Correlation between gene mutation status and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between mutation status of 79 genes and 12 molecular subtypes across 977 patients, 99 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

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

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

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

  • CBFB mutation correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • RUNX1 mutation correlated to 'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • CDKN1B mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • MAP2K4 mutation correlated to 'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • FOXA1 mutation correlated to 'CN_CNMF'.

  • GPS2 mutation correlated to 'MRNA_CNMF' and 'CN_CNMF'.

  • RB1 mutation correlated to 'RPPA_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • CTCF mutation correlated to 'CN_CNMF'.

  • RBMX mutation correlated to 'MRNASEQ_CNMF'.

  • NCOR1 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • ERBB2 mutation correlated to 'RPPA_CNMF'.

  • RAB42 mutation correlated to 'MRNA_CHIERARCHICAL'.

  • NBPF9 mutation correlated to 'CN_CNMF'.

  • MYB mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • TGS1 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • USP36 mutation correlated to 'MRNA_CHIERARCHICAL'.

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

  • ZFP36L1 mutation correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • ACTL6B mutation correlated to 'CN_CNMF'.

  • ZFP36L2 mutation correlated to 'CN_CNMF'.

  • MED23 mutation correlated to 'MIRSEQ_CNMF'.

  • ANKRD20A4 mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • DLG1 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • GPRASP2 mutation correlated to 'MIRSEQ_CNMF'.

  • CCDC82 mutation correlated to 'RPPA_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 79 genes and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 99 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
PIK3CA 316 (32%) 661 0.00805
(0.0978) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256) 		3e-05
(0.000694) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256) 		3e-05
(0.000694) 		1e-05
(0.000256)
TP53 296 (30%) 681 1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256)
CDH1 107 (11%) 870 0.00207
(0.0322) 		0.00102
(0.0173) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256)
GATA3 97 (10%) 880 0.00876
(0.105) 		9e-05
(0.00198) 		0.00012
(0.00253) 		7e-05
(0.00158) 		0.00023
(0.00445) 		1e-05
(0.000256) 		1e-05
(0.000256) 		1e-05
(0.000256) 		0.00024
(0.00446) 		1e-05
(0.000256) 		1e-05
(0.000256) 		0.0736
(0.421)
MAP3K1 71 (7%) 906 0.00168
(0.0275) 		0.00203
(0.0321) 		3e-05
(0.000694) 		0.0243
(0.235) 		0.00022
(0.00434) 		1e-05
(0.000256) 		0.00022
(0.00434) 		0.00031
(0.00565) 		0.0004
(0.00715) 		0.00013
(0.00268) 		0.00448
(0.0616) 		0.0999
(0.504)
MAP2K4 32 (3%) 945 0.066
(0.409) 		0.0692
(0.415) 		0.0522
(0.375) 		0.0321
(0.287) 		0.0357
(0.307) 		0.0113
(0.128) 		0.00796
(0.0978) 		0.0037
(0.0524) 		0.00216
(0.033) 		0.00024
(0.00446) 		0.0334
(0.293) 		0.00066
(0.0116)
CBFB 22 (2%) 955 0.662
(0.966) 		0.468
(0.867) 		0.00069
(0.0119) 		0.0612
(0.403) 		0.0491
(0.364) 		0.202
(0.64) 		2e-05
(0.000499) 		0.613
(0.938) 		0.0496
(0.364) 		0.00011
(0.00237) 		0.00577
(0.076) 		0.00224
(0.0337)
RUNX1 29 (3%) 948 0.246
(0.701) 		0.0413
(0.324) 		0.0306
(0.276) 		0.318
(0.777) 		0.428
(0.837) 		0.412
(0.835) 		0.068
(0.414) 		0.011
(0.125) 		0.00467
(0.0632) 		0.00362
(0.052) 		0.374
(0.829) 		0.373
(0.829)
GPS2 10 (1%) 967 0.00643
(0.0824) 		0.607
(0.936) 		0.00725
(0.0916) 		0.392
(0.834) 		0.072
(0.421) 		0.886
(1.00) 		0.484
(0.868) 		0.0667
(0.409) 		0.332
(0.789) 		0.595
(0.931) 		0.327
(0.788) 		0.0379
(0.321)
RB1 19 (2%) 958 0.189
(0.631) 		0.265
(0.712) 		0.15
(0.586) 		0.123
(0.565) 		0.00738
(0.0921) 		0.16
(0.595) 		0.217
(0.655) 		0.261
(0.709) 		0.289
(0.753) 		0.118
(0.565) 		0.0235
(0.231) 		0.263
(0.709)
EYS 21 (2%) 956 0.19
(0.631) 		0.178
(0.624) 		0.151
(0.586) 		0.484
(0.868) 		0.0409
(0.324) 		0.0785
(0.438) 		0.0108
(0.125) 		0.201
(0.64) 		0.0368
(0.314) 		0.0146
(0.159) 		0.199
(0.64) 		0.0885
(0.458)
ZFP36L1 8 (1%) 969 0.204
(0.641) 		0.581
(0.928) 		0.00105
(0.0175) 		0.418
(0.837) 		0.954
(1.00) 		0.434
(0.84) 		0.239
(0.689) 		0.732
(0.989) 		0.0206
(0.215) 		0.538
(0.903) 		0.71
(0.978) 		0.818
(1.00)
CCDC82 6 (1%) 971 0.217
(0.655) 		0.302
(0.769) 		0.91
(1.00) 		0.013
(0.143) 		0.586
(0.928) 		0.412
(0.835) 		0.00255
(0.0378) 		0.387
(0.831) 		0.0592
(0.402) 		0.896
(1.00) 		1
(1.00)
CDKN1B 10 (1%) 967 1
(1.00) 		0.33
(0.789) 		0.117
(0.565) 		0.324
(0.785) 		0.792
(1.00) 		0.148
(0.586) 		0.0821
(0.445) 		0.464
(0.867) 		0.107
(0.528) 		0.316
(0.775) 		0.328
(0.789) 		0.017
(0.181)
FOXA1 23 (2%) 954 0.0748
(0.424) 		0.341
(0.794) 		0.0233
(0.231) 		0.0795
(0.441) 		0.569
(0.919) 		0.0873
(0.455) 		0.0505
(0.368) 		0.16
(0.595) 		0.258
(0.709) 		0.6
(0.932) 		0.226
(0.674) 		0.491
(0.868)
CTCF 16 (2%) 961 0.0479
(0.358) 		0.0596
(0.402) 		0.0108
(0.125) 		0.0996
(0.504) 		0.667
(0.969) 		0.202
(0.64) 		0.295
(0.763) 		0.489
(0.868) 		0.118
(0.565) 		0.0598
(0.402) 		0.972
(1.00) 		0.751
(1.00)
RBMX 13 (1%) 964 0.771
(1.00) 		0.127
(0.568) 		0.14
(0.582) 		0.135
(0.571) 		0.0848
(0.451) 		0.18
(0.626) 		0.0236
(0.231) 		0.0283
(0.264) 		0.681
(0.969) 		0.616
(0.94) 		0.229
(0.678) 		1
(1.00)
NCOR1 40 (4%) 937 0.907
(1.00) 		0.947
(1.00) 		0.849
(1.00) 		0.304
(0.772) 		0.352
(0.81) 		0.944
(1.00) 		0.313
(0.773) 		0.532
(0.898) 		0.896
(1.00) 		0.0208
(0.215) 		0.423
(0.837) 		0.714
(0.98)
ERBB2 20 (2%) 957 0.2
(0.64) 		0.167
(0.608) 		0.38
(0.829) 		0.156
(0.592) 		0.0191
(0.201) 		0.359
(0.812) 		0.0689
(0.415) 		0.133
(0.57) 		0.0551
(0.388) 		0.0569
(0.397) 		0.919
(1.00) 		0.497
(0.869)
RAB42 4 (0%) 973 0.82
(1.00) 		0.026
(0.249) 		0.292
(0.757) 		0.402
(0.835) 		0.119
(0.565) 		0.212
(0.654) 		0.157
(0.592) 		0.447
(0.848) 		0.344
(0.798)
NBPF9 5 (1%) 972 0.315
(0.775) 		0.849
(1.00) 		0.00409
(0.057) 		0.937
(1.00) 		1
(1.00) 		0.952
(1.00) 		0.155
(0.592) 		0.353
(0.81) 		0.561
(0.918)
MYB 12 (1%) 965 0.386
(0.831) 		0.587
(0.928) 		0.151
(0.586) 		0.555
(0.918) 		0.151
(0.586) 		1
(1.00) 		0.895
(1.00) 		0.899
(1.00) 		0.245
(0.698) 		0.313
(0.773) 		0.0866
(0.455) 		0.00177
(0.0284)
TGS1 13 (1%) 964 0.21
(0.649) 		0.262
(0.709) 		0.625
(0.946) 		0.285
(0.752) 		0.835
(1.00) 		0.564
(0.918) 		0.745
(0.999) 		0.249
(0.703) 		0.689
(0.969) 		0.0235
(0.231) 		0.0869
(0.455) 		0.319
(0.777)
USP36 8 (1%) 969 0.336
(0.792) 		0.006
(0.0779) 		0.882
(1.00) 		0.927
(1.00) 		0.454
(0.857) 		0.499
(0.869) 		0.409
(0.835) 		0.0759
(0.428) 		0.596
(0.931) 		0.749
(1.00)
ACTL6B 10 (1%) 967 0.676
(0.969) 		0.4
(0.835) 		0.00576
(0.076) 		0.312
(0.773) 		0.163
(0.601) 		0.566
(0.918) 		0.686
(0.969) 		0.197
(0.638) 		0.782
(1.00) 		0.913
(1.00) 		0.515
(0.882) 		0.848
(1.00)
ZFP36L2 7 (1%) 970 0.82
(1.00) 		1
(1.00) 		0.0107
(0.125) 		0.42
(0.837) 		0.654
(0.96) 		0.442
(0.84) 		0.688
(0.969) 		0.568
(0.918) 		0.614
(0.938) 		0.737
(0.993) 		0.316
(0.775) 		0.85
(1.00)
MED23 14 (1%) 963 0.388
(0.831) 		0.251
(0.706) 		0.274
(0.727) 		0.198
(0.639) 		0.17
(0.612) 		0.0577
(0.399) 		0.184
(0.631) 		0.0737
(0.421) 		0.0164
(0.177) 		0.117
(0.565) 		0.267
(0.713) 		0.534
(0.899)
ANKRD20A4 7 (1%) 970 0.607
(0.936) 		1
(1.00) 		0.606
(0.936) 		0.408
(0.835) 		0.922
(1.00) 		0.882
(1.00) 		0.0725
(0.421) 		0.332
(0.789) 		0.847
(1.00) 		0.813
(1.00) 		0.688
(0.969) 		0.0236
(0.231)
DLG1 13 (1%) 964 0.795
(1.00) 		0.249
(0.703) 		0.872
(1.00) 		0.13
(0.57) 		0.634
(0.951) 		0.827
(1.00) 		0.262
(0.709) 		0.189
(0.631) 		0.919
(1.00) 		0.0117
(0.13) 		0.436
(0.84) 		1
(1.00)
GPRASP2 10 (1%) 967 0.433
(0.84) 		0.33
(0.789) 		0.66
(0.966) 		0.655
(0.96) 		0.397
(0.835) 		0.44
(0.84) 		0.146
(0.585) 		0.253
(0.709) 		0.00291
(0.0424) 		0.231
(0.678) 		0.379
(0.829) 		0.672
(0.969)
PTEN 35 (4%) 942 1
(1.00) 		0.695
(0.969) 		0.276
(0.731) 		0.321
(0.78) 		0.206
(0.641) 		0.726
(0.988) 		0.289
(0.753) 		0.573
(0.923) 		0.15
(0.586) 		0.153
(0.587) 		0.421
(0.837) 		0.549
(0.915)
MLL3 70 (7%) 907 0.634
(0.951) 		0.781
(1.00) 		0.168
(0.608) 		0.236
(0.687) 		0.674
(0.969) 		0.109
(0.531) 		0.0306
(0.276) 		0.415
(0.837) 		0.0389
(0.323) 		0.121
(0.565) 		0.336
(0.792) 		0.661
(0.966)
ARID1A 27 (3%) 950 1
(1.00) 		1
(1.00) 		0.21
(0.649) 		0.494
(0.868) 		0.384
(0.831) 		0.485
(0.868) 		0.141
(0.582) 		0.644
(0.956) 		0.441
(0.84) 		0.363
(0.82) 		0.196
(0.638) 		0.311
(0.773)
TBX3 27 (3%) 950 0.187
(0.631) 		0.518
(0.883) 		0.0428
(0.33) 		0.424
(0.837) 		0.14
(0.582) 		0.0648
(0.409) 		0.081
(0.445) 		0.134
(0.57) 		0.0602
(0.402) 		0.133
(0.57) 		0.83
(1.00) 		0.594
(0.931)
HRNR 31 (3%) 946 0.874
(1.00) 		0.646
(0.956) 		0.216
(0.655) 		0.516
(0.882) 		0.626
(0.947) 		0.393
(0.835) 		0.99
(1.00) 		0.677
(0.969) 		0.643
(0.956) 		0.835
(1.00) 		0.621
(0.945) 		0.743
(0.998)
ZMYM3 15 (2%) 962 0.323
(0.783) 		0.253
(0.709) 		0.397
(0.835) 		0.679
(0.969) 		0.497
(0.869) 		0.0475
(0.358) 		0.398
(0.835) 		0.487
(0.868) 		0.48
(0.868) 		0.425
(0.837) 		0.714
(0.98) 		0.85
(1.00)
GPRIN2 11 (1%) 966 0.792
(1.00) 		0.69
(0.969) 		0.961
(1.00) 		0.61
(0.937) 		0.933
(1.00) 		0.263
(0.709) 		0.771
(1.00) 		0.425
(0.837) 		0.67
(0.969) 		0.248
(0.703) 		0.56
(0.918) 		1
(1.00)
SPEN 32 (3%) 945 0.877
(1.00) 		0.53
(0.896) 		0.507
(0.876) 		0.421
(0.837) 		0.945
(1.00) 		1
(1.00) 		0.209
(0.649) 		0.12
(0.565) 		0.0666
(0.409) 		0.204
(0.641) 		0.526
(0.891) 		0.541
(0.905)
NF1 28 (3%) 949 1
(1.00) 		0.94
(1.00) 		0.139
(0.582) 		0.216
(0.655) 		0.441
(0.84) 		0.866
(1.00) 		0.128
(0.568) 		0.418
(0.837) 		0.29
(0.753) 		0.556
(0.918) 		0.915
(1.00) 		0.787
(1.00)
TCP11 6 (1%) 971 0.872
(1.00) 		1
(1.00) 		0.46
(0.866) 		0.789
(1.00) 		1
(1.00) 		0.762
(1.00) 		0.376
(0.829) 		0.647
(0.956) 		0.399
(0.835)
SF3B1 16 (2%) 961 0.73
(0.988) 		0.453
(0.856) 		0.508
(0.876) 		0.172
(0.614) 		0.174
(0.617) 		0.26
(0.709) 		0.646
(0.956) 		0.354
(0.81) 		0.338
(0.792) 		0.19
(0.631) 		0.624
(0.946) 		0.183
(0.63)
CDC42EP1 5 (1%) 972 0.82
(1.00) 		0.172
(0.614) 		0.174
(0.617) 		0.346
(0.799) 		0.77
(1.00) 		0.739
(0.994) 		0.259
(0.709) 		0.559
(0.918) 		0.692
(0.969) 		0.218
(0.655)
KDM6A 15 (2%) 962 0.0841
(0.451) 		0.573
(0.923) 		0.371
(0.829) 		0.348
(0.803) 		0.26
(0.709) 		0.153
(0.587) 		0.54
(0.905) 		0.405
(0.835) 		0.931
(1.00) 		0.987
(1.00) 		0.801
(1.00) 		0.401
(0.835)
AQP12A 6 (1%) 971 0.467
(0.867) 		1
(1.00) 		0.562
(0.918) 		0.777
(1.00) 		0.937
(1.00) 		0.185
(0.631) 		0.777
(1.00) 		1
(1.00) 		0.93
(1.00) 		0.559
(0.918) 		0.202
(0.64) 		1
(1.00)
KRAS 6 (1%) 971 0.565
(0.918) 		0.826
(1.00) 		0.178
(0.624) 		0.355
(0.811) 		0.632
(0.951) 		1
(1.00) 		0.565
(0.918) 		0.0851
(0.451) 		0.693
(0.969) 		0.0391
(0.323) 		0.722
(0.987) 		0.192
(0.631)
ZNF362 5 (1%) 972 0.0996
(0.504) 		0.714
(0.98) 		0.181
(0.627) 		0.776
(1.00) 		0.473
(0.868) 		0.462
(0.866) 		0.909
(1.00) 		0.178
(0.624) 		0.0701
(0.416)
TBL1XR1 9 (1%) 968 0.0631
(0.407) 		0.34
(0.794) 		0.0983
(0.504) 		0.474
(0.868) 		1
(1.00) 		0.0417
(0.324) 		0.566
(0.918) 		0.425
(0.837) 		0.2
(0.64) 		0.9
(1.00) 		0.103
(0.512)
SP3 7 (1%) 970 1
(1.00) 		0.3
(0.768) 		0.492
(0.868) 		0.947
(1.00) 		0.836
(1.00) 		0.821
(1.00) 		0.194
(0.636) 		0.442
(0.84) 		0.519
(0.883) 		0.0652
(0.409) 		0.38
(0.829) 		1
(1.00)
FGFR2 11 (1%) 966 0.498
(0.869) 		1
(1.00) 		0.639
(0.953) 		0.559
(0.918) 		0.0416
(0.324) 		0.313
(0.773) 		0.194
(0.636) 		0.428
(0.837) 		0.219
(0.655) 		0.0721
(0.421) 		0.828
(1.00) 		0.673
(0.969)
ZBTB7C 5 (1%) 972 0.126
(0.565) 		1
(1.00) 		0.704
(0.976) 		1
(1.00) 		0.881
(1.00) 		0.677
(0.969) 		0.83
(1.00) 		0.597
(0.931)
NCDN 4 (0%) 973 0.8
(1.00) 		0.157
(0.592) 		0.916
(1.00) 		0.952
(1.00) 		1
(1.00) 		0.88
(1.00) 		0.913
(1.00) 		0.501
(0.87) 		0.468
(0.867)
MUC6 14 (1%) 963 0.631
(0.951) 		0.904
(1.00) 		0.125
(0.565) 		0.135
(0.571) 		0.485
(0.868) 		0.168
(0.608) 		0.0623
(0.405) 		0.205
(0.641) 		0.492
(0.868) 		0.033
(0.292) 		0.587
(0.928) 		0.052
(0.375)
TFE3 7 (1%) 970 0.192
(0.631) 		0.149
(0.586) 		0.407
(0.835) 		0.694
(0.969) 		0.357
(0.812) 		1
(1.00) 		0.722
(0.987) 		0.647
(0.956) 		0.958
(1.00) 		0.165
(0.605) 		1
(1.00) 		0.311
(0.773)
IRS4 11 (1%) 966 0.191
(0.631) 		0.125
(0.565) 		0.231
(0.678) 		0.638
(0.953) 		0.166
(0.606) 		0.0652
(0.409) 		0.146
(0.585) 		0.47
(0.867) 		0.0614
(0.403) 		0.815
(1.00) 		0.709
(0.978) 		0.817
(1.00)
NLGN3 11 (1%) 966 0.242
(0.695) 		1
(1.00) 		0.791
(1.00) 		0.876
(1.00) 		0.124
(0.565) 		0.396
(0.835) 		0.928
(1.00) 		0.0819
(0.445) 		0.994
(1.00) 		0.996
(1.00) 		0.375
(0.829) 		0.673
(0.969)
IL1RAP 9 (1%) 968 0.427
(0.837) 		0.299
(0.767) 		0.337
(0.792) 		0.312
(0.773) 		0.873
(1.00) 		0.643
(0.956) 		0.575
(0.923) 		0.301
(0.768) 		0.833
(1.00) 		0.611
(0.937)
CASZ1 14 (1%) 963 0.896
(1.00) 		0.458
(0.862) 		0.972
(1.00) 		0.462
(0.866) 		0.493
(0.868) 		0.098
(0.504) 		0.986
(1.00) 		0.733
(0.99) 		0.483
(0.868) 		0.986
(1.00) 		0.707
(0.977) 		0.809
(1.00)
KCNN3 9 (1%) 968 0.379
(0.829) 		0.162
(0.598) 		0.386
(0.831) 		0.125
(0.565) 		0.0406
(0.324) 		0.495
(0.868) 		0.0729
(0.421) 		0.398
(0.835) 		0.142
(0.584) 		0.487
(0.868) 		0.491
(0.868) 		0.428
(0.837)
ICOSLG 5 (1%) 972 0.799
(1.00) 		0.157
(0.592) 		0.47
(0.867) 		1
(1.00) 		0.102
(0.507) 		0.383
(0.831) 		0.835
(1.00) 		0.968
(1.00) 		0.141
(0.582) 		0.682
(0.969)
MYH9 18 (2%) 959 0.478
(0.868) 		1
(1.00) 		0.144
(0.584) 		0.812
(1.00) 		0.39
(0.832) 		0.412
(0.835) 		0.338
(0.792) 		0.143
(0.584) 		0.633
(0.951) 		0.504
(0.873) 		0.906
(1.00) 		0.171
(0.614)
FBXW7 15 (2%) 962 0.767
(1.00) 		0.479
(0.868) 		0.133
(0.57) 		0.0272
(0.258) 		0.263
(0.709) 		0.101
(0.507) 		0.125
(0.565) 		0.148
(0.586) 		0.518
(0.883) 		0.403
(0.835) 		0.034
(0.296) 		0.81
(1.00)
FRMPD2 13 (1%) 964 0.441
(0.84) 		0.124
(0.565) 		0.23
(0.678) 		0.135
(0.571) 		0.133
(0.57) 		0.262
(0.709) 		0.575
(0.923) 		0.0541
(0.386) 		0.435
(0.84) 		0.29
(0.753) 		0.553
(0.918) 		0.579
(0.926)
TPP2 8 (1%) 969 0.358
(0.812) 		0.826
(1.00) 		0.908
(1.00) 		0.635
(0.951) 		0.937
(1.00) 		1
(1.00) 		0.598
(0.931) 		0.916
(1.00) 		0.595
(0.931) 		0.889
(1.00) 		0.487
(0.868) 		1
(1.00)
C17ORF95 5 (1%) 972 1
(1.00) 		1
(1.00) 		1
(1.00) 		0.953
(1.00) 		0.968
(1.00) 		0.513
(0.881) 		0.429
(0.837)
RUFY1 6 (1%) 971 1
(1.00) 		0.298
(0.767) 		0.38
(0.829) 		0.729
(0.988) 		0.07
(0.416) 		0.736
(0.993) 		0.878
(1.00) 		0.239
(0.69) 		0.697
(0.969) 		0.266
(0.713) 		0.369
(0.829) 		0.431
(0.839)
PAX2 4 (0%) 973 0.466
(0.867) 		0.583
(0.928) 		0.839
(1.00) 		0.805
(1.00) 		0.484
(0.868) 		0.376
(0.829) 		0.286
(0.752) 		0.388
(0.831) 		0.337
(0.792)
MED12 21 (2%) 956 0.728
(0.988) 		0.512
(0.881) 		0.545
(0.91) 		0.872
(1.00) 		0.697
(0.969) 		0.832
(1.00) 		0.663
(0.966) 		0.41
(0.835) 		0.707
(0.977) 		0.914
(1.00) 		0.537
(0.903) 		0.481
(0.868)
CHD4 19 (2%) 958 0.76
(1.00) 		0.494
(0.868) 		0.231
(0.678) 		0.0616
(0.403) 		0.715
(0.98) 		1
(1.00) 		0.0297
(0.274) 		0.269
(0.716) 		0.873
(1.00) 		0.0669
(0.409) 		0.818
(1.00) 		0.308
(0.773)
PFKP 6 (1%) 971 0.123
(0.565) 		0.0587
(0.402) 		0.697
(0.969) 		0.306
(0.773) 		0.687
(0.969) 		0.587
(0.928) 		0.302
(0.769) 		0.427
(0.837) 		0.131
(0.57)
RHBG 4 (0%) 973 1
(1.00) 		0.219
(0.655) 		0.107
(0.528) 		0.679
(0.969) 		0.289
(0.753)
PSIP1 8 (1%) 969 0.692
(0.969) 		1
(1.00) 		0.652
(0.96) 		0.902
(1.00) 		0.592
(0.931) 		0.585
(0.928) 		0.556
(0.918) 		0.935
(1.00) 		0.411
(0.835) 		0.909
(1.00) 		0.915
(1.00) 		0.429
(0.837)
LRIG2 7 (1%) 970 0.564
(0.918) 		0.0643
(0.409) 		0.624
(0.946) 		0.59
(0.931) 		0.406
(0.835) 		0.584
(0.928) 		0.368
(0.829) 		0.885
(1.00) 		0.331
(0.789) 		0.93
(1.00) 		1
(1.00) 		1
(1.00)
RIBC1 4 (0%) 973 0.357
(0.812) 		0.653
(0.96) 		0.7
(0.972) 		0.0395
(0.323) 		0.685
(0.969) 		0.608
(0.936) 		0.388
(0.831) 		0.412
(0.835)
PLK2 9 (1%) 968 0.606
(0.936) 		0.442
(0.84) 		1
(1.00) 		0.922
(1.00) 		0.342
(0.796) 		1
(1.00) 		0.908
(1.00) 		0.797
(1.00) 		0.982
(1.00) 		0.596
(0.931) 		0.829
(1.00) 		0.671
(0.969)
PHACTR1 7 (1%) 970 0.121
(0.565) 		1
(1.00) 		0.869
(1.00) 		0.237
(0.687) 		0.191
(0.631) 		0.0851
(0.451) 		0.132
(0.57) 		0.0784
(0.438) 		0.757
(1.00) 		0.0417
(0.324) 		0.897
(1.00) 		1
(1.00)
CCDC27 7 (1%) 970 0.216
(0.655) 		0.402
(0.835) 		0.129
(0.57) 		0.0284
(0.264) 		0.0813
(0.445) 		0.143
(0.584) 		0.0382
(0.321) 		0.263
(0.709) 		0.214
(0.655) 		0.0553
(0.388) 		0.232
(0.678) 		0.312
(0.773)
RHOA 6 (1%) 971 0.0459
(0.348) 		0.439
(0.84) 		0.526
(0.891) 		0.236
(0.687) 		0.481
(0.868) 		0.508
(0.876) 		0.889
(1.00) 		0.261
(0.709) 		0.727
(0.988) 		0.374
(0.829)
MAMLD1 10 (1%) 967 0.371
(0.829) 		0.189
(0.631) 		0.601
(0.932) 		0.467
(0.867) 		0.158
(0.593) 		0.5
(0.869) 		0.621
(0.945) 		0.653
(0.96) 		0.757
(1.00) 		0.727
(0.988) 		0.671
(0.969) 		1
(1.00)
OR8D1 5 (1%) 972 0.692
(0.969) 		0.0446
(0.341) 		0.769
(1.00) 		0.522
(0.888) 		0.188
(0.631) 		0.146
(0.585) 		0.243
(0.695) 		0.18
(0.627) 		0.475
(0.868) 		1
(1.00)
'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00805 (Fisher's exact test), Q value = 0.098

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
PIK3CA MUTATED 83 43 38
PIK3CA WILD-TYPE 144 74 127

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

'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
PIK3CA MUTATED 51 108 5
PIK3CA WILD-TYPE 104 157 84

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

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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 292 118 267 261 25
PIK3CA MUTATED 81 65 104 54 10
PIK3CA WILD-TYPE 211 53 163 207 15

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

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
PIK3CA MUTATED 83 52 41 8 32
PIK3CA WILD-TYPE 110 98 81 111 48

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 = 3e-05 (Fisher's exact test), Q value = 0.00069

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
PIK3CA MUTATED 26 75 12 81 35 22 1
PIK3CA WILD-TYPE 126 139 17 118 88 45 9

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

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
PIK3CA MUTATED 28 124 100
PIK3CA WILD-TYPE 187 206 149

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

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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 CLUS_7
ALL 233 159 130 205 184 45 18
PIK3CA MUTATED 45 57 60 115 12 17 10
PIK3CA WILD-TYPE 188 102 70 90 172 28 8

Figure S7.  Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

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

Figure S8.  Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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 129 243 177 184 184 41
PIK3CA MUTATED 33 45 68 74 76 18
PIK3CA WILD-TYPE 96 198 109 110 108 23

Figure S9.  Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
PIK3CA MUTATED 7 49 74 54 38 45 7 22 18
PIK3CA WILD-TYPE 57 70 82 113 31 66 138 32 55

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 = 3e-05 (Fisher's exact test), Q value = 0.00069

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
PIK3CA MUTATED 32 26 22 47 17 38
PIK3CA WILD-TYPE 82 37 28 73 105 61

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

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
PIK3CA MUTATED 51 71 60
PIK3CA WILD-TYPE 230 100 56

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

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
TP53 MUTATED 23 26 116
TP53 WILD-TYPE 204 91 49

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

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
TP53 MUTATED 11 85 69
TP53 WILD-TYPE 144 180 20

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

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
TP53 MUTATED 63 14 25 187 4
TP53 WILD-TYPE 229 104 242 74 21

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

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
TP53 MUTATED 21 46 34 90 6
TP53 WILD-TYPE 172 104 88 29 74

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

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
TP53 MUTATED 107 18 8 33 44 32 6
TP53 WILD-TYPE 45 196 21 166 79 35 4

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

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
TP53 MUTATED 153 54 41
TP53 WILD-TYPE 62 276 208

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

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
TP53 MUTATED 31 87 10 17 136 7 7
TP53 WILD-TYPE 202 72 120 188 48 38 11

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

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

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

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

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
TP53 MUTATED 36 166 14 28 38 7
TP53 WILD-TYPE 93 77 163 156 146 34

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

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
TP53 MUTATED 11 62 14 15 14 19 106 7 41
TP53 WILD-TYPE 53 57 142 152 55 92 39 47 32

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

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
TP53 MUTATED 15 11 14 23 93 16
TP53 WILD-TYPE 99 52 36 97 29 83

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

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
TP53 MUTATED 124 32 16
TP53 WILD-TYPE 157 139 100

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

'GATA3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00876 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
GATA3 MUTATED 38 10 12
GATA3 WILD-TYPE 189 107 153

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

'GATA3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.002

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
GATA3 MUTATED 29 30 1
GATA3 WILD-TYPE 126 235 88

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

'GATA3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0025

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
GATA3 MUTATED 38 15 33 8 2
GATA3 WILD-TYPE 254 103 234 253 23

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

'GATA3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
GATA3 MUTATED 24 18 5 1 11
GATA3 WILD-TYPE 169 132 117 118 69

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

'GATA3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0044

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
GATA3 MUTATED 7 40 1 12 14 8 1
GATA3 WILD-TYPE 145 174 28 187 109 59 9

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

'GATA3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
GATA3 MUTATED 4 58 21
GATA3 WILD-TYPE 211 272 228

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

'GATA3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
GATA3 MUTATED 40 8 13 33 1 1 0
GATA3 WILD-TYPE 193 151 117 172 183 44 18

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

'GATA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

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

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

'GATA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0045

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
GATA3 MUTATED 22 9 20 15 23 6
GATA3 WILD-TYPE 107 234 157 169 161 35

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

'GATA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
GATA3 MUTATED 16 8 11 24 15 11 0 4 6
GATA3 WILD-TYPE 48 111 145 143 54 100 145 50 67

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

'GATA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
GATA3 MUTATED 23 3 5 20 0 6
GATA3 WILD-TYPE 91 60 45 100 122 93

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

'GATA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0736 (Fisher's exact test), Q value = 0.42

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
GATA3 MUTATED 29 11 17
GATA3 WILD-TYPE 252 160 99
'MAP3K1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00168 (Fisher's exact test), Q value = 0.027

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
MAP3K1 MUTATED 27 9 4
MAP3K1 WILD-TYPE 200 108 161

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

'MAP3K1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00203 (Fisher's exact test), Q value = 0.032

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
MAP3K1 MUTATED 20 19 1
MAP3K1 WILD-TYPE 135 246 88

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

'MAP3K1 MUTATION STATUS' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00069

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
MAP3K1 MUTATED 16 11 33 6 5
MAP3K1 WILD-TYPE 276 107 234 255 20

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

'MAP3K1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.23

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
MAP3K1 MUTATED 19 4 9 3 5
MAP3K1 WILD-TYPE 174 146 113 116 75

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

'MAP3K1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0043

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
MAP3K1 MUTATED 3 25 4 21 3 2 0
MAP3K1 WILD-TYPE 149 189 25 178 120 65 10

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

'MAP3K1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
MAP3K1 MUTATED 1 34 23
MAP3K1 WILD-TYPE 214 296 226

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

'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0043

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
MAP3K1 MUTATED 21 4 16 23 4 3 0
MAP3K1 WILD-TYPE 212 155 114 182 180 42 18

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

'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0057

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

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

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

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0072

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
MAP3K1 MUTATED 10 4 20 17 15 5
MAP3K1 WILD-TYPE 119 239 157 167 169 36

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

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0027

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
MAP3K1 MUTATED 1 3 20 19 5 12 2 5 4
MAP3K1 WILD-TYPE 63 116 136 148 64 99 143 49 69

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

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00448 (Fisher's exact test), Q value = 0.062

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
MAP3K1 MUTATED 16 4 6 5 3 4
MAP3K1 WILD-TYPE 98 59 44 115 119 95

Figure S46.  Get High-res Image Gene #4: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'MAP3K1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0999 (Fisher's exact test), Q value = 0.5

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
MAP3K1 MUTATED 15 10 13
MAP3K1 WILD-TYPE 266 161 103
'CDH1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00207 (Fisher's exact test), Q value = 0.032

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
CDH1 MUTATED 14 15 4
CDH1 WILD-TYPE 213 102 161

Figure S47.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00102 (Fisher's exact test), Q value = 0.017

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
CDH1 MUTATED 5 27 1
CDH1 WILD-TYPE 150 238 88

Figure S48.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
CDH1 MUTATED 20 36 42 4 3
CDH1 WILD-TYPE 272 82 225 257 22

Figure S49.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
CDH1 MUTATED 28 19 24 0 17
CDH1 WILD-TYPE 165 131 98 119 63

Figure S50.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CDH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
CDH1 MUTATED 2 21 1 36 11 7 2
CDH1 WILD-TYPE 150 193 28 163 112 60 8

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

'CDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
CDH1 MUTATED 5 30 45
CDH1 WILD-TYPE 210 300 204

Figure S52.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
CDH1 MUTATED 10 12 32 37 1 14 1
CDH1 WILD-TYPE 223 147 98 168 183 31 17

Figure S53.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

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

Figure S54.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
CDH1 MUTATED 9 2 28 49 11 6
CDH1 WILD-TYPE 120 241 149 135 173 35

Figure S55.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
CDH1 MUTATED 2 6 56 11 8 10 0 11 1
CDH1 WILD-TYPE 62 113 100 156 61 101 145 43 72

Figure S56.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
CDH1 MUTATED 7 19 7 10 1 31
CDH1 WILD-TYPE 107 44 43 110 121 68

Figure S57.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
CDH1 MUTATED 8 56 11
CDH1 WILD-TYPE 273 115 105

Figure S58.  Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CBFB MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.662 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
CBFB MUTATED 6 2 2
CBFB WILD-TYPE 221 115 163
'CBFB MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.468 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
CBFB MUTATED 5 4 1
CBFB WILD-TYPE 150 261 88
'CBFB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.012

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
CBFB MUTATED 4 8 7 1 2
CBFB WILD-TYPE 288 110 260 260 23

Figure S59.  Get High-res Image Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CBFB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0612 (Fisher's exact test), Q value = 0.4

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
CBFB MUTATED 7 3 1 0 4
CBFB WILD-TYPE 186 147 121 119 76
'CBFB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.36

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
CBFB MUTATED 1 4 0 6 3 3 2
CBFB WILD-TYPE 151 210 29 193 120 64 8

Figure S60.  Get High-res Image Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'CBFB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.202 (Fisher's exact test), Q value = 0.64

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
CBFB MUTATED 2 11 6
CBFB WILD-TYPE 213 319 243
'CBFB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5e-04

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
CBFB MUTATED 0 2 3 16 1 0 0
CBFB WILD-TYPE 233 157 127 189 183 45 18

Figure S61.  Get High-res Image Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CBFB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.613 (Fisher's exact test), Q value = 0.94

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

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

P value = 0.0496 (Fisher's exact test), Q value = 0.36

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
CBFB MUTATED 2 1 3 5 8 2
CBFB WILD-TYPE 127 242 174 179 176 39

Figure S62.  Get High-res Image Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CBFB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.0024

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
CBFB MUTATED 0 1 5 1 7 6 0 1 0
CBFB WILD-TYPE 64 118 151 166 62 105 145 53 73

Figure S63.  Get High-res Image Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CBFB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00577 (Fisher's exact test), Q value = 0.076

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
CBFB MUTATED 2 0 2 8 0 1
CBFB WILD-TYPE 112 63 48 112 122 98

Figure S64.  Get High-res Image Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'CBFB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00224 (Fisher's exact test), Q value = 0.034

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
CBFB MUTATED 4 1 8
CBFB WILD-TYPE 277 170 108

Figure S65.  Get High-res Image Gene #6: 'CBFB MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
PTEN MUTATED 6 3 4
PTEN WILD-TYPE 221 114 161
'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.695 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
PTEN MUTATED 4 8 1
PTEN WILD-TYPE 151 257 88
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.276 (Fisher's exact test), Q value = 0.73

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
PTEN MUTATED 6 7 11 11 0
PTEN WILD-TYPE 286 111 256 250 25
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.321 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
PTEN MUTATED 4 9 7 6 3
PTEN WILD-TYPE 189 141 115 113 77
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.206 (Fisher's exact test), Q value = 0.64

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
PTEN MUTATED 4 7 2 9 2 6 0
PTEN WILD-TYPE 148 207 27 190 121 61 10
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.726 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
PTEN MUTATED 10 12 8
PTEN WILD-TYPE 205 318 241
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 0.75

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
PTEN MUTATED 6 9 8 6 4 1 1
PTEN WILD-TYPE 227 150 122 199 180 44 17
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.573 (Fisher's exact test), Q value = 0.92

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

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

P value = 0.15 (Fisher's exact test), Q value = 0.59

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
PTEN MUTATED 4 5 5 12 9 0
PTEN WILD-TYPE 125 238 172 172 175 41
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
PTEN MUTATED 1 5 11 2 1 7 5 1 2
PTEN WILD-TYPE 63 114 145 165 68 104 140 53 71
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.421 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
PTEN MUTATED 6 3 1 3 4 8
PTEN WILD-TYPE 108 60 49 117 118 91
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.549 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
PTEN MUTATED 11 10 4
PTEN WILD-TYPE 270 161 112
'RUNX1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.246 (Fisher's exact test), Q value = 0.7

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
RUNX1 MUTATED 7 7 4
RUNX1 WILD-TYPE 220 110 161
'RUNX1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0413 (Fisher's exact test), Q value = 0.32

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
RUNX1 MUTATED 4 14 0
RUNX1 WILD-TYPE 151 251 89

Figure S66.  Get High-res Image Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'RUNX1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.28

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
RUNX1 MUTATED 4 8 11 5 0
RUNX1 WILD-TYPE 288 110 256 256 25

Figure S67.  Get High-res Image Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'RUNX1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.318 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
RUNX1 MUTATED 4 5 5 1 4
RUNX1 WILD-TYPE 189 145 117 118 76
'RUNX1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.428 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
RUNX1 MUTATED 3 3 2 6 3 3 0
RUNX1 WILD-TYPE 149 211 27 193 120 64 10
'RUNX1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.412 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
RUNX1 MUTATED 4 7 9
RUNX1 WILD-TYPE 211 323 240
'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.068 (Fisher's exact test), Q value = 0.41

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
RUNX1 MUTATED 4 6 7 9 1 2 0
RUNX1 WILD-TYPE 229 153 123 196 183 43 18
'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.13

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

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

Figure S68.  Get High-res Image Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00467 (Fisher's exact test), Q value = 0.063

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
RUNX1 MUTATED 4 1 3 10 8 3
RUNX1 WILD-TYPE 125 242 174 174 176 38

Figure S69.  Get High-res Image Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00362 (Fisher's exact test), Q value = 0.052

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
RUNX1 MUTATED 1 3 13 3 2 6 1 0 0
RUNX1 WILD-TYPE 63 116 143 164 67 105 144 54 73

Figure S70.  Get High-res Image Gene #8: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.374 (Fisher's exact test), Q value = 0.83

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
RUNX1 MUTATED 3 1 4 5 2 4
RUNX1 WILD-TYPE 111 62 46 115 120 95
'RUNX1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.373 (Fisher's exact test), Q value = 0.83

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
RUNX1 MUTATED 7 6 6
RUNX1 WILD-TYPE 274 165 110
'MLL3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.634 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
MLL3 MUTATED 18 6 13
MLL3 WILD-TYPE 209 111 152
'MLL3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
MLL3 MUTATED 13 19 5
MLL3 WILD-TYPE 142 246 84
'MLL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.168 (Fisher's exact test), Q value = 0.61

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
MLL3 MUTATED 17 11 24 13 3
MLL3 WILD-TYPE 275 107 243 248 22
'MLL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.236 (Fisher's exact test), Q value = 0.69

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
MLL3 MUTATED 20 12 6 5 7
MLL3 WILD-TYPE 173 138 116 114 73
'MLL3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.674 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
MLL3 MUTATED 9 19 1 9 9 5 0
MLL3 WILD-TYPE 143 195 28 190 114 62 10
'MLL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.109 (Fisher's exact test), Q value = 0.53

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
MLL3 MUTATED 10 29 13
MLL3 WILD-TYPE 205 301 236
'MLL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.28

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
MLL3 MUTATED 16 14 8 24 8 0 0
MLL3 WILD-TYPE 217 145 122 181 176 45 18

Figure S71.  Get High-res Image Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'MLL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.415 (Fisher's exact test), Q value = 0.84

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

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

P value = 0.0389 (Fisher's exact test), Q value = 0.32

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
MLL3 MUTATED 9 8 16 11 18 5
MLL3 WILD-TYPE 120 235 161 173 166 36

Figure S72.  Get High-res Image Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MLL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.121 (Fisher's exact test), Q value = 0.56

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
MLL3 MUTATED 5 7 11 13 11 7 4 3 6
MLL3 WILD-TYPE 59 112 145 154 58 104 141 51 67
'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.336 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
MLL3 MUTATED 12 5 2 8 4 6
MLL3 WILD-TYPE 102 58 48 112 118 93
'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.661 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
MLL3 MUTATED 16 12 9
MLL3 WILD-TYPE 265 159 107
'CDKN1B MUTATION STATUS' versus 'MRNA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
CDKN1B MUTATED 3 1 2
CDKN1B WILD-TYPE 224 116 163
'CDKN1B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.33 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
CDKN1B MUTATED 1 5 0
CDKN1B WILD-TYPE 154 260 89
'CDKN1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.117 (Fisher's exact test), Q value = 0.56

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
CDKN1B MUTATED 1 3 2 3 1
CDKN1B WILD-TYPE 291 115 265 258 24
'CDKN1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
CDKN1B MUTATED 3 0 2 0 1
CDKN1B WILD-TYPE 190 150 120 119 79
'CDKN1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.792 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
CDKN1B MUTATED 1 5 0 2 1 0 0
CDKN1B WILD-TYPE 151 209 29 197 122 67 10
'CDKN1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.148 (Fisher's exact test), Q value = 0.59

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
CDKN1B MUTATED 0 6 3
CDKN1B WILD-TYPE 215 324 246
'CDKN1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0821 (Fisher's exact test), Q value = 0.44

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
CDKN1B MUTATED 1 2 1 5 0 0 1
CDKN1B WILD-TYPE 232 157 129 200 184 45 17
'CDKN1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.464 (Fisher's exact test), Q value = 0.87

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

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

P value = 0.107 (Fisher's exact test), Q value = 0.53

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
CDKN1B MUTATED 1 0 1 3 4 1
CDKN1B WILD-TYPE 128 243 176 181 180 40
'CDKN1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.316 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
CDKN1B MUTATED 1 0 3 2 2 2 0 0 0
CDKN1B WILD-TYPE 63 119 153 165 67 109 145 54 73
'CDKN1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.328 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
CDKN1B MUTATED 0 1 1 2 0 1
CDKN1B WILD-TYPE 114 62 49 118 122 98
'CDKN1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.017 (Fisher's exact test), Q value = 0.18

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
CDKN1B MUTATED 0 2 3
CDKN1B WILD-TYPE 281 169 113

Figure S73.  Get High-res Image Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MAP2K4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.066 (Fisher's exact test), Q value = 0.41

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
MAP2K4 MUTATED 10 7 2
MAP2K4 WILD-TYPE 217 110 163
'MAP2K4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0692 (Fisher's exact test), Q value = 0.42

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
MAP2K4 MUTATED 8 11 0
MAP2K4 WILD-TYPE 147 254 89
'MAP2K4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0522 (Fisher's exact test), Q value = 0.37

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
MAP2K4 MUTATED 10 8 8 4 2
MAP2K4 WILD-TYPE 282 110 259 257 23
'MAP2K4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 0.29

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
MAP2K4 MUTATED 14 6 2 1 2
MAP2K4 WILD-TYPE 179 144 120 118 78

Figure S74.  Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MAP2K4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.31

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
MAP2K4 MUTATED 0 9 0 8 8 1 0
MAP2K4 WILD-TYPE 152 205 29 191 115 66 10

Figure S75.  Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'MAP2K4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.13

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
MAP2K4 MUTATED 1 14 11
MAP2K4 WILD-TYPE 214 316 238

Figure S76.  Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'MAP2K4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00796 (Fisher's exact test), Q value = 0.098

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
MAP2K4 MUTATED 12 5 2 11 0 1 1
MAP2K4 WILD-TYPE 221 154 128 194 184 44 17

Figure S77.  Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'MAP2K4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0037 (Fisher's exact test), Q value = 0.052

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

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

Figure S78.  Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00216 (Fisher's exact test), Q value = 0.033

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
MAP2K4 MUTATED 4 1 8 4 13 2
MAP2K4 WILD-TYPE 125 242 169 180 171 39

Figure S79.  Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0045

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
MAP2K4 MUTATED 4 1 1 12 5 6 0 1 2
MAP2K4 WILD-TYPE 60 118 155 155 64 105 145 53 71

Figure S80.  Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.29

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
MAP2K4 MUTATED 4 0 3 6 0 4
MAP2K4 WILD-TYPE 110 63 47 114 122 95

Figure S81.  Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.012

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
MAP2K4 MUTATED 5 2 10
MAP2K4 WILD-TYPE 276 169 106

Figure S82.  Get High-res Image Gene #11: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MRNA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
ARID1A MUTATED 7 3 5
ARID1A WILD-TYPE 220 114 160
'ARID1A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
ARID1A MUTATED 5 8 2
ARID1A WILD-TYPE 150 257 87
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.21 (Fisher's exact test), Q value = 0.65

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
ARID1A MUTATED 12 1 8 4 1
ARID1A WILD-TYPE 280 117 259 257 24
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.494 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
ARID1A MUTATED 7 5 1 2 3
ARID1A WILD-TYPE 186 145 121 117 77
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 0.83

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
ARID1A MUTATED 3 5 1 3 7 1 0
ARID1A WILD-TYPE 149 209 28 196 116 66 10
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.485 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
ARID1A MUTATED 3 10 7
ARID1A WILD-TYPE 212 320 242
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 0.58

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
ARID1A MUTATED 13 5 3 3 2 1 0
ARID1A WILD-TYPE 220 154 127 202 182 44 18
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.644 (Fisher's exact test), Q value = 0.96

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

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

P value = 0.441 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
ARID1A MUTATED 6 5 7 3 6 0
ARID1A WILD-TYPE 123 238 170 181 178 41
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.363 (Fisher's exact test), Q value = 0.82

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
ARID1A MUTATED 3 4 2 9 1 2 2 1 3
ARID1A WILD-TYPE 61 115 154 158 68 109 143 53 70
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.196 (Fisher's exact test), Q value = 0.64

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
ARID1A MUTATED 1 3 2 1 1 3
ARID1A WILD-TYPE 113 60 48 119 121 96
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.311 (Fisher's exact test), Q value = 0.77

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
ARID1A MUTATED 3 5 3
ARID1A WILD-TYPE 278 166 113
'FOXA1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0748 (Fisher's exact test), Q value = 0.42

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
FOXA1 MUTATED 6 2 0
FOXA1 WILD-TYPE 221 115 165
'FOXA1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.341 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
FOXA1 MUTATED 4 4 0
FOXA1 WILD-TYPE 151 261 89
'FOXA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.23

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
FOXA1 MUTATED 6 5 10 1 1
FOXA1 WILD-TYPE 286 113 257 260 24

Figure S83.  Get High-res Image Gene #13: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FOXA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0795 (Fisher's exact test), Q value = 0.44

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
FOXA1 MUTATED 6 8 3 0 1
FOXA1 WILD-TYPE 187 142 119 119 79
'FOXA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.569 (Fisher's exact test), Q value = 0.92

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
FOXA1 MUTATED 1 8 0 4 3 2 0
FOXA1 WILD-TYPE 151 206 29 195 120 65 10
'FOXA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0873 (Fisher's exact test), Q value = 0.45

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
FOXA1 MUTATED 1 10 7
FOXA1 WILD-TYPE 214 320 242
'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0505 (Fisher's exact test), Q value = 0.37

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
FOXA1 MUTATED 4 4 2 8 1 4 0
FOXA1 WILD-TYPE 229 155 128 197 183 41 18
'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.16 (Fisher's exact test), Q value = 0.6

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

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

P value = 0.258 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
FOXA1 MUTATED 1 3 5 7 5 2
FOXA1 WILD-TYPE 128 240 172 177 179 39
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.6 (Fisher's exact test), Q value = 0.93

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
FOXA1 MUTATED 1 3 4 4 4 2 1 2 2
FOXA1 WILD-TYPE 63 116 152 163 65 109 144 52 71
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.226 (Fisher's exact test), Q value = 0.67

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
FOXA1 MUTATED 4 3 1 3 0 3
FOXA1 WILD-TYPE 110 60 49 117 122 96
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.491 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
FOXA1 MUTATED 5 6 3
FOXA1 WILD-TYPE 276 165 113
'GPS2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00643 (Fisher's exact test), Q value = 0.082

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
GPS2 MUTATED 2 5 0
GPS2 WILD-TYPE 225 112 165

Figure S84.  Get High-res Image Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'GPS2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.607 (Fisher's exact test), Q value = 0.94

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
GPS2 MUTATED 2 5 0
GPS2 WILD-TYPE 153 260 89
'GPS2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00725 (Fisher's exact test), Q value = 0.092

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
GPS2 MUTATED 1 1 7 0 1
GPS2 WILD-TYPE 291 117 260 261 24

Figure S85.  Get High-res Image Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'GPS2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.392 (Fisher's exact test), Q value = 0.83

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
GPS2 MUTATED 1 3 0 2 1
GPS2 WILD-TYPE 192 147 122 117 79
'GPS2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.072 (Fisher's exact test), Q value = 0.42

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
GPS2 MUTATED 0 1 0 2 0 3 0
GPS2 WILD-TYPE 152 213 29 197 123 64 10
'GPS2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.886 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
GPS2 MUTATED 2 2 2
GPS2 WILD-TYPE 213 328 247
'GPS2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.484 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
GPS2 MUTATED 3 3 1 2 0 1 0
GPS2 WILD-TYPE 230 156 129 203 184 44 18
'GPS2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0667 (Fisher's exact test), Q value = 0.41

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

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

P value = 0.332 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
GPS2 MUTATED 0 2 4 2 1 1
GPS2 WILD-TYPE 129 241 173 182 183 40
'GPS2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.595 (Fisher's exact test), Q value = 0.93

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
GPS2 MUTATED 0 2 2 2 0 3 0 0 1
GPS2 WILD-TYPE 64 117 154 165 69 108 145 54 72
'GPS2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.327 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
GPS2 MUTATED 0 1 1 2 0 1
GPS2 WILD-TYPE 114 62 49 118 122 98
'GPS2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0379 (Fisher's exact test), Q value = 0.32

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
GPS2 MUTATED 0 3 2
GPS2 WILD-TYPE 281 168 114

Figure S86.  Get High-res Image Gene #14: 'GPS2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TBX3 MUTATION STATUS' versus 'MRNA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
TBX3 MUTATED 10 4 2
TBX3 WILD-TYPE 217 113 163
'TBX3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.518 (Fisher's exact test), Q value = 0.88

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
TBX3 MUTATED 6 9 1
TBX3 WILD-TYPE 149 256 88
'TBX3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0428 (Fisher's exact test), Q value = 0.33

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
TBX3 MUTATED 6 6 10 3 2
TBX3 WILD-TYPE 286 112 257 258 23

Figure S87.  Get High-res Image Gene #15: 'TBX3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TBX3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.424 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
TBX3 MUTATED 7 2 3 1 3
TBX3 WILD-TYPE 186 148 119 118 77
'TBX3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.14 (Fisher's exact test), Q value = 0.58

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
TBX3 MUTATED 0 6 1 5 6 1 0
TBX3 WILD-TYPE 152 208 28 194 117 66 10
'TBX3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0648 (Fisher's exact test), Q value = 0.41

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
TBX3 MUTATED 3 5 11
TBX3 WILD-TYPE 212 325 238
'TBX3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.081 (Fisher's exact test), Q value = 0.44

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
TBX3 MUTATED 5 1 8 9 3 1 0
TBX3 WILD-TYPE 228 158 122 196 181 44 18
'TBX3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.134 (Fisher's exact test), Q value = 0.57

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

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

P value = 0.0602 (Fisher's exact test), Q value = 0.4

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
TBX3 MUTATED 2 3 10 7 3 2
TBX3 WILD-TYPE 127 240 167 177 181 39
'TBX3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.133 (Fisher's exact test), Q value = 0.57

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
TBX3 MUTATED 0 4 9 8 1 2 1 1 1
TBX3 WILD-TYPE 64 115 147 159 68 109 144 53 72
'TBX3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.83 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
TBX3 MUTATED 2 3 1 3 2 3
TBX3 WILD-TYPE 112 60 49 117 120 96
'TBX3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.594 (Fisher's exact test), Q value = 0.93

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
TBX3 MUTATED 6 6 2
TBX3 WILD-TYPE 275 165 114
'RB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.189 (Fisher's exact test), Q value = 0.63

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
RB1 MUTATED 6 0 4
RB1 WILD-TYPE 221 117 161
'RB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.265 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
RB1 MUTATED 1 6 3
RB1 WILD-TYPE 154 259 86
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.15 (Fisher's exact test), Q value = 0.59

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
RB1 MUTATED 3 4 3 9 0
RB1 WILD-TYPE 289 114 264 252 25
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.123 (Fisher's exact test), Q value = 0.56

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
RB1 MUTATED 2 3 0 5 1
RB1 WILD-TYPE 191 147 122 114 79
'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00738 (Fisher's exact test), Q value = 0.092

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
RB1 MUTATED 5 2 0 1 3 3 2
RB1 WILD-TYPE 147 212 29 198 120 64 8

Figure S88.  Get High-res Image Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.16 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
RB1 MUTATED 8 5 3
RB1 WILD-TYPE 207 325 246
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.217 (Fisher's exact test), Q value = 0.65

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
RB1 MUTATED 3 5 0 4 7 0 0
RB1 WILD-TYPE 230 154 130 201 177 45 18
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 0.71

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

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

P value = 0.289 (Fisher's exact test), Q value = 0.75

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
RB1 MUTATED 4 6 1 1 3 1
RB1 WILD-TYPE 125 237 176 183 181 40
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.118 (Fisher's exact test), Q value = 0.56

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
RB1 MUTATED 0 5 0 2 1 2 3 0 3
RB1 WILD-TYPE 64 114 156 165 68 109 142 54 70
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.23

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
RB1 MUTATED 1 0 2 2 7 0
RB1 WILD-TYPE 113 63 48 118 115 99

Figure S89.  Get High-res Image Gene #16: 'RB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.263 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
RB1 MUTATED 8 1 3
RB1 WILD-TYPE 273 170 113
'CTCF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0479 (Fisher's exact test), Q value = 0.36

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
CTCF MUTATED 10 2 1
CTCF WILD-TYPE 217 115 164

Figure S90.  Get High-res Image Gene #17: 'CTCF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CTCF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0596 (Fisher's exact test), Q value = 0.4

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
CTCF MUTATED 8 4 1
CTCF WILD-TYPE 147 261 88
'CTCF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.13

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
CTCF MUTATED 2 2 11 1 0
CTCF WILD-TYPE 290 116 256 260 25

Figure S91.  Get High-res Image Gene #17: 'CTCF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CTCF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0996 (Fisher's exact test), Q value = 0.5

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
CTCF MUTATED 7 1 1 0 1
CTCF WILD-TYPE 186 149 121 119 79
'CTCF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.667 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
CTCF MUTATED 1 5 1 4 1 1 0
CTCF WILD-TYPE 151 209 28 195 122 66 10
'CTCF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.202 (Fisher's exact test), Q value = 0.64

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
CTCF MUTATED 1 8 4
CTCF WILD-TYPE 214 322 245
'CTCF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.295 (Fisher's exact test), Q value = 0.76

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
CTCF MUTATED 3 1 3 7 1 1 0
CTCF WILD-TYPE 230 158 127 198 183 44 18
'CTCF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.489 (Fisher's exact test), Q value = 0.87

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

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

P value = 0.118 (Fisher's exact test), Q value = 0.56

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
CTCF MUTATED 1 1 7 4 3 0
CTCF WILD-TYPE 128 242 170 180 181 41
'CTCF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0598 (Fisher's exact test), Q value = 0.4

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
CTCF MUTATED 1 1 1 8 2 1 0 1 1
CTCF WILD-TYPE 63 118 155 159 67 110 145 53 72
'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.972 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
CTCF MUTATED 1 0 0 2 2 1
CTCF WILD-TYPE 113 63 50 118 120 98
'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
CTCF MUTATED 3 1 2
CTCF WILD-TYPE 278 170 114
'RBMX MUTATION STATUS' versus 'MRNA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
RBMX MUTATED 2 1 3
RBMX WILD-TYPE 225 116 162
'RBMX MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.127 (Fisher's exact test), Q value = 0.57

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
RBMX MUTATED 1 2 3
RBMX WILD-TYPE 154 263 86
'RBMX MUTATION STATUS' versus 'CN_CNMF'

P value = 0.14 (Fisher's exact test), Q value = 0.58

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
RBMX MUTATED 1 1 4 6 1
RBMX WILD-TYPE 291 117 263 255 24
'RBMX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.57

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
RBMX MUTATED 0 3 2 3 2
RBMX WILD-TYPE 193 147 120 116 78
'RBMX MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0848 (Fisher's exact test), Q value = 0.45

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
RBMX MUTATED 4 3 2 1 0 1 0
RBMX WILD-TYPE 148 211 27 198 123 66 10
'RBMX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.18 (Fisher's exact test), Q value = 0.63

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
RBMX MUTATED 5 5 1
RBMX WILD-TYPE 210 325 248
'RBMX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.23

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
RBMX MUTATED 0 1 2 2 6 1 1
RBMX WILD-TYPE 233 158 128 203 178 44 17

Figure S92.  Get High-res Image Gene #18: 'RBMX MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'RBMX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0283 (Fisher's exact test), Q value = 0.26

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

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

Figure S93.  Get High-res Image Gene #18: 'RBMX MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'RBMX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.681 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
RBMX MUTATED 1 6 1 2 3 0
RBMX WILD-TYPE 128 237 176 182 181 41
'RBMX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.616 (Fisher's exact test), Q value = 0.94

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
RBMX MUTATED 0 2 2 1 1 1 3 0 3
RBMX WILD-TYPE 64 117 154 166 68 110 142 54 70
'RBMX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.229 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
RBMX MUTATED 0 0 0 1 4 2
RBMX WILD-TYPE 114 63 50 119 118 97
'RBMX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
RBMX MUTATED 4 2 1
RBMX WILD-TYPE 277 169 115
'HRNR MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.874 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
HRNR MUTATED 8 5 7
HRNR WILD-TYPE 219 112 158
'HRNR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.646 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
HRNR MUTATED 5 10 5
HRNR WILD-TYPE 150 255 84
'HRNR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 0.65

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
HRNR MUTATED 5 5 10 9 2
HRNR WILD-TYPE 287 113 257 252 23
'HRNR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.516 (Fisher's exact test), Q value = 0.88

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
HRNR MUTATED 6 3 3 3 5
HRNR WILD-TYPE 187 147 119 116 75
'HRNR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.626 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
HRNR MUTATED 7 6 0 6 4 1 1
HRNR WILD-TYPE 145 208 29 193 119 66 9
'HRNR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.393 (Fisher's exact test), Q value = 0.83

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
HRNR MUTATED 9 11 5
HRNR WILD-TYPE 206 319 244
'HRNR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.99 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
HRNR MUTATED 6 6 4 7 7 1 0
HRNR WILD-TYPE 227 153 126 198 177 44 18
'HRNR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.677 (Fisher's exact test), Q value = 0.97

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

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

P value = 0.643 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
HRNR MUTATED 2 8 6 4 9 1
HRNR WILD-TYPE 127 235 171 180 175 40
'HRNR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.835 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
HRNR MUTATED 2 5 5 7 3 1 5 1 1
HRNR WILD-TYPE 62 114 151 160 66 110 140 53 72
'HRNR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.621 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
HRNR MUTATED 2 0 2 3 4 4
HRNR WILD-TYPE 112 63 48 117 118 95
'HRNR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
HRNR MUTATED 9 3 3
HRNR WILD-TYPE 272 168 113
'ZMYM3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.323 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
ZMYM3 MUTATED 3 2 6
ZMYM3 WILD-TYPE 224 115 159
'ZMYM3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.253 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
ZMYM3 MUTATED 2 5 4
ZMYM3 WILD-TYPE 153 260 85
'ZMYM3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
ZMYM3 MUTATED 2 1 7 5 0
ZMYM3 WILD-TYPE 290 117 260 256 25
'ZMYM3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.679 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
ZMYM3 MUTATED 2 2 1 3 0
ZMYM3 WILD-TYPE 191 148 121 116 80
'ZMYM3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.497 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
ZMYM3 MUTATED 4 3 0 1 1 2 0
ZMYM3 WILD-TYPE 148 211 29 198 122 65 10
'ZMYM3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0475 (Fisher's exact test), Q value = 0.36

Table S234.  Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
ZMYM3 MUTATED 4 7 0
ZMYM3 WILD-TYPE 211 323 249

Figure S94.  Get High-res Image Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'ZMYM3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.398 (Fisher's exact test), Q value = 0.84

Table S235.  Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
ZMYM3 MUTATED 4 1 0 6 4 0 0
ZMYM3 WILD-TYPE 229 158 130 199 180 45 18
'ZMYM3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.487 (Fisher's exact test), Q value = 0.87

Table S236.  Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
ZMYM3 MUTATED 2 3 0 6 4 0
ZMYM3 WILD-TYPE 261 148 79 255 164 52
'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.48 (Fisher's exact test), Q value = 0.87

Table S237.  Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
ZMYM3 MUTATED 1 6 4 1 2 1
ZMYM3 WILD-TYPE 128 237 173 183 182 40
'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.425 (Fisher's exact test), Q value = 0.84

Table S238.  Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
ZMYM3 MUTATED 0 3 1 2 1 1 3 3 1
ZMYM3 WILD-TYPE 64 116 155 165 68 110 142 51 72
'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.714 (Fisher's exact test), Q value = 0.98

Table S239.  Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
ZMYM3 MUTATED 2 1 0 1 0 1
ZMYM3 WILD-TYPE 112 62 50 119 122 98
'ZMYM3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.85 (Fisher's exact test), Q value = 1

Table S240.  Gene #20: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
ZMYM3 MUTATED 2 2 1
ZMYM3 WILD-TYPE 279 169 115
'NCOR1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S241.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
NCOR1 MUTATED 9 3 6
NCOR1 WILD-TYPE 218 114 159
'NCOR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.947 (Fisher's exact test), Q value = 1

Table S242.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
NCOR1 MUTATED 6 9 3
NCOR1 WILD-TYPE 149 256 86
'NCOR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.849 (Fisher's exact test), Q value = 1

Table S243.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
NCOR1 MUTATED 12 6 11 8 1
NCOR1 WILD-TYPE 280 112 256 253 24
'NCOR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.304 (Fisher's exact test), Q value = 0.77

Table S244.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
NCOR1 MUTATED 6 10 4 4 6
NCOR1 WILD-TYPE 187 140 118 115 74
'NCOR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.352 (Fisher's exact test), Q value = 0.81

Table S245.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
NCOR1 MUTATED 4 6 1 6 8 5 0
NCOR1 WILD-TYPE 148 208 28 193 115 62 10
'NCOR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.944 (Fisher's exact test), Q value = 1

Table S246.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
NCOR1 MUTATED 9 12 9
NCOR1 WILD-TYPE 206 318 240
'NCOR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.313 (Fisher's exact test), Q value = 0.77

Table S247.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
NCOR1 MUTATED 6 12 6 8 6 1 1
NCOR1 WILD-TYPE 227 147 124 197 178 44 17
'NCOR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.532 (Fisher's exact test), Q value = 0.9

Table S248.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
NCOR1 MUTATED 7 10 3 12 6 2
NCOR1 WILD-TYPE 256 141 76 249 162 50
'NCOR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.896 (Fisher's exact test), Q value = 1

Table S249.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
NCOR1 MUTATED 4 12 6 7 10 1
NCOR1 WILD-TYPE 125 231 171 177 174 40
'NCOR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0208 (Fisher's exact test), Q value = 0.21

Table S250.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
NCOR1 MUTATED 4 8 8 0 3 4 5 4 4
NCOR1 WILD-TYPE 60 111 148 167 66 107 140 50 69

Figure S95.  Get High-res Image Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'NCOR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.423 (Fisher's exact test), Q value = 0.84

Table S251.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
NCOR1 MUTATED 1 2 1 7 4 4
NCOR1 WILD-TYPE 113 61 49 113 118 95
'NCOR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.714 (Fisher's exact test), Q value = 0.98

Table S252.  Gene #21: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
NCOR1 MUTATED 8 6 5
NCOR1 WILD-TYPE 273 165 111
'GPRIN2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.792 (Fisher's exact test), Q value = 1

Table S253.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
GPRIN2 MUTATED 3 1 3
GPRIN2 WILD-TYPE 224 116 162
'GPRIN2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.69 (Fisher's exact test), Q value = 0.97

Table S254.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
GPRIN2 MUTATED 2 3 2
GPRIN2 WILD-TYPE 153 262 87
'GPRIN2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.961 (Fisher's exact test), Q value = 1

Table S255.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
GPRIN2 MUTATED 3 1 3 4 0
GPRIN2 WILD-TYPE 289 117 264 257 25
'GPRIN2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.61 (Fisher's exact test), Q value = 0.94

Table S256.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
GPRIN2 MUTATED 3 2 0 2 0
GPRIN2 WILD-TYPE 190 148 122 117 80
'GPRIN2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S257.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
GPRIN2 MUTATED 3 2 0 3 1 1 0
GPRIN2 WILD-TYPE 149 212 29 196 122 66 10
'GPRIN2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.263 (Fisher's exact test), Q value = 0.71

Table S258.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
GPRIN2 MUTATED 5 3 2
GPRIN2 WILD-TYPE 210 327 247
'GPRIN2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S259.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
GPRIN2 MUTATED 1 2 1 4 3 0 0
GPRIN2 WILD-TYPE 232 157 129 201 181 45 18
'GPRIN2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.425 (Fisher's exact test), Q value = 0.84

Table S260.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
GPRIN2 MUTATED 1 2 0 4 4 0
GPRIN2 WILD-TYPE 262 149 79 257 164 52
'GPRIN2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.67 (Fisher's exact test), Q value = 0.97

Table S261.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
GPRIN2 MUTATED 0 4 3 2 1 0
GPRIN2 WILD-TYPE 129 239 174 182 183 41
'GPRIN2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.248 (Fisher's exact test), Q value = 0.7

Table S262.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
GPRIN2 MUTATED 0 1 0 3 1 0 4 1 0
GPRIN2 WILD-TYPE 64 118 156 164 68 111 141 53 73
'GPRIN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.56 (Fisher's exact test), Q value = 0.92

Table S263.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
GPRIN2 MUTATED 0 1 0 1 3 1
GPRIN2 WILD-TYPE 114 62 50 119 119 98
'GPRIN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S264.  Gene #22: 'GPRIN2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
GPRIN2 MUTATED 3 2 1
GPRIN2 WILD-TYPE 278 169 115
'SPEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.877 (Fisher's exact test), Q value = 1

Table S265.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
SPEN MUTATED 8 5 7
SPEN WILD-TYPE 219 112 158
'SPEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.53 (Fisher's exact test), Q value = 0.9

Table S266.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
SPEN MUTATED 5 13 2
SPEN WILD-TYPE 150 252 87
'SPEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.507 (Fisher's exact test), Q value = 0.88

Table S267.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
SPEN MUTATED 9 4 12 5 0
SPEN WILD-TYPE 283 114 255 256 25
'SPEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.421 (Fisher's exact test), Q value = 0.84

Table S268.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
SPEN MUTATED 9 6 5 1 3
SPEN WILD-TYPE 184 144 117 118 77
'SPEN MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S269.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
SPEN MUTATED 4 7 0 8 3 1 0
SPEN WILD-TYPE 148 207 29 191 120 66 10
'SPEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S270.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
SPEN MUTATED 6 10 7
SPEN WILD-TYPE 209 320 242
'SPEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.209 (Fisher's exact test), Q value = 0.65

Table S271.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
SPEN MUTATED 8 5 4 9 2 2 2
SPEN WILD-TYPE 225 154 126 196 182 43 16
'SPEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.12 (Fisher's exact test), Q value = 0.56

Table S272.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
SPEN MUTATED 6 7 1 14 2 2
SPEN WILD-TYPE 257 144 78 247 166 50
'SPEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0666 (Fisher's exact test), Q value = 0.41

Table S273.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
SPEN MUTATED 5 4 6 3 12 2
SPEN WILD-TYPE 124 239 171 181 172 39
'SPEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.204 (Fisher's exact test), Q value = 0.64

Table S274.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
SPEN MUTATED 3 6 5 4 5 5 2 2 0
SPEN WILD-TYPE 61 113 151 163 64 106 143 52 73
'SPEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.526 (Fisher's exact test), Q value = 0.89

Table S275.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
SPEN MUTATED 4 3 1 2 1 2
SPEN WILD-TYPE 110 60 49 118 121 97
'SPEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.541 (Fisher's exact test), Q value = 0.91

Table S276.  Gene #23: 'SPEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
SPEN MUTATED 7 5 1
SPEN WILD-TYPE 274 166 115
'NF1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S277.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
NF1 MUTATED 7 3 5
NF1 WILD-TYPE 220 114 160
'NF1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.94 (Fisher's exact test), Q value = 1

Table S278.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
NF1 MUTATED 4 8 3
NF1 WILD-TYPE 151 257 86
'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.139 (Fisher's exact test), Q value = 0.58

Table S279.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
NF1 MUTATED 4 6 11 6 0
NF1 WILD-TYPE 288 112 256 255 25
'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 0.65

Table S280.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
NF1 MUTATED 3 7 6 2 1
NF1 WILD-TYPE 190 143 116 117 79
'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 0.84

Table S281.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
NF1 MUTATED 3 6 0 5 5 5 0
NF1 WILD-TYPE 149 208 29 194 118 62 10
'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S282.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
NF1 MUTATED 6 9 9
NF1 WILD-TYPE 209 321 240
'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.128 (Fisher's exact test), Q value = 0.57

Table S283.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
NF1 MUTATED 4 9 2 3 6 2 1
NF1 WILD-TYPE 229 150 128 202 178 43 17
'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.418 (Fisher's exact test), Q value = 0.84

Table S284.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
NF1 MUTATED 4 7 3 6 6 1
NF1 WILD-TYPE 259 144 76 255 162 51
'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.29 (Fisher's exact test), Q value = 0.75

Table S285.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
NF1 MUTATED 1 6 3 8 8 1
NF1 WILD-TYPE 128 237 174 176 176 40
'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.556 (Fisher's exact test), Q value = 0.92

Table S286.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
NF1 MUTATED 0 6 4 5 1 4 6 0 1
NF1 WILD-TYPE 64 113 152 162 68 107 139 54 72
'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.915 (Fisher's exact test), Q value = 1

Table S287.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
NF1 MUTATED 3 1 2 4 2 3
NF1 WILD-TYPE 111 62 48 116 120 96
'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.787 (Fisher's exact test), Q value = 1

Table S288.  Gene #24: 'NF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
NF1 MUTATED 9 4 2
NF1 WILD-TYPE 272 167 114
'TCP11 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.872 (Fisher's exact test), Q value = 1

Table S289.  Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
TCP11 MUTATED 2 2 2
TCP11 WILD-TYPE 225 115 163
'TCP11 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S290.  Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
TCP11 MUTATED 2 3 1
TCP11 WILD-TYPE 153 262 88
'TCP11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.46 (Fisher's exact test), Q value = 0.87

Table S291.  Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
TCP11 MUTATED 1 0 4 1 0
TCP11 WILD-TYPE 291 118 263 260 25
'TCP11 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S292.  Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
TCP11 MUTATED 2 1 0 2 0 0 0
TCP11 WILD-TYPE 150 213 29 197 123 67 10
'TCP11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S293.  Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
TCP11 MUTATED 1 2 2
TCP11 WILD-TYPE 214 328 247
'TCP11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.762 (Fisher's exact test), Q value = 1

Table S294.  Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
TCP11 MUTATED 2 0 2 1 1 0 0
TCP11 WILD-TYPE 231 159 128 204 183 45 18
'TCP11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.376 (Fisher's exact test), Q value = 0.83

Table S295.  Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
TCP11 MUTATED 1 1 2 1 1 0
TCP11 WILD-TYPE 262 150 77 260 167 52
'TCP11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.647 (Fisher's exact test), Q value = 0.96

Table S296.  Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
TCP11 MUTATED 1 1 1 1 1 1
TCP11 WILD-TYPE 128 242 176 183 183 40
'TCP11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.399 (Fisher's exact test), Q value = 0.84

Table S297.  Gene #25: 'TCP11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
TCP11 MUTATED 2 0 2 1 0 0 1 0 0
TCP11 WILD-TYPE 62 119 154 166 69 111 144 54 73
'SF3B1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.73 (Fisher's exact test), Q value = 0.99

Table S298.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
SF3B1 MUTATED 5 1 2
SF3B1 WILD-TYPE 222 116 163
'SF3B1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.453 (Fisher's exact test), Q value = 0.86

Table S299.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
SF3B1 MUTATED 1 6 1
SF3B1 WILD-TYPE 154 259 88
'SF3B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.508 (Fisher's exact test), Q value = 0.88

Table S300.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
SF3B1 MUTATED 7 3 4 2 0
SF3B1 WILD-TYPE 285 115 263 259 25
'SF3B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.172 (Fisher's exact test), Q value = 0.61

Table S301.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
SF3B1 MUTATED 6 5 1 0 2
SF3B1 WILD-TYPE 187 145 121 119 78
'SF3B1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.62

Table S302.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
SF3B1 MUTATED 1 1 1 6 1 2 0
SF3B1 WILD-TYPE 151 213 28 193 122 65 10
'SF3B1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.26 (Fisher's exact test), Q value = 0.71

Table S303.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
SF3B1 MUTATED 1 5 6
SF3B1 WILD-TYPE 214 325 243
'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.646 (Fisher's exact test), Q value = 0.96

Table S304.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
SF3B1 MUTATED 3 4 3 5 1 0 0
SF3B1 WILD-TYPE 230 155 127 200 183 45 18
'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.354 (Fisher's exact test), Q value = 0.81

Table S305.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
SF3B1 MUTATED 5 4 3 3 1 0
SF3B1 WILD-TYPE 258 147 76 258 167 52
'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.338 (Fisher's exact test), Q value = 0.79

Table S306.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
SF3B1 MUTATED 3 2 4 5 1 1
SF3B1 WILD-TYPE 126 241 173 179 183 40
'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.19 (Fisher's exact test), Q value = 0.63

Table S307.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
SF3B1 MUTATED 0 1 4 4 1 0 1 3 2
SF3B1 WILD-TYPE 64 118 152 163 68 111 144 51 71
'SF3B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.624 (Fisher's exact test), Q value = 0.95

Table S308.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
SF3B1 MUTATED 2 1 1 1 0 1
SF3B1 WILD-TYPE 112 62 49 119 122 98
'SF3B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.183 (Fisher's exact test), Q value = 0.63

Table S309.  Gene #26: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
SF3B1 MUTATED 1 3 2
SF3B1 WILD-TYPE 280 168 114
'ERBB2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.2 (Fisher's exact test), Q value = 0.64

Table S310.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
ERBB2 MUTATED 6 4 1
ERBB2 WILD-TYPE 221 113 164
'ERBB2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S311.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
ERBB2 MUTATED 1 9 1
ERBB2 WILD-TYPE 154 256 88
'ERBB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.38 (Fisher's exact test), Q value = 0.83

Table S312.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
ERBB2 MUTATED 5 5 6 3 0
ERBB2 WILD-TYPE 287 113 261 258 25
'ERBB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.156 (Fisher's exact test), Q value = 0.59

Table S313.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
ERBB2 MUTATED 1 4 4 1 3
ERBB2 WILD-TYPE 192 146 118 118 77
'ERBB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.2

Table S314.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
ERBB2 MUTATED 0 2 1 6 1 3 1
ERBB2 WILD-TYPE 152 212 28 193 122 64 9

Figure S96.  Get High-res Image Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'ERBB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.359 (Fisher's exact test), Q value = 0.81

Table S315.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
ERBB2 MUTATED 3 4 7
ERBB2 WILD-TYPE 212 326 242
'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0689 (Fisher's exact test), Q value = 0.42

Table S316.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
ERBB2 MUTATED 2 8 4 5 1 0 0
ERBB2 WILD-TYPE 231 151 126 200 183 45 18
'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.133 (Fisher's exact test), Q value = 0.57

Table S317.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
ERBB2 MUTATED 3 3 2 8 1 3
ERBB2 WILD-TYPE 260 148 77 253 167 49
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0551 (Fisher's exact test), Q value = 0.39

Table S318.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
ERBB2 MUTATED 0 2 6 4 6 2
ERBB2 WILD-TYPE 129 241 171 180 178 39
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0569 (Fisher's exact test), Q value = 0.4

Table S319.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
ERBB2 MUTATED 1 3 8 3 3 1 0 1 0
ERBB2 WILD-TYPE 63 116 148 164 66 110 145 53 73
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.919 (Fisher's exact test), Q value = 1

Table S320.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
ERBB2 MUTATED 2 1 0 3 1 2
ERBB2 WILD-TYPE 112 62 50 117 121 97
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.497 (Fisher's exact test), Q value = 0.87

Table S321.  Gene #27: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
ERBB2 MUTATED 3 3 3
ERBB2 WILD-TYPE 278 168 113
'RAB42 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S322.  Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
RAB42 MUTATED 1 1 2
RAB42 WILD-TYPE 226 116 163
'RAB42 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.25

Table S323.  Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
RAB42 MUTATED 0 1 3
RAB42 WILD-TYPE 155 264 86

Figure S97.  Get High-res Image Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'RAB42 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.292 (Fisher's exact test), Q value = 0.76

Table S324.  Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
RAB42 MUTATED 1 0 0 3 0
RAB42 WILD-TYPE 291 118 267 258 25
'RAB42 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.402 (Fisher's exact test), Q value = 0.84

Table S325.  Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
RAB42 MUTATED 1 0 0 1 0 1 0
RAB42 WILD-TYPE 151 214 29 198 123 66 10
'RAB42 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S326.  Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
RAB42 MUTATED 2 0 1
RAB42 WILD-TYPE 213 330 248
'RAB42 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.212 (Fisher's exact test), Q value = 0.65

Table S327.  Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
RAB42 MUTATED 0 0 0 1 3 0 0
RAB42 WILD-TYPE 233 159 130 204 181 45 18
'RAB42 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.157 (Fisher's exact test), Q value = 0.59

Table S328.  Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
RAB42 MUTATED 0 0 0 1 3 0
RAB42 WILD-TYPE 263 151 79 260 165 52
'RAB42 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.447 (Fisher's exact test), Q value = 0.85

Table S329.  Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
RAB42 MUTATED 0 3 0 0 1 0
RAB42 WILD-TYPE 129 240 177 184 183 41
'RAB42 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.344 (Fisher's exact test), Q value = 0.8

Table S330.  Gene #28: 'RAB42 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
RAB42 MUTATED 0 0 0 1 0 0 3 0 0
RAB42 WILD-TYPE 64 119 156 166 69 111 142 54 73
'CDC42EP1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S331.  Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
CDC42EP1 MUTATED 1 1 2
CDC42EP1 WILD-TYPE 226 116 163
'CDC42EP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.172 (Fisher's exact test), Q value = 0.61

Table S332.  Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
CDC42EP1 MUTATED 1 1 2
CDC42EP1 WILD-TYPE 154 264 87
'CDC42EP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.62

Table S333.  Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
CDC42EP1 MUTATED 0 2 1 2 0
CDC42EP1 WILD-TYPE 292 116 266 259 25
'CDC42EP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.346 (Fisher's exact test), Q value = 0.8

Table S334.  Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
CDC42EP1 MUTATED 1 0 2 0 0
CDC42EP1 WILD-TYPE 192 150 120 119 80
'CDC42EP1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S335.  Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
CDC42EP1 MUTATED 1 2 0 1 0 1 0
CDC42EP1 WILD-TYPE 151 212 29 198 123 66 10
'CDC42EP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.739 (Fisher's exact test), Q value = 0.99

Table S336.  Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
CDC42EP1 MUTATED 2 2 1
CDC42EP1 WILD-TYPE 213 328 248
'CDC42EP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.259 (Fisher's exact test), Q value = 0.71

Table S337.  Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
CDC42EP1 MUTATED 1 0 1 0 2 1 0
CDC42EP1 WILD-TYPE 232 159 129 205 182 44 18
'CDC42EP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.559 (Fisher's exact test), Q value = 0.92

Table S338.  Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
CDC42EP1 MUTATED 1 0 1 1 2 0
CDC42EP1 WILD-TYPE 262 151 78 260 166 52
'CDC42EP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.692 (Fisher's exact test), Q value = 0.97

Table S339.  Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
CDC42EP1 MUTATED 0 2 2 0 1 0
CDC42EP1 WILD-TYPE 129 241 175 184 183 41
'CDC42EP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.218 (Fisher's exact test), Q value = 0.66

Table S340.  Gene #29: 'CDC42EP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
CDC42EP1 MUTATED 0 0 2 0 0 0 1 0 2
CDC42EP1 WILD-TYPE 64 119 154 167 69 111 144 54 71
'KDM6A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0841 (Fisher's exact test), Q value = 0.45

Table S341.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
KDM6A MUTATED 1 4 3
KDM6A WILD-TYPE 226 113 162
'KDM6A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.573 (Fisher's exact test), Q value = 0.92

Table S342.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
KDM6A MUTATED 1 5 2
KDM6A WILD-TYPE 154 260 87
'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.371 (Fisher's exact test), Q value = 0.83

Table S343.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
KDM6A MUTATED 5 3 4 2 1
KDM6A WILD-TYPE 287 115 263 259 24
'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 0.8

Table S344.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
KDM6A MUTATED 2 3 0 3 2
KDM6A WILD-TYPE 191 147 122 116 78
'KDM6A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.26 (Fisher's exact test), Q value = 0.71

Table S345.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
KDM6A MUTATED 4 2 1 2 1 3 0
KDM6A WILD-TYPE 148 212 28 197 122 64 10
'KDM6A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S346.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
KDM6A MUTATED 5 7 1
KDM6A WILD-TYPE 210 323 248
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.54 (Fisher's exact test), Q value = 0.9

Table S347.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
KDM6A MUTATED 3 2 3 1 5 1 0
KDM6A WILD-TYPE 230 157 127 204 179 44 18
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.405 (Fisher's exact test), Q value = 0.84

Table S348.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
KDM6A MUTATED 2 3 0 5 5 0
KDM6A WILD-TYPE 261 148 79 256 163 52
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.931 (Fisher's exact test), Q value = 1

Table S349.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
KDM6A MUTATED 3 5 2 2 3 0
KDM6A WILD-TYPE 126 238 175 182 181 41
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.987 (Fisher's exact test), Q value = 1

Table S350.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
KDM6A MUTATED 1 2 2 3 1 1 4 0 1
KDM6A WILD-TYPE 63 117 154 164 68 110 141 54 72
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S351.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
KDM6A MUTATED 2 0 0 3 3 1
KDM6A WILD-TYPE 112 63 50 117 119 98
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.401 (Fisher's exact test), Q value = 0.84

Table S352.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
KDM6A MUTATED 5 1 3
KDM6A WILD-TYPE 276 170 113
'AQP12A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 0.87

Table S353.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
AQP12A MUTATED 2 1 0
AQP12A WILD-TYPE 225 116 165
'AQP12A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S354.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
AQP12A MUTATED 1 2 0
AQP12A WILD-TYPE 154 263 89
'AQP12A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.562 (Fisher's exact test), Q value = 0.92

Table S355.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
AQP12A MUTATED 4 0 1 1 0
AQP12A WILD-TYPE 288 118 266 260 25
'AQP12A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.777 (Fisher's exact test), Q value = 1

Table S356.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
AQP12A MUTATED 2 2 0 1 0
AQP12A WILD-TYPE 191 148 122 118 80
'AQP12A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.937 (Fisher's exact test), Q value = 1

Table S357.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
AQP12A MUTATED 1 2 0 2 0 0 0
AQP12A WILD-TYPE 151 212 29 197 123 67 10
'AQP12A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.185 (Fisher's exact test), Q value = 0.63

Table S358.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
AQP12A MUTATED 1 4 0
AQP12A WILD-TYPE 214 326 249
'AQP12A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.777 (Fisher's exact test), Q value = 1

Table S359.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
AQP12A MUTATED 2 2 1 1 0 0 0
AQP12A WILD-TYPE 231 157 129 204 184 45 18
'AQP12A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S360.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
AQP12A MUTATED 2 1 0 2 1 0
AQP12A WILD-TYPE 261 150 79 259 167 52
'AQP12A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.93 (Fisher's exact test), Q value = 1

Table S361.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
AQP12A MUTATED 0 2 1 1 2 0
AQP12A WILD-TYPE 129 241 176 183 182 41
'AQP12A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.559 (Fisher's exact test), Q value = 0.92

Table S362.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
AQP12A MUTATED 0 0 0 3 1 1 1 0 0
AQP12A WILD-TYPE 64 119 156 164 68 110 144 54 73
'AQP12A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.202 (Fisher's exact test), Q value = 0.64

Table S363.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
AQP12A MUTATED 2 1 0 0 0 0
AQP12A WILD-TYPE 112 62 50 120 122 99
'AQP12A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S364.  Gene #31: 'AQP12A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
AQP12A MUTATED 2 1 0
AQP12A WILD-TYPE 279 170 116
'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.565 (Fisher's exact test), Q value = 0.92

Table S365.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
KRAS MUTATED 3 0 1
KRAS WILD-TYPE 224 117 164
'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S366.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
KRAS MUTATED 1 3 0
KRAS WILD-TYPE 154 262 89
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.178 (Fisher's exact test), Q value = 0.62

Table S367.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
KRAS MUTATED 0 1 4 1 0
KRAS WILD-TYPE 292 117 263 260 25
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.355 (Fisher's exact test), Q value = 0.81

Table S368.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
KRAS MUTATED 2 0 2 0 0
KRAS WILD-TYPE 191 150 120 119 80
'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.632 (Fisher's exact test), Q value = 0.95

Table S369.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
KRAS MUTATED 0 1 0 1 2 0 0
KRAS WILD-TYPE 152 213 29 198 121 67 10
'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S370.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
KRAS MUTATED 1 2 1
KRAS WILD-TYPE 214 328 248
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.565 (Fisher's exact test), Q value = 0.92

Table S371.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
KRAS MUTATED 0 1 1 3 1 0 0
KRAS WILD-TYPE 233 158 129 202 183 45 18
'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0851 (Fisher's exact test), Q value = 0.45

Table S372.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
KRAS MUTATED 2 0 2 1 0 1
KRAS WILD-TYPE 261 151 77 260 168 51
'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.693 (Fisher's exact test), Q value = 0.97

Table S373.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
KRAS MUTATED 0 1 1 1 3 0
KRAS WILD-TYPE 129 242 176 183 181 41
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0391 (Fisher's exact test), Q value = 0.32

Table S374.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
KRAS MUTATED 0 4 2 0 0 0 0 0 0
KRAS WILD-TYPE 64 115 154 167 69 111 145 54 73

Figure S98.  Get High-res Image Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.722 (Fisher's exact test), Q value = 0.99

Table S375.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
KRAS MUTATED 0 0 0 2 1 0
KRAS WILD-TYPE 114 63 50 118 121 99
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S376.  Gene #32: 'KRAS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
KRAS MUTATED 1 0 2
KRAS WILD-TYPE 280 171 114
'NBPF9 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.315 (Fisher's exact test), Q value = 0.78

Table S377.  Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
NBPF9 MUTATED 4 0 1
NBPF9 WILD-TYPE 223 117 164
'NBPF9 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.849 (Fisher's exact test), Q value = 1

Table S378.  Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
NBPF9 MUTATED 2 2 1
NBPF9 WILD-TYPE 153 263 88
'NBPF9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00409 (Fisher's exact test), Q value = 0.057

Table S379.  Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
NBPF9 MUTATED 1 1 0 1 2
NBPF9 WILD-TYPE 291 117 267 260 23

Figure S99.  Get High-res Image Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'NBPF9 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.937 (Fisher's exact test), Q value = 1

Table S380.  Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
NBPF9 MUTATED 1 2 0 2 0 0 0
NBPF9 WILD-TYPE 151 212 29 197 123 67 10
'NBPF9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S381.  Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
NBPF9 MUTATED 1 2 2
NBPF9 WILD-TYPE 214 328 247
'NBPF9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.952 (Fisher's exact test), Q value = 1

Table S382.  Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
NBPF9 MUTATED 1 1 0 2 1 0 0
NBPF9 WILD-TYPE 232 158 130 203 183 45 18
'NBPF9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S383.  Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
NBPF9 MUTATED 1 3 0 0 1 0
NBPF9 WILD-TYPE 262 148 79 261 167 52
'NBPF9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.353 (Fisher's exact test), Q value = 0.81

Table S384.  Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
NBPF9 MUTATED 0 2 1 0 1 1
NBPF9 WILD-TYPE 129 241 176 184 183 40
'NBPF9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.561 (Fisher's exact test), Q value = 0.92

Table S385.  Gene #33: 'NBPF9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
NBPF9 MUTATED 0 0 0 1 0 2 1 0 1
NBPF9 WILD-TYPE 64 119 156 166 69 109 144 54 72
'MYB MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.386 (Fisher's exact test), Q value = 0.83

Table S386.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
MYB MUTATED 6 2 1
MYB WILD-TYPE 221 115 164
'MYB MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.587 (Fisher's exact test), Q value = 0.93

Table S387.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
MYB MUTATED 4 3 2
MYB WILD-TYPE 151 262 87
'MYB MUTATION STATUS' versus 'CN_CNMF'

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

Table S388.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
MYB MUTATED 1 3 6 2 0
MYB WILD-TYPE 291 115 261 259 25
'MYB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.555 (Fisher's exact test), Q value = 0.92

Table S389.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
MYB MUTATED 1 1 0 2 1
MYB WILD-TYPE 192 149 122 117 79
'MYB MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S390.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
MYB MUTATED 0 2 0 0 3 1 0
MYB WILD-TYPE 152 212 29 199 120 66 10
'MYB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S391.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
MYB MUTATED 1 3 2
MYB WILD-TYPE 214 327 247
'MYB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.895 (Fisher's exact test), Q value = 1

Table S392.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
MYB MUTATED 3 1 1 3 3 1 0
MYB WILD-TYPE 230 158 129 202 181 44 18
'MYB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.899 (Fisher's exact test), Q value = 1

Table S393.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
MYB MUTATED 4 1 0 4 3 0
MYB WILD-TYPE 259 150 79 257 165 52
'MYB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.245 (Fisher's exact test), Q value = 0.7

Table S394.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
MYB MUTATED 0 2 4 1 4 1
MYB WILD-TYPE 129 241 173 183 180 40
'MYB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.313 (Fisher's exact test), Q value = 0.77

Table S395.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
MYB MUTATED 1 0 0 4 1 3 2 0 1
MYB WILD-TYPE 63 119 156 163 68 108 143 54 72
'MYB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0866 (Fisher's exact test), Q value = 0.45

Table S396.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
MYB MUTATED 1 0 2 1 0 0
MYB WILD-TYPE 113 63 48 119 122 99
'MYB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00177 (Fisher's exact test), Q value = 0.028

Table S397.  Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
MYB MUTATED 0 0 4
MYB WILD-TYPE 281 171 112

Figure S100.  Get High-res Image Gene #34: 'MYB MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ZNF362 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0996 (Fisher's exact test), Q value = 0.5

Table S398.  Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
ZNF362 MUTATED 2 3 0
ZNF362 WILD-TYPE 225 114 165
'ZNF362 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.714 (Fisher's exact test), Q value = 0.98

Table S399.  Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
ZNF362 MUTATED 2 3 0
ZNF362 WILD-TYPE 153 262 89
'ZNF362 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.181 (Fisher's exact test), Q value = 0.63

Table S400.  Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
ZNF362 MUTATED 3 1 0 0 0
ZNF362 WILD-TYPE 289 117 267 261 25
'ZNF362 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.776 (Fisher's exact test), Q value = 1

Table S401.  Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
ZNF362 MUTATED 0 2 0 2 0 0 0
ZNF362 WILD-TYPE 152 212 29 197 123 67 10
'ZNF362 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.473 (Fisher's exact test), Q value = 0.87

Table S402.  Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
ZNF362 MUTATED 0 3 1
ZNF362 WILD-TYPE 215 327 248
'ZNF362 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.462 (Fisher's exact test), Q value = 0.87

Table S403.  Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
ZNF362 MUTATED 3 1 1 0 0 0 0
ZNF362 WILD-TYPE 230 158 129 205 184 45 18
'ZNF362 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S404.  Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
ZNF362 MUTATED 2 1 0 2 0 0
ZNF362 WILD-TYPE 261 150 79 259 168 52
'ZNF362 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.178 (Fisher's exact test), Q value = 0.62

Table S405.  Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
ZNF362 MUTATED 1 0 1 0 3 0
ZNF362 WILD-TYPE 128 243 176 184 181 41
'ZNF362 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0701 (Fisher's exact test), Q value = 0.42

Table S406.  Gene #35: 'ZNF362 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
ZNF362 MUTATED 0 0 0 4 1 0 0 0 0
ZNF362 WILD-TYPE 64 119 156 163 68 111 145 54 73
'TBL1XR1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0631 (Fisher's exact test), Q value = 0.41

Table S407.  Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
TBL1XR1 MUTATED 7 0 1
TBL1XR1 WILD-TYPE 220 117 164
'TBL1XR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.34 (Fisher's exact test), Q value = 0.79

Table S408.  Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
TBL1XR1 MUTATED 4 4 0
TBL1XR1 WILD-TYPE 151 261 89
'TBL1XR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0983 (Fisher's exact test), Q value = 0.5

Table S409.  Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
TBL1XR1 MUTATED 2 3 4 0 0
TBL1XR1 WILD-TYPE 290 115 263 261 25
'TBL1XR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.474 (Fisher's exact test), Q value = 0.87

Table S410.  Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
TBL1XR1 MUTATED 1 2 1 3 0 1 0
TBL1XR1 WILD-TYPE 151 212 28 196 123 66 10
'TBL1XR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S411.  Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
TBL1XR1 MUTATED 2 3 3
TBL1XR1 WILD-TYPE 213 327 246
'TBL1XR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.32

Table S412.  Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
TBL1XR1 MUTATED 0 2 1 6 0 0 0
TBL1XR1 WILD-TYPE 233 157 129 199 184 45 18

Figure S101.  Get High-res Image Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TBL1XR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.566 (Fisher's exact test), Q value = 0.92

Table S413.  Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
TBL1XR1 MUTATED 4 1 0 4 0 0
TBL1XR1 WILD-TYPE 259 150 79 257 168 52
'TBL1XR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 0.84

Table S414.  Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
TBL1XR1 MUTATED 0 1 2 2 3 1
TBL1XR1 WILD-TYPE 129 242 175 182 181 40
'TBL1XR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.2 (Fisher's exact test), Q value = 0.64

Table S415.  Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
TBL1XR1 MUTATED 0 1 1 2 3 2 0 0 0
TBL1XR1 WILD-TYPE 64 118 155 165 66 109 145 54 73
'TBL1XR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.9 (Fisher's exact test), Q value = 1

Table S416.  Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
TBL1XR1 MUTATED 1 0 0 1 1 2
TBL1XR1 WILD-TYPE 113 63 50 119 121 97
'TBL1XR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.103 (Fisher's exact test), Q value = 0.51

Table S417.  Gene #36: 'TBL1XR1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
TBL1XR1 MUTATED 1 1 3
TBL1XR1 WILD-TYPE 280 170 113
'SP3 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S418.  Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
SP3 MUTATED 2 1 1
SP3 WILD-TYPE 225 116 164
'SP3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.3 (Fisher's exact test), Q value = 0.77

Table S419.  Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
SP3 MUTATED 0 4 0
SP3 WILD-TYPE 155 261 89
'SP3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.492 (Fisher's exact test), Q value = 0.87

Table S420.  Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
SP3 MUTATED 3 1 2 0 0
SP3 WILD-TYPE 289 117 265 261 25
'SP3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.947 (Fisher's exact test), Q value = 1

Table S421.  Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
SP3 MUTATED 2 1 1 0 0
SP3 WILD-TYPE 191 149 121 119 80
'SP3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.836 (Fisher's exact test), Q value = 1

Table S422.  Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
SP3 MUTATED 0 1 0 2 1 0 0
SP3 WILD-TYPE 152 213 29 197 122 67 10
'SP3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.821 (Fisher's exact test), Q value = 1

Table S423.  Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
SP3 MUTATED 1 1 2
SP3 WILD-TYPE 214 329 247
'SP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.194 (Fisher's exact test), Q value = 0.64

Table S424.  Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
SP3 MUTATED 2 2 2 0 0 1 0
SP3 WILD-TYPE 231 157 128 205 184 44 18
'SP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.442 (Fisher's exact test), Q value = 0.84

Table S425.  Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
SP3 MUTATED 1 2 0 4 0 0
SP3 WILD-TYPE 262 149 79 257 168 52
'SP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.519 (Fisher's exact test), Q value = 0.88

Table S426.  Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
SP3 MUTATED 3 1 1 1 1 0
SP3 WILD-TYPE 126 242 176 183 183 41
'SP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0652 (Fisher's exact test), Q value = 0.41

Table S427.  Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
SP3 MUTATED 2 1 0 2 0 0 0 0 2
SP3 WILD-TYPE 62 118 156 165 69 111 145 54 71
'SP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.38 (Fisher's exact test), Q value = 0.83

Table S428.  Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
SP3 MUTATED 2 1 0 0 0 1
SP3 WILD-TYPE 112 62 50 120 122 98
'SP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S429.  Gene #37: 'SP3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
SP3 MUTATED 2 1 1
SP3 WILD-TYPE 279 170 115
'FGFR2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.498 (Fisher's exact test), Q value = 0.87

Table S430.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
FGFR2 MUTATED 4 0 2
FGFR2 WILD-TYPE 223 117 163
'FGFR2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S431.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
FGFR2 MUTATED 2 3 1
FGFR2 WILD-TYPE 153 262 88
'FGFR2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.639 (Fisher's exact test), Q value = 0.95

Table S432.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
FGFR2 MUTATED 3 3 2 3 0
FGFR2 WILD-TYPE 289 115 265 258 25
'FGFR2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.559 (Fisher's exact test), Q value = 0.92

Table S433.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
FGFR2 MUTATED 2 3 1 0 0
FGFR2 WILD-TYPE 191 147 121 119 80
'FGFR2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.32

Table S434.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
FGFR2 MUTATED 2 3 1 0 3 0 1
FGFR2 WILD-TYPE 150 211 28 199 120 67 9

Figure S102.  Get High-res Image Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'FGFR2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.313 (Fisher's exact test), Q value = 0.77

Table S435.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
FGFR2 MUTATED 4 5 1
FGFR2 WILD-TYPE 211 325 248
'FGFR2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.194 (Fisher's exact test), Q value = 0.64

Table S436.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
FGFR2 MUTATED 2 4 0 3 1 0 1
FGFR2 WILD-TYPE 231 155 130 202 183 45 17
'FGFR2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.428 (Fisher's exact test), Q value = 0.84

Table S437.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
FGFR2 MUTATED 2 4 0 3 1 1
FGFR2 WILD-TYPE 261 147 79 258 167 51
'FGFR2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 0.66

Table S438.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
FGFR2 MUTATED 1 5 3 0 1 1
FGFR2 WILD-TYPE 128 238 174 184 183 40
'FGFR2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0721 (Fisher's exact test), Q value = 0.42

Table S439.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
FGFR2 MUTATED 1 5 0 3 0 0 1 0 1
FGFR2 WILD-TYPE 63 114 156 164 69 111 144 54 72
'FGFR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.828 (Fisher's exact test), Q value = 1

Table S440.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
FGFR2 MUTATED 1 1 0 0 1 1
FGFR2 WILD-TYPE 113 62 50 120 121 98
'FGFR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.673 (Fisher's exact test), Q value = 0.97

Table S441.  Gene #38: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
FGFR2 MUTATED 2 2 0
FGFR2 WILD-TYPE 279 169 116
'ZBTB7C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.126 (Fisher's exact test), Q value = 0.56

Table S442.  Gene #39: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
ZBTB7C MUTATED 2 2 0 0 0
ZBTB7C WILD-TYPE 290 116 267 261 25
'ZBTB7C MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S443.  Gene #39: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
ZBTB7C MUTATED 1 1 1 0 0
ZBTB7C WILD-TYPE 192 149 121 119 80
'ZBTB7C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.704 (Fisher's exact test), Q value = 0.98

Table S444.  Gene #39: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
ZBTB7C MUTATED 0 2 0 1 1 1 0
ZBTB7C WILD-TYPE 152 212 29 198 122 66 10
'ZBTB7C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S445.  Gene #39: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
ZBTB7C MUTATED 1 2 2
ZBTB7C WILD-TYPE 214 328 247
'ZBTB7C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.881 (Fisher's exact test), Q value = 1

Table S446.  Gene #39: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
ZBTB7C MUTATED 2 1 1 1 0 0 0
ZBTB7C WILD-TYPE 231 158 129 204 184 45 18
'ZBTB7C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.677 (Fisher's exact test), Q value = 0.97

Table S447.  Gene #39: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
ZBTB7C MUTATED 1 1 1 2 0 0
ZBTB7C WILD-TYPE 262 150 78 259 168 52
'ZBTB7C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.83 (Fisher's exact test), Q value = 1

Table S448.  Gene #39: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
ZBTB7C MUTATED 1 1 0 2 1 0
ZBTB7C WILD-TYPE 128 242 177 182 183 41
'ZBTB7C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.597 (Fisher's exact test), Q value = 0.93

Table S449.  Gene #39: 'ZBTB7C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
ZBTB7C MUTATED 0 1 2 0 0 1 0 0 1
ZBTB7C WILD-TYPE 64 118 154 167 69 110 145 54 72
'NCDN MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S450.  Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
NCDN MUTATED 2 0 1
NCDN WILD-TYPE 225 117 164
'NCDN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.157 (Fisher's exact test), Q value = 0.59

Table S451.  Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
NCDN MUTATED 2 0 1
NCDN WILD-TYPE 153 265 88
'NCDN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.916 (Fisher's exact test), Q value = 1

Table S452.  Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
NCDN MUTATED 1 0 2 1 0
NCDN WILD-TYPE 291 118 265 260 25
'NCDN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.952 (Fisher's exact test), Q value = 1

Table S453.  Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
NCDN MUTATED 1 2 0 1 0 0 0
NCDN WILD-TYPE 151 212 29 198 123 67 10
'NCDN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S454.  Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
NCDN MUTATED 1 2 1
NCDN WILD-TYPE 214 328 248
'NCDN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.88 (Fisher's exact test), Q value = 1

Table S455.  Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
NCDN MUTATED 1 0 0 2 1 0 0
NCDN WILD-TYPE 232 159 130 203 183 45 18
'NCDN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.913 (Fisher's exact test), Q value = 1

Table S456.  Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
NCDN MUTATED 1 0 0 2 1 0
NCDN WILD-TYPE 262 151 79 259 167 52
'NCDN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.501 (Fisher's exact test), Q value = 0.87

Table S457.  Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
NCDN MUTATED 0 2 0 0 2 0
NCDN WILD-TYPE 129 241 177 184 182 41
'NCDN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.468 (Fisher's exact test), Q value = 0.87

Table S458.  Gene #40: 'NCDN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
NCDN MUTATED 1 0 0 1 1 0 1 0 0
NCDN WILD-TYPE 63 119 156 166 68 111 144 54 73
'MUC6 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 0.95

Table S459.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
MUC6 MUTATED 4 1 4
MUC6 WILD-TYPE 223 116 161
'MUC6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S460.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
MUC6 MUTATED 2 5 2
MUC6 WILD-TYPE 153 260 87
'MUC6 MUTATION STATUS' versus 'CN_CNMF'

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

Table S461.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
MUC6 MUTATED 4 0 2 7 1
MUC6 WILD-TYPE 288 118 265 254 24
'MUC6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.57

Table S462.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
MUC6 MUTATED 0 3 2 3 2
MUC6 WILD-TYPE 193 147 120 116 78
'MUC6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.485 (Fisher's exact test), Q value = 0.87

Table S463.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
MUC6 MUTATED 2 1 1 5 2 1 0
MUC6 WILD-TYPE 150 213 28 194 121 66 10
'MUC6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.168 (Fisher's exact test), Q value = 0.61

Table S464.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
MUC6 MUTATED 5 2 5
MUC6 WILD-TYPE 210 328 244
'MUC6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0623 (Fisher's exact test), Q value = 0.4

Table S465.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
MUC6 MUTATED 0 4 1 2 6 1 0
MUC6 WILD-TYPE 233 155 129 203 178 44 18
'MUC6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.205 (Fisher's exact test), Q value = 0.64

Table S466.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
MUC6 MUTATED 1 3 0 4 5 1
MUC6 WILD-TYPE 262 148 79 257 163 51
'MUC6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.492 (Fisher's exact test), Q value = 0.87

Table S467.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
MUC6 MUTATED 1 7 2 1 3 0
MUC6 WILD-TYPE 128 236 175 183 181 41
'MUC6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.033 (Fisher's exact test), Q value = 0.29

Table S468.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
MUC6 MUTATED 0 4 0 3 1 0 6 0 0
MUC6 WILD-TYPE 64 115 156 164 68 111 139 54 73

Figure S103.  Get High-res Image Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'MUC6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.587 (Fisher's exact test), Q value = 0.93

Table S469.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
MUC6 MUTATED 2 0 0 1 3 0
MUC6 WILD-TYPE 112 63 50 119 119 99
'MUC6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.052 (Fisher's exact test), Q value = 0.37

Table S470.  Gene #41: 'MUC6 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
MUC6 MUTATED 6 0 0
MUC6 WILD-TYPE 275 171 116
'TGS1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.21 (Fisher's exact test), Q value = 0.65

Table S471.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
TGS1 MUTATED 1 1 4
TGS1 WILD-TYPE 226 116 161
'TGS1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.262 (Fisher's exact test), Q value = 0.71

Table S472.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
TGS1 MUTATED 0 5 1
TGS1 WILD-TYPE 155 260 88
'TGS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.625 (Fisher's exact test), Q value = 0.95

Table S473.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
TGS1 MUTATED 3 1 6 2 0
TGS1 WILD-TYPE 289 117 261 259 25
'TGS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.285 (Fisher's exact test), Q value = 0.75

Table S474.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
TGS1 MUTATED 4 4 3 0 0
TGS1 WILD-TYPE 189 146 119 119 80
'TGS1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.835 (Fisher's exact test), Q value = 1

Table S475.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
TGS1 MUTATED 2 4 0 1 2 1 0
TGS1 WILD-TYPE 150 210 29 198 121 66 10
'TGS1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.564 (Fisher's exact test), Q value = 0.92

Table S476.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
TGS1 MUTATED 2 6 2
TGS1 WILD-TYPE 213 324 247
'TGS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S477.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
TGS1 MUTATED 2 4 1 3 2 1 0
TGS1 WILD-TYPE 231 155 129 202 182 44 18
'TGS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.249 (Fisher's exact test), Q value = 0.7

Table S478.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
TGS1 MUTATED 2 5 0 4 1 1
TGS1 WILD-TYPE 261 146 79 257 167 51
'TGS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.689 (Fisher's exact test), Q value = 0.97

Table S479.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
TGS1 MUTATED 2 2 2 2 5 0
TGS1 WILD-TYPE 127 241 175 182 179 41
'TGS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0235 (Fisher's exact test), Q value = 0.23

Table S480.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
TGS1 MUTATED 1 3 1 1 1 1 0 4 1
TGS1 WILD-TYPE 63 116 155 166 68 110 145 50 72

Figure S104.  Get High-res Image Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TGS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0869 (Fisher's exact test), Q value = 0.45

Table S481.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
TGS1 MUTATED 3 2 0 0 0 2
TGS1 WILD-TYPE 111 61 50 120 122 97
'TGS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.319 (Fisher's exact test), Q value = 0.78

Table S482.  Gene #42: 'TGS1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
TGS1 MUTATED 2 4 1
TGS1 WILD-TYPE 279 167 115
'TFE3 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S483.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
TFE3 MUTATED 1 3 3
TFE3 WILD-TYPE 226 114 162
'TFE3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.149 (Fisher's exact test), Q value = 0.59

Table S484.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
TFE3 MUTATED 0 5 2
TFE3 WILD-TYPE 155 260 87
'TFE3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.407 (Fisher's exact test), Q value = 0.84

Table S485.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
TFE3 MUTATED 3 1 0 3 0
TFE3 WILD-TYPE 289 117 267 258 25
'TFE3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.694 (Fisher's exact test), Q value = 0.97

Table S486.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
TFE3 MUTATED 1 0 1 1 1
TFE3 WILD-TYPE 192 150 121 118 79
'TFE3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.357 (Fisher's exact test), Q value = 0.81

Table S487.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
TFE3 MUTATED 0 0 0 1 1 1 0
TFE3 WILD-TYPE 152 214 29 198 122 66 10
'TFE3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S488.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
TFE3 MUTATED 1 1 1
TFE3 WILD-TYPE 214 329 248
'TFE3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.722 (Fisher's exact test), Q value = 0.99

Table S489.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
TFE3 MUTATED 2 2 1 0 2 0 0
TFE3 WILD-TYPE 231 157 129 205 182 45 18
'TFE3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.647 (Fisher's exact test), Q value = 0.96

Table S490.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
TFE3 MUTATED 2 1 0 1 2 1
TFE3 WILD-TYPE 261 150 79 260 166 51
'TFE3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.958 (Fisher's exact test), Q value = 1

Table S491.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
TFE3 MUTATED 1 3 1 1 1 0
TFE3 WILD-TYPE 128 240 176 183 183 41
'TFE3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.165 (Fisher's exact test), Q value = 0.6

Table S492.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
TFE3 MUTATED 0 0 2 1 0 0 1 0 3
TFE3 WILD-TYPE 64 119 154 166 69 111 144 54 70
'TFE3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S493.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
TFE3 MUTATED 1 0 0 1 1 0
TFE3 WILD-TYPE 113 63 50 119 121 99
'TFE3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.311 (Fisher's exact test), Q value = 0.77

Table S494.  Gene #43: 'TFE3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
TFE3 MUTATED 3 0 0
TFE3 WILD-TYPE 278 171 116
'IRS4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.191 (Fisher's exact test), Q value = 0.63

Table S495.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
IRS4 MUTATED 1 3 3
IRS4 WILD-TYPE 226 114 162
'IRS4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S496.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
IRS4 MUTATED 0 6 1
IRS4 WILD-TYPE 155 259 88
'IRS4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.231 (Fisher's exact test), Q value = 0.68

Table S497.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
IRS4 MUTATED 4 0 1 6 0
IRS4 WILD-TYPE 288 118 266 255 25
'IRS4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.638 (Fisher's exact test), Q value = 0.95

Table S498.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
IRS4 MUTATED 1 2 3 2 1
IRS4 WILD-TYPE 192 148 119 117 79
'IRS4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.166 (Fisher's exact test), Q value = 0.61

Table S499.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
IRS4 MUTATED 1 3 1 0 3 0 0
IRS4 WILD-TYPE 151 211 28 199 120 67 10
'IRS4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0652 (Fisher's exact test), Q value = 0.41

Table S500.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
IRS4 MUTATED 2 6 0
IRS4 WILD-TYPE 213 324 249
'IRS4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.146 (Fisher's exact test), Q value = 0.59

Table S501.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
IRS4 MUTATED 3 1 2 0 3 1 1
IRS4 WILD-TYPE 230 158 128 205 181 44 17
'IRS4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.47 (Fisher's exact test), Q value = 0.87

Table S502.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
IRS4 MUTATED 2 0 1 4 3 1
IRS4 WILD-TYPE 261 151 78 257 165 51
'IRS4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0614 (Fisher's exact test), Q value = 0.4

Table S503.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
IRS4 MUTATED 4 3 0 0 3 0
IRS4 WILD-TYPE 125 240 177 184 181 41
'IRS4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S504.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
IRS4 MUTATED 2 1 1 1 1 1 2 0 1
IRS4 WILD-TYPE 62 118 155 166 68 110 143 54 72
'IRS4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.709 (Fisher's exact test), Q value = 0.98

Table S505.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
IRS4 MUTATED 2 0 0 0 1 1
IRS4 WILD-TYPE 112 63 50 120 121 98
'IRS4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.817 (Fisher's exact test), Q value = 1

Table S506.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
IRS4 MUTATED 3 1 0
IRS4 WILD-TYPE 278 170 116
'NLGN3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 0.69

Table S507.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
NLGN3 MUTATED 2 1 5
NLGN3 WILD-TYPE 225 116 160
'NLGN3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S508.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
NLGN3 MUTATED 2 5 1
NLGN3 WILD-TYPE 153 260 88
'NLGN3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.791 (Fisher's exact test), Q value = 1

Table S509.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
NLGN3 MUTATED 3 1 5 2 0
NLGN3 WILD-TYPE 289 117 262 259 25
'NLGN3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.876 (Fisher's exact test), Q value = 1

Table S510.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
NLGN3 MUTATED 2 1 0 1 1
NLGN3 WILD-TYPE 191 149 122 118 79
'NLGN3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S511.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
NLGN3 MUTATED 2 0 0 1 3 2 0
NLGN3 WILD-TYPE 150 214 29 198 120 65 10
'NLGN3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.396 (Fisher's exact test), Q value = 0.84

Table S512.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
NLGN3 MUTATED 2 5 1
NLGN3 WILD-TYPE 213 325 248
'NLGN3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.928 (Fisher's exact test), Q value = 1

Table S513.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
NLGN3 MUTATED 4 2 1 3 1 0 0
NLGN3 WILD-TYPE 229 157 129 202 183 45 18
'NLGN3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0819 (Fisher's exact test), Q value = 0.44

Table S514.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
NLGN3 MUTATED 4 4 1 0 1 1
NLGN3 WILD-TYPE 259 147 78 261 167 51
'NLGN3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S515.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
NLGN3 MUTATED 1 3 2 3 2 0
NLGN3 WILD-TYPE 128 240 175 181 182 41
'NLGN3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.996 (Fisher's exact test), Q value = 1

Table S516.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
NLGN3 MUTATED 1 1 2 2 0 2 2 0 1
NLGN3 WILD-TYPE 63 118 154 165 69 109 143 54 72
'NLGN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.375 (Fisher's exact test), Q value = 0.83

Table S517.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
NLGN3 MUTATED 2 1 0 0 0 1
NLGN3 WILD-TYPE 112 62 50 120 122 98
'NLGN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.673 (Fisher's exact test), Q value = 0.97

Table S518.  Gene #45: 'NLGN3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
NLGN3 MUTATED 2 2 0
NLGN3 WILD-TYPE 279 169 116
'IL1RAP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.427 (Fisher's exact test), Q value = 0.84

Table S519.  Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
IL1RAP MUTATED 2 1 1 5 0
IL1RAP WILD-TYPE 290 117 266 256 25
'IL1RAP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.299 (Fisher's exact test), Q value = 0.77

Table S520.  Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
IL1RAP MUTATED 1 2 0 3 1
IL1RAP WILD-TYPE 192 148 122 116 79
'IL1RAP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.337 (Fisher's exact test), Q value = 0.79

Table S521.  Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
IL1RAP MUTATED 0 3 0 1 2 2 0
IL1RAP WILD-TYPE 152 211 29 198 121 65 10
'IL1RAP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.312 (Fisher's exact test), Q value = 0.77

Table S522.  Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
IL1RAP MUTATED 4 3 1
IL1RAP WILD-TYPE 211 327 248
'IL1RAP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.873 (Fisher's exact test), Q value = 1

Table S523.  Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
IL1RAP MUTATED 2 2 0 3 2 0 0
IL1RAP WILD-TYPE 231 157 130 202 182 45 18
'IL1RAP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.643 (Fisher's exact test), Q value = 0.96

Table S524.  Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
IL1RAP MUTATED 1 2 0 3 2 1
IL1RAP WILD-TYPE 262 149 79 258 166 51
'IL1RAP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.575 (Fisher's exact test), Q value = 0.92

Table S525.  Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
IL1RAP MUTATED 0 3 1 1 2 1
IL1RAP WILD-TYPE 129 240 176 183 182 40
'IL1RAP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.301 (Fisher's exact test), Q value = 0.77

Table S526.  Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
IL1RAP MUTATED 0 1 0 0 1 2 2 1 1
IL1RAP WILD-TYPE 64 118 156 167 68 109 143 53 72
'IL1RAP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S527.  Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
IL1RAP MUTATED 1 0 0 2 3 1
IL1RAP WILD-TYPE 113 63 50 118 119 98
'IL1RAP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.611 (Fisher's exact test), Q value = 0.94

Table S528.  Gene #46: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
IL1RAP MUTATED 5 1 1
IL1RAP WILD-TYPE 276 170 115
'USP36 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.336 (Fisher's exact test), Q value = 0.79

Table S529.  Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
USP36 MUTATED 4 0 3
USP36 WILD-TYPE 223 117 162
'USP36 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.006 (Fisher's exact test), Q value = 0.078

Table S530.  Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
USP36 MUTATED 4 0 3
USP36 WILD-TYPE 151 265 86

Figure S105.  Get High-res Image Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'USP36 MUTATION STATUS' versus 'CN_CNMF'

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

Table S531.  Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
USP36 MUTATED 3 0 2 3 0
USP36 WILD-TYPE 289 118 265 258 25
'USP36 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S532.  Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
USP36 MUTATED 1 1 0 1 0
USP36 WILD-TYPE 192 149 122 118 80
'USP36 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.454 (Fisher's exact test), Q value = 0.86

Table S533.  Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
USP36 MUTATED 2 4 0 0 1 1 0
USP36 WILD-TYPE 150 210 29 199 122 66 10
'USP36 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.499 (Fisher's exact test), Q value = 0.87

Table S534.  Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
USP36 MUTATED 3 4 1
USP36 WILD-TYPE 212 326 248
'USP36 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.409 (Fisher's exact test), Q value = 0.84

Table S535.  Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
USP36 MUTATED 4 0 0 1 3 0 0
USP36 WILD-TYPE 229 159 130 204 181 45 18
'USP36 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0759 (Fisher's exact test), Q value = 0.43

Table S536.  Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
USP36 MUTATED 5 0 0 0 3 0
USP36 WILD-TYPE 258 151 79 261 165 52
'USP36 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.596 (Fisher's exact test), Q value = 0.93

Table S537.  Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
USP36 MUTATED 2 3 2 0 1 0
USP36 WILD-TYPE 127 240 175 184 183 41
'USP36 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S538.  Gene #47: 'USP36 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
USP36 MUTATED 1 0 2 1 0 1 3 0 0
USP36 WILD-TYPE 63 119 154 166 69 110 142 54 73
'CASZ1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.896 (Fisher's exact test), Q value = 1

Table S539.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
CASZ1 MUTATED 4 1 2
CASZ1 WILD-TYPE 223 116 163
'CASZ1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.458 (Fisher's exact test), Q value = 0.86

Table S540.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
CASZ1 MUTATED 1 4 2
CASZ1 WILD-TYPE 154 261 87
'CASZ1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.972 (Fisher's exact test), Q value = 1

Table S541.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
CASZ1 MUTATED 5 1 4 3 0
CASZ1 WILD-TYPE 287 117 263 258 25
'CASZ1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.462 (Fisher's exact test), Q value = 0.87

Table S542.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
CASZ1 MUTATED 2 4 1 3 0
CASZ1 WILD-TYPE 191 146 121 116 80
'CASZ1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.493 (Fisher's exact test), Q value = 0.87

Table S543.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
CASZ1 MUTATED 1 1 0 5 2 0 0
CASZ1 WILD-TYPE 151 213 29 194 121 67 10
'CASZ1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.098 (Fisher's exact test), Q value = 0.5

Table S544.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
CASZ1 MUTATED 1 2 6
CASZ1 WILD-TYPE 214 328 243
'CASZ1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.986 (Fisher's exact test), Q value = 1

Table S545.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
CASZ1 MUTATED 3 2 2 3 4 0 0
CASZ1 WILD-TYPE 230 157 128 202 180 45 18
'CASZ1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.733 (Fisher's exact test), Q value = 0.99

Table S546.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
CASZ1 MUTATED 2 2 1 5 4 0
CASZ1 WILD-TYPE 261 149 78 256 164 52
'CASZ1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 0.87

Table S547.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
CASZ1 MUTATED 3 2 2 4 1 1
CASZ1 WILD-TYPE 126 241 175 180 183 40
'CASZ1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.986 (Fisher's exact test), Q value = 1

Table S548.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
CASZ1 MUTATED 1 2 2 2 0 1 3 1 1
CASZ1 WILD-TYPE 63 117 154 165 69 110 142 53 72
'CASZ1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.707 (Fisher's exact test), Q value = 0.98

Table S549.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
CASZ1 MUTATED 2 0 0 2 1 3
CASZ1 WILD-TYPE 112 63 50 118 121 96
'CASZ1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.809 (Fisher's exact test), Q value = 1

Table S550.  Gene #48: 'CASZ1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
CASZ1 MUTATED 5 2 1
CASZ1 WILD-TYPE 276 169 115
'EYS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.19 (Fisher's exact test), Q value = 0.63

Table S551.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
EYS MUTATED 4 1 7
EYS WILD-TYPE 223 116 158
'EYS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.178 (Fisher's exact test), Q value = 0.62

Table S552.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
EYS MUTATED 1 9 2
EYS WILD-TYPE 154 256 87
'EYS MUTATION STATUS' versus 'CN_CNMF'

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

Table S553.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
EYS MUTATED 7 0 4 10 0
EYS WILD-TYPE 285 118 263 251 25
'EYS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.484 (Fisher's exact test), Q value = 0.87

Table S554.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
EYS MUTATED 2 4 1 4 1
EYS WILD-TYPE 191 146 121 115 79
'EYS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.32

Table S555.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
EYS MUTATED 6 3 2 1 5 0 0
EYS WILD-TYPE 146 211 27 198 118 67 10

Figure S106.  Get High-res Image Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'EYS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0785 (Fisher's exact test), Q value = 0.44

Table S556.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
EYS MUTATED 9 5 3
EYS WILD-TYPE 206 325 246
'EYS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.13

Table S557.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
EYS MUTATED 3 7 1 3 4 0 3
EYS WILD-TYPE 230 152 129 202 180 45 15

Figure S107.  Get High-res Image Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'EYS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.201 (Fisher's exact test), Q value = 0.64

Table S558.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
EYS MUTATED 2 4 1 7 4 3
EYS WILD-TYPE 261 147 78 254 164 49
'EYS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.31

Table S559.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
EYS MUTATED 6 9 3 1 1 1
EYS WILD-TYPE 123 234 174 183 183 40

Figure S108.  Get High-res Image Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'EYS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.16

Table S560.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
EYS MUTATED 1 7 1 0 1 3 3 1 4
EYS WILD-TYPE 63 112 155 167 68 108 142 53 69

Figure S109.  Get High-res Image Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'EYS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 0.64

Table S561.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
EYS MUTATED 2 1 0 1 7 3
EYS WILD-TYPE 112 62 50 119 115 96
'EYS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0885 (Fisher's exact test), Q value = 0.46

Table S562.  Gene #49: 'EYS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
EYS MUTATED 10 4 0
EYS WILD-TYPE 271 167 116
'KCNN3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.379 (Fisher's exact test), Q value = 0.83

Table S563.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
KCNN3 MUTATED 2 0 3
KCNN3 WILD-TYPE 225 117 162
'KCNN3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S564.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
KCNN3 MUTATED 0 3 2
KCNN3 WILD-TYPE 155 262 87
'KCNN3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.386 (Fisher's exact test), Q value = 0.83

Table S565.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
KCNN3 MUTATED 3 0 1 5 0
KCNN3 WILD-TYPE 289 118 266 256 25
'KCNN3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S566.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
KCNN3 MUTATED 2 0 0 3 0
KCNN3 WILD-TYPE 191 150 122 116 80
'KCNN3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0406 (Fisher's exact test), Q value = 0.32

Table S567.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
KCNN3 MUTATED 5 0 0 1 0 1 0
KCNN3 WILD-TYPE 147 214 29 198 123 66 10

Figure S110.  Get High-res Image Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'KCNN3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.495 (Fisher's exact test), Q value = 0.87

Table S568.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
KCNN3 MUTATED 3 3 1
KCNN3 WILD-TYPE 212 327 248
'KCNN3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0729 (Fisher's exact test), Q value = 0.42

Table S569.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
KCNN3 MUTATED 1 3 1 0 2 1 1
KCNN3 WILD-TYPE 232 156 129 205 182 44 17
'KCNN3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.398 (Fisher's exact test), Q value = 0.84

Table S570.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
KCNN3 MUTATED 1 3 0 2 2 1
KCNN3 WILD-TYPE 262 148 79 259 166 51
'KCNN3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 0.58

Table S571.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
KCNN3 MUTATED 3 4 0 0 2 0
KCNN3 WILD-TYPE 126 239 177 184 182 41
'KCNN3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.487 (Fisher's exact test), Q value = 0.87

Table S572.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
KCNN3 MUTATED 0 1 0 1 1 3 2 0 1
KCNN3 WILD-TYPE 64 118 156 166 68 108 143 54 72
'KCNN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.491 (Fisher's exact test), Q value = 0.87

Table S573.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
KCNN3 MUTATED 2 0 0 0 2 0
KCNN3 WILD-TYPE 112 63 50 120 120 99
'KCNN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.428 (Fisher's exact test), Q value = 0.84

Table S574.  Gene #50: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
KCNN3 MUTATED 3 0 1
KCNN3 WILD-TYPE 278 171 115
'ZFP36L1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.204 (Fisher's exact test), Q value = 0.64

Table S575.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
ZFP36L1 MUTATED 4 1 0
ZFP36L1 WILD-TYPE 223 116 165
'ZFP36L1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.581 (Fisher's exact test), Q value = 0.93

Table S576.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
ZFP36L1 MUTATED 1 4 0
ZFP36L1 WILD-TYPE 154 261 89
'ZFP36L1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.017

Table S577.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
ZFP36L1 MUTATED 3 4 0 0 1
ZFP36L1 WILD-TYPE 289 114 267 261 24

Figure S111.  Get High-res Image Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ZFP36L1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.418 (Fisher's exact test), Q value = 0.84

Table S578.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
ZFP36L1 MUTATED 1 3 0 1 0
ZFP36L1 WILD-TYPE 192 147 122 118 80
'ZFP36L1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S579.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
ZFP36L1 MUTATED 1 2 0 3 1 0 0
ZFP36L1 WILD-TYPE 151 212 29 196 122 67 10
'ZFP36L1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.434 (Fisher's exact test), Q value = 0.84

Table S580.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
ZFP36L1 MUTATED 1 2 4
ZFP36L1 WILD-TYPE 214 328 245
'ZFP36L1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.239 (Fisher's exact test), Q value = 0.69

Table S581.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
ZFP36L1 MUTATED 5 2 0 0 1 0 0
ZFP36L1 WILD-TYPE 228 157 130 205 183 45 18
'ZFP36L1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.732 (Fisher's exact test), Q value = 0.99

Table S582.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
ZFP36L1 MUTATED 4 2 0 1 1 0
ZFP36L1 WILD-TYPE 259 149 79 260 167 52
'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.21

Table S583.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
ZFP36L1 MUTATED 3 1 1 0 1 2
ZFP36L1 WILD-TYPE 126 242 176 184 183 39

Figure S112.  Get High-res Image Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.538 (Fisher's exact test), Q value = 0.9

Table S584.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
ZFP36L1 MUTATED 0 2 0 1 0 2 1 1 1
ZFP36L1 WILD-TYPE 64 117 156 166 69 109 144 53 72
'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.71 (Fisher's exact test), Q value = 0.98

Table S585.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
ZFP36L1 MUTATED 2 0 0 0 1 1
ZFP36L1 WILD-TYPE 112 63 50 120 121 98
'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S586.  Gene #51: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
ZFP36L1 MUTATED 3 1 0
ZFP36L1 WILD-TYPE 278 170 116
'ICOSLG MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S587.  Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
ICOSLG MUTATED 2 0 1
ICOSLG WILD-TYPE 225 117 164
'ICOSLG MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.157 (Fisher's exact test), Q value = 0.59

Table S588.  Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
ICOSLG MUTATED 2 0 1
ICOSLG WILD-TYPE 153 265 88
'ICOSLG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.47 (Fisher's exact test), Q value = 0.87

Table S589.  Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
ICOSLG MUTATED 3 0 0 2 0
ICOSLG WILD-TYPE 289 118 267 259 25
'ICOSLG MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S590.  Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
ICOSLG MUTATED 1 1 1 1 0
ICOSLG WILD-TYPE 192 149 121 118 80
'ICOSLG MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.51

Table S591.  Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
ICOSLG MUTATED 0 2 0 0 0 2 0
ICOSLG WILD-TYPE 152 212 29 199 123 65 10
'ICOSLG MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.383 (Fisher's exact test), Q value = 0.83

Table S592.  Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
ICOSLG MUTATED 1 3 0
ICOSLG WILD-TYPE 214 327 249
'ICOSLG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.835 (Fisher's exact test), Q value = 1

Table S593.  Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
ICOSLG MUTATED 2 0 0 2 1 0 0
ICOSLG WILD-TYPE 231 159 130 203 183 45 18
'ICOSLG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.968 (Fisher's exact test), Q value = 1

Table S594.  Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
ICOSLG MUTATED 1 1 0 2 1 0
ICOSLG WILD-TYPE 262 150 79 259 167 52
'ICOSLG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 0.58

Table S595.  Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
ICOSLG MUTATED 1 1 2 0 0 1
ICOSLG WILD-TYPE 128 242 175 184 184 40
'ICOSLG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.682 (Fisher's exact test), Q value = 0.97

Table S596.  Gene #52: 'ICOSLG MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
ICOSLG MUTATED 0 0 0 1 1 1 1 0 1
ICOSLG WILD-TYPE 64 119 156 166 68 110 144 54 72
'ACTL6B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.676 (Fisher's exact test), Q value = 0.97

Table S597.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
ACTL6B MUTATED 3 2 1
ACTL6B WILD-TYPE 224 115 164
'ACTL6B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.4 (Fisher's exact test), Q value = 0.84

Table S598.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
ACTL6B MUTATED 2 2 2
ACTL6B WILD-TYPE 153 263 87
'ACTL6B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00576 (Fisher's exact test), Q value = 0.076

Table S599.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
ACTL6B MUTATED 3 0 0 5 2
ACTL6B WILD-TYPE 289 118 267 256 23

Figure S113.  Get High-res Image Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ACTL6B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.312 (Fisher's exact test), Q value = 0.77

Table S600.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
ACTL6B MUTATED 3 1 0 3 0
ACTL6B WILD-TYPE 190 149 122 116 80
'ACTL6B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S601.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
ACTL6B MUTATED 2 1 0 2 0 1 1
ACTL6B WILD-TYPE 150 213 29 197 123 66 9
'ACTL6B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.566 (Fisher's exact test), Q value = 0.92

Table S602.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
ACTL6B MUTATED 3 2 2
ACTL6B WILD-TYPE 212 328 247
'ACTL6B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 0.97

Table S603.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
ACTL6B MUTATED 2 2 0 2 3 1 0
ACTL6B WILD-TYPE 231 157 130 203 181 44 18
'ACTL6B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.197 (Fisher's exact test), Q value = 0.64

Table S604.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
ACTL6B MUTATED 3 3 1 0 3 0
ACTL6B WILD-TYPE 260 148 78 261 165 52
'ACTL6B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.782 (Fisher's exact test), Q value = 1

Table S605.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
ACTL6B MUTATED 2 2 1 2 2 1
ACTL6B WILD-TYPE 127 241 176 182 182 40
'ACTL6B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.913 (Fisher's exact test), Q value = 1

Table S606.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
ACTL6B MUTATED 0 1 1 3 1 1 3 0 0
ACTL6B WILD-TYPE 64 118 155 164 68 110 142 54 73
'ACTL6B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.515 (Fisher's exact test), Q value = 0.88

Table S607.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
ACTL6B MUTATED 2 0 0 1 0 2
ACTL6B WILD-TYPE 112 63 50 119 122 97
'ACTL6B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S608.  Gene #53: 'ACTL6B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
ACTL6B MUTATED 2 2 1
ACTL6B WILD-TYPE 279 169 115
'MYH9 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.478 (Fisher's exact test), Q value = 0.87

Table S609.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
MYH9 MUTATED 2 2 4
MYH9 WILD-TYPE 225 115 161
'MYH9 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S610.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
MYH9 MUTATED 2 5 1
MYH9 WILD-TYPE 153 260 88
'MYH9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.144 (Fisher's exact test), Q value = 0.58

Table S611.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
MYH9 MUTATED 4 0 8 3 1
MYH9 WILD-TYPE 288 118 259 258 24
'MYH9 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S612.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
MYH9 MUTATED 5 4 1 2 2
MYH9 WILD-TYPE 188 146 121 117 78
'MYH9 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.39 (Fisher's exact test), Q value = 0.83

Table S613.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
MYH9 MUTATED 2 4 0 3 4 4 0
MYH9 WILD-TYPE 150 210 29 196 119 63 10
'MYH9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.412 (Fisher's exact test), Q value = 0.84

Table S614.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
MYH9 MUTATED 7 5 5
MYH9 WILD-TYPE 208 325 244
'MYH9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.338 (Fisher's exact test), Q value = 0.79

Table S615.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
MYH9 MUTATED 1 5 2 6 3 1 0
MYH9 WILD-TYPE 232 154 128 199 181 44 18
'MYH9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.143 (Fisher's exact test), Q value = 0.58

Table S616.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
MYH9 MUTATED 1 3 1 8 3 2
MYH9 WILD-TYPE 262 148 78 253 165 50
'MYH9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.633 (Fisher's exact test), Q value = 0.95

Table S617.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
MYH9 MUTATED 3 4 3 2 4 2
MYH9 WILD-TYPE 126 239 174 182 180 39
'MYH9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.504 (Fisher's exact test), Q value = 0.87

Table S618.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
MYH9 MUTATED 0 3 3 2 2 2 3 3 0
MYH9 WILD-TYPE 64 116 153 165 67 109 142 51 73
'MYH9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.906 (Fisher's exact test), Q value = 1

Table S619.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
MYH9 MUTATED 3 2 0 2 2 2
MYH9 WILD-TYPE 111 61 50 118 120 97
'MYH9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.171 (Fisher's exact test), Q value = 0.61

Table S620.  Gene #54: 'MYH9 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
MYH9 MUTATED 6 5 0
MYH9 WILD-TYPE 275 166 116
'FBXW7 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S621.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
FBXW7 MUTATED 2 1 3
FBXW7 WILD-TYPE 225 116 162
'FBXW7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.479 (Fisher's exact test), Q value = 0.87

Table S622.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
FBXW7 MUTATED 1 3 2
FBXW7 WILD-TYPE 154 262 87
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.133 (Fisher's exact test), Q value = 0.57

Table S623.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
FBXW7 MUTATED 2 0 5 8 0
FBXW7 WILD-TYPE 290 118 262 253 25
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S624.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
FBXW7 MUTATED 3 0 1 6 1
FBXW7 WILD-TYPE 190 150 121 113 79

Figure S114.  Get High-res Image Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.263 (Fisher's exact test), Q value = 0.71

Table S625.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
FBXW7 MUTATED 6 2 0 1 2 1 0
FBXW7 WILD-TYPE 146 212 29 198 121 66 10
'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.101 (Fisher's exact test), Q value = 0.51

Table S626.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
FBXW7 MUTATED 6 5 1
FBXW7 WILD-TYPE 209 325 248
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S627.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
FBXW7 MUTATED 1 1 1 5 7 0 0
FBXW7 WILD-TYPE 232 158 129 200 177 45 18
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.148 (Fisher's exact test), Q value = 0.59

Table S628.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
FBXW7 MUTATED 3 1 0 4 7 0
FBXW7 WILD-TYPE 260 150 79 257 161 52
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.518 (Fisher's exact test), Q value = 0.88

Table S629.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
FBXW7 MUTATED 1 7 3 1 3 0
FBXW7 WILD-TYPE 128 236 174 183 181 41
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.403 (Fisher's exact test), Q value = 0.84

Table S630.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
FBXW7 MUTATED 0 2 3 1 0 1 6 1 1
FBXW7 WILD-TYPE 64 117 153 166 69 110 139 53 72
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.3

Table S631.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
FBXW7 MUTATED 0 0 1 0 5 2
FBXW7 WILD-TYPE 114 63 49 120 117 97

Figure S115.  Get High-res Image Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.81 (Fisher's exact test), Q value = 1

Table S632.  Gene #55: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
FBXW7 MUTATED 5 2 1
FBXW7 WILD-TYPE 276 169 115
'FRMPD2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 0.84

Table S633.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
FRMPD2 MUTATED 2 1 4
FRMPD2 WILD-TYPE 225 116 161
'FRMPD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S634.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
FRMPD2 MUTATED 0 6 1
FRMPD2 WILD-TYPE 155 259 88
'FRMPD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.23 (Fisher's exact test), Q value = 0.68

Table S635.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
FRMPD2 MUTATED 3 0 3 6 1
FRMPD2 WILD-TYPE 289 118 264 255 24
'FRMPD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.57

Table S636.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
FRMPD2 MUTATED 0 3 2 3 2
FRMPD2 WILD-TYPE 193 147 120 116 78
'FRMPD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.133 (Fisher's exact test), Q value = 0.57

Table S637.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
FRMPD2 MUTATED 3 1 1 2 1 1 1
FRMPD2 WILD-TYPE 149 213 28 197 122 66 9
'FRMPD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.262 (Fisher's exact test), Q value = 0.71

Table S638.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
FRMPD2 MUTATED 5 3 2
FRMPD2 WILD-TYPE 210 327 247
'FRMPD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.575 (Fisher's exact test), Q value = 0.92

Table S639.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
FRMPD2 MUTATED 1 3 2 2 4 1 0
FRMPD2 WILD-TYPE 232 156 128 203 180 44 18
'FRMPD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0541 (Fisher's exact test), Q value = 0.39

Table S640.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
FRMPD2 MUTATED 0 4 0 5 4 0
FRMPD2 WILD-TYPE 263 147 79 256 164 52
'FRMPD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.435 (Fisher's exact test), Q value = 0.84

Table S641.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
FRMPD2 MUTATED 0 4 1 4 3 1
FRMPD2 WILD-TYPE 129 239 176 180 181 40
'FRMPD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.29 (Fisher's exact test), Q value = 0.75

Table S642.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
FRMPD2 MUTATED 0 5 3 1 0 1 3 0 0
FRMPD2 WILD-TYPE 64 114 153 166 69 110 142 54 73
'FRMPD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.553 (Fisher's exact test), Q value = 0.92

Table S643.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
FRMPD2 MUTATED 0 0 1 1 2 2
FRMPD2 WILD-TYPE 114 63 49 119 120 97
'FRMPD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.579 (Fisher's exact test), Q value = 0.93

Table S644.  Gene #56: 'FRMPD2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
FRMPD2 MUTATED 2 3 1
FRMPD2 WILD-TYPE 279 168 115
'ZFP36L2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S645.  Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
ZFP36L2 MUTATED 1 1 2
ZFP36L2 WILD-TYPE 226 116 163
'ZFP36L2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S646.  Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
ZFP36L2 MUTATED 1 2 1
ZFP36L2 WILD-TYPE 154 263 88
'ZFP36L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.13

Table S647.  Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
ZFP36L2 MUTATED 2 1 0 2 2
ZFP36L2 WILD-TYPE 290 117 267 259 23

Figure S116.  Get High-res Image Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ZFP36L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.42 (Fisher's exact test), Q value = 0.84

Table S648.  Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
ZFP36L2 MUTATED 1 3 0 1 0
ZFP36L2 WILD-TYPE 192 147 122 118 80
'ZFP36L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.654 (Fisher's exact test), Q value = 0.96

Table S649.  Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
ZFP36L2 MUTATED 1 1 0 3 0 1 0
ZFP36L2 WILD-TYPE 151 213 29 196 123 66 10
'ZFP36L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.442 (Fisher's exact test), Q value = 0.84

Table S650.  Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
ZFP36L2 MUTATED 2 1 3
ZFP36L2 WILD-TYPE 213 329 246
'ZFP36L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.688 (Fisher's exact test), Q value = 0.97

Table S651.  Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
ZFP36L2 MUTATED 2 3 0 1 1 0 0
ZFP36L2 WILD-TYPE 231 156 130 204 183 45 18
'ZFP36L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.568 (Fisher's exact test), Q value = 0.92

Table S652.  Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
ZFP36L2 MUTATED 2 3 0 1 1 0
ZFP36L2 WILD-TYPE 261 148 79 260 167 52
'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.614 (Fisher's exact test), Q value = 0.94

Table S653.  Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
ZFP36L2 MUTATED 1 1 2 1 1 1
ZFP36L2 WILD-TYPE 128 242 175 183 183 40
'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.737 (Fisher's exact test), Q value = 0.99

Table S654.  Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
ZFP36L2 MUTATED 0 2 1 1 1 0 1 1 0
ZFP36L2 WILD-TYPE 64 117 155 166 68 111 144 53 73
'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.316 (Fisher's exact test), Q value = 0.78

Table S655.  Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
ZFP36L2 MUTATED 1 0 0 0 1 3
ZFP36L2 WILD-TYPE 113 63 50 120 121 96
'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.85 (Fisher's exact test), Q value = 1

Table S656.  Gene #57: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
ZFP36L2 MUTATED 2 2 1
ZFP36L2 WILD-TYPE 279 169 115
'TPP2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.358 (Fisher's exact test), Q value = 0.81

Table S657.  Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
TPP2 MUTATED 3 1 0
TPP2 WILD-TYPE 224 116 165
'TPP2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S658.  Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
TPP2 MUTATED 1 3 0
TPP2 WILD-TYPE 154 262 89
'TPP2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.908 (Fisher's exact test), Q value = 1

Table S659.  Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
TPP2 MUTATED 3 0 3 2 0
TPP2 WILD-TYPE 289 118 264 259 25
'TPP2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.635 (Fisher's exact test), Q value = 0.95

Table S660.  Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
TPP2 MUTATED 2 1 0 2 0
TPP2 WILD-TYPE 191 149 122 117 80
'TPP2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.937 (Fisher's exact test), Q value = 1

Table S661.  Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
TPP2 MUTATED 1 2 0 2 0 0 0
TPP2 WILD-TYPE 151 212 29 197 123 67 10
'TPP2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S662.  Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
TPP2 MUTATED 1 2 2
TPP2 WILD-TYPE 214 328 247
'TPP2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.598 (Fisher's exact test), Q value = 0.93

Table S663.  Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
TPP2 MUTATED 1 1 0 4 2 0 0
TPP2 WILD-TYPE 232 158 130 201 182 45 18
'TPP2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.916 (Fisher's exact test), Q value = 1

Table S664.  Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
TPP2 MUTATED 2 2 0 2 2 0
TPP2 WILD-TYPE 261 149 79 259 166 52
'TPP2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.595 (Fisher's exact test), Q value = 0.93

Table S665.  Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
TPP2 MUTATED 2 3 2 0 1 0
TPP2 WILD-TYPE 127 240 175 184 183 41
'TPP2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.889 (Fisher's exact test), Q value = 1

Table S666.  Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
TPP2 MUTATED 0 2 1 2 1 0 2 0 0
TPP2 WILD-TYPE 64 117 155 165 68 111 143 54 73
'TPP2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.487 (Fisher's exact test), Q value = 0.87

Table S667.  Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
TPP2 MUTATED 0 0 0 1 3 1
TPP2 WILD-TYPE 114 63 50 119 119 98
'TPP2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S668.  Gene #58: 'TPP2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
TPP2 MUTATED 3 1 1
TPP2 WILD-TYPE 278 170 115
'C17ORF95 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S669.  Gene #59: 'C17ORF95 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
C17ORF95 MUTATED 2 1 1
C17ORF95 WILD-TYPE 225 116 164
'C17ORF95 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S670.  Gene #59: 'C17ORF95 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
C17ORF95 MUTATED 1 2 1
C17ORF95 WILD-TYPE 154 263 88
'C17ORF95 MUTATION STATUS' versus 'CN_CNMF'

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

Table S671.  Gene #59: 'C17ORF95 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
C17ORF95 MUTATED 2 0 2 1 0
C17ORF95 WILD-TYPE 290 118 265 260 25
'C17ORF95 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.953 (Fisher's exact test), Q value = 1

Table S672.  Gene #59: 'C17ORF95 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
C17ORF95 MUTATED 1 1 0 2 1 0 0
C17ORF95 WILD-TYPE 232 158 130 203 183 45 18
'C17ORF95 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.968 (Fisher's exact test), Q value = 1

Table S673.  Gene #59: 'C17ORF95 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
C17ORF95 MUTATED 1 1 0 2 1 0
C17ORF95 WILD-TYPE 262 150 79 259 167 52
'C17ORF95 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.513 (Fisher's exact test), Q value = 0.88

Table S674.  Gene #59: 'C17ORF95 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
C17ORF95 MUTATED 1 2 2 0 0 0
C17ORF95 WILD-TYPE 128 241 175 184 184 41
'C17ORF95 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.429 (Fisher's exact test), Q value = 0.84

Table S675.  Gene #59: 'C17ORF95 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
C17ORF95 MUTATED 0 2 0 0 0 1 1 0 1
C17ORF95 WILD-TYPE 64 117 156 167 69 110 144 54 72
'RUFY1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S676.  Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
RUFY1 MUTATED 1 1 1
RUFY1 WILD-TYPE 226 116 164
'RUFY1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.298 (Fisher's exact test), Q value = 0.77

Table S677.  Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
RUFY1 MUTATED 0 3 0
RUFY1 WILD-TYPE 155 262 89
'RUFY1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.38 (Fisher's exact test), Q value = 0.83

Table S678.  Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
RUFY1 MUTATED 0 1 2 3 0
RUFY1 WILD-TYPE 292 117 265 258 25
'RUFY1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.729 (Fisher's exact test), Q value = 0.99

Table S679.  Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
RUFY1 MUTATED 1 2 0 1 0
RUFY1 WILD-TYPE 192 148 122 118 80
'RUFY1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.07 (Fisher's exact test), Q value = 0.42

Table S680.  Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
RUFY1 MUTATED 2 0 1 0 1 1 0
RUFY1 WILD-TYPE 150 214 28 199 122 66 10
'RUFY1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.736 (Fisher's exact test), Q value = 0.99

Table S681.  Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
RUFY1 MUTATED 2 2 1
RUFY1 WILD-TYPE 213 328 248
'RUFY1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.878 (Fisher's exact test), Q value = 1

Table S682.  Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
RUFY1 MUTATED 3 1 0 1 1 0 0
RUFY1 WILD-TYPE 230 158 130 204 183 45 18
'RUFY1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.239 (Fisher's exact test), Q value = 0.69

Table S683.  Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
RUFY1 MUTATED 0 3 0 2 1 0
RUFY1 WILD-TYPE 263 148 79 259 167 52
'RUFY1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.697 (Fisher's exact test), Q value = 0.97

Table S684.  Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
RUFY1 MUTATED 0 1 1 1 3 0
RUFY1 WILD-TYPE 129 242 176 183 181 41
'RUFY1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.266 (Fisher's exact test), Q value = 0.71

Table S685.  Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
RUFY1 MUTATED 1 2 0 0 0 2 1 0 0
RUFY1 WILD-TYPE 63 117 156 167 69 109 144 54 73
'RUFY1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.369 (Fisher's exact test), Q value = 0.83

Table S686.  Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
RUFY1 MUTATED 2 0 1 0 1 0
RUFY1 WILD-TYPE 112 63 49 120 121 99
'RUFY1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.431 (Fisher's exact test), Q value = 0.84

Table S687.  Gene #60: 'RUFY1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
RUFY1 MUTATED 3 0 1
RUFY1 WILD-TYPE 278 171 115
'MED23 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.388 (Fisher's exact test), Q value = 0.83

Table S688.  Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
MED23 MUTATED 3 3 1
MED23 WILD-TYPE 224 114 164
'MED23 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.251 (Fisher's exact test), Q value = 0.71

Table S689.  Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
MED23 MUTATED 1 6 0
MED23 WILD-TYPE 154 259 89
'MED23 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.274 (Fisher's exact test), Q value = 0.73

Table S690.  Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
MED23 MUTATED 4 3 6 1 0
MED23 WILD-TYPE 288 115 261 260 25
'MED23 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 0.64

Table S691.  Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
MED23 MUTATED 5 2 1 0 3
MED23 WILD-TYPE 188 148 121 119 77
'MED23 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 0.61

Table S692.  Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
MED23 MUTATED 0 1 1 5 2 1 0
MED23 WILD-TYPE 152 213 28 194 121 66 10
'MED23 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0577 (Fisher's exact test), Q value = 0.4

Table S693.  Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
MED23 MUTATED 0 4 6
MED23 WILD-TYPE 215 326 243
'MED23 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.184 (Fisher's exact test), Q value = 0.63

Table S694.  Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
MED23 MUTATED 4 0 3 4 1 2 0
MED23 WILD-TYPE 229 159 127 201 183 43 18
'MED23 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0737 (Fisher's exact test), Q value = 0.42

Table S695.  Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
MED23 MUTATED 3 1 1 9 0 0
MED23 WILD-TYPE 260 150 78 252 168 52
'MED23 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.18

Table S696.  Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
MED23 MUTATED 2 0 4 5 1 2
MED23 WILD-TYPE 127 243 173 179 183 39

Figure S117.  Get High-res Image Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MED23 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.117 (Fisher's exact test), Q value = 0.56

Table S697.  Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
MED23 MUTATED 0 0 3 5 2 1 0 2 1
MED23 WILD-TYPE 64 119 153 162 67 110 145 52 72
'MED23 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.267 (Fisher's exact test), Q value = 0.71

Table S698.  Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
MED23 MUTATED 2 1 2 1 0 1
MED23 WILD-TYPE 112 62 48 119 122 98
'MED23 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.534 (Fisher's exact test), Q value = 0.9

Table S699.  Gene #61: 'MED23 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
MED23 MUTATED 2 3 2
MED23 WILD-TYPE 279 168 114
'PAX2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.466 (Fisher's exact test), Q value = 0.87

Table S700.  Gene #62: 'PAX2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
PAX2 MUTATED 2 1 0
PAX2 WILD-TYPE 225 116 165
'PAX2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.583 (Fisher's exact test), Q value = 0.93

Table S701.  Gene #62: 'PAX2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
PAX2 MUTATED 2 1 0
PAX2 WILD-TYPE 153 264 89
'PAX2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.839 (Fisher's exact test), Q value = 1

Table S702.  Gene #62: 'PAX2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
PAX2 MUTATED 1 0 1 2 0
PAX2 WILD-TYPE 291 118 266 259 25
'PAX2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.805 (Fisher's exact test), Q value = 1

Table S703.  Gene #62: 'PAX2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
PAX2 MUTATED 0 1 0 2 0 0 0
PAX2 WILD-TYPE 152 213 29 197 123 67 10
'PAX2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.484 (Fisher's exact test), Q value = 0.87

Table S704.  Gene #62: 'PAX2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
PAX2 MUTATED 0 1 2
PAX2 WILD-TYPE 215 329 247
'PAX2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 0.83

Table S705.  Gene #62: 'PAX2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
PAX2 MUTATED 3 1 0 0 0 0 0
PAX2 WILD-TYPE 230 158 130 205 184 45 18
'PAX2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.286 (Fisher's exact test), Q value = 0.75

Table S706.  Gene #62: 'PAX2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
PAX2 MUTATED 2 2 0 0 0 0
PAX2 WILD-TYPE 261 149 79 261 168 52
'PAX2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.388 (Fisher's exact test), Q value = 0.83

Table S707.  Gene #62: 'PAX2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
PAX2 MUTATED 1 0 1 0 2 0
PAX2 WILD-TYPE 128 243 176 184 182 41
'PAX2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.337 (Fisher's exact test), Q value = 0.79

Table S708.  Gene #62: 'PAX2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
PAX2 MUTATED 1 0 0 1 1 1 0 0 0
PAX2 WILD-TYPE 63 119 156 166 68 110 145 54 73
'MED12 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.728 (Fisher's exact test), Q value = 0.99

Table S709.  Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
MED12 MUTATED 5 1 2
MED12 WILD-TYPE 222 116 163
'MED12 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.512 (Fisher's exact test), Q value = 0.88

Table S710.  Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
MED12 MUTATED 4 3 1
MED12 WILD-TYPE 151 262 88
'MED12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.545 (Fisher's exact test), Q value = 0.91

Table S711.  Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
MED12 MUTATED 6 1 9 4 0
MED12 WILD-TYPE 286 117 258 257 25
'MED12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.872 (Fisher's exact test), Q value = 1

Table S712.  Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
MED12 MUTATED 4 4 3 2 3
MED12 WILD-TYPE 189 146 119 117 77
'MED12 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.697 (Fisher's exact test), Q value = 0.97

Table S713.  Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
MED12 MUTATED 4 5 0 5 2 1 1
MED12 WILD-TYPE 148 209 29 194 121 66 9
'MED12 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.832 (Fisher's exact test), Q value = 1

Table S714.  Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
MED12 MUTATED 4 9 5
MED12 WILD-TYPE 211 321 244
'MED12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.663 (Fisher's exact test), Q value = 0.97

Table S715.  Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
MED12 MUTATED 4 5 3 7 2 0 0
MED12 WILD-TYPE 229 154 127 198 182 45 18
'MED12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.41 (Fisher's exact test), Q value = 0.84

Table S716.  Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
MED12 MUTATED 8 2 3 4 2 2
MED12 WILD-TYPE 255 149 76 257 166 50
'MED12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.707 (Fisher's exact test), Q value = 0.98

Table S717.  Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
MED12 MUTATED 2 3 4 5 6 1
MED12 WILD-TYPE 127 240 173 179 178 40
'MED12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.914 (Fisher's exact test), Q value = 1

Table S718.  Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
MED12 MUTATED 2 3 4 5 1 1 2 2 1
MED12 WILD-TYPE 62 116 152 162 68 110 143 52 72
'MED12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.537 (Fisher's exact test), Q value = 0.9

Table S719.  Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
MED12 MUTATED 2 1 1 1 1 4
MED12 WILD-TYPE 112 62 49 119 121 95
'MED12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.481 (Fisher's exact test), Q value = 0.87

Table S720.  Gene #63: 'MED12 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
MED12 MUTATED 4 5 1
MED12 WILD-TYPE 277 166 115
'CHD4 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S721.  Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
CHD4 MUTATED 3 2 4
CHD4 WILD-TYPE 224 115 161
'CHD4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 0.87

Table S722.  Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
CHD4 MUTATED 1 6 2
CHD4 WILD-TYPE 154 259 87
'CHD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.231 (Fisher's exact test), Q value = 0.68

Table S723.  Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
CHD4 MUTATED 3 2 9 4 1
CHD4 WILD-TYPE 289 116 258 257 24
'CHD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0616 (Fisher's exact test), Q value = 0.4

Table S724.  Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
CHD4 MUTATED 1 5 4 1 4
CHD4 WILD-TYPE 192 145 118 118 76
'CHD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.715 (Fisher's exact test), Q value = 0.98

Table S725.  Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
CHD4 MUTATED 4 2 0 4 4 1 0
CHD4 WILD-TYPE 148 212 29 195 119 66 10
'CHD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S726.  Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
CHD4 MUTATED 4 6 5
CHD4 WILD-TYPE 211 324 244
'CHD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.27

Table S727.  Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
CHD4 MUTATED 0 4 5 6 3 0 1
CHD4 WILD-TYPE 233 155 125 199 181 45 17

Figure S118.  Get High-res Image Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CHD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.269 (Fisher's exact test), Q value = 0.72

Table S728.  Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
CHD4 MUTATED 2 5 3 6 3 0
CHD4 WILD-TYPE 261 146 76 255 165 52
'CHD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.873 (Fisher's exact test), Q value = 1

Table S729.  Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
CHD4 MUTATED 3 3 4 5 4 0
CHD4 WILD-TYPE 126 240 173 179 180 41
'CHD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0669 (Fisher's exact test), Q value = 0.41

Table S730.  Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
CHD4 MUTATED 0 5 8 2 0 1 3 0 0
CHD4 WILD-TYPE 64 114 148 165 69 110 142 54 73
'CHD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S731.  Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
CHD4 MUTATED 1 2 1 2 2 3
CHD4 WILD-TYPE 113 61 49 118 120 96
'CHD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.308 (Fisher's exact test), Q value = 0.77

Table S732.  Gene #64: 'CHD4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
CHD4 MUTATED 3 5 3
CHD4 WILD-TYPE 278 166 113
'PFKP MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.123 (Fisher's exact test), Q value = 0.56

Table S733.  Gene #65: 'PFKP MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
PFKP MUTATED 1 0 4
PFKP WILD-TYPE 226 117 161
'PFKP MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0587 (Fisher's exact test), Q value = 0.4

Table S734.  Gene #65: 'PFKP MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
PFKP MUTATED 1 1 3
PFKP WILD-TYPE 154 264 86
'PFKP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.697 (Fisher's exact test), Q value = 0.97

Table S735.  Gene #65: 'PFKP MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
PFKP MUTATED 2 0 1 3 0
PFKP WILD-TYPE 290 118 266 258 25
'PFKP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.306 (Fisher's exact test), Q value = 0.77

Table S736.  Gene #65: 'PFKP MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
PFKP MUTATED 2 0 0 1 0 1 0
PFKP WILD-TYPE 150 214 29 198 123 66 10
'PFKP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.687 (Fisher's exact test), Q value = 0.97

Table S737.  Gene #65: 'PFKP MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
PFKP MUTATED 2 1 1
PFKP WILD-TYPE 213 329 248
'PFKP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.587 (Fisher's exact test), Q value = 0.93

Table S738.  Gene #65: 'PFKP MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
PFKP MUTATED 2 0 0 1 3 0 0
PFKP WILD-TYPE 231 159 130 204 181 45 18
'PFKP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.302 (Fisher's exact test), Q value = 0.77

Table S739.  Gene #65: 'PFKP MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
PFKP MUTATED 2 1 0 0 3 0
PFKP WILD-TYPE 261 150 79 261 165 52
'PFKP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.427 (Fisher's exact test), Q value = 0.84

Table S740.  Gene #65: 'PFKP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
PFKP MUTATED 0 4 1 0 1 0
PFKP WILD-TYPE 129 239 176 184 183 41
'PFKP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.131 (Fisher's exact test), Q value = 0.57

Table S741.  Gene #65: 'PFKP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
PFKP MUTATED 1 2 0 0 0 0 3 0 0
PFKP WILD-TYPE 63 117 156 167 69 111 142 54 73
'RHBG MUTATION STATUS' versus 'CN_CNMF'

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

Table S742.  Gene #66: 'RHBG MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
RHBG MUTATED 2 0 1 1 0
RHBG WILD-TYPE 290 118 266 260 25
'RHBG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 0.66

Table S743.  Gene #66: 'RHBG MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
RHBG MUTATED 0 2 0 0 2 0 0
RHBG WILD-TYPE 233 157 130 205 182 45 18
'RHBG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.107 (Fisher's exact test), Q value = 0.53

Table S744.  Gene #66: 'RHBG MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
RHBG MUTATED 0 2 0 0 2 0
RHBG WILD-TYPE 263 149 79 261 166 52
'RHBG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.679 (Fisher's exact test), Q value = 0.97

Table S745.  Gene #66: 'RHBG MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
RHBG MUTATED 1 2 0 0 1 0
RHBG WILD-TYPE 128 241 177 184 183 41
'RHBG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.289 (Fisher's exact test), Q value = 0.75

Table S746.  Gene #66: 'RHBG MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
RHBG MUTATED 0 2 0 0 0 0 2 0 0
RHBG WILD-TYPE 64 117 156 167 69 111 143 54 73
'PSIP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.692 (Fisher's exact test), Q value = 0.97

Table S747.  Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
PSIP1 MUTATED 2 0 2
PSIP1 WILD-TYPE 225 117 163
'PSIP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S748.  Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
PSIP1 MUTATED 1 2 1
PSIP1 WILD-TYPE 154 263 88
'PSIP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.652 (Fisher's exact test), Q value = 0.96

Table S749.  Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
PSIP1 MUTATED 3 2 2 1 0
PSIP1 WILD-TYPE 289 116 265 260 25
'PSIP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.902 (Fisher's exact test), Q value = 1

Table S750.  Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
PSIP1 MUTATED 2 1 1 0 1
PSIP1 WILD-TYPE 191 149 121 119 79
'PSIP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.592 (Fisher's exact test), Q value = 0.93

Table S751.  Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
PSIP1 MUTATED 0 2 0 1 2 1 0
PSIP1 WILD-TYPE 152 212 29 198 121 66 10
'PSIP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.585 (Fisher's exact test), Q value = 0.93

Table S752.  Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
PSIP1 MUTATED 1 4 1
PSIP1 WILD-TYPE 214 326 248
'PSIP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.556 (Fisher's exact test), Q value = 0.92

Table S753.  Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
PSIP1 MUTATED 1 1 0 3 2 1 0
PSIP1 WILD-TYPE 232 158 130 202 182 44 18
'PSIP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S754.  Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
PSIP1 MUTATED 3 2 0 2 1 0
PSIP1 WILD-TYPE 260 149 79 259 167 52
'PSIP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.411 (Fisher's exact test), Q value = 0.84

Table S755.  Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
PSIP1 MUTATED 2 0 2 1 2 0
PSIP1 WILD-TYPE 127 243 175 183 182 41
'PSIP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S756.  Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
PSIP1 MUTATED 0 1 2 2 0 1 0 0 1
PSIP1 WILD-TYPE 64 118 154 165 69 110 145 54 72
'PSIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.915 (Fisher's exact test), Q value = 1

Table S757.  Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
PSIP1 MUTATED 1 0 0 2 1 0
PSIP1 WILD-TYPE 113 63 50 118 121 99
'PSIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.429 (Fisher's exact test), Q value = 0.84

Table S758.  Gene #67: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
PSIP1 MUTATED 3 0 1
PSIP1 WILD-TYPE 278 171 115
'LRIG2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.564 (Fisher's exact test), Q value = 0.92

Table S759.  Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
LRIG2 MUTATED 3 0 1
LRIG2 WILD-TYPE 224 117 164
'LRIG2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0643 (Fisher's exact test), Q value = 0.41

Table S760.  Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
LRIG2 MUTATED 3 0 1
LRIG2 WILD-TYPE 152 265 88
'LRIG2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.624 (Fisher's exact test), Q value = 0.95

Table S761.  Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
LRIG2 MUTATED 4 0 1 2 0
LRIG2 WILD-TYPE 288 118 266 259 25
'LRIG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.59 (Fisher's exact test), Q value = 0.93

Table S762.  Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
LRIG2 MUTATED 1 1 0 2 0
LRIG2 WILD-TYPE 192 149 122 117 80
'LRIG2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.406 (Fisher's exact test), Q value = 0.84

Table S763.  Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
LRIG2 MUTATED 1 3 1 1 0 0 0
LRIG2 WILD-TYPE 151 211 28 198 123 67 10
'LRIG2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.584 (Fisher's exact test), Q value = 0.93

Table S764.  Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
LRIG2 MUTATED 1 4 1
LRIG2 WILD-TYPE 214 326 248
'LRIG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.368 (Fisher's exact test), Q value = 0.83

Table S765.  Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
LRIG2 MUTATED 4 2 0 0 1 0 0
LRIG2 WILD-TYPE 229 157 130 205 183 45 18
'LRIG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.885 (Fisher's exact test), Q value = 1

Table S766.  Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
LRIG2 MUTATED 2 1 0 2 1 1
LRIG2 WILD-TYPE 261 150 79 259 167 51
'LRIG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 0.79

Table S767.  Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
LRIG2 MUTATED 2 2 1 0 1 1
LRIG2 WILD-TYPE 127 241 176 184 183 40
'LRIG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.93 (Fisher's exact test), Q value = 1

Table S768.  Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
LRIG2 MUTATED 1 1 1 1 0 2 1 0 0
LRIG2 WILD-TYPE 63 118 155 166 69 109 144 54 73
'LRIG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S769.  Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
LRIG2 MUTATED 1 0 0 1 1 0
LRIG2 WILD-TYPE 113 63 50 119 121 99
'LRIG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S770.  Gene #68: 'LRIG2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
LRIG2 MUTATED 2 1 0
LRIG2 WILD-TYPE 279 170 116
'RIBC1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.357 (Fisher's exact test), Q value = 0.81

Table S771.  Gene #69: 'RIBC1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
RIBC1 MUTATED 3 1 0
RIBC1 WILD-TYPE 224 116 165
'RIBC1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.653 (Fisher's exact test), Q value = 0.96

Table S772.  Gene #69: 'RIBC1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
RIBC1 MUTATED 2 2 0
RIBC1 WILD-TYPE 153 263 89
'RIBC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.7 (Fisher's exact test), Q value = 0.97

Table S773.  Gene #69: 'RIBC1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
RIBC1 MUTATED 2 0 2 0 0
RIBC1 WILD-TYPE 290 118 265 261 25
'RIBC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0395 (Fisher's exact test), Q value = 0.32

Table S774.  Gene #69: 'RIBC1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
RIBC1 MUTATED 0 1 0 0 2
RIBC1 WILD-TYPE 193 149 122 119 78

Figure S119.  Get High-res Image Gene #69: 'RIBC1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'RIBC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.685 (Fisher's exact test), Q value = 0.97

Table S775.  Gene #69: 'RIBC1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
RIBC1 MUTATED 1 0 1 2 0 0 0
RIBC1 WILD-TYPE 232 159 129 203 184 45 18
'RIBC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.608 (Fisher's exact test), Q value = 0.94

Table S776.  Gene #69: 'RIBC1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
RIBC1 MUTATED 1 0 0 3 0 0
RIBC1 WILD-TYPE 262 151 79 258 168 52
'RIBC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.388 (Fisher's exact test), Q value = 0.83

Table S777.  Gene #69: 'RIBC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
RIBC1 MUTATED 1 0 1 0 2 0
RIBC1 WILD-TYPE 128 243 176 184 182 41
'RIBC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.412 (Fisher's exact test), Q value = 0.84

Table S778.  Gene #69: 'RIBC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
RIBC1 MUTATED 0 1 1 0 1 0 0 0 1
RIBC1 WILD-TYPE 64 118 155 167 68 111 145 54 72
'PLK2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.606 (Fisher's exact test), Q value = 0.94

Table S779.  Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
PLK2 MUTATED 1 0 2
PLK2 WILD-TYPE 226 117 163
'PLK2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.442 (Fisher's exact test), Q value = 0.84

Table S780.  Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
PLK2 MUTATED 0 2 1
PLK2 WILD-TYPE 155 263 88
'PLK2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S781.  Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
PLK2 MUTATED 3 1 3 2 0
PLK2 WILD-TYPE 289 117 264 259 25
'PLK2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S782.  Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
PLK2 MUTATED 2 1 1 2 1
PLK2 WILD-TYPE 191 149 121 117 79
'PLK2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.342 (Fisher's exact test), Q value = 0.8

Table S783.  Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
PLK2 MUTATED 0 2 1 1 1 1 0
PLK2 WILD-TYPE 152 212 28 198 122 66 10
'PLK2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S784.  Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
PLK2 MUTATED 1 3 2
PLK2 WILD-TYPE 214 327 247
'PLK2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.908 (Fisher's exact test), Q value = 1

Table S785.  Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
PLK2 MUTATED 1 2 1 3 2 0 0
PLK2 WILD-TYPE 232 157 129 202 182 45 18
'PLK2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S786.  Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
PLK2 MUTATED 1 2 1 3 2 0
PLK2 WILD-TYPE 262 149 78 258 166 52
'PLK2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.982 (Fisher's exact test), Q value = 1

Table S787.  Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
PLK2 MUTATED 1 3 2 2 1 0
PLK2 WILD-TYPE 128 240 175 182 183 41
'PLK2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.596 (Fisher's exact test), Q value = 0.93

Table S788.  Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
PLK2 MUTATED 0 3 2 1 0 0 2 1 0
PLK2 WILD-TYPE 64 116 154 166 69 111 143 53 73
'PLK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S789.  Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
PLK2 MUTATED 1 1 0 0 1 1
PLK2 WILD-TYPE 113 62 50 120 121 98
'PLK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.671 (Fisher's exact test), Q value = 0.97

Table S790.  Gene #70: 'PLK2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
PLK2 MUTATED 2 2 0
PLK2 WILD-TYPE 279 169 116
'ANKRD20A4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.607 (Fisher's exact test), Q value = 0.94

Table S791.  Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
ANKRD20A4 MUTATED 1 0 2
ANKRD20A4 WILD-TYPE 226 117 163
'ANKRD20A4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S792.  Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
ANKRD20A4 MUTATED 1 2 0
ANKRD20A4 WILD-TYPE 154 263 89
'ANKRD20A4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.606 (Fisher's exact test), Q value = 0.94

Table S793.  Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
ANKRD20A4 MUTATED 1 0 3 3 0
ANKRD20A4 WILD-TYPE 291 118 264 258 25
'ANKRD20A4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.408 (Fisher's exact test), Q value = 0.84

Table S794.  Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
ANKRD20A4 MUTATED 3 0 1 0 1
ANKRD20A4 WILD-TYPE 190 150 121 119 79
'ANKRD20A4 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S795.  Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
ANKRD20A4 MUTATED 1 2 0 1 1 1 0
ANKRD20A4 WILD-TYPE 151 212 29 198 122 66 10
'ANKRD20A4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S796.  Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
ANKRD20A4 MUTATED 2 2 2
ANKRD20A4 WILD-TYPE 213 328 247
'ANKRD20A4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0725 (Fisher's exact test), Q value = 0.42

Table S797.  Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
ANKRD20A4 MUTATED 0 3 2 1 0 1 0
ANKRD20A4 WILD-TYPE 233 156 128 204 184 44 18
'ANKRD20A4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.332 (Fisher's exact test), Q value = 0.79

Table S798.  Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
ANKRD20A4 MUTATED 2 0 1 3 0 1
ANKRD20A4 WILD-TYPE 261 151 78 258 168 51
'ANKRD20A4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.847 (Fisher's exact test), Q value = 1

Table S799.  Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
ANKRD20A4 MUTATED 2 1 1 2 1 0
ANKRD20A4 WILD-TYPE 127 242 176 182 183 41
'ANKRD20A4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.813 (Fisher's exact test), Q value = 1

Table S800.  Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
ANKRD20A4 MUTATED 0 1 2 2 0 1 0 1 0
ANKRD20A4 WILD-TYPE 64 118 154 165 69 110 145 53 73
'ANKRD20A4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.688 (Fisher's exact test), Q value = 0.97

Table S801.  Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
ANKRD20A4 MUTATED 0 1 1 1 1 1
ANKRD20A4 WILD-TYPE 114 62 49 119 121 98
'ANKRD20A4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0236 (Fisher's exact test), Q value = 0.23

Table S802.  Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
ANKRD20A4 MUTATED 0 4 1
ANKRD20A4 WILD-TYPE 281 167 115

Figure S120.  Get High-res Image Gene #71: 'ANKRD20A4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PHACTR1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.121 (Fisher's exact test), Q value = 0.56

Table S803.  Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
PHACTR1 MUTATED 1 0 4
PHACTR1 WILD-TYPE 226 117 161
'PHACTR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S804.  Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
PHACTR1 MUTATED 1 3 1
PHACTR1 WILD-TYPE 154 262 88
'PHACTR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.869 (Fisher's exact test), Q value = 1

Table S805.  Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
PHACTR1 MUTATED 1 1 2 2 0
PHACTR1 WILD-TYPE 291 117 265 259 25
'PHACTR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.237 (Fisher's exact test), Q value = 0.69

Table S806.  Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
PHACTR1 MUTATED 0 2 0 1 1
PHACTR1 WILD-TYPE 193 148 122 118 79
'PHACTR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.191 (Fisher's exact test), Q value = 0.63

Table S807.  Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
PHACTR1 MUTATED 4 1 0 0 1 1 0
PHACTR1 WILD-TYPE 148 213 29 199 122 66 10
'PHACTR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0851 (Fisher's exact test), Q value = 0.45

Table S808.  Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
PHACTR1 MUTATED 4 3 0
PHACTR1 WILD-TYPE 211 327 249
'PHACTR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.132 (Fisher's exact test), Q value = 0.57

Table S809.  Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
PHACTR1 MUTATED 0 4 0 1 2 0 0
PHACTR1 WILD-TYPE 233 155 130 204 182 45 18
'PHACTR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0784 (Fisher's exact test), Q value = 0.44

Table S810.  Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
PHACTR1 MUTATED 0 3 0 1 2 1
PHACTR1 WILD-TYPE 263 148 79 260 166 51
'PHACTR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.757 (Fisher's exact test), Q value = 1

Table S811.  Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
PHACTR1 MUTATED 1 3 0 1 2 0
PHACTR1 WILD-TYPE 128 240 177 183 182 41
'PHACTR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0417 (Fisher's exact test), Q value = 0.32

Table S812.  Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
PHACTR1 MUTATED 0 2 0 0 2 0 1 0 2
PHACTR1 WILD-TYPE 64 117 156 167 67 111 144 54 71

Figure S121.  Get High-res Image Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PHACTR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.897 (Fisher's exact test), Q value = 1

Table S813.  Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
PHACTR1 MUTATED 1 0 0 0 1 1
PHACTR1 WILD-TYPE 113 63 50 120 121 98
'PHACTR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S814.  Gene #72: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
PHACTR1 MUTATED 2 1 0
PHACTR1 WILD-TYPE 279 170 116
'DLG1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.795 (Fisher's exact test), Q value = 1

Table S815.  Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
DLG1 MUTATED 3 1 3
DLG1 WILD-TYPE 224 116 162
'DLG1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.249 (Fisher's exact test), Q value = 0.7

Table S816.  Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
DLG1 MUTATED 1 6 0
DLG1 WILD-TYPE 154 259 89
'DLG1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.872 (Fisher's exact test), Q value = 1

Table S817.  Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
DLG1 MUTATED 3 1 4 5 0
DLG1 WILD-TYPE 289 117 263 256 25
'DLG1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 0.57

Table S818.  Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
DLG1 MUTATED 1 1 4 3 0
DLG1 WILD-TYPE 192 149 118 116 80
'DLG1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.634 (Fisher's exact test), Q value = 0.95

Table S819.  Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
DLG1 MUTATED 2 3 0 2 4 2 0
DLG1 WILD-TYPE 150 211 29 197 119 65 10
'DLG1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.827 (Fisher's exact test), Q value = 1

Table S820.  Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
DLG1 MUTATED 4 6 3
DLG1 WILD-TYPE 211 324 246
'DLG1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 0.71

Table S821.  Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
DLG1 MUTATED 2 4 2 1 2 1 1
DLG1 WILD-TYPE 231 155 128 204 182 44 17
'DLG1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.189 (Fisher's exact test), Q value = 0.63

Table S822.  Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
DLG1 MUTATED 1 3 1 5 1 2
DLG1 WILD-TYPE 262 148 78 256 167 50
'DLG1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.919 (Fisher's exact test), Q value = 1

Table S823.  Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
DLG1 MUTATED 2 4 2 3 1 0
DLG1 WILD-TYPE 127 239 175 181 183 41
'DLG1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.13

Table S824.  Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
DLG1 MUTATED 0 4 0 3 0 0 1 0 4
DLG1 WILD-TYPE 64 115 156 164 69 111 144 54 69

Figure S122.  Get High-res Image Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'DLG1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.436 (Fisher's exact test), Q value = 0.84

Table S825.  Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
DLG1 MUTATED 0 2 1 1 2 2
DLG1 WILD-TYPE 114 61 49 119 120 97
'DLG1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S826.  Gene #73: 'DLG1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
DLG1 MUTATED 4 2 2
DLG1 WILD-TYPE 277 169 114
'GPRASP2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.433 (Fisher's exact test), Q value = 0.84

Table S827.  Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
GPRASP2 MUTATED 3 0 3
GPRASP2 WILD-TYPE 224 117 162
'GPRASP2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.33 (Fisher's exact test), Q value = 0.79

Table S828.  Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
GPRASP2 MUTATED 1 5 0
GPRASP2 WILD-TYPE 154 260 89
'GPRASP2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.66 (Fisher's exact test), Q value = 0.97

Table S829.  Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
GPRASP2 MUTATED 4 1 1 4 0
GPRASP2 WILD-TYPE 288 117 266 257 25
'GPRASP2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.655 (Fisher's exact test), Q value = 0.96

Table S830.  Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
GPRASP2 MUTATED 2 1 2 0 0
GPRASP2 WILD-TYPE 191 149 120 119 80
'GPRASP2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 0.84

Table S831.  Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
GPRASP2 MUTATED 3 5 0 1 0 0 0
GPRASP2 WILD-TYPE 149 209 29 198 123 67 10
'GPRASP2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.44 (Fisher's exact test), Q value = 0.84

Table S832.  Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
GPRASP2 MUTATED 3 5 1
GPRASP2 WILD-TYPE 212 325 248
'GPRASP2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.146 (Fisher's exact test), Q value = 0.59

Table S833.  Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
GPRASP2 MUTATED 1 3 0 4 1 0 1
GPRASP2 WILD-TYPE 232 156 130 201 183 45 17
'GPRASP2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.253 (Fisher's exact test), Q value = 0.71

Table S834.  Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
GPRASP2 MUTATED 1 4 0 3 1 1
GPRASP2 WILD-TYPE 262 147 79 258 167 51
'GPRASP2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00291 (Fisher's exact test), Q value = 0.042

Table S835.  Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
GPRASP2 MUTATED 2 4 0 1 0 3
GPRASP2 WILD-TYPE 127 239 177 183 184 38

Figure S123.  Get High-res Image Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'GPRASP2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.231 (Fisher's exact test), Q value = 0.68

Table S836.  Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
GPRASP2 MUTATED 0 1 3 0 2 3 1 0 0
GPRASP2 WILD-TYPE 64 118 153 167 67 108 144 54 73
'GPRASP2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.379 (Fisher's exact test), Q value = 0.83

Table S837.  Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
GPRASP2 MUTATED 2 1 0 0 0 1
GPRASP2 WILD-TYPE 112 62 50 120 122 98
'GPRASP2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.672 (Fisher's exact test), Q value = 0.97

Table S838.  Gene #74: 'GPRASP2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
GPRASP2 MUTATED 2 2 0
GPRASP2 WILD-TYPE 279 169 116
'CCDC82 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.217 (Fisher's exact test), Q value = 0.65

Table S839.  Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
CCDC82 MUTATED 1 0 3
CCDC82 WILD-TYPE 226 117 162
'CCDC82 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.302 (Fisher's exact test), Q value = 0.77

Table S840.  Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
CCDC82 MUTATED 0 4 0
CCDC82 WILD-TYPE 155 261 89
'CCDC82 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.91 (Fisher's exact test), Q value = 1

Table S841.  Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
CCDC82 MUTATED 2 1 1 2 0
CCDC82 WILD-TYPE 290 117 266 259 25
'CCDC82 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.14

Table S842.  Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
CCDC82 MUTATED 4 0 0 0 0 2 0
CCDC82 WILD-TYPE 148 214 29 199 123 65 10

Figure S124.  Get High-res Image Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'CCDC82 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.586 (Fisher's exact test), Q value = 0.93

Table S843.  Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
CCDC82 MUTATED 1 4 1
CCDC82 WILD-TYPE 214 326 248
'CCDC82 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.412 (Fisher's exact test), Q value = 0.84

Table S844.  Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
CCDC82 MUTATED 4 1 0 0 1 0 0
CCDC82 WILD-TYPE 229 158 130 205 183 45 18
'CCDC82 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00255 (Fisher's exact test), Q value = 0.038

Table S845.  Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
CCDC82 MUTATED 0 5 0 0 1 0
CCDC82 WILD-TYPE 263 146 79 261 167 52

Figure S125.  Get High-res Image Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CCDC82 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.387 (Fisher's exact test), Q value = 0.83

Table S846.  Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
CCDC82 MUTATED 2 2 0 0 2 0
CCDC82 WILD-TYPE 127 241 177 184 182 41
'CCDC82 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0592 (Fisher's exact test), Q value = 0.4

Table S847.  Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
CCDC82 MUTATED 2 1 0 0 1 0 1 1 0
CCDC82 WILD-TYPE 62 118 156 167 68 111 144 53 73
'CCDC82 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.896 (Fisher's exact test), Q value = 1

Table S848.  Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
CCDC82 MUTATED 1 0 0 0 1 1
CCDC82 WILD-TYPE 113 63 50 120 121 98
'CCDC82 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S849.  Gene #75: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
CCDC82 MUTATED 2 1 0
CCDC82 WILD-TYPE 279 170 116
'CCDC27 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 0.65

Table S850.  Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
CCDC27 MUTATED 1 0 3
CCDC27 WILD-TYPE 226 117 162
'CCDC27 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.402 (Fisher's exact test), Q value = 0.84

Table S851.  Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
CCDC27 MUTATED 0 3 1
CCDC27 WILD-TYPE 155 262 88
'CCDC27 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.129 (Fisher's exact test), Q value = 0.57

Table S852.  Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
CCDC27 MUTATED 2 0 0 5 0
CCDC27 WILD-TYPE 290 118 267 256 25
'CCDC27 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0284 (Fisher's exact test), Q value = 0.26

Table S853.  Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
CCDC27 MUTATED 0 0 2 3 0
CCDC27 WILD-TYPE 193 150 120 116 80

Figure S126.  Get High-res Image Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CCDC27 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0813 (Fisher's exact test), Q value = 0.44

Table S854.  Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
CCDC27 MUTATED 2 0 0 0 1 2 0
CCDC27 WILD-TYPE 150 214 29 199 122 65 10
'CCDC27 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.143 (Fisher's exact test), Q value = 0.58

Table S855.  Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
CCDC27 MUTATED 3 2 0
CCDC27 WILD-TYPE 212 328 249
'CCDC27 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0382 (Fisher's exact test), Q value = 0.32

Table S856.  Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
CCDC27 MUTATED 0 3 0 0 4 0 0
CCDC27 WILD-TYPE 233 156 130 205 180 45 18

Figure S127.  Get High-res Image Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CCDC27 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.263 (Fisher's exact test), Q value = 0.71

Table S857.  Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
CCDC27 MUTATED 1 1 0 1 4 0
CCDC27 WILD-TYPE 262 150 79 260 164 52
'CCDC27 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 0.65

Table S858.  Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
CCDC27 MUTATED 2 4 0 1 0 0
CCDC27 WILD-TYPE 127 239 177 183 184 41
'CCDC27 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0553 (Fisher's exact test), Q value = 0.39

Table S859.  Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
CCDC27 MUTATED 0 0 0 1 0 0 4 0 2
CCDC27 WILD-TYPE 64 119 156 166 69 111 141 54 71
'CCDC27 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.232 (Fisher's exact test), Q value = 0.68

Table S860.  Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
CCDC27 MUTATED 0 1 0 0 2 0
CCDC27 WILD-TYPE 114 62 50 120 120 99
'CCDC27 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.312 (Fisher's exact test), Q value = 0.77

Table S861.  Gene #76: 'CCDC27 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
CCDC27 MUTATED 3 0 0
CCDC27 WILD-TYPE 278 171 116
'RHOA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0459 (Fisher's exact test), Q value = 0.35

Table S862.  Gene #77: 'RHOA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
RHOA MUTATED 0 0 3
RHOA WILD-TYPE 227 117 162

Figure S128.  Get High-res Image Gene #77: 'RHOA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'RHOA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.439 (Fisher's exact test), Q value = 0.84

Table S863.  Gene #77: 'RHOA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
RHOA MUTATED 0 2 1
RHOA WILD-TYPE 155 263 88
'RHOA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.526 (Fisher's exact test), Q value = 0.89

Table S864.  Gene #77: 'RHOA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
RHOA MUTATED 1 2 2 1 0
RHOA WILD-TYPE 291 116 265 260 25
'RHOA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.236 (Fisher's exact test), Q value = 0.69

Table S865.  Gene #77: 'RHOA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
RHOA MUTATED 0 2 0 1 1
RHOA WILD-TYPE 193 148 122 118 79
'RHOA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.481 (Fisher's exact test), Q value = 0.87

Table S866.  Gene #77: 'RHOA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
RHOA MUTATED 2 1 1 1 1 0 0
RHOA WILD-TYPE 150 213 28 198 122 67 10
'RHOA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.508 (Fisher's exact test), Q value = 0.88

Table S867.  Gene #77: 'RHOA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
RHOA MUTATED 3 2 1
RHOA WILD-TYPE 212 328 248
'RHOA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.889 (Fisher's exact test), Q value = 1

Table S868.  Gene #77: 'RHOA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
RHOA MUTATED 2 2 0 1 1 0 0
RHOA WILD-TYPE 231 157 130 204 183 45 18
'RHOA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 0.71

Table S869.  Gene #77: 'RHOA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
RHOA MUTATED 0 2 0 2 1 1
RHOA WILD-TYPE 263 149 79 259 167 51
'RHOA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.727 (Fisher's exact test), Q value = 0.99

Table S870.  Gene #77: 'RHOA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
RHOA MUTATED 0 2 0 2 2 0
RHOA WILD-TYPE 129 241 177 182 182 41
'RHOA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.374 (Fisher's exact test), Q value = 0.83

Table S871.  Gene #77: 'RHOA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
RHOA MUTATED 1 2 1 0 0 0 1 1 0
RHOA WILD-TYPE 63 117 155 167 69 111 144 53 73
'MAMLD1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.371 (Fisher's exact test), Q value = 0.83

Table S872.  Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
MAMLD1 MUTATED 1 2 3
MAMLD1 WILD-TYPE 226 115 162
'MAMLD1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.189 (Fisher's exact test), Q value = 0.63

Table S873.  Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
MAMLD1 MUTATED 0 4 2
MAMLD1 WILD-TYPE 155 261 87
'MAMLD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.601 (Fisher's exact test), Q value = 0.93

Table S874.  Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
MAMLD1 MUTATED 1 1 3 4 0
MAMLD1 WILD-TYPE 291 117 264 257 25
'MAMLD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 0.87

Table S875.  Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
MAMLD1 MUTATED 1 0 1 2 1
MAMLD1 WILD-TYPE 192 150 121 117 79
'MAMLD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.158 (Fisher's exact test), Q value = 0.59

Table S876.  Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
MAMLD1 MUTATED 3 3 0 0 0 2 0
MAMLD1 WILD-TYPE 149 211 29 199 123 65 10
'MAMLD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.5 (Fisher's exact test), Q value = 0.87

Table S877.  Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
MAMLD1 MUTATED 3 4 1
MAMLD1 WILD-TYPE 212 326 248
'MAMLD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.621 (Fisher's exact test), Q value = 0.95

Table S878.  Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
MAMLD1 MUTATED 3 0 1 2 4 0 0
MAMLD1 WILD-TYPE 230 159 129 203 180 45 18
'MAMLD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.653 (Fisher's exact test), Q value = 0.96

Table S879.  Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
MAMLD1 MUTATED 2 1 0 3 4 0
MAMLD1 WILD-TYPE 261 150 79 258 164 52
'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.757 (Fisher's exact test), Q value = 1

Table S880.  Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
MAMLD1 MUTATED 1 5 1 2 1 0
MAMLD1 WILD-TYPE 128 238 176 182 183 41
'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.727 (Fisher's exact test), Q value = 0.99

Table S881.  Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
MAMLD1 MUTATED 0 1 1 3 0 1 4 0 0
MAMLD1 WILD-TYPE 64 118 155 164 69 110 141 54 73
'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.671 (Fisher's exact test), Q value = 0.97

Table S882.  Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 114 63 50 120 122 99
MAMLD1 MUTATED 0 0 1 1 1 1
MAMLD1 WILD-TYPE 114 63 49 119 121 98
'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S883.  Gene #78: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 281 171 116
MAMLD1 MUTATED 2 1 1
MAMLD1 WILD-TYPE 279 170 115
'OR8D1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.692 (Fisher's exact test), Q value = 0.97

Table S884.  Gene #79: 'OR8D1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 227 117 165
OR8D1 MUTATED 2 0 2
OR8D1 WILD-TYPE 225 117 163
'OR8D1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0446 (Fisher's exact test), Q value = 0.34

Table S885.  Gene #79: 'OR8D1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 155 265 89
OR8D1 MUTATED 2 0 2
OR8D1 WILD-TYPE 153 265 87

Figure S129.  Get High-res Image Gene #79: 'OR8D1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'OR8D1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.769 (Fisher's exact test), Q value = 1

Table S886.  Gene #79: 'OR8D1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 292 118 267 261 25
OR8D1 MUTATED 1 1 1 1 0
OR8D1 WILD-TYPE 291 117 266 260 25
'OR8D1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.522 (Fisher's exact test), Q value = 0.89

Table S887.  Gene #79: 'OR8D1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 193 150 122 119 80
OR8D1 MUTATED 2 0 1 2 0
OR8D1 WILD-TYPE 191 150 121 117 80
'OR8D1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.188 (Fisher's exact test), Q value = 0.63

Table S888.  Gene #79: 'OR8D1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 152 214 29 199 123 67 10
OR8D1 MUTATED 1 2 0 0 0 2 0
OR8D1 WILD-TYPE 151 212 29 199 123 65 10
'OR8D1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 0.59

Table S889.  Gene #79: 'OR8D1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 215 330 249
OR8D1 MUTATED 3 2 0
OR8D1 WILD-TYPE 212 328 249
'OR8D1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.243 (Fisher's exact test), Q value = 0.69

Table S890.  Gene #79: 'OR8D1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 233 159 130 205 184 45 18
OR8D1 MUTATED 0 0 0 2 3 0 0
OR8D1 WILD-TYPE 233 159 130 203 181 45 18
'OR8D1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.18 (Fisher's exact test), Q value = 0.63

Table S891.  Gene #79: 'OR8D1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 263 151 79 261 168 52
OR8D1 MUTATED 2 0 0 0 3 0
OR8D1 WILD-TYPE 261 151 79 261 165 52
'OR8D1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.475 (Fisher's exact test), Q value = 0.87

Table S892.  Gene #79: 'OR8D1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 129 243 177 184 184 41
OR8D1 MUTATED 1 1 2 0 0 0
OR8D1 WILD-TYPE 128 242 175 184 184 41
'OR8D1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S893.  Gene #79: 'OR8D1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 64 119 156 167 69 111 145 54 73
OR8D1 MUTATED 0 1 1 1 0 0 1 0 0
OR8D1 WILD-TYPE 64 118 155 166 69 111 144 54 73
Methods & Data
Input

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BRCA-TP/22824019/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BRCA-TP/22595637/BRCA-TP.transferedmergedcluster.txt

  • Number of patients = 977

  • Number of significantly mutated genes = 79

  • Number of Molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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