Correlation between gene mutation status and molecular subtypes
Pan-kidney cohort (KICH+KIRC+KIRP) (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1ST7P3R
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1ST7P3R
Overview
Introduction

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

Summary

Testing the association between mutation status of 57 genes and 12 molecular subtypes across 663 patients, 174 significant findings detected with P value < 0.05 and Q value < 0.25.

  • FAM18B2 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • PTEN mutation correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • KDM5C mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • SETD2 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • PBRM1 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • NEFH mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

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

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

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

  • NF2 mutation correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • TDG mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • MUC5B mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • ZNF814 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • CSGALNACT2 mutation correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • GPR50 mutation correlated to 'RPPA_CNMF'.

  • STAG2 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • NFE2L2 mutation correlated to 'MRNASEQ_CNMF'.

  • MTOR mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • EMG1 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • RIMBP3 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • ZNF598 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • KDM6A mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • STAM mutation correlated to 'METHLYATION_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • PARD6B mutation correlated to 'RPPA_CNMF'.

  • SLC16A1 mutation correlated to 'RPPA_CNMF' and 'RPPA_CHIERARCHICAL'.

  • SKI mutation correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

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

  • FAT1 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • MLL3 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • PAM mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • GAPDHS mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • RPL7A mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • AHNAK2 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • AMAC1L3 mutation correlated to 'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • MED16 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 57 genes and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 174 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
PBRM1 138 (21%) 525 0.00374
(0.0277) 		0.0022
(0.0188) 		1e-05
(0.000175) 		1e-05
(0.000175) 		0.0349
(0.149) 		0.00195
(0.0175) 		1e-05
(0.000175) 		1e-05
(0.000175) 		1e-05
(0.000175) 		1e-05
(0.000175) 		1e-05
(0.000175) 		1e-05
(0.000175)
VHL 195 (29%) 468 0.00148
(0.0143) 		0.002
(0.0178) 		1e-05
(0.000175) 		1e-05
(0.000175) 		0.0414
(0.171) 		1e-05
(0.000175) 		1e-05
(0.000175) 		1e-05
(0.000175) 		1e-05
(0.000175) 		1e-05
(0.000175) 		1e-05
(0.000175) 		1e-05
(0.000175)
FAM18B2 35 (5%) 628 0.00232
(0.0194) 		0.0191
(0.0928) 		1e-05
(0.000175) 		1e-05
(0.000175) 		0.786
(1.00) 		0.101
(0.321) 		1e-05
(0.000175) 		1e-05
(0.000175) 		1e-05
(0.000175) 		1e-05
(0.000175) 		1e-05
(0.000175) 		1e-05
(0.000175)
TP53 35 (5%) 628 1e-05
(0.000175) 		1e-05
(0.000175) 		0.935
(1.00) 		0.0127
(0.0707) 		1e-05
(0.000175) 		1e-05
(0.000175) 		1e-05
(0.000175) 		1e-05
(0.000175) 		1e-05
(0.000175) 		1e-05
(0.000175)
MET 19 (3%) 644 0.00906
(0.0525) 		1e-05
(0.000175) 		0.0465
(0.186) 		0.693
(1.00) 		1e-05
(0.000175) 		1e-05
(0.000175) 		3e-05
(5e-04) 		1e-05
(0.000175) 		0.00095
(0.0104) 		0.00013
(0.00198)
MUC5B 32 (5%) 631 0.00408
(0.0294) 		4e-05
(0.000651) 		0.565
(0.946) 		0.0296
(0.134) 		0.00015
(0.00223) 		2e-05
(0.000342) 		1e-05
(0.000175) 		1e-05
(0.000175) 		0.0396
(0.166) 		0.00697
(0.0431)
HNRNPM 12 (2%) 651 0.0273
(0.124) 		0.00144
(0.0141) 		0.422
(0.8) 		0.366
(0.728) 		0.00083
(0.00946) 		0.00183
(0.0174) 		0.00104
(0.0111) 		0.0001
(0.00155) 		0.0331
(0.143) 		0.031
(0.138)
ZNF598 11 (2%) 652 0.0314
(0.139) 		0.00194
(0.0175) 		0.58
(0.951) 		0.486
(0.859) 		0.00213
(0.0184) 		0.0011
(0.0116) 		0.00131
(0.0132) 		0.00023
(0.00328) 		0.0873
(0.294) 		0.00064
(0.00742)
ZNF814 13 (2%) 650 0.00745
(0.0455) 		0.00644
(0.0408) 		0.646
(1.00) 		0.787
(1.00) 		0.00189
(0.0175) 		0.0152
(0.0795) 		0.0109
(0.0609) 		0.00144
(0.0141) 		0.448
(0.824) 		0.361
(0.723)
MTOR 32 (5%) 631 0.00062
(0.00731) 		0.00847
(0.0513) 		0.0169
(0.0868) 		0.0217
(0.102) 		0.142
(0.386) 		0.089
(0.296) 		0.00116
(0.012) 		0.00441
(0.0305) 		0.401
(0.773) 		0.0737
(0.261)
SKI 9 (1%) 654 0.00096
(0.0104) 		0.126
(0.36) 		0.626
(0.991) 		0.358
(0.718) 		0.00018
(0.00262) 		0.00247
(0.0201) 		0.00055
(0.00672) 		0.00297
(0.0232) 		0.0229
(0.106) 		0.0828
(0.286)
MLL3 38 (6%) 625 0.775
(1.00) 		0.625
(0.991) 		0.0233
(0.108) 		0.0107
(0.0608) 		0.265
(0.605) 		0.662
(1.00) 		0.0257
(0.118) 		0.0216
(0.102) 		0.00439
(0.0305) 		0.00088
(0.00987) 		0.212
(0.519) 		0.594
(0.97)
PAM 4 (1%) 659 0.02
(0.0956) 		0.00581
(0.0375) 		0.145
(0.388) 		0.109
(0.329) 		0.00278
(0.0221) 		0.0129
(0.0708) 		0.013
(0.0708) 		0.0152
(0.0795)
KDM5C 28 (4%) 635 0.0688
(0.248) 		0.0191
(0.0928) 		0.329
(0.683) 		0.303
(0.658) 		0.0316
(0.139) 		0.009
(0.0525) 		0.00123
(0.0126) 		0.00678
(0.0425) 		0.811
(1.00) 		0.669
(1.00)
NF2 16 (2%) 647 0.0775
(0.272) 		0.11
(0.329) 		0.9
(1.00) 		0.167
(0.433) 		0.0033
(0.0248) 		0.0003
(0.00419) 		0.0721
(0.257) 		0.00031
(0.00424) 		0.00242
(0.0199) 		0.0187
(0.092)
CSGALNACT2 8 (1%) 655 0.00377
(0.0277) 		0.247
(0.575) 		0.521
(0.904) 		0.389
(0.759) 		0.0105
(0.06) 		0.0496
(0.196) 		0.0403
(0.168) 		0.0101
(0.0581) 		0.0871
(0.294) 		0.222
(0.537)
EMG1 4 (1%) 659 0.00419
(0.0299) 		0.0044
(0.0305) 		0.0684
(0.248) 		0.0186
(0.092) 		0.00306
(0.0235) 		0.821
(1.00) 		0.00488
(0.033)
KDM6A 10 (2%) 653 0.0977
(0.315) 		0.00516
(0.0346) 		0.229
(0.548) 		0.295
(0.647) 		0.00466
(0.0319) 		0.0056
(0.0368) 		0.00574
(0.0374) 		0.00227
(0.0192) 		0.329
(0.683) 		0.194
(0.487)
FAT1 21 (3%) 642 0.11
(0.329) 		0.0306
(0.138) 		0.963
(1.00) 		0.188
(0.476) 		0.00038
(0.005) 		0.0004
(0.00516) 		0.0141
(0.0747) 		0.00062
(0.00731) 		0.231
(0.551) 		0.0643
(0.239)
AHNAK2 33 (5%) 630 0.178
(0.451) 		0.0523
(0.203) 		0.561
(0.946) 		0.0333
(0.143) 		0.889
(1.00) 		0.401
(0.773) 		0.00617
(0.0394) 		0.00044
(0.00557) 		0.0171
(0.0868) 		0.00873
(0.0521) 		0.681
(1.00) 		0.357
(0.718)
AMAC1L3 8 (1%) 655 0.481
(0.855) 		0.00314
(0.0239) 		0.0879
(0.295) 		0.00206
(0.0181) 		0.00195
(0.0175) 		0.00052
(0.00647) 		0.242
(0.567) 		0.00038
(0.005) 		0.326
(0.683) 		0.33
(0.683)
PTEN 26 (4%) 637 0.616
(0.991) 		0.92
(1.00) 		0.0532
(0.204) 		0.424
(0.801) 		0.397
(0.77) 		0.29
(0.643) 		0.0171
(0.0868) 		0.00557
(0.0368) 		0.342
(0.699) 		0.0525
(0.203) 		0.0187
(0.092) 		0.00265
(0.0213)
NEFH 16 (2%) 647 0.124
(0.358) 		0.0221
(0.103) 		0.0623
(0.233) 		0.287
(0.639) 		0.0039
(0.0284) 		0.00876
(0.0521) 		0.0562
(0.215) 		0.00886
(0.0522) 		0.21
(0.517) 		0.148
(0.391)
SETD2 56 (8%) 607 0.54
(0.92) 		0.58
(0.951) 		0.0653
(0.242) 		0.0135
(0.0729) 		0.48
(0.855) 		0.371
(0.729) 		0.144
(0.388) 		5e-05
(0.000795) 		0.326
(0.683) 		0.114
(0.335) 		0.0462
(0.186) 		0.0756
(0.266)
TDG 5 (1%) 658 0.033
(0.143) 		0.0365
(0.154) 		0.878
(1.00) 		0.646
(1.00) 		0.0365
(0.154) 		0.114
(0.335) 		0.122
(0.355) 		0.0519
(0.203) 		0.104
(0.325) 		0.0611
(0.231)
STAM 6 (1%) 657 1
(1.00) 		0.0129
(0.0708) 		0.342
(0.699) 		0.129
(0.36) 		0.368
(0.728) 		0.125
(0.36) 		0.324
(0.683) 		0.236
(0.557) 		0.00298
(0.0232) 		0.057
(0.217)
SLC16A1 3 (0%) 660 1
(1.00) 		1
(1.00) 		0.0422
(0.172) 		0.0137
(0.0731) 		1
(1.00) 		0.955
(1.00) 		0.799
(1.00) 		1
(1.00)
NASP 4 (1%) 659 0.318
(0.678) 		0.0671
(0.246) 		0.343
(0.699) 		0.305
(0.658) 		0.041
(0.17) 		0.146
(0.388) 		0.213
(0.519) 		0.0498
(0.196) 		0.0868
(0.294) 		0.134
(0.368)
GPR50 5 (1%) 658 1
(1.00) 		0.618
(0.991) 		0.0194
(0.0934) 		0.31
(0.666) 		0.422
(0.8) 		0.568
(0.946) 		0.856
(1.00) 		0.626
(0.991)
STAG2 14 (2%) 649 1
(1.00) 		0.856
(1.00) 		0.545
(0.924) 		0.129
(0.36) 		0.565
(0.946) 		0.00699
(0.0431) 		0.202
(0.5) 		0.137
(0.375) 		0.129
(0.36) 		0.229
(0.548)
NFE2L2 10 (2%) 653 0.527
(0.908) 		0.109
(0.329) 		0.605
(0.98) 		0.169
(0.438) 		0.0474
(0.188) 		0.138
(0.377) 		0.5
(0.875) 		0.291
(0.644) 		0.296
(0.647) 		0.101
(0.321)
RIMBP3 5 (1%) 658 0.447
(0.824) 		0.174
(0.447) 		0.49
(0.862) 		0.751
(1.00) 		0.624
(0.991) 		0.0161
(0.0835) 		0.449
(0.824) 		0.431
(0.809)
PARD6B 5 (1%) 658 0.322
(0.683) 		0.128
(0.36) 		0.0422
(0.172) 		0.0618
(0.232) 		0.146
(0.388) 		0.0963
(0.312) 		0.453
(0.824) 		0.225
(0.542) 		0.531
(0.913) 		0.451
(0.824)
GAPDHS 5 (1%) 658 0.643
(1.00) 		0.261
(0.597) 		0.462
(0.832) 		1
(1.00) 		0.147
(0.388) 		0.0179
(0.09) 		0.12
(0.35) 		0.107
(0.329)
RPL7A 3 (0%) 660 1
(1.00) 		0.0986
(0.317) 		1
(1.00) 		0.133
(0.368) 		0.0871
(0.294) 		0.0933
(0.306) 		0.237
(0.557) 		0.032
(0.14)
MED16 4 (1%) 659 0.46
(0.83) 		0.421
(0.8) 		1
(1.00) 		0.203
(0.502) 		0.907
(1.00) 		0.0461
(0.186) 		0.82
(1.00) 		0.127
(0.36) 		0.384
(0.75) 		0.277
(0.627)
KDELR3 6 (1%) 657 1
(1.00) 		0.2
(0.496) 		0.509
(0.888) 		0.495
(0.868) 		0.0711
(0.255) 		0.295
(0.647) 		0.869
(1.00) 		0.237
(0.557) 		0.112
(0.332) 		0.285
(0.636)
ATM 16 (2%) 647 0.566
(0.946) 		0.458
(0.828) 		0.913
(1.00) 		0.988
(1.00) 		0.25
(0.578) 		0.235
(0.557) 		0.331
(0.685) 		0.0885
(0.295) 		0.758
(1.00) 		0.543
(0.923)
EGFR 6 (1%) 657 0.296
(0.647) 		0.428
(0.806) 		0.773
(1.00) 		0.876
(1.00) 		0.35
(0.706) 		0.724
(1.00) 		0.25
(0.578) 		1
(1.00)
SLC6A14 5 (1%) 658 0.856
(1.00) 		0.0996
(0.318) 		0.878
(1.00) 		0.175
(0.447) 		0.756
(1.00) 		0.571
(0.946) 		0.526
(0.908) 		0.107
(0.329) 		0.109
(0.329) 		0.142
(0.386)
PIK3CA 12 (2%) 651 0.194
(0.487) 		0.784
(1.00) 		0.892
(1.00) 		0.605
(0.98) 		0.215
(0.521) 		0.34
(0.699) 		0.651
(1.00) 		0.686
(1.00)
RAI1 7 (1%) 656 0.102
(0.322) 		0.743
(1.00) 		0.57
(0.946) 		0.884
(1.00) 		0.908
(1.00) 		0.347
(0.704) 		1
(1.00) 		0.416
(0.797) 		0.11
(0.329) 		0.284
(0.636)
FAM160B2 4 (1%) 659 0.84
(1.00) 		1
(1.00) 		0.751
(1.00) 		0.702
(1.00) 		0.905
(1.00) 		0.833
(1.00) 		0.452
(0.824) 		0.744
(1.00)
DPCR1 8 (1%) 655 1
(1.00) 		0.799
(1.00) 		0.651
(1.00) 		0.967
(1.00) 		0.83
(1.00) 		0.893
(1.00) 		1
(1.00) 		0.565
(0.946)
CYP4F11 5 (1%) 658 0.449
(0.824) 		0.786
(1.00) 		0.414
(0.796) 		0.0674
(0.246) 		0.37
(0.729) 		0.846
(1.00) 		0.249
(0.578) 		1
(1.00)
NUDT11 5 (1%) 658 0.163
(0.428) 		0.718
(1.00) 		0.574
(0.948) 		0.91
(1.00) 		0.93
(1.00) 		0.711
(1.00) 		0.854
(1.00) 		1
(1.00)
RHEB 3 (0%) 660 0.785
(1.00) 		0.367
(0.728) 		0.253
(0.582) 		1
(1.00) 		0.474
(0.848) 		0.166
(0.433) 		1
(1.00) 		0.438
(0.816) 		0.916
(1.00)
THBS1 10 (2%) 653 0.486
(0.859) 		0.348
(0.704) 		0.417
(0.797) 		0.304
(0.658) 		0.252
(0.581) 		0.144
(0.388) 		0.717
(1.00) 		0.571
(0.946) 		0.622
(0.991) 		0.859
(1.00)
SH3BP2 4 (1%) 659 0.0686
(0.248) 		0.278
(0.627) 		0.901
(1.00) 		0.465
(0.835) 		0.112
(0.332) 		0.0916
(0.303) 		0.213
(0.519) 		0.128
(0.36)
CACNA1C 17 (3%) 646 1
(1.00) 		1
(1.00) 		0.525
(0.908) 		0.628
(0.991) 		0.583
(0.954) 		0.432
(0.809) 		0.49
(0.862) 		0.765
(1.00) 		0.536
(0.917) 		0.533
(0.914) 		0.452
(0.824) 		0.605
(0.98)
PCK1 5 (1%) 658 1
(1.00) 		0.606
(0.98) 		0.925
(1.00) 		0.868
(1.00) 		0.609
(0.983) 		0.314
(0.673) 		1
(1.00)
TPPP 3 (0%) 660 1
(1.00) 		0.175
(0.447) 		1
(1.00) 		0.368
(0.728) 		0.514
(0.894) 		0.196
(0.49) 		1
(1.00) 		0.457
(0.828)
TMCO3 7 (1%) 656 0.0785
(0.274) 		0.273
(0.621) 		0.183
(0.464) 		0.945
(1.00) 		0.867
(1.00) 		0.0852
(0.293) 		0.342
(0.699) 		0.624
(0.991)
ARHGAP35 7 (1%) 656 0.638
(1.00) 		0.302
(0.658) 		0.761
(1.00) 		0.848
(1.00) 		1
(1.00) 		0.657
(1.00) 		0.11
(0.329) 		1
(1.00)
JMJD1C 10 (2%) 653 0.855
(1.00) 		0.434
(0.81) 		0.0826
(0.286) 		0.316
(0.676) 		0.117
(0.343) 		0.868
(1.00) 		0.17
(0.439) 		1
(1.00) 		0.327
(0.683) 		0.481
(0.855)
TTLL6 6 (1%) 657 1
(1.00) 		0.0934
(0.306) 		0.575
(0.948) 		0.557
(0.943) 		0.0961
(0.312) 		0.395
(0.767) 		0.769
(1.00) 		0.107
(0.329) 		0.279
(0.628) 		0.836
(1.00)
TRAPPC9 5 (1%) 658 0.854
(1.00) 		0.129
(0.36) 		0.38
(0.744) 		0.925
(1.00) 		0.147
(0.388) 		0.328
(0.683) 		0.453
(0.824) 		0.109
(0.329)
'FAM18B2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00232 (Fisher's exact test), Q value = 0.019

Table S1.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 16 10 13
FAM18B2 MUTATED 0 0 0 4
FAM18B2 WILD-TYPE 17 16 10 9

Figure S1.  Get High-res Image Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'FAM18B2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0191 (Fisher's exact test), Q value = 0.093

Table S2.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 7 16 14 10 9
FAM18B2 MUTATED 0 0 4 0 0
FAM18B2 WILD-TYPE 7 16 10 10 9

Figure S2.  Get High-res Image Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'FAM18B2 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S3.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
FAM18B2 MUTATED 23 8 4
FAM18B2 WILD-TYPE 156 231 238

Figure S3.  Get High-res Image Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FAM18B2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S4.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
FAM18B2 MUTATED 6 2 23
FAM18B2 WILD-TYPE 97 253 96

Figure S4.  Get High-res Image Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'FAM18B2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S5.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
FAM18B2 MUTATED 5 5 8 7
FAM18B2 WILD-TYPE 143 134 132 150
'FAM18B2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.101 (Fisher's exact test), Q value = 0.32

Table S6.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
FAM18B2 MUTATED 6 5 2 2 2 4 4
FAM18B2 WILD-TYPE 144 39 94 118 46 47 71
'FAM18B2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S7.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
FAM18B2 MUTATED 2 4 0 29
FAM18B2 WILD-TYPE 97 169 241 119

Figure S5.  Get High-res Image Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'FAM18B2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S8.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
FAM18B2 MUTATED 1 14 0 0 0 20
FAM18B2 WILD-TYPE 79 77 173 137 90 70

Figure S6.  Get High-res Image Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'FAM18B2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S9.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
FAM18B2 MUTATED 28 7 0
FAM18B2 WILD-TYPE 184 142 293

Figure S7.  Get High-res Image Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'FAM18B2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S10.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
FAM18B2 MUTATED 0 34 1
FAM18B2 WILD-TYPE 72 146 401

Figure S8.  Get High-res Image Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'FAM18B2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S11.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
FAM18B2 MUTATED 18 4 6 1
FAM18B2 WILD-TYPE 59 56 36 98

Figure S9.  Get High-res Image Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'FAM18B2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S12.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
FAM18B2 MUTATED 1 16 12 0 0
FAM18B2 WILD-TYPE 23 33 52 95 46

Figure S10.  Get High-res Image Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S13.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
TP53 MUTATED 22 3 10
TP53 WILD-TYPE 157 236 232

Figure S11.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S14.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
TP53 MUTATED 26 4 3
TP53 WILD-TYPE 77 251 116

Figure S12.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S15.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
TP53 MUTATED 9 7 8 7
TP53 WILD-TYPE 139 132 132 150
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.071

Table S16.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
TP53 MUTATED 10 4 11 4 1 0 1
TP53 WILD-TYPE 140 40 85 116 47 51 74

Figure S13.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S17.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
TP53 MUTATED 24 5 2 4
TP53 WILD-TYPE 75 168 239 144

Figure S14.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S18.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
TP53 MUTATED 23 6 2 2 1 1
TP53 WILD-TYPE 57 85 171 135 89 89

Figure S15.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S19.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
TP53 MUTATED 27 3 5
TP53 WILD-TYPE 185 146 288

Figure S16.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S20.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
TP53 MUTATED 23 7 5
TP53 WILD-TYPE 49 173 397

Figure S17.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S21.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
TP53 MUTATED 2 18 3 2
TP53 WILD-TYPE 75 42 39 97

Figure S18.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S22.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
TP53 MUTATED 0 1 4 2 18
TP53 WILD-TYPE 24 48 60 93 28

Figure S19.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.616 (Fisher's exact test), Q value = 0.99

Table S23.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 16 10 13
PTEN MUTATED 0 1 1 1
PTEN WILD-TYPE 17 15 9 12
'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.92 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 7 16 14 10 9
PTEN MUTATED 0 1 1 0 1
PTEN WILD-TYPE 7 15 13 10 8
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0532 (Fisher's exact test), Q value = 0.2

Table S25.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
PTEN MUTATED 12 5 8
PTEN WILD-TYPE 167 234 234
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.424 (Fisher's exact test), Q value = 0.8

Table S26.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
PTEN MUTATED 6 8 5
PTEN WILD-TYPE 97 247 114
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 0.77

Table S27.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
PTEN MUTATED 5 8 3 8
PTEN WILD-TYPE 143 131 137 149
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.29 (Fisher's exact test), Q value = 0.64

Table S28.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
PTEN MUTATED 7 0 5 9 1 1 1
PTEN WILD-TYPE 143 44 91 111 47 50 74
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.087

Table S29.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
PTEN MUTATED 7 10 3 6
PTEN WILD-TYPE 92 163 238 142

Figure S20.  Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00557 (Fisher's exact test), Q value = 0.037

Table S30.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
PTEN MUTATED 7 0 4 8 1 6
PTEN WILD-TYPE 73 91 169 129 89 84

Figure S21.  Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.342 (Fisher's exact test), Q value = 0.7

Table S31.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
PTEN MUTATED 12 4 10
PTEN WILD-TYPE 200 145 283
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0525 (Fisher's exact test), Q value = 0.2

Table S32.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
PTEN MUTATED 7 6 13
PTEN WILD-TYPE 65 174 389
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.092

Table S33.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
PTEN MUTATED 6 5 0 1
PTEN WILD-TYPE 71 55 42 98

Figure S22.  Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00265 (Fisher's exact test), Q value = 0.021

Table S34.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
PTEN MUTATED 1 5 0 1 5
PTEN WILD-TYPE 23 44 64 94 41

Figure S23.  Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KDM5C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0688 (Fisher's exact test), Q value = 0.25

Table S35.  Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
KDM5C MUTATED 4 8 16
KDM5C WILD-TYPE 175 231 226
'KDM5C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.093

Table S36.  Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
KDM5C MUTATED 1 17 2
KDM5C WILD-TYPE 102 238 117

Figure S24.  Get High-res Image Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'KDM5C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.329 (Fisher's exact test), Q value = 0.68

Table S37.  Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
KDM5C MUTATED 5 8 3 9
KDM5C WILD-TYPE 143 131 137 148
'KDM5C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.303 (Fisher's exact test), Q value = 0.66

Table S38.  Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
KDM5C MUTATED 10 0 6 6 1 1 1
KDM5C WILD-TYPE 140 44 90 114 47 50 74
'KDM5C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0316 (Fisher's exact test), Q value = 0.14

Table S39.  Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
KDM5C MUTATED 1 10 14 2
KDM5C WILD-TYPE 98 163 227 146

Figure S25.  Get High-res Image Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'KDM5C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.009 (Fisher's exact test), Q value = 0.053

Table S40.  Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
KDM5C MUTATED 1 0 15 6 3 2
KDM5C WILD-TYPE 79 91 158 131 87 88

Figure S26.  Get High-res Image Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KDM5C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.013

Table S41.  Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
KDM5C MUTATED 3 3 22
KDM5C WILD-TYPE 209 146 271

Figure S27.  Get High-res Image Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'KDM5C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00678 (Fisher's exact test), Q value = 0.043

Table S42.  Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
KDM5C MUTATED 1 2 25
KDM5C WILD-TYPE 71 178 377

Figure S28.  Get High-res Image Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'KDM5C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.811 (Fisher's exact test), Q value = 1

Table S43.  Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
KDM5C MUTATED 1 1 0 3
KDM5C WILD-TYPE 76 59 42 96
'KDM5C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S44.  Gene #4: 'KDM5C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
KDM5C MUTATED 0 1 0 3 1
KDM5C WILD-TYPE 24 48 64 92 45
'SETD2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.54 (Fisher's exact test), Q value = 0.92

Table S45.  Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 16 10 13
SETD2 MUTATED 1 2 0 0
SETD2 WILD-TYPE 16 14 10 13
'SETD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.58 (Fisher's exact test), Q value = 0.95

Table S46.  Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 7 16 14 10 9
SETD2 MUTATED 0 2 0 1 0
SETD2 WILD-TYPE 7 14 14 9 9
'SETD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0653 (Fisher's exact test), Q value = 0.24

Table S47.  Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
SETD2 MUTATED 8 24 24
SETD2 WILD-TYPE 171 215 218
'SETD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.073

Table S48.  Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
SETD2 MUTATED 3 31 9
SETD2 WILD-TYPE 100 224 110

Figure S29.  Get High-res Image Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'SETD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.48 (Fisher's exact test), Q value = 0.86

Table S49.  Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
SETD2 MUTATED 12 11 9 18
SETD2 WILD-TYPE 136 128 131 139
'SETD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.371 (Fisher's exact test), Q value = 0.73

Table S50.  Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
SETD2 MUTATED 17 5 10 5 3 3 7
SETD2 WILD-TYPE 133 39 86 115 45 48 68
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.144 (Fisher's exact test), Q value = 0.39

Table S51.  Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
SETD2 MUTATED 3 15 25 13
SETD2 WILD-TYPE 96 158 216 135
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 8e-04

Table S52.  Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
SETD2 MUTATED 2 14 23 12 5 0
SETD2 WILD-TYPE 78 77 150 125 85 90

Figure S30.  Get High-res Image Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.326 (Fisher's exact test), Q value = 0.68

Table S53.  Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
SETD2 MUTATED 13 12 29
SETD2 WILD-TYPE 199 137 264
'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.114 (Fisher's exact test), Q value = 0.34

Table S54.  Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
SETD2 MUTATED 2 13 39
SETD2 WILD-TYPE 70 167 363
'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0462 (Fisher's exact test), Q value = 0.19

Table S55.  Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
SETD2 MUTATED 6 1 3 14
SETD2 WILD-TYPE 71 59 39 85

Figure S31.  Get High-res Image Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0756 (Fisher's exact test), Q value = 0.27

Table S56.  Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
SETD2 MUTATED 0 3 7 13 1
SETD2 WILD-TYPE 24 46 57 82 45
'PBRM1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00374 (Fisher's exact test), Q value = 0.028

Table S57.  Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 16 10 13
PBRM1 MUTATED 9 3 1 0
PBRM1 WILD-TYPE 8 13 9 13

Figure S32.  Get High-res Image Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'PBRM1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0022 (Fisher's exact test), Q value = 0.019

Table S58.  Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 7 16 14 10 9
PBRM1 MUTATED 5 3 0 4 1
PBRM1 WILD-TYPE 2 13 14 6 8

Figure S33.  Get High-res Image Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S59.  Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
PBRM1 MUTATED 5 68 65
PBRM1 WILD-TYPE 174 171 177

Figure S34.  Get High-res Image Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PBRM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S60.  Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
PBRM1 MUTATED 1 92 5
PBRM1 WILD-TYPE 102 163 114

Figure S35.  Get High-res Image Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PBRM1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.15

Table S61.  Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
PBRM1 MUTATED 23 36 26 43
PBRM1 WILD-TYPE 125 103 114 114

Figure S36.  Get High-res Image Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'PBRM1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00195 (Fisher's exact test), Q value = 0.018

Table S62.  Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
PBRM1 MUTATED 42 4 12 35 12 13 10
PBRM1 WILD-TYPE 108 40 84 85 36 38 65

Figure S37.  Get High-res Image Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S63.  Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
PBRM1 MUTATED 2 37 91 7
PBRM1 WILD-TYPE 97 136 150 141

Figure S38.  Get High-res Image Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S64.  Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
PBRM1 MUTATED 2 6 70 27 31 1
PBRM1 WILD-TYPE 78 85 103 110 59 89

Figure S39.  Get High-res Image Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S65.  Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
PBRM1 MUTATED 7 23 104
PBRM1 WILD-TYPE 205 126 189

Figure S40.  Get High-res Image Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S66.  Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
PBRM1 MUTATED 1 8 125
PBRM1 WILD-TYPE 71 172 277

Figure S41.  Get High-res Image Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S67.  Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
PBRM1 MUTATED 4 1 2 31
PBRM1 WILD-TYPE 73 59 40 68

Figure S42.  Get High-res Image Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S68.  Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
PBRM1 MUTATED 0 1 5 31 1
PBRM1 WILD-TYPE 24 48 59 64 45

Figure S43.  Get High-res Image Gene #6: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NEFH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.124 (Fisher's exact test), Q value = 0.36

Table S69.  Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
NEFH MUTATED 8 5 3
NEFH WILD-TYPE 171 234 239
'NEFH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.1

Table S70.  Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
NEFH MUTATED 1 5 8
NEFH WILD-TYPE 102 250 111

Figure S44.  Get High-res Image Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'NEFH MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0623 (Fisher's exact test), Q value = 0.23

Table S71.  Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
NEFH MUTATED 3 0 3 7
NEFH WILD-TYPE 145 139 137 150
'NEFH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.287 (Fisher's exact test), Q value = 0.64

Table S72.  Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
NEFH MUTATED 4 2 2 0 2 1 2
NEFH WILD-TYPE 146 42 94 120 46 50 73
'NEFH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0039 (Fisher's exact test), Q value = 0.028

Table S73.  Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
NEFH MUTATED 1 1 4 10
NEFH WILD-TYPE 98 172 237 138

Figure S45.  Get High-res Image Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NEFH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00876 (Fisher's exact test), Q value = 0.052

Table S74.  Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
NEFH MUTATED 0 6 3 2 0 5
NEFH WILD-TYPE 80 85 170 135 90 85

Figure S46.  Get High-res Image Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'NEFH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0562 (Fisher's exact test), Q value = 0.21

Table S75.  Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
NEFH MUTATED 10 2 4
NEFH WILD-TYPE 202 147 289
'NEFH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00886 (Fisher's exact test), Q value = 0.052

Table S76.  Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
NEFH MUTATED 0 10 6
NEFH WILD-TYPE 72 170 396

Figure S47.  Get High-res Image Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.21 (Fisher's exact test), Q value = 0.52

Table S77.  Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
NEFH MUTATED 4 0 0 3
NEFH WILD-TYPE 73 60 42 96
'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.148 (Fisher's exact test), Q value = 0.39

Table S78.  Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
NEFH MUTATED 0 4 1 2 0
NEFH WILD-TYPE 24 45 63 93 46
'VHL MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00148 (Fisher's exact test), Q value = 0.014

Table S79.  Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 16 10 13
VHL MUTATED 10 5 1 0
VHL WILD-TYPE 7 11 9 13

Figure S48.  Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'VHL MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.002 (Fisher's exact test), Q value = 0.018

Table S80.  Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 7 16 14 10 9
VHL MUTATED 4 5 0 6 1
VHL WILD-TYPE 3 11 14 4 8

Figure S49.  Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S81.  Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
VHL MUTATED 4 103 88
VHL WILD-TYPE 175 136 154

Figure S50.  Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'VHL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S82.  Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
VHL MUTATED 1 120 1
VHL WILD-TYPE 102 135 118

Figure S51.  Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'VHL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0414 (Fisher's exact test), Q value = 0.17

Table S83.  Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
VHL MUTATED 50 47 30 54
VHL WILD-TYPE 98 92 110 103

Figure S52.  Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'VHL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S84.  Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
VHL MUTATED 49 0 23 48 17 20 24
VHL WILD-TYPE 101 44 73 72 31 31 51

Figure S53.  Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S85.  Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
VHL MUTATED 4 66 123 2
VHL WILD-TYPE 95 107 118 146

Figure S54.  Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'VHL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S86.  Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
VHL MUTATED 2 2 83 61 47 0
VHL WILD-TYPE 78 89 90 76 43 90

Figure S55.  Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S87.  Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
VHL MUTATED 4 52 135
VHL WILD-TYPE 208 97 158

Figure S56.  Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'VHL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S88.  Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
VHL MUTATED 1 1 189
VHL WILD-TYPE 71 179 213

Figure S57.  Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S89.  Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
VHL MUTATED 0 1 0 50
VHL WILD-TYPE 77 59 42 49

Figure S58.  Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S90.  Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
VHL MUTATED 0 0 3 47 1
VHL WILD-TYPE 24 49 61 48 45

Figure S59.  Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MET MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00906 (Fisher's exact test), Q value = 0.053

Table S91.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
MET MUTATED 11 4 3
MET WILD-TYPE 168 235 239

Figure S60.  Get High-res Image Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'MET MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S92.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
MET MUTATED 1 3 13
MET WILD-TYPE 102 252 106

Figure S61.  Get High-res Image Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MET MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0465 (Fisher's exact test), Q value = 0.19

Table S93.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
MET MUTATED 7 7 1 2
MET WILD-TYPE 141 132 139 155

Figure S62.  Get High-res Image Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'MET MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.693 (Fisher's exact test), Q value = 1

Table S94.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
MET MUTATED 4 0 4 5 1 0 3
MET WILD-TYPE 146 44 92 115 47 51 72
'MET MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S95.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
MET MUTATED 0 1 1 17
MET WILD-TYPE 99 172 240 131

Figure S63.  Get High-res Image Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'MET MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S96.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
MET MUTATED 0 4 1 0 0 14
MET WILD-TYPE 80 87 172 137 90 76

Figure S64.  Get High-res Image Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'MET MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 5e-04

Table S97.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
MET MUTATED 15 3 1
MET WILD-TYPE 197 146 292

Figure S65.  Get High-res Image Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MET MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S98.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
MET MUTATED 0 18 1
MET WILD-TYPE 72 162 401

Figure S66.  Get High-res Image Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.01

Table S99.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
MET MUTATED 9 0 3 1
MET WILD-TYPE 68 60 39 98

Figure S67.  Get High-res Image Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.002

Table S100.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
MET MUTATED 4 5 4 0 0
MET WILD-TYPE 20 44 60 95 46

Figure S68.  Get High-res Image Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HNRNPM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.12

Table S101.  Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
HNRNPM MUTATED 7 4 1
HNRNPM WILD-TYPE 172 235 241

Figure S69.  Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'HNRNPM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.014

Table S102.  Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
HNRNPM MUTATED 4 1 7
HNRNPM WILD-TYPE 99 254 112

Figure S70.  Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'HNRNPM MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.422 (Fisher's exact test), Q value = 0.8

Table S103.  Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
HNRNPM MUTATED 3 4 4 1
HNRNPM WILD-TYPE 145 135 136 156
'HNRNPM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.366 (Fisher's exact test), Q value = 0.73

Table S104.  Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
HNRNPM MUTATED 2 3 1 3 0 1 2
HNRNPM WILD-TYPE 148 41 95 117 48 50 73
'HNRNPM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0095

Table S105.  Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
HNRNPM MUTATED 2 2 0 8
HNRNPM WILD-TYPE 97 171 241 140

Figure S71.  Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'HNRNPM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00183 (Fisher's exact test), Q value = 0.017

Table S106.  Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
HNRNPM MUTATED 2 5 0 1 0 4
HNRNPM WILD-TYPE 78 86 173 136 90 86

Figure S72.  Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'HNRNPM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.011

Table S107.  Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
HNRNPM MUTATED 8 4 0
HNRNPM WILD-TYPE 204 145 293

Figure S73.  Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'HNRNPM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.0016

Table S108.  Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
HNRNPM MUTATED 1 10 1
HNRNPM WILD-TYPE 71 170 401

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

'HNRNPM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0331 (Fisher's exact test), Q value = 0.14

Table S109.  Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
HNRNPM MUTATED 5 3 2 0
HNRNPM WILD-TYPE 72 57 40 99

Figure S75.  Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'HNRNPM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.031 (Fisher's exact test), Q value = 0.14

Table S110.  Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
HNRNPM MUTATED 2 3 4 0 1
HNRNPM WILD-TYPE 22 46 60 95 45

Figure S76.  Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0775 (Fisher's exact test), Q value = 0.27

Table S111.  Gene #11: 'NF2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
NF2 MUTATED 7 2 7
NF2 WILD-TYPE 172 237 235
'NF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 0.33

Table S112.  Gene #11: 'NF2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
NF2 MUTATED 4 3 5
NF2 WILD-TYPE 99 252 114
'NF2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.9 (Fisher's exact test), Q value = 1

Table S113.  Gene #11: 'NF2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
NF2 MUTATED 3 4 3 5
NF2 WILD-TYPE 145 135 137 152
'NF2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.167 (Fisher's exact test), Q value = 0.43

Table S114.  Gene #11: 'NF2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
NF2 MUTATED 3 2 4 0 2 1 3
NF2 WILD-TYPE 147 42 92 120 46 50 72
'NF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0033 (Fisher's exact test), Q value = 0.025

Table S115.  Gene #11: 'NF2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
NF2 MUTATED 1 5 1 9
NF2 WILD-TYPE 98 168 240 139

Figure S77.  Get High-res Image Gene #11: 'NF2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0042

Table S116.  Gene #11: 'NF2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
NF2 MUTATED 0 8 1 3 0 4
NF2 WILD-TYPE 80 83 172 134 90 86

Figure S78.  Get High-res Image Gene #11: 'NF2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'NF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0721 (Fisher's exact test), Q value = 0.26

Table S117.  Gene #11: 'NF2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
NF2 MUTATED 9 4 3
NF2 WILD-TYPE 203 145 290
'NF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0042

Table S118.  Gene #11: 'NF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
NF2 MUTATED 0 12 4
NF2 WILD-TYPE 72 168 398

Figure S79.  Get High-res Image Gene #11: 'NF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00242 (Fisher's exact test), Q value = 0.02

Table S119.  Gene #11: 'NF2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
NF2 MUTATED 3 0 4 0
NF2 WILD-TYPE 74 60 38 99

Figure S80.  Get High-res Image Gene #11: 'NF2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0187 (Fisher's exact test), Q value = 0.092

Table S120.  Gene #11: 'NF2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
NF2 MUTATED 0 3 4 0 0
NF2 WILD-TYPE 24 46 60 95 46

Figure S81.  Get High-res Image Gene #11: 'NF2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TDG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.14

Table S121.  Gene #12: 'TDG MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
TDG MUTATED 4 0 1
TDG WILD-TYPE 175 239 241

Figure S82.  Get High-res Image Gene #12: 'TDG MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TDG MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 0.15

Table S122.  Gene #12: 'TDG MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
TDG MUTATED 0 1 4
TDG WILD-TYPE 103 254 115

Figure S83.  Get High-res Image Gene #12: 'TDG MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'TDG MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.878 (Fisher's exact test), Q value = 1

Table S123.  Gene #12: 'TDG MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
TDG MUTATED 1 1 2 1
TDG WILD-TYPE 147 138 138 156
'TDG MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.646 (Fisher's exact test), Q value = 1

Table S124.  Gene #12: 'TDG MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
TDG MUTATED 2 1 1 0 0 0 1
TDG WILD-TYPE 148 43 95 120 48 51 74
'TDG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 0.15

Table S125.  Gene #12: 'TDG MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
TDG MUTATED 0 0 1 4
TDG WILD-TYPE 99 173 240 144

Figure S84.  Get High-res Image Gene #12: 'TDG MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TDG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.114 (Fisher's exact test), Q value = 0.33

Table S126.  Gene #12: 'TDG MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
TDG MUTATED 0 2 0 1 0 2
TDG WILD-TYPE 80 89 173 136 90 88
'TDG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.122 (Fisher's exact test), Q value = 0.35

Table S127.  Gene #12: 'TDG MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
TDG MUTATED 4 0 1
TDG WILD-TYPE 208 149 292
'TDG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0519 (Fisher's exact test), Q value = 0.2

Table S128.  Gene #12: 'TDG MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
TDG MUTATED 0 4 1
TDG WILD-TYPE 72 176 401
'TDG MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.104 (Fisher's exact test), Q value = 0.32

Table S129.  Gene #12: 'TDG MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
TDG MUTATED 4 0 0 1
TDG WILD-TYPE 73 60 42 98
'TDG MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0611 (Fisher's exact test), Q value = 0.23

Table S130.  Gene #12: 'TDG MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
TDG MUTATED 1 3 0 1 0
TDG WILD-TYPE 23 46 64 94 46
'MUC5B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00408 (Fisher's exact test), Q value = 0.029

Table S131.  Gene #13: 'MUC5B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
MUC5B MUTATED 17 6 9
MUC5B WILD-TYPE 162 233 233

Figure S85.  Get High-res Image Gene #13: 'MUC5B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'MUC5B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00065

Table S132.  Gene #13: 'MUC5B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
MUC5B MUTATED 14 5 11
MUC5B WILD-TYPE 89 250 108

Figure S86.  Get High-res Image Gene #13: 'MUC5B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MUC5B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.565 (Fisher's exact test), Q value = 0.95

Table S133.  Gene #13: 'MUC5B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
MUC5B MUTATED 8 7 7 4
MUC5B WILD-TYPE 140 132 133 153
'MUC5B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0296 (Fisher's exact test), Q value = 0.13

Table S134.  Gene #13: 'MUC5B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
MUC5B MUTATED 9 5 7 2 0 2 1
MUC5B WILD-TYPE 141 39 89 118 48 49 74

Figure S87.  Get High-res Image Gene #13: 'MUC5B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'MUC5B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0022

Table S135.  Gene #13: 'MUC5B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
MUC5B MUTATED 11 4 4 13
MUC5B WILD-TYPE 88 169 237 135

Figure S88.  Get High-res Image Gene #13: 'MUC5B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'MUC5B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00034

Table S136.  Gene #13: 'MUC5B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
MUC5B MUTATED 11 10 4 2 0 5
MUC5B WILD-TYPE 69 81 169 135 90 85

Figure S89.  Get High-res Image Gene #13: 'MUC5B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'MUC5B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S137.  Gene #13: 'MUC5B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
MUC5B MUTATED 24 3 5
MUC5B WILD-TYPE 188 146 288

Figure S90.  Get High-res Image Gene #13: 'MUC5B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MUC5B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00018

Table S138.  Gene #13: 'MUC5B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
MUC5B MUTATED 11 14 7
MUC5B WILD-TYPE 61 166 395

Figure S91.  Get High-res Image Gene #13: 'MUC5B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'MUC5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0396 (Fisher's exact test), Q value = 0.17

Table S139.  Gene #13: 'MUC5B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
MUC5B MUTATED 8 9 4 3
MUC5B WILD-TYPE 69 51 38 96

Figure S92.  Get High-res Image Gene #13: 'MUC5B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'MUC5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00697 (Fisher's exact test), Q value = 0.043

Table S140.  Gene #13: 'MUC5B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
MUC5B MUTATED 3 4 6 2 9
MUC5B WILD-TYPE 21 45 58 93 37

Figure S93.  Get High-res Image Gene #13: 'MUC5B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ZNF814 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00745 (Fisher's exact test), Q value = 0.045

Table S141.  Gene #14: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
ZNF814 MUTATED 6 0 7
ZNF814 WILD-TYPE 173 239 235

Figure S94.  Get High-res Image Gene #14: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ZNF814 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00644 (Fisher's exact test), Q value = 0.041

Table S142.  Gene #14: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
ZNF814 MUTATED 4 2 7
ZNF814 WILD-TYPE 99 253 112

Figure S95.  Get High-res Image Gene #14: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'ZNF814 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.646 (Fisher's exact test), Q value = 1

Table S143.  Gene #14: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
ZNF814 MUTATED 5 2 3 2
ZNF814 WILD-TYPE 143 137 137 155
'ZNF814 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.787 (Fisher's exact test), Q value = 1

Table S144.  Gene #14: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
ZNF814 MUTATED 4 2 2 1 1 1 1
ZNF814 WILD-TYPE 146 42 94 119 47 50 74
'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.018

Table S145.  Gene #14: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
ZNF814 MUTATED 3 1 1 8
ZNF814 WILD-TYPE 96 172 240 140

Figure S96.  Get High-res Image Gene #14: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.08

Table S146.  Gene #14: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
ZNF814 MUTATED 3 5 1 1 0 3
ZNF814 WILD-TYPE 77 86 172 136 90 87

Figure S97.  Get High-res Image Gene #14: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.061

Table S147.  Gene #14: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
ZNF814 MUTATED 7 5 1
ZNF814 WILD-TYPE 205 144 292

Figure S98.  Get High-res Image Gene #14: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00144 (Fisher's exact test), Q value = 0.014

Table S148.  Gene #14: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
ZNF814 MUTATED 3 8 2
ZNF814 WILD-TYPE 69 172 400

Figure S99.  Get High-res Image Gene #14: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.448 (Fisher's exact test), Q value = 0.82

Table S149.  Gene #14: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
ZNF814 MUTATED 5 2 1 2
ZNF814 WILD-TYPE 72 58 41 97
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.361 (Fisher's exact test), Q value = 0.72

Table S150.  Gene #14: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
ZNF814 MUTATED 1 2 4 1 2
ZNF814 WILD-TYPE 23 47 60 94 44
'CSGALNACT2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00377 (Fisher's exact test), Q value = 0.028

Table S151.  Gene #15: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
CSGALNACT2 MUTATED 6 0 2
CSGALNACT2 WILD-TYPE 173 239 240

Figure S100.  Get High-res Image Gene #15: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CSGALNACT2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.247 (Fisher's exact test), Q value = 0.58

Table S152.  Gene #15: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
CSGALNACT2 MUTATED 3 2 3
CSGALNACT2 WILD-TYPE 100 253 116
'CSGALNACT2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.521 (Fisher's exact test), Q value = 0.9

Table S153.  Gene #15: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
CSGALNACT2 MUTATED 2 0 2 3
CSGALNACT2 WILD-TYPE 146 139 138 154
'CSGALNACT2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.389 (Fisher's exact test), Q value = 0.76

Table S154.  Gene #15: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
CSGALNACT2 MUTATED 1 1 3 1 1 0 0
CSGALNACT2 WILD-TYPE 149 43 93 119 47 51 75
'CSGALNACT2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.06

Table S155.  Gene #15: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
CSGALNACT2 MUTATED 3 1 0 4
CSGALNACT2 WILD-TYPE 96 172 241 144

Figure S101.  Get High-res Image Gene #15: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CSGALNACT2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0496 (Fisher's exact test), Q value = 0.2

Table S156.  Gene #15: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
CSGALNACT2 MUTATED 2 3 0 1 0 2
CSGALNACT2 WILD-TYPE 78 88 173 136 90 88

Figure S102.  Get High-res Image Gene #15: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0403 (Fisher's exact test), Q value = 0.17

Table S157.  Gene #15: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
CSGALNACT2 MUTATED 6 1 1
CSGALNACT2 WILD-TYPE 206 148 292

Figure S103.  Get High-res Image Gene #15: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.058

Table S158.  Gene #15: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
CSGALNACT2 MUTATED 2 5 1
CSGALNACT2 WILD-TYPE 70 175 401

Figure S104.  Get High-res Image Gene #15: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0871 (Fisher's exact test), Q value = 0.29

Table S159.  Gene #15: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
CSGALNACT2 MUTATED 0 2 1 0
CSGALNACT2 WILD-TYPE 77 58 41 99
'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.222 (Fisher's exact test), Q value = 0.54

Table S160.  Gene #15: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
CSGALNACT2 MUTATED 0 0 2 0 1
CSGALNACT2 WILD-TYPE 24 49 62 95 45
'GPR50 MUTATION STATUS' versus 'CN_CNMF'

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

Table S161.  Gene #16: 'GPR50 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
GPR50 MUTATED 1 2 2
GPR50 WILD-TYPE 178 237 240
'GPR50 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.618 (Fisher's exact test), Q value = 0.99

Table S162.  Gene #16: 'GPR50 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
GPR50 MUTATED 2 2 1
GPR50 WILD-TYPE 101 253 118
'GPR50 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.093

Table S163.  Gene #16: 'GPR50 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
GPR50 MUTATED 1 0 4 0
GPR50 WILD-TYPE 147 139 136 157

Figure S105.  Get High-res Image Gene #16: 'GPR50 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'GPR50 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.31 (Fisher's exact test), Q value = 0.67

Table S164.  Gene #16: 'GPR50 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
GPR50 MUTATED 0 1 1 2 0 1 0
GPR50 WILD-TYPE 150 43 95 118 48 50 75
'GPR50 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.422 (Fisher's exact test), Q value = 0.8

Table S165.  Gene #16: 'GPR50 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
GPR50 MUTATED 2 1 1 1
GPR50 WILD-TYPE 97 172 240 147
'GPR50 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.568 (Fisher's exact test), Q value = 0.95

Table S166.  Gene #16: 'GPR50 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
GPR50 MUTATED 1 1 0 1 1 1
GPR50 WILD-TYPE 79 90 173 136 89 89
'GPR50 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.856 (Fisher's exact test), Q value = 1

Table S167.  Gene #16: 'GPR50 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
GPR50 MUTATED 1 1 3
GPR50 WILD-TYPE 211 148 290
'GPR50 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S168.  Gene #16: 'GPR50 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
GPR50 MUTATED 1 1 3
GPR50 WILD-TYPE 71 179 399
'STAG2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S169.  Gene #17: 'STAG2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
STAG2 MUTATED 4 5 5
STAG2 WILD-TYPE 175 234 237
'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.856 (Fisher's exact test), Q value = 1

Table S170.  Gene #17: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
STAG2 MUTATED 3 7 2
STAG2 WILD-TYPE 100 248 117
'STAG2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.545 (Fisher's exact test), Q value = 0.92

Table S171.  Gene #17: 'STAG2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
STAG2 MUTATED 3 1 3 5
STAG2 WILD-TYPE 145 138 137 152
'STAG2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.129 (Fisher's exact test), Q value = 0.36

Table S172.  Gene #17: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
STAG2 MUTATED 1 3 1 3 2 0 2
STAG2 WILD-TYPE 149 41 95 117 46 51 73
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.565 (Fisher's exact test), Q value = 0.95

Table S173.  Gene #17: 'STAG2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
STAG2 MUTATED 3 5 3 3
STAG2 WILD-TYPE 96 168 238 145
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00699 (Fisher's exact test), Q value = 0.043

Table S174.  Gene #17: 'STAG2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
STAG2 MUTATED 0 6 1 4 3 0
STAG2 WILD-TYPE 80 85 172 133 87 90

Figure S106.  Get High-res Image Gene #17: 'STAG2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.202 (Fisher's exact test), Q value = 0.5

Table S175.  Gene #17: 'STAG2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
STAG2 MUTATED 4 6 4
STAG2 WILD-TYPE 208 143 289
'STAG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.137 (Fisher's exact test), Q value = 0.38

Table S176.  Gene #17: 'STAG2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
STAG2 MUTATED 0 7 7
STAG2 WILD-TYPE 72 173 395
'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.129 (Fisher's exact test), Q value = 0.36

Table S177.  Gene #17: 'STAG2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
STAG2 MUTATED 1 1 4 3
STAG2 WILD-TYPE 76 59 38 96
'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.229 (Fisher's exact test), Q value = 0.55

Table S178.  Gene #17: 'STAG2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
STAG2 MUTATED 0 1 5 3 0
STAG2 WILD-TYPE 24 48 59 92 46
'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.527 (Fisher's exact test), Q value = 0.91

Table S179.  Gene #18: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
NFE2L2 MUTATED 4 2 4
NFE2L2 WILD-TYPE 175 237 238
'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.33

Table S180.  Gene #18: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
NFE2L2 MUTATED 0 3 4
NFE2L2 WILD-TYPE 103 252 115
'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.605 (Fisher's exact test), Q value = 0.98

Table S181.  Gene #18: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
NFE2L2 MUTATED 2 1 4 3
NFE2L2 WILD-TYPE 146 138 136 154
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.169 (Fisher's exact test), Q value = 0.44

Table S182.  Gene #18: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
NFE2L2 MUTATED 2 2 1 1 2 2 0
NFE2L2 WILD-TYPE 148 42 95 119 46 49 75
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0474 (Fisher's exact test), Q value = 0.19

Table S183.  Gene #18: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
NFE2L2 MUTATED 0 4 1 5
NFE2L2 WILD-TYPE 99 169 240 143

Figure S107.  Get High-res Image Gene #18: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.138 (Fisher's exact test), Q value = 0.38

Table S184.  Gene #18: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
NFE2L2 MUTATED 0 2 1 4 0 3
NFE2L2 WILD-TYPE 80 89 172 133 90 87
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.5 (Fisher's exact test), Q value = 0.87

Table S185.  Gene #18: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
NFE2L2 MUTATED 5 2 3
NFE2L2 WILD-TYPE 207 147 290
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S186.  Gene #18: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
NFE2L2 MUTATED 0 5 5
NFE2L2 WILD-TYPE 72 175 397
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.296 (Fisher's exact test), Q value = 0.65

Table S187.  Gene #18: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
NFE2L2 MUTATED 3 0 0 1
NFE2L2 WILD-TYPE 74 60 42 98
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.101 (Fisher's exact test), Q value = 0.32

Table S188.  Gene #18: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
NFE2L2 MUTATED 0 3 0 1 0
NFE2L2 WILD-TYPE 24 46 64 94 46
'KDELR3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S189.  Gene #19: 'KDELR3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
KDELR3 MUTATED 2 2 2
KDELR3 WILD-TYPE 177 237 240
'KDELR3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.2 (Fisher's exact test), Q value = 0.5

Table S190.  Gene #19: 'KDELR3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
KDELR3 MUTATED 3 2 1
KDELR3 WILD-TYPE 100 253 118
'KDELR3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.509 (Fisher's exact test), Q value = 0.89

Table S191.  Gene #19: 'KDELR3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
KDELR3 MUTATED 2 1 0 3
KDELR3 WILD-TYPE 146 138 140 154
'KDELR3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.495 (Fisher's exact test), Q value = 0.87

Table S192.  Gene #19: 'KDELR3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
KDELR3 MUTATED 2 0 2 0 0 0 2
KDELR3 WILD-TYPE 148 44 94 120 48 51 73
'KDELR3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0711 (Fisher's exact test), Q value = 0.25

Table S193.  Gene #19: 'KDELR3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
KDELR3 MUTATED 2 3 0 1
KDELR3 WILD-TYPE 97 170 241 147
'KDELR3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.295 (Fisher's exact test), Q value = 0.65

Table S194.  Gene #19: 'KDELR3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
KDELR3 MUTATED 1 2 0 2 0 1
KDELR3 WILD-TYPE 79 89 173 135 90 89
'KDELR3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.869 (Fisher's exact test), Q value = 1

Table S195.  Gene #19: 'KDELR3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
KDELR3 MUTATED 2 2 2
KDELR3 WILD-TYPE 210 147 291
'KDELR3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.237 (Fisher's exact test), Q value = 0.56

Table S196.  Gene #19: 'KDELR3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
KDELR3 MUTATED 1 3 2
KDELR3 WILD-TYPE 71 177 400
'KDELR3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 0.33

Table S197.  Gene #19: 'KDELR3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
KDELR3 MUTATED 1 1 2 0
KDELR3 WILD-TYPE 76 59 40 99
'KDELR3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.285 (Fisher's exact test), Q value = 0.64

Table S198.  Gene #19: 'KDELR3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
KDELR3 MUTATED 0 1 2 0 1
KDELR3 WILD-TYPE 24 48 62 95 45
'ATM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.566 (Fisher's exact test), Q value = 0.95

Table S199.  Gene #20: 'ATM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
ATM MUTATED 3 8 5
ATM WILD-TYPE 176 231 237
'ATM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.458 (Fisher's exact test), Q value = 0.83

Table S200.  Gene #20: 'ATM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
ATM MUTATED 3 8 1
ATM WILD-TYPE 100 247 118
'ATM MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.913 (Fisher's exact test), Q value = 1

Table S201.  Gene #20: 'ATM MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
ATM MUTATED 5 3 3 4
ATM WILD-TYPE 143 136 137 153
'ATM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S202.  Gene #20: 'ATM MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
ATM MUTATED 4 1 3 3 1 2 1
ATM WILD-TYPE 146 43 93 117 47 49 74
'ATM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.25 (Fisher's exact test), Q value = 0.58

Table S203.  Gene #20: 'ATM MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
ATM MUTATED 3 3 9 1
ATM WILD-TYPE 96 170 232 147
'ATM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.235 (Fisher's exact test), Q value = 0.56

Table S204.  Gene #20: 'ATM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
ATM MUTATED 3 0 6 2 4 1
ATM WILD-TYPE 77 91 167 135 86 89
'ATM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 0.68

Table S205.  Gene #20: 'ATM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
ATM MUTATED 5 1 9
ATM WILD-TYPE 207 148 284
'ATM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0885 (Fisher's exact test), Q value = 0.3

Table S206.  Gene #20: 'ATM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
ATM MUTATED 3 1 11
ATM WILD-TYPE 69 179 391
'ATM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.758 (Fisher's exact test), Q value = 1

Table S207.  Gene #20: 'ATM MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
ATM MUTATED 1 2 0 2
ATM WILD-TYPE 76 58 42 97
'ATM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.543 (Fisher's exact test), Q value = 0.92

Table S208.  Gene #20: 'ATM MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
ATM MUTATED 0 1 0 2 2
ATM WILD-TYPE 24 48 64 93 44
'MTOR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0073

Table S209.  Gene #21: 'MTOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
MTOR MUTATED 1 11 20
MTOR WILD-TYPE 178 228 222

Figure S108.  Get High-res Image Gene #21: 'MTOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'MTOR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00847 (Fisher's exact test), Q value = 0.051

Table S210.  Gene #21: 'MTOR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
MTOR MUTATED 5 21 1
MTOR WILD-TYPE 98 234 118

Figure S109.  Get High-res Image Gene #21: 'MTOR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MTOR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.087

Table S211.  Gene #21: 'MTOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
MTOR MUTATED 3 7 4 15
MTOR WILD-TYPE 145 132 136 142

Figure S110.  Get High-res Image Gene #21: 'MTOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'MTOR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0217 (Fisher's exact test), Q value = 0.1

Table S212.  Gene #21: 'MTOR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
MTOR MUTATED 13 3 2 5 5 0 1
MTOR WILD-TYPE 137 41 94 115 43 51 74

Figure S111.  Get High-res Image Gene #21: 'MTOR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'MTOR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 0.39

Table S213.  Gene #21: 'MTOR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
MTOR MUTATED 3 12 14 3
MTOR WILD-TYPE 96 161 227 145
'MTOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.089 (Fisher's exact test), Q value = 0.3

Table S214.  Gene #21: 'MTOR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
MTOR MUTATED 2 4 7 9 9 1
MTOR WILD-TYPE 78 87 166 128 81 89
'MTOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.012

Table S215.  Gene #21: 'MTOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
MTOR MUTATED 2 9 21
MTOR WILD-TYPE 210 140 272

Figure S112.  Get High-res Image Gene #21: 'MTOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MTOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00441 (Fisher's exact test), Q value = 0.03

Table S216.  Gene #21: 'MTOR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
MTOR MUTATED 0 4 28
MTOR WILD-TYPE 72 176 374

Figure S113.  Get High-res Image Gene #21: 'MTOR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'MTOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.401 (Fisher's exact test), Q value = 0.77

Table S217.  Gene #21: 'MTOR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
MTOR MUTATED 1 2 2 6
MTOR WILD-TYPE 76 58 40 93
'MTOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0737 (Fisher's exact test), Q value = 0.26

Table S218.  Gene #21: 'MTOR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
MTOR MUTATED 0 0 4 7 0
MTOR WILD-TYPE 24 49 60 88 46
'EGFR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.296 (Fisher's exact test), Q value = 0.65

Table S219.  Gene #22: 'EGFR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
EGFR MUTATED 0 3 3
EGFR WILD-TYPE 179 236 239
'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.428 (Fisher's exact test), Q value = 0.81

Table S220.  Gene #22: 'EGFR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
EGFR MUTATED 0 3 0
EGFR WILD-TYPE 103 252 119
'EGFR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.773 (Fisher's exact test), Q value = 1

Table S221.  Gene #22: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
EGFR MUTATED 1 2 2 1
EGFR WILD-TYPE 147 137 138 156
'EGFR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.876 (Fisher's exact test), Q value = 1

Table S222.  Gene #22: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
EGFR MUTATED 3 0 1 1 0 1 0
EGFR WILD-TYPE 147 44 95 119 48 50 75
'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 0.71

Table S223.  Gene #22: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
EGFR MUTATED 0 2 4 0
EGFR WILD-TYPE 99 171 237 148
'EGFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S224.  Gene #22: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
EGFR MUTATED 0 0 3 2 1 0
EGFR WILD-TYPE 80 91 170 135 89 90
'EGFR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.25 (Fisher's exact test), Q value = 0.58

Table S225.  Gene #22: 'EGFR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
EGFR MUTATED 0 2 3
EGFR WILD-TYPE 212 147 290
'EGFR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S226.  Gene #22: 'EGFR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
EGFR MUTATED 0 1 4
EGFR WILD-TYPE 72 179 398
'SLC6A14 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.856 (Fisher's exact test), Q value = 1

Table S227.  Gene #23: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
SLC6A14 MUTATED 2 1 2
SLC6A14 WILD-TYPE 177 238 240
'SLC6A14 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0996 (Fisher's exact test), Q value = 0.32

Table S228.  Gene #23: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
SLC6A14 MUTATED 1 0 2
SLC6A14 WILD-TYPE 102 255 117
'SLC6A14 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.878 (Fisher's exact test), Q value = 1

Table S229.  Gene #23: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
SLC6A14 MUTATED 1 1 2 1
SLC6A14 WILD-TYPE 147 138 138 156
'SLC6A14 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.175 (Fisher's exact test), Q value = 0.45

Table S230.  Gene #23: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
SLC6A14 MUTATED 0 1 0 1 1 1 1
SLC6A14 WILD-TYPE 150 43 96 119 47 50 74
'SLC6A14 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.756 (Fisher's exact test), Q value = 1

Table S231.  Gene #23: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
SLC6A14 MUTATED 1 2 1 1
SLC6A14 WILD-TYPE 98 171 240 147
'SLC6A14 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.571 (Fisher's exact test), Q value = 0.95

Table S232.  Gene #23: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
SLC6A14 MUTATED 1 1 0 1 1 1
SLC6A14 WILD-TYPE 79 90 173 136 89 89
'SLC6A14 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.526 (Fisher's exact test), Q value = 0.91

Table S233.  Gene #23: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
SLC6A14 MUTATED 2 2 1
SLC6A14 WILD-TYPE 210 147 292
'SLC6A14 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.107 (Fisher's exact test), Q value = 0.33

Table S234.  Gene #23: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
SLC6A14 MUTATED 1 3 1
SLC6A14 WILD-TYPE 71 177 401
'SLC6A14 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.33

Table S235.  Gene #23: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
SLC6A14 MUTATED 1 1 2 0
SLC6A14 WILD-TYPE 76 59 40 99
'SLC6A14 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.142 (Fisher's exact test), Q value = 0.39

Table S236.  Gene #23: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
SLC6A14 MUTATED 1 0 2 0 1
SLC6A14 WILD-TYPE 23 49 62 95 45
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.194 (Fisher's exact test), Q value = 0.49

Table S237.  Gene #24: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
PIK3CA MUTATED 1 4 7
PIK3CA WILD-TYPE 178 235 235
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S238.  Gene #24: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
PIK3CA MUTATED 1 5 1
PIK3CA WILD-TYPE 102 250 118
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.892 (Fisher's exact test), Q value = 1

Table S239.  Gene #24: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
PIK3CA MUTATED 2 2 3 4
PIK3CA WILD-TYPE 146 137 137 153
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.605 (Fisher's exact test), Q value = 0.98

Table S240.  Gene #24: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
PIK3CA MUTATED 2 0 1 3 2 2 1
PIK3CA WILD-TYPE 148 44 95 117 46 49 74
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.215 (Fisher's exact test), Q value = 0.52

Table S241.  Gene #24: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
PIK3CA MUTATED 0 5 6 1
PIK3CA WILD-TYPE 99 168 235 147
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.34 (Fisher's exact test), Q value = 0.7

Table S242.  Gene #24: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
PIK3CA MUTATED 0 1 2 5 3 1
PIK3CA WILD-TYPE 80 90 171 132 87 89
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.651 (Fisher's exact test), Q value = 1

Table S243.  Gene #24: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
PIK3CA MUTATED 3 4 5
PIK3CA WILD-TYPE 209 145 288
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.686 (Fisher's exact test), Q value = 1

Table S244.  Gene #24: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
PIK3CA MUTATED 0 4 8
PIK3CA WILD-TYPE 72 176 394
'EMG1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00419 (Fisher's exact test), Q value = 0.03

Table S245.  Gene #25: 'EMG1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 16 10 13
EMG1 MUTATED 0 0 3 0
EMG1 WILD-TYPE 17 16 7 13

Figure S114.  Get High-res Image Gene #25: 'EMG1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'EMG1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0044 (Fisher's exact test), Q value = 0.03

Table S246.  Gene #25: 'EMG1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 7 16 14 10 9
EMG1 MUTATED 0 0 0 0 3
EMG1 WILD-TYPE 7 16 14 10 6

Figure S115.  Get High-res Image Gene #25: 'EMG1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'EMG1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0684 (Fisher's exact test), Q value = 0.25

Table S247.  Gene #25: 'EMG1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
EMG1 MUTATED 3 1 0
EMG1 WILD-TYPE 176 238 242
'EMG1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.092

Table S248.  Gene #25: 'EMG1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
EMG1 MUTATED 3 0 1 0
EMG1 WILD-TYPE 96 173 240 148

Figure S116.  Get High-res Image Gene #25: 'EMG1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'EMG1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00306 (Fisher's exact test), Q value = 0.024

Table S249.  Gene #25: 'EMG1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
EMG1 MUTATED 3 0 0 0 1 0
EMG1 WILD-TYPE 77 91 173 137 89 90

Figure S117.  Get High-res Image Gene #25: 'EMG1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'EMG1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.821 (Fisher's exact test), Q value = 1

Table S250.  Gene #25: 'EMG1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
EMG1 MUTATED 2 1 1
EMG1 WILD-TYPE 210 148 292
'EMG1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00488 (Fisher's exact test), Q value = 0.033

Table S251.  Gene #25: 'EMG1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
EMG1 MUTATED 3 0 1
EMG1 WILD-TYPE 69 180 401

Figure S118.  Get High-res Image Gene #25: 'EMG1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'RIMBP3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.447 (Fisher's exact test), Q value = 0.82

Table S252.  Gene #26: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
RIMBP3 MUTATED 0 2 3
RIMBP3 WILD-TYPE 179 237 239
'RIMBP3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.45

Table S253.  Gene #26: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
RIMBP3 MUTATED 2 1 0
RIMBP3 WILD-TYPE 101 254 119
'RIMBP3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.49 (Fisher's exact test), Q value = 0.86

Table S254.  Gene #26: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
RIMBP3 MUTATED 0 2 2 1
RIMBP3 WILD-TYPE 148 137 138 156
'RIMBP3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S255.  Gene #26: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
RIMBP3 MUTATED 2 0 1 0 0 1 1
RIMBP3 WILD-TYPE 148 44 95 120 48 50 74
'RIMBP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S256.  Gene #26: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
RIMBP3 MUTATED 1 1 3 0
RIMBP3 WILD-TYPE 98 172 238 148
'RIMBP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.084

Table S257.  Gene #26: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
RIMBP3 MUTATED 1 1 0 0 3 0
RIMBP3 WILD-TYPE 79 90 173 137 87 90

Figure S119.  Get High-res Image Gene #26: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'RIMBP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.449 (Fisher's exact test), Q value = 0.82

Table S258.  Gene #26: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
RIMBP3 MUTATED 1 2 1
RIMBP3 WILD-TYPE 211 147 292
'RIMBP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.431 (Fisher's exact test), Q value = 0.81

Table S259.  Gene #26: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
RIMBP3 MUTATED 1 1 2
RIMBP3 WILD-TYPE 71 179 400
'RAI1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.32

Table S260.  Gene #27: 'RAI1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
RAI1 MUTATED 3 0 4
RAI1 WILD-TYPE 176 239 238
'RAI1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S261.  Gene #27: 'RAI1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
RAI1 MUTATED 2 3 1
RAI1 WILD-TYPE 101 252 118
'RAI1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 0.95

Table S262.  Gene #27: 'RAI1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
RAI1 MUTATED 0 2 2 2
RAI1 WILD-TYPE 148 137 138 155
'RAI1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S263.  Gene #27: 'RAI1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
RAI1 MUTATED 2 1 1 2 0 0 0
RAI1 WILD-TYPE 148 43 95 118 48 51 75
'RAI1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.908 (Fisher's exact test), Q value = 1

Table S264.  Gene #27: 'RAI1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
RAI1 MUTATED 1 1 3 2
RAI1 WILD-TYPE 98 172 238 146
'RAI1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.347 (Fisher's exact test), Q value = 0.7

Table S265.  Gene #27: 'RAI1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
RAI1 MUTATED 1 2 1 0 2 1
RAI1 WILD-TYPE 79 89 172 137 88 89
'RAI1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S266.  Gene #27: 'RAI1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
RAI1 MUTATED 2 2 3
RAI1 WILD-TYPE 210 147 290
'RAI1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.416 (Fisher's exact test), Q value = 0.8

Table S267.  Gene #27: 'RAI1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
RAI1 MUTATED 1 3 3
RAI1 WILD-TYPE 71 177 399
'RAI1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 0.33

Table S268.  Gene #27: 'RAI1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
RAI1 MUTATED 1 1 2 0
RAI1 WILD-TYPE 76 59 40 99
'RAI1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.284 (Fisher's exact test), Q value = 0.64

Table S269.  Gene #27: 'RAI1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
RAI1 MUTATED 0 1 2 0 1
RAI1 WILD-TYPE 24 48 62 95 45
'FAM160B2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.84 (Fisher's exact test), Q value = 1

Table S270.  Gene #28: 'FAM160B2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
FAM160B2 MUTATED 1 2 1
FAM160B2 WILD-TYPE 178 237 241
'FAM160B2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S271.  Gene #28: 'FAM160B2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
FAM160B2 MUTATED 1 2 1
FAM160B2 WILD-TYPE 102 253 118
'FAM160B2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S272.  Gene #28: 'FAM160B2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
FAM160B2 MUTATED 0 1 1 2
FAM160B2 WILD-TYPE 148 138 139 155
'FAM160B2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.702 (Fisher's exact test), Q value = 1

Table S273.  Gene #28: 'FAM160B2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
FAM160B2 MUTATED 2 1 0 1 0 0 0
FAM160B2 WILD-TYPE 148 43 96 119 48 51 75
'FAM160B2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.905 (Fisher's exact test), Q value = 1

Table S274.  Gene #28: 'FAM160B2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
FAM160B2 MUTATED 1 1 1 1
FAM160B2 WILD-TYPE 98 172 240 147
'FAM160B2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S275.  Gene #28: 'FAM160B2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
FAM160B2 MUTATED 1 0 1 1 0 1
FAM160B2 WILD-TYPE 79 91 172 136 90 89
'FAM160B2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.452 (Fisher's exact test), Q value = 0.82

Table S276.  Gene #28: 'FAM160B2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
FAM160B2 MUTATED 1 2 1
FAM160B2 WILD-TYPE 211 147 292
'FAM160B2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S277.  Gene #28: 'FAM160B2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
FAM160B2 MUTATED 0 2 2
FAM160B2 WILD-TYPE 72 178 400
'ZNF598 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.14

Table S278.  Gene #29: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
ZNF598 MUTATED 7 2 2
ZNF598 WILD-TYPE 172 237 240

Figure S120.  Get High-res Image Gene #29: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ZNF598 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00194 (Fisher's exact test), Q value = 0.018

Table S279.  Gene #29: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
ZNF598 MUTATED 2 1 7
ZNF598 WILD-TYPE 101 254 112

Figure S121.  Get High-res Image Gene #29: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'ZNF598 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.58 (Fisher's exact test), Q value = 0.95

Table S280.  Gene #29: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
ZNF598 MUTATED 4 3 1 2
ZNF598 WILD-TYPE 144 136 139 155
'ZNF598 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.486 (Fisher's exact test), Q value = 0.86

Table S281.  Gene #29: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
ZNF598 MUTATED 1 1 1 3 0 1 3
ZNF598 WILD-TYPE 149 43 95 117 48 50 72
'ZNF598 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00213 (Fisher's exact test), Q value = 0.018

Table S282.  Gene #29: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
ZNF598 MUTATED 1 1 1 8
ZNF598 WILD-TYPE 98 172 240 140

Figure S122.  Get High-res Image Gene #29: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'ZNF598 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0011 (Fisher's exact test), Q value = 0.012

Table S283.  Gene #29: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
ZNF598 MUTATED 1 3 0 1 0 6
ZNF598 WILD-TYPE 79 88 173 136 90 84

Figure S123.  Get High-res Image Gene #29: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'ZNF598 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.013

Table S284.  Gene #29: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
ZNF598 MUTATED 8 3 0
ZNF598 WILD-TYPE 204 146 293

Figure S124.  Get High-res Image Gene #29: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'ZNF598 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.0033

Table S285.  Gene #29: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
ZNF598 MUTATED 1 9 1
ZNF598 WILD-TYPE 71 171 401

Figure S125.  Get High-res Image Gene #29: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'ZNF598 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0873 (Fisher's exact test), Q value = 0.29

Table S286.  Gene #29: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
ZNF598 MUTATED 3 3 4 1
ZNF598 WILD-TYPE 74 57 38 98
'ZNF598 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0074

Table S287.  Gene #29: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
ZNF598 MUTATED 5 0 4 1 1
ZNF598 WILD-TYPE 19 49 60 94 45

Figure S126.  Get High-res Image Gene #29: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0977 (Fisher's exact test), Q value = 0.32

Table S288.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
KDM6A MUTATED 6 2 2
KDM6A WILD-TYPE 173 237 240
'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00516 (Fisher's exact test), Q value = 0.035

Table S289.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
KDM6A MUTATED 1 1 6
KDM6A WILD-TYPE 102 254 113

Figure S127.  Get High-res Image Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'KDM6A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.229 (Fisher's exact test), Q value = 0.55

Table S290.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
KDM6A MUTATED 0 2 4 2
KDM6A WILD-TYPE 148 137 136 155
'KDM6A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.295 (Fisher's exact test), Q value = 0.65

Table S291.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
KDM6A MUTATED 2 2 0 2 1 1 0
KDM6A WILD-TYPE 148 42 96 118 47 50 75
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00466 (Fisher's exact test), Q value = 0.032

Table S292.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
KDM6A MUTATED 1 0 2 7
KDM6A WILD-TYPE 98 173 239 141

Figure S128.  Get High-res Image Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0056 (Fisher's exact test), Q value = 0.037

Table S293.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
KDM6A MUTATED 0 4 0 1 1 4
KDM6A WILD-TYPE 80 87 173 136 89 86

Figure S129.  Get High-res Image Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00574 (Fisher's exact test), Q value = 0.037

Table S294.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
KDM6A MUTATED 8 0 2
KDM6A WILD-TYPE 204 149 291

Figure S130.  Get High-res Image Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00227 (Fisher's exact test), Q value = 0.019

Table S295.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
KDM6A MUTATED 0 8 2
KDM6A WILD-TYPE 72 172 400

Figure S131.  Get High-res Image Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.329 (Fisher's exact test), Q value = 0.68

Table S296.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
KDM6A MUTATED 2 1 0 0
KDM6A WILD-TYPE 75 59 42 99
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.194 (Fisher's exact test), Q value = 0.49

Table S297.  Gene #30: 'KDM6A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
KDM6A MUTATED 0 2 1 0 0
KDM6A WILD-TYPE 24 47 63 95 46
'DPCR1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S298.  Gene #31: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
DPCR1 MUTATED 2 3 3
DPCR1 WILD-TYPE 177 236 239
'DPCR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S299.  Gene #31: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
DPCR1 MUTATED 2 5 1
DPCR1 WILD-TYPE 101 250 118
'DPCR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.651 (Fisher's exact test), Q value = 1

Table S300.  Gene #31: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
DPCR1 MUTATED 3 1 1 3
DPCR1 WILD-TYPE 145 138 139 154
'DPCR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S301.  Gene #31: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
DPCR1 MUTATED 2 1 1 2 1 0 1
DPCR1 WILD-TYPE 148 43 95 118 47 51 74
'DPCR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S302.  Gene #31: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
DPCR1 MUTATED 2 2 3 1
DPCR1 WILD-TYPE 97 171 238 147
'DPCR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.893 (Fisher's exact test), Q value = 1

Table S303.  Gene #31: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
DPCR1 MUTATED 1 1 2 3 0 1
DPCR1 WILD-TYPE 79 90 171 134 90 89
'DPCR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S304.  Gene #31: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
DPCR1 MUTATED 2 2 4
DPCR1 WILD-TYPE 210 147 289
'DPCR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.565 (Fisher's exact test), Q value = 0.95

Table S305.  Gene #31: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
DPCR1 MUTATED 1 1 6
DPCR1 WILD-TYPE 71 179 396
'CYP4F11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.449 (Fisher's exact test), Q value = 0.82

Table S306.  Gene #32: 'CYP4F11 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
CYP4F11 MUTATED 0 2 3
CYP4F11 WILD-TYPE 179 237 239
'CYP4F11 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S307.  Gene #32: 'CYP4F11 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
CYP4F11 MUTATED 1 2 0
CYP4F11 WILD-TYPE 102 253 119
'CYP4F11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.414 (Fisher's exact test), Q value = 0.8

Table S308.  Gene #32: 'CYP4F11 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
CYP4F11 MUTATED 1 0 1 3
CYP4F11 WILD-TYPE 147 139 139 154
'CYP4F11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0674 (Fisher's exact test), Q value = 0.25

Table S309.  Gene #32: 'CYP4F11 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
CYP4F11 MUTATED 1 0 4 0 0 0 0
CYP4F11 WILD-TYPE 149 44 92 120 48 51 75
'CYP4F11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.37 (Fisher's exact test), Q value = 0.73

Table S310.  Gene #32: 'CYP4F11 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
CYP4F11 MUTATED 0 3 2 0
CYP4F11 WILD-TYPE 99 170 239 148
'CYP4F11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.846 (Fisher's exact test), Q value = 1

Table S311.  Gene #32: 'CYP4F11 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
CYP4F11 MUTATED 0 1 1 2 1 0
CYP4F11 WILD-TYPE 80 90 172 135 89 90
'CYP4F11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.249 (Fisher's exact test), Q value = 0.58

Table S312.  Gene #32: 'CYP4F11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
CYP4F11 MUTATED 0 2 3
CYP4F11 WILD-TYPE 212 147 290
'CYP4F11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S313.  Gene #32: 'CYP4F11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
CYP4F11 MUTATED 0 1 4
CYP4F11 WILD-TYPE 72 179 398
'STAM MUTATION STATUS' versus 'CN_CNMF'

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

Table S314.  Gene #33: 'STAM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
STAM MUTATED 2 2 2
STAM WILD-TYPE 177 237 240
'STAM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.071

Table S315.  Gene #33: 'STAM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
STAM MUTATED 4 1 0
STAM WILD-TYPE 99 254 119

Figure S132.  Get High-res Image Gene #33: 'STAM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'STAM MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.342 (Fisher's exact test), Q value = 0.7

Table S316.  Gene #33: 'STAM MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
STAM MUTATED 3 0 1 1
STAM WILD-TYPE 145 139 139 156
'STAM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.129 (Fisher's exact test), Q value = 0.36

Table S317.  Gene #33: 'STAM MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
STAM MUTATED 0 1 2 0 0 1 1
STAM WILD-TYPE 150 43 94 120 48 50 74
'STAM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.368 (Fisher's exact test), Q value = 0.73

Table S318.  Gene #33: 'STAM MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
STAM MUTATED 2 2 2 0
STAM WILD-TYPE 97 171 239 148
'STAM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.125 (Fisher's exact test), Q value = 0.36

Table S319.  Gene #33: 'STAM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
STAM MUTATED 1 3 1 0 1 0
STAM WILD-TYPE 79 88 172 137 89 90
'STAM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 0.68

Table S320.  Gene #33: 'STAM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
STAM MUTATED 1 3 2
STAM WILD-TYPE 211 146 291
'STAM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.236 (Fisher's exact test), Q value = 0.56

Table S321.  Gene #33: 'STAM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
STAM MUTATED 1 3 2
STAM WILD-TYPE 71 177 400
'STAM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00298 (Fisher's exact test), Q value = 0.023

Table S322.  Gene #33: 'STAM MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
STAM MUTATED 0 0 3 0
STAM WILD-TYPE 77 60 39 99

Figure S133.  Get High-res Image Gene #33: 'STAM MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'STAM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.057 (Fisher's exact test), Q value = 0.22

Table S323.  Gene #33: 'STAM MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
STAM MUTATED 0 0 3 0 0
STAM WILD-TYPE 24 49 61 95 46
'NUDT11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.163 (Fisher's exact test), Q value = 0.43

Table S324.  Gene #34: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
NUDT11 MUTATED 0 4 1
NUDT11 WILD-TYPE 179 235 241
'NUDT11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.718 (Fisher's exact test), Q value = 1

Table S325.  Gene #34: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
NUDT11 MUTATED 0 4 1
NUDT11 WILD-TYPE 103 251 118
'NUDT11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.574 (Fisher's exact test), Q value = 0.95

Table S326.  Gene #34: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
NUDT11 MUTATED 0 2 1 2
NUDT11 WILD-TYPE 148 137 139 155
'NUDT11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.91 (Fisher's exact test), Q value = 1

Table S327.  Gene #34: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
NUDT11 MUTATED 2 0 1 1 1 0 0
NUDT11 WILD-TYPE 148 44 95 119 47 51 75
'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.93 (Fisher's exact test), Q value = 1

Table S328.  Gene #34: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
NUDT11 MUTATED 0 2 2 1
NUDT11 WILD-TYPE 99 171 239 147
'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S329.  Gene #34: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
NUDT11 MUTATED 0 0 3 1 0 1
NUDT11 WILD-TYPE 80 91 170 136 90 89
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.854 (Fisher's exact test), Q value = 1

Table S330.  Gene #34: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
NUDT11 MUTATED 1 1 3
NUDT11 WILD-TYPE 211 148 290
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S331.  Gene #34: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
NUDT11 MUTATED 0 1 4
NUDT11 WILD-TYPE 72 179 398
'PARD6B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.322 (Fisher's exact test), Q value = 0.68

Table S332.  Gene #35: 'PARD6B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
PARD6B MUTATED 3 1 1
PARD6B WILD-TYPE 176 238 241
'PARD6B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.128 (Fisher's exact test), Q value = 0.36

Table S333.  Gene #35: 'PARD6B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
PARD6B MUTATED 1 1 3
PARD6B WILD-TYPE 102 254 116
'PARD6B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.17

Table S334.  Gene #35: 'PARD6B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
PARD6B MUTATED 0 1 3 0
PARD6B WILD-TYPE 148 138 137 157

Figure S134.  Get High-res Image Gene #35: 'PARD6B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'PARD6B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0618 (Fisher's exact test), Q value = 0.23

Table S335.  Gene #35: 'PARD6B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
PARD6B MUTATED 1 1 0 0 0 2 0
PARD6B WILD-TYPE 149 43 96 120 48 49 75
'PARD6B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.146 (Fisher's exact test), Q value = 0.39

Table S336.  Gene #35: 'PARD6B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
PARD6B MUTATED 1 0 1 3
PARD6B WILD-TYPE 98 173 240 145
'PARD6B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0963 (Fisher's exact test), Q value = 0.31

Table S337.  Gene #35: 'PARD6B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
PARD6B MUTATED 0 3 1 0 0 1
PARD6B WILD-TYPE 80 88 172 137 90 89
'PARD6B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.453 (Fisher's exact test), Q value = 0.82

Table S338.  Gene #35: 'PARD6B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
PARD6B MUTATED 3 1 1
PARD6B WILD-TYPE 209 148 292
'PARD6B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.225 (Fisher's exact test), Q value = 0.54

Table S339.  Gene #35: 'PARD6B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
PARD6B MUTATED 0 3 2
PARD6B WILD-TYPE 72 177 400
'PARD6B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.531 (Fisher's exact test), Q value = 0.91

Table S340.  Gene #35: 'PARD6B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
PARD6B MUTATED 2 0 1 1
PARD6B WILD-TYPE 75 60 41 98
'PARD6B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.451 (Fisher's exact test), Q value = 0.82

Table S341.  Gene #35: 'PARD6B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
PARD6B MUTATED 0 2 0 2 0
PARD6B WILD-TYPE 24 47 64 93 46
'RHEB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.785 (Fisher's exact test), Q value = 1

Table S342.  Gene #36: 'RHEB MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
RHEB MUTATED 0 1 2
RHEB WILD-TYPE 179 238 240
'RHEB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.367 (Fisher's exact test), Q value = 0.73

Table S343.  Gene #36: 'RHEB MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
RHEB MUTATED 2 0 1 0
RHEB WILD-TYPE 146 139 139 157
'RHEB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.253 (Fisher's exact test), Q value = 0.58

Table S344.  Gene #36: 'RHEB MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
RHEB MUTATED 0 0 1 0 1 0 1
RHEB WILD-TYPE 150 44 95 120 47 51 74
'RHEB MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S345.  Gene #36: 'RHEB MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
RHEB MUTATED 0 1 1 1
RHEB WILD-TYPE 99 172 240 147
'RHEB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.474 (Fisher's exact test), Q value = 0.85

Table S346.  Gene #36: 'RHEB MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
RHEB MUTATED 0 1 0 1 1 0
RHEB WILD-TYPE 80 90 173 136 89 90
'RHEB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.166 (Fisher's exact test), Q value = 0.43

Table S347.  Gene #36: 'RHEB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
RHEB MUTATED 0 2 1
RHEB WILD-TYPE 212 147 292
'RHEB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S348.  Gene #36: 'RHEB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
RHEB MUTATED 0 1 2
RHEB WILD-TYPE 72 179 400
'RHEB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.438 (Fisher's exact test), Q value = 0.82

Table S349.  Gene #36: 'RHEB MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
RHEB MUTATED 0 0 1 2
RHEB WILD-TYPE 77 60 41 97
'RHEB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.916 (Fisher's exact test), Q value = 1

Table S350.  Gene #36: 'RHEB MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
RHEB MUTATED 0 0 1 2 0
RHEB WILD-TYPE 24 49 63 93 46
'SLC16A1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S351.  Gene #37: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
SLC16A1 MUTATED 1 1 1
SLC16A1 WILD-TYPE 178 238 241
'SLC16A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S352.  Gene #37: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
SLC16A1 MUTATED 0 2 1
SLC16A1 WILD-TYPE 103 253 118
'SLC16A1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.17

Table S353.  Gene #37: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
SLC16A1 MUTATED 3 0 0 0
SLC16A1 WILD-TYPE 145 139 140 157

Figure S135.  Get High-res Image Gene #37: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'SLC16A1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.073

Table S354.  Gene #37: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
SLC16A1 MUTATED 0 0 0 0 0 0 3
SLC16A1 WILD-TYPE 150 44 96 120 48 51 72

Figure S136.  Get High-res Image Gene #37: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'SLC16A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S355.  Gene #37: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
SLC16A1 MUTATED 0 1 1 1
SLC16A1 WILD-TYPE 99 172 240 147
'SLC16A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.955 (Fisher's exact test), Q value = 1

Table S356.  Gene #37: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
SLC16A1 MUTATED 0 0 1 1 0 1
SLC16A1 WILD-TYPE 80 91 172 136 90 89
'SLC16A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S357.  Gene #37: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
SLC16A1 MUTATED 1 0 2
SLC16A1 WILD-TYPE 211 149 291
'SLC16A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S358.  Gene #37: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
SLC16A1 MUTATED 0 1 2
SLC16A1 WILD-TYPE 72 179 400
'SKI MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.01

Table S359.  Gene #38: 'SKI MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
SKI MUTATED 7 2 0
SKI WILD-TYPE 172 237 242

Figure S137.  Get High-res Image Gene #38: 'SKI MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'SKI MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.126 (Fisher's exact test), Q value = 0.36

Table S360.  Gene #38: 'SKI MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
SKI MUTATED 2 2 4
SKI WILD-TYPE 101 253 115
'SKI MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S361.  Gene #38: 'SKI MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
SKI MUTATED 2 1 3 1
SKI WILD-TYPE 146 138 137 156
'SKI MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.358 (Fisher's exact test), Q value = 0.72

Table S362.  Gene #38: 'SKI MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
SKI MUTATED 2 2 0 1 0 1 1
SKI WILD-TYPE 148 42 96 119 48 50 74
'SKI MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0026

Table S363.  Gene #38: 'SKI MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
SKI MUTATED 3 0 0 6
SKI WILD-TYPE 96 173 241 142

Figure S138.  Get High-res Image Gene #38: 'SKI MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'SKI MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00247 (Fisher's exact test), Q value = 0.02

Table S364.  Gene #38: 'SKI MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
SKI MUTATED 3 3 0 0 0 3
SKI WILD-TYPE 77 88 173 137 90 87

Figure S139.  Get High-res Image Gene #38: 'SKI MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SKI MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0067

Table S365.  Gene #38: 'SKI MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
SKI MUTATED 8 1 0
SKI WILD-TYPE 204 148 293

Figure S140.  Get High-res Image Gene #38: 'SKI MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'SKI MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00297 (Fisher's exact test), Q value = 0.023

Table S366.  Gene #38: 'SKI MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
SKI MUTATED 3 5 1
SKI WILD-TYPE 69 175 401

Figure S141.  Get High-res Image Gene #38: 'SKI MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'SKI MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0229 (Fisher's exact test), Q value = 0.11

Table S367.  Gene #38: 'SKI MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
SKI MUTATED 1 2 3 0
SKI WILD-TYPE 76 58 39 99

Figure S142.  Get High-res Image Gene #38: 'SKI MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'SKI MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0828 (Fisher's exact test), Q value = 0.29

Table S368.  Gene #38: 'SKI MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
SKI MUTATED 0 1 4 0 1
SKI WILD-TYPE 24 48 60 95 45
'THBS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.486 (Fisher's exact test), Q value = 0.86

Table S369.  Gene #39: 'THBS1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
THBS1 MUTATED 4 4 2
THBS1 WILD-TYPE 175 235 240
'THBS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 0.7

Table S370.  Gene #39: 'THBS1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
THBS1 MUTATED 0 5 3
THBS1 WILD-TYPE 103 250 116
'THBS1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.417 (Fisher's exact test), Q value = 0.8

Table S371.  Gene #39: 'THBS1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
THBS1 MUTATED 1 2 4 1
THBS1 WILD-TYPE 147 137 136 156
'THBS1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.304 (Fisher's exact test), Q value = 0.66

Table S372.  Gene #39: 'THBS1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
THBS1 MUTATED 2 0 0 3 1 2 0
THBS1 WILD-TYPE 148 44 96 117 47 49 75
'THBS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.252 (Fisher's exact test), Q value = 0.58

Table S373.  Gene #39: 'THBS1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
THBS1 MUTATED 0 1 5 4
THBS1 WILD-TYPE 99 172 236 144
'THBS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.144 (Fisher's exact test), Q value = 0.39

Table S374.  Gene #39: 'THBS1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
THBS1 MUTATED 0 3 5 0 1 1
THBS1 WILD-TYPE 80 88 168 137 89 89
'THBS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.717 (Fisher's exact test), Q value = 1

Table S375.  Gene #39: 'THBS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
THBS1 MUTATED 2 3 5
THBS1 WILD-TYPE 210 146 288
'THBS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.571 (Fisher's exact test), Q value = 0.95

Table S376.  Gene #39: 'THBS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
THBS1 MUTATED 0 4 6
THBS1 WILD-TYPE 72 176 396
'THBS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 0.99

Table S377.  Gene #39: 'THBS1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
THBS1 MUTATED 2 0 1 3
THBS1 WILD-TYPE 75 60 41 96
'THBS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.859 (Fisher's exact test), Q value = 1

Table S378.  Gene #39: 'THBS1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
THBS1 MUTATED 0 1 2 3 0
THBS1 WILD-TYPE 24 48 62 92 46
'SH3BP2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0686 (Fisher's exact test), Q value = 0.25

Table S379.  Gene #40: 'SH3BP2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
SH3BP2 MUTATED 3 1 0
SH3BP2 WILD-TYPE 176 238 242
'SH3BP2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.278 (Fisher's exact test), Q value = 0.63

Table S380.  Gene #40: 'SH3BP2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
SH3BP2 MUTATED 0 1 2
SH3BP2 WILD-TYPE 103 254 117
'SH3BP2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.901 (Fisher's exact test), Q value = 1

Table S381.  Gene #40: 'SH3BP2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
SH3BP2 MUTATED 1 1 0 1
SH3BP2 WILD-TYPE 147 138 140 156
'SH3BP2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.465 (Fisher's exact test), Q value = 0.83

Table S382.  Gene #40: 'SH3BP2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
SH3BP2 MUTATED 3 0 0 0 0 0 0
SH3BP2 WILD-TYPE 147 44 96 120 48 51 75
'SH3BP2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 0.33

Table S383.  Gene #40: 'SH3BP2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
SH3BP2 MUTATED 0 0 1 3
SH3BP2 WILD-TYPE 99 173 240 145
'SH3BP2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0916 (Fisher's exact test), Q value = 0.3

Table S384.  Gene #40: 'SH3BP2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
SH3BP2 MUTATED 0 1 0 0 1 2
SH3BP2 WILD-TYPE 80 90 173 137 89 88
'SH3BP2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.213 (Fisher's exact test), Q value = 0.52

Table S385.  Gene #40: 'SH3BP2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
SH3BP2 MUTATED 3 0 1
SH3BP2 WILD-TYPE 209 149 292
'SH3BP2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.128 (Fisher's exact test), Q value = 0.36

Table S386.  Gene #40: 'SH3BP2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
SH3BP2 MUTATED 0 3 1
SH3BP2 WILD-TYPE 72 177 401
'NASP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.318 (Fisher's exact test), Q value = 0.68

Table S387.  Gene #41: 'NASP MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
NASP MUTATED 2 0 2
NASP WILD-TYPE 177 239 240
'NASP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0671 (Fisher's exact test), Q value = 0.25

Table S388.  Gene #41: 'NASP MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
NASP MUTATED 3 1 0
NASP WILD-TYPE 100 254 119
'NASP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.343 (Fisher's exact test), Q value = 0.7

Table S389.  Gene #41: 'NASP MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
NASP MUTATED 2 0 0 2
NASP WILD-TYPE 146 139 140 155
'NASP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.305 (Fisher's exact test), Q value = 0.66

Table S390.  Gene #41: 'NASP MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
NASP MUTATED 0 0 2 1 1 0 0
NASP WILD-TYPE 150 44 94 119 47 51 75
'NASP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.041 (Fisher's exact test), Q value = 0.17

Table S391.  Gene #41: 'NASP MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
NASP MUTATED 2 2 0 0
NASP WILD-TYPE 97 171 241 148

Figure S143.  Get High-res Image Gene #41: 'NASP MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NASP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 0.39

Table S392.  Gene #41: 'NASP MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
NASP MUTATED 2 1 0 1 0 0
NASP WILD-TYPE 78 90 173 136 90 90
'NASP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.213 (Fisher's exact test), Q value = 0.52

Table S393.  Gene #41: 'NASP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
NASP MUTATED 3 0 1
NASP WILD-TYPE 209 149 292
'NASP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0498 (Fisher's exact test), Q value = 0.2

Table S394.  Gene #41: 'NASP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
NASP MUTATED 2 1 1
NASP WILD-TYPE 70 179 401

Figure S144.  Get High-res Image Gene #41: 'NASP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'NASP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0868 (Fisher's exact test), Q value = 0.29

Table S395.  Gene #41: 'NASP MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
NASP MUTATED 0 2 1 0
NASP WILD-TYPE 77 58 41 99
'NASP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.134 (Fisher's exact test), Q value = 0.37

Table S396.  Gene #41: 'NASP MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
NASP MUTATED 0 0 1 0 2
NASP WILD-TYPE 24 49 63 95 44
'FAT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 0.33

Table S397.  Gene #42: 'FAT1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
FAT1 MUTATED 10 5 6
FAT1 WILD-TYPE 169 234 236
'FAT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.14

Table S398.  Gene #42: 'FAT1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
FAT1 MUTATED 4 5 9
FAT1 WILD-TYPE 99 250 110

Figure S145.  Get High-res Image Gene #42: 'FAT1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'FAT1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.963 (Fisher's exact test), Q value = 1

Table S399.  Gene #42: 'FAT1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
FAT1 MUTATED 5 4 5 4
FAT1 WILD-TYPE 143 135 135 153
'FAT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.188 (Fisher's exact test), Q value = 0.48

Table S400.  Gene #42: 'FAT1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
FAT1 MUTATED 4 3 2 1 1 2 5
FAT1 WILD-TYPE 146 41 94 119 47 49 70
'FAT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.005

Table S401.  Gene #42: 'FAT1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
FAT1 MUTATED 2 4 2 13
FAT1 WILD-TYPE 97 169 239 135

Figure S146.  Get High-res Image Gene #42: 'FAT1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'FAT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0052

Table S402.  Gene #42: 'FAT1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
FAT1 MUTATED 1 9 1 3 1 6
FAT1 WILD-TYPE 79 82 172 134 89 84

Figure S147.  Get High-res Image Gene #42: 'FAT1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'FAT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.075

Table S403.  Gene #42: 'FAT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
FAT1 MUTATED 13 4 4
FAT1 WILD-TYPE 199 145 289

Figure S148.  Get High-res Image Gene #42: 'FAT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'FAT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0073

Table S404.  Gene #42: 'FAT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
FAT1 MUTATED 1 14 6
FAT1 WILD-TYPE 71 166 396

Figure S149.  Get High-res Image Gene #42: 'FAT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.231 (Fisher's exact test), Q value = 0.55

Table S405.  Gene #42: 'FAT1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
FAT1 MUTATED 5 1 3 2
FAT1 WILD-TYPE 72 59 39 97
'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0643 (Fisher's exact test), Q value = 0.24

Table S406.  Gene #42: 'FAT1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
FAT1 MUTATED 0 3 6 1 1
FAT1 WILD-TYPE 24 46 58 94 45
'CACNA1C MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S407.  Gene #43: 'CACNA1C MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 16 10 13
CACNA1C MUTATED 1 1 0 1
CACNA1C WILD-TYPE 16 15 10 12
'CACNA1C MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S408.  Gene #43: 'CACNA1C MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 7 16 14 10 9
CACNA1C MUTATED 0 1 1 1 0
CACNA1C WILD-TYPE 7 15 13 9 9
'CACNA1C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.525 (Fisher's exact test), Q value = 0.91

Table S409.  Gene #43: 'CACNA1C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
CACNA1C MUTATED 6 4 7
CACNA1C WILD-TYPE 173 235 235
'CACNA1C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.628 (Fisher's exact test), Q value = 0.99

Table S410.  Gene #43: 'CACNA1C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
CACNA1C MUTATED 4 8 2
CACNA1C WILD-TYPE 99 247 117
'CACNA1C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.583 (Fisher's exact test), Q value = 0.95

Table S411.  Gene #43: 'CACNA1C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
CACNA1C MUTATED 4 1 4 4
CACNA1C WILD-TYPE 144 138 136 153
'CACNA1C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.432 (Fisher's exact test), Q value = 0.81

Table S412.  Gene #43: 'CACNA1C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
CACNA1C MUTATED 2 1 3 2 3 0 2
CACNA1C WILD-TYPE 148 43 93 118 45 51 73
'CACNA1C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.49 (Fisher's exact test), Q value = 0.86

Table S413.  Gene #43: 'CACNA1C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
CACNA1C MUTATED 4 4 4 5
CACNA1C WILD-TYPE 95 169 237 143
'CACNA1C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.765 (Fisher's exact test), Q value = 1

Table S414.  Gene #43: 'CACNA1C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
CACNA1C MUTATED 4 2 4 4 1 2
CACNA1C WILD-TYPE 76 89 169 133 89 88
'CACNA1C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.536 (Fisher's exact test), Q value = 0.92

Table S415.  Gene #43: 'CACNA1C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
CACNA1C MUTATED 7 2 8
CACNA1C WILD-TYPE 205 147 285
'CACNA1C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.533 (Fisher's exact test), Q value = 0.91

Table S416.  Gene #43: 'CACNA1C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
CACNA1C MUTATED 3 5 9
CACNA1C WILD-TYPE 69 175 393
'CACNA1C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.452 (Fisher's exact test), Q value = 0.82

Table S417.  Gene #43: 'CACNA1C MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
CACNA1C MUTATED 2 3 1 1
CACNA1C WILD-TYPE 75 57 41 98
'CACNA1C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.605 (Fisher's exact test), Q value = 0.98

Table S418.  Gene #43: 'CACNA1C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
CACNA1C MUTATED 1 1 2 1 2
CACNA1C WILD-TYPE 23 48 62 94 44
'PCK1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S419.  Gene #44: 'PCK1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
PCK1 MUTATED 1 2 2
PCK1 WILD-TYPE 178 237 240
'PCK1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.606 (Fisher's exact test), Q value = 0.98

Table S420.  Gene #44: 'PCK1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
PCK1 MUTATED 1 2 0 1
PCK1 WILD-TYPE 147 137 140 156
'PCK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S421.  Gene #44: 'PCK1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
PCK1 MUTATED 2 0 0 1 0 0 1
PCK1 WILD-TYPE 148 44 96 119 48 51 74
'PCK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.868 (Fisher's exact test), Q value = 1

Table S422.  Gene #44: 'PCK1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
PCK1 MUTATED 0 1 3 1
PCK1 WILD-TYPE 99 172 238 147
'PCK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.609 (Fisher's exact test), Q value = 0.98

Table S423.  Gene #44: 'PCK1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
PCK1 MUTATED 0 0 1 1 2 1
PCK1 WILD-TYPE 80 91 172 136 88 89
'PCK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.314 (Fisher's exact test), Q value = 0.67

Table S424.  Gene #44: 'PCK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
PCK1 MUTATED 1 0 4
PCK1 WILD-TYPE 211 149 289
'PCK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S425.  Gene #44: 'PCK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
PCK1 MUTATED 0 1 4
PCK1 WILD-TYPE 72 179 398
'TPPP MUTATION STATUS' versus 'CN_CNMF'

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

Table S426.  Gene #45: 'TPPP MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
TPPP MUTATED 1 1 1
TPPP WILD-TYPE 178 238 241
'TPPP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.175 (Fisher's exact test), Q value = 0.45

Table S427.  Gene #45: 'TPPP MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
TPPP MUTATED 2 1 0
TPPP WILD-TYPE 101 254 119
'TPPP MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S428.  Gene #45: 'TPPP MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
TPPP MUTATED 1 0 1 1
TPPP WILD-TYPE 147 139 139 156
'TPPP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.368 (Fisher's exact test), Q value = 0.73

Table S429.  Gene #45: 'TPPP MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
TPPP MUTATED 1 1 0 0 0 0 1
TPPP WILD-TYPE 149 43 96 120 48 51 74
'TPPP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.514 (Fisher's exact test), Q value = 0.89

Table S430.  Gene #45: 'TPPP MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
TPPP MUTATED 1 0 1 1
TPPP WILD-TYPE 98 173 240 147
'TPPP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.196 (Fisher's exact test), Q value = 0.49

Table S431.  Gene #45: 'TPPP MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
TPPP MUTATED 1 1 0 0 1 0
TPPP WILD-TYPE 79 90 173 137 89 90
'TPPP MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S432.  Gene #45: 'TPPP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
TPPP MUTATED 1 1 1
TPPP WILD-TYPE 211 148 292
'TPPP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.457 (Fisher's exact test), Q value = 0.83

Table S433.  Gene #45: 'TPPP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
TPPP MUTATED 0 2 1
TPPP WILD-TYPE 72 178 401
'MLL3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.775 (Fisher's exact test), Q value = 1

Table S434.  Gene #46: 'MLL3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 16 10 13
MLL3 MUTATED 1 0 1 1
MLL3 WILD-TYPE 16 16 9 12
'MLL3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.625 (Fisher's exact test), Q value = 0.99

Table S435.  Gene #46: 'MLL3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 7 16 14 10 9
MLL3 MUTATED 0 0 1 1 1
MLL3 WILD-TYPE 7 16 13 9 8
'MLL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.11

Table S436.  Gene #46: 'MLL3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
MLL3 MUTATED 18 10 10
MLL3 WILD-TYPE 161 229 232

Figure S150.  Get High-res Image Gene #46: 'MLL3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'MLL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.061

Table S437.  Gene #46: 'MLL3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
MLL3 MUTATED 13 10 9
MLL3 WILD-TYPE 90 245 110

Figure S151.  Get High-res Image Gene #46: 'MLL3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MLL3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.265 (Fisher's exact test), Q value = 0.6

Table S438.  Gene #46: 'MLL3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
MLL3 MUTATED 10 12 5 7
MLL3 WILD-TYPE 138 127 135 150
'MLL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.662 (Fisher's exact test), Q value = 1

Table S439.  Gene #46: 'MLL3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
MLL3 MUTATED 11 1 7 5 1 3 6
MLL3 WILD-TYPE 139 43 89 115 47 48 69
'MLL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0257 (Fisher's exact test), Q value = 0.12

Table S440.  Gene #46: 'MLL3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
MLL3 MUTATED 10 6 9 13
MLL3 WILD-TYPE 89 167 232 135

Figure S152.  Get High-res Image Gene #46: 'MLL3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'MLL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.1

Table S441.  Gene #46: 'MLL3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
MLL3 MUTATED 9 8 6 3 4 8
MLL3 WILD-TYPE 71 83 167 134 86 82

Figure S153.  Get High-res Image Gene #46: 'MLL3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'MLL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00439 (Fisher's exact test), Q value = 0.03

Table S442.  Gene #46: 'MLL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
MLL3 MUTATED 22 5 11
MLL3 WILD-TYPE 190 144 282

Figure S154.  Get High-res Image Gene #46: 'MLL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MLL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.0099

Table S443.  Gene #46: 'MLL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
MLL3 MUTATED 9 16 13
MLL3 WILD-TYPE 63 164 389

Figure S155.  Get High-res Image Gene #46: 'MLL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.212 (Fisher's exact test), Q value = 0.52

Table S444.  Gene #46: 'MLL3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
MLL3 MUTATED 6 7 5 4
MLL3 WILD-TYPE 71 53 37 95
'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.594 (Fisher's exact test), Q value = 0.97

Table S445.  Gene #46: 'MLL3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
MLL3 MUTATED 2 4 5 5 6
MLL3 WILD-TYPE 22 45 59 90 40
'PAM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.096

Table S446.  Gene #47: 'PAM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
PAM MUTATED 3 0 0
PAM WILD-TYPE 176 239 242

Figure S156.  Get High-res Image Gene #47: 'PAM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PAM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00581 (Fisher's exact test), Q value = 0.037

Table S447.  Gene #47: 'PAM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
PAM MUTATED 0 0 4
PAM WILD-TYPE 103 255 115

Figure S157.  Get High-res Image Gene #47: 'PAM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PAM MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.145 (Fisher's exact test), Q value = 0.39

Table S448.  Gene #47: 'PAM MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
PAM MUTATED 3 0 0 1
PAM WILD-TYPE 145 139 140 156
'PAM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.109 (Fisher's exact test), Q value = 0.33

Table S449.  Gene #47: 'PAM MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
PAM MUTATED 1 0 0 0 2 0 1
PAM WILD-TYPE 149 44 96 120 46 51 74
'PAM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00278 (Fisher's exact test), Q value = 0.022

Table S450.  Gene #47: 'PAM MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
PAM MUTATED 0 0 0 4
PAM WILD-TYPE 99 173 241 144

Figure S158.  Get High-res Image Gene #47: 'PAM MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PAM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0129 (Fisher's exact test), Q value = 0.071

Table S451.  Gene #47: 'PAM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
PAM MUTATED 0 1 0 0 0 3
PAM WILD-TYPE 80 90 173 137 90 87

Figure S159.  Get High-res Image Gene #47: 'PAM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PAM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.071

Table S452.  Gene #47: 'PAM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
PAM MUTATED 4 0 0
PAM WILD-TYPE 208 149 293

Figure S160.  Get High-res Image Gene #47: 'PAM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PAM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.08

Table S453.  Gene #47: 'PAM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
PAM MUTATED 0 4 0
PAM WILD-TYPE 72 176 402

Figure S161.  Get High-res Image Gene #47: 'PAM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'GAPDHS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.643 (Fisher's exact test), Q value = 1

Table S454.  Gene #48: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
GAPDHS MUTATED 1 1 3
GAPDHS WILD-TYPE 178 238 239
'GAPDHS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.261 (Fisher's exact test), Q value = 0.6

Table S455.  Gene #48: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
GAPDHS MUTATED 2 1 2
GAPDHS WILD-TYPE 101 254 117
'GAPDHS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.462 (Fisher's exact test), Q value = 0.83

Table S456.  Gene #48: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
GAPDHS MUTATED 0 1 0 2
GAPDHS WILD-TYPE 148 138 140 155
'GAPDHS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S457.  Gene #48: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
GAPDHS MUTATED 1 0 1 1 0 0 0
GAPDHS WILD-TYPE 149 44 95 119 48 51 75
'GAPDHS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.147 (Fisher's exact test), Q value = 0.39

Table S458.  Gene #48: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
GAPDHS MUTATED 1 0 1 3
GAPDHS WILD-TYPE 98 173 240 145
'GAPDHS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.09

Table S459.  Gene #48: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
GAPDHS MUTATED 1 3 0 0 1 0
GAPDHS WILD-TYPE 79 88 173 137 89 90

Figure S162.  Get High-res Image Gene #48: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'GAPDHS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.12 (Fisher's exact test), Q value = 0.35

Table S460.  Gene #48: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
GAPDHS MUTATED 4 0 1
GAPDHS WILD-TYPE 208 149 292
'GAPDHS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.107 (Fisher's exact test), Q value = 0.33

Table S461.  Gene #48: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
GAPDHS MUTATED 1 3 1
GAPDHS WILD-TYPE 71 177 401
'TMCO3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0785 (Fisher's exact test), Q value = 0.27

Table S462.  Gene #49: 'TMCO3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
TMCO3 MUTATED 2 0 5
TMCO3 WILD-TYPE 177 239 237
'TMCO3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 0.62

Table S463.  Gene #49: 'TMCO3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
TMCO3 MUTATED 0 1 2
TMCO3 WILD-TYPE 103 254 117
'TMCO3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.183 (Fisher's exact test), Q value = 0.46

Table S464.  Gene #49: 'TMCO3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
TMCO3 MUTATED 0 0 1 3
TMCO3 WILD-TYPE 148 139 139 154
'TMCO3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S465.  Gene #49: 'TMCO3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
TMCO3 MUTATED 1 0 1 2 0 0 0
TMCO3 WILD-TYPE 149 44 95 118 48 51 75
'TMCO3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S466.  Gene #49: 'TMCO3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
TMCO3 MUTATED 0 2 3 2
TMCO3 WILD-TYPE 99 171 238 146
'TMCO3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0852 (Fisher's exact test), Q value = 0.29

Table S467.  Gene #49: 'TMCO3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
TMCO3 MUTATED 0 1 0 1 3 2
TMCO3 WILD-TYPE 80 90 173 136 87 88
'TMCO3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.342 (Fisher's exact test), Q value = 0.7

Table S468.  Gene #49: 'TMCO3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
TMCO3 MUTATED 3 0 4
TMCO3 WILD-TYPE 209 149 289
'TMCO3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S469.  Gene #49: 'TMCO3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
TMCO3 MUTATED 0 3 4
TMCO3 WILD-TYPE 72 177 398
'RPL7A MUTATION STATUS' versus 'CN_CNMF'

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

Table S470.  Gene #50: 'RPL7A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
RPL7A MUTATED 1 1 1
RPL7A WILD-TYPE 178 238 241
'RPL7A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0986 (Fisher's exact test), Q value = 0.32

Table S471.  Gene #50: 'RPL7A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
RPL7A MUTATED 1 0 2
RPL7A WILD-TYPE 102 255 117
'RPL7A MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S472.  Gene #50: 'RPL7A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
RPL7A MUTATED 1 0 1 1
RPL7A WILD-TYPE 147 139 139 156
'RPL7A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.133 (Fisher's exact test), Q value = 0.37

Table S473.  Gene #50: 'RPL7A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
RPL7A MUTATED 0 0 1 0 1 1 0
RPL7A WILD-TYPE 150 44 95 120 47 50 75
'RPL7A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0871 (Fisher's exact test), Q value = 0.29

Table S474.  Gene #50: 'RPL7A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
RPL7A MUTATED 1 0 0 2
RPL7A WILD-TYPE 98 173 241 146
'RPL7A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0933 (Fisher's exact test), Q value = 0.31

Table S475.  Gene #50: 'RPL7A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
RPL7A MUTATED 0 2 0 0 0 1
RPL7A WILD-TYPE 80 89 173 137 90 89
'RPL7A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.237 (Fisher's exact test), Q value = 0.56

Table S476.  Gene #50: 'RPL7A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
RPL7A MUTATED 2 1 0
RPL7A WILD-TYPE 210 148 293
'RPL7A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.032 (Fisher's exact test), Q value = 0.14

Table S477.  Gene #50: 'RPL7A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
RPL7A MUTATED 0 3 0
RPL7A WILD-TYPE 72 177 402

Figure S163.  Get High-res Image Gene #50: 'RPL7A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'ARHGAP35 MUTATION STATUS' versus 'CN_CNMF'

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

Table S478.  Gene #51: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
ARHGAP35 MUTATED 1 2 4
ARHGAP35 WILD-TYPE 178 237 238
'ARHGAP35 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.302 (Fisher's exact test), Q value = 0.66

Table S479.  Gene #51: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
ARHGAP35 MUTATED 1 5 0
ARHGAP35 WILD-TYPE 102 250 119
'ARHGAP35 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.761 (Fisher's exact test), Q value = 1

Table S480.  Gene #51: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
ARHGAP35 MUTATED 1 2 1 3
ARHGAP35 WILD-TYPE 147 137 139 154
'ARHGAP35 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S481.  Gene #51: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
ARHGAP35 MUTATED 2 0 2 1 0 0 2
ARHGAP35 WILD-TYPE 148 44 94 119 48 51 73
'ARHGAP35 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S482.  Gene #51: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
ARHGAP35 MUTATED 1 2 3 1
ARHGAP35 WILD-TYPE 98 171 238 147
'ARHGAP35 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.657 (Fisher's exact test), Q value = 1

Table S483.  Gene #51: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
ARHGAP35 MUTATED 0 2 3 1 1 0
ARHGAP35 WILD-TYPE 80 89 170 136 89 90
'ARHGAP35 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 0.33

Table S484.  Gene #51: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
ARHGAP35 MUTATED 0 3 4
ARHGAP35 WILD-TYPE 212 146 289
'ARHGAP35 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S485.  Gene #51: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
ARHGAP35 MUTATED 0 2 5
ARHGAP35 WILD-TYPE 72 178 397
'AHNAK2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.178 (Fisher's exact test), Q value = 0.45

Table S486.  Gene #52: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 16 10 13
AHNAK2 MUTATED 3 0 0 2
AHNAK2 WILD-TYPE 14 16 10 11
'AHNAK2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0523 (Fisher's exact test), Q value = 0.2

Table S487.  Gene #52: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 7 16 14 10 9
AHNAK2 MUTATED 0 0 2 3 0
AHNAK2 WILD-TYPE 7 16 12 7 9
'AHNAK2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.561 (Fisher's exact test), Q value = 0.95

Table S488.  Gene #52: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
AHNAK2 MUTATED 10 9 14
AHNAK2 WILD-TYPE 169 230 228
'AHNAK2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0333 (Fisher's exact test), Q value = 0.14

Table S489.  Gene #52: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
AHNAK2 MUTATED 11 10 4
AHNAK2 WILD-TYPE 92 245 115

Figure S164.  Get High-res Image Gene #52: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'AHNAK2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.889 (Fisher's exact test), Q value = 1

Table S490.  Gene #52: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
AHNAK2 MUTATED 7 6 8 6
AHNAK2 WILD-TYPE 141 133 132 151
'AHNAK2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.401 (Fisher's exact test), Q value = 0.77

Table S491.  Gene #52: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
AHNAK2 MUTATED 6 4 7 6 1 2 1
AHNAK2 WILD-TYPE 144 40 89 114 47 49 74
'AHNAK2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00617 (Fisher's exact test), Q value = 0.039

Table S492.  Gene #52: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
AHNAK2 MUTATED 10 2 12 9
AHNAK2 WILD-TYPE 89 171 229 139

Figure S165.  Get High-res Image Gene #52: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'AHNAK2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.0056

Table S493.  Gene #52: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
AHNAK2 MUTATED 10 6 4 1 8 4
AHNAK2 WILD-TYPE 70 85 169 136 82 86

Figure S166.  Get High-res Image Gene #52: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.087

Table S494.  Gene #52: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
AHNAK2 MUTATED 18 3 12
AHNAK2 WILD-TYPE 194 146 281

Figure S167.  Get High-res Image Gene #52: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00873 (Fisher's exact test), Q value = 0.052

Table S495.  Gene #52: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
AHNAK2 MUTATED 9 10 14
AHNAK2 WILD-TYPE 63 170 388

Figure S168.  Get High-res Image Gene #52: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.681 (Fisher's exact test), Q value = 1

Table S496.  Gene #52: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
AHNAK2 MUTATED 5 5 2 4
AHNAK2 WILD-TYPE 72 55 40 95
'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.357 (Fisher's exact test), Q value = 0.72

Table S497.  Gene #52: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
AHNAK2 MUTATED 1 4 3 3 5
AHNAK2 WILD-TYPE 23 45 61 92 41
'JMJD1C MUTATION STATUS' versus 'CN_CNMF'

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

Table S498.  Gene #53: 'JMJD1C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
JMJD1C MUTATED 3 4 3
JMJD1C WILD-TYPE 176 235 239
'JMJD1C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.434 (Fisher's exact test), Q value = 0.81

Table S499.  Gene #53: 'JMJD1C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
JMJD1C MUTATED 1 4 4
JMJD1C WILD-TYPE 102 251 115
'JMJD1C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0826 (Fisher's exact test), Q value = 0.29

Table S500.  Gene #53: 'JMJD1C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
JMJD1C MUTATED 1 6 2 1
JMJD1C WILD-TYPE 147 133 138 156
'JMJD1C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.316 (Fisher's exact test), Q value = 0.68

Table S501.  Gene #53: 'JMJD1C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
JMJD1C MUTATED 5 1 0 3 1 0 0
JMJD1C WILD-TYPE 145 43 96 117 47 51 75
'JMJD1C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.117 (Fisher's exact test), Q value = 0.34

Table S502.  Gene #53: 'JMJD1C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
JMJD1C MUTATED 1 0 5 4
JMJD1C WILD-TYPE 98 173 236 144
'JMJD1C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.868 (Fisher's exact test), Q value = 1

Table S503.  Gene #53: 'JMJD1C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
JMJD1C MUTATED 1 2 2 1 2 2
JMJD1C WILD-TYPE 79 89 171 136 88 88
'JMJD1C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 0.44

Table S504.  Gene #53: 'JMJD1C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
JMJD1C MUTATED 5 0 5
JMJD1C WILD-TYPE 207 149 288
'JMJD1C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S505.  Gene #53: 'JMJD1C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
JMJD1C MUTATED 1 3 6
JMJD1C WILD-TYPE 71 177 396
'JMJD1C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.327 (Fisher's exact test), Q value = 0.68

Table S506.  Gene #53: 'JMJD1C MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
JMJD1C MUTATED 2 1 0 0
JMJD1C WILD-TYPE 75 59 42 99
'JMJD1C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.481 (Fisher's exact test), Q value = 0.86

Table S507.  Gene #53: 'JMJD1C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
JMJD1C MUTATED 0 1 1 0 1
JMJD1C WILD-TYPE 24 48 63 95 45
'TTLL6 MUTATION STATUS' versus 'CN_CNMF'

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

Table S508.  Gene #54: 'TTLL6 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
TTLL6 MUTATED 2 2 2
TTLL6 WILD-TYPE 177 237 240
'TTLL6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0934 (Fisher's exact test), Q value = 0.31

Table S509.  Gene #54: 'TTLL6 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
TTLL6 MUTATED 3 2 0
TTLL6 WILD-TYPE 100 253 119
'TTLL6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.575 (Fisher's exact test), Q value = 0.95

Table S510.  Gene #54: 'TTLL6 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
TTLL6 MUTATED 0 2 1 2
TTLL6 WILD-TYPE 148 137 139 155
'TTLL6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.557 (Fisher's exact test), Q value = 0.94

Table S511.  Gene #54: 'TTLL6 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
TTLL6 MUTATED 3 0 1 0 0 1 0
TTLL6 WILD-TYPE 147 44 95 120 48 50 75
'TTLL6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0961 (Fisher's exact test), Q value = 0.31

Table S512.  Gene #54: 'TTLL6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
TTLL6 MUTATED 3 0 2 1
TTLL6 WILD-TYPE 96 173 239 147
'TTLL6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.395 (Fisher's exact test), Q value = 0.77

Table S513.  Gene #54: 'TTLL6 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
TTLL6 MUTATED 2 1 1 0 1 1
TTLL6 WILD-TYPE 78 90 172 137 89 89
'TTLL6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.769 (Fisher's exact test), Q value = 1

Table S514.  Gene #54: 'TTLL6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
TTLL6 MUTATED 3 1 2
TTLL6 WILD-TYPE 209 148 291
'TTLL6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.107 (Fisher's exact test), Q value = 0.33

Table S515.  Gene #54: 'TTLL6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
TTLL6 MUTATED 2 2 2
TTLL6 WILD-TYPE 70 178 400
'TTLL6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.279 (Fisher's exact test), Q value = 0.63

Table S516.  Gene #54: 'TTLL6 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
TTLL6 MUTATED 0 2 0 1
TTLL6 WILD-TYPE 77 58 42 98
'TTLL6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.836 (Fisher's exact test), Q value = 1

Table S517.  Gene #54: 'TTLL6 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
TTLL6 MUTATED 0 0 1 1 1
TTLL6 WILD-TYPE 24 49 63 94 45
'AMAC1L3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.481 (Fisher's exact test), Q value = 0.86

Table S518.  Gene #55: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
AMAC1L3 MUTATED 4 2 2
AMAC1L3 WILD-TYPE 175 237 240
'AMAC1L3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00314 (Fisher's exact test), Q value = 0.024

Table S519.  Gene #55: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
AMAC1L3 MUTATED 6 1 1
AMAC1L3 WILD-TYPE 97 254 118

Figure S169.  Get High-res Image Gene #55: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'AMAC1L3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0879 (Fisher's exact test), Q value = 0.29

Table S520.  Gene #55: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
AMAC1L3 MUTATED 1 2 4 0
AMAC1L3 WILD-TYPE 147 137 136 157
'AMAC1L3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00206 (Fisher's exact test), Q value = 0.018

Table S521.  Gene #55: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
AMAC1L3 MUTATED 1 4 2 0 0 0 0
AMAC1L3 WILD-TYPE 149 40 94 120 48 51 75

Figure S170.  Get High-res Image Gene #55: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'AMAC1L3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00195 (Fisher's exact test), Q value = 0.018

Table S522.  Gene #55: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
AMAC1L3 MUTATED 5 0 1 2
AMAC1L3 WILD-TYPE 94 173 240 146

Figure S171.  Get High-res Image Gene #55: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'AMAC1L3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0065

Table S523.  Gene #55: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
AMAC1L3 MUTATED 5 2 0 0 1 0
AMAC1L3 WILD-TYPE 75 89 173 137 89 90

Figure S172.  Get High-res Image Gene #55: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'AMAC1L3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 0.57

Table S524.  Gene #55: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
AMAC1L3 MUTATED 5 1 2
AMAC1L3 WILD-TYPE 207 148 291
'AMAC1L3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.005

Table S525.  Gene #55: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
AMAC1L3 MUTATED 5 2 1
AMAC1L3 WILD-TYPE 67 178 401

Figure S173.  Get High-res Image Gene #55: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'AMAC1L3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.326 (Fisher's exact test), Q value = 0.68

Table S526.  Gene #55: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
AMAC1L3 MUTATED 1 3 1 1
AMAC1L3 WILD-TYPE 76 57 41 98
'AMAC1L3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.33 (Fisher's exact test), Q value = 0.68

Table S527.  Gene #55: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
AMAC1L3 MUTATED 0 1 1 1 3
AMAC1L3 WILD-TYPE 24 48 63 94 43
'TRAPPC9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.854 (Fisher's exact test), Q value = 1

Table S528.  Gene #56: 'TRAPPC9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
TRAPPC9 MUTATED 2 1 2
TRAPPC9 WILD-TYPE 177 238 240
'TRAPPC9 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.129 (Fisher's exact test), Q value = 0.36

Table S529.  Gene #56: 'TRAPPC9 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
TRAPPC9 MUTATED 1 1 3
TRAPPC9 WILD-TYPE 102 254 116
'TRAPPC9 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.38 (Fisher's exact test), Q value = 0.74

Table S530.  Gene #56: 'TRAPPC9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
TRAPPC9 MUTATED 1 2 1 0
TRAPPC9 WILD-TYPE 147 137 139 157
'TRAPPC9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S531.  Gene #56: 'TRAPPC9 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
TRAPPC9 MUTATED 2 0 0 1 0 0 1
TRAPPC9 WILD-TYPE 148 44 96 119 48 51 74
'TRAPPC9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.147 (Fisher's exact test), Q value = 0.39

Table S532.  Gene #56: 'TRAPPC9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
TRAPPC9 MUTATED 1 0 1 3
TRAPPC9 WILD-TYPE 98 173 240 145
'TRAPPC9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.328 (Fisher's exact test), Q value = 0.68

Table S533.  Gene #56: 'TRAPPC9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
TRAPPC9 MUTATED 1 1 1 0 0 2
TRAPPC9 WILD-TYPE 79 90 172 137 90 88
'TRAPPC9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.453 (Fisher's exact test), Q value = 0.82

Table S534.  Gene #56: 'TRAPPC9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
TRAPPC9 MUTATED 3 1 1
TRAPPC9 WILD-TYPE 209 148 292
'TRAPPC9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.109 (Fisher's exact test), Q value = 0.33

Table S535.  Gene #56: 'TRAPPC9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
TRAPPC9 MUTATED 1 3 1
TRAPPC9 WILD-TYPE 71 177 401
'MED16 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.46 (Fisher's exact test), Q value = 0.83

Table S536.  Gene #57: 'MED16 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 179 239 242
MED16 MUTATED 0 1 3
MED16 WILD-TYPE 179 238 239
'MED16 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.421 (Fisher's exact test), Q value = 0.8

Table S537.  Gene #57: 'MED16 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
MED16 MUTATED 1 1 2
MED16 WILD-TYPE 102 254 117
'MED16 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S538.  Gene #57: 'MED16 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 148 139 140 157
MED16 MUTATED 1 1 1 1
MED16 WILD-TYPE 147 138 139 156
'MED16 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.203 (Fisher's exact test), Q value = 0.5

Table S539.  Gene #57: 'MED16 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 150 44 96 120 48 51 75
MED16 MUTATED 0 1 0 1 1 0 1
MED16 WILD-TYPE 150 43 96 119 47 51 74
'MED16 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S540.  Gene #57: 'MED16 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 173 241 148
MED16 MUTATED 1 1 1 1
MED16 WILD-TYPE 98 172 240 147
'MED16 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0461 (Fisher's exact test), Q value = 0.19

Table S541.  Gene #57: 'MED16 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 91 173 137 90 90
MED16 MUTATED 0 3 1 0 0 0
MED16 WILD-TYPE 80 88 172 137 90 90

Figure S174.  Get High-res Image Gene #57: 'MED16 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'MED16 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.82 (Fisher's exact test), Q value = 1

Table S542.  Gene #57: 'MED16 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 212 149 293
MED16 MUTATED 2 1 1
MED16 WILD-TYPE 210 148 292
'MED16 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.127 (Fisher's exact test), Q value = 0.36

Table S543.  Gene #57: 'MED16 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 180 402
MED16 MUTATED 0 3 1
MED16 WILD-TYPE 72 177 401
'MED16 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 0.75

Table S544.  Gene #57: 'MED16 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 60 42 99
MED16 MUTATED 1 1 1 0
MED16 WILD-TYPE 76 59 41 99
'MED16 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S545.  Gene #57: 'MED16 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 49 64 95 46
MED16 MUTATED 0 1 2 0 0
MED16 WILD-TYPE 24 48 62 95 46
Methods & Data
Input

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIPAN-TP/20230421/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIPAN-TP/20125873/KIPAN-TP.transferedmergedcluster.txt

  • Number of patients = 663

  • Number of significantly mutated genes = 57

  • Number of Molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
Copyright © 2015 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle