Correlation between gene mutation status and molecular subtypes
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
04 October 2018  |  None
Maintainer Information
Maintained by Broad Institute GDAC (Broad Institute of MIT & Harvard)
Overview
Introduction

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

Summary

Testing the association between mutation status of 388 genes and 3 molecular subtypes across 100 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.

  • No gene mutations related to molecuar subtypes.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 388 genes and 3 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, no significant finding detected.

Clinical
Features 		MRNA
CHIERARCHICAL 		METHYLATION
CNMF 		METHYLATION
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test
PTEN 73 (73%) 27 0.0218
(0.4) 		0.0673
(0.455) 		0.00582
(0.317)
ARID1A 40 (40%) 60 0.837
(0.94) 		0.00396
(0.317) 		0.0004
(0.255)
KRAS 32 (32%) 68 0.376
(0.681) 		0.727
(0.885) 		0.432
(0.716)
PIK3R1 29 (29%) 71 0.188
(0.559) 		0.181
(0.559) 		0.14
(0.524)
RPL22 19 (19%) 81 0.78
(0.917) 		0.0131
(0.395) 		0.00089
(0.255)
LMAN1 17 (17%) 83 0.573
(0.782) 		0.0812
(0.47) 		0.0159
(0.395)
CTCF 23 (23%) 77 0.694
(0.863) 		0.594
(0.801) 		0.109
(0.482)
TP53 24 (24%) 76 0.216
(0.575) 		0.0409
(0.416) 		0.0412
(0.416)
SRPR 16 (16%) 84 0.626
(0.83) 		0.0487
(0.426) 		0.0173
(0.4)
INPPL1 22 (22%) 78 0.769
(0.907) 		0.182
(0.559) 		0.112
(0.482)
RNF43 14 (14%) 86 0.879
(0.956) 		0.0529
(0.428) 		0.0437
(0.416)
JAK1 15 (15%) 85 0.819
(0.932) 		0.00169
(0.255) 		0.006
(0.317)
PHF2 16 (16%) 84 0.821
(0.932) 		0.394
(0.687) 		0.0952
(0.473)
FBXW7 19 (19%) 81 0.775
(0.912) 		1
(1.00) 		0.486
(0.745)
ACVR2A 11 (11%) 89 0.564
(0.782) 		0.0157
(0.395) 		0.0273
(0.416)
ADNP 9 (9%) 91 0.647
(0.843) 		0.947
(0.995) 		0.416
(0.694)
ZFP36L2 10 (10%) 90 0.265
(0.632) 		0.117
(0.485) 		0.254
(0.629)
SEC31A 19 (19%) 81 0.94
(0.991) 		0.014
(0.395) 		0.00097
(0.255)
CMTM1 7 (7%) 93 0.708
(0.874) 		0.549
(0.774) 		0.317
(0.649)
TEAD2 8 (8%) 92 0.748
(0.894) 		0.843
(0.944) 		0.0521
(0.428)
NCOR2 15 (15%) 85 0.701
(0.867) 		0.00136
(0.255) 		0.133
(0.512)
WDTC1 9 (9%) 91 0.276
(0.632) 		0.0464
(0.416) 		0.191
(0.561)
NDUFC2 6 (6%) 94 0.807
(0.93) 		0.12
(0.489) 		0.606
(0.81)
ZBTB20 11 (11%) 89 0.925
(0.984) 		0.185
(0.559) 		0.131
(0.509)
ARID5B 12 (12%) 88 0.568
(0.782) 		0.0266
(0.416) 		0.169
(0.559)
CEL 11 (11%) 89 0.621
(0.826) 		0.291
(0.637) 		0.292
(0.637)
RNF145 8 (8%) 92 0.745
(0.892) 		0.531
(0.766) 		0.487
(0.745)
BAX 7 (7%) 93 0.845
(0.944) 		0.0766
(0.466) 		0.211
(0.575)
ARSJ 6 (6%) 94 0.594
(0.801) 		0.105
(0.477) 		0.193
(0.561)
FAHD2A 5 (5%) 95 0.378
(0.681) 		0.398
(0.688) 		0.389
(0.685)
KIAA1919 8 (8%) 92 0.268
(0.632) 		0.0403
(0.416) 		0.041
(0.416)
PHTF1 9 (9%) 91 0.484
(0.745) 		0.0667
(0.455) 		0.0378
(0.416)
ZFHX3 21 (21%) 79 0.32
(0.649) 		0.0192
(0.4) 		0.00358
(0.317)
ESRP1 10 (10%) 90 0.122
(0.494) 		0.117
(0.485) 		0.0329
(0.416)
PROM1 9 (9%) 91 0.569
(0.782) 		0.0139
(0.395) 		0.0522
(0.428)
SFRS15 15 (15%) 85 0.936
(0.991) 		0.0464
(0.416) 		0.0447
(0.416)
USP35 9 (9%) 91 0.442
(0.725) 		0.256
(0.629) 		0.193
(0.561)
PRRG1 6 (6%) 94 0.849
(0.944) 		0.163
(0.559) 		0.276
(0.632)
CTNNB1 28 (28%) 72 0.727
(0.885) 		0.0237
(0.4) 		0.00132
(0.255)
HNRNPL 6 (6%) 94 0.808
(0.93) 		0.57
(0.782) 		0.371
(0.681)
MLL4 23 (23%) 77 0.709
(0.876) 		0.0187
(0.4) 		0.0658
(0.455)
SNRK 6 (6%) 94 0.483
(0.745) 		0.0923
(0.47) 		0.197
(0.565)
OR6C75 5 (5%) 95 0.722
(0.884) 		0.0537
(0.428) 		0.382
(0.681)
CCDC73 12 (12%) 88 0.784
(0.917) 		0.0201
(0.4) 		0.0422
(0.416)
SLAMF1 5 (5%) 95 0.893
(0.965) 		0.335
(0.668) 		0.249
(0.627)
SLC3A2 6 (6%) 94 0.849
(0.944) 		1
(1.00) 		0.14
(0.524)
CHD3 15 (15%) 85 0.0279
(0.416) 		0.0705
(0.464) 		0.0745
(0.466)
XPOT 9 (9%) 91 0.226
(0.589) 		0.13
(0.509) 		0.0914
(0.47)
NRIP1 8 (8%) 92 0.3
(0.648) 		0.311
(0.649) 		0.182
(0.559)
MAZ 4 (4%) 96 0.484
(0.745) 		0.183
(0.559) 		0.726
(0.885)
LCE4A 8 (8%) 92 0.717
(0.884) 		0.44
(0.724) 		0.879
(0.956)
NFE2L2 6 (6%) 94 0.77
(0.908) 		0.0909
(0.47) 		0.216
(0.575)
VEGFB 6 (6%) 94 0.166
(0.559) 		0.0909
(0.47) 		0.494
(0.746)
SENP1 6 (6%) 94 0.482
(0.745) 		0.736
(0.889) 		0.791
(0.921)
USP9X 16 (16%) 84 0.647
(0.843) 		0.324
(0.654) 		0.066
(0.455)
ADAM28 6 (6%) 94 0.644
(0.843) 		0.0911
(0.47) 		0.277
(0.632)
SVIL 14 (14%) 86 0.396
(0.688) 		0.0776
(0.466) 		0.0739
(0.466)
KDM5A 11 (11%) 89 0.836
(0.94) 		0.0231
(0.4) 		0.0722
(0.466)
PIK3CA 43 (43%) 57 0.452
(0.729) 		0.219
(0.578) 		0.847
(0.944)
TBC1D23 7 (7%) 93 0.978
(1.00) 		0.132
(0.509) 		0.316
(0.649)
C13ORF33 6 (6%) 94 0.13
(0.509) 		0.044
(0.416) 		0.148
(0.535)
KIAA0182 6 (6%) 94 0.538
(0.771) 		0.103
(0.477) 		0.198
(0.566)
CKAP2 5 (5%) 95 0.405
(0.688) 		0.16
(0.557) 		0.354
(0.676)
WBP1 6 (6%) 94 0.102
(0.477) 		0.113
(0.482) 		0.111
(0.482)
SAFB2 9 (9%) 91 0.275
(0.632) 		0.528
(0.763) 		0.486
(0.745)
XYLT2 5 (5%) 95 0.605
(0.81) 		0.00434
(0.317) 		0.181
(0.559)
LRPPRC 11 (11%) 89 0.668
(0.849) 		0.206
(0.575) 		0.193
(0.561)
SLC12A7 5 (5%) 95 0.892
(0.965) 		0.162
(0.559) 		0.181
(0.559)
ZFR 4 (4%) 96 0.326
(0.656) 		0.354
(0.676) 		0.31
(0.649)
SYNJ2 8 (8%) 92 0.886
(0.962) 		0.0756
(0.466) 		0.0795
(0.466)
RALGAPB 6 (6%) 94 0.667
(0.848) 		0.186
(0.559) 		0.299
(0.647)
TCEB3 7 (7%) 93 0.571
(0.782) 		0.288
(0.635) 		0.219
(0.578)
QSOX1 5 (5%) 95 0.292
(0.637) 		0.736
(0.889) 		0.474
(0.745)
MFRP 5 (5%) 95 0.593
(0.801) 		0.364
(0.681) 		0.536
(0.771)
CCDC28A 4 (4%) 96 0.401
(0.688) 		0.182
(0.559) 		0.576
(0.784)
FGFR2 13 (13%) 87 0.494
(0.746) 		0.157
(0.556) 		0.32
(0.649)
ZMIZ1 7 (7%) 93 0.241
(0.617) 		0.631
(0.836) 		0.277
(0.632)
ARHGAP35 12 (12%) 88 0.455
(0.729) 		0.382
(0.681) 		0.477
(0.745)
TFE3 4 (4%) 96 0.202
(0.573) 		0.122
(0.494) 		0.573
(0.782)
SIPA1L1 13 (13%) 87 0.892
(0.965) 		0.112
(0.482) 		0.0765
(0.466)
EIF2B3 6 (6%) 94 0.848
(0.944) 		0.569
(0.782) 		0.211
(0.575)
NBEAL1 9 (9%) 91 0.426
(0.708) 		0.35
(0.676) 		0.116
(0.485)
HPS1 6 (6%) 94 0.515
(0.758) 		0.166
(0.559) 		0.275
(0.632)
DOCK3 19 (19%) 81 0.676
(0.854) 		0.289
(0.635) 		0.145
(0.534)
SLC16A4 4 (4%) 96 0.0648
(0.455) 		0.232
(0.598) 		0.402
(0.688)
DYNC1LI1 4 (4%) 96 0.939
(0.991) 		0.0676
(0.455) 		0.105
(0.477)
CHD9 11 (11%) 89 0.407
(0.688) 		0.199
(0.566) 		0.0613
(0.454)
RPE65 7 (7%) 93 0.64
(0.842) 		0.0409
(0.416) 		0.113
(0.482)
C1QTNF5 4 (4%) 96 0.328
(0.659) 		0.124
(0.496) 		0.576
(0.784)
LANCL1 5 (5%) 95 0.832
(0.94) 		0.737
(0.889) 		1
(1.00)
TMEM60 5 (5%) 95 0.435
(0.721) 		0.918
(0.984) 		0.0679
(0.455)
SLC30A8 5 (5%) 95 0.924
(0.984) 		0.0121
(0.395) 		0.00996
(0.395)
U2AF1 5 (5%) 95 0.492
(0.746) 		0.188
(0.559) 		0.456
(0.729)
AP1S1 6 (6%) 94 0.393
(0.687) 		0.0437
(0.416) 		0.149
(0.536)
TP53BP2 8 (8%) 92 0.769
(0.907) 		0.0465
(0.416) 		0.145
(0.534)
ZMYM2 12 (12%) 88 0.167
(0.559) 		0.489
(0.746) 		0.155
(0.551)
BRD3 6 (6%) 94 0.81
(0.931) 		0.0903
(0.47) 		0.277
(0.632)
C6ORF89 5 (5%) 95 0.957
(1.00) 		0.246
(0.627) 		0.0987
(0.477)
STAMBPL1 6 (6%) 94 0.506
(0.754) 		0.935
(0.991) 		0.794
(0.921)
NES 12 (12%) 88 0.99
(1.00) 		0.124
(0.496) 		0.0564
(0.432)
MBD6 8 (8%) 92 0.436
(0.721) 		0.0646
(0.455) 		0.212
(0.575)
SHC1 9 (9%) 91 0.798
(0.922) 		0.351
(0.676) 		0.222
(0.582)
PEX1 6 (6%) 94 0.204
(0.575) 		0.538
(0.771) 		0.797
(0.922)
MCPH1 6 (6%) 94 0.972
(1.00) 		0.166
(0.559) 		0.247
(0.627)
TTLL11 8 (8%) 92 0.383
(0.681) 		0.554
(0.775) 		0.689
(0.863)
ZNF800 11 (11%) 89 0.837
(0.94) 		0.00367
(0.317) 		0.0212
(0.4)
HNF1A 7 (7%) 93 0.487
(0.745) 		0.112
(0.482) 		0.0973
(0.476)
PAPD4 6 (6%) 94 0.48
(0.745) 		0.821
(0.932) 		0.605
(0.81)
NSD1 16 (16%) 84 0.764
(0.903) 		0.0357
(0.416) 		0.0422
(0.416)
RANBP10 6 (6%) 94 0.101
(0.477) 		0.45
(0.729) 		0.415
(0.692)
WNT1 4 (4%) 96 0.663
(0.847) 		0.185
(0.559) 		0.157
(0.556)
IPO11 7 (7%) 93 0.474
(0.745) 		0.0421
(0.416) 		0.0317
(0.416)
FBXL3 4 (4%) 96 0.721
(0.884) 		1
(1.00) 		0.963
(1.00)
LNPEP 6 (6%) 94 0.0856
(0.47) 		0.541
(0.773) 		0.454
(0.729)
LINGO4 4 (4%) 96 0.754
(0.897) 		1
(1.00) 		0.897
(0.968)
CPNE7 6 (6%) 94 1
(1.00) 		0.174
(0.559) 		0.443
(0.725)
DPCR1 10 (10%) 90 1
(1.00) 		0.00934
(0.395) 		0.0521
(0.428)
SMTN 9 (9%) 91 0.455
(0.729) 		0.231
(0.598) 		0.115
(0.482)
ATP2A1 6 (6%) 94 0.302
(0.648) 		0.239
(0.617) 		0.251
(0.629)
PIGO 7 (7%) 93 0.811
(0.931) 		0.406
(0.688) 		0.248
(0.627)
RRAS2 5 (5%) 95 1
(1.00) 		0.403
(0.688) 		0.679
(0.854)
DRD5 8 (8%) 92 0.816
(0.932) 		0.672
(0.852) 		0.411
(0.692)
PRR25 5 (5%) 95 0.258
(0.63) 		0.135
(0.514) 		0.229
(0.596)
PAX2 4 (4%) 96 0.0913
(0.47) 		0.00597
(0.317) 		0.127
(0.503)
KIF24 4 (4%) 96 0.0926
(0.47) 		0.719
(0.884) 		0.962
(1.00)
NOS3 7 (7%) 93 0.486
(0.745) 		0.0411
(0.416) 		0.174
(0.559)
ANAPC1 6 (6%) 94 0.055
(0.429) 		0.112
(0.482) 		0.275
(0.632)
DNHD1 16 (16%) 84 0.301
(0.648) 		0.0181
(0.4) 		0.452
(0.729)
IL27 4 (4%) 96 0.0019
(0.255) 		0.809
(0.93) 		0.172
(0.559)
RYR2 19 (19%) 81 0.256
(0.629) 		0.00044
(0.255) 		0.00816
(0.395)
CHPF2 8 (8%) 92 0.0558
(0.432) 		0.366
(0.681) 		0.0641
(0.455)
TNK2 9 (9%) 91 0.614
(0.818) 		0.0271
(0.416) 		0.366
(0.681)
PPP2R1A 10 (10%) 90 0.834
(0.94) 		1
(1.00) 		0.679
(0.854)
KBTBD10 6 (6%) 94 0.454
(0.729) 		0.539
(0.771) 		0.248
(0.627)
ERMP1 5 (5%) 95 0.832
(0.94) 		0.267
(0.632) 		0.354
(0.676)
DAB2IP 10 (10%) 90 0.24
(0.617) 		0.35
(0.676) 		0.0731
(0.466)
BCOR 11 (11%) 89 0.836
(0.94) 		0.0119
(0.395) 		0.0422
(0.416)
C22ORF28 5 (5%) 95 0.492
(0.746) 		0.52
(0.758) 		0.756
(0.897)
LHX1 8 (8%) 92 0.741
(0.89) 		0.365
(0.681) 		0.262
(0.632)
USP26 9 (9%) 91 0.452
(0.729) 		0.739
(0.889) 		0.347
(0.676)
RBM27 11 (11%) 89 0.0851
(0.47) 		0.556
(0.776) 		0.292
(0.637)
CCDC43 7 (7%) 93 0.639
(0.842) 		0.55
(0.774) 		0.278
(0.632)
LIN54 4 (4%) 96 0.504
(0.754) 		0.319
(0.649) 		0.482
(0.745)
FAM8A1 6 (6%) 94 0.315
(0.649) 		0.569
(0.782) 		0.405
(0.688)
ZDHHC8 6 (6%) 94 0.255
(0.629) 		0.542
(0.773) 		0.413
(0.692)
PHKG2 4 (4%) 96 0.0937
(0.47) 		0.0652
(0.455) 		0.105
(0.477)
POLE 9 (9%) 91 0.904
(0.974) 		0.0821
(0.47) 		0.515
(0.758)
TCERG1 9 (9%) 91 0.568
(0.782) 		0.00523
(0.317) 		0.0256
(0.416)
TTLL10 4 (4%) 96 0.0933
(0.47) 		0.354
(0.676) 		0.4
(0.688)
EBPL 4 (4%) 96 0.123
(0.494) 		0.184
(0.559) 		0.483
(0.745)
NOSTRIN 4 (4%) 96 0.755
(0.897) 		0.381
(0.681) 		0.285
(0.635)
DAZAP1 7 (7%) 93 0.397
(0.688) 		0.168
(0.559) 		0.274
(0.632)
C6ORF10 3 (3%) 97 0.551
(0.774) 		0.864
(0.944) 		0.367
(0.681)
C19ORF2 8 (8%) 92 0.649
(0.843) 		0.0843
(0.47) 		0.213
(0.575)
HOXA11 5 (5%) 95 0.958
(1.00) 		0.352
(0.676) 		0.309
(0.649)
ZRSR2 6 (6%) 94 0.452
(0.729) 		0.176
(0.559) 		0.276
(0.632)
NR4A2 6 (6%) 94 0.0151
(0.395) 		0.819
(0.932) 		0.368
(0.681)
COIL 6 (6%) 94 0.406
(0.688) 		0.447
(0.729) 		0.372
(0.681)
CDS1 5 (5%) 95 0.957
(1.00) 		0.266
(0.632) 		0.297
(0.645)
MTMR9 4 (4%) 96 0.278
(0.632) 		0.257
(0.63) 		0.79
(0.921)
LRP2BP 5 (5%) 95 0.0215
(0.4) 		0.176
(0.559) 		0.362
(0.681)
REPIN1 7 (7%) 93 0.844
(0.944) 		0.0228
(0.4) 		0.389
(0.685)
DHX57 9 (9%) 91 0.333
(0.665) 		0.663
(0.847) 		0.849
(0.944)
FHOD3 9 (9%) 91 0.132
(0.51) 		0.0434
(0.416) 		0.0534
(0.428)
SLC25A24 5 (5%) 95 0.0381
(0.416) 		0.187
(0.559) 		0.298
(0.645)
PPRC1 4 (4%) 96 0.442
(0.725) 		0.653
(0.843) 		0.188
(0.559)
ZMYM3 10 (10%) 90 0.256
(0.629) 		0.104
(0.477) 		0.0349
(0.416)
C1ORF114 7 (7%) 93 0.64
(0.842) 		0.352
(0.676) 		0.193
(0.561)
TEX10 9 (9%) 91 0.982
(1.00) 		0.0182
(0.4) 		0.019
(0.4)
WAC 6 (6%) 94 0.351
(0.676) 		0.111
(0.482) 		0.0966
(0.476)
CADPS 10 (10%) 90 0.567
(0.782) 		0.309
(0.649) 		0.288
(0.635)
FAM60A 6 (6%) 94 0.304
(0.649) 		0.934
(0.991) 		0.856
(0.944)
PSG1 5 (5%) 95 0.958
(1.00) 		0.793
(0.921) 		0.145
(0.534)
MLH3 6 (6%) 94 0.101
(0.477) 		0.0359
(0.416) 		0.11
(0.482)
NFASC 10 (10%) 90 0.302
(0.648) 		0.0416
(0.416) 		0.0387
(0.416)
ENTPD2 4 (4%) 96 0.552
(0.775) 		0.652
(0.843) 		0.0876
(0.47)
SFRS2B 3 (3%) 97 0.549
(0.774) 		0.603
(0.809) 		0.55
(0.774)
XKR6 5 (5%) 95 0.182
(0.559) 		0.104
(0.477) 		0.377
(0.681)
KIAA1267 10 (10%) 90 0.19
(0.561) 		0.0278
(0.416) 		0.145
(0.534)
SGOL2 7 (7%) 93 0.217
(0.575) 		0.037
(0.416) 		0.217
(0.575)
MSH6 8 (8%) 92 0.719
(0.884) 		0.412
(0.692) 		0.185
(0.559)
TP53BP1 10 (10%) 90 0.179
(0.559) 		0.00539
(0.317) 		0.0717
(0.466)
IFIH1 7 (7%) 93 0.667
(0.848) 		0.102
(0.477) 		0.146
(0.534)
MRI1 3 (3%) 97 0.37
(0.681) 		0.333
(0.665) 		0.49
(0.746)
PAPPA2 12 (12%) 88 0.657
(0.845) 		0.0147
(0.395) 		0.0142
(0.395)
KRTAP10-1 3 (3%) 97 1
(1.00) 		0.382
(0.681) 		0.491
(0.746)
PIK3R2 8 (8%) 92 0.104
(0.477) 		0.945
(0.994) 		0.849
(0.944)
SDAD1 4 (4%) 96 0.00755
(0.382) 		0.353
(0.676) 		0.403
(0.688)
GOLGA5 3 (3%) 97 0.37
(0.681) 		0.505
(0.754) 		0.518
(0.758)
MAGI1 5 (5%) 95 0.0843
(0.47) 		0.737
(0.889) 		0.793
(0.921)
PRUNE2 12 (12%) 88 0.405
(0.688) 		0.677
(0.854) 		0.386
(0.685)
MXRA8 5 (5%) 95 1
(1.00) 		1
(1.00) 		0.904
(0.974)
WDR47 7 (7%) 93 0.567
(0.782) 		0.0937
(0.47) 		0.217
(0.575)
ANK3 13 (13%) 87 0.314
(0.649) 		0.00573
(0.317) 		0.0246
(0.409)
MED25 5 (5%) 95 0.591
(0.8) 		0.265
(0.632) 		0.382
(0.681)
LRCH2 8 (8%) 92 0.312
(0.649) 		0.55
(0.774) 		0.868
(0.947)
SALL4 7 (7%) 93 0.755
(0.897) 		0.166
(0.559) 		0.12
(0.489)
RTKN2 5 (5%) 95 0.0781
(0.466) 		0.189
(0.559) 		0.309
(0.649)
TTC39B 3 (3%) 97 0.287
(0.635) 		0.38
(0.681) 		0.497
(0.749)
CDH24 4 (4%) 96 0.86
(0.944) 		0.32
(0.649) 		0.573
(0.782)
PRR12 8 (8%) 92 0.551
(0.774) 		0.151
(0.542) 		0.115
(0.482)
MSL3 9 (9%) 91 0.719
(0.884) 		0.178
(0.559) 		0.279
(0.632)
PAX6 6 (6%) 94 0.206
(0.575) 		0.82
(0.932) 		0.262
(0.632)
FLJ10357 10 (10%) 90 0.763
(0.903) 		0.0135
(0.395) 		0.0382
(0.416)
USMG5 3 (3%) 97 0.684
(0.859) 		0.00543
(0.317) 		0.52
(0.758)
TFDP1 6 (6%) 94 0.27
(0.632) 		0.535
(0.77) 		0.473
(0.745)
WIF1 5 (5%) 95 0.338
(0.672) 		0.918
(0.984) 		0.405
(0.688)
ATXN2L 9 (9%) 91 0.557
(0.777) 		0.0497
(0.428) 		0.0695
(0.46)
FLT3LG 4 (4%) 96 0.723
(0.884) 		0.649
(0.843) 		0.791
(0.921)
POLG 10 (10%) 90 0.461
(0.736) 		0.0174
(0.4) 		0.068
(0.455)
EIF2AK3 9 (9%) 91 0.983
(1.00) 		0.0666
(0.455) 		0.0915
(0.47)
GLTSCR1 12 (12%) 88 0.39
(0.685) 		0.0376
(0.416) 		0.553
(0.775)
CYTSB 9 (9%) 91 0.725
(0.885) 		0.0134
(0.395) 		0.0472
(0.417)
NAP1L5 4 (4%) 96 0.859
(0.944) 		0.395
(0.687) 		0.835
(0.94)
DDX10 8 (8%) 92 0.632
(0.836) 		0.352
(0.676) 		0.855
(0.944)
LIMK2 8 (8%) 92 0.844
(0.944) 		0.549
(0.774) 		0.641
(0.842)
POLD1 6 (6%) 94 0.871
(0.949) 		1
(1.00) 		0.55
(0.774)
SBNO1 9 (9%) 91 0.0915
(0.47) 		0.0384
(0.416) 		0.0921
(0.47)
CACHD1 6 (6%) 94 0.209
(0.575) 		0.11
(0.482) 		0.442
(0.725)
FAM200A 4 (4%) 96 0.203
(0.575) 		0.393
(0.687) 		0.213
(0.575)
KIAA1370 8 (8%) 92 0.521
(0.758) 		0.0314
(0.416) 		0.136
(0.514)
C7ORF63 6 (6%) 94 0.749
(0.895) 		0.16
(0.557) 		0.182
(0.559)
BAT3 7 (7%) 93 0.06
(0.454) 		0.0982
(0.477) 		0.0837
(0.47)
WNK4 11 (11%) 89 0.387
(0.685) 		0.147
(0.535) 		0.0796
(0.466)
VPRBP 6 (6%) 94 0.00322
(0.317) 		0.45
(0.729) 		0.795
(0.921)
DOCK5 7 (7%) 93 0.377
(0.681) 		0.819
(0.932) 		0.606
(0.81)
PPM1D 7 (7%) 93 0.438
(0.722) 		0.0898
(0.47) 		0.276
(0.632)
MAPRE3 3 (3%) 97 0.784
(0.917) 		0.505
(0.754) 		0.52
(0.758)
SHPRH 10 (10%) 90 0.815
(0.932) 		0.0293
(0.416) 		0.0167
(0.4)
KSR1 8 (8%) 92 0.208
(0.575) 		0.909
(0.977) 		0.641
(0.842)
ZNF195 7 (7%) 93 0.282
(0.635) 		0.0368
(0.416) 		0.32
(0.649)
CANX 5 (5%) 95 0.957
(1.00) 		0.264
(0.632) 		0.479
(0.745)
WHSC1 10 (10%) 90 0.339
(0.673) 		0.0849
(0.47) 		0.289
(0.635)
TAOK3 6 (6%) 94 0.405
(0.688) 		0.0532
(0.428) 		0.25
(0.628)
GIPC1 3 (3%) 97 0.856
(0.944) 		0.862
(0.944) 		0.368
(0.681)
LOR 4 (4%) 96 0.14
(0.524) 		0.319
(0.649) 		0.479
(0.745)
SMAP1 6 (6%) 94 0.696
(0.863) 		0.0913
(0.47) 		0.276
(0.632)
HERC6 5 (5%) 95 0.834
(0.94) 		0.174
(0.559) 		0.353
(0.676)
KIAA0913 4 (4%) 96 0.382
(0.681) 		0.0159
(0.395) 		0.211
(0.575)
FKBP11 3 (3%) 97 0.288
(0.635) 		0.863
(0.944) 		0.369
(0.681)
C5ORF36 8 (8%) 92 0.623
(0.827) 		0.0415
(0.416) 		0.113
(0.482)
FAT2 16 (16%) 84 0.517
(0.758) 		0.0497
(0.428) 		0.0666
(0.455)
XRRA1 3 (3%) 97 0.0778
(0.466) 		0.503
(0.754) 		0.519
(0.758)
ZNF583 4 (4%) 96 0.82
(0.932) 		0.35
(0.676) 		0.312
(0.649)
FOXM1 7 (7%) 93 0.602
(0.809) 		0.0225
(0.4) 		0.147
(0.535)
INF2 5 (5%) 95 0.0769
(0.466) 		0.261
(0.632) 		0.375
(0.681)
SLC16A1 4 (4%) 96 1
(1.00) 		0.319
(0.649) 		0.482
(0.745)
SMAD7 5 (5%) 95 0.923
(0.984) 		0.738
(0.889) 		0.869
(0.947)
CELSR1 11 (11%) 89 0.654
(0.843) 		0.0406
(0.416) 		0.0887
(0.47)
C14ORF43 4 (4%) 96 1
(1.00) 		0.519
(0.758) 		0.962
(1.00)
SEC63 6 (6%) 94 0.0431
(0.416) 		0.568
(0.782) 		0.314
(0.649)
USP47 6 (6%) 94 0.944
(0.994) 		0.0897
(0.47) 		0.275
(0.632)
ZNF253 6 (6%) 94 0.189
(0.559) 		0.54
(0.772) 		0.413
(0.692)
C1ORF141 6 (6%) 94 0.256
(0.629) 		0.176
(0.559) 		0.274
(0.632)
COL5A1 12 (12%) 88 0.517
(0.758) 		0.0232
(0.4) 		0.0973
(0.476)
RAB3IL1 5 (5%) 95 0.589
(0.799) 		0.918
(0.984) 		0.179
(0.559)
C15ORF42 7 (7%) 93 0.508
(0.754) 		0.316
(0.649) 		0.744
(0.891)
SPTY2D1 5 (5%) 95 0.114
(0.482) 		0.173
(0.559) 		0.383
(0.681)
C19ORF66 3 (3%) 97 0.589
(0.799) 		0.382
(0.681) 		0.494
(0.746)
MYO1A 10 (10%) 90 0.792
(0.921) 		0.0315
(0.416) 		0.103
(0.477)
DMXL2 11 (11%) 89 0.352
(0.676) 		0.0156
(0.395) 		0.0284
(0.416)
ZIC5 7 (7%) 93 0.319
(0.649) 		0.287
(0.635) 		0.317
(0.649)
DSC1 8 (8%) 92 0.652
(0.843) 		0.171
(0.559) 		0.214
(0.575)
CCKBR 4 (4%) 96 0.551
(0.774) 		0.355
(0.676) 		0.309
(0.649)
QKI 4 (4%) 96 0.858
(0.944) 		0.351
(0.676) 		0.4
(0.688)
DLGAP3 6 (6%) 94 0.616
(0.821) 		0.167
(0.559) 		0.279
(0.632)
ZNF626 9 (9%) 91 0.762
(0.903) 		0.791
(0.921) 		0.805
(0.929)
MGA 14 (14%) 86 0.558
(0.778) 		0.0771
(0.466) 		0.0514
(0.428)
C3ORF23 5 (5%) 95 0.438
(0.722) 		0.522
(0.758) 		0.752
(0.897)
ALPPL2 5 (5%) 95 0.722
(0.884) 		0.733
(0.889) 		0.534
(0.769)
EFHC1 9 (9%) 91 0.597
(0.804) 		0.0734
(0.466) 		0.0383
(0.416)
HNRNPA3 4 (4%) 96 0.665
(0.847) 		0.508
(0.754) 		0.696
(0.863)
UBB 4 (4%) 96 0.755
(0.897) 		0.0213
(0.4) 		0.48
(0.745)
SNX25 4 (4%) 96 0.86
(0.944) 		0.122
(0.494) 		0.573
(0.782)
GDF7 4 (4%) 96 1
(1.00) 		0.722
(0.884) 		0.623
(0.827)
MFI2 5 (5%) 95 0.105
(0.477) 		0.189
(0.559) 		0.297
(0.645)
AKT1 4 (4%) 96 1
(1.00) 		0.38
(0.681) 		0.494
(0.746)
DENND4C 7 (7%) 93 0.937
(0.991) 		0.0586
(0.446) 		0.176
(0.559)
ACSM4 4 (4%) 96 0.94
(0.991) 		1
(1.00) 		0.52
(0.758)
TNRC18 9 (9%) 91 0.523
(0.759) 		0.375
(0.681) 		0.105
(0.477)
CACNA1F 14 (14%) 86 0.922
(0.984) 		0.00376
(0.317) 		0.0346
(0.416)
RASA1 8 (8%) 92 0.136
(0.514) 		0.0463
(0.416) 		0.213
(0.575)
IRX5 7 (7%) 93 0.0651
(0.455) 		0.197
(0.565) 		0.688
(0.863)
TBX10 3 (3%) 97 0.855
(0.944) 		1
(1.00) 		0.653
(0.843)
PRIC285 14 (14%) 86 0.691
(0.863) 		0.0517
(0.428) 		0.0407
(0.416)
MAX 4 (4%) 96 0.484
(0.745) 		1
(1.00) 		0.834
(0.94)
IQSEC2 11 (11%) 89 0.925
(0.984) 		0.164
(0.559) 		0.154
(0.551)
KIAA1804 7 (7%) 93 0.229
(0.596) 		0.406
(0.688) 		0.114
(0.482)
IPO9 5 (5%) 95 0.924
(0.984) 		0.367
(0.681) 		0.588
(0.799)
TPP2 8 (8%) 92 0.305
(0.649) 		0.0748
(0.466) 		0.0796
(0.466)
CDC73 7 (7%) 93 0.485
(0.745) 		0.256
(0.629) 		0.251
(0.629)
HRASLS5 5 (5%) 95 0.959
(1.00) 		0.162
(0.559) 		0.183
(0.559)
ARID4B 6 (6%) 94 0.56
(0.779) 		0.74
(0.89) 		0.452
(0.729)
SLC2A5 5 (5%) 95 0.833
(0.94) 		0.114
(0.482) 		0.473
(0.745)
TUBB4 6 (6%) 94 0.768
(0.907) 		0.0907
(0.47) 		0.412
(0.692)
ARID3B 6 (6%) 94 0.0788
(0.466) 		0.345
(0.676) 		0.369
(0.681)
AADACL3 4 (4%) 96 0.246
(0.627) 		0.352
(0.676) 		0.309
(0.649)
TXNDC11 6 (6%) 94 0.454
(0.729) 		0.0523
(0.428) 		0.252
(0.629)
TULP4 7 (7%) 93 0.197
(0.565) 		0.132
(0.509) 		0.114
(0.482)
CALB1 5 (5%) 95 0.642
(0.842) 		0.738
(0.889) 		0.638
(0.842)
OXER1 3 (3%) 97 0.734
(0.889) 		0.282
(0.635) 		0.697
(0.863)
BCLAF1 9 (9%) 91 0.782
(0.917) 		0.363
(0.681) 		0.524
(0.759)
IDH3A 4 (4%) 96 0.82
(0.932) 		0.319
(0.649) 		0.48
(0.745)
SYNM 3 (3%) 97 1
(1.00) 		0.504
(0.754) 		0.521
(0.758)
C20ORF194 4 (4%) 96 0.663
(0.847) 		1
(1.00) 		0.674
(0.852)
FRG1 7 (7%) 93 0.979
(1.00) 		0.109
(0.482) 		0.209
(0.575)
DOCK9 8 (8%) 92 0.321
(0.649) 		0.411
(0.692) 		0.261
(0.632)
LMOD2 6 (6%) 94 0.642
(0.842) 		0.365
(0.681) 		0.904
(0.974)
IGF2R 10 (10%) 90 0.601
(0.809) 		0.131
(0.509) 		0.14
(0.524)
POTEE 5 (5%) 95 0.169
(0.559) 		0.517
(0.758) 		0.963
(1.00)
N4BP2 11 (11%) 89 0.138
(0.521) 		0.406
(0.688) 		0.262
(0.632)
RUFY2 5 (5%) 95 0.892
(0.965) 		0.0469
(0.417) 		0.352
(0.676)
UBQLN2 6 (6%) 94 0.348
(0.676) 		0.104
(0.477) 		0.193
(0.561)
PIGB 6 (6%) 94 0.694
(0.863) 		0.177
(0.559) 		0.247
(0.627)
TSPAN10 3 (3%) 97 0.783
(0.917) 		1
(1.00) 		0.821
(0.932)
SFRS8 6 (6%) 94 0.392
(0.687) 		0.45
(0.729) 		0.855
(0.944)
TSTD2 6 (6%) 94 0.303
(0.649) 		0.0898
(0.47) 		0.194
(0.561)
WDR5 4 (4%) 96 0.131
(0.509) 		0.507
(0.754) 		0.52
(0.758)
LPIN1 5 (5%) 95 0.0856
(0.47) 		0.182
(0.559) 		0.158
(0.556)
OR2A4 3 (3%) 97 1
(1.00) 		0.286
(0.635) 		0.696
(0.863)
RAPGEF4 9 (9%) 91 0.256
(0.629) 		0.0302
(0.416) 		0.214
(0.575)
KCNA4 9 (9%) 91 0.647
(0.843) 		0.361
(0.681) 		0.326
(0.656)
LYSMD1 3 (3%) 97 1
(1.00) 		0.384
(0.681) 		0.693
(0.863)
MYH4 7 (7%) 93 0.118
(0.486) 		0.548
(0.774) 		0.318
(0.649)
SEMA6C 6 (6%) 94 1
(1.00) 		0.178
(0.559) 		0.248
(0.627)
LIMCH1 8 (8%) 92 0.93
(0.987) 		0.55
(0.774) 		0.691
(0.863)
CTSA 4 (4%) 96 0.0641
(0.455) 		0.0543
(0.429) 		0.0371
(0.416)
MAP3K4 13 (13%) 87 0.92
(0.984) 		0.0438
(0.416) 		0.0377
(0.416)
SGK1 4 (4%) 96 0.664
(0.847) 		0.32
(0.649) 		0.389
(0.685)
NFE2L1 3 (3%) 97 0.0788
(0.466) 		0.861
(0.944) 		0.186
(0.559)
WASF3 7 (7%) 93 0.119
(0.489) 		0.0899
(0.47) 		0.0375
(0.416)
ARNTL 5 (5%) 95 1
(1.00) 		0.0462
(0.416) 		0.533
(0.769)
EDC4 4 (4%) 96 0.279
(0.632) 		0.517
(0.758) 		0.146
(0.534)
TBC1D22A 5 (5%) 95 0.0796
(0.466) 		0.736
(0.889) 		0.453
(0.729)
ALPK1 8 (8%) 92 0.0232
(0.4) 		0.0106
(0.395) 		0.124
(0.496)
SYTL2 5 (5%) 95 0.275
(0.632) 		0.266
(0.632) 		0.355
(0.676)
OAT 3 (3%) 97 0.0439
(0.416) 		0.0548
(0.429) 		0.0612
(0.454)
HSP90B1 7 (7%) 93 0.743
(0.891) 		0.0607
(0.454) 		0.159
(0.557)
PTCH1 9 (9%) 91 0.925
(0.984) 		0.0227
(0.4) 		0.069
(0.459)
SULT1E1 3 (3%) 97 0.21
(0.575) 		0.285
(0.635) 		0.649
(0.843)
UPF3A 5 (5%) 95 0.209
(0.575) 		0.103
(0.477) 		0.127
(0.503)
DNAH8 12 (12%) 88 0.221
(0.582) 		0.00197
(0.255) 		0.046
(0.416)
SYCP2 12 (12%) 88 0.754
(0.897) 		0.0101
(0.395) 		0.0156
(0.395)
ATG5 3 (3%) 97 0.287
(0.635) 		0.603
(0.809) 		0.654
(0.843)
RTN2 6 (6%) 94 0.56
(0.779) 		0.0563
(0.432) 		0.373
(0.681)
AP2A2 3 (3%) 97 0.0143
(0.395) 		0.0235
(0.4) 		0.211
(0.575)
ECT2 3 (3%) 97 1
(1.00) 		0.383
(0.681) 		0.654
(0.843)
ZNF174 3 (3%) 97 0.786
(0.918) 		0.861
(0.944) 		0.581
(0.789)
JAM3 6 (6%) 94 0.67
(0.851) 		0.167
(0.559) 		0.275
(0.632)
EEA1 9 (9%) 91 0.663
(0.847) 		0.474
(0.745) 		0.422
(0.703)
RTN3 9 (9%) 91 0.216
(0.575) 		0.0132
(0.395) 		0.134
(0.512)
ZBTB7B 4 (4%) 96 0.16
(0.557) 		0.38
(0.681) 		0.493
(0.746)
ZC3H18 7 (7%) 93 0.57
(0.782) 		0.805
(0.929) 		0.213
(0.575)
FAHD2B 3 (3%) 97 1
(1.00)
SETD7 3 (3%) 97 0.548
(0.774) 		0.504
(0.754) 		0.695
(0.863)
ZNF510 4 (4%) 96 0.224
(0.585) 		0.318
(0.649) 		0.482
(0.745)
KIAA0408 8 (8%) 92 0.663
(0.847) 		0.407
(0.688) 		0.374
(0.681)
PRR5L 3 (3%) 97 0.286
(0.635) 		1
(1.00) 		1
(1.00)
DST 14 (14%) 86 0.948
(0.996) 		0.045
(0.416) 		0.0503
(0.428)
NPY 3 (3%) 97 0.372
(0.681) 		0.863
(0.944) 		0.922
(0.984)
VASP 4 (4%) 96 0.939
(0.991) 		1
(1.00) 		0.656
(0.843)
COL5A3 5 (5%) 95 0.0658
(0.455) 		0.173
(0.559) 		0.458
(0.732)
KCNQ3 10 (10%) 90 0.909
(0.977) 		0.0723
(0.466) 		0.376
(0.681)
PLXNA1 11 (11%) 89 0.281
(0.635) 		0.0629
(0.455) 		0.0949
(0.473)
ZNF395 3 (3%) 97 0.855
(0.944) 		0.332
(0.665) 		0.209
(0.575)
PLA2G4C 6 (6%) 94 0.0965
(0.476) 		0.0911
(0.47) 		0.414
(0.692)
RBM6 10 (10%) 90 0.696
(0.863) 		0.231
(0.598) 		0.169
(0.559)
COL18A1 11 (11%) 89 0.222
(0.582) 		0.673
(0.852) 		0.368
(0.681)
ERBB3 7 (7%) 93 0.187
(0.559) 		0.198
(0.566) 		0.467
(0.743)
PRDM2 13 (13%) 87 0.154
(0.551) 		0.502
(0.754) 		0.204
(0.575)
C7ORF50 3 (3%) 97 1
(1.00) 		0.282
(0.635) 		0.651
(0.843)
ARFGAP2 3 (3%) 97 1
(1.00) 		1
(1.00) 		0.651
(0.843)
FAM81B 6 (6%) 94 0.85
(0.944) 		0.0909
(0.47) 		0.411
(0.692)
LIN37 3 (3%) 97 0.784
(0.917) 		0.333
(0.665) 		0.212
(0.575)
SPRYD5 7 (7%) 93 0.109
(0.482) 		0.35
(0.676) 		0.319
(0.649)
INHBA 3 (3%) 97 0.286
(0.635) 		0.508
(0.754) 		0.366
(0.681)
SOX8 5 (5%) 95 1
(1.00) 		0.266
(0.632) 		0.356
(0.677)
WDR60 9 (9%) 91 0.424
(0.706) 		0.00956
(0.395) 		0.0199
(0.4)
TCP10L 4 (4%) 96 0.484
(0.745) 		0.185
(0.559) 		0.479
(0.745)
MGAT4C 5 (5%) 95 0.892
(0.965) 		0.189
(0.559) 		0.181
(0.559)
ATP6V1C1 4 (4%) 96 0.724
(0.885) 		0.516
(0.758) 		0.674
(0.852)
MNT 6 (6%) 94 0.196
(0.565) 		0.346
(0.676) 		0.467
(0.743)
PLXNB1 8 (8%) 92 0.947
(0.995) 		0.0157
(0.395) 		0.101
(0.477)
STIM2 6 (6%) 94 0.482
(0.745) 		0.266
(0.632) 		0.456
(0.729)
CYB5R4 4 (4%) 96 0.819
(0.932) 		1
(1.00) 		0.392
(0.687)
SIAH2 3 (3%) 97 0.161
(0.559) 		0.865
(0.945) 		0.26
(0.632)
NUP210L 11 (11%) 89 0.858
(0.944) 		0.0415
(0.416) 		0.039
(0.416)
ZNF609 5 (5%) 95 0.684
(0.859) 		0.112
(0.482) 		0.148
(0.535)
'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.4

Table S1.  Gene #1: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PTEN MUTATED 19 19 10 11 14
PTEN WILD-TYPE 9 1 1 9 7

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

'PTEN MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0673 (Fisher's exact test), Q value = 0.45

Table S2.  Gene #1: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PTEN MUTATED 30 24 8 9
PTEN WILD-TYPE 5 9 8 3
'PTEN MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00582 (Fisher's exact test), Q value = 0.32

Table S3.  Gene #1: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PTEN MUTATED 28 3 8 5 4 14 9
PTEN WILD-TYPE 6 8 1 2 2 6 0

Figure S2.  Get High-res Image Gene #1: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.837 (Fisher's exact test), Q value = 0.94

Table S4.  Gene #2: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ARID1A MUTATED 13 8 5 6 8
ARID1A WILD-TYPE 15 12 6 14 13
'ARID1A MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.00396 (Fisher's exact test), Q value = 0.32

Table S5.  Gene #2: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ARID1A MUTATED 21 6 6 6
ARID1A WILD-TYPE 14 27 10 6

Figure S3.  Get High-res Image Gene #2: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'ARID1A MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.25

Table S6.  Gene #2: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ARID1A MUTATED 24 1 2 3 3 4 2
ARID1A WILD-TYPE 10 10 7 4 3 16 7

Figure S4.  Get High-res Image Gene #2: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.376 (Fisher's exact test), Q value = 0.68

Table S7.  Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
KRAS MUTATED 7 10 4 6 5
KRAS WILD-TYPE 21 10 7 14 16
'KRAS MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.727 (Fisher's exact test), Q value = 0.88

Table S8.  Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
KRAS MUTATED 10 12 4 5
KRAS WILD-TYPE 25 21 12 7
'KRAS MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.432 (Fisher's exact test), Q value = 0.72

Table S9.  Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
KRAS MUTATED 12 2 1 2 3 6 5
KRAS WILD-TYPE 22 9 8 5 3 14 4
'PIK3R1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.188 (Fisher's exact test), Q value = 0.56

Table S10.  Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PIK3R1 MUTATED 6 4 2 10 7
PIK3R1 WILD-TYPE 22 16 9 10 14
'PIK3R1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.181 (Fisher's exact test), Q value = 0.56

Table S11.  Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PIK3R1 MUTATED 14 6 4 5
PIK3R1 WILD-TYPE 21 27 12 7
'PIK3R1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.14 (Fisher's exact test), Q value = 0.52

Table S12.  Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PIK3R1 MUTATED 12 2 5 2 3 2 3
PIK3R1 WILD-TYPE 22 9 4 5 3 18 6
'RPL22 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.78 (Fisher's exact test), Q value = 0.92

Table S13.  Gene #5: 'RPL22 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
RPL22 MUTATED 6 2 3 4 4
RPL22 WILD-TYPE 22 18 8 16 17
'RPL22 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.39

Table S14.  Gene #5: 'RPL22 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
RPL22 MUTATED 9 1 4 4
RPL22 WILD-TYPE 26 32 12 8

Figure S5.  Get High-res Image Gene #5: 'RPL22 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'RPL22 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.25

Table S15.  Gene #5: 'RPL22 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
RPL22 MUTATED 11 0 0 3 3 0 1
RPL22 WILD-TYPE 23 11 9 4 3 20 8

Figure S6.  Get High-res Image Gene #5: 'RPL22 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'LMAN1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.573 (Fisher's exact test), Q value = 0.78

Table S16.  Gene #6: 'LMAN1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
LMAN1 MUTATED 5 4 0 3 5
LMAN1 WILD-TYPE 23 16 11 17 16
'LMAN1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0812 (Fisher's exact test), Q value = 0.47

Table S17.  Gene #6: 'LMAN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
LMAN1 MUTATED 7 2 4 4
LMAN1 WILD-TYPE 28 31 12 8
'LMAN1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.39

Table S18.  Gene #6: 'LMAN1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
LMAN1 MUTATED 10 0 0 2 3 1 1
LMAN1 WILD-TYPE 24 11 9 5 3 19 8

Figure S7.  Get High-res Image Gene #6: 'LMAN1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'CTCF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.694 (Fisher's exact test), Q value = 0.86

Table S19.  Gene #7: 'CTCF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CTCF MUTATED 7 5 4 4 3
CTCF WILD-TYPE 21 15 7 16 18
'CTCF MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.594 (Fisher's exact test), Q value = 0.8

Table S20.  Gene #7: 'CTCF MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CTCF MUTATED 10 5 4 3
CTCF WILD-TYPE 25 28 12 9
'CTCF MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.109 (Fisher's exact test), Q value = 0.48

Table S21.  Gene #7: 'CTCF MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CTCF MUTATED 12 1 0 3 2 3 1
CTCF WILD-TYPE 22 10 9 4 4 17 8
'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.216 (Fisher's exact test), Q value = 0.58

Table S22.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TP53 MUTATED 10 2 1 6 5
TP53 WILD-TYPE 18 18 10 14 16
'TP53 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.42

Table S23.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TP53 MUTATED 6 6 8 1
TP53 WILD-TYPE 29 27 8 11

Figure S8.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'TP53 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0412 (Fisher's exact test), Q value = 0.42

Table S24.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TP53 MUTATED 6 7 2 2 0 3 1
TP53 WILD-TYPE 28 4 7 5 6 17 8

Figure S9.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'SRPR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.626 (Fisher's exact test), Q value = 0.83

Table S25.  Gene #9: 'SRPR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SRPR MUTATED 3 4 3 2 4
SRPR WILD-TYPE 25 16 8 18 17
'SRPR MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.43

Table S26.  Gene #9: 'SRPR MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SRPR MUTATED 6 2 6 2
SRPR WILD-TYPE 29 31 10 10

Figure S10.  Get High-res Image Gene #9: 'SRPR MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'SRPR MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0173 (Fisher's exact test), Q value = 0.4

Table S27.  Gene #9: 'SRPR MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SRPR MUTATED 10 1 0 3 1 0 1
SRPR WILD-TYPE 24 10 9 4 5 20 8

Figure S11.  Get High-res Image Gene #9: 'SRPR MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'INPPL1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.769 (Fisher's exact test), Q value = 0.91

Table S28.  Gene #10: 'INPPL1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
INPPL1 MUTATED 6 5 1 6 4
INPPL1 WILD-TYPE 22 15 10 14 17
'INPPL1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 0.56

Table S29.  Gene #10: 'INPPL1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
INPPL1 MUTATED 10 3 4 3
INPPL1 WILD-TYPE 25 30 12 9
'INPPL1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.112 (Fisher's exact test), Q value = 0.48

Table S30.  Gene #10: 'INPPL1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
INPPL1 MUTATED 12 0 1 1 2 2 2
INPPL1 WILD-TYPE 22 11 8 6 4 18 7
'RNF43 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.879 (Fisher's exact test), Q value = 0.96

Table S31.  Gene #11: 'RNF43 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
RNF43 MUTATED 5 2 2 3 2
RNF43 WILD-TYPE 23 18 9 17 19
'RNF43 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0529 (Fisher's exact test), Q value = 0.43

Table S32.  Gene #11: 'RNF43 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
RNF43 MUTATED 6 1 4 3
RNF43 WILD-TYPE 29 32 12 9
'RNF43 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0437 (Fisher's exact test), Q value = 0.42

Table S33.  Gene #11: 'RNF43 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
RNF43 MUTATED 7 0 1 2 3 1 0
RNF43 WILD-TYPE 27 11 8 5 3 19 9

Figure S12.  Get High-res Image Gene #11: 'RNF43 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'JAK1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.819 (Fisher's exact test), Q value = 0.93

Table S34.  Gene #12: 'JAK1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
JAK1 MUTATED 5 4 2 2 2
JAK1 WILD-TYPE 23 16 9 18 19
'JAK1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.00169 (Fisher's exact test), Q value = 0.25

Table S35.  Gene #12: 'JAK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
JAK1 MUTATED 9 0 5 1
JAK1 WILD-TYPE 26 33 11 11

Figure S13.  Get High-res Image Gene #12: 'JAK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'JAK1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.006 (Fisher's exact test), Q value = 0.32

Table S36.  Gene #12: 'JAK1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
JAK1 MUTATED 10 0 1 3 1 0 0
JAK1 WILD-TYPE 24 11 8 4 5 20 9

Figure S14.  Get High-res Image Gene #12: 'JAK1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'PHF2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.821 (Fisher's exact test), Q value = 0.93

Table S37.  Gene #13: 'PHF2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PHF2 MUTATED 3 4 1 4 4
PHF2 WILD-TYPE 25 16 10 16 17
'PHF2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.394 (Fisher's exact test), Q value = 0.69

Table S38.  Gene #13: 'PHF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PHF2 MUTATED 6 3 4 3
PHF2 WILD-TYPE 29 30 12 9
'PHF2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0952 (Fisher's exact test), Q value = 0.47

Table S39.  Gene #13: 'PHF2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PHF2 MUTATED 6 1 0 3 3 2 1
PHF2 WILD-TYPE 28 10 9 4 3 18 8
'FBXW7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.775 (Fisher's exact test), Q value = 0.91

Table S40.  Gene #14: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
FBXW7 MUTATED 4 3 2 4 6
FBXW7 WILD-TYPE 24 17 9 16 15
'FBXW7 MUTATION STATUS' versus 'METHYLATION_CNMF'

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

Table S41.  Gene #14: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
FBXW7 MUTATED 7 6 3 2
FBXW7 WILD-TYPE 28 27 13 10
'FBXW7 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.486 (Fisher's exact test), Q value = 0.75

Table S42.  Gene #14: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
FBXW7 MUTATED 8 2 1 3 0 2 2
FBXW7 WILD-TYPE 26 9 8 4 6 18 7
'ACVR2A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.564 (Fisher's exact test), Q value = 0.78

Table S43.  Gene #15: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ACVR2A MUTATED 2 2 0 3 4
ACVR2A WILD-TYPE 26 18 11 17 17
'ACVR2A MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.39

Table S44.  Gene #15: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ACVR2A MUTATED 8 0 2 1
ACVR2A WILD-TYPE 27 33 14 11

Figure S15.  Get High-res Image Gene #15: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'ACVR2A MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0273 (Fisher's exact test), Q value = 0.42

Table S45.  Gene #15: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ACVR2A MUTATED 9 0 0 1 1 0 0
ACVR2A WILD-TYPE 25 11 9 6 5 20 9

Figure S16.  Get High-res Image Gene #15: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'ADNP MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.647 (Fisher's exact test), Q value = 0.84

Table S46.  Gene #16: 'ADNP MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ADNP MUTATED 1 2 1 3 2
ADNP WILD-TYPE 27 18 10 17 19
'ADNP MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.947 (Fisher's exact test), Q value = 1

Table S47.  Gene #16: 'ADNP MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ADNP MUTATED 4 2 1 1
ADNP WILD-TYPE 31 31 15 11
'ADNP MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.416 (Fisher's exact test), Q value = 0.69

Table S48.  Gene #16: 'ADNP MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ADNP MUTATED 3 0 0 1 1 1 2
ADNP WILD-TYPE 31 11 9 6 5 19 7
'ZFP36L2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.265 (Fisher's exact test), Q value = 0.63

Table S49.  Gene #17: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ZFP36L2 MUTATED 2 2 0 1 5
ZFP36L2 WILD-TYPE 26 18 11 19 16
'ZFP36L2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.117 (Fisher's exact test), Q value = 0.48

Table S50.  Gene #17: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ZFP36L2 MUTATED 2 2 3 3
ZFP36L2 WILD-TYPE 33 31 13 9
'ZFP36L2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.254 (Fisher's exact test), Q value = 0.63

Table S51.  Gene #17: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ZFP36L2 MUTATED 4 1 1 1 2 0 1
ZFP36L2 WILD-TYPE 30 10 8 6 4 20 8
'SEC31A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.94 (Fisher's exact test), Q value = 0.99

Table S52.  Gene #18: 'SEC31A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SEC31A MUTATED 5 3 3 4 4
SEC31A WILD-TYPE 23 17 8 16 17
'SEC31A MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.39

Table S53.  Gene #18: 'SEC31A MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SEC31A MUTATED 9 1 5 3
SEC31A WILD-TYPE 26 32 11 9

Figure S17.  Get High-res Image Gene #18: 'SEC31A MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'SEC31A MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00097 (Fisher's exact test), Q value = 0.25

Table S54.  Gene #18: 'SEC31A MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SEC31A MUTATED 10 0 0 4 3 1 0
SEC31A WILD-TYPE 24 11 9 3 3 19 9

Figure S18.  Get High-res Image Gene #18: 'SEC31A MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'CMTM1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.708 (Fisher's exact test), Q value = 0.87

Table S55.  Gene #19: 'CMTM1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CMTM1 MUTATED 4 1 0 1 1
CMTM1 WILD-TYPE 24 19 11 19 20
'CMTM1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.549 (Fisher's exact test), Q value = 0.77

Table S56.  Gene #19: 'CMTM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CMTM1 MUTATED 3 1 2 1
CMTM1 WILD-TYPE 32 32 14 11
'CMTM1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.317 (Fisher's exact test), Q value = 0.65

Table S57.  Gene #19: 'CMTM1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CMTM1 MUTATED 5 0 0 1 0 0 1
CMTM1 WILD-TYPE 29 11 9 6 6 20 8
'TEAD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.748 (Fisher's exact test), Q value = 0.89

Table S58.  Gene #20: 'TEAD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TEAD2 MUTATED 2 1 2 1 2
TEAD2 WILD-TYPE 26 19 9 19 19
'TEAD2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.843 (Fisher's exact test), Q value = 0.94

Table S59.  Gene #20: 'TEAD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TEAD2 MUTATED 2 2 2 1
TEAD2 WILD-TYPE 33 31 14 11
'TEAD2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0521 (Fisher's exact test), Q value = 0.43

Table S60.  Gene #20: 'TEAD2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TEAD2 MUTATED 2 0 0 2 1 0 2
TEAD2 WILD-TYPE 32 11 9 5 5 20 7
'NCOR2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.701 (Fisher's exact test), Q value = 0.87

Table S61.  Gene #21: 'NCOR2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
NCOR2 MUTATED 5 4 0 3 3
NCOR2 WILD-TYPE 23 16 11 17 18
'NCOR2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.00136 (Fisher's exact test), Q value = 0.25

Table S62.  Gene #21: 'NCOR2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
NCOR2 MUTATED 12 1 2 0
NCOR2 WILD-TYPE 23 32 14 12

Figure S19.  Get High-res Image Gene #21: 'NCOR2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'NCOR2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.133 (Fisher's exact test), Q value = 0.51

Table S63.  Gene #21: 'NCOR2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
NCOR2 MUTATED 9 2 2 1 0 0 1
NCOR2 WILD-TYPE 25 9 7 6 6 20 8
'WDTC1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.276 (Fisher's exact test), Q value = 0.63

Table S64.  Gene #22: 'WDTC1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
WDTC1 MUTATED 5 2 1 0 1
WDTC1 WILD-TYPE 23 18 10 20 20
'WDTC1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0464 (Fisher's exact test), Q value = 0.42

Table S65.  Gene #22: 'WDTC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
WDTC1 MUTATED 5 0 3 1
WDTC1 WILD-TYPE 30 33 13 11

Figure S20.  Get High-res Image Gene #22: 'WDTC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'WDTC1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.191 (Fisher's exact test), Q value = 0.56

Table S66.  Gene #22: 'WDTC1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
WDTC1 MUTATED 6 0 0 1 1 0 1
WDTC1 WILD-TYPE 28 11 9 6 5 20 8
'NDUFC2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.807 (Fisher's exact test), Q value = 0.93

Table S67.  Gene #23: 'NDUFC2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
NDUFC2 MUTATED 1 2 0 1 2
NDUFC2 WILD-TYPE 27 18 11 19 19
'NDUFC2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.12 (Fisher's exact test), Q value = 0.49

Table S68.  Gene #23: 'NDUFC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
NDUFC2 MUTATED 1 1 3 1
NDUFC2 WILD-TYPE 34 32 13 11
'NDUFC2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.606 (Fisher's exact test), Q value = 0.81

Table S69.  Gene #23: 'NDUFC2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
NDUFC2 MUTATED 3 0 0 1 1 1 0
NDUFC2 WILD-TYPE 31 11 9 6 5 19 9
'ZBTB20 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.925 (Fisher's exact test), Q value = 0.98

Table S70.  Gene #24: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ZBTB20 MUTATED 4 1 1 2 3
ZBTB20 WILD-TYPE 24 19 10 18 18
'ZBTB20 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 0.56

Table S71.  Gene #24: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ZBTB20 MUTATED 5 1 3 2
ZBTB20 WILD-TYPE 30 32 13 10
'ZBTB20 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.131 (Fisher's exact test), Q value = 0.51

Table S72.  Gene #24: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ZBTB20 MUTATED 7 0 0 1 2 1 0
ZBTB20 WILD-TYPE 27 11 9 6 4 19 9
'ARID5B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.568 (Fisher's exact test), Q value = 0.78

Table S73.  Gene #25: 'ARID5B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ARID5B MUTATED 3 4 2 2 1
ARID5B WILD-TYPE 25 16 9 18 20
'ARID5B MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 0.42

Table S74.  Gene #25: 'ARID5B MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ARID5B MUTATED 9 3 0 0
ARID5B WILD-TYPE 26 30 16 12

Figure S21.  Get High-res Image Gene #25: 'ARID5B MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'ARID5B MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.169 (Fisher's exact test), Q value = 0.56

Table S75.  Gene #25: 'ARID5B MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ARID5B MUTATED 6 0 2 0 0 1 3
ARID5B WILD-TYPE 28 11 7 7 6 19 6
'CEL MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.621 (Fisher's exact test), Q value = 0.83

Table S76.  Gene #26: 'CEL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CEL MUTATED 4 1 2 1 3
CEL WILD-TYPE 24 19 9 19 18
'CEL MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.291 (Fisher's exact test), Q value = 0.64

Table S77.  Gene #26: 'CEL MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CEL MUTATED 4 2 4 1
CEL WILD-TYPE 31 31 12 11
'CEL MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.292 (Fisher's exact test), Q value = 0.64

Table S78.  Gene #26: 'CEL MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CEL MUTATED 6 0 0 2 1 1 1
CEL WILD-TYPE 28 11 9 5 5 19 8
'RNF145 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.745 (Fisher's exact test), Q value = 0.89

Table S79.  Gene #27: 'RNF145 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
RNF145 MUTATED 2 1 2 1 2
RNF145 WILD-TYPE 26 19 9 19 19
'RNF145 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.531 (Fisher's exact test), Q value = 0.77

Table S80.  Gene #27: 'RNF145 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
RNF145 MUTATED 4 1 2 1
RNF145 WILD-TYPE 31 32 14 11
'RNF145 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.487 (Fisher's exact test), Q value = 0.75

Table S81.  Gene #27: 'RNF145 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
RNF145 MUTATED 4 0 2 1 0 1 0
RNF145 WILD-TYPE 30 11 7 6 6 19 9
'BAX MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.845 (Fisher's exact test), Q value = 0.94

Table S82.  Gene #28: 'BAX MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
BAX MUTATED 3 1 0 2 1
BAX WILD-TYPE 25 19 11 18 20
'BAX MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0766 (Fisher's exact test), Q value = 0.47

Table S83.  Gene #28: 'BAX MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
BAX MUTATED 3 0 3 1
BAX WILD-TYPE 32 33 13 11
'BAX MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.211 (Fisher's exact test), Q value = 0.58

Table S84.  Gene #28: 'BAX MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
BAX MUTATED 5 0 0 1 1 0 0
BAX WILD-TYPE 29 11 9 6 5 20 9
'ARSJ MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.594 (Fisher's exact test), Q value = 0.8

Table S85.  Gene #29: 'ARSJ MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ARSJ MUTATED 3 0 0 1 2
ARSJ WILD-TYPE 25 20 11 19 19
'ARSJ MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.105 (Fisher's exact test), Q value = 0.48

Table S86.  Gene #29: 'ARSJ MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ARSJ MUTATED 4 0 2 0
ARSJ WILD-TYPE 31 33 14 12
'ARSJ MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.193 (Fisher's exact test), Q value = 0.56

Table S87.  Gene #29: 'ARSJ MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ARSJ MUTATED 6 0 0 0 0 0 0
ARSJ WILD-TYPE 28 11 9 7 6 20 9
'FAHD2A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.378 (Fisher's exact test), Q value = 0.68

Table S88.  Gene #30: 'FAHD2A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
FAHD2A MUTATED 2 2 1 0 0
FAHD2A WILD-TYPE 26 18 10 20 21
'FAHD2A MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.398 (Fisher's exact test), Q value = 0.69

Table S89.  Gene #30: 'FAHD2A MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
FAHD2A MUTATED 1 1 2 0
FAHD2A WILD-TYPE 34 32 14 12
'FAHD2A MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.389 (Fisher's exact test), Q value = 0.68

Table S90.  Gene #30: 'FAHD2A MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
FAHD2A MUTATED 2 0 0 1 0 0 1
FAHD2A WILD-TYPE 32 11 9 6 6 20 8
'KIAA1919 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.268 (Fisher's exact test), Q value = 0.63

Table S91.  Gene #31: 'KIAA1919 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
KIAA1919 MUTATED 2 3 2 0 1
KIAA1919 WILD-TYPE 26 17 9 20 20
'KIAA1919 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0403 (Fisher's exact test), Q value = 0.42

Table S92.  Gene #31: 'KIAA1919 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
KIAA1919 MUTATED 3 0 3 2
KIAA1919 WILD-TYPE 32 33 13 10

Figure S22.  Get High-res Image Gene #31: 'KIAA1919 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'KIAA1919 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.041 (Fisher's exact test), Q value = 0.42

Table S93.  Gene #31: 'KIAA1919 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
KIAA1919 MUTATED 4 0 0 2 2 0 0
KIAA1919 WILD-TYPE 30 11 9 5 4 20 9

Figure S23.  Get High-res Image Gene #31: 'KIAA1919 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'PHTF1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.484 (Fisher's exact test), Q value = 0.75

Table S94.  Gene #32: 'PHTF1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PHTF1 MUTATED 3 1 0 1 4
PHTF1 WILD-TYPE 25 19 11 19 17
'PHTF1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0667 (Fisher's exact test), Q value = 0.45

Table S95.  Gene #32: 'PHTF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PHTF1 MUTATED 5 0 2 2
PHTF1 WILD-TYPE 30 33 14 10
'PHTF1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0378 (Fisher's exact test), Q value = 0.42

Table S96.  Gene #32: 'PHTF1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PHTF1 MUTATED 5 0 0 2 2 0 0
PHTF1 WILD-TYPE 29 11 9 5 4 20 9

Figure S24.  Get High-res Image Gene #32: 'PHTF1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'ZFHX3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.32 (Fisher's exact test), Q value = 0.65

Table S97.  Gene #33: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ZFHX3 MUTATED 3 5 3 3 7
ZFHX3 WILD-TYPE 25 15 8 17 14
'ZFHX3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.4

Table S98.  Gene #33: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ZFHX3 MUTATED 9 2 5 5
ZFHX3 WILD-TYPE 26 31 11 7

Figure S25.  Get High-res Image Gene #33: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'ZFHX3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00358 (Fisher's exact test), Q value = 0.32

Table S99.  Gene #33: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ZFHX3 MUTATED 11 0 1 3 4 1 1
ZFHX3 WILD-TYPE 23 11 8 4 2 19 8

Figure S26.  Get High-res Image Gene #33: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'ESRP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.122 (Fisher's exact test), Q value = 0.49

Table S100.  Gene #34: 'ESRP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ESRP1 MUTATED 0 2 1 3 4
ESRP1 WILD-TYPE 28 18 10 17 17
'ESRP1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.117 (Fisher's exact test), Q value = 0.48

Table S101.  Gene #34: 'ESRP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ESRP1 MUTATED 2 2 3 3
ESRP1 WILD-TYPE 33 31 13 9
'ESRP1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0329 (Fisher's exact test), Q value = 0.42

Table S102.  Gene #34: 'ESRP1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ESRP1 MUTATED 3 0 0 2 3 2 0
ESRP1 WILD-TYPE 31 11 9 5 3 18 9

Figure S27.  Get High-res Image Gene #34: 'ESRP1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'PROM1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.569 (Fisher's exact test), Q value = 0.78

Table S103.  Gene #35: 'PROM1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PROM1 MUTATED 4 1 2 1 1
PROM1 WILD-TYPE 24 19 9 19 20
'PROM1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0139 (Fisher's exact test), Q value = 0.39

Table S104.  Gene #35: 'PROM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PROM1 MUTATED 7 0 2 0
PROM1 WILD-TYPE 28 33 14 12

Figure S28.  Get High-res Image Gene #35: 'PROM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'PROM1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0522 (Fisher's exact test), Q value = 0.43

Table S105.  Gene #35: 'PROM1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PROM1 MUTATED 8 0 0 1 0 0 0
PROM1 WILD-TYPE 26 11 9 6 6 20 9
'SFRS15 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.936 (Fisher's exact test), Q value = 0.99

Table S106.  Gene #36: 'SFRS15 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SFRS15 MUTATED 5 3 1 2 4
SFRS15 WILD-TYPE 23 17 10 18 17
'SFRS15 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0464 (Fisher's exact test), Q value = 0.42

Table S107.  Gene #36: 'SFRS15 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SFRS15 MUTATED 9 1 2 2
SFRS15 WILD-TYPE 26 32 14 10

Figure S29.  Get High-res Image Gene #36: 'SFRS15 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'SFRS15 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0447 (Fisher's exact test), Q value = 0.42

Table S108.  Gene #36: 'SFRS15 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SFRS15 MUTATED 10 0 1 1 1 0 1
SFRS15 WILD-TYPE 24 11 8 6 5 20 8

Figure S30.  Get High-res Image Gene #36: 'SFRS15 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'USP35 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.442 (Fisher's exact test), Q value = 0.72

Table S109.  Gene #37: 'USP35 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
USP35 MUTATED 1 3 2 1 2
USP35 WILD-TYPE 27 17 9 19 19
'USP35 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.256 (Fisher's exact test), Q value = 0.63

Table S110.  Gene #37: 'USP35 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
USP35 MUTATED 5 1 1 2
USP35 WILD-TYPE 30 32 15 10
'USP35 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.193 (Fisher's exact test), Q value = 0.56

Table S111.  Gene #37: 'USP35 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
USP35 MUTATED 6 0 0 1 1 0 1
USP35 WILD-TYPE 28 11 9 6 5 20 8
'PRRG1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.849 (Fisher's exact test), Q value = 0.94

Table S112.  Gene #38: 'PRRG1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PRRG1 MUTATED 1 2 1 1 1
PRRG1 WILD-TYPE 27 18 10 19 20
'PRRG1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.163 (Fisher's exact test), Q value = 0.56

Table S113.  Gene #38: 'PRRG1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PRRG1 MUTATED 3 0 2 1
PRRG1 WILD-TYPE 32 33 14 11
'PRRG1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.276 (Fisher's exact test), Q value = 0.63

Table S114.  Gene #38: 'PRRG1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PRRG1 MUTATED 4 0 0 1 1 0 0
PRRG1 WILD-TYPE 30 11 9 6 5 20 9
'CTNNB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.727 (Fisher's exact test), Q value = 0.88

Table S115.  Gene #39: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CTNNB1 MUTATED 8 6 2 4 8
CTNNB1 WILD-TYPE 20 14 9 16 13
'CTNNB1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.4

Table S116.  Gene #39: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CTNNB1 MUTATED 15 7 1 5
CTNNB1 WILD-TYPE 20 26 15 7

Figure S31.  Get High-res Image Gene #39: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'CTNNB1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00132 (Fisher's exact test), Q value = 0.25

Table S117.  Gene #39: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CTNNB1 MUTATED 14 0 6 0 1 7 0
CTNNB1 WILD-TYPE 20 11 3 7 5 13 9

Figure S32.  Get High-res Image Gene #39: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'HNRNPL MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.808 (Fisher's exact test), Q value = 0.93

Table S118.  Gene #40: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
HNRNPL MUTATED 1 2 0 1 2
HNRNPL WILD-TYPE 27 18 11 19 19
'HNRNPL MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 0.78

Table S119.  Gene #40: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
HNRNPL MUTATED 2 1 2 1
HNRNPL WILD-TYPE 33 32 14 11
'HNRNPL MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.371 (Fisher's exact test), Q value = 0.68

Table S120.  Gene #40: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
HNRNPL MUTATED 4 0 0 0 1 0 1
HNRNPL WILD-TYPE 30 11 9 7 5 20 8
'MLL4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.709 (Fisher's exact test), Q value = 0.88

Table S121.  Gene #41: 'MLL4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
MLL4 MUTATED 5 7 2 4 5
MLL4 WILD-TYPE 23 13 9 16 16
'MLL4 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.4

Table S122.  Gene #41: 'MLL4 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
MLL4 MUTATED 12 2 5 3
MLL4 WILD-TYPE 23 31 11 9

Figure S33.  Get High-res Image Gene #41: 'MLL4 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'MLL4 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0658 (Fisher's exact test), Q value = 0.45

Table S123.  Gene #41: 'MLL4 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
MLL4 MUTATED 12 0 2 3 2 2 1
MLL4 WILD-TYPE 22 11 7 4 4 18 8
'SNRK MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.483 (Fisher's exact test), Q value = 0.75

Table S124.  Gene #42: 'SNRK MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SNRK MUTATED 1 0 1 2 2
SNRK WILD-TYPE 27 20 10 18 19
'SNRK MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0923 (Fisher's exact test), Q value = 0.47

Table S125.  Gene #42: 'SNRK MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SNRK MUTATED 5 0 1 0
SNRK WILD-TYPE 30 33 15 12
'SNRK MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.197 (Fisher's exact test), Q value = 0.57

Table S126.  Gene #42: 'SNRK MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SNRK MUTATED 6 0 0 0 0 0 0
SNRK WILD-TYPE 28 11 9 7 6 20 9
'OR6C75 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.722 (Fisher's exact test), Q value = 0.88

Table S127.  Gene #43: 'OR6C75 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
OR6C75 MUTATED 2 2 0 0 1
OR6C75 WILD-TYPE 26 18 11 20 20
'OR6C75 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0537 (Fisher's exact test), Q value = 0.43

Table S128.  Gene #43: 'OR6C75 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
OR6C75 MUTATED 2 0 3 0
OR6C75 WILD-TYPE 33 33 13 12
'OR6C75 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.382 (Fisher's exact test), Q value = 0.68

Table S129.  Gene #43: 'OR6C75 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
OR6C75 MUTATED 4 0 0 1 0 0 0
OR6C75 WILD-TYPE 30 11 9 6 6 20 9
'CCDC73 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.784 (Fisher's exact test), Q value = 0.92

Table S130.  Gene #44: 'CCDC73 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CCDC73 MUTATED 4 3 2 1 2
CCDC73 WILD-TYPE 24 17 9 19 19
'CCDC73 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.4

Table S131.  Gene #44: 'CCDC73 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CCDC73 MUTATED 7 0 3 1
CCDC73 WILD-TYPE 28 33 13 11

Figure S34.  Get High-res Image Gene #44: 'CCDC73 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'CCDC73 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0422 (Fisher's exact test), Q value = 0.42

Table S132.  Gene #44: 'CCDC73 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CCDC73 MUTATED 8 0 1 2 0 0 0
CCDC73 WILD-TYPE 26 11 8 5 6 20 9

Figure S35.  Get High-res Image Gene #44: 'CCDC73 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'SLAMF1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.893 (Fisher's exact test), Q value = 0.97

Table S133.  Gene #45: 'SLAMF1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SLAMF1 MUTATED 1 1 0 2 1
SLAMF1 WILD-TYPE 27 19 11 18 20
'SLAMF1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.335 (Fisher's exact test), Q value = 0.67

Table S134.  Gene #45: 'SLAMF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SLAMF1 MUTATED 1 1 2 1
SLAMF1 WILD-TYPE 34 32 14 11
'SLAMF1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.249 (Fisher's exact test), Q value = 0.63

Table S135.  Gene #45: 'SLAMF1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SLAMF1 MUTATED 2 0 0 1 1 0 1
SLAMF1 WILD-TYPE 32 11 9 6 5 20 8
'SLC3A2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.849 (Fisher's exact test), Q value = 0.94

Table S136.  Gene #46: 'SLC3A2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SLC3A2 MUTATED 1 2 1 1 1
SLC3A2 WILD-TYPE 27 18 10 19 20
'SLC3A2 MUTATION STATUS' versus 'METHYLATION_CNMF'

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

Table S137.  Gene #46: 'SLC3A2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SLC3A2 MUTATED 2 2 1 1
SLC3A2 WILD-TYPE 33 31 15 11
'SLC3A2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.14 (Fisher's exact test), Q value = 0.52

Table S138.  Gene #46: 'SLC3A2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SLC3A2 MUTATED 2 0 0 1 1 0 2
SLC3A2 WILD-TYPE 32 11 9 6 5 20 7
'CHD3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0279 (Fisher's exact test), Q value = 0.42

Table S139.  Gene #47: 'CHD3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CHD3 MUTATED 2 5 2 0 6
CHD3 WILD-TYPE 26 15 9 20 15

Figure S36.  Get High-res Image Gene #47: 'CHD3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'CHD3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0705 (Fisher's exact test), Q value = 0.46

Table S140.  Gene #47: 'CHD3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CHD3 MUTATED 7 1 3 3
CHD3 WILD-TYPE 28 32 13 9
'CHD3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0745 (Fisher's exact test), Q value = 0.47

Table S141.  Gene #47: 'CHD3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CHD3 MUTATED 8 0 2 2 1 0 1
CHD3 WILD-TYPE 26 11 7 5 5 20 8
'XPOT MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.226 (Fisher's exact test), Q value = 0.59

Table S142.  Gene #48: 'XPOT MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
XPOT MUTATED 1 2 3 1 2
XPOT WILD-TYPE 27 18 8 19 19
'XPOT MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 0.51

Table S143.  Gene #48: 'XPOT MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
XPOT MUTATED 4 1 1 3
XPOT WILD-TYPE 31 32 15 9
'XPOT MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0914 (Fisher's exact test), Q value = 0.47

Table S144.  Gene #48: 'XPOT MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
XPOT MUTATED 5 2 0 0 2 0 0
XPOT WILD-TYPE 29 9 9 7 4 20 9
'NRIP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.3 (Fisher's exact test), Q value = 0.65

Table S145.  Gene #49: 'NRIP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
NRIP1 MUTATED 1 4 0 1 2
NRIP1 WILD-TYPE 27 16 11 19 19
'NRIP1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.311 (Fisher's exact test), Q value = 0.65

Table S146.  Gene #49: 'NRIP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
NRIP1 MUTATED 3 1 2 2
NRIP1 WILD-TYPE 32 32 14 10
'NRIP1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.182 (Fisher's exact test), Q value = 0.56

Table S147.  Gene #49: 'NRIP1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
NRIP1 MUTATED 4 0 0 1 1 0 2
NRIP1 WILD-TYPE 30 11 9 6 5 20 7
'MAZ MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.484 (Fisher's exact test), Q value = 0.75

Table S148.  Gene #50: 'MAZ MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
MAZ MUTATED 2 0 1 1 0
MAZ WILD-TYPE 26 20 10 19 21
'MAZ MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.183 (Fisher's exact test), Q value = 0.56

Table S149.  Gene #50: 'MAZ MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
MAZ MUTATED 2 0 2 0
MAZ WILD-TYPE 33 33 14 12
'MAZ MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.726 (Fisher's exact test), Q value = 0.88

Table S150.  Gene #50: 'MAZ MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
MAZ MUTATED 3 1 0 0 0 0 0
MAZ WILD-TYPE 31 10 9 7 6 20 9
'LCE4A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.717 (Fisher's exact test), Q value = 0.88

Table S151.  Gene #51: 'LCE4A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
LCE4A MUTATED 2 2 0 3 1
LCE4A WILD-TYPE 26 18 11 17 20
'LCE4A MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 0.72

Table S152.  Gene #51: 'LCE4A MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
LCE4A MUTATED 2 2 3 1
LCE4A WILD-TYPE 33 31 13 11
'LCE4A MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.879 (Fisher's exact test), Q value = 0.96

Table S153.  Gene #51: 'LCE4A MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
LCE4A MUTATED 3 2 1 0 0 2 0
LCE4A WILD-TYPE 31 9 8 7 6 18 9
'NFE2L2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.77 (Fisher's exact test), Q value = 0.91

Table S154.  Gene #52: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
NFE2L2 MUTATED 1 2 0 2 1
NFE2L2 WILD-TYPE 27 18 11 18 20
'NFE2L2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0909 (Fisher's exact test), Q value = 0.47

Table S155.  Gene #52: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
NFE2L2 MUTATED 5 0 1 0
NFE2L2 WILD-TYPE 30 33 15 12
'NFE2L2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.216 (Fisher's exact test), Q value = 0.58

Table S156.  Gene #52: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
NFE2L2 MUTATED 3 0 0 1 0 0 2
NFE2L2 WILD-TYPE 31 11 9 6 6 20 7
'VEGFB MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.166 (Fisher's exact test), Q value = 0.56

Table S157.  Gene #53: 'VEGFB MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
VEGFB MUTATED 0 3 0 2 1
VEGFB WILD-TYPE 28 17 11 18 20
'VEGFB MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0909 (Fisher's exact test), Q value = 0.47

Table S158.  Gene #53: 'VEGFB MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
VEGFB MUTATED 5 0 1 0
VEGFB WILD-TYPE 30 33 15 12
'VEGFB MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 0.75

Table S159.  Gene #53: 'VEGFB MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
VEGFB MUTATED 4 0 1 0 0 0 1
VEGFB WILD-TYPE 30 11 8 7 6 20 8
'SENP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.482 (Fisher's exact test), Q value = 0.75

Table S160.  Gene #54: 'SENP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SENP1 MUTATED 1 0 1 2 2
SENP1 WILD-TYPE 27 20 10 18 19
'SENP1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.736 (Fisher's exact test), Q value = 0.89

Table S161.  Gene #54: 'SENP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SENP1 MUTATED 3 1 1 0
SENP1 WILD-TYPE 32 32 15 12
'SENP1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.791 (Fisher's exact test), Q value = 0.92

Table S162.  Gene #54: 'SENP1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SENP1 MUTATED 3 0 0 1 0 1 0
SENP1 WILD-TYPE 31 11 9 6 6 19 9
'USP9X MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.647 (Fisher's exact test), Q value = 0.84

Table S163.  Gene #55: 'USP9X MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
USP9X MUTATED 5 4 2 1 4
USP9X WILD-TYPE 23 16 9 19 17
'USP9X MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 0.65

Table S164.  Gene #55: 'USP9X MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
USP9X MUTATED 9 3 2 2
USP9X WILD-TYPE 26 30 14 10
'USP9X MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.066 (Fisher's exact test), Q value = 0.45

Table S165.  Gene #55: 'USP9X MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
USP9X MUTATED 10 0 0 2 1 1 2
USP9X WILD-TYPE 24 11 9 5 5 19 7
'ADAM28 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.644 (Fisher's exact test), Q value = 0.84

Table S166.  Gene #56: 'ADAM28 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ADAM28 MUTATED 2 0 0 2 2
ADAM28 WILD-TYPE 26 20 11 18 19
'ADAM28 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0911 (Fisher's exact test), Q value = 0.47

Table S167.  Gene #56: 'ADAM28 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ADAM28 MUTATED 5 0 1 0
ADAM28 WILD-TYPE 30 33 15 12
'ADAM28 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.277 (Fisher's exact test), Q value = 0.63

Table S168.  Gene #56: 'ADAM28 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ADAM28 MUTATED 5 0 0 1 0 0 0
ADAM28 WILD-TYPE 29 11 9 6 6 20 9
'SVIL MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.396 (Fisher's exact test), Q value = 0.69

Table S169.  Gene #57: 'SVIL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SVIL MUTATED 3 2 1 2 6
SVIL WILD-TYPE 25 18 10 18 15
'SVIL MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0776 (Fisher's exact test), Q value = 0.47

Table S170.  Gene #57: 'SVIL MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SVIL MUTATED 8 1 3 2
SVIL WILD-TYPE 27 32 13 10
'SVIL MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0739 (Fisher's exact test), Q value = 0.47

Table S171.  Gene #57: 'SVIL MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SVIL MUTATED 8 0 2 2 1 0 1
SVIL WILD-TYPE 26 11 7 5 5 20 8
'KDM5A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.836 (Fisher's exact test), Q value = 0.94

Table S172.  Gene #58: 'KDM5A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
KDM5A MUTATED 2 3 2 2 2
KDM5A WILD-TYPE 26 17 9 18 19
'KDM5A MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.4

Table S173.  Gene #58: 'KDM5A MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
KDM5A MUTATED 7 0 2 2
KDM5A WILD-TYPE 28 33 14 10

Figure S37.  Get High-res Image Gene #58: 'KDM5A MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'KDM5A MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0722 (Fisher's exact test), Q value = 0.47

Table S174.  Gene #58: 'KDM5A MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
KDM5A MUTATED 7 0 1 2 1 0 0
KDM5A WILD-TYPE 27 11 8 5 5 20 9
'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.452 (Fisher's exact test), Q value = 0.73

Table S175.  Gene #59: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PIK3CA MUTATED 10 10 6 6 11
PIK3CA WILD-TYPE 18 10 5 14 10
'PIK3CA MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 0.58

Table S176.  Gene #59: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PIK3CA MUTATED 19 13 4 4
PIK3CA WILD-TYPE 16 20 12 8
'PIK3CA MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.847 (Fisher's exact test), Q value = 0.94

Table S177.  Gene #59: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PIK3CA MUTATED 17 3 3 2 2 9 4
PIK3CA WILD-TYPE 17 8 6 5 4 11 5
'TBC1D23 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.978 (Fisher's exact test), Q value = 1

Table S178.  Gene #60: 'TBC1D23 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TBC1D23 MUTATED 2 2 1 1 1
TBC1D23 WILD-TYPE 26 18 10 19 20
'TBC1D23 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.132 (Fisher's exact test), Q value = 0.51

Table S179.  Gene #60: 'TBC1D23 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TBC1D23 MUTATED 4 0 2 1
TBC1D23 WILD-TYPE 31 33 14 11
'TBC1D23 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.316 (Fisher's exact test), Q value = 0.65

Table S180.  Gene #60: 'TBC1D23 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TBC1D23 MUTATED 4 0 0 1 1 0 1
TBC1D23 WILD-TYPE 30 11 9 6 5 20 8
'C13ORF33 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.13 (Fisher's exact test), Q value = 0.51

Table S181.  Gene #61: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
C13ORF33 MUTATED 2 0 2 2 0
C13ORF33 WILD-TYPE 26 20 9 18 21
'C13ORF33 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.044 (Fisher's exact test), Q value = 0.42

Table S182.  Gene #61: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
C13ORF33 MUTATED 3 0 3 0
C13ORF33 WILD-TYPE 32 33 13 12

Figure S38.  Get High-res Image Gene #61: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'C13ORF33 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.148 (Fisher's exact test), Q value = 0.54

Table S183.  Gene #61: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
C13ORF33 MUTATED 4 0 0 2 0 0 0
C13ORF33 WILD-TYPE 30 11 9 5 6 20 9
'KIAA0182 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.538 (Fisher's exact test), Q value = 0.77

Table S184.  Gene #62: 'KIAA0182 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
KIAA0182 MUTATED 3 2 0 0 1
KIAA0182 WILD-TYPE 25 18 11 20 20
'KIAA0182 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.103 (Fisher's exact test), Q value = 0.48

Table S185.  Gene #62: 'KIAA0182 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
KIAA0182 MUTATED 4 0 2 0
KIAA0182 WILD-TYPE 31 33 14 12
'KIAA0182 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.198 (Fisher's exact test), Q value = 0.57

Table S186.  Gene #62: 'KIAA0182 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
KIAA0182 MUTATED 6 0 0 0 0 0 0
KIAA0182 WILD-TYPE 28 11 9 7 6 20 9
'CKAP2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.405 (Fisher's exact test), Q value = 0.69

Table S187.  Gene #63: 'CKAP2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CKAP2 MUTATED 0 2 0 1 2
CKAP2 WILD-TYPE 28 18 11 19 19
'CKAP2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.16 (Fisher's exact test), Q value = 0.56

Table S188.  Gene #63: 'CKAP2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CKAP2 MUTATED 3 0 2 0
CKAP2 WILD-TYPE 32 33 14 12
'CKAP2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.354 (Fisher's exact test), Q value = 0.68

Table S189.  Gene #63: 'CKAP2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CKAP2 MUTATED 5 0 0 0 0 0 0
CKAP2 WILD-TYPE 29 11 9 7 6 20 9
'WBP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.102 (Fisher's exact test), Q value = 0.48

Table S190.  Gene #64: 'WBP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
WBP1 MUTATED 1 0 0 1 4
WBP1 WILD-TYPE 27 20 11 19 17
'WBP1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.113 (Fisher's exact test), Q value = 0.48

Table S191.  Gene #64: 'WBP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
WBP1 MUTATED 3 0 1 2
WBP1 WILD-TYPE 32 33 15 10
'WBP1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.111 (Fisher's exact test), Q value = 0.48

Table S192.  Gene #64: 'WBP1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
WBP1 MUTATED 4 0 0 0 2 0 0
WBP1 WILD-TYPE 30 11 9 7 4 20 9
'SAFB2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 0.63

Table S193.  Gene #65: 'SAFB2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SAFB2 MUTATED 3 0 2 3 1
SAFB2 WILD-TYPE 25 20 9 17 20
'SAFB2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.528 (Fisher's exact test), Q value = 0.76

Table S194.  Gene #65: 'SAFB2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SAFB2 MUTATED 4 1 2 1
SAFB2 WILD-TYPE 31 32 14 11
'SAFB2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.486 (Fisher's exact test), Q value = 0.75

Table S195.  Gene #65: 'SAFB2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SAFB2 MUTATED 5 0 0 1 1 1 0
SAFB2 WILD-TYPE 29 11 9 6 5 19 9
'XYLT2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.605 (Fisher's exact test), Q value = 0.81

Table S196.  Gene #66: 'XYLT2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
XYLT2 MUTATED 3 1 0 1 0
XYLT2 WILD-TYPE 25 19 11 19 21
'XYLT2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.00434 (Fisher's exact test), Q value = 0.32

Table S197.  Gene #66: 'XYLT2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
XYLT2 MUTATED 1 0 4 0
XYLT2 WILD-TYPE 34 33 12 12

Figure S39.  Get High-res Image Gene #66: 'XYLT2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'XYLT2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.181 (Fisher's exact test), Q value = 0.56

Table S198.  Gene #66: 'XYLT2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
XYLT2 MUTATED 3 0 0 2 0 0 0
XYLT2 WILD-TYPE 31 11 9 5 6 20 9
'LRPPRC MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.668 (Fisher's exact test), Q value = 0.85

Table S199.  Gene #67: 'LRPPRC MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
LRPPRC MUTATED 3 4 1 2 1
LRPPRC WILD-TYPE 25 16 10 18 20
'LRPPRC MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.206 (Fisher's exact test), Q value = 0.58

Table S200.  Gene #67: 'LRPPRC MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
LRPPRC MUTATED 3 3 4 0
LRPPRC WILD-TYPE 32 30 12 12
'LRPPRC MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.193 (Fisher's exact test), Q value = 0.56

Table S201.  Gene #67: 'LRPPRC MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
LRPPRC MUTATED 4 1 0 3 0 1 1
LRPPRC WILD-TYPE 30 10 9 4 6 19 8
'SLC12A7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.892 (Fisher's exact test), Q value = 0.97

Table S202.  Gene #68: 'SLC12A7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SLC12A7 MUTATED 1 1 0 2 1
SLC12A7 WILD-TYPE 27 19 11 18 20
'SLC12A7 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.162 (Fisher's exact test), Q value = 0.56

Table S203.  Gene #68: 'SLC12A7 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SLC12A7 MUTATED 3 0 2 0
SLC12A7 WILD-TYPE 32 33 14 12
'SLC12A7 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.181 (Fisher's exact test), Q value = 0.56

Table S204.  Gene #68: 'SLC12A7 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SLC12A7 MUTATED 3 0 0 2 0 0 0
SLC12A7 WILD-TYPE 31 11 9 5 6 20 9
'ZFR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.326 (Fisher's exact test), Q value = 0.66

Table S205.  Gene #69: 'ZFR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ZFR MUTATED 3 0 0 1 0
ZFR WILD-TYPE 25 20 11 19 21
'ZFR MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.354 (Fisher's exact test), Q value = 0.68

Table S206.  Gene #69: 'ZFR MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ZFR MUTATED 2 0 1 1
ZFR WILD-TYPE 33 33 15 11
'ZFR MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.31 (Fisher's exact test), Q value = 0.65

Table S207.  Gene #69: 'ZFR MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ZFR MUTATED 2 0 0 1 1 0 0
ZFR WILD-TYPE 32 11 9 6 5 20 9
'SYNJ2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.886 (Fisher's exact test), Q value = 0.96

Table S208.  Gene #70: 'SYNJ2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SYNJ2 MUTATED 3 1 0 2 2
SYNJ2 WILD-TYPE 25 19 11 18 19
'SYNJ2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0756 (Fisher's exact test), Q value = 0.47

Table S209.  Gene #70: 'SYNJ2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SYNJ2 MUTATED 4 0 2 2
SYNJ2 WILD-TYPE 31 33 14 10
'SYNJ2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0795 (Fisher's exact test), Q value = 0.47

Table S210.  Gene #70: 'SYNJ2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SYNJ2 MUTATED 5 0 0 1 2 0 0
SYNJ2 WILD-TYPE 29 11 9 6 4 20 9
'RALGAPB MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.667 (Fisher's exact test), Q value = 0.85

Table S211.  Gene #71: 'RALGAPB MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
RALGAPB MUTATED 3 1 1 0 1
RALGAPB WILD-TYPE 25 19 10 20 20
'RALGAPB MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.186 (Fisher's exact test), Q value = 0.56

Table S212.  Gene #71: 'RALGAPB MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
RALGAPB MUTATED 2 0 2 1
RALGAPB WILD-TYPE 33 33 14 11
'RALGAPB MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.299 (Fisher's exact test), Q value = 0.65

Table S213.  Gene #71: 'RALGAPB MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
RALGAPB MUTATED 3 0 0 1 1 0 0
RALGAPB WILD-TYPE 31 11 9 6 5 20 9
'TCEB3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.571 (Fisher's exact test), Q value = 0.78

Table S214.  Gene #72: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TCEB3 MUTATED 1 3 0 1 2
TCEB3 WILD-TYPE 27 17 11 19 19
'TCEB3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.288 (Fisher's exact test), Q value = 0.64

Table S215.  Gene #72: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TCEB3 MUTATED 5 1 1 0
TCEB3 WILD-TYPE 30 32 15 12
'TCEB3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.219 (Fisher's exact test), Q value = 0.58

Table S216.  Gene #72: 'TCEB3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TCEB3 MUTATED 6 0 0 0 0 0 1
TCEB3 WILD-TYPE 28 11 9 7 6 20 8
'QSOX1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.292 (Fisher's exact test), Q value = 0.64

Table S217.  Gene #73: 'QSOX1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
QSOX1 MUTATED 1 3 0 0 1
QSOX1 WILD-TYPE 27 17 11 20 20
'QSOX1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.736 (Fisher's exact test), Q value = 0.89

Table S218.  Gene #73: 'QSOX1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
QSOX1 MUTATED 3 1 1 0
QSOX1 WILD-TYPE 32 32 15 12
'QSOX1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.474 (Fisher's exact test), Q value = 0.75

Table S219.  Gene #73: 'QSOX1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
QSOX1 MUTATED 2 1 0 1 0 0 1
QSOX1 WILD-TYPE 32 10 9 6 6 20 8
'MFRP MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.593 (Fisher's exact test), Q value = 0.8

Table S220.  Gene #74: 'MFRP MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
MFRP MUTATED 1 1 1 0 2
MFRP WILD-TYPE 27 19 10 20 19
'MFRP MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.364 (Fisher's exact test), Q value = 0.68

Table S221.  Gene #74: 'MFRP MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
MFRP MUTATED 4 1 0 0
MFRP WILD-TYPE 31 32 16 12
'MFRP MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.536 (Fisher's exact test), Q value = 0.77

Table S222.  Gene #74: 'MFRP MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
MFRP MUTATED 4 0 0 0 0 0 1
MFRP WILD-TYPE 30 11 9 7 6 20 8
'CCDC28A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.401 (Fisher's exact test), Q value = 0.69

Table S223.  Gene #75: 'CCDC28A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CCDC28A MUTATED 2 0 0 0 2
CCDC28A WILD-TYPE 26 20 11 20 19
'CCDC28A MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 0.56

Table S224.  Gene #75: 'CCDC28A MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CCDC28A MUTATED 2 0 2 0
CCDC28A WILD-TYPE 33 33 14 12
'CCDC28A MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.576 (Fisher's exact test), Q value = 0.78

Table S225.  Gene #75: 'CCDC28A MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CCDC28A MUTATED 4 0 0 0 0 0 0
CCDC28A WILD-TYPE 30 11 9 7 6 20 9
'FGFR2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 0.75

Table S226.  Gene #76: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
FGFR2 MUTATED 3 3 1 1 5
FGFR2 WILD-TYPE 25 17 10 19 16
'FGFR2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.157 (Fisher's exact test), Q value = 0.56

Table S227.  Gene #76: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
FGFR2 MUTATED 7 2 1 3
FGFR2 WILD-TYPE 28 31 15 9
'FGFR2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.32 (Fisher's exact test), Q value = 0.65

Table S228.  Gene #76: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
FGFR2 MUTATED 6 0 1 1 2 1 2
FGFR2 WILD-TYPE 28 11 8 6 4 19 7
'ZMIZ1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.241 (Fisher's exact test), Q value = 0.62

Table S229.  Gene #77: 'ZMIZ1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ZMIZ1 MUTATED 0 1 1 2 3
ZMIZ1 WILD-TYPE 28 19 10 18 18
'ZMIZ1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 0.84

Table S230.  Gene #77: 'ZMIZ1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ZMIZ1 MUTATED 4 1 1 1
ZMIZ1 WILD-TYPE 31 32 15 11
'ZMIZ1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.277 (Fisher's exact test), Q value = 0.63

Table S231.  Gene #77: 'ZMIZ1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ZMIZ1 MUTATED 5 0 0 0 1 0 1
ZMIZ1 WILD-TYPE 29 11 9 7 5 20 8
'ARHGAP35 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.455 (Fisher's exact test), Q value = 0.73

Table S232.  Gene #78: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ARHGAP35 MUTATED 2 4 1 1 4
ARHGAP35 WILD-TYPE 26 16 10 19 17
'ARHGAP35 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 0.68

Table S233.  Gene #78: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ARHGAP35 MUTATED 5 5 0 2
ARHGAP35 WILD-TYPE 30 28 16 10
'ARHGAP35 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.477 (Fisher's exact test), Q value = 0.75

Table S234.  Gene #78: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ARHGAP35 MUTATED 3 2 1 0 2 2 2
ARHGAP35 WILD-TYPE 31 9 8 7 4 18 7
'TFE3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.202 (Fisher's exact test), Q value = 0.57

Table S235.  Gene #79: 'TFE3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TFE3 MUTATED 0 1 1 2 0
TFE3 WILD-TYPE 28 19 10 18 21
'TFE3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.122 (Fisher's exact test), Q value = 0.49

Table S236.  Gene #79: 'TFE3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TFE3 MUTATED 4 0 0 0
TFE3 WILD-TYPE 31 33 16 12
'TFE3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.573 (Fisher's exact test), Q value = 0.78

Table S237.  Gene #79: 'TFE3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TFE3 MUTATED 4 0 0 0 0 0 0
TFE3 WILD-TYPE 30 11 9 7 6 20 9
'SIPA1L1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.892 (Fisher's exact test), Q value = 0.97

Table S238.  Gene #80: 'SIPA1L1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SIPA1L1 MUTATED 3 2 1 3 4
SIPA1L1 WILD-TYPE 25 18 10 17 17
'SIPA1L1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 0.48

Table S239.  Gene #80: 'SIPA1L1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SIPA1L1 MUTATED 7 1 3 2
SIPA1L1 WILD-TYPE 28 32 13 10
'SIPA1L1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0765 (Fisher's exact test), Q value = 0.47

Table S240.  Gene #80: 'SIPA1L1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SIPA1L1 MUTATED 7 1 0 2 2 0 1
SIPA1L1 WILD-TYPE 27 10 9 5 4 20 8
'EIF2B3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.848 (Fisher's exact test), Q value = 0.94

Table S241.  Gene #81: 'EIF2B3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
EIF2B3 MUTATED 1 1 1 2 1
EIF2B3 WILD-TYPE 27 19 10 18 20
'EIF2B3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.569 (Fisher's exact test), Q value = 0.78

Table S242.  Gene #81: 'EIF2B3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
EIF2B3 MUTATED 2 1 2 1
EIF2B3 WILD-TYPE 33 32 14 11
'EIF2B3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.211 (Fisher's exact test), Q value = 0.58

Table S243.  Gene #81: 'EIF2B3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
EIF2B3 MUTATED 2 0 0 2 1 1 0
EIF2B3 WILD-TYPE 32 11 9 5 5 19 9
'NBEAL1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.426 (Fisher's exact test), Q value = 0.71

Table S244.  Gene #82: 'NBEAL1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
NBEAL1 MUTATED 3 2 2 0 2
NBEAL1 WILD-TYPE 25 18 9 20 19
'NBEAL1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 0.68

Table S245.  Gene #82: 'NBEAL1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
NBEAL1 MUTATED 4 1 2 2
NBEAL1 WILD-TYPE 31 32 14 10
'NBEAL1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.116 (Fisher's exact test), Q value = 0.48

Table S246.  Gene #82: 'NBEAL1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
NBEAL1 MUTATED 4 0 0 2 2 1 0
NBEAL1 WILD-TYPE 30 11 9 5 4 19 9
'HPS1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.515 (Fisher's exact test), Q value = 0.76

Table S247.  Gene #83: 'HPS1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
HPS1 MUTATED 1 1 2 1 1
HPS1 WILD-TYPE 27 19 9 19 20
'HPS1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.166 (Fisher's exact test), Q value = 0.56

Table S248.  Gene #83: 'HPS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
HPS1 MUTATED 3 0 2 1
HPS1 WILD-TYPE 32 33 14 11
'HPS1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 0.63

Table S249.  Gene #83: 'HPS1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
HPS1 MUTATED 4 0 0 1 1 0 0
HPS1 WILD-TYPE 30 11 9 6 5 20 9
'DOCK3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.676 (Fisher's exact test), Q value = 0.85

Table S250.  Gene #84: 'DOCK3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
DOCK3 MUTATED 5 5 3 4 2
DOCK3 WILD-TYPE 23 15 8 16 19
'DOCK3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 0.64

Table S251.  Gene #84: 'DOCK3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DOCK3 MUTATED 9 3 4 2
DOCK3 WILD-TYPE 26 30 12 10
'DOCK3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 0.53

Table S252.  Gene #84: 'DOCK3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DOCK3 MUTATED 9 0 1 3 2 2 1
DOCK3 WILD-TYPE 25 11 8 4 4 18 8
'SLC16A4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0648 (Fisher's exact test), Q value = 0.45

Table S253.  Gene #85: 'SLC16A4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SLC16A4 MUTATED 0 1 2 0 1
SLC16A4 WILD-TYPE 28 19 9 20 20
'SLC16A4 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.232 (Fisher's exact test), Q value = 0.6

Table S254.  Gene #85: 'SLC16A4 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SLC16A4 MUTATED 3 0 0 1
SLC16A4 WILD-TYPE 32 33 16 11
'SLC16A4 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.402 (Fisher's exact test), Q value = 0.69

Table S255.  Gene #85: 'SLC16A4 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SLC16A4 MUTATED 3 0 0 0 1 0 0
SLC16A4 WILD-TYPE 31 11 9 7 5 20 9
'DYNC1LI1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.939 (Fisher's exact test), Q value = 0.99

Table S256.  Gene #86: 'DYNC1LI1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
DYNC1LI1 MUTATED 2 0 0 1 1
DYNC1LI1 WILD-TYPE 26 20 11 19 20
'DYNC1LI1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0676 (Fisher's exact test), Q value = 0.45

Table S257.  Gene #86: 'DYNC1LI1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DYNC1LI1 MUTATED 2 0 0 2
DYNC1LI1 WILD-TYPE 33 33 16 10
'DYNC1LI1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.105 (Fisher's exact test), Q value = 0.48

Table S258.  Gene #86: 'DYNC1LI1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DYNC1LI1 MUTATED 2 0 0 0 2 0 0
DYNC1LI1 WILD-TYPE 32 11 9 7 4 20 9
'CHD9 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.407 (Fisher's exact test), Q value = 0.69

Table S259.  Gene #87: 'CHD9 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CHD9 MUTATED 4 3 1 0 3
CHD9 WILD-TYPE 24 17 10 20 18
'CHD9 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 0.57

Table S260.  Gene #87: 'CHD9 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CHD9 MUTATED 6 1 2 2
CHD9 WILD-TYPE 29 32 14 10
'CHD9 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0613 (Fisher's exact test), Q value = 0.45

Table S261.  Gene #87: 'CHD9 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CHD9 MUTATED 7 0 0 1 2 0 1
CHD9 WILD-TYPE 27 11 9 6 4 20 8
'RPE65 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.64 (Fisher's exact test), Q value = 0.84

Table S262.  Gene #88: 'RPE65 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
RPE65 MUTATED 1 3 1 1 1
RPE65 WILD-TYPE 27 17 10 19 20
'RPE65 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.42

Table S263.  Gene #88: 'RPE65 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
RPE65 MUTATED 4 0 3 0
RPE65 WILD-TYPE 31 33 13 12

Figure S40.  Get High-res Image Gene #88: 'RPE65 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'RPE65 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.113 (Fisher's exact test), Q value = 0.48

Table S264.  Gene #88: 'RPE65 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
RPE65 MUTATED 5 0 0 2 0 0 0
RPE65 WILD-TYPE 29 11 9 5 6 20 9
'C1QTNF5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.328 (Fisher's exact test), Q value = 0.66

Table S265.  Gene #89: 'C1QTNF5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
C1QTNF5 MUTATED 3 0 0 1 0
C1QTNF5 WILD-TYPE 25 20 11 19 21
'C1QTNF5 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.124 (Fisher's exact test), Q value = 0.5

Table S266.  Gene #89: 'C1QTNF5 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
C1QTNF5 MUTATED 4 0 0 0
C1QTNF5 WILD-TYPE 31 33 16 12
'C1QTNF5 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.576 (Fisher's exact test), Q value = 0.78

Table S267.  Gene #89: 'C1QTNF5 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
C1QTNF5 MUTATED 4 0 0 0 0 0 0
C1QTNF5 WILD-TYPE 30 11 9 7 6 20 9
'LANCL1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.832 (Fisher's exact test), Q value = 0.94

Table S268.  Gene #90: 'LANCL1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
LANCL1 MUTATED 2 0 1 1 1
LANCL1 WILD-TYPE 26 20 10 19 20
'LANCL1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.737 (Fisher's exact test), Q value = 0.89

Table S269.  Gene #90: 'LANCL1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
LANCL1 MUTATED 3 2 0 0
LANCL1 WILD-TYPE 32 31 16 12
'LANCL1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

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

Table S270.  Gene #90: 'LANCL1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
LANCL1 MUTATED 3 1 0 0 0 1 0
LANCL1 WILD-TYPE 31 10 9 7 6 19 9
'TMEM60 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.435 (Fisher's exact test), Q value = 0.72

Table S271.  Gene #91: 'TMEM60 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TMEM60 MUTATED 0 2 1 1 1
TMEM60 WILD-TYPE 28 18 10 19 20
'TMEM60 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.918 (Fisher's exact test), Q value = 0.98

Table S272.  Gene #91: 'TMEM60 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TMEM60 MUTATED 2 1 1 1
TMEM60 WILD-TYPE 33 32 15 11
'TMEM60 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0679 (Fisher's exact test), Q value = 0.45

Table S273.  Gene #91: 'TMEM60 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TMEM60 MUTATED 1 0 0 1 1 0 2
TMEM60 WILD-TYPE 33 11 9 6 5 20 7
'SLC30A8 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.924 (Fisher's exact test), Q value = 0.98

Table S274.  Gene #92: 'SLC30A8 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SLC30A8 MUTATED 1 1 0 1 2
SLC30A8 WILD-TYPE 27 19 11 19 19
'SLC30A8 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.39

Table S275.  Gene #92: 'SLC30A8 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SLC30A8 MUTATED 2 0 0 3
SLC30A8 WILD-TYPE 33 33 16 9

Figure S41.  Get High-res Image Gene #92: 'SLC30A8 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'SLC30A8 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00996 (Fisher's exact test), Q value = 0.39

Table S276.  Gene #92: 'SLC30A8 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SLC30A8 MUTATED 2 0 0 0 3 0 0
SLC30A8 WILD-TYPE 32 11 9 7 3 20 9

Figure S42.  Get High-res Image Gene #92: 'SLC30A8 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'U2AF1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.492 (Fisher's exact test), Q value = 0.75

Table S277.  Gene #93: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
U2AF1 MUTATED 1 0 0 2 2
U2AF1 WILD-TYPE 27 20 11 18 19
'U2AF1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.188 (Fisher's exact test), Q value = 0.56

Table S278.  Gene #93: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
U2AF1 MUTATED 2 0 2 1
U2AF1 WILD-TYPE 33 33 14 11
'U2AF1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.456 (Fisher's exact test), Q value = 0.73

Table S279.  Gene #93: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
U2AF1 MUTATED 3 0 1 1 0 0 0
U2AF1 WILD-TYPE 31 11 8 6 6 20 9
'AP1S1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.393 (Fisher's exact test), Q value = 0.69

Table S280.  Gene #94: 'AP1S1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
AP1S1 MUTATED 2 3 0 1 0
AP1S1 WILD-TYPE 26 17 11 19 21
'AP1S1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0437 (Fisher's exact test), Q value = 0.42

Table S281.  Gene #94: 'AP1S1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AP1S1 MUTATED 3 0 3 0
AP1S1 WILD-TYPE 32 33 13 12

Figure S43.  Get High-res Image Gene #94: 'AP1S1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'AP1S1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.149 (Fisher's exact test), Q value = 0.54

Table S282.  Gene #94: 'AP1S1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AP1S1 MUTATED 4 0 0 2 0 0 0
AP1S1 WILD-TYPE 30 11 9 5 6 20 9
'TP53BP2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.769 (Fisher's exact test), Q value = 0.91

Table S283.  Gene #95: 'TP53BP2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TP53BP2 MUTATED 2 3 0 1 2
TP53BP2 WILD-TYPE 26 17 11 19 19
'TP53BP2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0465 (Fisher's exact test), Q value = 0.42

Table S284.  Gene #95: 'TP53BP2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TP53BP2 MUTATED 6 0 1 1
TP53BP2 WILD-TYPE 29 33 15 11

Figure S44.  Get High-res Image Gene #95: 'TP53BP2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'TP53BP2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 0.53

Table S285.  Gene #95: 'TP53BP2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TP53BP2 MUTATED 6 0 0 1 1 0 0
TP53BP2 WILD-TYPE 28 11 9 6 5 20 9
'ZMYM2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.167 (Fisher's exact test), Q value = 0.56

Table S286.  Gene #96: 'ZMYM2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ZMYM2 MUTATED 1 3 2 1 5
ZMYM2 WILD-TYPE 27 17 9 19 16
'ZMYM2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.489 (Fisher's exact test), Q value = 0.75

Table S287.  Gene #96: 'ZMYM2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ZMYM2 MUTATED 5 2 3 2
ZMYM2 WILD-TYPE 30 31 13 10
'ZMYM2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.155 (Fisher's exact test), Q value = 0.55

Table S288.  Gene #96: 'ZMYM2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ZMYM2 MUTATED 6 0 0 2 2 1 1
ZMYM2 WILD-TYPE 28 11 9 5 4 19 8
'BRD3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.81 (Fisher's exact test), Q value = 0.93

Table S289.  Gene #97: 'BRD3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
BRD3 MUTATED 1 2 0 1 2
BRD3 WILD-TYPE 27 18 11 19 19
'BRD3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0903 (Fisher's exact test), Q value = 0.47

Table S290.  Gene #97: 'BRD3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
BRD3 MUTATED 5 0 1 0
BRD3 WILD-TYPE 30 33 15 12
'BRD3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.277 (Fisher's exact test), Q value = 0.63

Table S291.  Gene #97: 'BRD3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
BRD3 MUTATED 5 0 0 1 0 0 0
BRD3 WILD-TYPE 29 11 9 6 6 20 9
'C6ORF89 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.957 (Fisher's exact test), Q value = 1

Table S292.  Gene #98: 'C6ORF89 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
C6ORF89 MUTATED 1 1 1 1 1
C6ORF89 WILD-TYPE 27 19 10 19 20
'C6ORF89 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.246 (Fisher's exact test), Q value = 0.63

Table S293.  Gene #98: 'C6ORF89 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
C6ORF89 MUTATED 1 1 1 2
C6ORF89 WILD-TYPE 34 32 15 10
'C6ORF89 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0987 (Fisher's exact test), Q value = 0.48

Table S294.  Gene #98: 'C6ORF89 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
C6ORF89 MUTATED 1 0 0 1 2 1 0
C6ORF89 WILD-TYPE 33 11 9 6 4 19 9
'STAMBPL1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.506 (Fisher's exact test), Q value = 0.75

Table S295.  Gene #99: 'STAMBPL1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
STAMBPL1 MUTATED 3 2 0 1 0
STAMBPL1 WILD-TYPE 25 18 11 19 21
'STAMBPL1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.935 (Fisher's exact test), Q value = 0.99

Table S296.  Gene #99: 'STAMBPL1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
STAMBPL1 MUTATED 3 2 1 0
STAMBPL1 WILD-TYPE 32 31 15 12
'STAMBPL1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.794 (Fisher's exact test), Q value = 0.92

Table S297.  Gene #99: 'STAMBPL1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
STAMBPL1 MUTATED 3 0 0 1 0 1 1
STAMBPL1 WILD-TYPE 31 11 9 6 6 19 8
'NES MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S298.  Gene #100: 'NES MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
NES MUTATED 3 3 1 2 3
NES WILD-TYPE 25 17 10 18 18
'NES MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.124 (Fisher's exact test), Q value = 0.5

Table S299.  Gene #100: 'NES MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
NES MUTATED 7 1 3 1
NES WILD-TYPE 28 32 13 11
'NES MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0564 (Fisher's exact test), Q value = 0.43

Table S300.  Gene #100: 'NES MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
NES MUTATED 7 0 0 2 1 0 2
NES WILD-TYPE 27 11 9 5 5 20 7
'MBD6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.436 (Fisher's exact test), Q value = 0.72

Table S301.  Gene #101: 'MBD6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
MBD6 MUTATED 2 0 2 2 2
MBD6 WILD-TYPE 26 20 9 18 19
'MBD6 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0646 (Fisher's exact test), Q value = 0.45

Table S302.  Gene #101: 'MBD6 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
MBD6 MUTATED 4 1 0 3
MBD6 WILD-TYPE 31 32 16 9
'MBD6 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.212 (Fisher's exact test), Q value = 0.58

Table S303.  Gene #101: 'MBD6 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
MBD6 MUTATED 5 0 0 0 2 1 0
MBD6 WILD-TYPE 29 11 9 7 4 19 9
'SHC1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.798 (Fisher's exact test), Q value = 0.92

Table S304.  Gene #102: 'SHC1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SHC1 MUTATED 2 2 0 3 2
SHC1 WILD-TYPE 26 18 11 17 19
'SHC1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.351 (Fisher's exact test), Q value = 0.68

Table S305.  Gene #102: 'SHC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SHC1 MUTATED 4 1 2 2
SHC1 WILD-TYPE 31 32 14 10
'SHC1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.222 (Fisher's exact test), Q value = 0.58

Table S306.  Gene #102: 'SHC1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SHC1 MUTATED 5 0 0 1 2 1 0
SHC1 WILD-TYPE 29 11 9 6 4 19 9
'PEX1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.204 (Fisher's exact test), Q value = 0.57

Table S307.  Gene #103: 'PEX1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PEX1 MUTATED 0 3 1 1 1
PEX1 WILD-TYPE 28 17 10 19 20
'PEX1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.538 (Fisher's exact test), Q value = 0.77

Table S308.  Gene #103: 'PEX1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PEX1 MUTATED 4 1 1 0
PEX1 WILD-TYPE 31 32 15 12
'PEX1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.797 (Fisher's exact test), Q value = 0.92

Table S309.  Gene #103: 'PEX1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PEX1 MUTATED 3 0 0 1 0 1 1
PEX1 WILD-TYPE 31 11 9 6 6 19 8
'MCPH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S310.  Gene #104: 'MCPH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
MCPH1 MUTATED 2 1 0 1 2
MCPH1 WILD-TYPE 26 19 11 19 19
'MCPH1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.166 (Fisher's exact test), Q value = 0.56

Table S311.  Gene #104: 'MCPH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
MCPH1 MUTATED 3 0 2 1
MCPH1 WILD-TYPE 32 33 14 11
'MCPH1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.247 (Fisher's exact test), Q value = 0.63

Table S312.  Gene #104: 'MCPH1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
MCPH1 MUTATED 5 0 0 0 1 0 0
MCPH1 WILD-TYPE 29 11 9 7 5 20 9
'TTLL11 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.383 (Fisher's exact test), Q value = 0.68

Table S313.  Gene #105: 'TTLL11 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TTLL11 MUTATED 2 4 0 1 1
TTLL11 WILD-TYPE 26 16 11 19 20
'TTLL11 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.554 (Fisher's exact test), Q value = 0.77

Table S314.  Gene #105: 'TTLL11 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TTLL11 MUTATED 5 2 1 0
TTLL11 WILD-TYPE 30 31 15 12
'TTLL11 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.689 (Fisher's exact test), Q value = 0.86

Table S315.  Gene #105: 'TTLL11 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TTLL11 MUTATED 5 0 0 1 0 2 0
TTLL11 WILD-TYPE 29 11 9 6 6 18 9
'ZNF800 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.837 (Fisher's exact test), Q value = 0.94

Table S316.  Gene #106: 'ZNF800 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ZNF800 MUTATED 2 3 2 2 2
ZNF800 WILD-TYPE 26 17 9 18 19
'ZNF800 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.00367 (Fisher's exact test), Q value = 0.32

Table S317.  Gene #106: 'ZNF800 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ZNF800 MUTATED 7 0 4 0
ZNF800 WILD-TYPE 28 33 12 12

Figure S45.  Get High-res Image Gene #106: 'ZNF800 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'ZNF800 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0212 (Fisher's exact test), Q value = 0.4

Table S318.  Gene #106: 'ZNF800 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ZNF800 MUTATED 7 0 0 3 0 0 1
ZNF800 WILD-TYPE 27 11 9 4 6 20 8

Figure S46.  Get High-res Image Gene #106: 'ZNF800 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'HNF1A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.487 (Fisher's exact test), Q value = 0.75

Table S319.  Gene #107: 'HNF1A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
HNF1A MUTATED 2 0 1 1 3
HNF1A WILD-TYPE 26 20 10 19 18
'HNF1A MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 0.48

Table S320.  Gene #107: 'HNF1A MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
HNF1A MUTATED 3 0 1 2
HNF1A WILD-TYPE 32 33 15 10
'HNF1A MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0973 (Fisher's exact test), Q value = 0.48

Table S321.  Gene #107: 'HNF1A MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
HNF1A MUTATED 3 0 0 1 2 0 0
HNF1A WILD-TYPE 31 11 9 6 4 20 9
'PAPD4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.48 (Fisher's exact test), Q value = 0.75

Table S322.  Gene #108: 'PAPD4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PAPD4 MUTATED 1 2 1 0 2
PAPD4 WILD-TYPE 27 18 10 20 19
'PAPD4 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.821 (Fisher's exact test), Q value = 0.93

Table S323.  Gene #108: 'PAPD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PAPD4 MUTATED 3 1 1 1
PAPD4 WILD-TYPE 32 32 15 11
'PAPD4 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.605 (Fisher's exact test), Q value = 0.81

Table S324.  Gene #108: 'PAPD4 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PAPD4 MUTATED 3 0 0 1 1 1 0
PAPD4 WILD-TYPE 31 11 9 6 5 19 9
'NSD1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.764 (Fisher's exact test), Q value = 0.9

Table S325.  Gene #109: 'NSD1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
NSD1 MUTATED 5 5 1 2 3
NSD1 WILD-TYPE 23 15 10 18 18
'NSD1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.42

Table S326.  Gene #109: 'NSD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
NSD1 MUTATED 7 1 5 2
NSD1 WILD-TYPE 28 32 11 10

Figure S47.  Get High-res Image Gene #109: 'NSD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'NSD1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0422 (Fisher's exact test), Q value = 0.42

Table S327.  Gene #109: 'NSD1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
NSD1 MUTATED 8 0 0 3 2 1 1
NSD1 WILD-TYPE 26 11 9 4 4 19 8

Figure S48.  Get High-res Image Gene #109: 'NSD1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'RANBP10 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.101 (Fisher's exact test), Q value = 0.48

Table S328.  Gene #110: 'RANBP10 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
RANBP10 MUTATED 1 1 0 0 4
RANBP10 WILD-TYPE 27 19 11 20 17
'RANBP10 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.45 (Fisher's exact test), Q value = 0.73

Table S329.  Gene #110: 'RANBP10 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
RANBP10 MUTATED 3 1 2 0
RANBP10 WILD-TYPE 32 32 14 12
'RANBP10 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.415 (Fisher's exact test), Q value = 0.69

Table S330.  Gene #110: 'RANBP10 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
RANBP10 MUTATED 4 0 0 1 0 0 1
RANBP10 WILD-TYPE 30 11 9 6 6 20 8
'WNT1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.663 (Fisher's exact test), Q value = 0.85

Table S331.  Gene #111: 'WNT1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
WNT1 MUTATED 1 0 0 2 1
WNT1 WILD-TYPE 27 20 11 18 20
'WNT1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 0.56

Table S332.  Gene #111: 'WNT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
WNT1 MUTATED 2 0 2 0
WNT1 WILD-TYPE 33 33 14 12
'WNT1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.157 (Fisher's exact test), Q value = 0.56

Table S333.  Gene #111: 'WNT1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
WNT1 MUTATED 2 0 0 2 0 0 0
WNT1 WILD-TYPE 32 11 9 5 6 20 9
'IPO11 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.474 (Fisher's exact test), Q value = 0.75

Table S334.  Gene #112: 'IPO11 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
IPO11 MUTATED 2 3 1 0 1
IPO11 WILD-TYPE 26 17 10 20 20
'IPO11 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0421 (Fisher's exact test), Q value = 0.42

Table S335.  Gene #112: 'IPO11 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
IPO11 MUTATED 4 0 3 0
IPO11 WILD-TYPE 31 33 13 12

Figure S49.  Get High-res Image Gene #112: 'IPO11 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'IPO11 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0317 (Fisher's exact test), Q value = 0.42

Table S336.  Gene #112: 'IPO11 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
IPO11 MUTATED 4 0 0 3 0 0 0
IPO11 WILD-TYPE 30 11 9 4 6 20 9

Figure S50.  Get High-res Image Gene #112: 'IPO11 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'FBXL3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.721 (Fisher's exact test), Q value = 0.88

Table S337.  Gene #113: 'FBXL3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
FBXL3 MUTATED 1 1 0 0 2
FBXL3 WILD-TYPE 27 19 11 20 19
'FBXL3 MUTATION STATUS' versus 'METHYLATION_CNMF'

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

Table S338.  Gene #113: 'FBXL3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
FBXL3 MUTATED 2 1 1 0
FBXL3 WILD-TYPE 33 32 15 12
'FBXL3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.963 (Fisher's exact test), Q value = 1

Table S339.  Gene #113: 'FBXL3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
FBXL3 MUTATED 3 0 0 0 0 1 0
FBXL3 WILD-TYPE 31 11 9 7 6 19 9
'LNPEP MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0856 (Fisher's exact test), Q value = 0.47

Table S340.  Gene #114: 'LNPEP MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
LNPEP MUTATED 1 4 0 1 0
LNPEP WILD-TYPE 27 16 11 19 21
'LNPEP MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.541 (Fisher's exact test), Q value = 0.77

Table S341.  Gene #114: 'LNPEP MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
LNPEP MUTATED 4 1 1 0
LNPEP WILD-TYPE 31 32 15 12
'LNPEP MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.454 (Fisher's exact test), Q value = 0.73

Table S342.  Gene #114: 'LNPEP MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
LNPEP MUTATED 3 0 1 1 0 0 1
LNPEP WILD-TYPE 31 11 8 6 6 20 8
'LINGO4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.754 (Fisher's exact test), Q value = 0.9

Table S343.  Gene #115: 'LINGO4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
LINGO4 MUTATED 1 1 1 1 0
LINGO4 WILD-TYPE 27 19 10 19 21
'LINGO4 MUTATION STATUS' versus 'METHYLATION_CNMF'

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

Table S344.  Gene #115: 'LINGO4 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
LINGO4 MUTATED 2 2 0 0
LINGO4 WILD-TYPE 33 31 16 12
'LINGO4 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.897 (Fisher's exact test), Q value = 0.97

Table S345.  Gene #115: 'LINGO4 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
LINGO4 MUTATED 2 0 0 0 0 1 1
LINGO4 WILD-TYPE 32 11 9 7 6 19 8
'CPNE7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S346.  Gene #116: 'CPNE7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CPNE7 MUTATED 2 1 1 1 1
CPNE7 WILD-TYPE 26 19 10 19 20
'CPNE7 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.56

Table S347.  Gene #116: 'CPNE7 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CPNE7 MUTATED 4 0 1 1
CPNE7 WILD-TYPE 31 33 15 11
'CPNE7 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.443 (Fisher's exact test), Q value = 0.72

Table S348.  Gene #116: 'CPNE7 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CPNE7 MUTATED 4 1 0 0 1 0 0
CPNE7 WILD-TYPE 30 10 9 7 5 20 9
'DPCR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S349.  Gene #117: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
DPCR1 MUTATED 3 2 1 2 2
DPCR1 WILD-TYPE 25 18 10 18 19
'DPCR1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.00934 (Fisher's exact test), Q value = 0.39

Table S350.  Gene #117: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DPCR1 MUTATED 7 0 3 0
DPCR1 WILD-TYPE 28 33 13 12

Figure S51.  Get High-res Image Gene #117: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'DPCR1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0521 (Fisher's exact test), Q value = 0.43

Table S351.  Gene #117: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DPCR1 MUTATED 5 0 1 3 0 0 1
DPCR1 WILD-TYPE 29 11 8 4 6 20 8
'SMTN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.455 (Fisher's exact test), Q value = 0.73

Table S352.  Gene #118: 'SMTN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SMTN MUTATED 2 4 0 1 2
SMTN WILD-TYPE 26 16 11 19 19
'SMTN MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.231 (Fisher's exact test), Q value = 0.6

Table S353.  Gene #118: 'SMTN MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SMTN MUTATED 6 1 1 1
SMTN WILD-TYPE 29 32 15 11
'SMTN MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.115 (Fisher's exact test), Q value = 0.48

Table S354.  Gene #118: 'SMTN MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SMTN MUTATED 7 0 0 0 1 0 1
SMTN WILD-TYPE 27 11 9 7 5 20 8
'ATP2A1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.302 (Fisher's exact test), Q value = 0.65

Table S355.  Gene #119: 'ATP2A1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ATP2A1 MUTATED 1 0 0 2 3
ATP2A1 WILD-TYPE 27 20 11 18 18
'ATP2A1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.239 (Fisher's exact test), Q value = 0.62

Table S356.  Gene #119: 'ATP2A1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ATP2A1 MUTATED 3 1 0 2
ATP2A1 WILD-TYPE 32 32 16 10
'ATP2A1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.251 (Fisher's exact test), Q value = 0.63

Table S357.  Gene #119: 'ATP2A1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ATP2A1 MUTATED 3 0 0 0 2 1 0
ATP2A1 WILD-TYPE 31 11 9 7 4 19 9
'PIGO MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.811 (Fisher's exact test), Q value = 0.93

Table S358.  Gene #120: 'PIGO MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PIGO MUTATED 1 2 1 1 2
PIGO WILD-TYPE 27 18 10 19 19
'PIGO MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.406 (Fisher's exact test), Q value = 0.69

Table S359.  Gene #120: 'PIGO MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PIGO MUTATED 3 1 1 2
PIGO WILD-TYPE 32 32 15 10
'PIGO MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.248 (Fisher's exact test), Q value = 0.63

Table S360.  Gene #120: 'PIGO MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PIGO MUTATED 4 0 0 0 2 1 0
PIGO WILD-TYPE 30 11 9 7 4 19 9
'RRAS2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S361.  Gene #121: 'RRAS2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
RRAS2 MUTATED 2 1 0 1 1
RRAS2 WILD-TYPE 26 19 11 19 20
'RRAS2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.403 (Fisher's exact test), Q value = 0.69

Table S362.  Gene #121: 'RRAS2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
RRAS2 MUTATED 1 2 2 0
RRAS2 WILD-TYPE 34 31 14 12
'RRAS2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.679 (Fisher's exact test), Q value = 0.85

Table S363.  Gene #121: 'RRAS2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
RRAS2 MUTATED 2 2 0 0 0 1 0
RRAS2 WILD-TYPE 32 9 9 7 6 19 9
'DRD5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.816 (Fisher's exact test), Q value = 0.93

Table S364.  Gene #122: 'DRD5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
DRD5 MUTATED 2 3 1 1 1
DRD5 WILD-TYPE 26 17 10 19 20
'DRD5 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.672 (Fisher's exact test), Q value = 0.85

Table S365.  Gene #122: 'DRD5 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DRD5 MUTATED 2 3 1 2
DRD5 WILD-TYPE 33 30 15 10
'DRD5 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.411 (Fisher's exact test), Q value = 0.69

Table S366.  Gene #122: 'DRD5 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DRD5 MUTATED 3 1 0 0 2 1 1
DRD5 WILD-TYPE 31 10 9 7 4 19 8
'PRR25 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.258 (Fisher's exact test), Q value = 0.63

Table S367.  Gene #123: 'PRR25 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PRR25 MUTATED 1 3 0 1 0
PRR25 WILD-TYPE 27 17 11 19 21
'PRR25 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.51

Table S368.  Gene #123: 'PRR25 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PRR25 MUTATED 0 3 2 0
PRR25 WILD-TYPE 35 30 14 12
'PRR25 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.229 (Fisher's exact test), Q value = 0.6

Table S369.  Gene #123: 'PRR25 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PRR25 MUTATED 1 0 0 1 0 1 2
PRR25 WILD-TYPE 33 11 9 6 6 19 7
'PAX2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0913 (Fisher's exact test), Q value = 0.47

Table S370.  Gene #124: 'PAX2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PAX2 MUTATED 0 0 0 1 3
PAX2 WILD-TYPE 28 20 11 19 18
'PAX2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.00597 (Fisher's exact test), Q value = 0.32

Table S371.  Gene #124: 'PAX2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PAX2 MUTATED 0 1 0 3
PAX2 WILD-TYPE 35 32 16 9

Figure S52.  Get High-res Image Gene #124: 'PAX2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'PAX2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.127 (Fisher's exact test), Q value = 0.5

Table S372.  Gene #124: 'PAX2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PAX2 MUTATED 1 0 0 0 2 1 0
PAX2 WILD-TYPE 33 11 9 7 4 19 9
'KIF24 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0926 (Fisher's exact test), Q value = 0.47

Table S373.  Gene #125: 'KIF24 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
KIF24 MUTATED 0 0 0 1 3
KIF24 WILD-TYPE 28 20 11 19 18
'KIF24 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.719 (Fisher's exact test), Q value = 0.88

Table S374.  Gene #125: 'KIF24 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
KIF24 MUTATED 2 1 0 1
KIF24 WILD-TYPE 33 32 16 11
'KIF24 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.962 (Fisher's exact test), Q value = 1

Table S375.  Gene #125: 'KIF24 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
KIF24 MUTATED 3 0 0 0 0 1 0
KIF24 WILD-TYPE 31 11 9 7 6 19 9
'NOS3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.486 (Fisher's exact test), Q value = 0.75

Table S376.  Gene #126: 'NOS3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
NOS3 MUTATED 2 1 1 0 3
NOS3 WILD-TYPE 26 19 10 20 18
'NOS3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0411 (Fisher's exact test), Q value = 0.42

Table S377.  Gene #126: 'NOS3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
NOS3 MUTATED 4 0 3 0
NOS3 WILD-TYPE 31 33 13 12

Figure S53.  Get High-res Image Gene #126: 'NOS3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'NOS3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.174 (Fisher's exact test), Q value = 0.56

Table S378.  Gene #126: 'NOS3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
NOS3 MUTATED 6 0 0 1 0 0 0
NOS3 WILD-TYPE 28 11 9 6 6 20 9
'ANAPC1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.055 (Fisher's exact test), Q value = 0.43

Table S379.  Gene #127: 'ANAPC1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ANAPC1 MUTATED 1 0 3 1 1
ANAPC1 WILD-TYPE 27 20 8 19 20
'ANAPC1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 0.48

Table S380.  Gene #127: 'ANAPC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ANAPC1 MUTATED 3 0 1 2
ANAPC1 WILD-TYPE 32 33 15 10
'ANAPC1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 0.63

Table S381.  Gene #127: 'ANAPC1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ANAPC1 MUTATED 4 0 0 1 1 0 0
ANAPC1 WILD-TYPE 30 11 9 6 5 20 9
'DNHD1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.301 (Fisher's exact test), Q value = 0.65

Table S382.  Gene #128: 'DNHD1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
DNHD1 MUTATED 4 5 1 5 1
DNHD1 WILD-TYPE 24 15 10 15 20
'DNHD1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.4

Table S383.  Gene #128: 'DNHD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DNHD1 MUTATED 9 2 5 0
DNHD1 WILD-TYPE 26 31 11 12

Figure S54.  Get High-res Image Gene #128: 'DNHD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'DNHD1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.452 (Fisher's exact test), Q value = 0.73

Table S384.  Gene #128: 'DNHD1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DNHD1 MUTATED 7 1 1 3 0 2 2
DNHD1 WILD-TYPE 27 10 8 4 6 18 7
'IL27 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0019 (Fisher's exact test), Q value = 0.25

Table S385.  Gene #129: 'IL27 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
IL27 MUTATED 0 1 3 0 0
IL27 WILD-TYPE 28 19 8 20 21

Figure S55.  Get High-res Image Gene #129: 'IL27 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'IL27 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.809 (Fisher's exact test), Q value = 0.93

Table S386.  Gene #129: 'IL27 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
IL27 MUTATED 1 2 1 0
IL27 WILD-TYPE 34 31 15 12
'IL27 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.172 (Fisher's exact test), Q value = 0.56

Table S387.  Gene #129: 'IL27 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
IL27 MUTATED 0 0 1 1 0 2 0
IL27 WILD-TYPE 34 11 8 6 6 18 9
'RYR2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.256 (Fisher's exact test), Q value = 0.63

Table S388.  Gene #130: 'RYR2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
RYR2 MUTATED 6 6 3 1 3
RYR2 WILD-TYPE 22 14 8 19 18
'RYR2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.25

Table S389.  Gene #130: 'RYR2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
RYR2 MUTATED 12 0 5 2
RYR2 WILD-TYPE 23 33 11 10

Figure S56.  Get High-res Image Gene #130: 'RYR2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'RYR2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00816 (Fisher's exact test), Q value = 0.39

Table S390.  Gene #130: 'RYR2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
RYR2 MUTATED 11 1 2 3 2 0 0
RYR2 WILD-TYPE 23 10 7 4 4 20 9

Figure S57.  Get High-res Image Gene #130: 'RYR2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'CHPF2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0558 (Fisher's exact test), Q value = 0.43

Table S391.  Gene #131: 'CHPF2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CHPF2 MUTATED 0 4 0 1 3
CHPF2 WILD-TYPE 28 16 11 19 18
'CHPF2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.366 (Fisher's exact test), Q value = 0.68

Table S392.  Gene #131: 'CHPF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CHPF2 MUTATED 4 1 1 2
CHPF2 WILD-TYPE 31 32 15 10
'CHPF2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0641 (Fisher's exact test), Q value = 0.45

Table S393.  Gene #131: 'CHPF2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CHPF2 MUTATED 3 0 0 1 2 0 2
CHPF2 WILD-TYPE 31 11 9 6 4 20 7
'TNK2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.614 (Fisher's exact test), Q value = 0.82

Table S394.  Gene #132: 'TNK2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TNK2 MUTATED 2 1 2 1 3
TNK2 WILD-TYPE 26 19 9 19 18
'TNK2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0271 (Fisher's exact test), Q value = 0.42

Table S395.  Gene #132: 'TNK2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TNK2 MUTATED 2 2 5 0
TNK2 WILD-TYPE 33 31 11 12

Figure S58.  Get High-res Image Gene #132: 'TNK2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'TNK2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.366 (Fisher's exact test), Q value = 0.68

Table S396.  Gene #132: 'TNK2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TNK2 MUTATED 5 0 0 2 0 1 1
TNK2 WILD-TYPE 29 11 9 5 6 19 8
'PPP2R1A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.834 (Fisher's exact test), Q value = 0.94

Table S397.  Gene #133: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PPP2R1A MUTATED 3 2 0 3 2
PPP2R1A WILD-TYPE 25 18 11 17 19
'PPP2R1A MUTATION STATUS' versus 'METHYLATION_CNMF'

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

Table S398.  Gene #133: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PPP2R1A MUTATED 4 4 1 1
PPP2R1A WILD-TYPE 31 29 15 11
'PPP2R1A MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.679 (Fisher's exact test), Q value = 0.85

Table S399.  Gene #133: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PPP2R1A MUTATED 3 1 0 0 1 3 2
PPP2R1A WILD-TYPE 31 10 9 7 5 17 7
'KBTBD10 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.454 (Fisher's exact test), Q value = 0.73

Table S400.  Gene #134: 'KBTBD10 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
KBTBD10 MUTATED 2 1 0 0 3
KBTBD10 WILD-TYPE 26 19 11 20 18
'KBTBD10 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.539 (Fisher's exact test), Q value = 0.77

Table S401.  Gene #134: 'KBTBD10 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
KBTBD10 MUTATED 4 2 0 0
KBTBD10 WILD-TYPE 31 31 16 12
'KBTBD10 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.248 (Fisher's exact test), Q value = 0.63

Table S402.  Gene #134: 'KBTBD10 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
KBTBD10 MUTATED 4 0 0 0 0 0 2
KBTBD10 WILD-TYPE 30 11 9 7 6 20 7
'ERMP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.832 (Fisher's exact test), Q value = 0.94

Table S403.  Gene #135: 'ERMP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ERMP1 MUTATED 2 1 1 0 1
ERMP1 WILD-TYPE 26 19 10 20 20
'ERMP1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.267 (Fisher's exact test), Q value = 0.63

Table S404.  Gene #135: 'ERMP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ERMP1 MUTATED 3 0 1 1
ERMP1 WILD-TYPE 32 33 15 11
'ERMP1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.354 (Fisher's exact test), Q value = 0.68

Table S405.  Gene #135: 'ERMP1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ERMP1 MUTATED 4 0 0 0 1 0 0
ERMP1 WILD-TYPE 30 11 9 7 5 20 9
'DAB2IP MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.24 (Fisher's exact test), Q value = 0.62

Table S406.  Gene #136: 'DAB2IP MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
DAB2IP MUTATED 3 1 0 1 5
DAB2IP WILD-TYPE 25 19 11 19 16
'DAB2IP MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 0.68

Table S407.  Gene #136: 'DAB2IP MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DAB2IP MUTATED 4 1 2 2
DAB2IP WILD-TYPE 31 32 14 10
'DAB2IP MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0731 (Fisher's exact test), Q value = 0.47

Table S408.  Gene #136: 'DAB2IP MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DAB2IP MUTATED 6 0 0 0 2 0 1
DAB2IP WILD-TYPE 28 11 9 7 4 20 8
'BCOR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.836 (Fisher's exact test), Q value = 0.94

Table S409.  Gene #137: 'BCOR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
BCOR MUTATED 2 3 2 2 2
BCOR WILD-TYPE 26 17 9 18 19
'BCOR MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.39

Table S410.  Gene #137: 'BCOR MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
BCOR MUTATED 9 1 0 1
BCOR WILD-TYPE 26 32 16 11

Figure S59.  Get High-res Image Gene #137: 'BCOR MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'BCOR MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0422 (Fisher's exact test), Q value = 0.42

Table S411.  Gene #137: 'BCOR MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
BCOR MUTATED 9 1 0 0 1 0 0
BCOR WILD-TYPE 25 10 9 7 5 20 9

Figure S60.  Get High-res Image Gene #137: 'BCOR MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'C22ORF28 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.492 (Fisher's exact test), Q value = 0.75

Table S412.  Gene #138: 'C22ORF28 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
C22ORF28 MUTATED 1 0 0 2 2
C22ORF28 WILD-TYPE 27 20 11 18 19
'C22ORF28 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.52 (Fisher's exact test), Q value = 0.76

Table S413.  Gene #138: 'C22ORF28 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
C22ORF28 MUTATED 3 1 0 1
C22ORF28 WILD-TYPE 32 32 16 11
'C22ORF28 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.756 (Fisher's exact test), Q value = 0.9

Table S414.  Gene #138: 'C22ORF28 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
C22ORF28 MUTATED 3 0 0 0 1 1 0
C22ORF28 WILD-TYPE 31 11 9 7 5 19 9
'LHX1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.741 (Fisher's exact test), Q value = 0.89

Table S415.  Gene #139: 'LHX1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
LHX1 MUTATED 3 1 0 1 3
LHX1 WILD-TYPE 25 19 11 19 18
'LHX1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 0.68

Table S416.  Gene #139: 'LHX1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
LHX1 MUTATED 4 1 1 2
LHX1 WILD-TYPE 31 32 15 10
'LHX1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.262 (Fisher's exact test), Q value = 0.63

Table S417.  Gene #139: 'LHX1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
LHX1 MUTATED 5 0 0 1 1 0 1
LHX1 WILD-TYPE 29 11 9 6 5 20 8
'USP26 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.452 (Fisher's exact test), Q value = 0.73

Table S418.  Gene #140: 'USP26 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
USP26 MUTATED 2 4 0 1 2
USP26 WILD-TYPE 26 16 11 19 19
'USP26 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.739 (Fisher's exact test), Q value = 0.89

Table S419.  Gene #140: 'USP26 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
USP26 MUTATED 5 2 1 1
USP26 WILD-TYPE 30 31 15 11
'USP26 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.347 (Fisher's exact test), Q value = 0.68

Table S420.  Gene #140: 'USP26 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
USP26 MUTATED 4 1 1 0 1 0 2
USP26 WILD-TYPE 30 10 8 7 5 20 7
'RBM27 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0851 (Fisher's exact test), Q value = 0.47

Table S421.  Gene #141: 'RBM27 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
RBM27 MUTATED 3 5 0 0 3
RBM27 WILD-TYPE 25 15 11 20 18
'RBM27 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.556 (Fisher's exact test), Q value = 0.78

Table S422.  Gene #141: 'RBM27 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
RBM27 MUTATED 5 2 3 1
RBM27 WILD-TYPE 30 31 13 11
'RBM27 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.292 (Fisher's exact test), Q value = 0.64

Table S423.  Gene #141: 'RBM27 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
RBM27 MUTATED 6 0 0 2 1 1 1
RBM27 WILD-TYPE 28 11 9 5 5 19 8
'CCDC43 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.639 (Fisher's exact test), Q value = 0.84

Table S424.  Gene #142: 'CCDC43 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CCDC43 MUTATED 1 1 1 3 1
CCDC43 WILD-TYPE 27 19 10 17 20
'CCDC43 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.55 (Fisher's exact test), Q value = 0.77

Table S425.  Gene #142: 'CCDC43 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CCDC43 MUTATED 3 1 2 1
CCDC43 WILD-TYPE 32 32 14 11
'CCDC43 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.278 (Fisher's exact test), Q value = 0.63

Table S426.  Gene #142: 'CCDC43 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CCDC43 MUTATED 3 0 0 2 1 1 0
CCDC43 WILD-TYPE 31 11 9 5 5 19 9
'LIN54 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.504 (Fisher's exact test), Q value = 0.75

Table S427.  Gene #143: 'LIN54 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
LIN54 MUTATED 0 1 0 1 2
LIN54 WILD-TYPE 28 19 11 19 19
'LIN54 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.319 (Fisher's exact test), Q value = 0.65

Table S428.  Gene #143: 'LIN54 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
LIN54 MUTATED 3 0 1 0
LIN54 WILD-TYPE 32 33 15 12
'LIN54 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.482 (Fisher's exact test), Q value = 0.75

Table S429.  Gene #143: 'LIN54 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
LIN54 MUTATED 3 0 0 1 0 0 0
LIN54 WILD-TYPE 31 11 9 6 6 20 9
'FAM8A1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.315 (Fisher's exact test), Q value = 0.65

Table S430.  Gene #144: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
FAM8A1 MUTATED 1 3 1 0 1
FAM8A1 WILD-TYPE 27 17 10 20 20
'FAM8A1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.569 (Fisher's exact test), Q value = 0.78

Table S431.  Gene #144: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
FAM8A1 MUTATED 2 1 2 1
FAM8A1 WILD-TYPE 33 32 14 11
'FAM8A1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.405 (Fisher's exact test), Q value = 0.69

Table S432.  Gene #144: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
FAM8A1 MUTATED 1 1 1 1 1 1 0
FAM8A1 WILD-TYPE 33 10 8 6 5 19 9
'ZDHHC8 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.255 (Fisher's exact test), Q value = 0.63

Table S433.  Gene #145: 'ZDHHC8 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ZDHHC8 MUTATED 1 1 2 0 2
ZDHHC8 WILD-TYPE 27 19 9 20 19
'ZDHHC8 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.542 (Fisher's exact test), Q value = 0.77

Table S434.  Gene #145: 'ZDHHC8 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ZDHHC8 MUTATED 4 1 1 0
ZDHHC8 WILD-TYPE 31 32 15 12
'ZDHHC8 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.413 (Fisher's exact test), Q value = 0.69

Table S435.  Gene #145: 'ZDHHC8 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ZDHHC8 MUTATED 4 0 0 1 0 0 1
ZDHHC8 WILD-TYPE 30 11 9 6 6 20 8
'PHKG2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0937 (Fisher's exact test), Q value = 0.47

Table S436.  Gene #146: 'PHKG2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PHKG2 MUTATED 0 0 0 1 3
PHKG2 WILD-TYPE 28 20 11 19 18
'PHKG2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0652 (Fisher's exact test), Q value = 0.45

Table S437.  Gene #146: 'PHKG2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PHKG2 MUTATED 2 0 0 2
PHKG2 WILD-TYPE 33 33 16 10
'PHKG2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.105 (Fisher's exact test), Q value = 0.48

Table S438.  Gene #146: 'PHKG2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PHKG2 MUTATED 2 0 0 0 2 0 0
PHKG2 WILD-TYPE 32 11 9 7 4 20 9
'POLE MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.904 (Fisher's exact test), Q value = 0.97

Table S439.  Gene #147: 'POLE MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
POLE MUTATED 2 3 1 1 2
POLE WILD-TYPE 26 17 10 19 19
'POLE MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0821 (Fisher's exact test), Q value = 0.47

Table S440.  Gene #147: 'POLE MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
POLE MUTATED 7 1 1 0
POLE WILD-TYPE 28 32 15 12
'POLE MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.515 (Fisher's exact test), Q value = 0.76

Table S441.  Gene #147: 'POLE MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
POLE MUTATED 6 0 1 1 0 1 0
POLE WILD-TYPE 28 11 8 6 6 19 9
'TCERG1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.568 (Fisher's exact test), Q value = 0.78

Table S442.  Gene #148: 'TCERG1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TCERG1 MUTATED 1 3 1 1 3
TCERG1 WILD-TYPE 27 17 10 19 18
'TCERG1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.00523 (Fisher's exact test), Q value = 0.32

Table S443.  Gene #148: 'TCERG1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TCERG1 MUTATED 3 0 5 1
TCERG1 WILD-TYPE 32 33 11 11

Figure S61.  Get High-res Image Gene #148: 'TCERG1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'TCERG1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0256 (Fisher's exact test), Q value = 0.42

Table S444.  Gene #148: 'TCERG1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TCERG1 MUTATED 5 0 0 3 1 0 0
TCERG1 WILD-TYPE 29 11 9 4 5 20 9

Figure S62.  Get High-res Image Gene #148: 'TCERG1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'TTLL10 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0933 (Fisher's exact test), Q value = 0.47

Table S445.  Gene #149: 'TTLL10 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TTLL10 MUTATED 0 1 0 0 3
TTLL10 WILD-TYPE 28 19 11 20 18
'TTLL10 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.354 (Fisher's exact test), Q value = 0.68

Table S446.  Gene #149: 'TTLL10 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TTLL10 MUTATED 2 0 1 1
TTLL10 WILD-TYPE 33 33 15 11
'TTLL10 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.4 (Fisher's exact test), Q value = 0.69

Table S447.  Gene #149: 'TTLL10 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TTLL10 MUTATED 3 0 0 0 1 0 0
TTLL10 WILD-TYPE 31 11 9 7 5 20 9
'EBPL MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.123 (Fisher's exact test), Q value = 0.49

Table S448.  Gene #150: 'EBPL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
EBPL MUTATED 1 0 0 3 0
EBPL WILD-TYPE 27 20 11 17 21
'EBPL MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.184 (Fisher's exact test), Q value = 0.56

Table S449.  Gene #150: 'EBPL MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
EBPL MUTATED 2 0 2 0
EBPL WILD-TYPE 33 33 14 12
'EBPL MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.483 (Fisher's exact test), Q value = 0.75

Table S450.  Gene #150: 'EBPL MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
EBPL MUTATED 3 0 0 1 0 0 0
EBPL WILD-TYPE 31 11 9 6 6 20 9
'NOSTRIN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.755 (Fisher's exact test), Q value = 0.9

Table S451.  Gene #151: 'NOSTRIN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
NOSTRIN MUTATED 1 1 1 1 0
NOSTRIN WILD-TYPE 27 19 10 19 21
'NOSTRIN MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 0.68

Table S452.  Gene #151: 'NOSTRIN MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
NOSTRIN MUTATED 2 0 0 1
NOSTRIN WILD-TYPE 33 33 16 11
'NOSTRIN MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.285 (Fisher's exact test), Q value = 0.64

Table S453.  Gene #151: 'NOSTRIN MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
NOSTRIN MUTATED 1 0 0 0 1 0 1
NOSTRIN WILD-TYPE 33 11 9 7 5 20 8
'DAZAP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.397 (Fisher's exact test), Q value = 0.69

Table S454.  Gene #152: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
DAZAP1 MUTATED 3 1 0 0 3
DAZAP1 WILD-TYPE 25 19 11 20 18
'DAZAP1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.168 (Fisher's exact test), Q value = 0.56

Table S455.  Gene #152: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DAZAP1 MUTATED 3 0 2 1
DAZAP1 WILD-TYPE 32 33 14 11
'DAZAP1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.274 (Fisher's exact test), Q value = 0.63

Table S456.  Gene #152: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DAZAP1 MUTATED 4 0 0 1 1 0 0
DAZAP1 WILD-TYPE 30 11 9 6 5 20 9
'C6ORF10 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.551 (Fisher's exact test), Q value = 0.77

Table S457.  Gene #153: 'C6ORF10 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
C6ORF10 MUTATED 1 1 1 0 0
C6ORF10 WILD-TYPE 27 19 10 20 21
'C6ORF10 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.864 (Fisher's exact test), Q value = 0.94

Table S458.  Gene #153: 'C6ORF10 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
C6ORF10 MUTATED 1 1 1 0
C6ORF10 WILD-TYPE 34 32 15 12
'C6ORF10 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.367 (Fisher's exact test), Q value = 0.68

Table S459.  Gene #153: 'C6ORF10 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
C6ORF10 MUTATED 1 0 0 1 0 0 1
C6ORF10 WILD-TYPE 33 11 9 6 6 20 8
'C19ORF2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.649 (Fisher's exact test), Q value = 0.84

Table S460.  Gene #154: 'C19ORF2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
C19ORF2 MUTATED 1 2 1 1 3
C19ORF2 WILD-TYPE 27 18 10 19 18
'C19ORF2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0843 (Fisher's exact test), Q value = 0.47

Table S461.  Gene #154: 'C19ORF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
C19ORF2 MUTATED 5 0 2 1
C19ORF2 WILD-TYPE 30 33 14 11
'C19ORF2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.213 (Fisher's exact test), Q value = 0.58

Table S462.  Gene #154: 'C19ORF2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
C19ORF2 MUTATED 6 0 0 1 0 0 1
C19ORF2 WILD-TYPE 28 11 9 6 6 20 8
'HOXA11 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.958 (Fisher's exact test), Q value = 1

Table S463.  Gene #155: 'HOXA11 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
HOXA11 MUTATED 1 1 1 1 1
HOXA11 WILD-TYPE 27 19 10 19 20
'HOXA11 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.352 (Fisher's exact test), Q value = 0.68

Table S464.  Gene #155: 'HOXA11 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
HOXA11 MUTATED 2 0 1 1
HOXA11 WILD-TYPE 33 33 15 11
'HOXA11 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.309 (Fisher's exact test), Q value = 0.65

Table S465.  Gene #155: 'HOXA11 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
HOXA11 MUTATED 2 0 0 1 1 0 0
HOXA11 WILD-TYPE 32 11 9 6 5 20 9
'ZRSR2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.452 (Fisher's exact test), Q value = 0.73

Table S466.  Gene #156: 'ZRSR2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ZRSR2 MUTATED 2 1 0 0 3
ZRSR2 WILD-TYPE 26 19 11 20 18
'ZRSR2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.176 (Fisher's exact test), Q value = 0.56

Table S467.  Gene #156: 'ZRSR2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ZRSR2 MUTATED 4 0 1 1
ZRSR2 WILD-TYPE 31 33 15 11
'ZRSR2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.276 (Fisher's exact test), Q value = 0.63

Table S468.  Gene #156: 'ZRSR2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ZRSR2 MUTATED 4 0 0 1 1 0 0
ZRSR2 WILD-TYPE 30 11 9 6 5 20 9
'NR4A2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.39

Table S469.  Gene #157: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
NR4A2 MUTATED 0 4 0 0 2
NR4A2 WILD-TYPE 28 16 11 20 19

Figure S63.  Get High-res Image Gene #157: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'NR4A2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.819 (Fisher's exact test), Q value = 0.93

Table S470.  Gene #157: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
NR4A2 MUTATED 3 1 1 1
NR4A2 WILD-TYPE 32 32 15 11
'NR4A2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.368 (Fisher's exact test), Q value = 0.68

Table S471.  Gene #157: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
NR4A2 MUTATED 4 0 0 0 1 0 1
NR4A2 WILD-TYPE 30 11 9 7 5 20 8
'COIL MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.406 (Fisher's exact test), Q value = 0.69

Table S472.  Gene #158: 'COIL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
COIL MUTATED 2 0 2 1 1
COIL WILD-TYPE 26 20 9 19 20
'COIL MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.447 (Fisher's exact test), Q value = 0.73

Table S473.  Gene #158: 'COIL MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
COIL MUTATED 3 1 2 0
COIL WILD-TYPE 32 32 14 12
'COIL MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.372 (Fisher's exact test), Q value = 0.68

Table S474.  Gene #158: 'COIL MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
COIL MUTATED 3 0 0 2 0 1 0
COIL WILD-TYPE 31 11 9 5 6 19 9
'CDS1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.957 (Fisher's exact test), Q value = 1

Table S475.  Gene #159: 'CDS1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CDS1 MUTATED 1 1 1 1 1
CDS1 WILD-TYPE 27 19 10 19 20
'CDS1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.266 (Fisher's exact test), Q value = 0.63

Table S476.  Gene #159: 'CDS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CDS1 MUTATED 3 0 1 1
CDS1 WILD-TYPE 32 33 15 11
'CDS1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.297 (Fisher's exact test), Q value = 0.65

Table S477.  Gene #159: 'CDS1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CDS1 MUTATED 3 0 0 1 1 0 0
CDS1 WILD-TYPE 31 11 9 6 5 20 9
'MTMR9 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.278 (Fisher's exact test), Q value = 0.63

Table S478.  Gene #160: 'MTMR9 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
MTMR9 MUTATED 1 2 1 0 0
MTMR9 WILD-TYPE 27 18 10 20 21
'MTMR9 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.257 (Fisher's exact test), Q value = 0.63

Table S479.  Gene #160: 'MTMR9 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
MTMR9 MUTATED 0 3 1 0
MTMR9 WILD-TYPE 35 30 15 12
'MTMR9 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.79 (Fisher's exact test), Q value = 0.92

Table S480.  Gene #160: 'MTMR9 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
MTMR9 MUTATED 1 1 0 0 0 1 1
MTMR9 WILD-TYPE 33 10 9 7 6 19 8
'LRP2BP MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0215 (Fisher's exact test), Q value = 0.4

Table S481.  Gene #161: 'LRP2BP MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
LRP2BP MUTATED 0 4 0 0 1
LRP2BP WILD-TYPE 28 16 11 20 20

Figure S64.  Get High-res Image Gene #161: 'LRP2BP MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'LRP2BP MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.176 (Fisher's exact test), Q value = 0.56

Table S482.  Gene #161: 'LRP2BP MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
LRP2BP MUTATED 4 0 1 0
LRP2BP WILD-TYPE 31 33 15 12
'LRP2BP MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.362 (Fisher's exact test), Q value = 0.68

Table S483.  Gene #161: 'LRP2BP MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
LRP2BP MUTATED 2 0 1 1 0 0 1
LRP2BP WILD-TYPE 32 11 8 6 6 20 8
'REPIN1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.844 (Fisher's exact test), Q value = 0.94

Table S484.  Gene #162: 'REPIN1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
REPIN1 MUTATED 3 2 0 1 1
REPIN1 WILD-TYPE 25 18 11 19 20
'REPIN1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.4

Table S485.  Gene #162: 'REPIN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
REPIN1 MUTATED 6 0 0 1
REPIN1 WILD-TYPE 29 33 16 11

Figure S65.  Get High-res Image Gene #162: 'REPIN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'REPIN1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.389 (Fisher's exact test), Q value = 0.68

Table S486.  Gene #162: 'REPIN1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
REPIN1 MUTATED 5 0 1 0 0 0 1
REPIN1 WILD-TYPE 29 11 8 7 6 20 8
'DHX57 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.333 (Fisher's exact test), Q value = 0.67

Table S487.  Gene #163: 'DHX57 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
DHX57 MUTATED 2 2 3 1 1
DHX57 WILD-TYPE 26 18 8 19 20
'DHX57 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.663 (Fisher's exact test), Q value = 0.85

Table S488.  Gene #163: 'DHX57 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DHX57 MUTATED 5 3 1 0
DHX57 WILD-TYPE 30 30 15 12
'DHX57 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.849 (Fisher's exact test), Q value = 0.94

Table S489.  Gene #163: 'DHX57 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DHX57 MUTATED 5 1 0 1 0 1 1
DHX57 WILD-TYPE 29 10 9 6 6 19 8
'FHOD3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.132 (Fisher's exact test), Q value = 0.51

Table S490.  Gene #164: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
FHOD3 MUTATED 1 3 1 0 4
FHOD3 WILD-TYPE 27 17 10 20 17
'FHOD3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 0.42

Table S491.  Gene #164: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
FHOD3 MUTATED 4 0 3 2
FHOD3 WILD-TYPE 31 33 13 10

Figure S66.  Get High-res Image Gene #164: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'FHOD3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0534 (Fisher's exact test), Q value = 0.43

Table S492.  Gene #164: 'FHOD3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
FHOD3 MUTATED 4 0 1 2 2 0 0
FHOD3 WILD-TYPE 30 11 8 5 4 20 9
'SLC25A24 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0381 (Fisher's exact test), Q value = 0.42

Table S493.  Gene #165: 'SLC25A24 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SLC25A24 MUTATED 0 2 2 1 0
SLC25A24 WILD-TYPE 28 18 9 19 21

Figure S67.  Get High-res Image Gene #165: 'SLC25A24 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'SLC25A24 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.187 (Fisher's exact test), Q value = 0.56

Table S494.  Gene #165: 'SLC25A24 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SLC25A24 MUTATED 2 0 2 1
SLC25A24 WILD-TYPE 33 33 14 11
'SLC25A24 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.298 (Fisher's exact test), Q value = 0.65

Table S495.  Gene #165: 'SLC25A24 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SLC25A24 MUTATED 3 0 0 1 1 0 0
SLC25A24 WILD-TYPE 31 11 9 6 5 20 9
'PPRC1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.442 (Fisher's exact test), Q value = 0.72

Table S496.  Gene #166: 'PPRC1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PPRC1 MUTATED 0 2 0 1 1
PPRC1 WILD-TYPE 28 18 11 19 20
'PPRC1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.653 (Fisher's exact test), Q value = 0.84

Table S497.  Gene #166: 'PPRC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PPRC1 MUTATED 1 1 1 1
PPRC1 WILD-TYPE 34 32 15 11
'PPRC1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.188 (Fisher's exact test), Q value = 0.56

Table S498.  Gene #166: 'PPRC1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PPRC1 MUTATED 1 0 0 1 1 0 1
PPRC1 WILD-TYPE 33 11 9 6 5 20 8
'ZMYM3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.256 (Fisher's exact test), Q value = 0.63

Table S499.  Gene #167: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ZMYM3 MUTATED 2 3 1 0 4
ZMYM3 WILD-TYPE 26 17 10 20 17
'ZMYM3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.104 (Fisher's exact test), Q value = 0.48

Table S500.  Gene #167: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ZMYM3 MUTATED 5 1 1 3
ZMYM3 WILD-TYPE 30 32 15 9
'ZMYM3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0349 (Fisher's exact test), Q value = 0.42

Table S501.  Gene #167: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ZMYM3 MUTATED 4 0 1 1 3 0 1
ZMYM3 WILD-TYPE 30 11 8 6 3 20 8

Figure S68.  Get High-res Image Gene #167: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'C1ORF114 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.64 (Fisher's exact test), Q value = 0.84

Table S502.  Gene #168: 'C1ORF114 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
C1ORF114 MUTATED 1 3 1 1 1
C1ORF114 WILD-TYPE 27 17 10 19 20
'C1ORF114 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.352 (Fisher's exact test), Q value = 0.68

Table S503.  Gene #168: 'C1ORF114 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
C1ORF114 MUTATED 4 1 2 0
C1ORF114 WILD-TYPE 31 32 14 12
'C1ORF114 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.193 (Fisher's exact test), Q value = 0.56

Table S504.  Gene #168: 'C1ORF114 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
C1ORF114 MUTATED 3 0 1 2 0 0 1
C1ORF114 WILD-TYPE 31 11 8 5 6 20 8
'TEX10 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.982 (Fisher's exact test), Q value = 1

Table S505.  Gene #169: 'TEX10 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TEX10 MUTATED 3 2 1 1 2
TEX10 WILD-TYPE 25 18 10 19 19
'TEX10 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.4

Table S506.  Gene #169: 'TEX10 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TEX10 MUTATED 6 0 3 0
TEX10 WILD-TYPE 29 33 13 12

Figure S69.  Get High-res Image Gene #169: 'TEX10 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'TEX10 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.019 (Fisher's exact test), Q value = 0.4

Table S507.  Gene #169: 'TEX10 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TEX10 MUTATED 6 0 0 3 0 0 0
TEX10 WILD-TYPE 28 11 9 4 6 20 9

Figure S70.  Get High-res Image Gene #169: 'TEX10 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'WAC MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.351 (Fisher's exact test), Q value = 0.68

Table S508.  Gene #170: 'WAC MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
WAC MUTATED 1 1 1 0 3
WAC WILD-TYPE 27 19 10 20 18
'WAC MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.111 (Fisher's exact test), Q value = 0.48

Table S509.  Gene #170: 'WAC MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
WAC MUTATED 3 0 1 2
WAC WILD-TYPE 32 33 15 10
'WAC MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0966 (Fisher's exact test), Q value = 0.48

Table S510.  Gene #170: 'WAC MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
WAC MUTATED 3 0 0 1 2 0 0
WAC WILD-TYPE 31 11 9 6 4 20 9
'CADPS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.567 (Fisher's exact test), Q value = 0.78

Table S511.  Gene #171: 'CADPS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CADPS MUTATED 1 3 1 3 2
CADPS WILD-TYPE 27 17 10 17 19
'CADPS MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.309 (Fisher's exact test), Q value = 0.65

Table S512.  Gene #171: 'CADPS MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CADPS MUTATED 5 2 3 0
CADPS WILD-TYPE 30 31 13 12
'CADPS MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.288 (Fisher's exact test), Q value = 0.64

Table S513.  Gene #171: 'CADPS MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CADPS MUTATED 6 0 0 2 0 1 1
CADPS WILD-TYPE 28 11 9 5 6 19 8
'FAM60A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.304 (Fisher's exact test), Q value = 0.65

Table S514.  Gene #172: 'FAM60A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
FAM60A MUTATED 1 2 0 0 3
FAM60A WILD-TYPE 27 18 11 20 18
'FAM60A MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.934 (Fisher's exact test), Q value = 0.99

Table S515.  Gene #172: 'FAM60A MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
FAM60A MUTATED 3 2 1 0
FAM60A WILD-TYPE 32 31 15 12
'FAM60A MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.856 (Fisher's exact test), Q value = 0.94

Table S516.  Gene #172: 'FAM60A MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
FAM60A MUTATED 4 0 0 0 0 1 1
FAM60A WILD-TYPE 30 11 9 7 6 19 8
'PSG1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.958 (Fisher's exact test), Q value = 1

Table S517.  Gene #173: 'PSG1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PSG1 MUTATED 1 1 1 1 1
PSG1 WILD-TYPE 27 19 10 19 20
'PSG1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.793 (Fisher's exact test), Q value = 0.92

Table S518.  Gene #173: 'PSG1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PSG1 MUTATED 1 2 1 1
PSG1 WILD-TYPE 34 31 15 11
'PSG1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 0.53

Table S519.  Gene #173: 'PSG1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PSG1 MUTATED 1 2 0 0 1 0 1
PSG1 WILD-TYPE 33 9 9 7 5 20 8
'MLH3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.101 (Fisher's exact test), Q value = 0.48

Table S520.  Gene #174: 'MLH3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
MLH3 MUTATED 1 1 0 0 4
MLH3 WILD-TYPE 27 19 11 20 17
'MLH3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.42

Table S521.  Gene #174: 'MLH3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
MLH3 MUTATED 4 0 0 2
MLH3 WILD-TYPE 31 33 16 10

Figure S71.  Get High-res Image Gene #174: 'MLH3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'MLH3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.11 (Fisher's exact test), Q value = 0.48

Table S522.  Gene #174: 'MLH3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
MLH3 MUTATED 4 0 0 0 2 0 0
MLH3 WILD-TYPE 30 11 9 7 4 20 9
'NFASC MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.302 (Fisher's exact test), Q value = 0.65

Table S523.  Gene #175: 'NFASC MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
NFASC MUTATED 2 1 1 1 5
NFASC WILD-TYPE 26 19 10 19 16
'NFASC MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.42

Table S524.  Gene #175: 'NFASC MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
NFASC MUTATED 6 0 2 2
NFASC WILD-TYPE 29 33 14 10

Figure S72.  Get High-res Image Gene #175: 'NFASC MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'NFASC MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0387 (Fisher's exact test), Q value = 0.42

Table S525.  Gene #175: 'NFASC MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
NFASC MUTATED 7 0 0 1 2 0 0
NFASC WILD-TYPE 27 11 9 6 4 20 9

Figure S73.  Get High-res Image Gene #175: 'NFASC MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'ENTPD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.552 (Fisher's exact test), Q value = 0.77

Table S526.  Gene #176: 'ENTPD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ENTPD2 MUTATED 0 1 1 1 1
ENTPD2 WILD-TYPE 28 19 10 19 20
'ENTPD2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.652 (Fisher's exact test), Q value = 0.84

Table S527.  Gene #176: 'ENTPD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ENTPD2 MUTATED 1 1 1 1
ENTPD2 WILD-TYPE 34 32 15 11
'ENTPD2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0876 (Fisher's exact test), Q value = 0.47

Table S528.  Gene #176: 'ENTPD2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ENTPD2 MUTATED 0 0 0 1 1 1 1
ENTPD2 WILD-TYPE 34 11 9 6 5 19 8
'SFRS2B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.549 (Fisher's exact test), Q value = 0.77

Table S529.  Gene #177: 'SFRS2B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SFRS2B MUTATED 1 0 1 1 0
SFRS2B WILD-TYPE 27 20 10 19 21
'SFRS2B MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.603 (Fisher's exact test), Q value = 0.81

Table S530.  Gene #177: 'SFRS2B MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SFRS2B MUTATED 1 1 0 1
SFRS2B WILD-TYPE 34 32 16 11
'SFRS2B MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.55 (Fisher's exact test), Q value = 0.77

Table S531.  Gene #177: 'SFRS2B MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SFRS2B MUTATED 1 0 0 0 1 1 0
SFRS2B WILD-TYPE 33 11 9 7 5 19 9
'XKR6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.182 (Fisher's exact test), Q value = 0.56

Table S532.  Gene #178: 'XKR6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
XKR6 MUTATED 0 2 1 0 2
XKR6 WILD-TYPE 28 18 10 20 19
'XKR6 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.104 (Fisher's exact test), Q value = 0.48

Table S533.  Gene #178: 'XKR6 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
XKR6 MUTATED 4 0 0 1
XKR6 WILD-TYPE 31 33 16 11
'XKR6 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.377 (Fisher's exact test), Q value = 0.68

Table S534.  Gene #178: 'XKR6 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
XKR6 MUTATED 3 0 0 0 1 0 1
XKR6 WILD-TYPE 31 11 9 7 5 20 8
'KIAA1267 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.19 (Fisher's exact test), Q value = 0.56

Table S535.  Gene #179: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
KIAA1267 MUTATED 3 0 2 1 4
KIAA1267 WILD-TYPE 25 20 9 19 17
'KIAA1267 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0278 (Fisher's exact test), Q value = 0.42

Table S536.  Gene #179: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
KIAA1267 MUTATED 8 1 0 1
KIAA1267 WILD-TYPE 27 32 16 11

Figure S74.  Get High-res Image Gene #179: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'KIAA1267 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 0.53

Table S537.  Gene #179: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
KIAA1267 MUTATED 8 0 0 0 1 1 0
KIAA1267 WILD-TYPE 26 11 9 7 5 19 9
'SGOL2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.217 (Fisher's exact test), Q value = 0.58

Table S538.  Gene #180: 'SGOL2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SGOL2 MUTATED 0 2 0 2 3
SGOL2 WILD-TYPE 28 18 11 18 18
'SGOL2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.42

Table S539.  Gene #180: 'SGOL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SGOL2 MUTATED 6 0 1 0
SGOL2 WILD-TYPE 29 33 15 12

Figure S75.  Get High-res Image Gene #180: 'SGOL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'SGOL2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.217 (Fisher's exact test), Q value = 0.58

Table S540.  Gene #180: 'SGOL2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SGOL2 MUTATED 6 0 1 0 0 0 0
SGOL2 WILD-TYPE 28 11 8 7 6 20 9
'MSH6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.719 (Fisher's exact test), Q value = 0.88

Table S541.  Gene #181: 'MSH6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
MSH6 MUTATED 2 2 0 3 1
MSH6 WILD-TYPE 26 18 11 17 20
'MSH6 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.412 (Fisher's exact test), Q value = 0.69

Table S542.  Gene #181: 'MSH6 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
MSH6 MUTATED 5 1 1 1
MSH6 WILD-TYPE 30 32 15 11
'MSH6 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.185 (Fisher's exact test), Q value = 0.56

Table S543.  Gene #181: 'MSH6 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
MSH6 MUTATED 6 0 0 0 1 0 1
MSH6 WILD-TYPE 28 11 9 7 5 20 8
'TP53BP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.179 (Fisher's exact test), Q value = 0.56

Table S544.  Gene #182: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TP53BP1 MUTATED 2 4 2 0 2
TP53BP1 WILD-TYPE 26 16 9 20 19
'TP53BP1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.00539 (Fisher's exact test), Q value = 0.32

Table S545.  Gene #182: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TP53BP1 MUTATED 9 1 0 0
TP53BP1 WILD-TYPE 26 32 16 12

Figure S76.  Get High-res Image Gene #182: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'TP53BP1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0717 (Fisher's exact test), Q value = 0.47

Table S546.  Gene #182: 'TP53BP1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TP53BP1 MUTATED 9 0 0 0 0 1 0
TP53BP1 WILD-TYPE 25 11 9 7 6 19 9
'IFIH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.667 (Fisher's exact test), Q value = 0.85

Table S547.  Gene #183: 'IFIH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
IFIH1 MUTATED 3 1 1 0 2
IFIH1 WILD-TYPE 25 19 10 20 19
'IFIH1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.48

Table S548.  Gene #183: 'IFIH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
IFIH1 MUTATED 4 0 2 0
IFIH1 WILD-TYPE 31 33 14 12
'IFIH1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 0.53

Table S549.  Gene #183: 'IFIH1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
IFIH1 MUTATED 4 0 0 2 0 0 0
IFIH1 WILD-TYPE 30 11 9 5 6 20 9
'MRI1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.37 (Fisher's exact test), Q value = 0.68

Table S550.  Gene #184: 'MRI1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
MRI1 MUTATED 0 1 1 0 1
MRI1 WILD-TYPE 28 19 10 20 20
'MRI1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.333 (Fisher's exact test), Q value = 0.67

Table S551.  Gene #184: 'MRI1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
MRI1 MUTATED 1 0 1 1
MRI1 WILD-TYPE 34 33 15 11
'MRI1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.49 (Fisher's exact test), Q value = 0.75

Table S552.  Gene #184: 'MRI1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
MRI1 MUTATED 2 0 0 0 1 0 0
MRI1 WILD-TYPE 32 11 9 7 5 20 9
'PAPPA2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.657 (Fisher's exact test), Q value = 0.84

Table S553.  Gene #185: 'PAPPA2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PAPPA2 MUTATED 4 2 0 2 4
PAPPA2 WILD-TYPE 24 18 11 18 17
'PAPPA2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.39

Table S554.  Gene #185: 'PAPPA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PAPPA2 MUTATED 6 0 3 3
PAPPA2 WILD-TYPE 29 33 13 9

Figure S77.  Get High-res Image Gene #185: 'PAPPA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'PAPPA2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.39

Table S555.  Gene #185: 'PAPPA2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PAPPA2 MUTATED 8 0 0 2 2 0 0
PAPPA2 WILD-TYPE 26 11 9 5 4 20 9

Figure S78.  Get High-res Image Gene #185: 'PAPPA2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'KRTAP10-1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S556.  Gene #186: 'KRTAP10-1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
KRTAP10-1 MUTATED 1 0 0 1 1
KRTAP10-1 WILD-TYPE 27 20 11 19 20
'KRTAP10-1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 0.68

Table S557.  Gene #186: 'KRTAP10-1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
KRTAP10-1 MUTATED 2 0 0 1
KRTAP10-1 WILD-TYPE 33 33 16 11
'KRTAP10-1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.491 (Fisher's exact test), Q value = 0.75

Table S558.  Gene #186: 'KRTAP10-1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
KRTAP10-1 MUTATED 2 0 0 0 1 0 0
KRTAP10-1 WILD-TYPE 32 11 9 7 5 20 9
'PIK3R2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.104 (Fisher's exact test), Q value = 0.48

Table S559.  Gene #187: 'PIK3R2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PIK3R2 MUTATED 1 1 0 1 5
PIK3R2 WILD-TYPE 27 19 11 19 16
'PIK3R2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.945 (Fisher's exact test), Q value = 0.99

Table S560.  Gene #187: 'PIK3R2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PIK3R2 MUTATED 2 3 1 1
PIK3R2 WILD-TYPE 33 30 15 11
'PIK3R2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.849 (Fisher's exact test), Q value = 0.94

Table S561.  Gene #187: 'PIK3R2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PIK3R2 MUTATED 3 1 0 0 1 1 1
PIK3R2 WILD-TYPE 31 10 9 7 5 19 8
'SDAD1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00755 (Fisher's exact test), Q value = 0.38

Table S562.  Gene #188: 'SDAD1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SDAD1 MUTATED 0 0 0 0 4
SDAD1 WILD-TYPE 28 20 11 20 17

Figure S79.  Get High-res Image Gene #188: 'SDAD1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'SDAD1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.353 (Fisher's exact test), Q value = 0.68

Table S563.  Gene #188: 'SDAD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SDAD1 MUTATED 2 0 1 1
SDAD1 WILD-TYPE 33 33 15 11
'SDAD1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.403 (Fisher's exact test), Q value = 0.69

Table S564.  Gene #188: 'SDAD1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SDAD1 MUTATED 3 0 0 0 1 0 0
SDAD1 WILD-TYPE 31 11 9 7 5 20 9
'GOLGA5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.37 (Fisher's exact test), Q value = 0.68

Table S565.  Gene #189: 'GOLGA5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
GOLGA5 MUTATED 0 1 1 0 1
GOLGA5 WILD-TYPE 28 19 10 20 20
'GOLGA5 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.505 (Fisher's exact test), Q value = 0.75

Table S566.  Gene #189: 'GOLGA5 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
GOLGA5 MUTATED 2 0 1 0
GOLGA5 WILD-TYPE 33 33 15 12
'GOLGA5 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.518 (Fisher's exact test), Q value = 0.76

Table S567.  Gene #189: 'GOLGA5 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
GOLGA5 MUTATED 2 0 0 1 0 0 0
GOLGA5 WILD-TYPE 32 11 9 6 6 20 9
'MAGI1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0843 (Fisher's exact test), Q value = 0.47

Table S568.  Gene #190: 'MAGI1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
MAGI1 MUTATED 0 0 1 3 1
MAGI1 WILD-TYPE 28 20 10 17 20
'MAGI1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.737 (Fisher's exact test), Q value = 0.89

Table S569.  Gene #190: 'MAGI1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
MAGI1 MUTATED 3 1 1 0
MAGI1 WILD-TYPE 32 32 15 12
'MAGI1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.793 (Fisher's exact test), Q value = 0.92

Table S570.  Gene #190: 'MAGI1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
MAGI1 MUTATED 3 0 0 1 0 1 0
MAGI1 WILD-TYPE 31 11 9 6 6 19 9
'PRUNE2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.405 (Fisher's exact test), Q value = 0.69

Table S571.  Gene #191: 'PRUNE2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PRUNE2 MUTATED 2 4 1 4 1
PRUNE2 WILD-TYPE 26 16 10 16 20
'PRUNE2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.677 (Fisher's exact test), Q value = 0.85

Table S572.  Gene #191: 'PRUNE2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PRUNE2 MUTATED 5 4 2 0
PRUNE2 WILD-TYPE 30 29 14 12
'PRUNE2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.386 (Fisher's exact test), Q value = 0.68

Table S573.  Gene #191: 'PRUNE2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PRUNE2 MUTATED 4 0 1 2 0 4 0
PRUNE2 WILD-TYPE 30 11 8 5 6 16 9
'MXRA8 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S574.  Gene #192: 'MXRA8 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
MXRA8 MUTATED 2 1 0 1 1
MXRA8 WILD-TYPE 26 19 11 19 20
'MXRA8 MUTATION STATUS' versus 'METHYLATION_CNMF'

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

Table S575.  Gene #192: 'MXRA8 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
MXRA8 MUTATED 2 2 1 0
MXRA8 WILD-TYPE 33 31 15 12
'MXRA8 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.904 (Fisher's exact test), Q value = 0.97

Table S576.  Gene #192: 'MXRA8 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
MXRA8 MUTATED 3 0 0 0 0 1 1
MXRA8 WILD-TYPE 31 11 9 7 6 19 8
'WDR47 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.567 (Fisher's exact test), Q value = 0.78

Table S577.  Gene #193: 'WDR47 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
WDR47 MUTATED 1 3 0 1 2
WDR47 WILD-TYPE 27 17 11 19 19
'WDR47 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0937 (Fisher's exact test), Q value = 0.47

Table S578.  Gene #193: 'WDR47 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
WDR47 MUTATED 6 1 0 0
WDR47 WILD-TYPE 29 32 16 12
'WDR47 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.217 (Fisher's exact test), Q value = 0.58

Table S579.  Gene #193: 'WDR47 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
WDR47 MUTATED 6 0 0 0 0 0 1
WDR47 WILD-TYPE 28 11 9 7 6 20 8
'ANK3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.314 (Fisher's exact test), Q value = 0.65

Table S580.  Gene #194: 'ANK3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ANK3 MUTATED 1 4 2 2 4
ANK3 WILD-TYPE 27 16 9 18 17
'ANK3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.00573 (Fisher's exact test), Q value = 0.32

Table S581.  Gene #194: 'ANK3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ANK3 MUTATED 9 0 3 1
ANK3 WILD-TYPE 26 33 13 11

Figure S80.  Get High-res Image Gene #194: 'ANK3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'ANK3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0246 (Fisher's exact test), Q value = 0.41

Table S582.  Gene #194: 'ANK3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ANK3 MUTATED 10 0 0 1 1 0 1
ANK3 WILD-TYPE 24 11 9 6 5 20 8

Figure S81.  Get High-res Image Gene #194: 'ANK3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'MED25 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.591 (Fisher's exact test), Q value = 0.8

Table S583.  Gene #195: 'MED25 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
MED25 MUTATED 1 0 1 1 2
MED25 WILD-TYPE 27 20 10 19 19
'MED25 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.265 (Fisher's exact test), Q value = 0.63

Table S584.  Gene #195: 'MED25 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
MED25 MUTATED 3 0 1 1
MED25 WILD-TYPE 32 33 15 11
'MED25 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.382 (Fisher's exact test), Q value = 0.68

Table S585.  Gene #195: 'MED25 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
MED25 MUTATED 4 0 0 1 0 0 0
MED25 WILD-TYPE 30 11 9 6 6 20 9
'LRCH2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.312 (Fisher's exact test), Q value = 0.65

Table S586.  Gene #196: 'LRCH2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
LRCH2 MUTATED 1 4 1 1 1
LRCH2 WILD-TYPE 27 16 10 19 20
'LRCH2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.55 (Fisher's exact test), Q value = 0.77

Table S587.  Gene #196: 'LRCH2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
LRCH2 MUTATED 5 2 1 0
LRCH2 WILD-TYPE 30 31 15 12
'LRCH2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.868 (Fisher's exact test), Q value = 0.95

Table S588.  Gene #196: 'LRCH2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
LRCH2 MUTATED 4 0 1 1 0 2 0
LRCH2 WILD-TYPE 30 11 8 6 6 18 9
'SALL4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.755 (Fisher's exact test), Q value = 0.9

Table S589.  Gene #197: 'SALL4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SALL4 MUTATED 2 1 0 1 3
SALL4 WILD-TYPE 26 19 11 19 18
'SALL4 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.166 (Fisher's exact test), Q value = 0.56

Table S590.  Gene #197: 'SALL4 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SALL4 MUTATED 4 1 0 2
SALL4 WILD-TYPE 31 32 16 10
'SALL4 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.12 (Fisher's exact test), Q value = 0.49

Table S591.  Gene #197: 'SALL4 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SALL4 MUTATED 4 0 0 0 2 0 1
SALL4 WILD-TYPE 30 11 9 7 4 20 8
'RTKN2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0781 (Fisher's exact test), Q value = 0.47

Table S592.  Gene #198: 'RTKN2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
RTKN2 MUTATED 0 0 0 2 3
RTKN2 WILD-TYPE 28 20 11 18 18
'RTKN2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.189 (Fisher's exact test), Q value = 0.56

Table S593.  Gene #198: 'RTKN2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
RTKN2 MUTATED 2 0 2 1
RTKN2 WILD-TYPE 33 33 14 11
'RTKN2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.309 (Fisher's exact test), Q value = 0.65

Table S594.  Gene #198: 'RTKN2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
RTKN2 MUTATED 2 1 0 1 1 0 0
RTKN2 WILD-TYPE 32 10 9 6 5 20 9
'TTC39B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.287 (Fisher's exact test), Q value = 0.64

Table S595.  Gene #199: 'TTC39B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TTC39B MUTATED 0 1 0 0 2
TTC39B WILD-TYPE 28 19 11 20 19
'TTC39B MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.38 (Fisher's exact test), Q value = 0.68

Table S596.  Gene #199: 'TTC39B MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TTC39B MUTATED 2 0 0 1
TTC39B WILD-TYPE 33 33 16 11
'TTC39B MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.497 (Fisher's exact test), Q value = 0.75

Table S597.  Gene #199: 'TTC39B MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TTC39B MUTATED 2 0 0 0 1 0 0
TTC39B WILD-TYPE 32 11 9 7 5 20 9
'CDH24 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.86 (Fisher's exact test), Q value = 0.94

Table S598.  Gene #200: 'CDH24 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CDH24 MUTATED 2 1 0 1 0
CDH24 WILD-TYPE 26 19 11 19 21
'CDH24 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.32 (Fisher's exact test), Q value = 0.65

Table S599.  Gene #200: 'CDH24 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CDH24 MUTATED 3 0 1 0
CDH24 WILD-TYPE 32 33 15 12
'CDH24 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.573 (Fisher's exact test), Q value = 0.78

Table S600.  Gene #200: 'CDH24 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CDH24 MUTATED 4 0 0 0 0 0 0
CDH24 WILD-TYPE 30 11 9 7 6 20 9
'PRR12 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.551 (Fisher's exact test), Q value = 0.77

Table S601.  Gene #201: 'PRR12 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PRR12 MUTATED 1 1 2 2 2
PRR12 WILD-TYPE 27 19 9 18 19
'PRR12 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.151 (Fisher's exact test), Q value = 0.54

Table S602.  Gene #201: 'PRR12 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PRR12 MUTATED 3 1 1 3
PRR12 WILD-TYPE 32 32 15 9
'PRR12 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.115 (Fisher's exact test), Q value = 0.48

Table S603.  Gene #201: 'PRR12 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PRR12 MUTATED 4 0 0 1 2 0 1
PRR12 WILD-TYPE 30 11 9 6 4 20 8
'MSL3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.719 (Fisher's exact test), Q value = 0.88

Table S604.  Gene #202: 'MSL3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
MSL3 MUTATED 3 3 0 1 2
MSL3 WILD-TYPE 25 17 11 19 19
'MSL3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.178 (Fisher's exact test), Q value = 0.56

Table S605.  Gene #202: 'MSL3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
MSL3 MUTATED 4 1 3 0
MSL3 WILD-TYPE 31 32 13 12
'MSL3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.279 (Fisher's exact test), Q value = 0.63

Table S606.  Gene #202: 'MSL3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
MSL3 MUTATED 3 1 1 2 0 0 1
MSL3 WILD-TYPE 31 10 8 5 6 20 8
'PAX6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.206 (Fisher's exact test), Q value = 0.58

Table S607.  Gene #203: 'PAX6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PAX6 MUTATED 0 3 1 1 1
PAX6 WILD-TYPE 28 17 10 19 20
'PAX6 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.82 (Fisher's exact test), Q value = 0.93

Table S608.  Gene #203: 'PAX6 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PAX6 MUTATED 3 1 1 1
PAX6 WILD-TYPE 32 32 15 11
'PAX6 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.262 (Fisher's exact test), Q value = 0.63

Table S609.  Gene #203: 'PAX6 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PAX6 MUTATED 2 0 1 1 1 0 1
PAX6 WILD-TYPE 32 11 8 6 5 20 8
'FLJ10357 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.763 (Fisher's exact test), Q value = 0.9

Table S610.  Gene #204: 'FLJ10357 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
FLJ10357 MUTATED 2 3 0 2 3
FLJ10357 WILD-TYPE 26 17 11 18 18
'FLJ10357 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.39

Table S611.  Gene #204: 'FLJ10357 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
FLJ10357 MUTATED 3 0 3 3
FLJ10357 WILD-TYPE 32 33 13 9

Figure S82.  Get High-res Image Gene #204: 'FLJ10357 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'FLJ10357 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0382 (Fisher's exact test), Q value = 0.42

Table S612.  Gene #204: 'FLJ10357 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
FLJ10357 MUTATED 5 0 0 2 2 0 0
FLJ10357 WILD-TYPE 29 11 9 5 4 20 9

Figure S83.  Get High-res Image Gene #204: 'FLJ10357 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'USMG5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.684 (Fisher's exact test), Q value = 0.86

Table S613.  Gene #205: 'USMG5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
USMG5 MUTATED 2 1 0 0 0
USMG5 WILD-TYPE 26 19 11 20 21
'USMG5 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.00543 (Fisher's exact test), Q value = 0.32

Table S614.  Gene #205: 'USMG5 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
USMG5 MUTATED 0 0 3 0
USMG5 WILD-TYPE 35 33 13 12

Figure S84.  Get High-res Image Gene #205: 'USMG5 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'USMG5 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.52 (Fisher's exact test), Q value = 0.76

Table S615.  Gene #205: 'USMG5 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
USMG5 MUTATED 2 0 0 1 0 0 0
USMG5 WILD-TYPE 32 11 9 6 6 20 9
'TFDP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.27 (Fisher's exact test), Q value = 0.63

Table S616.  Gene #206: 'TFDP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TFDP1 MUTATED 1 3 0 0 2
TFDP1 WILD-TYPE 27 17 11 20 19
'TFDP1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.535 (Fisher's exact test), Q value = 0.77

Table S617.  Gene #206: 'TFDP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TFDP1 MUTATED 4 1 1 0
TFDP1 WILD-TYPE 31 32 15 12
'TFDP1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.473 (Fisher's exact test), Q value = 0.75

Table S618.  Gene #206: 'TFDP1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TFDP1 MUTATED 4 1 0 1 0 0 0
TFDP1 WILD-TYPE 30 10 9 6 6 20 9
'WIF1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.338 (Fisher's exact test), Q value = 0.67

Table S619.  Gene #207: 'WIF1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
WIF1 MUTATED 1 1 0 0 3
WIF1 WILD-TYPE 27 19 11 20 18
'WIF1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.918 (Fisher's exact test), Q value = 0.98

Table S620.  Gene #207: 'WIF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
WIF1 MUTATED 2 1 1 1
WIF1 WILD-TYPE 33 32 15 11
'WIF1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.405 (Fisher's exact test), Q value = 0.69

Table S621.  Gene #207: 'WIF1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
WIF1 MUTATED 2 1 0 0 1 0 1
WIF1 WILD-TYPE 32 10 9 7 5 20 8
'ATXN2L MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.557 (Fisher's exact test), Q value = 0.78

Table S622.  Gene #208: 'ATXN2L MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ATXN2L MUTATED 3 0 1 2 3
ATXN2L WILD-TYPE 25 20 10 18 18
'ATXN2L MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0497 (Fisher's exact test), Q value = 0.43

Table S623.  Gene #208: 'ATXN2L MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ATXN2L MUTATED 6 0 2 1
ATXN2L WILD-TYPE 29 33 14 11

Figure S85.  Get High-res Image Gene #208: 'ATXN2L MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'ATXN2L MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0695 (Fisher's exact test), Q value = 0.46

Table S624.  Gene #208: 'ATXN2L MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ATXN2L MUTATED 6 0 0 2 1 0 0
ATXN2L WILD-TYPE 28 11 9 5 5 20 9
'FLT3LG MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.723 (Fisher's exact test), Q value = 0.88

Table S625.  Gene #209: 'FLT3LG MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
FLT3LG MUTATED 1 1 0 0 2
FLT3LG WILD-TYPE 27 19 11 20 19
'FLT3LG MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.649 (Fisher's exact test), Q value = 0.84

Table S626.  Gene #209: 'FLT3LG MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
FLT3LG MUTATED 1 1 1 1
FLT3LG WILD-TYPE 34 32 15 11
'FLT3LG MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.791 (Fisher's exact test), Q value = 0.92

Table S627.  Gene #209: 'FLT3LG MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
FLT3LG MUTATED 2 0 0 0 1 1 0
FLT3LG WILD-TYPE 32 11 9 7 5 19 9
'POLG MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.461 (Fisher's exact test), Q value = 0.74

Table S628.  Gene #210: 'POLG MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
POLG MUTATED 3 3 1 0 3
POLG WILD-TYPE 25 17 10 20 18
'POLG MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.4

Table S629.  Gene #210: 'POLG MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
POLG MUTATED 4 0 4 2
POLG WILD-TYPE 31 33 12 10

Figure S86.  Get High-res Image Gene #210: 'POLG MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'POLG MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.068 (Fisher's exact test), Q value = 0.45

Table S630.  Gene #210: 'POLG MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
POLG MUTATED 7 0 1 2 0 0 0
POLG WILD-TYPE 27 11 8 5 6 20 9
'EIF2AK3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.983 (Fisher's exact test), Q value = 1

Table S631.  Gene #211: 'EIF2AK3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
EIF2AK3 MUTATED 3 2 1 1 2
EIF2AK3 WILD-TYPE 25 18 10 19 19
'EIF2AK3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0666 (Fisher's exact test), Q value = 0.45

Table S632.  Gene #211: 'EIF2AK3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
EIF2AK3 MUTATED 5 0 2 2
EIF2AK3 WILD-TYPE 30 33 14 10
'EIF2AK3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0915 (Fisher's exact test), Q value = 0.47

Table S633.  Gene #211: 'EIF2AK3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
EIF2AK3 MUTATED 7 0 0 1 1 0 0
EIF2AK3 WILD-TYPE 27 11 9 6 5 20 9
'GLTSCR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.39 (Fisher's exact test), Q value = 0.68

Table S634.  Gene #212: 'GLTSCR1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
GLTSCR1 MUTATED 6 1 1 3 1
GLTSCR1 WILD-TYPE 22 19 10 17 20
'GLTSCR1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.42

Table S635.  Gene #212: 'GLTSCR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
GLTSCR1 MUTATED 4 1 5 1
GLTSCR1 WILD-TYPE 31 32 11 11

Figure S87.  Get High-res Image Gene #212: 'GLTSCR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'GLTSCR1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.553 (Fisher's exact test), Q value = 0.77

Table S636.  Gene #212: 'GLTSCR1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
GLTSCR1 MUTATED 5 1 1 2 1 1 0
GLTSCR1 WILD-TYPE 29 10 8 5 5 19 9
'CYTSB MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.725 (Fisher's exact test), Q value = 0.88

Table S637.  Gene #213: 'CYTSB MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CYTSB MUTATED 2 2 2 2 1
CYTSB WILD-TYPE 26 18 9 18 20
'CYTSB MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.39

Table S638.  Gene #213: 'CYTSB MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CYTSB MUTATED 7 0 2 0
CYTSB WILD-TYPE 28 33 14 12

Figure S88.  Get High-res Image Gene #213: 'CYTSB MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'CYTSB MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0472 (Fisher's exact test), Q value = 0.42

Table S639.  Gene #213: 'CYTSB MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CYTSB MUTATED 7 0 0 2 0 0 0
CYTSB WILD-TYPE 27 11 9 5 6 20 9

Figure S89.  Get High-res Image Gene #213: 'CYTSB MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'NAP1L5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.859 (Fisher's exact test), Q value = 0.94

Table S640.  Gene #214: 'NAP1L5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
NAP1L5 MUTATED 2 1 0 1 0
NAP1L5 WILD-TYPE 26 19 11 19 21
'NAP1L5 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.395 (Fisher's exact test), Q value = 0.69

Table S641.  Gene #214: 'NAP1L5 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
NAP1L5 MUTATED 1 1 2 0
NAP1L5 WILD-TYPE 34 32 14 12
'NAP1L5 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.835 (Fisher's exact test), Q value = 0.94

Table S642.  Gene #214: 'NAP1L5 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
NAP1L5 MUTATED 2 0 0 1 0 1 0
NAP1L5 WILD-TYPE 32 11 9 6 6 19 9
'DDX10 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.632 (Fisher's exact test), Q value = 0.84

Table S643.  Gene #215: 'DDX10 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
DDX10 MUTATED 3 1 2 1 1
DDX10 WILD-TYPE 25 19 9 19 20
'DDX10 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.352 (Fisher's exact test), Q value = 0.68

Table S644.  Gene #215: 'DDX10 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DDX10 MUTATED 4 1 2 0
DDX10 WILD-TYPE 31 32 14 12
'DDX10 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.855 (Fisher's exact test), Q value = 0.94

Table S645.  Gene #215: 'DDX10 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DDX10 MUTATED 4 1 0 1 0 1 0
DDX10 WILD-TYPE 30 10 9 6 6 19 9
'LIMK2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.844 (Fisher's exact test), Q value = 0.94

Table S646.  Gene #216: 'LIMK2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
LIMK2 MUTATED 1 2 1 2 2
LIMK2 WILD-TYPE 27 18 10 18 19
'LIMK2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.549 (Fisher's exact test), Q value = 0.77

Table S647.  Gene #216: 'LIMK2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
LIMK2 MUTATED 5 2 1 0
LIMK2 WILD-TYPE 30 31 15 12
'LIMK2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.641 (Fisher's exact test), Q value = 0.84

Table S648.  Gene #216: 'LIMK2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
LIMK2 MUTATED 5 0 0 1 0 1 1
LIMK2 WILD-TYPE 29 11 9 6 6 19 8
'POLD1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.871 (Fisher's exact test), Q value = 0.95

Table S649.  Gene #217: 'POLD1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
POLD1 MUTATED 1 1 1 1 2
POLD1 WILD-TYPE 27 19 10 19 19
'POLD1 MUTATION STATUS' versus 'METHYLATION_CNMF'

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

Table S650.  Gene #217: 'POLD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
POLD1 MUTATED 2 2 1 1
POLD1 WILD-TYPE 33 31 15 11
'POLD1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.55 (Fisher's exact test), Q value = 0.77

Table S651.  Gene #217: 'POLD1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
POLD1 MUTATED 2 0 0 1 1 1 1
POLD1 WILD-TYPE 32 11 9 6 5 19 8
'SBNO1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0915 (Fisher's exact test), Q value = 0.47

Table S652.  Gene #218: 'SBNO1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SBNO1 MUTATED 0 3 1 1 4
SBNO1 WILD-TYPE 28 17 10 19 17
'SBNO1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.42

Table S653.  Gene #218: 'SBNO1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SBNO1 MUTATED 6 0 1 2
SBNO1 WILD-TYPE 29 33 15 10

Figure S90.  Get High-res Image Gene #218: 'SBNO1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'SBNO1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0921 (Fisher's exact test), Q value = 0.47

Table S654.  Gene #218: 'SBNO1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SBNO1 MUTATED 7 0 0 1 1 0 0
SBNO1 WILD-TYPE 27 11 9 6 5 20 9
'CACHD1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.209 (Fisher's exact test), Q value = 0.58

Table S655.  Gene #219: 'CACHD1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CACHD1 MUTATED 2 0 1 0 3
CACHD1 WILD-TYPE 26 20 10 20 18
'CACHD1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 0.48

Table S656.  Gene #219: 'CACHD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CACHD1 MUTATED 3 0 1 2
CACHD1 WILD-TYPE 32 33 15 10
'CACHD1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.442 (Fisher's exact test), Q value = 0.72

Table S657.  Gene #219: 'CACHD1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CACHD1 MUTATED 4 1 0 0 1 0 0
CACHD1 WILD-TYPE 30 10 9 7 5 20 9
'FAM200A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.203 (Fisher's exact test), Q value = 0.57

Table S658.  Gene #220: 'FAM200A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
FAM200A MUTATED 0 2 1 1 0
FAM200A WILD-TYPE 28 18 10 19 21
'FAM200A MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.393 (Fisher's exact test), Q value = 0.69

Table S659.  Gene #220: 'FAM200A MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
FAM200A MUTATED 1 1 2 0
FAM200A WILD-TYPE 34 32 14 12
'FAM200A MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.213 (Fisher's exact test), Q value = 0.58

Table S660.  Gene #220: 'FAM200A MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
FAM200A MUTATED 1 0 0 2 0 1 0
FAM200A WILD-TYPE 33 11 9 5 6 19 9
'KIAA1370 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.521 (Fisher's exact test), Q value = 0.76

Table S661.  Gene #221: 'KIAA1370 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
KIAA1370 MUTATED 2 3 1 0 2
KIAA1370 WILD-TYPE 26 17 10 20 19
'KIAA1370 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.42

Table S662.  Gene #221: 'KIAA1370 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
KIAA1370 MUTATED 5 0 3 0
KIAA1370 WILD-TYPE 30 33 13 12

Figure S91.  Get High-res Image Gene #221: 'KIAA1370 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'KIAA1370 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.136 (Fisher's exact test), Q value = 0.51

Table S663.  Gene #221: 'KIAA1370 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
KIAA1370 MUTATED 5 0 0 2 0 0 1
KIAA1370 WILD-TYPE 29 11 9 5 6 20 8
'C7ORF63 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.749 (Fisher's exact test), Q value = 0.9

Table S664.  Gene #222: 'C7ORF63 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
C7ORF63 MUTATED 2 1 1 0 2
C7ORF63 WILD-TYPE 26 19 10 20 19
'C7ORF63 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.16 (Fisher's exact test), Q value = 0.56

Table S665.  Gene #222: 'C7ORF63 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
C7ORF63 MUTATED 3 0 2 0
C7ORF63 WILD-TYPE 32 33 14 12
'C7ORF63 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.182 (Fisher's exact test), Q value = 0.56

Table S666.  Gene #222: 'C7ORF63 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
C7ORF63 MUTATED 3 0 0 2 0 0 0
C7ORF63 WILD-TYPE 31 11 9 5 6 20 9
'BAT3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.06 (Fisher's exact test), Q value = 0.45

Table S667.  Gene #223: 'BAT3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
BAT3 MUTATED 3 0 0 0 4
BAT3 WILD-TYPE 25 20 11 20 17
'BAT3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0982 (Fisher's exact test), Q value = 0.48

Table S668.  Gene #223: 'BAT3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
BAT3 MUTATED 4 0 1 2
BAT3 WILD-TYPE 31 33 15 10
'BAT3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0837 (Fisher's exact test), Q value = 0.47

Table S669.  Gene #223: 'BAT3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
BAT3 MUTATED 5 0 0 0 2 0 0
BAT3 WILD-TYPE 29 11 9 7 4 20 9
'WNK4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.387 (Fisher's exact test), Q value = 0.68

Table S670.  Gene #224: 'WNK4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
WNK4 MUTATED 6 2 0 1 2
WNK4 WILD-TYPE 22 18 11 19 19
'WNK4 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.147 (Fisher's exact test), Q value = 0.54

Table S671.  Gene #224: 'WNK4 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
WNK4 MUTATED 7 1 2 1
WNK4 WILD-TYPE 28 32 14 11
'WNK4 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0796 (Fisher's exact test), Q value = 0.47

Table S672.  Gene #224: 'WNK4 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
WNK4 MUTATED 8 0 0 1 1 0 1
WNK4 WILD-TYPE 26 11 9 6 5 20 8
'VPRBP MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00322 (Fisher's exact test), Q value = 0.32

Table S673.  Gene #225: 'VPRBP MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
VPRBP MUTATED 0 5 0 0 1
VPRBP WILD-TYPE 28 15 11 20 20

Figure S92.  Get High-res Image Gene #225: 'VPRBP MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'VPRBP MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.45 (Fisher's exact test), Q value = 0.73

Table S674.  Gene #225: 'VPRBP MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
VPRBP MUTATED 3 1 2 0
VPRBP WILD-TYPE 32 32 14 12
'VPRBP MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.795 (Fisher's exact test), Q value = 0.92

Table S675.  Gene #225: 'VPRBP MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
VPRBP MUTATED 3 0 1 1 0 1 0
VPRBP WILD-TYPE 31 11 8 6 6 19 9
'DOCK5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.377 (Fisher's exact test), Q value = 0.68

Table S676.  Gene #226: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
DOCK5 MUTATED 0 2 1 2 2
DOCK5 WILD-TYPE 28 18 10 18 19
'DOCK5 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.819 (Fisher's exact test), Q value = 0.93

Table S677.  Gene #226: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DOCK5 MUTATED 3 1 1 1
DOCK5 WILD-TYPE 32 32 15 11
'DOCK5 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.606 (Fisher's exact test), Q value = 0.81

Table S678.  Gene #226: 'DOCK5 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DOCK5 MUTATED 3 0 0 1 1 1 0
DOCK5 WILD-TYPE 31 11 9 6 5 19 9
'PPM1D MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.438 (Fisher's exact test), Q value = 0.72

Table S679.  Gene #227: 'PPM1D MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PPM1D MUTATED 4 1 1 0 1
PPM1D WILD-TYPE 24 19 10 20 20
'PPM1D MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0898 (Fisher's exact test), Q value = 0.47

Table S680.  Gene #227: 'PPM1D MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PPM1D MUTATED 5 0 1 0
PPM1D WILD-TYPE 30 33 15 12
'PPM1D MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.276 (Fisher's exact test), Q value = 0.63

Table S681.  Gene #227: 'PPM1D MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PPM1D MUTATED 5 0 0 1 0 0 0
PPM1D WILD-TYPE 29 11 9 6 6 20 9
'MAPRE3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.784 (Fisher's exact test), Q value = 0.92

Table S682.  Gene #228: 'MAPRE3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
MAPRE3 MUTATED 0 1 0 1 1
MAPRE3 WILD-TYPE 28 19 11 19 20
'MAPRE3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.505 (Fisher's exact test), Q value = 0.75

Table S683.  Gene #228: 'MAPRE3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
MAPRE3 MUTATED 2 0 1 0
MAPRE3 WILD-TYPE 33 33 15 12
'MAPRE3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.52 (Fisher's exact test), Q value = 0.76

Table S684.  Gene #228: 'MAPRE3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
MAPRE3 MUTATED 2 0 0 1 0 0 0
MAPRE3 WILD-TYPE 32 11 9 6 6 20 9
'SHPRH MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.815 (Fisher's exact test), Q value = 0.93

Table S685.  Gene #229: 'SHPRH MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SHPRH MUTATED 3 1 2 2 2
SHPRH WILD-TYPE 25 19 9 18 19
'SHPRH MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.42

Table S686.  Gene #229: 'SHPRH MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SHPRH MUTATED 4 0 2 3
SHPRH WILD-TYPE 31 33 14 9

Figure S93.  Get High-res Image Gene #229: 'SHPRH MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'SHPRH MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.4

Table S687.  Gene #229: 'SHPRH MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SHPRH MUTATED 5 0 0 1 3 0 0
SHPRH WILD-TYPE 29 11 9 6 3 20 9

Figure S94.  Get High-res Image Gene #229: 'SHPRH MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'KSR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.208 (Fisher's exact test), Q value = 0.58

Table S688.  Gene #230: 'KSR1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
KSR1 MUTATED 0 2 2 2 2
KSR1 WILD-TYPE 28 18 9 18 19
'KSR1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.909 (Fisher's exact test), Q value = 0.98

Table S689.  Gene #230: 'KSR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
KSR1 MUTATED 3 2 2 1
KSR1 WILD-TYPE 32 31 14 11
'KSR1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.641 (Fisher's exact test), Q value = 0.84

Table S690.  Gene #230: 'KSR1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
KSR1 MUTATED 4 0 0 1 1 1 1
KSR1 WILD-TYPE 30 11 9 6 5 19 8
'ZNF195 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.282 (Fisher's exact test), Q value = 0.64

Table S691.  Gene #231: 'ZNF195 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ZNF195 MUTATED 1 3 1 0 2
ZNF195 WILD-TYPE 27 17 10 20 19
'ZNF195 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.42

Table S692.  Gene #231: 'ZNF195 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ZNF195 MUTATED 6 0 1 0
ZNF195 WILD-TYPE 29 33 15 12

Figure S95.  Get High-res Image Gene #231: 'ZNF195 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'ZNF195 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.32 (Fisher's exact test), Q value = 0.65

Table S693.  Gene #231: 'ZNF195 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ZNF195 MUTATED 5 0 1 1 0 0 0
ZNF195 WILD-TYPE 29 11 8 6 6 20 9
'CANX MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.957 (Fisher's exact test), Q value = 1

Table S694.  Gene #232: 'CANX MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CANX MUTATED 1 1 1 1 1
CANX WILD-TYPE 27 19 10 19 20
'CANX MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.264 (Fisher's exact test), Q value = 0.63

Table S695.  Gene #232: 'CANX MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CANX MUTATED 3 0 1 1
CANX WILD-TYPE 32 33 15 11
'CANX MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.479 (Fisher's exact test), Q value = 0.75

Table S696.  Gene #232: 'CANX MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CANX MUTATED 3 1 0 0 1 0 0
CANX WILD-TYPE 31 10 9 7 5 20 9
'WHSC1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.339 (Fisher's exact test), Q value = 0.67

Table S697.  Gene #233: 'WHSC1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
WHSC1 MUTATED 1 4 1 1 3
WHSC1 WILD-TYPE 27 16 10 19 18
'WHSC1 MUTATION STATUS' versus 'METHYLATION_CNMF'

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

Table S698.  Gene #233: 'WHSC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
WHSC1 MUTATED 6 1 3 0
WHSC1 WILD-TYPE 29 32 13 12
'WHSC1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.289 (Fisher's exact test), Q value = 0.64

Table S699.  Gene #233: 'WHSC1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
WHSC1 MUTATED 6 0 0 2 0 1 1
WHSC1 WILD-TYPE 28 11 9 5 6 19 8
'TAOK3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.405 (Fisher's exact test), Q value = 0.69

Table S700.  Gene #234: 'TAOK3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TAOK3 MUTATED 2 1 2 0 1
TAOK3 WILD-TYPE 26 19 9 20 20
'TAOK3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0532 (Fisher's exact test), Q value = 0.43

Table S701.  Gene #234: 'TAOK3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TAOK3 MUTATED 5 0 0 1
TAOK3 WILD-TYPE 30 33 16 11
'TAOK3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.25 (Fisher's exact test), Q value = 0.63

Table S702.  Gene #234: 'TAOK3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TAOK3 MUTATED 5 0 0 0 1 0 0
TAOK3 WILD-TYPE 29 11 9 7 5 20 9
'GIPC1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.856 (Fisher's exact test), Q value = 0.94

Table S703.  Gene #235: 'GIPC1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
GIPC1 MUTATED 1 1 0 1 0
GIPC1 WILD-TYPE 27 19 11 19 21
'GIPC1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.862 (Fisher's exact test), Q value = 0.94

Table S704.  Gene #235: 'GIPC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
GIPC1 MUTATED 1 1 1 0
GIPC1 WILD-TYPE 34 32 15 12
'GIPC1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.368 (Fisher's exact test), Q value = 0.68

Table S705.  Gene #235: 'GIPC1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
GIPC1 MUTATED 1 0 0 1 0 0 1
GIPC1 WILD-TYPE 33 11 9 6 6 20 8
'LOR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.14 (Fisher's exact test), Q value = 0.52

Table S706.  Gene #236: 'LOR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
LOR MUTATED 3 0 1 0 0
LOR WILD-TYPE 25 20 10 20 21
'LOR MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.319 (Fisher's exact test), Q value = 0.65

Table S707.  Gene #236: 'LOR MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
LOR MUTATED 3 0 1 0
LOR WILD-TYPE 32 33 15 12
'LOR MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.479 (Fisher's exact test), Q value = 0.75

Table S708.  Gene #236: 'LOR MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
LOR MUTATED 3 0 0 1 0 0 0
LOR WILD-TYPE 31 11 9 6 6 20 9
'SMAP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.696 (Fisher's exact test), Q value = 0.86

Table S709.  Gene #237: 'SMAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SMAP1 MUTATED 2 2 1 1 0
SMAP1 WILD-TYPE 26 18 10 19 21
'SMAP1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0913 (Fisher's exact test), Q value = 0.47

Table S710.  Gene #237: 'SMAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SMAP1 MUTATED 5 0 1 0
SMAP1 WILD-TYPE 30 33 15 12
'SMAP1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.276 (Fisher's exact test), Q value = 0.63

Table S711.  Gene #237: 'SMAP1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SMAP1 MUTATED 5 0 0 1 0 0 0
SMAP1 WILD-TYPE 29 11 9 6 6 20 9
'HERC6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.834 (Fisher's exact test), Q value = 0.94

Table S712.  Gene #238: 'HERC6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
HERC6 MUTATED 2 1 1 0 1
HERC6 WILD-TYPE 26 19 10 20 20
'HERC6 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.56

Table S713.  Gene #238: 'HERC6 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
HERC6 MUTATED 4 0 1 0
HERC6 WILD-TYPE 31 33 15 12
'HERC6 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.353 (Fisher's exact test), Q value = 0.68

Table S714.  Gene #238: 'HERC6 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
HERC6 MUTATED 5 0 0 0 0 0 0
HERC6 WILD-TYPE 29 11 9 7 6 20 9
'KIAA0913 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.382 (Fisher's exact test), Q value = 0.68

Table S715.  Gene #239: 'KIAA0913 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
KIAA0913 MUTATED 2 0 0 2 0
KIAA0913 WILD-TYPE 26 20 11 18 21
'KIAA0913 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.39

Table S716.  Gene #239: 'KIAA0913 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
KIAA0913 MUTATED 0 1 3 0
KIAA0913 WILD-TYPE 35 32 13 12

Figure S96.  Get High-res Image Gene #239: 'KIAA0913 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'KIAA0913 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.211 (Fisher's exact test), Q value = 0.58

Table S717.  Gene #239: 'KIAA0913 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
KIAA0913 MUTATED 1 0 0 2 0 1 0
KIAA0913 WILD-TYPE 33 11 9 5 6 19 9
'FKBP11 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.288 (Fisher's exact test), Q value = 0.64

Table S718.  Gene #240: 'FKBP11 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
FKBP11 MUTATED 0 1 0 0 2
FKBP11 WILD-TYPE 28 19 11 20 19
'FKBP11 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.863 (Fisher's exact test), Q value = 0.94

Table S719.  Gene #240: 'FKBP11 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
FKBP11 MUTATED 1 1 1 0
FKBP11 WILD-TYPE 34 32 15 12
'FKBP11 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.369 (Fisher's exact test), Q value = 0.68

Table S720.  Gene #240: 'FKBP11 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
FKBP11 MUTATED 1 0 0 1 0 0 1
FKBP11 WILD-TYPE 33 11 9 6 6 20 8
'C5ORF36 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.623 (Fisher's exact test), Q value = 0.83

Table S721.  Gene #241: 'C5ORF36 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
C5ORF36 MUTATED 1 3 1 1 2
C5ORF36 WILD-TYPE 27 17 10 19 19
'C5ORF36 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 0.42

Table S722.  Gene #241: 'C5ORF36 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
C5ORF36 MUTATED 4 0 3 0
C5ORF36 WILD-TYPE 31 33 13 12

Figure S97.  Get High-res Image Gene #241: 'C5ORF36 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'C5ORF36 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.113 (Fisher's exact test), Q value = 0.48

Table S723.  Gene #241: 'C5ORF36 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
C5ORF36 MUTATED 5 0 0 2 0 0 0
C5ORF36 WILD-TYPE 29 11 9 5 6 20 9
'FAT2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.517 (Fisher's exact test), Q value = 0.76

Table S724.  Gene #242: 'FAT2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
FAT2 MUTATED 5 4 1 1 5
FAT2 WILD-TYPE 23 16 10 19 16
'FAT2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0497 (Fisher's exact test), Q value = 0.43

Table S725.  Gene #242: 'FAT2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
FAT2 MUTATED 8 1 3 3
FAT2 WILD-TYPE 27 32 13 9

Figure S98.  Get High-res Image Gene #242: 'FAT2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'FAT2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0666 (Fisher's exact test), Q value = 0.45

Table S726.  Gene #242: 'FAT2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
FAT2 MUTATED 9 0 1 2 2 1 0
FAT2 WILD-TYPE 25 11 8 5 4 19 9
'XRRA1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0778 (Fisher's exact test), Q value = 0.47

Table S727.  Gene #243: 'XRRA1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
XRRA1 MUTATED 0 2 1 0 0
XRRA1 WILD-TYPE 28 18 10 20 21
'XRRA1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.503 (Fisher's exact test), Q value = 0.75

Table S728.  Gene #243: 'XRRA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
XRRA1 MUTATED 2 0 1 0
XRRA1 WILD-TYPE 33 33 15 12
'XRRA1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.519 (Fisher's exact test), Q value = 0.76

Table S729.  Gene #243: 'XRRA1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
XRRA1 MUTATED 2 0 0 1 0 0 0
XRRA1 WILD-TYPE 32 11 9 6 6 20 9
'ZNF583 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.82 (Fisher's exact test), Q value = 0.93

Table S730.  Gene #244: 'ZNF583 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ZNF583 MUTATED 1 1 1 0 1
ZNF583 WILD-TYPE 27 19 10 20 20
'ZNF583 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 0.68

Table S731.  Gene #244: 'ZNF583 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ZNF583 MUTATED 2 0 1 1
ZNF583 WILD-TYPE 33 33 15 11
'ZNF583 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.312 (Fisher's exact test), Q value = 0.65

Table S732.  Gene #244: 'ZNF583 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ZNF583 MUTATED 2 0 0 1 1 0 0
ZNF583 WILD-TYPE 32 11 9 6 5 20 9
'FOXM1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.602 (Fisher's exact test), Q value = 0.81

Table S733.  Gene #245: 'FOXM1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
FOXM1 MUTATED 1 2 0 1 3
FOXM1 WILD-TYPE 27 18 11 19 18
'FOXM1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.4

Table S734.  Gene #245: 'FOXM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
FOXM1 MUTATED 6 0 0 1
FOXM1 WILD-TYPE 29 33 16 11

Figure S99.  Get High-res Image Gene #245: 'FOXM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'FOXM1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.147 (Fisher's exact test), Q value = 0.54

Table S735.  Gene #245: 'FOXM1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
FOXM1 MUTATED 6 0 0 0 1 0 0
FOXM1 WILD-TYPE 28 11 9 7 5 20 9
'INF2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0769 (Fisher's exact test), Q value = 0.47

Table S736.  Gene #246: 'INF2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
INF2 MUTATED 0 2 0 0 3
INF2 WILD-TYPE 28 18 11 20 18
'INF2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.261 (Fisher's exact test), Q value = 0.63

Table S737.  Gene #246: 'INF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
INF2 MUTATED 3 0 1 1
INF2 WILD-TYPE 32 33 15 11
'INF2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.375 (Fisher's exact test), Q value = 0.68

Table S738.  Gene #246: 'INF2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
INF2 MUTATED 3 0 0 0 1 0 1
INF2 WILD-TYPE 31 11 9 7 5 20 8
'SLC16A1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S739.  Gene #247: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SLC16A1 MUTATED 1 1 0 1 1
SLC16A1 WILD-TYPE 27 19 11 19 20
'SLC16A1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.319 (Fisher's exact test), Q value = 0.65

Table S740.  Gene #247: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SLC16A1 MUTATED 3 0 1 0
SLC16A1 WILD-TYPE 32 33 15 12
'SLC16A1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.482 (Fisher's exact test), Q value = 0.75

Table S741.  Gene #247: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SLC16A1 MUTATED 3 0 0 1 0 0 0
SLC16A1 WILD-TYPE 31 11 9 6 6 20 9
'SMAD7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.923 (Fisher's exact test), Q value = 0.98

Table S742.  Gene #248: 'SMAD7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SMAD7 MUTATED 1 1 0 1 2
SMAD7 WILD-TYPE 27 19 11 19 19
'SMAD7 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.738 (Fisher's exact test), Q value = 0.89

Table S743.  Gene #248: 'SMAD7 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SMAD7 MUTATED 3 2 0 0
SMAD7 WILD-TYPE 32 31 16 12
'SMAD7 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.869 (Fisher's exact test), Q value = 0.95

Table S744.  Gene #248: 'SMAD7 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SMAD7 MUTATED 2 0 0 0 0 2 1
SMAD7 WILD-TYPE 32 11 9 7 6 18 8
'CELSR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.654 (Fisher's exact test), Q value = 0.84

Table S745.  Gene #249: 'CELSR1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CELSR1 MUTATED 2 3 0 3 3
CELSR1 WILD-TYPE 26 17 11 17 18
'CELSR1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0406 (Fisher's exact test), Q value = 0.42

Table S746.  Gene #249: 'CELSR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CELSR1 MUTATED 8 1 2 0
CELSR1 WILD-TYPE 27 32 14 12

Figure S100.  Get High-res Image Gene #249: 'CELSR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'CELSR1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0887 (Fisher's exact test), Q value = 0.47

Table S747.  Gene #249: 'CELSR1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CELSR1 MUTATED 8 0 0 2 0 1 0
CELSR1 WILD-TYPE 26 11 9 5 6 19 9
'C14ORF43 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S748.  Gene #250: 'C14ORF43 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
C14ORF43 MUTATED 1 1 0 1 1
C14ORF43 WILD-TYPE 27 19 11 19 20
'C14ORF43 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.519 (Fisher's exact test), Q value = 0.76

Table S749.  Gene #250: 'C14ORF43 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
C14ORF43 MUTATED 3 1 0 0
C14ORF43 WILD-TYPE 32 32 16 12
'C14ORF43 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.962 (Fisher's exact test), Q value = 1

Table S750.  Gene #250: 'C14ORF43 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
C14ORF43 MUTATED 3 0 0 0 0 1 0
C14ORF43 WILD-TYPE 31 11 9 7 6 19 9
'SEC63 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0431 (Fisher's exact test), Q value = 0.42

Table S751.  Gene #251: 'SEC63 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SEC63 MUTATED 0 3 0 0 3
SEC63 WILD-TYPE 28 17 11 20 18

Figure S101.  Get High-res Image Gene #251: 'SEC63 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'SEC63 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.568 (Fisher's exact test), Q value = 0.78

Table S752.  Gene #251: 'SEC63 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SEC63 MUTATED 2 1 2 1
SEC63 WILD-TYPE 33 32 14 11
'SEC63 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.314 (Fisher's exact test), Q value = 0.65

Table S753.  Gene #251: 'SEC63 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SEC63 MUTATED 3 0 0 1 1 0 1
SEC63 WILD-TYPE 31 11 9 6 5 20 8
'USP47 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.944 (Fisher's exact test), Q value = 0.99

Table S754.  Gene #252: 'USP47 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
USP47 MUTATED 2 2 0 1 1
USP47 WILD-TYPE 26 18 11 19 20
'USP47 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0897 (Fisher's exact test), Q value = 0.47

Table S755.  Gene #252: 'USP47 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
USP47 MUTATED 5 0 1 0
USP47 WILD-TYPE 30 33 15 12
'USP47 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 0.63

Table S756.  Gene #252: 'USP47 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
USP47 MUTATED 5 0 0 1 0 0 0
USP47 WILD-TYPE 29 11 9 6 6 20 9
'ZNF253 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.189 (Fisher's exact test), Q value = 0.56

Table S757.  Gene #253: 'ZNF253 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ZNF253 MUTATED 0 3 0 1 2
ZNF253 WILD-TYPE 28 17 11 19 19
'ZNF253 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.54 (Fisher's exact test), Q value = 0.77

Table S758.  Gene #253: 'ZNF253 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ZNF253 MUTATED 4 1 1 0
ZNF253 WILD-TYPE 31 32 15 12
'ZNF253 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.413 (Fisher's exact test), Q value = 0.69

Table S759.  Gene #253: 'ZNF253 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ZNF253 MUTATED 4 0 0 1 0 0 1
ZNF253 WILD-TYPE 30 11 9 6 6 20 8
'C1ORF141 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.256 (Fisher's exact test), Q value = 0.63

Table S760.  Gene #254: 'C1ORF141 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
C1ORF141 MUTATED 1 1 2 0 2
C1ORF141 WILD-TYPE 27 19 9 20 19
'C1ORF141 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.176 (Fisher's exact test), Q value = 0.56

Table S761.  Gene #254: 'C1ORF141 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
C1ORF141 MUTATED 4 0 1 1
C1ORF141 WILD-TYPE 31 33 15 11
'C1ORF141 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.274 (Fisher's exact test), Q value = 0.63

Table S762.  Gene #254: 'C1ORF141 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
C1ORF141 MUTATED 4 0 0 1 1 0 0
C1ORF141 WILD-TYPE 30 11 9 6 5 20 9
'COL5A1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.517 (Fisher's exact test), Q value = 0.76

Table S763.  Gene #255: 'COL5A1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
COL5A1 MUTATED 3 2 1 1 5
COL5A1 WILD-TYPE 25 18 10 19 16
'COL5A1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.4

Table S764.  Gene #255: 'COL5A1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
COL5A1 MUTATED 7 0 2 2
COL5A1 WILD-TYPE 28 33 14 10

Figure S102.  Get High-res Image Gene #255: 'COL5A1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'COL5A1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0973 (Fisher's exact test), Q value = 0.48

Table S765.  Gene #255: 'COL5A1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
COL5A1 MUTATED 8 1 0 1 1 0 0
COL5A1 WILD-TYPE 26 10 9 6 5 20 9
'RAB3IL1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.589 (Fisher's exact test), Q value = 0.8

Table S766.  Gene #256: 'RAB3IL1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
RAB3IL1 MUTATED 1 1 1 0 2
RAB3IL1 WILD-TYPE 27 19 10 20 19
'RAB3IL1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.918 (Fisher's exact test), Q value = 0.98

Table S767.  Gene #256: 'RAB3IL1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
RAB3IL1 MUTATED 2 2 0 1
RAB3IL1 WILD-TYPE 33 31 16 11
'RAB3IL1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.179 (Fisher's exact test), Q value = 0.56

Table S768.  Gene #256: 'RAB3IL1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
RAB3IL1 MUTATED 2 0 0 0 1 0 2
RAB3IL1 WILD-TYPE 32 11 9 7 5 20 7
'C15ORF42 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.508 (Fisher's exact test), Q value = 0.75

Table S769.  Gene #257: 'C15ORF42 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
C15ORF42 MUTATED 1 2 2 1 1
C15ORF42 WILD-TYPE 27 18 9 19 20
'C15ORF42 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.316 (Fisher's exact test), Q value = 0.65

Table S770.  Gene #257: 'C15ORF42 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
C15ORF42 MUTATED 2 2 3 0
C15ORF42 WILD-TYPE 33 31 13 12
'C15ORF42 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.744 (Fisher's exact test), Q value = 0.89

Table S771.  Gene #257: 'C15ORF42 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
C15ORF42 MUTATED 4 0 0 1 0 1 1
C15ORF42 WILD-TYPE 30 11 9 6 6 19 8
'SPTY2D1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.114 (Fisher's exact test), Q value = 0.48

Table S772.  Gene #258: 'SPTY2D1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SPTY2D1 MUTATED 1 0 1 3 0
SPTY2D1 WILD-TYPE 27 20 10 17 21
'SPTY2D1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.173 (Fisher's exact test), Q value = 0.56

Table S773.  Gene #258: 'SPTY2D1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SPTY2D1 MUTATED 4 0 1 0
SPTY2D1 WILD-TYPE 31 33 15 12
'SPTY2D1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.383 (Fisher's exact test), Q value = 0.68

Table S774.  Gene #258: 'SPTY2D1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SPTY2D1 MUTATED 4 0 0 1 0 0 0
SPTY2D1 WILD-TYPE 30 11 9 6 6 20 9
'C19ORF66 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.589 (Fisher's exact test), Q value = 0.8

Table S775.  Gene #259: 'C19ORF66 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
C19ORF66 MUTATED 1 0 1 0 1
C19ORF66 WILD-TYPE 27 20 10 20 20
'C19ORF66 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 0.68

Table S776.  Gene #259: 'C19ORF66 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
C19ORF66 MUTATED 2 0 0 1
C19ORF66 WILD-TYPE 33 33 16 11
'C19ORF66 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 0.75

Table S777.  Gene #259: 'C19ORF66 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
C19ORF66 MUTATED 2 0 0 0 1 0 0
C19ORF66 WILD-TYPE 32 11 9 7 5 20 9
'MYO1A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.792 (Fisher's exact test), Q value = 0.92

Table S778.  Gene #260: 'MYO1A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
MYO1A MUTATED 2 3 1 1 3
MYO1A WILD-TYPE 26 17 10 19 18
'MYO1A MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0315 (Fisher's exact test), Q value = 0.42

Table S779.  Gene #260: 'MYO1A MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
MYO1A MUTATED 6 0 3 1
MYO1A WILD-TYPE 29 33 13 11

Figure S103.  Get High-res Image Gene #260: 'MYO1A MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'MYO1A MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.103 (Fisher's exact test), Q value = 0.48

Table S780.  Gene #260: 'MYO1A MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
MYO1A MUTATED 6 0 1 2 1 0 0
MYO1A WILD-TYPE 28 11 8 5 5 20 9
'DMXL2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.352 (Fisher's exact test), Q value = 0.68

Table S781.  Gene #261: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
DMXL2 MUTATED 3 3 2 0 3
DMXL2 WILD-TYPE 25 17 9 20 18
'DMXL2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.39

Table S782.  Gene #261: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DMXL2 MUTATED 8 0 2 1
DMXL2 WILD-TYPE 27 33 14 11

Figure S104.  Get High-res Image Gene #261: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'DMXL2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0284 (Fisher's exact test), Q value = 0.42

Table S783.  Gene #261: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DMXL2 MUTATED 8 0 0 2 1 0 0
DMXL2 WILD-TYPE 26 11 9 5 5 20 9

Figure S105.  Get High-res Image Gene #261: 'DMXL2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'ZIC5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.319 (Fisher's exact test), Q value = 0.65

Table S784.  Gene #262: 'ZIC5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ZIC5 MUTATED 1 2 1 0 3
ZIC5 WILD-TYPE 27 18 10 20 18
'ZIC5 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.287 (Fisher's exact test), Q value = 0.64

Table S785.  Gene #262: 'ZIC5 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ZIC5 MUTATED 5 1 1 0
ZIC5 WILD-TYPE 30 32 15 12
'ZIC5 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.317 (Fisher's exact test), Q value = 0.65

Table S786.  Gene #262: 'ZIC5 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ZIC5 MUTATED 5 0 0 1 0 0 1
ZIC5 WILD-TYPE 29 11 9 6 6 20 8
'DSC1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.652 (Fisher's exact test), Q value = 0.84

Table S787.  Gene #263: 'DSC1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
DSC1 MUTATED 1 2 1 1 3
DSC1 WILD-TYPE 27 18 10 19 18
'DSC1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.171 (Fisher's exact test), Q value = 0.56

Table S788.  Gene #263: 'DSC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DSC1 MUTATED 6 1 1 0
DSC1 WILD-TYPE 29 32 15 12
'DSC1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.214 (Fisher's exact test), Q value = 0.58

Table S789.  Gene #263: 'DSC1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DSC1 MUTATED 6 0 0 1 0 0 1
DSC1 WILD-TYPE 28 11 9 6 6 20 8
'CCKBR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.551 (Fisher's exact test), Q value = 0.77

Table S790.  Gene #264: 'CCKBR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CCKBR MUTATED 0 1 1 1 1
CCKBR WILD-TYPE 28 19 10 19 20
'CCKBR MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.355 (Fisher's exact test), Q value = 0.68

Table S791.  Gene #264: 'CCKBR MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CCKBR MUTATED 2 0 1 1
CCKBR WILD-TYPE 33 33 15 11
'CCKBR MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.309 (Fisher's exact test), Q value = 0.65

Table S792.  Gene #264: 'CCKBR MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CCKBR MUTATED 2 0 0 1 1 0 0
CCKBR WILD-TYPE 32 11 9 6 5 20 9
'QKI MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.858 (Fisher's exact test), Q value = 0.94

Table S793.  Gene #265: 'QKI MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
QKI MUTATED 2 1 0 1 0
QKI WILD-TYPE 26 19 11 19 21
'QKI MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.351 (Fisher's exact test), Q value = 0.68

Table S794.  Gene #265: 'QKI MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
QKI MUTATED 2 0 1 1
QKI WILD-TYPE 33 33 15 11
'QKI MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.4 (Fisher's exact test), Q value = 0.69

Table S795.  Gene #265: 'QKI MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
QKI MUTATED 3 0 0 0 1 0 0
QKI WILD-TYPE 31 11 9 7 5 20 9
'DLGAP3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.616 (Fisher's exact test), Q value = 0.82

Table S796.  Gene #266: 'DLGAP3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
DLGAP3 MUTATED 1 1 0 1 3
DLGAP3 WILD-TYPE 27 19 11 19 18
'DLGAP3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.167 (Fisher's exact test), Q value = 0.56

Table S797.  Gene #266: 'DLGAP3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DLGAP3 MUTATED 3 0 2 1
DLGAP3 WILD-TYPE 32 33 14 11
'DLGAP3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.279 (Fisher's exact test), Q value = 0.63

Table S798.  Gene #266: 'DLGAP3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DLGAP3 MUTATED 4 0 0 1 1 0 0
DLGAP3 WILD-TYPE 30 11 9 6 5 20 9
'ZNF626 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.762 (Fisher's exact test), Q value = 0.9

Table S799.  Gene #267: 'ZNF626 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ZNF626 MUTATED 3 2 0 1 3
ZNF626 WILD-TYPE 25 18 11 19 18
'ZNF626 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.791 (Fisher's exact test), Q value = 0.92

Table S800.  Gene #267: 'ZNF626 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ZNF626 MUTATED 4 3 2 0
ZNF626 WILD-TYPE 31 30 14 12
'ZNF626 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.805 (Fisher's exact test), Q value = 0.93

Table S801.  Gene #267: 'ZNF626 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ZNF626 MUTATED 5 0 0 1 0 2 1
ZNF626 WILD-TYPE 29 11 9 6 6 18 8
'MGA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.558 (Fisher's exact test), Q value = 0.78

Table S802.  Gene #268: 'MGA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
MGA MUTATED 4 3 1 1 5
MGA WILD-TYPE 24 17 10 19 16
'MGA MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0771 (Fisher's exact test), Q value = 0.47

Table S803.  Gene #268: 'MGA MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
MGA MUTATED 8 1 3 2
MGA WILD-TYPE 27 32 13 10
'MGA MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0514 (Fisher's exact test), Q value = 0.43

Table S804.  Gene #268: 'MGA MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
MGA MUTATED 7 0 1 3 2 1 0
MGA WILD-TYPE 27 11 8 4 4 19 9
'C3ORF23 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.438 (Fisher's exact test), Q value = 0.72

Table S805.  Gene #269: 'C3ORF23 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
C3ORF23 MUTATED 0 1 1 2 1
C3ORF23 WILD-TYPE 28 19 10 18 20
'C3ORF23 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.522 (Fisher's exact test), Q value = 0.76

Table S806.  Gene #269: 'C3ORF23 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
C3ORF23 MUTATED 3 1 0 1
C3ORF23 WILD-TYPE 32 32 16 11
'C3ORF23 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.752 (Fisher's exact test), Q value = 0.9

Table S807.  Gene #269: 'C3ORF23 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
C3ORF23 MUTATED 3 0 0 0 1 1 0
C3ORF23 WILD-TYPE 31 11 9 7 5 19 9
'ALPPL2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.722 (Fisher's exact test), Q value = 0.88

Table S808.  Gene #270: 'ALPPL2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ALPPL2 MUTATED 2 2 0 0 1
ALPPL2 WILD-TYPE 26 18 11 20 20
'ALPPL2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.733 (Fisher's exact test), Q value = 0.89

Table S809.  Gene #270: 'ALPPL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ALPPL2 MUTATED 3 1 1 0
ALPPL2 WILD-TYPE 32 32 15 12
'ALPPL2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.534 (Fisher's exact test), Q value = 0.77

Table S810.  Gene #270: 'ALPPL2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ALPPL2 MUTATED 4 0 0 0 0 0 1
ALPPL2 WILD-TYPE 30 11 9 7 6 20 8
'EFHC1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.597 (Fisher's exact test), Q value = 0.8

Table S811.  Gene #271: 'EFHC1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
EFHC1 MUTATED 2 3 2 1 1
EFHC1 WILD-TYPE 26 17 9 19 20
'EFHC1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0734 (Fisher's exact test), Q value = 0.47

Table S812.  Gene #271: 'EFHC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
EFHC1 MUTATED 4 1 4 0
EFHC1 WILD-TYPE 31 32 12 12
'EFHC1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 0.42

Table S813.  Gene #271: 'EFHC1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
EFHC1 MUTATED 5 0 0 3 0 0 1
EFHC1 WILD-TYPE 29 11 9 4 6 20 8

Figure S106.  Get High-res Image Gene #271: 'EFHC1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'HNRNPA3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.665 (Fisher's exact test), Q value = 0.85

Table S814.  Gene #272: 'HNRNPA3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
HNRNPA3 MUTATED 1 2 0 0 1
HNRNPA3 WILD-TYPE 27 18 11 20 20
'HNRNPA3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.508 (Fisher's exact test), Q value = 0.75

Table S815.  Gene #272: 'HNRNPA3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
HNRNPA3 MUTATED 2 0 1 0
HNRNPA3 WILD-TYPE 33 33 15 12
'HNRNPA3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.696 (Fisher's exact test), Q value = 0.86

Table S816.  Gene #272: 'HNRNPA3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
HNRNPA3 MUTATED 3 0 0 0 0 0 0
HNRNPA3 WILD-TYPE 31 11 9 7 6 20 9
'UBB MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.755 (Fisher's exact test), Q value = 0.9

Table S817.  Gene #273: 'UBB MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
UBB MUTATED 1 1 1 1 0
UBB WILD-TYPE 27 19 10 19 21
'UBB MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0213 (Fisher's exact test), Q value = 0.4

Table S818.  Gene #273: 'UBB MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
UBB MUTATED 1 0 3 0
UBB WILD-TYPE 34 33 13 12

Figure S107.  Get High-res Image Gene #273: 'UBB MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'UBB MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.48 (Fisher's exact test), Q value = 0.75

Table S819.  Gene #273: 'UBB MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
UBB MUTATED 3 0 0 1 0 0 0
UBB WILD-TYPE 31 11 9 6 6 20 9
'SNX25 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.86 (Fisher's exact test), Q value = 0.94

Table S820.  Gene #274: 'SNX25 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SNX25 MUTATED 2 1 0 1 0
SNX25 WILD-TYPE 26 19 11 19 21
'SNX25 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.122 (Fisher's exact test), Q value = 0.49

Table S821.  Gene #274: 'SNX25 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SNX25 MUTATED 4 0 0 0
SNX25 WILD-TYPE 31 33 16 12
'SNX25 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.573 (Fisher's exact test), Q value = 0.78

Table S822.  Gene #274: 'SNX25 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SNX25 MUTATED 4 0 0 0 0 0 0
SNX25 WILD-TYPE 30 11 9 7 6 20 9
'GDF7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S823.  Gene #275: 'GDF7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
GDF7 MUTATED 1 1 0 1 1
GDF7 WILD-TYPE 27 19 11 19 20
'GDF7 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.722 (Fisher's exact test), Q value = 0.88

Table S824.  Gene #275: 'GDF7 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
GDF7 MUTATED 2 1 0 1
GDF7 WILD-TYPE 33 32 16 11
'GDF7 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.623 (Fisher's exact test), Q value = 0.83

Table S825.  Gene #275: 'GDF7 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
GDF7 MUTATED 3 0 0 0 0 0 1
GDF7 WILD-TYPE 31 11 9 7 6 20 8
'MFI2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.105 (Fisher's exact test), Q value = 0.48

Table S826.  Gene #276: 'MFI2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
MFI2 MUTATED 1 0 2 0 2
MFI2 WILD-TYPE 27 20 9 20 19
'MFI2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.189 (Fisher's exact test), Q value = 0.56

Table S827.  Gene #276: 'MFI2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
MFI2 MUTATED 2 0 2 1
MFI2 WILD-TYPE 33 33 14 11
'MFI2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.297 (Fisher's exact test), Q value = 0.65

Table S828.  Gene #276: 'MFI2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
MFI2 MUTATED 3 0 0 1 1 0 0
MFI2 WILD-TYPE 31 11 9 6 5 20 9
'AKT1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S829.  Gene #277: 'AKT1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
AKT1 MUTATED 1 1 0 1 1
AKT1 WILD-TYPE 27 19 11 19 20
'AKT1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.38 (Fisher's exact test), Q value = 0.68

Table S830.  Gene #277: 'AKT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AKT1 MUTATED 2 0 0 1
AKT1 WILD-TYPE 33 33 16 11
'AKT1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 0.75

Table S831.  Gene #277: 'AKT1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AKT1 MUTATED 2 0 0 0 1 0 0
AKT1 WILD-TYPE 32 11 9 7 5 20 9
'DENND4C MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.937 (Fisher's exact test), Q value = 0.99

Table S832.  Gene #278: 'DENND4C MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
DENND4C MUTATED 3 1 1 1 1
DENND4C WILD-TYPE 25 19 10 19 20
'DENND4C MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0586 (Fisher's exact test), Q value = 0.45

Table S833.  Gene #278: 'DENND4C MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DENND4C MUTATED 5 0 2 0
DENND4C WILD-TYPE 30 33 14 12
'DENND4C MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.176 (Fisher's exact test), Q value = 0.56

Table S834.  Gene #278: 'DENND4C MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DENND4C MUTATED 6 0 0 1 0 0 0
DENND4C WILD-TYPE 28 11 9 6 6 20 9
'ACSM4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.94 (Fisher's exact test), Q value = 0.99

Table S835.  Gene #279: 'ACSM4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ACSM4 MUTATED 2 1 0 0 1
ACSM4 WILD-TYPE 26 19 11 20 20
'ACSM4 MUTATION STATUS' versus 'METHYLATION_CNMF'

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

Table S836.  Gene #279: 'ACSM4 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ACSM4 MUTATED 2 1 1 0
ACSM4 WILD-TYPE 33 32 15 12
'ACSM4 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.52 (Fisher's exact test), Q value = 0.76

Table S837.  Gene #279: 'ACSM4 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ACSM4 MUTATED 2 1 0 1 0 0 0
ACSM4 WILD-TYPE 32 10 9 6 6 20 9
'TNRC18 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.523 (Fisher's exact test), Q value = 0.76

Table S838.  Gene #280: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TNRC18 MUTATED 2 1 0 2 4
TNRC18 WILD-TYPE 26 19 11 18 17
'TNRC18 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.375 (Fisher's exact test), Q value = 0.68

Table S839.  Gene #280: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TNRC18 MUTATED 5 1 2 1
TNRC18 WILD-TYPE 30 32 14 11
'TNRC18 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.105 (Fisher's exact test), Q value = 0.48

Table S840.  Gene #280: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TNRC18 MUTATED 6 0 0 2 0 0 1
TNRC18 WILD-TYPE 28 11 9 5 6 20 8
'CACNA1F MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.922 (Fisher's exact test), Q value = 0.98

Table S841.  Gene #281: 'CACNA1F MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CACNA1F MUTATED 4 4 1 2 3
CACNA1F WILD-TYPE 24 16 10 18 18
'CACNA1F MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.00376 (Fisher's exact test), Q value = 0.32

Table S842.  Gene #281: 'CACNA1F MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CACNA1F MUTATED 7 0 5 1
CACNA1F WILD-TYPE 28 33 11 11

Figure S108.  Get High-res Image Gene #281: 'CACNA1F MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'CACNA1F MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0346 (Fisher's exact test), Q value = 0.42

Table S843.  Gene #281: 'CACNA1F MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CACNA1F MUTATED 9 1 0 2 1 0 0
CACNA1F WILD-TYPE 25 10 9 5 5 20 9

Figure S109.  Get High-res Image Gene #281: 'CACNA1F MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'RASA1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.136 (Fisher's exact test), Q value = 0.51

Table S844.  Gene #282: 'RASA1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
RASA1 MUTATED 0 3 0 2 3
RASA1 WILD-TYPE 28 17 11 18 18
'RASA1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.42

Table S845.  Gene #282: 'RASA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
RASA1 MUTATED 6 0 1 1
RASA1 WILD-TYPE 29 33 15 11

Figure S110.  Get High-res Image Gene #282: 'RASA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'RASA1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.213 (Fisher's exact test), Q value = 0.58

Table S846.  Gene #282: 'RASA1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
RASA1 MUTATED 6 0 1 1 0 0 0
RASA1 WILD-TYPE 28 11 8 6 6 20 9
'IRX5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0651 (Fisher's exact test), Q value = 0.45

Table S847.  Gene #283: 'IRX5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
IRX5 MUTATED 0 1 0 4 2
IRX5 WILD-TYPE 28 19 11 16 19
'IRX5 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.197 (Fisher's exact test), Q value = 0.57

Table S848.  Gene #283: 'IRX5 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
IRX5 MUTATED 5 1 0 1
IRX5 WILD-TYPE 30 32 16 11
'IRX5 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.688 (Fisher's exact test), Q value = 0.86

Table S849.  Gene #283: 'IRX5 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
IRX5 MUTATED 4 0 1 0 1 1 0
IRX5 WILD-TYPE 30 11 8 7 5 19 9
'TBX10 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.855 (Fisher's exact test), Q value = 0.94

Table S850.  Gene #284: 'TBX10 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TBX10 MUTATED 1 1 0 1 0
TBX10 WILD-TYPE 27 19 11 19 21
'TBX10 MUTATION STATUS' versus 'METHYLATION_CNMF'

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

Table S851.  Gene #284: 'TBX10 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TBX10 MUTATED 2 1 0 0
TBX10 WILD-TYPE 33 32 16 12
'TBX10 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.653 (Fisher's exact test), Q value = 0.84

Table S852.  Gene #284: 'TBX10 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TBX10 MUTATED 2 0 0 0 0 0 1
TBX10 WILD-TYPE 32 11 9 7 6 20 8
'PRIC285 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.691 (Fisher's exact test), Q value = 0.86

Table S853.  Gene #285: 'PRIC285 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PRIC285 MUTATED 3 2 1 5 3
PRIC285 WILD-TYPE 25 18 10 15 18
'PRIC285 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0517 (Fisher's exact test), Q value = 0.43

Table S854.  Gene #285: 'PRIC285 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PRIC285 MUTATED 8 1 2 3
PRIC285 WILD-TYPE 27 32 14 9
'PRIC285 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0407 (Fisher's exact test), Q value = 0.42

Table S855.  Gene #285: 'PRIC285 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PRIC285 MUTATED 9 2 0 0 2 0 1
PRIC285 WILD-TYPE 25 9 9 7 4 20 8

Figure S111.  Get High-res Image Gene #285: 'PRIC285 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'MAX MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.484 (Fisher's exact test), Q value = 0.75

Table S856.  Gene #286: 'MAX MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
MAX MUTATED 2 0 1 1 0
MAX WILD-TYPE 26 20 10 19 21
'MAX MUTATION STATUS' versus 'METHYLATION_CNMF'

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

Table S857.  Gene #286: 'MAX MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
MAX MUTATED 2 1 1 0
MAX WILD-TYPE 33 32 15 12
'MAX MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.834 (Fisher's exact test), Q value = 0.94

Table S858.  Gene #286: 'MAX MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
MAX MUTATED 2 0 0 1 0 1 0
MAX WILD-TYPE 32 11 9 6 6 19 9
'IQSEC2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.925 (Fisher's exact test), Q value = 0.98

Table S859.  Gene #287: 'IQSEC2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
IQSEC2 MUTATED 4 1 1 2 3
IQSEC2 WILD-TYPE 24 19 10 18 18
'IQSEC2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.56

Table S860.  Gene #287: 'IQSEC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
IQSEC2 MUTATED 6 1 3 1
IQSEC2 WILD-TYPE 29 32 13 11
'IQSEC2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.154 (Fisher's exact test), Q value = 0.55

Table S861.  Gene #287: 'IQSEC2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
IQSEC2 MUTATED 7 0 0 2 1 1 0
IQSEC2 WILD-TYPE 27 11 9 5 5 19 9
'KIAA1804 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.229 (Fisher's exact test), Q value = 0.6

Table S862.  Gene #288: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
KIAA1804 MUTATED 0 3 1 1 2
KIAA1804 WILD-TYPE 28 17 10 19 19
'KIAA1804 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.406 (Fisher's exact test), Q value = 0.69

Table S863.  Gene #288: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
KIAA1804 MUTATED 3 1 1 2
KIAA1804 WILD-TYPE 32 32 15 10
'KIAA1804 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.114 (Fisher's exact test), Q value = 0.48

Table S864.  Gene #288: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
KIAA1804 MUTATED 2 1 0 1 2 0 1
KIAA1804 WILD-TYPE 32 10 9 6 4 20 8
'IPO9 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.924 (Fisher's exact test), Q value = 0.98

Table S865.  Gene #289: 'IPO9 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
IPO9 MUTATED 1 1 0 1 2
IPO9 WILD-TYPE 27 19 11 19 19
'IPO9 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.367 (Fisher's exact test), Q value = 0.68

Table S866.  Gene #289: 'IPO9 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
IPO9 MUTATED 4 1 0 0
IPO9 WILD-TYPE 31 32 16 12
'IPO9 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.588 (Fisher's exact test), Q value = 0.8

Table S867.  Gene #289: 'IPO9 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
IPO9 MUTATED 3 0 1 0 0 0 1
IPO9 WILD-TYPE 31 11 8 7 6 20 8
'TPP2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.305 (Fisher's exact test), Q value = 0.65

Table S868.  Gene #290: 'TPP2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TPP2 MUTATED 2 3 0 0 3
TPP2 WILD-TYPE 26 17 11 20 18
'TPP2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0748 (Fisher's exact test), Q value = 0.47

Table S869.  Gene #290: 'TPP2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TPP2 MUTATED 4 0 2 2
TPP2 WILD-TYPE 31 33 14 10
'TPP2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0796 (Fisher's exact test), Q value = 0.47

Table S870.  Gene #290: 'TPP2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TPP2 MUTATED 5 0 0 1 2 0 0
TPP2 WILD-TYPE 29 11 9 6 4 20 9
'CDC73 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.485 (Fisher's exact test), Q value = 0.75

Table S871.  Gene #291: 'CDC73 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CDC73 MUTATED 2 1 1 0 3
CDC73 WILD-TYPE 26 19 10 20 18
'CDC73 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.256 (Fisher's exact test), Q value = 0.63

Table S872.  Gene #291: 'CDC73 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CDC73 MUTATED 2 1 2 2
CDC73 WILD-TYPE 33 32 14 10
'CDC73 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.251 (Fisher's exact test), Q value = 0.63

Table S873.  Gene #291: 'CDC73 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CDC73 MUTATED 4 0 0 0 2 1 0
CDC73 WILD-TYPE 30 11 9 7 4 19 9
'HRASLS5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.959 (Fisher's exact test), Q value = 1

Table S874.  Gene #292: 'HRASLS5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
HRASLS5 MUTATED 1 1 1 1 1
HRASLS5 WILD-TYPE 27 19 10 19 20
'HRASLS5 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.162 (Fisher's exact test), Q value = 0.56

Table S875.  Gene #292: 'HRASLS5 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
HRASLS5 MUTATED 3 0 2 0
HRASLS5 WILD-TYPE 32 33 14 12
'HRASLS5 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.183 (Fisher's exact test), Q value = 0.56

Table S876.  Gene #292: 'HRASLS5 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
HRASLS5 MUTATED 3 0 0 2 0 0 0
HRASLS5 WILD-TYPE 31 11 9 5 6 20 9
'ARID4B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.56 (Fisher's exact test), Q value = 0.78

Table S877.  Gene #293: 'ARID4B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ARID4B MUTATED 1 3 0 1 1
ARID4B WILD-TYPE 27 17 11 19 20
'ARID4B MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.74 (Fisher's exact test), Q value = 0.89

Table S878.  Gene #293: 'ARID4B MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ARID4B MUTATED 3 1 1 0
ARID4B WILD-TYPE 32 32 15 12
'ARID4B MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.452 (Fisher's exact test), Q value = 0.73

Table S879.  Gene #293: 'ARID4B MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ARID4B MUTATED 3 0 0 1 0 0 1
ARID4B WILD-TYPE 31 11 9 6 6 20 8
'SLC2A5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.833 (Fisher's exact test), Q value = 0.94

Table S880.  Gene #294: 'SLC2A5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SLC2A5 MUTATED 2 1 1 0 1
SLC2A5 WILD-TYPE 26 19 10 20 20
'SLC2A5 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.114 (Fisher's exact test), Q value = 0.48

Table S881.  Gene #294: 'SLC2A5 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SLC2A5 MUTATED 1 1 3 0
SLC2A5 WILD-TYPE 34 32 13 12
'SLC2A5 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.473 (Fisher's exact test), Q value = 0.75

Table S882.  Gene #294: 'SLC2A5 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SLC2A5 MUTATED 2 1 0 1 0 0 1
SLC2A5 WILD-TYPE 32 10 9 6 6 20 8
'TUBB4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.768 (Fisher's exact test), Q value = 0.91

Table S883.  Gene #295: 'TUBB4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TUBB4 MUTATED 1 2 0 2 1
TUBB4 WILD-TYPE 27 18 11 18 20
'TUBB4 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0907 (Fisher's exact test), Q value = 0.47

Table S884.  Gene #295: 'TUBB4 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TUBB4 MUTATED 5 0 1 0
TUBB4 WILD-TYPE 30 33 15 12
'TUBB4 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.412 (Fisher's exact test), Q value = 0.69

Table S885.  Gene #295: 'TUBB4 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TUBB4 MUTATED 4 0 0 1 0 0 1
TUBB4 WILD-TYPE 30 11 9 6 6 20 8
'ARID3B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0788 (Fisher's exact test), Q value = 0.47

Table S886.  Gene #296: 'ARID3B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ARID3B MUTATED 0 1 0 1 4
ARID3B WILD-TYPE 28 19 11 19 17
'ARID3B MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.345 (Fisher's exact test), Q value = 0.68

Table S887.  Gene #296: 'ARID3B MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ARID3B MUTATED 4 1 0 1
ARID3B WILD-TYPE 31 32 16 11
'ARID3B MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.369 (Fisher's exact test), Q value = 0.68

Table S888.  Gene #296: 'ARID3B MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ARID3B MUTATED 5 0 0 0 0 0 1
ARID3B WILD-TYPE 29 11 9 7 6 20 8
'AADACL3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.246 (Fisher's exact test), Q value = 0.63

Table S889.  Gene #297: 'AADACL3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
AADACL3 MUTATED 0 1 1 0 2
AADACL3 WILD-TYPE 28 19 10 20 19
'AADACL3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.352 (Fisher's exact test), Q value = 0.68

Table S890.  Gene #297: 'AADACL3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AADACL3 MUTATED 2 0 1 1
AADACL3 WILD-TYPE 33 33 15 11
'AADACL3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.309 (Fisher's exact test), Q value = 0.65

Table S891.  Gene #297: 'AADACL3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AADACL3 MUTATED 2 0 0 1 1 0 0
AADACL3 WILD-TYPE 32 11 9 6 5 20 9
'TXNDC11 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.454 (Fisher's exact test), Q value = 0.73

Table S892.  Gene #298: 'TXNDC11 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TXNDC11 MUTATED 2 1 0 0 3
TXNDC11 WILD-TYPE 26 19 11 20 18
'TXNDC11 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0523 (Fisher's exact test), Q value = 0.43

Table S893.  Gene #298: 'TXNDC11 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TXNDC11 MUTATED 5 0 0 1
TXNDC11 WILD-TYPE 30 33 16 11
'TXNDC11 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.252 (Fisher's exact test), Q value = 0.63

Table S894.  Gene #298: 'TXNDC11 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TXNDC11 MUTATED 5 0 0 0 1 0 0
TXNDC11 WILD-TYPE 29 11 9 7 5 20 9
'TULP4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.197 (Fisher's exact test), Q value = 0.57

Table S895.  Gene #299: 'TULP4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TULP4 MUTATED 0 1 2 2 2
TULP4 WILD-TYPE 28 19 9 18 19
'TULP4 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.132 (Fisher's exact test), Q value = 0.51

Table S896.  Gene #299: 'TULP4 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TULP4 MUTATED 4 0 2 1
TULP4 WILD-TYPE 31 33 14 11
'TULP4 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.114 (Fisher's exact test), Q value = 0.48

Table S897.  Gene #299: 'TULP4 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TULP4 MUTATED 4 0 0 2 1 0 0
TULP4 WILD-TYPE 30 11 9 5 5 20 9
'CALB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.642 (Fisher's exact test), Q value = 0.84

Table S898.  Gene #300: 'CALB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CALB1 MUTATED 3 1 0 0 1
CALB1 WILD-TYPE 25 19 11 20 20
'CALB1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.738 (Fisher's exact test), Q value = 0.89

Table S899.  Gene #300: 'CALB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CALB1 MUTATED 3 1 1 0
CALB1 WILD-TYPE 32 32 15 12
'CALB1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.638 (Fisher's exact test), Q value = 0.84

Table S900.  Gene #300: 'CALB1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CALB1 MUTATED 3 1 0 0 0 0 1
CALB1 WILD-TYPE 31 10 9 7 6 20 8
'OXER1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.734 (Fisher's exact test), Q value = 0.89

Table S901.  Gene #301: 'OXER1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
OXER1 MUTATED 2 0 0 0 1
OXER1 WILD-TYPE 26 20 11 20 20
'OXER1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.282 (Fisher's exact test), Q value = 0.64

Table S902.  Gene #301: 'OXER1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
OXER1 MUTATED 3 0 0 0
OXER1 WILD-TYPE 32 33 16 12
'OXER1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.697 (Fisher's exact test), Q value = 0.86

Table S903.  Gene #301: 'OXER1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
OXER1 MUTATED 3 0 0 0 0 0 0
OXER1 WILD-TYPE 31 11 9 7 6 20 9
'BCLAF1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.782 (Fisher's exact test), Q value = 0.92

Table S904.  Gene #302: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
BCLAF1 MUTATED 2 2 2 1 2
BCLAF1 WILD-TYPE 26 18 9 19 19
'BCLAF1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.363 (Fisher's exact test), Q value = 0.68

Table S905.  Gene #302: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
BCLAF1 MUTATED 6 2 1 0
BCLAF1 WILD-TYPE 29 31 15 12
'BCLAF1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.524 (Fisher's exact test), Q value = 0.76

Table S906.  Gene #302: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
BCLAF1 MUTATED 5 1 1 1 0 0 1
BCLAF1 WILD-TYPE 29 10 8 6 6 20 8
'IDH3A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.82 (Fisher's exact test), Q value = 0.93

Table S907.  Gene #303: 'IDH3A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
IDH3A MUTATED 1 0 1 1 1
IDH3A WILD-TYPE 27 20 10 19 20
'IDH3A MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.319 (Fisher's exact test), Q value = 0.65

Table S908.  Gene #303: 'IDH3A MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
IDH3A MUTATED 3 0 1 0
IDH3A WILD-TYPE 32 33 15 12
'IDH3A MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.48 (Fisher's exact test), Q value = 0.75

Table S909.  Gene #303: 'IDH3A MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
IDH3A MUTATED 3 0 0 1 0 0 0
IDH3A WILD-TYPE 31 11 9 6 6 20 9
'SYNM MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S910.  Gene #304: 'SYNM MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SYNM MUTATED 1 1 0 0 1
SYNM WILD-TYPE 27 19 11 20 20
'SYNM MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.504 (Fisher's exact test), Q value = 0.75

Table S911.  Gene #304: 'SYNM MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SYNM MUTATED 2 0 1 0
SYNM WILD-TYPE 33 33 15 12
'SYNM MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.521 (Fisher's exact test), Q value = 0.76

Table S912.  Gene #304: 'SYNM MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SYNM MUTATED 2 0 0 1 0 0 0
SYNM WILD-TYPE 32 11 9 6 6 20 9
'C20ORF194 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.663 (Fisher's exact test), Q value = 0.85

Table S913.  Gene #305: 'C20ORF194 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
C20ORF194 MUTATED 1 2 0 0 1
C20ORF194 WILD-TYPE 27 18 11 20 20
'C20ORF194 MUTATION STATUS' versus 'METHYLATION_CNMF'

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

Table S914.  Gene #305: 'C20ORF194 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
C20ORF194 MUTATED 2 2 0 0
C20ORF194 WILD-TYPE 33 31 16 12
'C20ORF194 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.674 (Fisher's exact test), Q value = 0.85

Table S915.  Gene #305: 'C20ORF194 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
C20ORF194 MUTATED 2 1 0 0 0 0 1
C20ORF194 WILD-TYPE 32 10 9 7 6 20 8
'FRG1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.979 (Fisher's exact test), Q value = 1

Table S916.  Gene #306: 'FRG1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
FRG1 MUTATED 2 2 1 1 1
FRG1 WILD-TYPE 26 18 10 19 20
'FRG1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.48

Table S917.  Gene #306: 'FRG1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
FRG1 MUTATED 5 0 1 1
FRG1 WILD-TYPE 30 33 15 11
'FRG1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.209 (Fisher's exact test), Q value = 0.58

Table S918.  Gene #306: 'FRG1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
FRG1 MUTATED 5 0 0 1 1 0 0
FRG1 WILD-TYPE 29 11 9 6 5 20 9
'DOCK9 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.321 (Fisher's exact test), Q value = 0.65

Table S919.  Gene #307: 'DOCK9 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
DOCK9 MUTATED 1 2 0 1 4
DOCK9 WILD-TYPE 27 18 11 19 17
'DOCK9 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.411 (Fisher's exact test), Q value = 0.69

Table S920.  Gene #307: 'DOCK9 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DOCK9 MUTATED 5 1 1 1
DOCK9 WILD-TYPE 30 32 15 11
'DOCK9 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 0.63

Table S921.  Gene #307: 'DOCK9 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DOCK9 MUTATED 5 0 0 1 1 0 1
DOCK9 WILD-TYPE 29 11 9 6 5 20 8
'LMOD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.642 (Fisher's exact test), Q value = 0.84

Table S922.  Gene #308: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
LMOD2 MUTATED 2 2 0 0 2
LMOD2 WILD-TYPE 26 18 11 20 19
'LMOD2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 0.68

Table S923.  Gene #308: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
LMOD2 MUTATED 4 1 0 0
LMOD2 WILD-TYPE 31 32 16 12
'LMOD2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.904 (Fisher's exact test), Q value = 0.97

Table S924.  Gene #308: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
LMOD2 MUTATED 3 0 0 0 0 1 1
LMOD2 WILD-TYPE 31 11 9 7 6 19 8
'IGF2R MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.601 (Fisher's exact test), Q value = 0.81

Table S925.  Gene #309: 'IGF2R MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
IGF2R MUTATED 3 1 1 1 4
IGF2R WILD-TYPE 25 19 10 19 17
'IGF2R MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.131 (Fisher's exact test), Q value = 0.51

Table S926.  Gene #309: 'IGF2R MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
IGF2R MUTATED 7 1 1 1
IGF2R WILD-TYPE 28 32 15 11
'IGF2R MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.14 (Fisher's exact test), Q value = 0.52

Table S927.  Gene #309: 'IGF2R MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
IGF2R MUTATED 8 0 0 0 1 1 0
IGF2R WILD-TYPE 26 11 9 7 5 19 9
'POTEE MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.169 (Fisher's exact test), Q value = 0.56

Table S928.  Gene #310: 'POTEE MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
POTEE MUTATED 2 0 2 0 1
POTEE WILD-TYPE 26 20 9 20 20
'POTEE MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.517 (Fisher's exact test), Q value = 0.76

Table S929.  Gene #310: 'POTEE MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
POTEE MUTATED 3 1 0 0
POTEE WILD-TYPE 32 32 16 12
'POTEE MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.963 (Fisher's exact test), Q value = 1

Table S930.  Gene #310: 'POTEE MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
POTEE MUTATED 3 0 0 0 0 1 0
POTEE WILD-TYPE 31 11 9 7 6 19 9
'N4BP2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.138 (Fisher's exact test), Q value = 0.52

Table S931.  Gene #311: 'N4BP2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
N4BP2 MUTATED 1 5 2 1 2
N4BP2 WILD-TYPE 27 15 9 19 19
'N4BP2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.406 (Fisher's exact test), Q value = 0.69

Table S932.  Gene #311: 'N4BP2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
N4BP2 MUTATED 6 2 1 2
N4BP2 WILD-TYPE 29 31 15 10
'N4BP2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.262 (Fisher's exact test), Q value = 0.63

Table S933.  Gene #311: 'N4BP2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
N4BP2 MUTATED 5 1 1 1 2 0 1
N4BP2 WILD-TYPE 29 10 8 6 4 20 8
'RUFY2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.892 (Fisher's exact test), Q value = 0.97

Table S934.  Gene #312: 'RUFY2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
RUFY2 MUTATED 1 2 0 1 1
RUFY2 WILD-TYPE 27 18 11 19 20
'RUFY2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.42

Table S935.  Gene #312: 'RUFY2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
RUFY2 MUTATED 5 0 0 0
RUFY2 WILD-TYPE 30 33 16 12

Figure S112.  Get High-res Image Gene #312: 'RUFY2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'RUFY2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.352 (Fisher's exact test), Q value = 0.68

Table S936.  Gene #312: 'RUFY2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
RUFY2 MUTATED 5 0 0 0 0 0 0
RUFY2 WILD-TYPE 29 11 9 7 6 20 9
'UBQLN2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.348 (Fisher's exact test), Q value = 0.68

Table S937.  Gene #313: 'UBQLN2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
UBQLN2 MUTATED 1 1 1 0 3
UBQLN2 WILD-TYPE 27 19 10 20 18
'UBQLN2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.104 (Fisher's exact test), Q value = 0.48

Table S938.  Gene #313: 'UBQLN2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
UBQLN2 MUTATED 4 0 2 0
UBQLN2 WILD-TYPE 31 33 14 12
'UBQLN2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.193 (Fisher's exact test), Q value = 0.56

Table S939.  Gene #313: 'UBQLN2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
UBQLN2 MUTATED 6 0 0 0 0 0 0
UBQLN2 WILD-TYPE 28 11 9 7 6 20 9
'PIGB MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.694 (Fisher's exact test), Q value = 0.86

Table S940.  Gene #314: 'PIGB MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PIGB MUTATED 2 2 1 1 0
PIGB WILD-TYPE 26 18 10 19 21
'PIGB MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.177 (Fisher's exact test), Q value = 0.56

Table S941.  Gene #314: 'PIGB MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PIGB MUTATED 4 0 1 1
PIGB WILD-TYPE 31 33 15 11
'PIGB MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.247 (Fisher's exact test), Q value = 0.63

Table S942.  Gene #314: 'PIGB MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PIGB MUTATED 5 0 0 0 1 0 0
PIGB WILD-TYPE 29 11 9 7 5 20 9
'TSPAN10 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.783 (Fisher's exact test), Q value = 0.92

Table S943.  Gene #315: 'TSPAN10 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TSPAN10 MUTATED 0 1 0 1 1
TSPAN10 WILD-TYPE 28 19 11 19 20
'TSPAN10 MUTATION STATUS' versus 'METHYLATION_CNMF'

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

Table S944.  Gene #315: 'TSPAN10 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TSPAN10 MUTATED 2 1 0 0
TSPAN10 WILD-TYPE 33 32 16 12
'TSPAN10 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.821 (Fisher's exact test), Q value = 0.93

Table S945.  Gene #315: 'TSPAN10 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TSPAN10 MUTATED 2 1 0 0 0 0 0
TSPAN10 WILD-TYPE 32 10 9 7 6 20 9
'SFRS8 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.392 (Fisher's exact test), Q value = 0.69

Table S946.  Gene #316: 'SFRS8 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SFRS8 MUTATED 2 3 0 1 0
SFRS8 WILD-TYPE 26 17 11 19 21
'SFRS8 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.45 (Fisher's exact test), Q value = 0.73

Table S947.  Gene #316: 'SFRS8 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SFRS8 MUTATED 3 1 2 0
SFRS8 WILD-TYPE 32 32 14 12
'SFRS8 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.855 (Fisher's exact test), Q value = 0.94

Table S948.  Gene #316: 'SFRS8 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SFRS8 MUTATED 4 0 0 0 0 1 1
SFRS8 WILD-TYPE 30 11 9 7 6 19 8
'TSTD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.303 (Fisher's exact test), Q value = 0.65

Table S949.  Gene #317: 'TSTD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TSTD2 MUTATED 1 2 0 0 3
TSTD2 WILD-TYPE 27 18 11 20 18
'TSTD2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0898 (Fisher's exact test), Q value = 0.47

Table S950.  Gene #317: 'TSTD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TSTD2 MUTATED 5 0 1 0
TSTD2 WILD-TYPE 30 33 15 12
'TSTD2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.194 (Fisher's exact test), Q value = 0.56

Table S951.  Gene #317: 'TSTD2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TSTD2 MUTATED 6 0 0 0 0 0 0
TSTD2 WILD-TYPE 28 11 9 7 6 20 9
'WDR5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.131 (Fisher's exact test), Q value = 0.51

Table S952.  Gene #318: 'WDR5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
WDR5 MUTATED 1 0 2 0 1
WDR5 WILD-TYPE 27 20 9 20 20
'WDR5 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.507 (Fisher's exact test), Q value = 0.75

Table S953.  Gene #318: 'WDR5 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
WDR5 MUTATED 2 0 1 0
WDR5 WILD-TYPE 33 33 15 12
'WDR5 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.52 (Fisher's exact test), Q value = 0.76

Table S954.  Gene #318: 'WDR5 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
WDR5 MUTATED 2 0 0 1 0 0 0
WDR5 WILD-TYPE 32 11 9 6 6 20 9
'LPIN1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0856 (Fisher's exact test), Q value = 0.47

Table S955.  Gene #319: 'LPIN1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
LPIN1 MUTATED 0 3 1 0 1
LPIN1 WILD-TYPE 28 17 10 20 20
'LPIN1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 0.56

Table S956.  Gene #319: 'LPIN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
LPIN1 MUTATED 2 0 2 0
LPIN1 WILD-TYPE 33 33 14 12
'LPIN1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.158 (Fisher's exact test), Q value = 0.56

Table S957.  Gene #319: 'LPIN1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
LPIN1 MUTATED 2 0 0 2 0 0 0
LPIN1 WILD-TYPE 32 11 9 5 6 20 9
'OR2A4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S958.  Gene #320: 'OR2A4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
OR2A4 MUTATED 1 0 0 1 1
OR2A4 WILD-TYPE 27 20 11 19 20
'OR2A4 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.286 (Fisher's exact test), Q value = 0.64

Table S959.  Gene #320: 'OR2A4 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
OR2A4 MUTATED 3 0 0 0
OR2A4 WILD-TYPE 32 33 16 12
'OR2A4 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.696 (Fisher's exact test), Q value = 0.86

Table S960.  Gene #320: 'OR2A4 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
OR2A4 MUTATED 3 0 0 0 0 0 0
OR2A4 WILD-TYPE 31 11 9 7 6 20 9
'RAPGEF4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.256 (Fisher's exact test), Q value = 0.63

Table S961.  Gene #321: 'RAPGEF4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
RAPGEF4 MUTATED 3 3 0 3 0
RAPGEF4 WILD-TYPE 25 17 11 17 21
'RAPGEF4 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.42

Table S962.  Gene #321: 'RAPGEF4 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
RAPGEF4 MUTATED 5 0 3 0
RAPGEF4 WILD-TYPE 30 33 13 12

Figure S113.  Get High-res Image Gene #321: 'RAPGEF4 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'RAPGEF4 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.214 (Fisher's exact test), Q value = 0.58

Table S963.  Gene #321: 'RAPGEF4 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
RAPGEF4 MUTATED 6 0 1 1 0 0 0
RAPGEF4 WILD-TYPE 28 11 8 6 6 20 9
'KCNA4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.647 (Fisher's exact test), Q value = 0.84

Table S964.  Gene #322: 'KCNA4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
KCNA4 MUTATED 1 3 1 2 2
KCNA4 WILD-TYPE 27 17 10 18 19
'KCNA4 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.361 (Fisher's exact test), Q value = 0.68

Table S965.  Gene #322: 'KCNA4 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
KCNA4 MUTATED 6 2 1 0
KCNA4 WILD-TYPE 29 31 15 12
'KCNA4 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.326 (Fisher's exact test), Q value = 0.66

Table S966.  Gene #322: 'KCNA4 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
KCNA4 MUTATED 6 1 0 1 0 0 1
KCNA4 WILD-TYPE 28 10 9 6 6 20 8
'LYSMD1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S967.  Gene #323: 'LYSMD1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
LYSMD1 MUTATED 1 1 0 0 1
LYSMD1 WILD-TYPE 27 19 11 20 20
'LYSMD1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 0.68

Table S968.  Gene #323: 'LYSMD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
LYSMD1 MUTATED 2 0 0 1
LYSMD1 WILD-TYPE 33 33 16 11
'LYSMD1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.693 (Fisher's exact test), Q value = 0.86

Table S969.  Gene #323: 'LYSMD1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
LYSMD1 MUTATED 3 0 0 0 0 0 0
LYSMD1 WILD-TYPE 31 11 9 7 6 20 9
'MYH4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.118 (Fisher's exact test), Q value = 0.49

Table S970.  Gene #324: 'MYH4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
MYH4 MUTATED 0 3 0 1 3
MYH4 WILD-TYPE 28 17 11 19 18
'MYH4 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.548 (Fisher's exact test), Q value = 0.77

Table S971.  Gene #324: 'MYH4 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
MYH4 MUTATED 3 1 2 1
MYH4 WILD-TYPE 32 32 14 11
'MYH4 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.318 (Fisher's exact test), Q value = 0.65

Table S972.  Gene #324: 'MYH4 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
MYH4 MUTATED 4 0 0 1 1 0 1
MYH4 WILD-TYPE 30 11 9 6 5 20 8
'SEMA6C MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S973.  Gene #325: 'SEMA6C MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SEMA6C MUTATED 2 1 1 1 1
SEMA6C WILD-TYPE 26 19 10 19 20
'SEMA6C MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.178 (Fisher's exact test), Q value = 0.56

Table S974.  Gene #325: 'SEMA6C MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SEMA6C MUTATED 4 0 1 1
SEMA6C WILD-TYPE 31 33 15 11
'SEMA6C MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.248 (Fisher's exact test), Q value = 0.63

Table S975.  Gene #325: 'SEMA6C MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SEMA6C MUTATED 5 0 0 0 1 0 0
SEMA6C WILD-TYPE 29 11 9 7 5 20 9
'LIMCH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.93 (Fisher's exact test), Q value = 0.99

Table S976.  Gene #326: 'LIMCH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
LIMCH1 MUTATED 3 2 1 1 1
LIMCH1 WILD-TYPE 25 18 10 19 20
'LIMCH1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.55 (Fisher's exact test), Q value = 0.77

Table S977.  Gene #326: 'LIMCH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
LIMCH1 MUTATED 5 2 1 0
LIMCH1 WILD-TYPE 30 31 15 12
'LIMCH1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.691 (Fisher's exact test), Q value = 0.86

Table S978.  Gene #326: 'LIMCH1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
LIMCH1 MUTATED 5 0 0 1 0 2 0
LIMCH1 WILD-TYPE 29 11 9 6 6 18 9
'CTSA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0641 (Fisher's exact test), Q value = 0.45

Table S979.  Gene #327: 'CTSA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CTSA MUTATED 0 0 2 1 1
CTSA WILD-TYPE 28 20 9 19 20
'CTSA MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0543 (Fisher's exact test), Q value = 0.43

Table S980.  Gene #327: 'CTSA MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CTSA MUTATED 1 0 1 2
CTSA WILD-TYPE 34 33 15 10
'CTSA MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0371 (Fisher's exact test), Q value = 0.42

Table S981.  Gene #327: 'CTSA MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CTSA MUTATED 1 0 0 1 2 0 0
CTSA WILD-TYPE 33 11 9 6 4 20 9

Figure S114.  Get High-res Image Gene #327: 'CTSA MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'MAP3K4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.92 (Fisher's exact test), Q value = 0.98

Table S982.  Gene #328: 'MAP3K4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
MAP3K4 MUTATED 5 3 1 2 2
MAP3K4 WILD-TYPE 23 17 10 18 19
'MAP3K4 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0438 (Fisher's exact test), Q value = 0.42

Table S983.  Gene #328: 'MAP3K4 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
MAP3K4 MUTATED 9 1 2 1
MAP3K4 WILD-TYPE 26 32 14 11

Figure S115.  Get High-res Image Gene #328: 'MAP3K4 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'MAP3K4 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0377 (Fisher's exact test), Q value = 0.42

Table S984.  Gene #328: 'MAP3K4 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
MAP3K4 MUTATED 9 0 0 1 1 0 2
MAP3K4 WILD-TYPE 25 11 9 6 5 20 7

Figure S116.  Get High-res Image Gene #328: 'MAP3K4 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'SGK1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.664 (Fisher's exact test), Q value = 0.85

Table S985.  Gene #329: 'SGK1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SGK1 MUTATED 1 2 0 0 1
SGK1 WILD-TYPE 27 18 11 20 20
'SGK1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.32 (Fisher's exact test), Q value = 0.65

Table S986.  Gene #329: 'SGK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SGK1 MUTATED 3 0 1 0
SGK1 WILD-TYPE 32 33 15 12
'SGK1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.389 (Fisher's exact test), Q value = 0.68

Table S987.  Gene #329: 'SGK1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SGK1 MUTATED 2 0 1 1 0 0 0
SGK1 WILD-TYPE 32 11 8 6 6 20 9
'NFE2L1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0788 (Fisher's exact test), Q value = 0.47

Table S988.  Gene #330: 'NFE2L1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
NFE2L1 MUTATED 0 0 1 2 0
NFE2L1 WILD-TYPE 28 20 10 18 21
'NFE2L1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.861 (Fisher's exact test), Q value = 0.94

Table S989.  Gene #330: 'NFE2L1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
NFE2L1 MUTATED 1 1 1 0
NFE2L1 WILD-TYPE 34 32 15 12
'NFE2L1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.186 (Fisher's exact test), Q value = 0.56

Table S990.  Gene #330: 'NFE2L1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
NFE2L1 MUTATED 0 0 1 1 0 1 0
NFE2L1 WILD-TYPE 34 11 8 6 6 19 9
'WASF3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.119 (Fisher's exact test), Q value = 0.49

Table S991.  Gene #331: 'WASF3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
WASF3 MUTATED 0 3 0 1 3
WASF3 WILD-TYPE 28 17 11 19 18
'WASF3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0899 (Fisher's exact test), Q value = 0.47

Table S992.  Gene #331: 'WASF3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
WASF3 MUTATED 3 0 2 2
WASF3 WILD-TYPE 32 33 14 10
'WASF3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0375 (Fisher's exact test), Q value = 0.42

Table S993.  Gene #331: 'WASF3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
WASF3 MUTATED 3 0 0 2 2 0 0
WASF3 WILD-TYPE 31 11 9 5 4 20 9

Figure S117.  Get High-res Image Gene #331: 'WASF3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'ARNTL MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S994.  Gene #332: 'ARNTL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ARNTL MUTATED 2 1 0 1 1
ARNTL WILD-TYPE 26 19 11 19 20
'ARNTL MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0462 (Fisher's exact test), Q value = 0.42

Table S995.  Gene #332: 'ARNTL MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ARNTL MUTATED 5 0 0 0
ARNTL WILD-TYPE 30 33 16 12

Figure S118.  Get High-res Image Gene #332: 'ARNTL MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'ARNTL MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.533 (Fisher's exact test), Q value = 0.77

Table S996.  Gene #332: 'ARNTL MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ARNTL MUTATED 4 0 1 0 0 0 0
ARNTL WILD-TYPE 30 11 8 7 6 20 9
'EDC4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.279 (Fisher's exact test), Q value = 0.63

Table S997.  Gene #333: 'EDC4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
EDC4 MUTATED 1 2 1 0 0
EDC4 WILD-TYPE 27 18 10 20 21
'EDC4 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.517 (Fisher's exact test), Q value = 0.76

Table S998.  Gene #333: 'EDC4 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
EDC4 MUTATED 3 1 0 0
EDC4 WILD-TYPE 32 32 16 12
'EDC4 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 0.53

Table S999.  Gene #333: 'EDC4 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
EDC4 MUTATED 1 0 1 0 0 0 2
EDC4 WILD-TYPE 33 11 8 7 6 20 7
'TBC1D22A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0796 (Fisher's exact test), Q value = 0.47

Table S1000.  Gene #334: 'TBC1D22A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TBC1D22A MUTATED 0 2 0 0 3
TBC1D22A WILD-TYPE 28 18 11 20 18
'TBC1D22A MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.736 (Fisher's exact test), Q value = 0.89

Table S1001.  Gene #334: 'TBC1D22A MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TBC1D22A MUTATED 3 1 1 0
TBC1D22A WILD-TYPE 32 32 15 12
'TBC1D22A MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.453 (Fisher's exact test), Q value = 0.73

Table S1002.  Gene #334: 'TBC1D22A MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TBC1D22A MUTATED 3 0 0 1 0 0 1
TBC1D22A WILD-TYPE 31 11 9 6 6 20 8
'ALPK1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0232 (Fisher's exact test), Q value = 0.4

Table S1003.  Gene #335: 'ALPK1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ALPK1 MUTATED 0 3 1 0 4
ALPK1 WILD-TYPE 28 17 10 20 17

Figure S119.  Get High-res Image Gene #335: 'ALPK1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'ALPK1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.39

Table S1004.  Gene #335: 'ALPK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ALPK1 MUTATED 7 0 0 1
ALPK1 WILD-TYPE 28 33 16 11

Figure S120.  Get High-res Image Gene #335: 'ALPK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'ALPK1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.124 (Fisher's exact test), Q value = 0.5

Table S1005.  Gene #335: 'ALPK1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ALPK1 MUTATED 7 0 0 0 0 0 1
ALPK1 WILD-TYPE 27 11 9 7 6 20 8
'SYTL2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 0.63

Table S1006.  Gene #336: 'SYTL2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SYTL2 MUTATED 1 1 2 0 1
SYTL2 WILD-TYPE 27 19 9 20 20
'SYTL2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.266 (Fisher's exact test), Q value = 0.63

Table S1007.  Gene #336: 'SYTL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SYTL2 MUTATED 3 0 1 1
SYTL2 WILD-TYPE 32 33 15 11
'SYTL2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.355 (Fisher's exact test), Q value = 0.68

Table S1008.  Gene #336: 'SYTL2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SYTL2 MUTATED 4 0 0 0 1 0 0
SYTL2 WILD-TYPE 30 11 9 7 5 20 9
'OAT MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0439 (Fisher's exact test), Q value = 0.42

Table S1009.  Gene #337: 'OAT MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
OAT MUTATED 0 0 0 0 3
OAT WILD-TYPE 28 20 11 20 18

Figure S121.  Get High-res Image Gene #337: 'OAT MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'OAT MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0548 (Fisher's exact test), Q value = 0.43

Table S1010.  Gene #337: 'OAT MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
OAT MUTATED 1 0 0 2
OAT WILD-TYPE 34 33 16 10
'OAT MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0612 (Fisher's exact test), Q value = 0.45

Table S1011.  Gene #337: 'OAT MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
OAT MUTATED 1 0 0 0 2 0 0
OAT WILD-TYPE 33 11 9 7 4 20 9
'HSP90B1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.743 (Fisher's exact test), Q value = 0.89

Table S1012.  Gene #338: 'HSP90B1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
HSP90B1 MUTATED 2 3 0 1 1
HSP90B1 WILD-TYPE 26 17 11 19 20
'HSP90B1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0607 (Fisher's exact test), Q value = 0.45

Table S1013.  Gene #338: 'HSP90B1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
HSP90B1 MUTATED 5 0 2 0
HSP90B1 WILD-TYPE 30 33 14 12
'HSP90B1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.159 (Fisher's exact test), Q value = 0.56

Table S1014.  Gene #338: 'HSP90B1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
HSP90B1 MUTATED 4 0 1 2 0 0 0
HSP90B1 WILD-TYPE 30 11 8 5 6 20 9
'PTCH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.925 (Fisher's exact test), Q value = 0.98

Table S1015.  Gene #339: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PTCH1 MUTATED 2 2 1 1 3
PTCH1 WILD-TYPE 26 18 10 19 18
'PTCH1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.4

Table S1016.  Gene #339: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PTCH1 MUTATED 4 0 4 1
PTCH1 WILD-TYPE 31 33 12 11

Figure S122.  Get High-res Image Gene #339: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'PTCH1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.069 (Fisher's exact test), Q value = 0.46

Table S1017.  Gene #339: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PTCH1 MUTATED 6 0 0 2 1 0 0
PTCH1 WILD-TYPE 28 11 9 5 5 20 9
'SULT1E1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.21 (Fisher's exact test), Q value = 0.58

Table S1018.  Gene #340: 'SULT1E1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SULT1E1 MUTATED 0 2 0 0 1
SULT1E1 WILD-TYPE 28 18 11 20 20
'SULT1E1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.285 (Fisher's exact test), Q value = 0.64

Table S1019.  Gene #340: 'SULT1E1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SULT1E1 MUTATED 3 0 0 0
SULT1E1 WILD-TYPE 32 33 16 12
'SULT1E1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.649 (Fisher's exact test), Q value = 0.84

Table S1020.  Gene #340: 'SULT1E1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SULT1E1 MUTATED 2 0 1 0 0 0 0
SULT1E1 WILD-TYPE 32 11 8 7 6 20 9
'UPF3A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.209 (Fisher's exact test), Q value = 0.58

Table S1021.  Gene #341: 'UPF3A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
UPF3A MUTATED 2 0 0 0 3
UPF3A WILD-TYPE 26 20 11 20 18
'UPF3A MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.103 (Fisher's exact test), Q value = 0.48

Table S1022.  Gene #341: 'UPF3A MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
UPF3A MUTATED 2 0 1 2
UPF3A WILD-TYPE 33 33 15 10
'UPF3A MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.127 (Fisher's exact test), Q value = 0.5

Table S1023.  Gene #341: 'UPF3A MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
UPF3A MUTATED 3 0 0 0 2 0 0
UPF3A WILD-TYPE 31 11 9 7 4 20 9
'DNAH8 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.221 (Fisher's exact test), Q value = 0.58

Table S1024.  Gene #342: 'DNAH8 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
DNAH8 MUTATED 3 4 1 0 4
DNAH8 WILD-TYPE 25 16 10 20 17
'DNAH8 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.25

Table S1025.  Gene #342: 'DNAH8 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DNAH8 MUTATED 10 0 1 1
DNAH8 WILD-TYPE 25 33 15 11

Figure S123.  Get High-res Image Gene #342: 'DNAH8 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'DNAH8 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.046 (Fisher's exact test), Q value = 0.42

Table S1026.  Gene #342: 'DNAH8 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DNAH8 MUTATED 9 0 1 1 1 0 0
DNAH8 WILD-TYPE 25 11 8 6 5 20 9

Figure S124.  Get High-res Image Gene #342: 'DNAH8 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'SYCP2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.754 (Fisher's exact test), Q value = 0.9

Table S1027.  Gene #343: 'SYCP2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SYCP2 MUTATED 4 3 2 2 1
SYCP2 WILD-TYPE 24 17 9 18 20
'SYCP2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.39

Table S1028.  Gene #343: 'SYCP2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SYCP2 MUTATED 7 0 4 1
SYCP2 WILD-TYPE 28 33 12 11

Figure S125.  Get High-res Image Gene #343: 'SYCP2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'SYCP2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.39

Table S1029.  Gene #343: 'SYCP2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SYCP2 MUTATED 9 0 0 2 1 0 0
SYCP2 WILD-TYPE 25 11 9 5 5 20 9

Figure S126.  Get High-res Image Gene #343: 'SYCP2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'ATG5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.287 (Fisher's exact test), Q value = 0.64

Table S1030.  Gene #344: 'ATG5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ATG5 MUTATED 0 1 0 0 2
ATG5 WILD-TYPE 28 19 11 20 19
'ATG5 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.603 (Fisher's exact test), Q value = 0.81

Table S1031.  Gene #344: 'ATG5 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ATG5 MUTATED 1 1 0 1
ATG5 WILD-TYPE 34 32 16 11
'ATG5 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.654 (Fisher's exact test), Q value = 0.84

Table S1032.  Gene #344: 'ATG5 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ATG5 MUTATED 2 0 0 0 0 0 1
ATG5 WILD-TYPE 32 11 9 7 6 20 8
'RTN2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.56 (Fisher's exact test), Q value = 0.78

Table S1033.  Gene #345: 'RTN2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
RTN2 MUTATED 1 3 0 1 1
RTN2 WILD-TYPE 27 17 11 19 20
'RTN2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0563 (Fisher's exact test), Q value = 0.43

Table S1034.  Gene #345: 'RTN2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
RTN2 MUTATED 2 0 3 1
RTN2 WILD-TYPE 33 33 13 11
'RTN2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.373 (Fisher's exact test), Q value = 0.68

Table S1035.  Gene #345: 'RTN2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
RTN2 MUTATED 4 0 1 0 1 0 0
RTN2 WILD-TYPE 30 11 8 7 5 20 9
'AP2A2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.39

Table S1036.  Gene #346: 'AP2A2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
AP2A2 MUTATED 0 1 2 0 0
AP2A2 WILD-TYPE 28 19 9 20 21

Figure S127.  Get High-res Image Gene #346: 'AP2A2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

'AP2A2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.4

Table S1037.  Gene #346: 'AP2A2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
AP2A2 MUTATED 0 0 2 1
AP2A2 WILD-TYPE 35 33 14 11

Figure S128.  Get High-res Image Gene #346: 'AP2A2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'AP2A2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.211 (Fisher's exact test), Q value = 0.58

Table S1038.  Gene #346: 'AP2A2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
AP2A2 MUTATED 1 0 0 1 1 0 0
AP2A2 WILD-TYPE 33 11 9 6 5 20 9
'ECT2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S1039.  Gene #347: 'ECT2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ECT2 MUTATED 1 1 0 0 1
ECT2 WILD-TYPE 27 19 11 20 20
'ECT2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.383 (Fisher's exact test), Q value = 0.68

Table S1040.  Gene #347: 'ECT2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ECT2 MUTATED 2 0 0 1
ECT2 WILD-TYPE 33 33 16 11
'ECT2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.654 (Fisher's exact test), Q value = 0.84

Table S1041.  Gene #347: 'ECT2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ECT2 MUTATED 2 0 1 0 0 0 0
ECT2 WILD-TYPE 32 11 8 7 6 20 9
'ZNF174 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.786 (Fisher's exact test), Q value = 0.92

Table S1042.  Gene #348: 'ZNF174 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ZNF174 MUTATED 0 1 0 1 1
ZNF174 WILD-TYPE 28 19 11 19 20
'ZNF174 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.861 (Fisher's exact test), Q value = 0.94

Table S1043.  Gene #348: 'ZNF174 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ZNF174 MUTATED 1 1 1 0
ZNF174 WILD-TYPE 34 32 15 12
'ZNF174 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.581 (Fisher's exact test), Q value = 0.79

Table S1044.  Gene #348: 'ZNF174 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ZNF174 MUTATED 1 0 0 1 0 1 0
ZNF174 WILD-TYPE 33 11 9 6 6 19 9
'JAM3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.67 (Fisher's exact test), Q value = 0.85

Table S1045.  Gene #349: 'JAM3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
JAM3 MUTATED 3 1 1 0 1
JAM3 WILD-TYPE 25 19 10 20 20
'JAM3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.167 (Fisher's exact test), Q value = 0.56

Table S1046.  Gene #349: 'JAM3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
JAM3 MUTATED 3 0 2 1
JAM3 WILD-TYPE 32 33 14 11
'JAM3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 0.63

Table S1047.  Gene #349: 'JAM3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
JAM3 MUTATED 4 0 0 1 1 0 0
JAM3 WILD-TYPE 30 11 9 6 5 20 9
'EEA1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.663 (Fisher's exact test), Q value = 0.85

Table S1048.  Gene #350: 'EEA1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
EEA1 MUTATED 3 2 2 1 1
EEA1 WILD-TYPE 25 18 9 19 20
'EEA1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.474 (Fisher's exact test), Q value = 0.75

Table S1049.  Gene #350: 'EEA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
EEA1 MUTATED 5 2 2 0
EEA1 WILD-TYPE 30 31 14 12
'EEA1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.422 (Fisher's exact test), Q value = 0.7

Table S1050.  Gene #350: 'EEA1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
EEA1 MUTATED 5 1 0 2 0 1 0
EEA1 WILD-TYPE 29 10 9 5 6 19 9
'RTN3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.216 (Fisher's exact test), Q value = 0.58

Table S1051.  Gene #351: 'RTN3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
RTN3 MUTATED 1 4 0 1 3
RTN3 WILD-TYPE 27 16 11 19 18
'RTN3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.39

Table S1052.  Gene #351: 'RTN3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
RTN3 MUTATED 7 0 2 0
RTN3 WILD-TYPE 28 33 14 12

Figure S129.  Get High-res Image Gene #351: 'RTN3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'RTN3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.134 (Fisher's exact test), Q value = 0.51

Table S1053.  Gene #351: 'RTN3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
RTN3 MUTATED 7 0 1 1 0 0 0
RTN3 WILD-TYPE 27 11 8 6 6 20 9
'ZBTB7B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.16 (Fisher's exact test), Q value = 0.56

Table S1054.  Gene #352: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ZBTB7B MUTATED 1 0 0 0 3
ZBTB7B WILD-TYPE 27 20 11 20 18
'ZBTB7B MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.38 (Fisher's exact test), Q value = 0.68

Table S1055.  Gene #352: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ZBTB7B MUTATED 2 0 0 1
ZBTB7B WILD-TYPE 33 33 16 11
'ZBTB7B MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.493 (Fisher's exact test), Q value = 0.75

Table S1056.  Gene #352: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ZBTB7B MUTATED 2 0 0 0 1 0 0
ZBTB7B WILD-TYPE 32 11 9 7 5 20 9
'ZC3H18 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.57 (Fisher's exact test), Q value = 0.78

Table S1057.  Gene #353: 'ZC3H18 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ZC3H18 MUTATED 1 3 0 1 2
ZC3H18 WILD-TYPE 27 17 11 19 19
'ZC3H18 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.805 (Fisher's exact test), Q value = 0.93

Table S1058.  Gene #353: 'ZC3H18 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ZC3H18 MUTATED 4 2 1 0
ZC3H18 WILD-TYPE 31 31 15 12
'ZC3H18 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.213 (Fisher's exact test), Q value = 0.58

Table S1059.  Gene #353: 'ZC3H18 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ZC3H18 MUTATED 4 0 0 1 0 0 2
ZC3H18 WILD-TYPE 30 11 9 6 6 20 7
'FAHD2B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S1060.  Gene #354: 'FAHD2B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
FAHD2B MUTATED 1 1 0 0 1
FAHD2B WILD-TYPE 27 19 11 20 20
'SETD7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.548 (Fisher's exact test), Q value = 0.77

Table S1061.  Gene #355: 'SETD7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SETD7 MUTATED 1 0 1 1 0
SETD7 WILD-TYPE 27 20 10 19 21
'SETD7 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.504 (Fisher's exact test), Q value = 0.75

Table S1062.  Gene #355: 'SETD7 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SETD7 MUTATED 2 0 1 0
SETD7 WILD-TYPE 33 33 15 12
'SETD7 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.695 (Fisher's exact test), Q value = 0.86

Table S1063.  Gene #355: 'SETD7 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SETD7 MUTATED 3 0 0 0 0 0 0
SETD7 WILD-TYPE 31 11 9 7 6 20 9
'ZNF510 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.224 (Fisher's exact test), Q value = 0.59

Table S1064.  Gene #356: 'ZNF510 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ZNF510 MUTATED 0 2 1 0 1
ZNF510 WILD-TYPE 28 18 10 20 20
'ZNF510 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.318 (Fisher's exact test), Q value = 0.65

Table S1065.  Gene #356: 'ZNF510 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ZNF510 MUTATED 3 0 1 0
ZNF510 WILD-TYPE 32 33 15 12
'ZNF510 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.482 (Fisher's exact test), Q value = 0.75

Table S1066.  Gene #356: 'ZNF510 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ZNF510 MUTATED 3 0 0 1 0 0 0
ZNF510 WILD-TYPE 31 11 9 6 6 20 9
'KIAA0408 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.663 (Fisher's exact test), Q value = 0.85

Table S1067.  Gene #357: 'KIAA0408 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
KIAA0408 MUTATED 3 3 0 1 1
KIAA0408 WILD-TYPE 25 17 11 19 20
'KIAA0408 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.407 (Fisher's exact test), Q value = 0.69

Table S1068.  Gene #357: 'KIAA0408 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
KIAA0408 MUTATED 3 2 0 2
KIAA0408 WILD-TYPE 32 31 16 10
'KIAA0408 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.374 (Fisher's exact test), Q value = 0.68

Table S1069.  Gene #357: 'KIAA0408 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
KIAA0408 MUTATED 2 0 2 0 1 1 1
KIAA0408 WILD-TYPE 32 11 7 7 5 19 8
'PRR5L MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.286 (Fisher's exact test), Q value = 0.64

Table S1070.  Gene #358: 'PRR5L MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PRR5L MUTATED 0 0 0 1 2
PRR5L WILD-TYPE 28 20 11 19 19
'PRR5L MUTATION STATUS' versus 'METHYLATION_CNMF'

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

Table S1071.  Gene #358: 'PRR5L MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PRR5L MUTATED 2 1 0 0
PRR5L WILD-TYPE 33 32 16 12
'PRR5L MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

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

Table S1072.  Gene #358: 'PRR5L MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PRR5L MUTATED 2 0 0 0 0 1 0
PRR5L WILD-TYPE 32 11 9 7 6 19 9
'DST MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.948 (Fisher's exact test), Q value = 1

Table S1073.  Gene #359: 'DST MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
DST MUTATED 5 3 1 3 2
DST WILD-TYPE 23 17 10 17 19
'DST MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.045 (Fisher's exact test), Q value = 0.42

Table S1074.  Gene #359: 'DST MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
DST MUTATED 9 1 2 1
DST WILD-TYPE 26 32 14 11

Figure S130.  Get High-res Image Gene #359: 'DST MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'DST MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0503 (Fisher's exact test), Q value = 0.43

Table S1075.  Gene #359: 'DST MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
DST MUTATED 10 0 0 1 1 1 0
DST WILD-TYPE 24 11 9 6 5 19 9
'NPY MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.372 (Fisher's exact test), Q value = 0.68

Table S1076.  Gene #360: 'NPY MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
NPY MUTATED 0 1 1 0 1
NPY WILD-TYPE 28 19 10 20 20
'NPY MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.863 (Fisher's exact test), Q value = 0.94

Table S1077.  Gene #360: 'NPY MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
NPY MUTATED 1 2 0 0
NPY WILD-TYPE 34 31 16 12
'NPY MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.922 (Fisher's exact test), Q value = 0.98

Table S1078.  Gene #360: 'NPY MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
NPY MUTATED 1 1 0 0 0 1 0
NPY WILD-TYPE 33 10 9 7 6 19 9
'VASP MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.939 (Fisher's exact test), Q value = 0.99

Table S1079.  Gene #361: 'VASP MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
VASP MUTATED 2 1 0 0 1
VASP WILD-TYPE 26 19 11 20 20
'VASP MUTATION STATUS' versus 'METHYLATION_CNMF'

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

Table S1080.  Gene #361: 'VASP MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
VASP MUTATED 2 1 0 0
VASP WILD-TYPE 33 32 16 12
'VASP MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.656 (Fisher's exact test), Q value = 0.84

Table S1081.  Gene #361: 'VASP MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
VASP MUTATED 2 0 0 0 0 0 1
VASP WILD-TYPE 32 11 9 7 6 20 8
'COL5A3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0658 (Fisher's exact test), Q value = 0.45

Table S1082.  Gene #362: 'COL5A3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
COL5A3 MUTATED 0 3 0 0 2
COL5A3 WILD-TYPE 28 17 11 20 19
'COL5A3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.173 (Fisher's exact test), Q value = 0.56

Table S1083.  Gene #362: 'COL5A3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
COL5A3 MUTATED 4 0 1 0
COL5A3 WILD-TYPE 31 33 15 12
'COL5A3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.458 (Fisher's exact test), Q value = 0.73

Table S1084.  Gene #362: 'COL5A3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
COL5A3 MUTATED 3 0 1 1 0 0 0
COL5A3 WILD-TYPE 31 11 8 6 6 20 9
'KCNQ3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.909 (Fisher's exact test), Q value = 0.98

Table S1085.  Gene #363: 'KCNQ3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
KCNQ3 MUTATED 3 3 1 1 2
KCNQ3 WILD-TYPE 25 17 10 19 19
'KCNQ3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0723 (Fisher's exact test), Q value = 0.47

Table S1086.  Gene #363: 'KCNQ3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
KCNQ3 MUTATED 7 1 2 0
KCNQ3 WILD-TYPE 28 32 14 12
'KCNQ3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.376 (Fisher's exact test), Q value = 0.68

Table S1087.  Gene #363: 'KCNQ3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
KCNQ3 MUTATED 7 0 0 1 0 1 1
KCNQ3 WILD-TYPE 27 11 9 6 6 19 8
'PLXNA1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.281 (Fisher's exact test), Q value = 0.64

Table S1088.  Gene #364: 'PLXNA1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PLXNA1 MUTATED 1 3 0 3 4
PLXNA1 WILD-TYPE 27 17 11 17 17
'PLXNA1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0629 (Fisher's exact test), Q value = 0.45

Table S1089.  Gene #364: 'PLXNA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PLXNA1 MUTATED 8 1 1 1
PLXNA1 WILD-TYPE 27 32 15 11
'PLXNA1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0949 (Fisher's exact test), Q value = 0.47

Table S1090.  Gene #364: 'PLXNA1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PLXNA1 MUTATED 7 0 0 1 1 0 2
PLXNA1 WILD-TYPE 27 11 9 6 5 20 7
'ZNF395 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.855 (Fisher's exact test), Q value = 0.94

Table S1091.  Gene #365: 'ZNF395 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ZNF395 MUTATED 1 1 0 1 0
ZNF395 WILD-TYPE 27 19 11 19 21
'ZNF395 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.332 (Fisher's exact test), Q value = 0.67

Table S1092.  Gene #365: 'ZNF395 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ZNF395 MUTATED 1 0 1 1
ZNF395 WILD-TYPE 34 33 15 11
'ZNF395 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.209 (Fisher's exact test), Q value = 0.58

Table S1093.  Gene #365: 'ZNF395 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ZNF395 MUTATED 1 0 0 1 1 0 0
ZNF395 WILD-TYPE 33 11 9 6 5 20 9
'PLA2G4C MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0965 (Fisher's exact test), Q value = 0.48

Table S1094.  Gene #366: 'PLA2G4C MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PLA2G4C MUTATED 1 4 0 0 1
PLA2G4C WILD-TYPE 27 16 11 20 20
'PLA2G4C MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0911 (Fisher's exact test), Q value = 0.47

Table S1095.  Gene #366: 'PLA2G4C MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PLA2G4C MUTATED 5 0 1 0
PLA2G4C WILD-TYPE 30 33 15 12
'PLA2G4C MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.414 (Fisher's exact test), Q value = 0.69

Table S1096.  Gene #366: 'PLA2G4C MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PLA2G4C MUTATED 4 0 0 1 0 0 1
PLA2G4C WILD-TYPE 30 11 9 6 6 20 8
'RBM6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.696 (Fisher's exact test), Q value = 0.86

Table S1097.  Gene #367: 'RBM6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
RBM6 MUTATED 3 3 0 1 3
RBM6 WILD-TYPE 25 17 11 19 18
'RBM6 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.231 (Fisher's exact test), Q value = 0.6

Table S1098.  Gene #367: 'RBM6 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
RBM6 MUTATED 6 1 1 1
RBM6 WILD-TYPE 29 32 15 11
'RBM6 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.169 (Fisher's exact test), Q value = 0.56

Table S1099.  Gene #367: 'RBM6 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
RBM6 MUTATED 5 0 0 1 1 0 2
RBM6 WILD-TYPE 29 11 9 6 5 20 7
'COL18A1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.222 (Fisher's exact test), Q value = 0.58

Table S1100.  Gene #368: 'COL18A1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
COL18A1 MUTATED 6 0 1 2 2
COL18A1 WILD-TYPE 22 20 10 18 19
'COL18A1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.673 (Fisher's exact test), Q value = 0.85

Table S1101.  Gene #368: 'COL18A1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
COL18A1 MUTATED 5 3 2 0
COL18A1 WILD-TYPE 30 30 14 12
'COL18A1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.368 (Fisher's exact test), Q value = 0.68

Table S1102.  Gene #368: 'COL18A1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
COL18A1 MUTATED 5 0 0 2 0 3 0
COL18A1 WILD-TYPE 29 11 9 5 6 17 9
'ERBB3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.187 (Fisher's exact test), Q value = 0.56

Table S1103.  Gene #369: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ERBB3 MUTATED 1 0 0 3 3
ERBB3 WILD-TYPE 27 20 11 17 18
'ERBB3 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 0.57

Table S1104.  Gene #369: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ERBB3 MUTATED 5 1 0 1
ERBB3 WILD-TYPE 30 32 16 11
'ERBB3 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.467 (Fisher's exact test), Q value = 0.74

Table S1105.  Gene #369: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ERBB3 MUTATED 6 0 0 0 0 1 0
ERBB3 WILD-TYPE 28 11 9 7 6 19 9
'PRDM2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.154 (Fisher's exact test), Q value = 0.55

Table S1106.  Gene #370: 'PRDM2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PRDM2 MUTATED 5 3 3 0 2
PRDM2 WILD-TYPE 23 17 8 20 19
'PRDM2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.502 (Fisher's exact test), Q value = 0.75

Table S1107.  Gene #370: 'PRDM2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PRDM2 MUTATED 6 2 2 2
PRDM2 WILD-TYPE 29 31 14 10
'PRDM2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.204 (Fisher's exact test), Q value = 0.57

Table S1108.  Gene #370: 'PRDM2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PRDM2 MUTATED 7 0 0 1 2 1 1
PRDM2 WILD-TYPE 27 11 9 6 4 19 8
'C7ORF50 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S1109.  Gene #371: 'C7ORF50 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
C7ORF50 MUTATED 1 1 0 0 1
C7ORF50 WILD-TYPE 27 19 11 20 20
'C7ORF50 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.282 (Fisher's exact test), Q value = 0.64

Table S1110.  Gene #371: 'C7ORF50 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
C7ORF50 MUTATED 3 0 0 0
C7ORF50 WILD-TYPE 32 33 16 12
'C7ORF50 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.651 (Fisher's exact test), Q value = 0.84

Table S1111.  Gene #371: 'C7ORF50 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
C7ORF50 MUTATED 2 0 0 0 0 0 1
C7ORF50 WILD-TYPE 32 11 9 7 6 20 8
'ARFGAP2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S1112.  Gene #372: 'ARFGAP2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ARFGAP2 MUTATED 1 1 0 0 1
ARFGAP2 WILD-TYPE 27 19 11 20 20
'ARFGAP2 MUTATION STATUS' versus 'METHYLATION_CNMF'

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

Table S1113.  Gene #372: 'ARFGAP2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ARFGAP2 MUTATED 2 1 0 0
ARFGAP2 WILD-TYPE 33 32 16 12
'ARFGAP2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.651 (Fisher's exact test), Q value = 0.84

Table S1114.  Gene #372: 'ARFGAP2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ARFGAP2 MUTATED 2 0 0 0 0 0 1
ARFGAP2 WILD-TYPE 32 11 9 7 6 20 8
'FAM81B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.85 (Fisher's exact test), Q value = 0.94

Table S1115.  Gene #373: 'FAM81B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
FAM81B MUTATED 1 2 1 1 1
FAM81B WILD-TYPE 27 18 10 19 20
'FAM81B MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0909 (Fisher's exact test), Q value = 0.47

Table S1116.  Gene #373: 'FAM81B MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
FAM81B MUTATED 5 0 1 0
FAM81B WILD-TYPE 30 33 15 12
'FAM81B MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.411 (Fisher's exact test), Q value = 0.69

Table S1117.  Gene #373: 'FAM81B MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
FAM81B MUTATED 4 0 1 1 0 0 0
FAM81B WILD-TYPE 30 11 8 6 6 20 9
'LIN37 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.784 (Fisher's exact test), Q value = 0.92

Table S1118.  Gene #374: 'LIN37 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
LIN37 MUTATED 0 1 0 1 1
LIN37 WILD-TYPE 28 19 11 19 20
'LIN37 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.333 (Fisher's exact test), Q value = 0.67

Table S1119.  Gene #374: 'LIN37 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
LIN37 MUTATED 1 0 1 1
LIN37 WILD-TYPE 34 33 15 11
'LIN37 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.212 (Fisher's exact test), Q value = 0.58

Table S1120.  Gene #374: 'LIN37 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
LIN37 MUTATED 1 0 0 1 1 0 0
LIN37 WILD-TYPE 33 11 9 6 5 20 9
'SPRYD5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.109 (Fisher's exact test), Q value = 0.48

Table S1121.  Gene #375: 'SPRYD5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SPRYD5 MUTATED 1 4 0 0 2
SPRYD5 WILD-TYPE 27 16 11 20 19
'SPRYD5 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 0.68

Table S1122.  Gene #375: 'SPRYD5 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SPRYD5 MUTATED 4 1 2 0
SPRYD5 WILD-TYPE 31 32 14 12
'SPRYD5 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.319 (Fisher's exact test), Q value = 0.65

Table S1123.  Gene #375: 'SPRYD5 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SPRYD5 MUTATED 5 0 0 1 0 0 1
SPRYD5 WILD-TYPE 29 11 9 6 6 20 8
'INHBA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.286 (Fisher's exact test), Q value = 0.64

Table S1124.  Gene #376: 'INHBA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
INHBA MUTATED 0 0 0 1 2
INHBA WILD-TYPE 28 20 11 19 19
'INHBA MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.508 (Fisher's exact test), Q value = 0.75

Table S1125.  Gene #376: 'INHBA MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
INHBA MUTATED 2 0 1 0
INHBA WILD-TYPE 33 33 15 12
'INHBA MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.366 (Fisher's exact test), Q value = 0.68

Table S1126.  Gene #376: 'INHBA MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
INHBA MUTATED 1 0 1 1 0 0 0
INHBA WILD-TYPE 33 11 8 6 6 20 9
'SOX8 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S1127.  Gene #377: 'SOX8 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SOX8 MUTATED 2 1 0 1 1
SOX8 WILD-TYPE 26 19 11 19 20
'SOX8 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.266 (Fisher's exact test), Q value = 0.63

Table S1128.  Gene #377: 'SOX8 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SOX8 MUTATED 3 0 1 1
SOX8 WILD-TYPE 32 33 15 11
'SOX8 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.356 (Fisher's exact test), Q value = 0.68

Table S1129.  Gene #377: 'SOX8 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SOX8 MUTATED 4 0 0 0 1 0 0
SOX8 WILD-TYPE 30 11 9 7 5 20 9
'WDR60 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.424 (Fisher's exact test), Q value = 0.71

Table S1130.  Gene #378: 'WDR60 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
WDR60 MUTATED 3 2 2 0 2
WDR60 WILD-TYPE 25 18 9 20 19
'WDR60 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.00956 (Fisher's exact test), Q value = 0.39

Table S1131.  Gene #378: 'WDR60 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
WDR60 MUTATED 5 0 4 0
WDR60 WILD-TYPE 30 33 12 12

Figure S131.  Get High-res Image Gene #378: 'WDR60 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'WDR60 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.4

Table S1132.  Gene #378: 'WDR60 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
WDR60 MUTATED 6 0 0 3 0 0 0
WDR60 WILD-TYPE 28 11 9 4 6 20 9

Figure S132.  Get High-res Image Gene #378: 'WDR60 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'TCP10L MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.484 (Fisher's exact test), Q value = 0.75

Table S1133.  Gene #379: 'TCP10L MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
TCP10L MUTATED 2 1 1 0 0
TCP10L WILD-TYPE 26 19 10 20 21
'TCP10L MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 0.56

Table S1134.  Gene #379: 'TCP10L MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
TCP10L MUTATED 2 0 2 0
TCP10L WILD-TYPE 33 33 14 12
'TCP10L MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.479 (Fisher's exact test), Q value = 0.75

Table S1135.  Gene #379: 'TCP10L MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
TCP10L MUTATED 3 0 0 1 0 0 0
TCP10L WILD-TYPE 31 11 9 6 6 20 9
'MGAT4C MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.892 (Fisher's exact test), Q value = 0.97

Table S1136.  Gene #380: 'MGAT4C MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
MGAT4C MUTATED 1 1 0 2 1
MGAT4C WILD-TYPE 27 19 11 18 20
'MGAT4C MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.189 (Fisher's exact test), Q value = 0.56

Table S1137.  Gene #380: 'MGAT4C MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
MGAT4C MUTATED 2 0 2 1
MGAT4C WILD-TYPE 33 33 14 11
'MGAT4C MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.181 (Fisher's exact test), Q value = 0.56

Table S1138.  Gene #380: 'MGAT4C MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
MGAT4C MUTATED 3 0 0 2 0 0 0
MGAT4C WILD-TYPE 31 11 9 5 6 20 9
'ATP6V1C1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.724 (Fisher's exact test), Q value = 0.88

Table S1139.  Gene #381: 'ATP6V1C1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ATP6V1C1 MUTATED 1 1 0 0 2
ATP6V1C1 WILD-TYPE 27 19 11 20 19
'ATP6V1C1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.516 (Fisher's exact test), Q value = 0.76

Table S1140.  Gene #381: 'ATP6V1C1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ATP6V1C1 MUTATED 3 1 0 0
ATP6V1C1 WILD-TYPE 32 32 16 12
'ATP6V1C1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.674 (Fisher's exact test), Q value = 0.85

Table S1141.  Gene #381: 'ATP6V1C1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ATP6V1C1 MUTATED 2 1 1 0 0 0 0
ATP6V1C1 WILD-TYPE 32 10 8 7 6 20 9
'MNT MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.196 (Fisher's exact test), Q value = 0.57

Table S1142.  Gene #382: 'MNT MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
MNT MUTATED 0 2 0 1 3
MNT WILD-TYPE 28 18 11 19 18
'MNT MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.346 (Fisher's exact test), Q value = 0.68

Table S1143.  Gene #382: 'MNT MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
MNT MUTATED 4 1 0 1
MNT WILD-TYPE 31 32 16 11
'MNT MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.467 (Fisher's exact test), Q value = 0.74

Table S1144.  Gene #382: 'MNT MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
MNT MUTATED 3 1 0 0 1 0 1
MNT WILD-TYPE 31 10 9 7 5 20 8
'PLXNB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.947 (Fisher's exact test), Q value = 1

Table S1145.  Gene #383: 'PLXNB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
PLXNB1 MUTATED 3 1 1 1 2
PLXNB1 WILD-TYPE 25 19 10 19 19
'PLXNB1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.39

Table S1146.  Gene #383: 'PLXNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
PLXNB1 MUTATED 7 0 1 0
PLXNB1 WILD-TYPE 28 33 15 12

Figure S133.  Get High-res Image Gene #383: 'PLXNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'PLXNB1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.101 (Fisher's exact test), Q value = 0.48

Table S1147.  Gene #383: 'PLXNB1 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
PLXNB1 MUTATED 7 0 0 1 0 0 0
PLXNB1 WILD-TYPE 27 11 9 6 6 20 9
'STIM2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.482 (Fisher's exact test), Q value = 0.75

Table S1148.  Gene #384: 'STIM2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
STIM2 MUTATED 1 2 1 0 2
STIM2 WILD-TYPE 27 18 10 20 19
'STIM2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.266 (Fisher's exact test), Q value = 0.63

Table S1149.  Gene #384: 'STIM2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
STIM2 MUTATED 3 0 1 1
STIM2 WILD-TYPE 32 33 15 11
'STIM2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.456 (Fisher's exact test), Q value = 0.73

Table S1150.  Gene #384: 'STIM2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
STIM2 MUTATED 3 0 1 1 0 0 0
STIM2 WILD-TYPE 31 11 8 6 6 20 9
'CYB5R4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.819 (Fisher's exact test), Q value = 0.93

Table S1151.  Gene #385: 'CYB5R4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
CYB5R4 MUTATED 1 1 1 0 1
CYB5R4 WILD-TYPE 27 19 10 20 20
'CYB5R4 MUTATION STATUS' versus 'METHYLATION_CNMF'

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

Table S1152.  Gene #385: 'CYB5R4 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
CYB5R4 MUTATED 2 1 1 0
CYB5R4 WILD-TYPE 33 32 15 12
'CYB5R4 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.392 (Fisher's exact test), Q value = 0.69

Table S1153.  Gene #385: 'CYB5R4 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
CYB5R4 MUTATED 2 0 0 1 0 0 1
CYB5R4 WILD-TYPE 32 11 9 6 6 20 8
'SIAH2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.161 (Fisher's exact test), Q value = 0.56

Table S1154.  Gene #386: 'SIAH2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
SIAH2 MUTATED 0 1 0 2 0
SIAH2 WILD-TYPE 28 19 11 18 21
'SIAH2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.865 (Fisher's exact test), Q value = 0.94

Table S1155.  Gene #386: 'SIAH2 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
SIAH2 MUTATED 1 2 0 0
SIAH2 WILD-TYPE 34 31 16 12
'SIAH2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.26 (Fisher's exact test), Q value = 0.63

Table S1156.  Gene #386: 'SIAH2 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
SIAH2 MUTATED 0 0 0 0 0 2 1
SIAH2 WILD-TYPE 34 11 9 7 6 18 8
'NUP210L MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.858 (Fisher's exact test), Q value = 0.94

Table S1157.  Gene #387: 'NUP210L MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
NUP210L MUTATED 2 2 2 2 3
NUP210L WILD-TYPE 26 18 9 18 18
'NUP210L MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 0.42

Table S1158.  Gene #387: 'NUP210L MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
NUP210L MUTATED 6 0 2 2
NUP210L WILD-TYPE 29 33 14 10

Figure S134.  Get High-res Image Gene #387: 'NUP210L MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

'NUP210L MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.039 (Fisher's exact test), Q value = 0.42

Table S1159.  Gene #387: 'NUP210L MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
NUP210L MUTATED 7 0 0 1 2 0 0
NUP210L WILD-TYPE 27 11 9 6 4 20 9

Figure S135.  Get High-res Image Gene #387: 'NUP210L MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

'ZNF609 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.684 (Fisher's exact test), Q value = 0.86

Table S1160.  Gene #388: 'ZNF609 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 28 20 11 20 21
ZNF609 MUTATED 2 2 0 1 0
ZNF609 WILD-TYPE 26 18 11 19 21
'ZNF609 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 0.48

Table S1161.  Gene #388: 'ZNF609 MUTATION STATUS' versus Molecular Subtype #2: 'METHYLATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 16 12
ZNF609 MUTATED 1 1 3 0
ZNF609 WILD-TYPE 34 32 13 12
'ZNF609 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.148 (Fisher's exact test), Q value = 0.54

Table S1162.  Gene #388: 'ZNF609 MUTATION STATUS' versus Molecular Subtype #3: 'METHYLATION_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 34 11 9 7 6 20 9
ZNF609 MUTATED 2 0 0 2 0 0 1
ZNF609 WILD-TYPE 32 11 9 5 6 20 8
Methods & Data
Input

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /cromwell_root/fc-8b2df640-93e1-40a2-b735-5b7a14ef6398/dc84de78-e224-489d-a892-238209655610/correlate_genomic_events_all/381a4ae2-a2b0-4c20-81f1-89a7993687e1/call-preprocess_genomic_event/transformed.cor.cli.txt

  • Molecular subtypes file = /cromwell_root/fc-8b2df640-93e1-40a2-b735-5b7a14ef6398/10d02b45-07ea-40cc-ac82-013e5f89ebb2/aggregate_clusters_workflow/b0f8dcb2-0993-4424-ad42-552c0bd1a2d5/call-aggregate_clusters/CPTAC3-UCEC-TP.transposedmergedcluster.txt

  • Number of patients = 100

  • Number of significantly mutated genes = 388

  • Number of Molecular subtypes = 3

  • 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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