24: 'HIST1H3B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
HIST1H3B MUTATED 1 3 2
HIST1H3B WILD-TYPE 149 338 158
'FAM86B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.734 (Chi-square test), Q value = 1

Table S287.  Gene #25: 'FAM86B1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
FAM86B1 MUTATED 3 2 0 2 1
FAM86B1 WILD-TYPE 350 237 94 231 41
'FAM86B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.87 (Chi-square test), Q value = 1

Table S288.  Gene #25: 'FAM86B1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
FAM86B1 MUTATED 2 1 1 2 0 1
FAM86B1 WILD-TYPE 109 162 94 119 54 102
'FAM86B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.4 (Chi-square test), Q value = 1

Table S289.  Gene #25: 'FAM86B1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
FAM86B1 MUTATED 2 2 0 1 3 0
FAM86B1 WILD-TYPE 179 92 244 161 240 47
'FAM86B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S290.  Gene #25: 'FAM86B1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
FAM86B1 MUTATED 4 2 2
FAM86B1 WILD-TYPE 316 415 232
'FAM86B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.394 (Chi-square test), Q value = 1

Table S291.  Gene #25: 'FAM86B1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
FAM86B1 MUTATED 0 3 1 2 2 0
FAM86B1 WILD-TYPE 196 153 206 232 130 31
'FAM86B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S292.  Gene #25: 'FAM86B1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
FAM86B1 MUTATED 1 2 5
FAM86B1 WILD-TYPE 510 253 185

Figure S101.  Get High-res Image Gene #25: 'FAM86B1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'FAM86B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.893 (Fisher's exact test), Q value = 1

Table S293.  Gene #25: 'FAM86B1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
FAM86B1 MUTATED 2 3 2
FAM86B1 WILD-TYPE 245 204 195
'FAM86B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.593 (Fisher's exact test), Q value = 1

Table S294.  Gene #25: 'FAM86B1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
FAM86B1 MUTATED 1 3 3
FAM86B1 WILD-TYPE 149 338 157
'PIK3R1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0266 (Chi-square test), Q value = 1

Table S295.  Gene #26: 'PIK3R1 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
PIK3R1 MUTATED 0 0 1 1 1 5 0 0
PIK3R1 WILD-TYPE 21 38 113 96 107 68 19 39

Figure S102.  Get High-res Image Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'PIK3R1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S296.  Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
PIK3R1 MUTATED 1 3 4
PIK3R1 WILD-TYPE 121 123 257
'PIK3R1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.873 (Chi-square test), Q value = 1

Table S297.  Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
PIK3R1 MUTATED 4 5 1 4 1
PIK3R1 WILD-TYPE 349 234 93 229 41
'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0774 (Chi-square test), Q value = 1

Table S298.  Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
PIK3R1 MUTATED 3 1 3 0 0 0
PIK3R1 WILD-TYPE 108 162 92 121 54 103
'PIK3R1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 1

Table S299.  Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
PIK3R1 MUTATED 3 1 1
PIK3R1 WILD-TYPE 142 129 117
'PIK3R1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.452 (Fisher's exact test), Q value = 1

Table S300.  Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
PIK3R1 MUTATED 3 0 2
PIK3R1 WILD-TYPE 151 113 124
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.511 (Chi-square test), Q value = 1

Table S301.  Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
PIK3R1 MUTATED 3 1 4 5 2 0
PIK3R1 WILD-TYPE 178 93 240 157 241 47
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.484 (Fisher's exact test), Q value = 1

Table S302.  Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
PIK3R1 MUTATED 3 7 5
PIK3R1 WILD-TYPE 317 410 229
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0307 (Chi-square test), Q value = 1

Table S303.  Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
PIK3R1 MUTATED 5 0 2 5 0 2
PIK3R1 WILD-TYPE 191 156 205 229 132 29

Figure S103.  Get High-res Image Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.135 (Fisher's exact test), Q value = 1

Table S304.  Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
PIK3R1 MUTATED 10 4 0
PIK3R1 WILD-TYPE 501 251 190
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 1

Table S305.  Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
PIK3R1 MUTATED 7 1 3
PIK3R1 WILD-TYPE 240 206 194
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S306.  Gene #26: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
PIK3R1 MUTATED 3 7 1
PIK3R1 WILD-TYPE 147 334 159
'MYH9 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.711 (Chi-square test), Q value = 1

Table S307.  Gene #27: '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 = 0.182 (Fisher's exact test), Q value = 1

Table S308.  Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
MYH9 MUTATED 2 4 2
MYH9 WILD-TYPE 120 122 259
'MYH9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.123 (Chi-square test), Q value = 1

Table S309.  Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
MYH9 MUTATED 11 4 0 2 0
MYH9 WILD-TYPE 342 235 94 231 42
'MYH9 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.465 (Chi-square test), Q value = 1

Table S310.  Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
MYH9 MUTATED 2 5 4 2 0 1
MYH9 WILD-TYPE 109 158 91 119 54 102
'MYH9 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.822 (Fisher's exact test), Q value = 1

Table S311.  Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
MYH9 MUTATED 4 2 2
MYH9 WILD-TYPE 141 128 116
'MYH9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.606 (Fisher's exact test), Q value = 1

Table S312.  Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
MYH9 MUTATED 2 2 4
MYH9 WILD-TYPE 152 111 122
'MYH9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.869 (Chi-square test), Q value = 1

Table S313.  Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
MYH9 MUTATED 3 2 5 5 3 1
MYH9 WILD-TYPE 178 92 239 157 240 46
'MYH9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.286 (Fisher's exact test), Q value = 1

Table S314.  Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
MYH9 MUTATED 8 5 6
MYH9 WILD-TYPE 312 412 228
'MYH9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.354 (Chi-square test), Q value = 1

Table S315.  Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
MYH9 MUTATED 2 2 5 4 4 2
MYH9 WILD-TYPE 194 154 202 230 128 29
'MYH9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S316.  Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
MYH9 MUTATED 8 4 7
MYH9 WILD-TYPE 503 251 183
'MYH9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.66 (Fisher's exact test), Q value = 1

Table S317.  Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
MYH9 MUTATED 4 6 4
MYH9 WILD-TYPE 243 201 193
'MYH9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.134 (Fisher's exact test), Q value = 1

Table S318.  Gene #27: 'MYH9 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
MYH9 MUTATED 4 4 6
MYH9 WILD-TYPE 146 337 154
'CASP8 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S319.  Gene #28: 'CASP8 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
CASP8 MUTATED 0 0 1 0 3 0 0 1
CASP8 WILD-TYPE 21 38 113 97 105 73 19 38
'CASP8 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.358 (Fisher's exact test), Q value = 1

Table S320.  Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
CASP8 MUTATED 2 0 3
CASP8 WILD-TYPE 120 126 258
'CASP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0663 (Chi-square test), Q value = 1

Table S321.  Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
CASP8 MUTATED 4 1 4 3 0
CASP8 WILD-TYPE 349 238 90 230 42
'CASP8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.436 (Chi-square test), Q value = 1

Table S322.  Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
CASP8 MUTATED 2 4 0 0 1 2
CASP8 WILD-TYPE 109 159 95 121 53 101
'CASP8 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S323.  Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
CASP8 MUTATED 1 3 1
CASP8 WILD-TYPE 144 127 117
'CASP8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S324.  Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
CASP8 MUTATED 3 1 1
CASP8 WILD-TYPE 151 112 125
'CASP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0633 (Chi-square test), Q value = 1

Table S325.  Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
CASP8 MUTATED 3 0 7 0 1 1
CASP8 WILD-TYPE 178 94 237 162 242 46
'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S326.  Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
CASP8 MUTATED 4 5 3
CASP8 WILD-TYPE 316 412 231
'CASP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.436 (Chi-square test), Q value = 1

Table S327.  Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
CASP8 MUTATED 2 0 3 5 1 1
CASP8 WILD-TYPE 194 156 204 229 131 30
'CASP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.424 (Fisher's exact test), Q value = 1

Table S328.  Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
CASP8 MUTATED 6 5 1
CASP8 WILD-TYPE 505 250 189
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.741 (Fisher's exact test), Q value = 1

Table S329.  Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
CASP8 MUTATED 2 3 3
CASP8 WILD-TYPE 245 204 194
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.452 (Fisher's exact test), Q value = 1

Table S330.  Gene #28: 'CASP8 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
CASP8 MUTATED 3 3 2
CASP8 WILD-TYPE 147 338 158
'COL6A5 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.144 (Chi-square test), Q value = 1

Table S331.  Gene #29: 'COL6A5 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
COL6A5 MUTATED 0 1 1 4 6 0 0 0
COL6A5 WILD-TYPE 21 37 113 93 102 73 19 39
'COL6A5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.44 (Fisher's exact test), Q value = 1

Table S332.  Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
COL6A5 MUTATED 2 5 5
COL6A5 WILD-TYPE 120 121 256
'COL6A5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S333.  Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
COL6A5 MUTATED 10 5 2 7 0
COL6A5 WILD-TYPE 343 234 92 226 42
'COL6A5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.204 (Chi-square test), Q value = 1

Table S334.  Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
COL6A5 MUTATED 5 5 1 6 0 1
COL6A5 WILD-TYPE 106 158 94 115 54 102
'COL6A5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.075 (Fisher's exact test), Q value = 1

Table S335.  Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
COL6A5 MUTATED 5 5 0
COL6A5 WILD-TYPE 140 125 118
'COL6A5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.076 (Fisher's exact test), Q value = 1

Table S336.  Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
COL6A5 MUTATED 5 0 5
COL6A5 WILD-TYPE 149 113 121
'COL6A5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.208 (Chi-square test), Q value = 1

Table S337.  Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
COL6A5 MUTATED 9 1 7 4 4 0
COL6A5 WILD-TYPE 172 93 237 158 239 47
'COL6A5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.342 (Fisher's exact test), Q value = 1

Table S338.  Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
COL6A5 MUTATED 6 10 9
COL6A5 WILD-TYPE 314 407 225
'COL6A5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.578 (Chi-square test), Q value = 1

Table S339.  Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
COL6A5 MUTATED 4 3 3 9 5 1
COL6A5 WILD-TYPE 192 153 204 225 127 30
'COL6A5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 1

Table S340.  Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
COL6A5 MUTATED 13 11 1
COL6A5 WILD-TYPE 498 244 189

Figure S104.  Get High-res Image Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'COL6A5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0502 (Fisher's exact test), Q value = 1

Table S341.  Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
COL6A5 MUTATED 7 2 10
COL6A5 WILD-TYPE 240 205 187
'COL6A5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0577 (Fisher's exact test), Q value = 1

Table S342.  Gene #29: 'COL6A5 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
COL6A5 MUTATED 9 7 3
COL6A5 WILD-TYPE 141 334 157
'TBL1XR1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.123 (Chi-square test), Q value = 1

Table S343.  Gene #30: '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 = 0.238 (Fisher's exact test), Q value = 1

Table S344.  Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
TBL1XR1 MUTATED 2 0 6
TBL1XR1 WILD-TYPE 120 126 255
'TBL1XR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0497 (Chi-square test), Q value = 1

Table S345.  Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
TBL1XR1 MUTATED 6 1 3 0 0
TBL1XR1 WILD-TYPE 347 238 91 233 42

Figure S105.  Get High-res Image Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TBL1XR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S346.  Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
TBL1XR1 MUTATED 0 2 0 0 0 1
TBL1XR1 WILD-TYPE 111 161 95 121 54 102
'TBL1XR1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S347.  Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
TBL1XR1 MUTATED 2 4 1
TBL1XR1 WILD-TYPE 143 126 117
'TBL1XR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.568 (Fisher's exact test), Q value = 1

Table S348.  Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
TBL1XR1 MUTATED 4 2 1
TBL1XR1 WILD-TYPE 150 111 125
'TBL1XR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0228 (Chi-square test), Q value = 1

Table S349.  Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
TBL1XR1 MUTATED 0 1 7 2 0 0
TBL1XR1 WILD-TYPE 181 93 237 160 243 47

Figure S106.  Get High-res Image Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TBL1XR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 1

Table S350.  Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
TBL1XR1 MUTATED 5 5 0
TBL1XR1 WILD-TYPE 315 412 234
'TBL1XR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.475 (Chi-square test), Q value = 1

Table S351.  Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
TBL1XR1 MUTATED 3 2 3 1 0 1
TBL1XR1 WILD-TYPE 193 154 204 233 132 30
'TBL1XR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.042 (Fisher's exact test), Q value = 1

Table S352.  Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
TBL1XR1 MUTATED 9 0 1
TBL1XR1 WILD-TYPE 502 255 189

Figure S107.  Get High-res Image Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TBL1XR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.575 (Fisher's exact test), Q value = 1

Table S353.  Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
TBL1XR1 MUTATED 4 2 1
TBL1XR1 WILD-TYPE 243 205 196
'TBL1XR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.242 (Fisher's exact test), Q value = 1

Table S354.  Gene #30: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
TBL1XR1 MUTATED 0 6 1
TBL1XR1 WILD-TYPE 150 335 159
'ASXL2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.403 (Chi-square test), Q value = 1

Table S355.  Gene #31: 'ASXL2 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
ASXL2 MUTATED 1 1 1 5 2 1 0 0
ASXL2 WILD-TYPE 20 37 113 92 106 72 19 39
'ASXL2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0975 (Fisher's exact test), Q value = 1

Table S356.  Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
ASXL2 MUTATED 2 6 3
ASXL2 WILD-TYPE 120 120 258
'ASXL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.861 (Chi-square test), Q value = 1

Table S357.  Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
ASXL2 MUTATED 7 3 2 4 0
ASXL2 WILD-TYPE 346 236 92 229 42
'ASXL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.971 (Chi-square test), Q value = 1

Table S358.  Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
ASXL2 MUTATED 1 2 1 1 1 2
ASXL2 WILD-TYPE 110 161 94 120 53 101
'ASXL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.281 (Fisher's exact test), Q value = 1

Table S359.  Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
ASXL2 MUTATED 3 0 2
ASXL2 WILD-TYPE 142 130 116
'ASXL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00505 (Fisher's exact test), Q value = 1

Table S360.  Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
ASXL2 MUTATED 0 0 5
ASXL2 WILD-TYPE 154 113 121

Figure S108.  Get High-res Image Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'ASXL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.512 (Chi-square test), Q value = 1

Table S361.  Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
ASXL2 MUTATED 5 2 3 4 2 0
ASXL2 WILD-TYPE 176 92 241 158 241 47
'ASXL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.4 (Fisher's exact test), Q value = 1

Table S362.  Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
ASXL2 MUTATED 5 5 6
ASXL2 WILD-TYPE 315 412 228
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.803 (Chi-square test), Q value = 1

Table S363.  Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
ASXL2 MUTATED 5 2 2 4 2 0
ASXL2 WILD-TYPE 191 154 205 230 130 31
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.187 (Fisher's exact test), Q value = 1

Table S364.  Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
ASXL2 MUTATED 5 7 3
ASXL2 WILD-TYPE 506 248 187
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.741 (Fisher's exact test), Q value = 1

Table S365.  Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
ASXL2 MUTATED 2 3 3
ASXL2 WILD-TYPE 245 204 194
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.26 (Fisher's exact test), Q value = 1

Table S366.  Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
ASXL2 MUTATED 3 2 3
ASXL2 WILD-TYPE 147 339 157
'ARID1A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.135 (Chi-square test), Q value = 1

Table S367.  Gene #32: '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 = 0.943 (Fisher's exact test), Q value = 1

Table S368.  Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
ARID1A MUTATED 4 3 8
ARID1A WILD-TYPE 118 123 253
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.152 (Chi-square test), Q value = 1

Table S369.  Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
ARID1A MUTATED 9 11 1 3 2
ARID1A WILD-TYPE 344 228 93 230 40
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0615 (Chi-square test), Q value = 1

Table S370.  Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
ARID1A MUTATED 1 5 1 8 2 1
ARID1A WILD-TYPE 110 158 94 113 52 102
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S371.  Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
ARID1A MUTATED 4 3 3
ARID1A WILD-TYPE 141 127 115
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S372.  Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
ARID1A MUTATED 5 1 4
ARID1A WILD-TYPE 149 112 122
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0924 (Chi-square test), Q value = 1

Table S373.  Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
ARID1A MUTATED 2 1 5 5 13 1
ARID1A WILD-TYPE 179 93 239 157 230 46
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S374.  Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
ARID1A MUTATED 10 14 3
ARID1A WILD-TYPE 310 403 231
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.443 (Chi-square test), Q value = 1

Table S375.  Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
ARID1A MUTATED 5 3 7 4 7 1
ARID1A WILD-TYPE 191 153 200 230 125 30
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0936 (Fisher's exact test), Q value = 1

Table S376.  Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
ARID1A MUTATED 20 5 2
ARID1A WILD-TYPE 491 250 188
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.837 (Fisher's exact test), Q value = 1

Table S377.  Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
ARID1A MUTATED 6 5 3
ARID1A WILD-TYPE 241 202 194
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0456 (Fisher's exact test), Q value = 1

Table S378.  Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
ARID1A MUTATED 0 8 6
ARID1A WILD-TYPE 150 333 154

Figure S109.  Get High-res Image Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'AQP12A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.715 (Chi-square test), Q value = 1

Table S379.  Gene #33: '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 = 0.203 (Fisher's exact test), Q value = 1

Table S380.  Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
AQP12A MUTATED 2 0 1
AQP12A WILD-TYPE 120 126 260
'AQP12A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.207 (Chi-square test), Q value = 1

Table S381.  Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
AQP12A MUTATED 1 4 0 1 0
AQP12A WILD-TYPE 352 235 94 232 42
'AQP12A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0247 (Chi-square test), Q value = 1

Table S382.  Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
AQP12A MUTATED 1 0 3 0 0 0
AQP12A WILD-TYPE 110 163 92 121 54 103

Figure S110.  Get High-res Image Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'AQP12A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.201 (Fisher's exact test), Q value = 1

Table S383.  Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
AQP12A MUTATED 0 1 2
AQP12A WILD-TYPE 145 129 116
'AQP12A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.115 (Fisher's exact test), Q value = 1

Table S384.  Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
AQP12A MUTATED 3 0 0
AQP12A WILD-TYPE 151 113 126
'AQP12A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.69 (Chi-square test), Q value = 1

Table S385.  Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
AQP12A MUTATED 0 1 1 2 2 0
AQP12A WILD-TYPE 181 93 243 160 241 47
'AQP12A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S386.  Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
AQP12A MUTATED 2 3 1
AQP12A WILD-TYPE 318 414 233
'AQP12A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.689 (Chi-square test), Q value = 1

Table S387.  Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
AQP12A MUTATED 2 0 2 2 0 0
AQP12A WILD-TYPE 194 156 205 232 132 31
'AQP12A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S388.  Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
AQP12A MUTATED 4 1 1
AQP12A WILD-TYPE 507 254 189
'AQP12A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S389.  Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
AQP12A MUTATED 2 1 1
AQP12A WILD-TYPE 245 206 196
'AQP12A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S390.  Gene #33: 'AQP12A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
AQP12A MUTATED 1 2 1
AQP12A WILD-TYPE 149 339 159
'EPDR1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.379 (Chi-square test), Q value = 1

Table S391.  Gene #34: 'EPDR1 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
EPDR1 MUTATED 0 1 1 0 0 2 0 0
EPDR1 WILD-TYPE 21 37 113 97 108 71 19 39
'EPDR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S392.  Gene #34: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
EPDR1 MUTATED 1 1 2
EPDR1 WILD-TYPE 121 125 259
'EPDR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.79 (Chi-square test), Q value = 1

Table S393.  Gene #34: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
EPDR1 MUTATED 1 1 1 2 0
EPDR1 WILD-TYPE 352 238 93 231 42
'EPDR1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S394.  Gene #34: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
EPDR1 MUTATED 2 2 0
EPDR1 WILD-TYPE 143 128 118
'EPDR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.468 (Fisher's exact test), Q value = 1

Table S395.  Gene #34: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
EPDR1 MUTATED 3 0 1
EPDR1 WILD-TYPE 151 113 125
'EPDR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.191 (Chi-square test), Q value = 1

Table S396.  Gene #34: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
EPDR1 MUTATED 0 0 1 3 1 0
EPDR1 WILD-TYPE 181 94 243 159 242 47
'EPDR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S397.  Gene #34: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
EPDR1 MUTATED 2 2 1
EPDR1 WILD-TYPE 318 415 233
'EPDR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.599 (Chi-square test), Q value = 1

Table S398.  Gene #34: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
EPDR1 MUTATED 1 0 2 0 1 0
EPDR1 WILD-TYPE 195 156 205 234 131 31
'EPDR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S399.  Gene #34: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
EPDR1 MUTATED 2 1 1
EPDR1 WILD-TYPE 509 254 189
'EPDR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 1

Table S400.  Gene #34: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
EPDR1 MUTATED 0 2 1
EPDR1 WILD-TYPE 247 205 196
'EPDR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S401.  Gene #34: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
EPDR1 MUTATED 0 2 1
EPDR1 WILD-TYPE 150 339 159
'ERBB2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.886 (Chi-square test), Q value = 1

Table S402.  Gene #35: '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 2 1 3 3 0 1
ERBB2 WILD-TYPE 20 37 112 96 105 70 19 38
'ERBB2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.349 (Fisher's exact test), Q value = 1

Table S403.  Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
ERBB2 MUTATED 5 2 5
ERBB2 WILD-TYPE 117 124 256
'ERBB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0254 (Chi-square test), Q value = 1

Table S404.  Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
ERBB2 MUTATED 11 2 5 2 0
ERBB2 WILD-TYPE 342 237 89 231 42

Figure S111.  Get High-res Image Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ERBB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0101 (Chi-square test), Q value = 1

Table S405.  Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
ERBB2 MUTATED 0 1 4 0 3 4
ERBB2 WILD-TYPE 111 162 91 121 51 99

Figure S112.  Get High-res Image Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'ERBB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.549 (Fisher's exact test), Q value = 1

Table S406.  Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
ERBB2 MUTATED 2 2 4
ERBB2 WILD-TYPE 143 128 114
'ERBB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.906 (Fisher's exact test), Q value = 1

Table S407.  Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
ERBB2 MUTATED 4 2 2
ERBB2 WILD-TYPE 150 111 124
'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.296 (Chi-square test), Q value = 1

Table S408.  Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
ERBB2 MUTATED 1 4 5 5 4 2
ERBB2 WILD-TYPE 180 90 239 157 239 45
'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.658 (Fisher's exact test), Q value = 1

Table S409.  Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
ERBB2 MUTATED 9 8 4
ERBB2 WILD-TYPE 311 409 230
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.112 (Chi-square test), Q value = 1

Table S410.  Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
ERBB2 MUTATED 6 4 6 1 1 2
ERBB2 WILD-TYPE 190 152 201 233 131 29
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.183 (Fisher's exact test), Q value = 1

Table S411.  Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
ERBB2 MUTATED 10 3 7
ERBB2 WILD-TYPE 501 252 183
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.584 (Fisher's exact test), Q value = 1

Table S412.  Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
ERBB2 MUTATED 5 5 2
ERBB2 WILD-TYPE 242 202 195
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.503 (Fisher's exact test), Q value = 1

Table S413.  Gene #35: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
ERBB2 MUTATED 1 7 4
ERBB2 WILD-TYPE 149 334 156
'MYB MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.631 (Chi-square test), Q value = 1

Table S414.  Gene #36: '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 = 1 (Fisher's exact test), Q value = 1

Table S415.  Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
MYB MUTATED 2 2 5
MYB WILD-TYPE 120 124 256
'MYB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.23 (Chi-square test), Q value = 1

Table S416.  Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
MYB MUTATED 6 1 3 2 0
MYB WILD-TYPE 347 238 91 231 42
'MYB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.514 (Chi-square test), Q value = 1

Table S417.  Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
MYB MUTATED 2 1 1 0 1 0
MYB WILD-TYPE 109 162 94 121 53 103
'MYB MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S418.  Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
MYB MUTATED 2 2 1
MYB WILD-TYPE 143 128 117
'MYB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S419.  Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
MYB MUTATED 2 2 1
MYB WILD-TYPE 152 111 125
'MYB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.764 (Chi-square test), Q value = 1

Table S420.  Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
MYB MUTATED 3 0 4 1 3 1
MYB WILD-TYPE 178 94 240 161 240 46
'MYB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.657 (Fisher's exact test), Q value = 1

Table S421.  Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
MYB MUTATED 4 4 4
MYB WILD-TYPE 316 413 230
'MYB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0344 (Chi-square test), Q value = 1

Table S422.  Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
MYB MUTATED 3 0 7 2 0 0
MYB WILD-TYPE 193 156 200 232 132 31

Figure S113.  Get High-res Image Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MYB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S423.  Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
MYB MUTATED 9 3 0
MYB WILD-TYPE 502 252 190
'MYB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0683 (Fisher's exact test), Q value = 1

Table S424.  Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
MYB MUTATED 5 0 1
MYB WILD-TYPE 242 207 196
'MYB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.489 (Fisher's exact test), Q value = 1

Table S425.  Gene #36: 'MYB MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
MYB MUTATED 2 4 0
MYB WILD-TYPE 148 337 160
'TMEM151B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.915 (Chi-square test), Q value = 1

Table S426.  Gene #37: 'TMEM151B 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
TMEM151B MUTATED 0 0 0 1 1 1 0 0
TMEM151B WILD-TYPE 21 38 114 96 107 72 19 39
'TMEM151B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.297 (Fisher's exact test), Q value = 1

Table S427.  Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
TMEM151B MUTATED 0 2 1
TMEM151B WILD-TYPE 122 124 260
'TMEM151B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.115 (Chi-square test), Q value = 1

Table S428.  Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
TMEM151B MUTATED 0 1 1 4 0
TMEM151B WILD-TYPE 353 238 93 229 42
'TMEM151B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.576 (Chi-square test), Q value = 1

Table S429.  Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
TMEM151B MUTATED 1 1 0 2 0 0
TMEM151B WILD-TYPE 110 162 95 119 54 103
'TMEM151B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 1

Table S430.  Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
TMEM151B MUTATED 0 0 3
TMEM151B WILD-TYPE 145 130 115

Figure S114.  Get High-res Image Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'TMEM151B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 1

Table S431.  Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
TMEM151B MUTATED 0 2 1
TMEM151B WILD-TYPE 154 111 125
'TMEM151B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.514 (Chi-square test), Q value = 1

Table S432.  Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
TMEM151B MUTATED 2 0 2 2 0 0
TMEM151B WILD-TYPE 179 94 242 160 243 47
'TMEM151B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0313 (Fisher's exact test), Q value = 1

Table S433.  Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
TMEM151B MUTATED 0 2 4
TMEM151B WILD-TYPE 320 415 230

Figure S115.  Get High-res Image Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TMEM151B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.272 (Chi-square test), Q value = 1

Table S434.  Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
TMEM151B MUTATED 1 0 1 2 0 1
TMEM151B WILD-TYPE 195 156 206 232 132 30
'TMEM151B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S435.  Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
TMEM151B MUTATED 3 2 0
TMEM151B WILD-TYPE 508 253 190
'TMEM151B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 1

Table S436.  Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
TMEM151B MUTATED 1 0 2
TMEM151B WILD-TYPE 246 207 195
'TMEM151B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.191 (Fisher's exact test), Q value = 1

Table S437.  Gene #37: 'TMEM151B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
TMEM151B MUTATED 2 1 0
TMEM151B WILD-TYPE 148 340 160
'GALNTL6 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.921 (Chi-square test), Q value = 1

Table S438.  Gene #38: 'GALNTL6 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
GALNTL6 MUTATED 0 0 1 1 0 1 0 0
GALNTL6 WILD-TYPE 21 38 113 96 108 72 19 39
'GALNTL6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S439.  Gene #38: 'GALNTL6 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
GALNTL6 MUTATED 0 1 2
GALNTL6 WILD-TYPE 122 125 259
'GALNTL6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.225 (Chi-square test), Q value = 1

Table S440.  Gene #38: 'GALNTL6 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
GALNTL6 MUTATED 0 2 0 3 0
GALNTL6 WILD-TYPE 353 237 94 230 42
'GALNTL6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0124 (Chi-square test), Q value = 1

Table S441.  Gene #38: 'GALNTL6 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
GALNTL6 MUTATED 3 0 0 0 0 0
GALNTL6 WILD-TYPE 108 163 95 121 54 103

Figure S116.  Get High-res Image Gene #38: 'GALNTL6 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'GALNTL6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.427 (Chi-square test), Q value = 1

Table S442.  Gene #38: 'GALNTL6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
GALNTL6 MUTATED 2 0 0 2 1 0
GALNTL6 WILD-TYPE 179 94 244 160 242 47
'GALNTL6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S443.  Gene #38: 'GALNTL6 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
GALNTL6 MUTATED 0 2 3
GALNTL6 WILD-TYPE 320 415 231
'GALNTL6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.11 (Chi-square test), Q value = 1

Table S444.  Gene #38: 'GALNTL6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
GALNTL6 MUTATED 0 0 1 2 0 1
GALNTL6 WILD-TYPE 196 156 206 232 132 30
'GALNTL6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.654 (Fisher's exact test), Q value = 1

Table S445.  Gene #38: 'GALNTL6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
GALNTL6 MUTATED 2 2 0
GALNTL6 WILD-TYPE 509 253 190
'GALNTL6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 1

Table S446.  Gene #38: 'GALNTL6 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
GALNTL6 MUTATED 1 0 2
GALNTL6 WILD-TYPE 246 207 195
'GALNTL6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.191 (Fisher's exact test), Q value = 1

Table S447.  Gene #38: 'GALNTL6 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
GALNTL6 MUTATED 2 1 0
GALNTL6 WILD-TYPE 148 340 160
'AKD1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.44 (Chi-square test), Q value = 1

Table S448.  Gene #39: 'AKD1 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
AKD1 MUTATED 0 0 0 3 3 1 0 0
AKD1 WILD-TYPE 21 38 114 94 105 72 19 39
'AKD1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.598 (Fisher's exact test), Q value = 1

Table S449.  Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
AKD1 MUTATED 1 3 3
AKD1 WILD-TYPE 121 123 258
'AKD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.361 (Chi-square test), Q value = 1

Table S450.  Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
AKD1 MUTATED 6 2 3 5 2
AKD1 WILD-TYPE 347 237 91 228 40
'AKD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.532 (Chi-square test), Q value = 1

Table S451.  Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
AKD1 MUTATED 3 2 3 4 0 1
AKD1 WILD-TYPE 108 161 92 117 54 102
'AKD1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S452.  Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
AKD1 MUTATED 2 0 3
AKD1 WILD-TYPE 143 130 115
'AKD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.124 (Fisher's exact test), Q value = 1

Table S453.  Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
AKD1 MUTATED 0 2 3
AKD1 WILD-TYPE 154 111 123
'AKD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.242 (Chi-square test), Q value = 1

Table S454.  Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
AKD1 MUTATED 6 0 3 5 4 0
AKD1 WILD-TYPE 175 94 241 157 239 47
'AKD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0808 (Fisher's exact test), Q value = 1

Table S455.  Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
AKD1 MUTATED 2 9 7
AKD1 WILD-TYPE 318 408 227
'AKD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.896 (Chi-square test), Q value = 1

Table S456.  Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
AKD1 MUTATED 3 2 3 6 3 1
AKD1 WILD-TYPE 193 154 204 228 129 30
'AKD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.474 (Fisher's exact test), Q value = 1

Table S457.  Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
AKD1 MUTATED 8 7 3
AKD1 WILD-TYPE 503 248 187
'AKD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0812 (Fisher's exact test), Q value = 1

Table S458.  Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
AKD1 MUTATED 5 1 7
AKD1 WILD-TYPE 242 206 190
'AKD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.431 (Fisher's exact test), Q value = 1

Table S459.  Gene #39: 'AKD1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
AKD1 MUTATED 5 6 2
AKD1 WILD-TYPE 145 335 158
'AARS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.403 (Chi-square test), Q value = 1

Table S460.  Gene #40: 'AARS 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
AARS MUTATED 0 1 2 2 0 0 1 0
AARS WILD-TYPE 21 37 112 95 108 73 18 39
'AARS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 1

Table S461.  Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
AARS MUTATED 4 2 0
AARS WILD-TYPE 118 124 261

Figure S117.  Get High-res Image Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'AARS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.738 (Chi-square test), Q value = 1

Table S462.  Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
AARS MUTATED 3 1 1 3 1
AARS WILD-TYPE 350 238 93 230 41
'AARS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.424 (Chi-square test), Q value = 1

Table S463.  Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
AARS MUTATED 0 0 1 2 1 2
AARS WILD-TYPE 111 163 94 119 53 101
'AARS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.836 (Fisher's exact test), Q value = 1

Table S464.  Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
AARS MUTATED 1 2 1
AARS WILD-TYPE 144 128 117
'AARS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.563 (Fisher's exact test), Q value = 1

Table S465.  Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
AARS MUTATED 2 0 2
AARS WILD-TYPE 152 113 124
'AARS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00241 (Chi-square test), Q value = 1

Table S466.  Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
AARS MUTATED 2 1 1 2 0 3
AARS WILD-TYPE 179 93 243 160 243 44

Figure S118.  Get High-res Image Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'AARS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.472 (Fisher's exact test), Q value = 1

Table S467.  Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
AARS MUTATED 4 2 3
AARS WILD-TYPE 316 415 231
'AARS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.746 (Chi-square test), Q value = 1

Table S468.  Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
AARS MUTATED 2 1 1 3 1 1
AARS WILD-TYPE 194 155 206 231 131 30
'AARS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.319 (Fisher's exact test), Q value = 1

Table S469.  Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
AARS MUTATED 6 3 0
AARS WILD-TYPE 505 252 190
'AARS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0573 (Fisher's exact test), Q value = 1

Table S470.  Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
AARS MUTATED 1 0 4
AARS WILD-TYPE 246 207 193
'AARS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.072 (Fisher's exact test), Q value = 1

Table S471.  Gene #40: 'AARS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
AARS MUTATED 3 1 1
AARS WILD-TYPE 147 340 159
'HLA-C MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.316 (Chi-square test), Q value = 1

Table S472.  Gene #41: 'HLA-C 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
HLA-C MUTATED 0 1 0 0 0 1 0 1
HLA-C WILD-TYPE 21 37 114 97 108 72 19 38
'HLA-C MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.203 (Fisher's exact test), Q value = 1

Table S473.  Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
HLA-C MUTATED 2 0 1
HLA-C WILD-TYPE 120 126 260
'HLA-C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.58 (Chi-square test), Q value = 1

Table S474.  Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
HLA-C MUTATED 3 2 0 4 0
HLA-C WILD-TYPE 350 237 94 229 42
'HLA-C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.106 (Chi-square test), Q value = 1

Table S475.  Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
HLA-C MUTATED 4 3 1 0 0 0
HLA-C WILD-TYPE 107 160 94 121 54 103
'HLA-C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.399 (Fisher's exact test), Q value = 1

Table S476.  Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
HLA-C MUTATED 1 0 2
HLA-C WILD-TYPE 144 130 116
'HLA-C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.634 (Fisher's exact test), Q value = 1

Table S477.  Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
HLA-C MUTATED 2 1 0
HLA-C WILD-TYPE 152 112 126
'HLA-C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.27 (Chi-square test), Q value = 1

Table S478.  Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
HLA-C MUTATED 4 1 3 1 0 0
HLA-C WILD-TYPE 177 93 241 161 243 47
'HLA-C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.236 (Fisher's exact test), Q value = 1

Table S479.  Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
HLA-C MUTATED 1 4 4
HLA-C WILD-TYPE 319 413 230
'HLA-C MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S480.  Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
HLA-C MUTATED 1 0 3 5 0 0
HLA-C WILD-TYPE 195 156 204 229 132 31
'HLA-C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0717 (Fisher's exact test), Q value = 1

Table S481.  Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
HLA-C MUTATED 2 5 2
HLA-C WILD-TYPE 509 250 188
'HLA-C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 1

Table S482.  Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
HLA-C MUTATED 1 1 4
HLA-C WILD-TYPE 246 206 193
'HLA-C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0267 (Fisher's exact test), Q value = 1

Table S483.  Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
HLA-C MUTATED 4 1 1
HLA-C WILD-TYPE 146 340 159

Figure S119.  Get High-res Image Gene #41: 'HLA-C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'GPRIN2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.655 (Chi-square test), Q value = 1

Table S484.  Gene #42: '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 = 0.465 (Fisher's exact test), Q value = 1

Table S485.  Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
GPRIN2 MUTATED 2 3 2
GPRIN2 WILD-TYPE 120 123 259
'GPRIN2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.698 (Chi-square test), Q value = 1

Table S486.  Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
GPRIN2 MUTATED 4 4 0 3 0
GPRIN2 WILD-TYPE 349 235 94 230 42
'GPRIN2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.655 (Chi-square test), Q value = 1

Table S487.  Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
GPRIN2 MUTATED 2 2 2 1 0 0
GPRIN2 WILD-TYPE 109 161 93 120 54 103
'GPRIN2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.877 (Fisher's exact test), Q value = 1

Table S488.  Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
GPRIN2 MUTATED 3 2 1
GPRIN2 WILD-TYPE 142 128 117
'GPRIN2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.33 (Fisher's exact test), Q value = 1

Table S489.  Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
GPRIN2 MUTATED 3 0 3
GPRIN2 WILD-TYPE 151 113 123
'GPRIN2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.845 (Chi-square test), Q value = 1

Table S490.  Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
GPRIN2 MUTATED 3 1 3 2 1 1
GPRIN2 WILD-TYPE 178 93 241 160 242 46
'GPRIN2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.433 (Fisher's exact test), Q value = 1

Table S491.  Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
GPRIN2 MUTATED 4 3 4
GPRIN2 WILD-TYPE 316 414 230
'GPRIN2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.406 (Chi-square test), Q value = 1

Table S492.  Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
GPRIN2 MUTATED 1 1 4 4 0 0
GPRIN2 WILD-TYPE 195 155 203 230 132 31
'GPRIN2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.578 (Fisher's exact test), Q value = 1

Table S493.  Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
GPRIN2 MUTATED 4 4 2
GPRIN2 WILD-TYPE 507 251 188
'GPRIN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.7 (Fisher's exact test), Q value = 1

Table S494.  Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
GPRIN2 MUTATED 3 2 4
GPRIN2 WILD-TYPE 244 205 193
'GPRIN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.324 (Fisher's exact test), Q value = 1

Table S495.  Gene #42: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
GPRIN2 MUTATED 4 4 1
GPRIN2 WILD-TYPE 146 337 159
'TRPM5 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.237 (Chi-square test), Q value = 1

Table S496.  Gene #43: 'TRPM5 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
TRPM5 MUTATED 0 0 1 1 0 0 1 0
TRPM5 WILD-TYPE 21 38 113 96 108 73 18 39
'TRPM5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.615 (Fisher's exact test), Q value = 1

Table S497.  Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
TRPM5 MUTATED 1 1 1
TRPM5 WILD-TYPE 121 125 260
'TRPM5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S498.  Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
TRPM5 MUTATED 4 3 0 3 1
TRPM5 WILD-TYPE 349 236 94 230 41
'TRPM5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.251 (Chi-square test), Q value = 1

Table S499.  Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
TRPM5 MUTATED 4 1 0 1 1 2
TRPM5 WILD-TYPE 107 162 95 120 53 101
'TRPM5 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S500.  Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
TRPM5 MUTATED 2 1 0
TRPM5 WILD-TYPE 143 129 118
'TRPM5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.782 (Fisher's exact test), Q value = 1

Table S501.  Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
TRPM5 MUTATED 2 0 1
TRPM5 WILD-TYPE 152 113 125
'TRPM5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.288 (Chi-square test), Q value = 1

Table S502.  Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
TRPM5 MUTATED 5 1 1 2 2 0
TRPM5 WILD-TYPE 176 93 243 160 241 47
'TRPM5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0629 (Fisher's exact test), Q value = 1

Table S503.  Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
TRPM5 MUTATED 3 2 6
TRPM5 WILD-TYPE 317 415 228
'TRPM5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.288 (Chi-square test), Q value = 1

Table S504.  Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
TRPM5 MUTATED 1 2 1 6 1 0
TRPM5 WILD-TYPE 195 154 206 228 131 31
'TRPM5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.105 (Fisher's exact test), Q value = 1

Table S505.  Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
TRPM5 MUTATED 3 6 2
TRPM5 WILD-TYPE 508 249 188
'TRPM5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 1

Table S506.  Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
TRPM5 MUTATED 1 2 7
TRPM5 WILD-TYPE 246 205 190

Figure S120.  Get High-res Image Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'TRPM5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S507.  Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
TRPM5 MUTATED 6 2 2
TRPM5 WILD-TYPE 144 339 158

Figure S121.  Get High-res Image Gene #43: 'TRPM5 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ANKRD12 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.178 (Chi-square test), Q value = 1

Table S508.  Gene #44: 'ANKRD12 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
ANKRD12 MUTATED 0 1 6 0 2 1 0 0
ANKRD12 WILD-TYPE 21 37 108 97 106 72 19 39
'ANKRD12 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.115 (Fisher's exact test), Q value = 1

Table S509.  Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
ANKRD12 MUTATED 4 0 6
ANKRD12 WILD-TYPE 118 126 255
'ANKRD12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.66 (Chi-square test), Q value = 1

Table S510.  Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
ANKRD12 MUTATED 6 3 3 5 0
ANKRD12 WILD-TYPE 347 236 91 228 42
'ANKRD12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.863 (Chi-square test), Q value = 1

Table S511.  Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
ANKRD12 MUTATED 1 2 3 2 1 2
ANKRD12 WILD-TYPE 110 161 92 119 53 101
'ANKRD12 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 1

Table S512.  Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
ANKRD12 MUTATED 4 1 1
ANKRD12 WILD-TYPE 141 129 117
'ANKRD12 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.518 (Fisher's exact test), Q value = 1

Table S513.  Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
ANKRD12 MUTATED 4 1 1
ANKRD12 WILD-TYPE 150 112 125
'ANKRD12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.42 (Chi-square test), Q value = 1

Table S514.  Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
ANKRD12 MUTATED 1 1 4 3 7 2
ANKRD12 WILD-TYPE 180 93 240 159 236 45
'ANKRD12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.1 (Fisher's exact test), Q value = 1

Table S515.  Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
ANKRD12 MUTATED 9 8 1
ANKRD12 WILD-TYPE 311 409 233
'ANKRD12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.537 (Chi-square test), Q value = 1

Table S516.  Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
ANKRD12 MUTATED 5 1 5 3 4 0
ANKRD12 WILD-TYPE 191 155 202 231 128 31
'ANKRD12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.64 (Fisher's exact test), Q value = 1

Table S517.  Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
ANKRD12 MUTATED 11 3 4
ANKRD12 WILD-TYPE 500 252 186
'ANKRD12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S518.  Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
ANKRD12 MUTATED 3 3 3
ANKRD12 WILD-TYPE 244 204 194
'ANKRD12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.399 (Fisher's exact test), Q value = 1

Table S519.  Gene #44: 'ANKRD12 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
ANKRD12 MUTATED 1 4 4
ANKRD12 WILD-TYPE 149 337 156
'FBXW7 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.818 (Chi-square test), Q value = 1

Table S520.  Gene #45: '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 = 0.64 (Fisher's exact test), Q value = 1

Table S521.  Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
FBXW7 MUTATED 2 2 2
FBXW7 WILD-TYPE 120 124 259
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0841 (Chi-square test), Q value = 1

Table S522.  Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
FBXW7 MUTATED 5 1 1 8 0
FBXW7 WILD-TYPE 348 238 93 225 42
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0025 (Chi-square test), Q value = 1

Table S523.  Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
FBXW7 MUTATED 7 2 0 0 1 1
FBXW7 WILD-TYPE 104 161 95 121 53 102

Figure S122.  Get High-res Image Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S524.  Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
FBXW7 MUTATED 2 1 0
FBXW7 WILD-TYPE 143 129 118
'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.782 (Fisher's exact test), Q value = 1

Table S525.  Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
FBXW7 MUTATED 2 0 1
FBXW7 WILD-TYPE 152 113 125
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0582 (Chi-square test), Q value = 1

Table S526.  Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
FBXW7 MUTATED 7 1 5 1 1 0
FBXW7 WILD-TYPE 174 93 239 161 242 47
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.135 (Fisher's exact test), Q value = 1

Table S527.  Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
FBXW7 MUTATED 4 4 7
FBXW7 WILD-TYPE 316 413 227
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.426 (Chi-square test), Q value = 1

Table S528.  Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
FBXW7 MUTATED 3 1 2 7 2 0
FBXW7 WILD-TYPE 193 155 205 227 130 31
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.256 (Fisher's exact test), Q value = 1

Table S529.  Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
FBXW7 MUTATED 6 7 2
FBXW7 WILD-TYPE 505 248 188
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S530.  Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
FBXW7 MUTATED 3 2 5
FBXW7 WILD-TYPE 244 205 192
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.125 (Fisher's exact test), Q value = 1

Table S531.  Gene #45: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
FBXW7 MUTATED 5 3 2
FBXW7 WILD-TYPE 145 338 158
'PRICKLE3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.335 (Chi-square test), Q value = 1

Table S532.  Gene #46: 'PRICKLE3 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
PRICKLE3 MUTATED 1 0 0 3 1 2 0 0
PRICKLE3 WILD-TYPE 20 38 114 94 107 71 19 39
'PRICKLE3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.282 (Fisher's exact test), Q value = 1

Table S533.  Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
PRICKLE3 MUTATED 0 3 4
PRICKLE3 WILD-TYPE 122 123 257
'PRICKLE3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.951 (Chi-square test), Q value = 1

Table S534.  Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
PRICKLE3 MUTATED 4 2 1 3 0
PRICKLE3 WILD-TYPE 349 237 93 230 42
'PRICKLE3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.609 (Chi-square test), Q value = 1

Table S535.  Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
PRICKLE3 MUTATED 0 1 2 1 0 1
PRICKLE3 WILD-TYPE 111 162 93 120 54 102
'PRICKLE3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.509 (Fisher's exact test), Q value = 1

Table S536.  Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
PRICKLE3 MUTATED 4 1 2
PRICKLE3 WILD-TYPE 141 129 116
'PRICKLE3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.891 (Fisher's exact test), Q value = 1

Table S537.  Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
PRICKLE3 MUTATED 2 2 3
PRICKLE3 WILD-TYPE 152 111 123
'PRICKLE3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.327 (Chi-square test), Q value = 1

Table S538.  Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
PRICKLE3 MUTATED 3 0 3 4 1 0
PRICKLE3 WILD-TYPE 178 94 241 158 242 47
'PRICKLE3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.126 (Fisher's exact test), Q value = 1

Table S539.  Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
PRICKLE3 MUTATED 1 5 5
PRICKLE3 WILD-TYPE 319 412 229
'PRICKLE3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.491 (Chi-square test), Q value = 1

Table S540.  Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
PRICKLE3 MUTATED 3 3 1 4 0 0
PRICKLE3 WILD-TYPE 193 153 206 230 132 31
'PRICKLE3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.13 (Fisher's exact test), Q value = 1

Table S541.  Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
PRICKLE3 MUTATED 4 6 1
PRICKLE3 WILD-TYPE 507 249 189
'PRICKLE3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.598 (Fisher's exact test), Q value = 1

Table S542.  Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
PRICKLE3 MUTATED 2 1 3
PRICKLE3 WILD-TYPE 245 206 194
'PRICKLE3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 1

Table S543.  Gene #46: 'PRICKLE3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
PRICKLE3 MUTATED 3 2 1
PRICKLE3 WILD-TYPE 147 339 159
'WDR52 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.768 (Chi-square test), Q value = 1

Table S544.  Gene #47: 'WDR52 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
WDR52 MUTATED 0 1 1 2 1 1 1 0
WDR52 WILD-TYPE 21 37 113 95 107 72 18 39
'WDR52 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0565 (Fisher's exact test), Q value = 1

Table S545.  Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
WDR52 MUTATED 2 4 1
WDR52 WILD-TYPE 120 122 260
'WDR52 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.22 (Chi-square test), Q value = 1

Table S546.  Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
WDR52 MUTATED 4 5 0 7 0
WDR52 WILD-TYPE 349 234 94 226 42
'WDR52 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S547.  Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
WDR52 MUTATED 3 0 2 4 1 0
WDR52 WILD-TYPE 108 163 93 117 53 103
'WDR52 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00424 (Fisher's exact test), Q value = 1

Table S548.  Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
WDR52 MUTATED 6 0 0
WDR52 WILD-TYPE 139 130 118

Figure S123.  Get High-res Image Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'WDR52 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.137 (Fisher's exact test), Q value = 1

Table S549.  Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
WDR52 MUTATED 2 0 4
WDR52 WILD-TYPE 152 113 122
'WDR52 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0134 (Chi-square test), Q value = 1

Table S550.  Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
WDR52 MUTATED 3 1 1 8 3 0
WDR52 WILD-TYPE 178 93 243 154 240 47

Figure S124.  Get High-res Image Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'WDR52 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.4 (Fisher's exact test), Q value = 1

Table S551.  Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
WDR52 MUTATED 5 5 6
WDR52 WILD-TYPE 315 412 228
'WDR52 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.303 (Chi-square test), Q value = 1

Table S552.  Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
WDR52 MUTATED 2 2 1 7 3 0
WDR52 WILD-TYPE 194 154 206 227 129 31
'WDR52 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.477 (Fisher's exact test), Q value = 1

Table S553.  Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
WDR52 MUTATED 9 5 1
WDR52 WILD-TYPE 502 250 189
'WDR52 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0455 (Fisher's exact test), Q value = 1

Table S554.  Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
WDR52 MUTATED 4 0 5
WDR52 WILD-TYPE 243 207 192

Figure S125.  Get High-res Image Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'WDR52 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S555.  Gene #47: 'WDR52 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
WDR52 MUTATED 3 5 1
WDR52 WILD-TYPE 147 336 159
'CDC42EP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.579 (Chi-square test), Q value = 1

Table S556.  Gene #48: '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 = 0.452 (Fisher's exact test), Q value = 1

Table S557.  Gene #48: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
CDC42EP1 MUTATED 1 2 1
CDC42EP1 WILD-TYPE 121 124 260
'CDC42EP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.638 (Chi-square test), Q value = 1

Table S558.  Gene #48: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
CDC42EP1 MUTATED 2 0 1 2 0
CDC42EP1 WILD-TYPE 351 239 93 231 42
'CDC42EP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.242 (Chi-square test), Q value = 1

Table S559.  Gene #48: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
CDC42EP1 MUTATED 0 1 0 0 0 2
CDC42EP1 WILD-TYPE 111 162 95 121 54 101
'CDC42EP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.836 (Fisher's exact test), Q value = 1

Table S560.  Gene #48: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
CDC42EP1 MUTATED 1 2 1
CDC42EP1 WILD-TYPE 144 128 117
'CDC42EP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S561.  Gene #48: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
CDC42EP1 MUTATED 1 1 2
CDC42EP1 WILD-TYPE 153 112 124
'CDC42EP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.276 (Chi-square test), Q value = 1

Table S562.  Gene #48: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
CDC42EP1 MUTATED 2 1 0 0 1 1
CDC42EP1 WILD-TYPE 179 93 244 162 242 46
'CDC42EP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S563.  Gene #48: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
CDC42EP1 MUTATED 2 1 2
CDC42EP1 WILD-TYPE 318 416 232
'CDC42EP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.707 (Chi-square test), Q value = 1

Table S564.  Gene #48: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
CDC42EP1 MUTATED 1 0 2 2 0 0
CDC42EP1 WILD-TYPE 195 156 205 232 132 31
'CDC42EP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.124 (Fisher's exact test), Q value = 1

Table S565.  Gene #48: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
CDC42EP1 MUTATED 1 3 1
CDC42EP1 WILD-TYPE 510 252 189
'ERBB3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.412 (Chi-square test), Q value = 1

Table S566.  Gene #49: 'ERBB3 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
ERBB3 MUTATED 1 0 1 3 1 3 1 0
ERBB3 WILD-TYPE 20 38 113 94 107 70 18 39
'ERBB3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.225 (Fisher's exact test), Q value = 1

Table S567.  Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
ERBB3 MUTATED 2 5 3
ERBB3 WILD-TYPE 120 121 258
'ERBB3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.867 (Chi-square test), Q value = 1

Table S568.  Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
ERBB3 MUTATED 7 5 1 4 0
ERBB3 WILD-TYPE 346 234 93 229 42
'ERBB3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.522 (Chi-square test), Q value = 1

Table S569.  Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
ERBB3 MUTATED 1 1 2 3 1 0
ERBB3 WILD-TYPE 110 162 93 118 53 103
'ERBB3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.335 (Fisher's exact test), Q value = 1

Table S570.  Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
ERBB3 MUTATED 5 1 3
ERBB3 WILD-TYPE 140 129 115
'ERBB3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.298 (Fisher's exact test), Q value = 1

Table S571.  Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
ERBB3 MUTATED 3 1 5
ERBB3 WILD-TYPE 151 112 121
'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.031 (Chi-square test), Q value = 1

Table S572.  Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
ERBB3 MUTATED 4 0 3 8 3 0
ERBB3 WILD-TYPE 177 94 241 154 240 47

Figure S126.  Get High-res Image Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.211 (Fisher's exact test), Q value = 1

Table S573.  Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
ERBB3 MUTATED 3 8 7
ERBB3 WILD-TYPE 317 409 227
'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.143 (Chi-square test), Q value = 1

Table S574.  Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
ERBB3 MUTATED 6 1 1 5 5 0
ERBB3 WILD-TYPE 190 155 206 229 127 31
'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.81 (Fisher's exact test), Q value = 1

Table S575.  Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
ERBB3 MUTATED 9 6 3
ERBB3 WILD-TYPE 502 249 187
'ERBB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S576.  Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
ERBB3 MUTATED 5 4 4
ERBB3 WILD-TYPE 242 203 193
'ERBB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.817 (Fisher's exact test), Q value = 1

Table S577.  Gene #49: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
ERBB3 MUTATED 2 7 4
ERBB3 WILD-TYPE 148 334 156
'FHOD3 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S578.  Gene #50: 'FHOD3 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
FHOD3 MUTATED 0 1 1 5 0 0 0 0
FHOD3 WILD-TYPE 21 37 113 92 108 73 19 39

Figure S127.  Get High-res Image Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'FHOD3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 1

Table S579.  Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
FHOD3 MUTATED 1 5 1
FHOD3 WILD-TYPE 121 121 260

Figure S128.  Get High-res Image Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'FHOD3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.162 (Chi-square test), Q value = 1

Table S580.  Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
FHOD3 MUTATED 3 2 1 7 0
FHOD3 WILD-TYPE 350 237 93 226 42
'FHOD3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0262 (Chi-square test), Q value = 1

Table S581.  Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
FHOD3 MUTATED 3 0 2 0 3 1
FHOD3 WILD-TYPE 108 163 93 121 51 102

Figure S129.  Get High-res Image Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'FHOD3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 1

Table S582.  Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
FHOD3 MUTATED 4 1 1
FHOD3 WILD-TYPE 141 129 117
'FHOD3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0261 (Fisher's exact test), Q value = 1

Table S583.  Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
FHOD3 MUTATED 1 0 5
FHOD3 WILD-TYPE 153 113 121

Figure S130.  Get High-res Image Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'FHOD3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.129 (Chi-square test), Q value = 1

Table S584.  Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
FHOD3 MUTATED 6 2 1 2 2 0
FHOD3 WILD-TYPE 175 92 243 160 241 47
'FHOD3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00296 (Fisher's exact test), Q value = 1

Table S585.  Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
FHOD3 MUTATED 4 1 8
FHOD3 WILD-TYPE 316 416 226

Figure S131.  Get High-res Image Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'FHOD3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.17 (Chi-square test), Q value = 1

Table S586.  Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
FHOD3 MUTATED 2 1 1 7 1 1
FHOD3 WILD-TYPE 194 155 206 227 131 30
'FHOD3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S587.  Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
FHOD3 MUTATED 3 8 2
FHOD3 WILD-TYPE 508 247 188

Figure S132.  Get High-res Image Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'FHOD3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.7 (Fisher's exact test), Q value = 1

Table S588.  Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
FHOD3 MUTATED 3 2 4
FHOD3 WILD-TYPE 244 205 193
'FHOD3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0408 (Fisher's exact test), Q value = 1

Table S589.  Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
FHOD3 MUTATED 5 2 2
FHOD3 WILD-TYPE 145 339 158

Figure S133.  Get High-res Image Gene #50: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTHLH MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.442 (Chi-square test), Q value = 1

Table S590.  Gene #51: 'PTHLH 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
PTHLH MUTATED 0 1 0 0 1 2 0 1
PTHLH WILD-TYPE 21 37 114 97 107 71 19 38
'PTHLH MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.358 (Fisher's exact test), Q value = 1

Table S591.  Gene #51: 'PTHLH MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
PTHLH MUTATED 2 0 3
PTHLH WILD-TYPE 120 126 258
'PTHLH MUTATION STATUS' versus 'CN_CNMF'

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

Table S592.  Gene #51: 'PTHLH MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
PTHLH MUTATED 1 1 2 1 2
PTHLH WILD-TYPE 352 238 92 232 40

Figure S134.  Get High-res Image Gene #51: 'PTHLH MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PTHLH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0533 (Chi-square test), Q value = 1

Table S593.  Gene #51: 'PTHLH MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
PTHLH MUTATED 1 0 3 0 1 0
PTHLH WILD-TYPE 110 163 92 121 53 103
'PTHLH MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.69 (Fisher's exact test), Q value = 1

Table S594.  Gene #51: 'PTHLH MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
PTHLH MUTATED 1 1 2
PTHLH WILD-TYPE 144 129 116
'PTHLH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.392 (Fisher's exact test), Q value = 1

Table S595.  Gene #51: 'PTHLH MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
PTHLH MUTATED 2 2 0
PTHLH WILD-TYPE 152 111 126
'PTHLH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.721 (Chi-square test), Q value = 1

Table S596.  Gene #51: 'PTHLH MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
PTHLH MUTATED 0 1 2 1 2 1
PTHLH WILD-TYPE 181 93 242 161 241 46
'PTHLH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.341 (Fisher's exact test), Q value = 1

Table S597.  Gene #51: 'PTHLH MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
PTHLH MUTATED 3 4 0
PTHLH WILD-TYPE 317 413 234
'PTHLH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.231 (Chi-square test), Q value = 1

Table S598.  Gene #51: 'PTHLH MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
PTHLH MUTATED 3 0 0 1 2 0
PTHLH WILD-TYPE 193 156 207 233 130 31
'PTHLH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.29 (Fisher's exact test), Q value = 1

Table S599.  Gene #51: 'PTHLH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
PTHLH MUTATED 5 0 1
PTHLH WILD-TYPE 506 255 189
'SHISA4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0213 (Chi-square test), Q value = 1

Table S600.  Gene #52: 'SHISA4 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
SHISA4 MUTATED 0 2 1 0 0 0 0 0
SHISA4 WILD-TYPE 21 36 113 97 108 73 19 39

Figure S135.  Get High-res Image Gene #52: 'SHISA4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'SHISA4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.203 (Fisher's exact test), Q value = 1

Table S601.  Gene #52: 'SHISA4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
SHISA4 MUTATED 2 0 1
SHISA4 WILD-TYPE 120 126 260
'SHISA4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.218 (Chi-square test), Q value = 1

Table S602.  Gene #52: 'SHISA4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
SHISA4 MUTATED 0 1 1 2 1
SHISA4 WILD-TYPE 353 238 93 231 41
'SHISA4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.266 (Chi-square test), Q value = 1

Table S603.  Gene #52: 'SHISA4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
SHISA4 MUTATED 2 0 0 0 1 1
SHISA4 WILD-TYPE 109 163 95 121 53 102
'SHISA4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.272 (Chi-square test), Q value = 1

Table S604.  Gene #52: 'SHISA4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
SHISA4 MUTATED 1 2 0 1 1 0
SHISA4 WILD-TYPE 180 92 244 161 242 47
'SHISA4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.454 (Fisher's exact test), Q value = 1

Table S605.  Gene #52: 'SHISA4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
SHISA4 MUTATED 3 1 1
SHISA4 WILD-TYPE 317 416 233
'SHISA4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.342 (Chi-square test), Q value = 1

Table S606.  Gene #52: 'SHISA4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
SHISA4 MUTATED 2 0 1 0 2 0
SHISA4 WILD-TYPE 194 156 206 234 130 31
'SHISA4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S607.  Gene #52: 'SHISA4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
SHISA4 MUTATED 3 1 1
SHISA4 WILD-TYPE 508 254 189
'KCNN3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.321 (Chi-square test), Q value = 1

Table S608.  Gene #53: '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 = 0.839 (Fisher's exact test), Q value = 1

Table S609.  Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
KCNN3 MUTATED 1 2 2
KCNN3 WILD-TYPE 121 124 259
'KCNN3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.212 (Chi-square test), Q value = 1

Table S610.  Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
KCNN3 MUTATED 1 4 0 4 0
KCNN3 WILD-TYPE 352 235 94 229 42
'KCNN3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.27 (Chi-square test), Q value = 1

Table S611.  Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
KCNN3 MUTATED 2 0 0 2 1 0
KCNN3 WILD-TYPE 109 163 95 119 53 103
'KCNN3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.328 (Fisher's exact test), Q value = 1

Table S612.  Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
KCNN3 MUTATED 3 0 1
KCNN3 WILD-TYPE 142 130 117
'KCNN3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.144 (Fisher's exact test), Q value = 1

Table S613.  Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
KCNN3 MUTATED 0 1 3
KCNN3 WILD-TYPE 154 112 123
'KCNN3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.326 (Chi-square test), Q value = 1

Table S614.  Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
KCNN3 MUTATED 2 2 0 3 2 0
KCNN3 WILD-TYPE 179 92 244 159 241 47
'KCNN3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.236 (Fisher's exact test), Q value = 1

Table S615.  Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
KCNN3 MUTATED 1 4 4
KCNN3 WILD-TYPE 319 413 230
'KCNN3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.409 (Chi-square test), Q value = 1

Table S616.  Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
KCNN3 MUTATED 2 0 1 3 3 0
KCNN3 WILD-TYPE 194 156 206 231 129 31
'KCNN3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.906 (Fisher's exact test), Q value = 1

Table S617.  Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
KCNN3 MUTATED 5 3 1
KCNN3 WILD-TYPE 506 252 189
'KCNN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.165 (Fisher's exact test), Q value = 1

Table S618.  Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
KCNN3 MUTATED 4 0 1
KCNN3 WILD-TYPE 243 207 196
'KCNN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.613 (Fisher's exact test), Q value = 1

Table S619.  Gene #53: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
KCNN3 MUTATED 0 4 1
KCNN3 WILD-TYPE 150 337 159
'FGFR2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.841 (Chi-square test), Q value = 1

Table S620.  Gene #54: '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 S621.  Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
FGFR2 MUTATED 1 2 3
FGFR2 WILD-TYPE 121 124 258
'FGFR2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S622.  Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
FGFR2 MUTATED 4 3 2 2 0
FGFR2 WILD-TYPE 349 236 92 231 42
'FGFR2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.208 (Chi-square test), Q value = 1

Table S623.  Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
FGFR2 MUTATED 0 0 2 2 1 0
FGFR2 WILD-TYPE 111 163 93 119 53 103
'FGFR2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S624.  Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
FGFR2 MUTATED 2 2 1
FGFR2 WILD-TYPE 143 128 117
'FGFR2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S625.  Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
FGFR2 MUTATED 2 1 2
FGFR2 WILD-TYPE 152 112 124
'FGFR2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.443 (Chi-square test), Q value = 1

Table S626.  Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
FGFR2 MUTATED 1 0 3 4 3 0
FGFR2 WILD-TYPE 180 94 241 158 240 47
'FGFR2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S627.  Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
FGFR2 MUTATED 3 6 2
FGFR2 WILD-TYPE 317 411 232
'FGFR2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.666 (Chi-square test), Q value = 1

Table S628.  Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
FGFR2 MUTATED 1 1 3 4 1 1
FGFR2 WILD-TYPE 195 155 204 230 131 30
'FGFR2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S629.  Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
FGFR2 MUTATED 6 3 2
FGFR2 WILD-TYPE 505 252 188
'FGFR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S630.  Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
FGFR2 MUTATED 2 2 3
FGFR2 WILD-TYPE 245 205 194
'FGFR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.593 (Fisher's exact test), Q value = 1

Table S631.  Gene #54: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
FGFR2 MUTATED 1 3 3
FGFR2 WILD-TYPE 149 338 157
'HLA-DRB5 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00723 (Chi-square test), Q value = 1

Table S632.  Gene #55: 'HLA-DRB5 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
HLA-DRB5 MUTATED 0 2 0 0 0 0 0 1
HLA-DRB5 WILD-TYPE 21 36 114 97 108 73 19 38

Figure S136.  Get High-res Image Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'HLA-DRB5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 1

Table S633.  Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
HLA-DRB5 MUTATED 3 0 0
HLA-DRB5 WILD-TYPE 119 126 261

Figure S137.  Get High-res Image Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'HLA-DRB5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.248 (Chi-square test), Q value = 1

Table S634.  Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
HLA-DRB5 MUTATED 1 2 1 0 1
HLA-DRB5 WILD-TYPE 352 237 93 233 41
'HLA-DRB5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.876 (Chi-square test), Q value = 1

Table S635.  Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
HLA-DRB5 MUTATED 1 1 1 1 1 0
HLA-DRB5 WILD-TYPE 110 162 94 120 53 103
'HLA-DRB5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.253 (Chi-square test), Q value = 1

Table S636.  Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
HLA-DRB5 MUTATED 1 2 1 0 1 1
HLA-DRB5 WILD-TYPE 180 92 243 162 242 46
'HLA-DRB5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.77 (Fisher's exact test), Q value = 1

Table S637.  Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
HLA-DRB5 MUTATED 3 2 1
HLA-DRB5 WILD-TYPE 317 415 233
'HLA-DRB5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.224 (Chi-square test), Q value = 1

Table S638.  Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
HLA-DRB5 MUTATED 3 0 1 0 2 0
HLA-DRB5 WILD-TYPE 193 156 206 234 130 31
'HLA-DRB5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S639.  Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
HLA-DRB5 MUTATED 4 1 1
HLA-DRB5 WILD-TYPE 507 254 189
'HLA-DRB5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.78 (Fisher's exact test), Q value = 1

Table S640.  Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
HLA-DRB5 MUTATED 2 1 0
HLA-DRB5 WILD-TYPE 245 206 197
'HLA-DRB5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S641.  Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
HLA-DRB5 MUTATED 0 2 1
HLA-DRB5 WILD-TYPE 150 339 159
'ICOSLG MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.693 (Chi-square test), Q value = 1

Table S642.  Gene #56: '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 = 1 (Fisher's exact test), Q value = 1

Table S643.  Gene #56: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
ICOSLG MUTATED 0 1 2
ICOSLG WILD-TYPE 122 125 259
'ICOSLG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0103 (Chi-square test), Q value = 1

Table S644.  Gene #56: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
ICOSLG MUTATED 1 1 0 2 2
ICOSLG WILD-TYPE 352 238 94 231 40

Figure S138.  Get High-res Image Gene #56: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ICOSLG MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.623 (Chi-square test), Q value = 1

Table S645.  Gene #56: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
ICOSLG MUTATED 1 1 2 1 0 0
ICOSLG WILD-TYPE 110 162 93 120 54 103
'ICOSLG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.107 (Chi-square test), Q value = 1

Table S646.  Gene #56: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
ICOSLG MUTATED 1 0 0 0 4 1
ICOSLG WILD-TYPE 180 94 244 162 239 46
'ICOSLG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S647.  Gene #56: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
ICOSLG MUTATED 2 3 1
ICOSLG WILD-TYPE 318 414 233
'ICOSLG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.156 (Chi-square test), Q value = 1

Table S648.  Gene #56: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
ICOSLG MUTATED 0 0 3 1 1 1
ICOSLG WILD-TYPE 196 156 204 233 131 30
'ICOSLG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S649.  Gene #56: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
ICOSLG MUTATED 3 2 1
ICOSLG WILD-TYPE 508 253 189
'ICOSLG MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S650.  Gene #56: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
ICOSLG MUTATED 1 1 1
ICOSLG WILD-TYPE 246 206 196
'ICOSLG MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.607 (Fisher's exact test), Q value = 1

Table S651.  Gene #56: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
ICOSLG MUTATED 1 1 1
ICOSLG WILD-TYPE 149 340 159
'GYG2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.703 (Chi-square test), Q value = 1

Table S652.  Gene #57: 'GYG2 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
GYG2 MUTATED 0 1 3 1 1 0 0 0
GYG2 WILD-TYPE 21 37 111 96 107 73 19 39
'GYG2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S653.  Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
GYG2 MUTATED 1 1 4
GYG2 WILD-TYPE 121 125 257
'GYG2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S654.  Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
GYG2 MUTATED 2 5 0 1 0
GYG2 WILD-TYPE 351 234 94 232 42
'GYG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.714 (Chi-square test), Q value = 1

Table S655.  Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
GYG2 MUTATED 2 1 1 1 0 0
GYG2 WILD-TYPE 109 162 94 120 54 103
'GYG2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.156 (Fisher's exact test), Q value = 1

Table S656.  Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
GYG2 MUTATED 0 3 1
GYG2 WILD-TYPE 145 127 117
'GYG2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0398 (Fisher's exact test), Q value = 1

Table S657.  Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
GYG2 MUTATED 4 0 0
GYG2 WILD-TYPE 150 113 126

Figure S139.  Get High-res Image Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'GYG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.885 (Chi-square test), Q value = 1

Table S658.  Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
GYG2 MUTATED 2 1 1 1 3 0
GYG2 WILD-TYPE 179 93 243 161 240 47
'GYG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S659.  Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
GYG2 MUTATED 2 4 2
GYG2 WILD-TYPE 318 413 232
'GYG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.44 (Chi-square test), Q value = 1

Table S660.  Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
GYG2 MUTATED 0 1 3 2 1 1
GYG2 WILD-TYPE 196 155 204 232 131 30
'GYG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S661.  Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
GYG2 MUTATED 5 2 1
GYG2 WILD-TYPE 506 253 189
'GYG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 1

Table S662.  Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
GYG2 MUTATED 1 0 2
GYG2 WILD-TYPE 246 207 195
'GYG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.191 (Fisher's exact test), Q value = 1

Table S663.  Gene #57: 'GYG2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
GYG2 MUTATED 2 1 0
GYG2 WILD-TYPE 148 340 160
'PPEF1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.84 (Chi-square test), Q value = 1

Table S664.  Gene #58: 'PPEF1 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
PPEF1 MUTATED 0 0 3 2 1 1 0 0
PPEF1 WILD-TYPE 21 38 111 95 107 72 19 39
'PPEF1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S665.  Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
PPEF1 MUTATED 1 2 4
PPEF1 WILD-TYPE 121 124 257
'PPEF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.306 (Chi-square test), Q value = 1

Table S666.  Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
PPEF1 MUTATED 1 5 1 3 1
PPEF1 WILD-TYPE 352 234 93 230 41
'PPEF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.575 (Chi-square test), Q value = 1

Table S667.  Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
PPEF1 MUTATED 2 1 1 3 1 0
PPEF1 WILD-TYPE 109 162 94 118 53 103
'PPEF1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S668.  Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
PPEF1 MUTATED 2 2 2
PPEF1 WILD-TYPE 143 128 116
'PPEF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S669.  Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
PPEF1 MUTATED 2 2 2
PPEF1 WILD-TYPE 152 111 124
'PPEF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.823 (Chi-square test), Q value = 1

Table S670.  Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
PPEF1 MUTATED 3 0 2 2 3 1
PPEF1 WILD-TYPE 178 94 242 160 240 46
'PPEF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.634 (Fisher's exact test), Q value = 1

Table S671.  Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
PPEF1 MUTATED 2 6 3
PPEF1 WILD-TYPE 318 411 231
'PPEF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.259 (Chi-square test), Q value = 1

Table S672.  Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
PPEF1 MUTATED 0 1 2 5 3 0
PPEF1 WILD-TYPE 196 155 205 229 129 31
'PPEF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.33 (Fisher's exact test), Q value = 1

Table S673.  Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
PPEF1 MUTATED 4 5 2
PPEF1 WILD-TYPE 507 250 188
'PPEF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S674.  Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
PPEF1 MUTATED 2 2 3
PPEF1 WILD-TYPE 245 205 194
'PPEF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.785 (Fisher's exact test), Q value = 1

Table S675.  Gene #58: 'PPEF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
PPEF1 MUTATED 2 3 2
PPEF1 WILD-TYPE 148 338 158
'MAP4K1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.828 (Chi-square test), Q value = 1

Table S676.  Gene #59: 'MAP4K1 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
MAP4K1 MUTATED 0 0 1 2 1 0 0 0
MAP4K1 WILD-TYPE 21 38 113 95 107 73 19 39
'MAP4K1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.452 (Fisher's exact test), Q value = 1

Table S677.  Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
MAP4K1 MUTATED 1 2 1
MAP4K1 WILD-TYPE 121 124 260
'MAP4K1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.358 (Chi-square test), Q value = 1

Table S678.  Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
MAP4K1 MUTATED 1 4 1 4 0
MAP4K1 WILD-TYPE 352 235 93 229 42
'MAP4K1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.577 (Chi-square test), Q value = 1

Table S679.  Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
MAP4K1 MUTATED 2 2 1 3 0 0
MAP4K1 WILD-TYPE 109 161 94 118 54 103
'MAP4K1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S680.  Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
MAP4K1 MUTATED 1 1 1
MAP4K1 WILD-TYPE 144 129 117
'MAP4K1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.782 (Fisher's exact test), Q value = 1

Table S681.  Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
MAP4K1 MUTATED 2 0 1
MAP4K1 WILD-TYPE 152 113 125
'MAP4K1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.434 (Chi-square test), Q value = 1

Table S682.  Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
MAP4K1 MUTATED 3 0 3 0 4 0
MAP4K1 WILD-TYPE 178 94 241 162 239 47
'MAP4K1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.849 (Fisher's exact test), Q value = 1

Table S683.  Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
MAP4K1 MUTATED 3 4 3
MAP4K1 WILD-TYPE 317 413 231
'MAP4K1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.963 (Chi-square test), Q value = 1

Table S684.  Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
MAP4K1 MUTATED 2 1 2 3 2 0
MAP4K1 WILD-TYPE 194 155 205 231 130 31
'MAP4K1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.326 (Fisher's exact test), Q value = 1

Table S685.  Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
MAP4K1 MUTATED 7 3 0
MAP4K1 WILD-TYPE 504 252 190
'MAP4K1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.239 (Fisher's exact test), Q value = 1

Table S686.  Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
MAP4K1 MUTATED 5 1 1
MAP4K1 WILD-TYPE 242 206 196
'MAP4K1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.207 (Fisher's exact test), Q value = 1

Table S687.  Gene #59: 'MAP4K1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
MAP4K1 MUTATED 1 6 0
MAP4K1 WILD-TYPE 149 335 160
'ZNF41 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.81 (Chi-square test), Q value = 1

Table S688.  Gene #60: 'ZNF41 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
ZNF41 MUTATED 1 1 1 2 1 1 0 0
ZNF41 WILD-TYPE 20 37 113 95 107 72 19 39
'ZNF41 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.465 (Fisher's exact test), Q value = 1

Table S689.  Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
ZNF41 MUTATED 2 3 2
ZNF41 WILD-TYPE 120 123 259
'ZNF41 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.656 (Chi-square test), Q value = 1

Table S690.  Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
ZNF41 MUTATED 3 2 2 4 0
ZNF41 WILD-TYPE 350 237 92 229 42
'ZNF41 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.207 (Chi-square test), Q value = 1

Table S691.  Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
ZNF41 MUTATED 1 0 3 1 0 1
ZNF41 WILD-TYPE 110 163 92 120 54 102
'ZNF41 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.877 (Fisher's exact test), Q value = 1

Table S692.  Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
ZNF41 MUTATED 3 2 1
ZNF41 WILD-TYPE 142 128 117
'ZNF41 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.291 (Fisher's exact test), Q value = 1

Table S693.  Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
ZNF41 MUTATED 4 0 2
ZNF41 WILD-TYPE 150 113 124
'ZNF41 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.693 (Chi-square test), Q value = 1

Table S694.  Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
ZNF41 MUTATED 3 0 2 3 3 0
ZNF41 WILD-TYPE 178 94 242 159 240 47
'ZNF41 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S695.  Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
ZNF41 MUTATED 2 5 4
ZNF41 WILD-TYPE 318 412 230
'ZNF41 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0401 (Chi-square test), Q value = 1

Table S696.  Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
ZNF41 MUTATED 3 0 2 1 5 0
ZNF41 WILD-TYPE 193 156 205 233 127 31

Figure S140.  Get High-res Image Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'ZNF41 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S697.  Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
ZNF41 MUTATED 7 3 1
ZNF41 WILD-TYPE 504 252 189
'ZNF41 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0924 (Fisher's exact test), Q value = 1

Table S698.  Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
ZNF41 MUTATED 4 0 4
ZNF41 WILD-TYPE 243 207 193
'ZNF41 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S699.  Gene #60: 'ZNF41 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
ZNF41 MUTATED 1 6 1
ZNF41 WILD-TYPE 149 335 159
'FBXO17 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.82 (Chi-square test), Q value = 1

Table S700.  Gene #61: 'FBXO17 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
FBXO17 MUTATED 3 1 0 1 0
FBXO17 WILD-TYPE 350 238 94 232 42
'FBXO17 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.399 (Chi-square test), Q value = 1

Table S701.  Gene #61: 'FBXO17 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
FBXO17 MUTATED 0 1 0 2 0 2
FBXO17 WILD-TYPE 111 162 95 119 54 101
'FBXO17 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.579 (Chi-square test), Q value = 1

Table S702.  Gene #61: 'FBXO17 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
FBXO17 MUTATED 0 0 2 2 1 0
FBXO17 WILD-TYPE 181 94 242 160 242 47
'FBXO17 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.38 (Fisher's exact test), Q value = 1

Table S703.  Gene #61: 'FBXO17 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
FBXO17 MUTATED 3 2 0
FBXO17 WILD-TYPE 317 415 234
'FBXO17 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.000298 (Chi-square test), Q value = 0.23

Table S704.  Gene #61: 'FBXO17 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
FBXO17 MUTATED 0 1 0 1 1 2
FBXO17 WILD-TYPE 196 155 207 233 131 29

Figure S141.  Get High-res Image Gene #61: 'FBXO17 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'FBXO17 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S705.  Gene #61: 'FBXO17 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
FBXO17 MUTATED 3 1 1
FBXO17 WILD-TYPE 508 254 189
'FBXO17 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S706.  Gene #61: 'FBXO17 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
FBXO17 MUTATED 1 1 1
FBXO17 WILD-TYPE 246 206 196
'FBXO17 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S707.  Gene #61: 'FBXO17 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
FBXO17 MUTATED 0 2 1
FBXO17 WILD-TYPE 150 339 159
'HRNR MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.892 (Chi-square test), Q value = 1

Table S708.  Gene #62: '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 = 0.46 (Fisher's exact test), Q value = 1

Table S709.  Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
HRNR MUTATED 5 7 8
HRNR WILD-TYPE 117 119 253
'HRNR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0636 (Chi-square test), Q value = 1

Table S710.  Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
HRNR MUTATED 13 3 4 7 4
HRNR WILD-TYPE 340 236 90 226 38
'HRNR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.975 (Chi-square test), Q value = 1

Table S711.  Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
HRNR MUTATED 4 6 2 3 2 3
HRNR WILD-TYPE 107 157 93 118 52 100
'HRNR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.587 (Fisher's exact test), Q value = 1

Table S712.  Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
HRNR MUTATED 4 6 6
HRNR WILD-TYPE 141 124 112
'HRNR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.588 (Fisher's exact test), Q value = 1

Table S713.  Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
HRNR MUTATED 8 3 5
HRNR WILD-TYPE 146 110 121
'HRNR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.931 (Chi-square test), Q value = 1

Table S714.  Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
HRNR MUTATED 7 2 8 6 6 2
HRNR WILD-TYPE 174 92 236 156 237 45
'HRNR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S715.  Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
HRNR MUTATED 8 13 10
HRNR WILD-TYPE 312 404 224
'HRNR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.516 (Chi-square test), Q value = 1

Table S716.  Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
HRNR MUTATED 8 2 8 9 2 1
HRNR WILD-TYPE 188 154 199 225 130 30
'HRNR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.878 (Fisher's exact test), Q value = 1

Table S717.  Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
HRNR MUTATED 16 9 5
HRNR WILD-TYPE 495 246 185
'HRNR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.938 (Fisher's exact test), Q value = 1

Table S718.  Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
HRNR MUTATED 6 6 5
HRNR WILD-TYPE 241 201 192
'HRNR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.763 (Fisher's exact test), Q value = 1

Table S719.  Gene #62: 'HRNR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
HRNR MUTATED 5 8 4
HRNR WILD-TYPE 145 333 156
'STAG2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S720.  Gene #63: 'STAG2 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
STAG2 MUTATED 0 0 0 1 3 2 1 0
STAG2 WILD-TYPE 21 38 114 96 105 71 18 39
'STAG2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S721.  Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
STAG2 MUTATED 1 2 4
STAG2 WILD-TYPE 121 124 257
'STAG2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.226 (Chi-square test), Q value = 1

Table S722.  Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
STAG2 MUTATED 5 2 0 4 2
STAG2 WILD-TYPE 348 237 94 229 40
'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.337 (Chi-square test), Q value = 1

Table S723.  Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
STAG2 MUTATED 2 2 1 4 0 0
STAG2 WILD-TYPE 109 161 94 117 54 103
'STAG2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.877 (Fisher's exact test), Q value = 1

Table S724.  Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
STAG2 MUTATED 3 2 1
STAG2 WILD-TYPE 142 128 117
'STAG2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.676 (Fisher's exact test), Q value = 1

Table S725.  Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
STAG2 MUTATED 2 1 3
STAG2 WILD-TYPE 152 112 123
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.323 (Chi-square test), Q value = 1

Table S726.  Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
STAG2 MUTATED 2 0 3 5 2 1
STAG2 WILD-TYPE 179 94 241 157 241 46
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.727 (Fisher's exact test), Q value = 1

Table S727.  Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
STAG2 MUTATED 3 7 3
STAG2 WILD-TYPE 317 410 231
'STAG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.307 (Chi-square test), Q value = 1

Table S728.  Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
STAG2 MUTATED 0 1 3 5 3 1
STAG2 WILD-TYPE 196 155 204 229 129 30
'STAG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S729.  Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
STAG2 MUTATED 7 5 1
STAG2 WILD-TYPE 504 250 189
'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.508 (Fisher's exact test), Q value = 1

Table S730.  Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
STAG2 MUTATED 4 1 2
STAG2 WILD-TYPE 243 206 195
'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.687 (Fisher's exact test), Q value = 1

Table S731.  Gene #63: 'STAG2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
STAG2 MUTATED 1 5 1
STAG2 WILD-TYPE 149 336 159
'CEP57 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.324 (Chi-square test), Q value = 1

Table S732.  Gene #64: 'CEP57 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
CEP57 MUTATED 0 0 0 1 0 2 0 0
CEP57 WILD-TYPE 21 38 114 96 108 71 19 39
'CEP57 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S733.  Gene #64: 'CEP57 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
CEP57 MUTATED 0 1 2
CEP57 WILD-TYPE 122 125 259
'CEP57 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.112 (Chi-square test), Q value = 1

Table S734.  Gene #64: 'CEP57 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
CEP57 MUTATED 1 0 2 3 0
CEP57 WILD-TYPE 352 239 92 230 42
'CEP57 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.129 (Chi-square test), Q value = 1

Table S735.  Gene #64: 'CEP57 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
CEP57 MUTATED 0 1 1 0 0 3
CEP57 WILD-TYPE 111 162 94 121 54 100
'CEP57 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.154 (Chi-square test), Q value = 1

Table S736.  Gene #64: 'CEP57 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
CEP57 MUTATED 1 0 1 3 0 1
CEP57 WILD-TYPE 180 94 243 159 243 46
'CEP57 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S737.  Gene #64: 'CEP57 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
CEP57 MUTATED 2 3 1
CEP57 WILD-TYPE 318 414 233
'CEP57 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S738.  Gene #64: 'CEP57 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
CEP57 MUTATED 2 1 3 0 0 0
CEP57 WILD-TYPE 194 155 204 234 132 31
'CEP57 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0622 (Fisher's exact test), Q value = 1

Table S739.  Gene #64: 'CEP57 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
CEP57 MUTATED 1 2 3
CEP57 WILD-TYPE 510 253 187
'CEP57 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 1

Table S740.  Gene #64: 'CEP57 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
CEP57 MUTATED 0 2 1
CEP57 WILD-TYPE 247 205 196
'CEP57 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0267 (Fisher's exact test), Q value = 1

Table S741.  Gene #64: 'CEP57 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
CEP57 MUTATED 0 0 3
CEP57 WILD-TYPE 150 341 157

Figure S142.  Get High-res Image Gene #64: 'CEP57 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SPRR2B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.734 (Chi-square test), Q value = 1

Table S742.  Gene #65: 'SPRR2B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
SPRR2B MUTATED 2 0 0 1 0
SPRR2B WILD-TYPE 351 239 94 232 42
'SPRR2B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.505 (Chi-square test), Q value = 1

Table S743.  Gene #65: 'SPRR2B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
SPRR2B MUTATED 0 0 2 1 0 0
SPRR2B WILD-TYPE 181 94 242 161 243 47
'SPRR2B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.795 (Fisher's exact test), Q value = 1

Table S744.  Gene #65: 'SPRR2B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
SPRR2B MUTATED 1 2 0
SPRR2B WILD-TYPE 319 415 234
'SPRR2B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.909 (Chi-square test), Q value = 1

Table S745.  Gene #65: 'SPRR2B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
SPRR2B MUTATED 1 0 1 1 0 0
SPRR2B WILD-TYPE 195 156 206 233 132 31
'SPRR2B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.43 (Fisher's exact test), Q value = 1

Table S746.  Gene #65: 'SPRR2B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
SPRR2B MUTATED 3 0 0
SPRR2B WILD-TYPE 508 255 190
'ZFP36L2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.437 (Chi-square test), Q value = 1

Table S747.  Gene #66: '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 S748.  Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
ZFP36L2 MUTATED 1 1 2
ZFP36L2 WILD-TYPE 121 125 259
'ZFP36L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00951 (Chi-square test), Q value = 1

Table S749.  Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
ZFP36L2 MUTATED 0 3 1 1 2
ZFP36L2 WILD-TYPE 353 236 93 232 40

Figure S143.  Get High-res Image Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ZFP36L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.206 (Chi-square test), Q value = 1

Table S750.  Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
ZFP36L2 MUTATED 1 0 1 3 0 0
ZFP36L2 WILD-TYPE 110 163 94 118 54 103
'ZFP36L2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S751.  Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
ZFP36L2 MUTATED 1 1 1
ZFP36L2 WILD-TYPE 144 129 117
'ZFP36L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S752.  Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
ZFP36L2 MUTATED 1 1 1
ZFP36L2 WILD-TYPE 153 112 125
'ZFP36L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S753.  Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
ZFP36L2 MUTATED 1 0 1 3 2 0
ZFP36L2 WILD-TYPE 180 94 243 159 241 47
'ZFP36L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.798 (Fisher's exact test), Q value = 1

Table S754.  Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
ZFP36L2 MUTATED 2 4 1
ZFP36L2 WILD-TYPE 318 413 233
'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.66 (Chi-square test), Q value = 1

Table S755.  Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
ZFP36L2 MUTATED 1 1 2 1 1 1
ZFP36L2 WILD-TYPE 195 155 205 233 131 30
'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S756.  Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
ZFP36L2 MUTATED 4 1 2
ZFP36L2 WILD-TYPE 507 254 188
'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S757.  Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
ZFP36L2 MUTATED 2 2 1
ZFP36L2 WILD-TYPE 245 205 196
'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.836 (Fisher's exact test), Q value = 1

Table S758.  Gene #66: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
ZFP36L2 MUTATED 1 2 2
ZFP36L2 WILD-TYPE 149 339 158
'DMXL2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.697 (Chi-square test), Q value = 1

Table S759.  Gene #67: 'DMXL2 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
DMXL2 MUTATED 1 1 1 3 1 1 0 0
DMXL2 WILD-TYPE 20 37 113 94 107 72 19 39
'DMXL2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.182 (Fisher's exact test), Q value = 1

Table S760.  Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
DMXL2 MUTATED 2 4 2
DMXL2 WILD-TYPE 120 122 259
'DMXL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0502 (Chi-square test), Q value = 1

Table S761.  Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
DMXL2 MUTATED 2 5 3 9 0
DMXL2 WILD-TYPE 351 234 91 224 42
'DMXL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.158 (Chi-square test), Q value = 1

Table S762.  Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
DMXL2 MUTATED 5 0 1 3 2 3
DMXL2 WILD-TYPE 106 163 94 118 52 100
'DMXL2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S763.  Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
DMXL2 MUTATED 4 0 1
DMXL2 WILD-TYPE 141 130 117
'DMXL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0727 (Fisher's exact test), Q value = 1

Table S764.  Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
DMXL2 MUTATED 1 0 4
DMXL2 WILD-TYPE 153 113 122
'DMXL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00947 (Chi-square test), Q value = 1

Table S765.  Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
DMXL2 MUTATED 8 2 1 3 2 3
DMXL2 WILD-TYPE 173 92 243 159 241 44

Figure S144.  Get High-res Image Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'DMXL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0697 (Fisher's exact test), Q value = 1

Table S766.  Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
DMXL2 MUTATED 5 5 9
DMXL2 WILD-TYPE 315 412 225
'DMXL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0505 (Chi-square test), Q value = 1

Table S767.  Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
DMXL2 MUTATED 1 2 4 10 1 0
DMXL2 WILD-TYPE 195 154 203 224 131 31
'DMXL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.221 (Fisher's exact test), Q value = 1

Table S768.  Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
DMXL2 MUTATED 7 8 3
DMXL2 WILD-TYPE 504 247 187
'DMXL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.085 (Fisher's exact test), Q value = 1

Table S769.  Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
DMXL2 MUTATED 1 4 6
DMXL2 WILD-TYPE 246 203 191
'DMXL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.137 (Fisher's exact test), Q value = 1

Table S770.  Gene #67: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
DMXL2 MUTATED 5 3 3
DMXL2 WILD-TYPE 145 338 157
'ZBTB7C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.682 (Chi-square test), Q value = 1

Table S771.  Gene #68: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
ZBTB7C MUTATED 2 1 1 0 0
ZBTB7C WILD-TYPE 351 238 93 233 42
'ZBTB7C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.746 (Chi-square test), Q value = 1

Table S772.  Gene #68: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
ZBTB7C MUTATED 0 1 1 0 0 1
ZBTB7C WILD-TYPE 111 162 94 121 54 102
'ZBTB7C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.811 (Chi-square test), Q value = 1

Table S773.  Gene #68: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
ZBTB7C MUTATED 0 1 1 1 2 0
ZBTB7C WILD-TYPE 181 93 243 161 241 47
'ZBTB7C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.38 (Fisher's exact test), Q value = 1

Table S774.  Gene #68: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
ZBTB7C MUTATED 3 2 0
ZBTB7C WILD-TYPE 317 415 234
'ZBTB7C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.675 (Chi-square test), Q value = 1

Table S775.  Gene #68: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
ZBTB7C MUTATED 1 2 0 1 1 0
ZBTB7C WILD-TYPE 195 154 207 233 131 31
'ZBTB7C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.498 (Fisher's exact test), Q value = 1

Table S776.  Gene #68: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
ZBTB7C MUTATED 2 1 2
ZBTB7C WILD-TYPE 509 254 188
'ZBTB7C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.78 (Fisher's exact test), Q value = 1

Table S777.  Gene #68: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
ZBTB7C MUTATED 2 1 0
ZBTB7C WILD-TYPE 245 206 197
'ZBTB7C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S778.  Gene #68: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
ZBTB7C MUTATED 0 2 1
ZBTB7C WILD-TYPE 150 339 159
'MUC5B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.694 (Chi-square test), Q value = 1

Table S779.  Gene #69: 'MUC5B 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
MUC5B MUTATED 0 1 6 3 2 1 0 1
MUC5B WILD-TYPE 21 37 108 94 106 72 19 38
'MUC5B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S780.  Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
MUC5B MUTATED 4 3 7
MUC5B WILD-TYPE 118 123 254
'MUC5B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.414 (Chi-square test), Q value = 1

Table S781.  Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
MUC5B MUTATED 11 4 4 11 1
MUC5B WILD-TYPE 342 235 90 222 41
'MUC5B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.285 (Chi-square test), Q value = 1

Table S782.  Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
MUC5B MUTATED 4 3 6 6 0 4
MUC5B WILD-TYPE 107 160 89 115 54 99
'MUC5B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.915 (Fisher's exact test), Q value = 1

Table S783.  Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
MUC5B MUTATED 4 3 2
MUC5B WILD-TYPE 141 127 116
'MUC5B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.695 (Fisher's exact test), Q value = 1

Table S784.  Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
MUC5B MUTATED 5 2 2
MUC5B WILD-TYPE 149 111 124
'MUC5B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.371 (Chi-square test), Q value = 1

Table S785.  Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
MUC5B MUTATED 6 3 8 2 13 1
MUC5B WILD-TYPE 175 91 236 160 230 46
'MUC5B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S786.  Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
MUC5B MUTATED 12 15 6
MUC5B WILD-TYPE 308 402 228
'MUC5B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.779 (Chi-square test), Q value = 1

Table S787.  Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
MUC5B MUTATED 8 7 8 7 2 1
MUC5B WILD-TYPE 188 149 199 227 130 30
'MUC5B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.21 (Fisher's exact test), Q value = 1

Table S788.  Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
MUC5B MUTATED 22 8 3
MUC5B WILD-TYPE 489 247 187
'MUC5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.746 (Fisher's exact test), Q value = 1

Table S789.  Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
MUC5B MUTATED 9 8 5
MUC5B WILD-TYPE 238 199 192
'MUC5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.83 (Fisher's exact test), Q value = 1

Table S790.  Gene #69: 'MUC5B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
MUC5B MUTATED 4 13 5
MUC5B WILD-TYPE 146 328 155
'XBP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0164 (Chi-square test), Q value = 1

Table S791.  Gene #70: 'XBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
XBP1 MUTATED 0 4 0 0 0
XBP1 WILD-TYPE 353 235 94 233 42

Figure S145.  Get High-res Image Gene #70: 'XBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'XBP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.36 (Chi-square test), Q value = 1

Table S792.  Gene #70: 'XBP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
XBP1 MUTATED 0 1 0 2 0 0
XBP1 WILD-TYPE 111 162 95 119 54 103
'XBP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.347 (Chi-square test), Q value = 1

Table S793.  Gene #70: 'XBP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
XBP1 MUTATED 0 1 0 2 1 0
XBP1 WILD-TYPE 181 93 244 160 242 47
'XBP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S794.  Gene #70: 'XBP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
XBP1 MUTATED 1 2 1
XBP1 WILD-TYPE 319 415 233
'XBP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.394 (Chi-square test), Q value = 1

Table S795.  Gene #70: 'XBP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
XBP1 MUTATED 1 2 0 0 1 0
XBP1 WILD-TYPE 195 154 207 234 131 31
'XBP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.532 (Fisher's exact test), Q value = 1

Table S796.  Gene #70: 'XBP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
XBP1 MUTATED 3 0 1
XBP1 WILD-TYPE 508 255 189
'XBP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.393 (Fisher's exact test), Q value = 1

Table S797.  Gene #70: 'XBP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
XBP1 MUTATED 3 1 0
XBP1 WILD-TYPE 244 206 197
'XBP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S798.  Gene #70: 'XBP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
XBP1 MUTATED 0 3 1
XBP1 WILD-TYPE 150 338 159
'FXYD5 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.693 (Chi-square test), Q value = 1

Table S799.  Gene #71: 'FXYD5 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
FXYD5 MUTATED 0 1 1 1 0 0 0 0
FXYD5 WILD-TYPE 21 37 113 96 108 73 19 39
'FXYD5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.615 (Fisher's exact test), Q value = 1

Table S800.  Gene #71: 'FXYD5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
FXYD5 MUTATED 1 1 1
FXYD5 WILD-TYPE 121 125 260
'FXYD5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.335 (Chi-square test), Q value = 1

Table S801.  Gene #71: 'FXYD5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
FXYD5 MUTATED 4 0 0 1 0
FXYD5 WILD-TYPE 349 239 94 232 42
'FXYD5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.643 (Fisher's exact test), Q value = 1

Table S802.  Gene #71: 'FXYD5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
FXYD5 MUTATED 2 0 1
FXYD5 WILD-TYPE 143 130 117
'FXYD5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S803.  Gene #71: 'FXYD5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
FXYD5 MUTATED 1 1 1
FXYD5 WILD-TYPE 153 112 125
'FXYD5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.31 (Chi-square test), Q value = 1

Table S804.  Gene #71: 'FXYD5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
FXYD5 MUTATED 1 2 1 0 1 0
FXYD5 WILD-TYPE 180 92 243 162 242 47
'FXYD5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.454 (Fisher's exact test), Q value = 1

Table S805.  Gene #71: 'FXYD5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
FXYD5 MUTATED 3 1 1
FXYD5 WILD-TYPE 317 416 233
'FXYD5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.756 (Chi-square test), Q value = 1

Table S806.  Gene #71: 'FXYD5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
FXYD5 MUTATED 1 2 1 1 0 0
FXYD5 WILD-TYPE 195 154 206 233 132 31
'FXYD5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.498 (Fisher's exact test), Q value = 1

Table S807.  Gene #71: 'FXYD5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
FXYD5 MUTATED 2 1 2
FXYD5 WILD-TYPE 509 254 188
'ATXN2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.837 (Chi-square test), Q value = 1

Table S808.  Gene #72: 'ATXN2 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
ATXN2 MUTATED 0 0 2 3 2 2 0 0
ATXN2 WILD-TYPE 21 38 112 94 106 71 19 39
'ATXN2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.366 (Fisher's exact test), Q value = 1

Table S809.  Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 122 126 261
ATXN2 MUTATED 2 4 3
ATXN2 WILD-TYPE 120 122 258
'ATXN2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.392 (Chi-square test), Q value = 1

Table S810.  Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
ATXN2 MUTATED 7 2 0 5 0
ATXN2 WILD-TYPE 346 237 94 228 42
'ATXN2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.642 (Chi-square test), Q value = 1

Table S811.  Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
ATXN2 MUTATED 1 1 1 3 1 3
ATXN2 WILD-TYPE 110 162 94 118 53 100
'ATXN2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.234 (Fisher's exact test), Q value = 1

Table S812.  Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 145 130 118
ATXN2 MUTATED 5 1 1
ATXN2 WILD-TYPE 140 129 117
'ATXN2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0766 (Fisher's exact test), Q value = 1

Table S813.  Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 154 113 126
ATXN2 MUTATED 2 0 5
ATXN2 WILD-TYPE 152 113 121
'ATXN2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.757 (Chi-square test), Q value = 1

Table S814.  Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
ATXN2 MUTATED 4 1 3 4 3 0
ATXN2 WILD-TYPE 177 93 241 158 240 47
'ATXN2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.364 (Fisher's exact test), Q value = 1

Table S815.  Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
ATXN2 MUTATED 4 5 6
ATXN2 WILD-TYPE 316 412 228
'ATXN2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.538 (Chi-square test), Q value = 1

Table S816.  Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
ATXN2 MUTATED 2 1 3 5 4 0
ATXN2 WILD-TYPE 194 155 204 229 128 31
'ATXN2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.342 (Fisher's exact test), Q value = 1

Table S817.  Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
ATXN2 MUTATED 6 4 5
ATXN2 WILD-TYPE 505 251 185
'ATXN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.793 (Fisher's exact test), Q value = 1

Table S818.  Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 247 207 197
ATXN2 MUTATED 4 4 2
ATXN2 WILD-TYPE 243 203 195
'ATXN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.916 (Fisher's exact test), Q value = 1

Table S819.  Gene #72: 'ATXN2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 341 160
ATXN2 MUTATED 2 5 3
ATXN2 WILD-TYPE 148 336 157
'CCL13 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000182 (Chi-square test), Q value = 0.14

Table S820.  Gene #73: 'CCL13 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 353 239 94 233 42
CCL13 MUTATED 1 0 1 0 2
CCL13 WILD-TYPE 352 239 93 233 40

Figure S146.  Get High-res Image Gene #73: 'CCL13 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CCL13 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.36 (Chi-square test), Q value = 1

Table S821.  Gene #73: 'CCL13 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 111 163 95 121 54 103
CCL13 MUTATED 0 1 0 2 0 0
CCL13 WILD-TYPE 111 162 95 119 54 103
'CCL13 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.778 (Chi-square test), Q value = 1

Table S822.  Gene #73: 'CCL13 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 181 94 244 162 243 47
CCL13 MUTATED 0 0 2 1 1 0
CCL13 WILD-TYPE 181 94 242 161 242 47
'CCL13 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.568 (Fisher's exact test), Q value = 1

Table S823.  Gene #73: 'CCL13 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 320 417 234
CCL13 MUTATED 1 3 0
CCL13 WILD-TYPE 319 414 234
'CCL13 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.16 (Chi-square test), Q value = 1

Table S824.  Gene #73: 'CCL13 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 196 156 207 234 132 31
CCL13 MUTATED 1 0 1 0 1 1
CCL13 WILD-TYPE 195 156 206 234 131 30
'CCL13 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.532 (Fisher's exact test), Q value = 1

Table S825.  Gene #73: 'CCL13 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 511 255 190
CCL13 MUTATED 3 0 1
CCL13 WILD-TYPE 508 255 189
Methods & Data
Input

  • Mutation data file = transformed.cor.cli.txt

  • Molecular subtypes file = BRCA-TP.transferedmergedcluster.txt

  • Number of patients = 975

  • Number of significantly mutated genes = 73

  • Number of Molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

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

References
[1] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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