Correlation between gene mutation status and molecular subtypes
Bladder Urothelial Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1FN14XS
Overview
Introduction

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

Summary

Testing the association between mutation status of 35 genes and 10 molecular subtypes across 130 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.

  • No gene mutations related to molecuar subtypes.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 35 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, no significant finding detected.

Clinical
Features
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
TP53 64 (49%) 66 0.109
(1.00)
0.148
(1.00)
0.04
(1.00)
0.00663
(1.00)
0.244
(1.00)
0.299
(1.00)
0.453
(1.00)
0.315
(1.00)
0.46
(1.00)
0.316
(1.00)
KDM6A 31 (24%) 99 0.154
(1.00)
0.824
(1.00)
0.34
(1.00)
0.136
(1.00)
0.608
(1.00)
0.668
(1.00)
0.121
(1.00)
0.501
(1.00)
0.658
(1.00)
0.326
(1.00)
RB1 17 (13%) 113 0.00472
(1.00)
0.743
(1.00)
0.592
(1.00)
0.316
(1.00)
0.605
(1.00)
0.54
(1.00)
1
(1.00)
0.346
(1.00)
0.217
(1.00)
0.432
(1.00)
ARID1A 32 (25%) 98 0.68
(1.00)
0.828
(1.00)
0.589
(1.00)
0.0803
(1.00)
0.378
(1.00)
0.564
(1.00)
0.125
(1.00)
0.0926
(1.00)
0.376
(1.00)
0.282
(1.00)
CDKN1A 18 (14%) 112 0.9
(1.00)
0.0785
(1.00)
0.831
(1.00)
0.824
(1.00)
0.73
(1.00)
0.498
(1.00)
0.382
(1.00)
0.91
(1.00)
0.842
(1.00)
0.53
(1.00)
MLL2 36 (28%) 94 0.425
(1.00)
0.814
(1.00)
0.366
(1.00)
0.328
(1.00)
0.199
(1.00)
0.308
(1.00)
0.326
(1.00)
0.292
(1.00)
0.71
(1.00)
0.589
(1.00)
ELF3 11 (8%) 119 0.784
(1.00)
0.208
(1.00)
0.759
(1.00)
0.383
(1.00)
0.669
(1.00)
0.222
(1.00)
0.569
(1.00)
0.847
(1.00)
0.916
(1.00)
0.456
(1.00)
FGFR3 16 (12%) 114 0.0186
(1.00)
0.232
(1.00)
0.0924
(1.00)
0.00986
(1.00)
0.186
(1.00)
0.0473
(1.00)
0.197
(1.00)
0.00929
(1.00)
0.011
(1.00)
0.0414
(1.00)
CDKN2A 7 (5%) 123 0.141
(1.00)
0.563
(1.00)
0.389
(1.00)
0.183
(1.00)
0.799
(1.00)
0.866
(1.00)
0.331
(1.00)
0.283
(1.00)
0.301
(1.00)
1
(1.00)
STAG2 14 (11%) 116 0.318
(1.00)
0.183
(1.00)
0.301
(1.00)
0.553
(1.00)
0.322
(1.00)
0.144
(1.00)
0.19
(1.00)
0.26
(1.00)
0.249
(1.00)
0.0177
(1.00)
NFE2L2 11 (8%) 119 0.117
(1.00)
0.655
(1.00)
0.307
(1.00)
0.725
(1.00)
0.0957
(1.00)
0.0416
(1.00)
1
(1.00)
0.0163
(1.00)
0.843
(1.00)
0.75
(1.00)
ERCC2 16 (12%) 114 0.618
(1.00)
0.448
(1.00)
0.0867
(1.00)
0.0178
(1.00)
0.174
(1.00)
0.123
(1.00)
0.395
(1.00)
0.105
(1.00)
0.78
(1.00)
0.933
(1.00)
FBXW7 13 (10%) 117 0.288
(1.00)
0.0415
(1.00)
0.262
(1.00)
0.532
(1.00)
0.104
(1.00)
0.0904
(1.00)
0.214
(1.00)
0.0284
(1.00)
0.0264
(1.00)
0.187
(1.00)
RHOB 7 (5%) 123 1
(1.00)
0.705
(1.00)
0.564
(1.00)
0.317
(1.00)
0.796
(1.00)
0.345
(1.00)
0.704
(1.00)
0.544
(1.00)
0.299
(1.00)
0.498
(1.00)
TSC1 11 (8%) 119 0.167
(1.00)
0.699
(1.00)
0.416
(1.00)
0.569
(1.00)
0.244
(1.00)
0.141
(1.00)
0.621
(1.00)
0.496
(1.00)
0.413
(1.00)
0.0855
(1.00)
FOXQ1 7 (5%) 123 0.423
(1.00)
0.378
(1.00)
0.467
(1.00)
0.366
(1.00)
0.884
(1.00)
1
(1.00)
0.152
(1.00)
0.294
(1.00)
0.299
(1.00)
0.422
(1.00)
PIK3CA 26 (20%) 104 0.407
(1.00)
0.961
(1.00)
0.224
(1.00)
0.642
(1.00)
0.432
(1.00)
0.166
(1.00)
0.789
(1.00)
0.537
(1.00)
0.419
(1.00)
0.6
(1.00)
RXRA 12 (9%) 118 0.119
(1.00)
0.193
(1.00)
0.168
(1.00)
0.923
(1.00)
0.591
(1.00)
0.321
(1.00)
0.549
(1.00)
0.336
(1.00)
0.674
(1.00)
0.315
(1.00)
CREBBP 17 (13%) 113 0.299
(1.00)
0.849
(1.00)
0.921
(1.00)
0.546
(1.00)
0.213
(1.00)
0.288
(1.00)
0.193
(1.00)
0.911
(1.00)
0.651
(1.00)
0.247
(1.00)
ERBB3 14 (11%) 116 0.936
(1.00)
0.593
(1.00)
0.693
(1.00)
0.493
(1.00)
0.675
(1.00)
0.842
(1.00)
0.821
(1.00)
0.731
(1.00)
0.573
(1.00)
1
(1.00)
FAT1 15 (12%) 115 0.205
(1.00)
0.365
(1.00)
0.22
(1.00)
0.436
(1.00)
0.37
(1.00)
1
(1.00)
0.453
(1.00)
0.288
(1.00)
0.0884
(1.00)
0.0737
(1.00)
MLL 18 (14%) 112 0.845
(1.00)
0.984
(1.00)
0.0283
(1.00)
0.00499
(1.00)
0.325
(1.00)
0.532
(1.00)
0.813
(1.00)
0.705
(1.00)
0.891
(1.00)
0.881
(1.00)
HRAS 6 (5%) 124 0.57
(1.00)
0.799
(1.00)
0.0168
(1.00)
0.339
(1.00)
0.88
(1.00)
0.439
(1.00)
0.57
(1.00)
0.648
(1.00)
0.197
(1.00)
0.258
(1.00)
ACRC 4 (3%) 126 0.281
(1.00)
0.11
(1.00)
0.855
(1.00)
0.76
(1.00)
1
(1.00)
0.912
(1.00)
1
(1.00)
0.87
(1.00)
1
(1.00)
0.812
(1.00)
TXNIP 9 (7%) 121 0.588
(1.00)
0.274
(1.00)
0.872
(1.00)
0.703
(1.00)
1
(1.00)
0.0801
(1.00)
0.909
(1.00)
0.983
(1.00)
0.732
(1.00)
0.897
(1.00)
ECM1 5 (4%) 125 0.0794
(1.00)
0.268
(1.00)
0.947
(1.00)
0.181
(1.00)
0.733
(1.00)
0.55
(1.00)
0.52
(1.00)
0.186
(1.00)
0.416
(1.00)
0.698
(1.00)
KLF5 10 (8%) 120 0.0917
(1.00)
0.778
(1.00)
0.303
(1.00)
0.31
(1.00)
0.915
(1.00)
0.679
(1.00)
0.706
(1.00)
0.23
(1.00)
0.192
(1.00)
0.0234
(1.00)
RBM26 9 (7%) 121 0.619
(1.00)
0.964
(1.00)
0.255
(1.00)
0.725
(1.00)
0.382
(1.00)
0.566
(1.00)
0.0938
(1.00)
0.288
(1.00)
0.389
(1.00)
0.246
(1.00)
RAD51C 4 (3%) 126 1
(1.00)
0.165
(1.00)
0.182
(1.00)
1
(1.00)
0.0372
(1.00)
0.21
(1.00)
0.134
(1.00)
0.449
(1.00)
0.134
(1.00)
0.375
(1.00)
CEP192 5 (4%) 125 0.85
(1.00)
0.725
(1.00)
0.895
(1.00)
0.696
(1.00)
0.733
(1.00)
0.587
(1.00)
0.734
(1.00)
0.0615
(1.00)
0.591
(1.00)
0.699
(1.00)
ASXL2 9 (7%) 121 0.0475
(1.00)
0.508
(1.00)
0.348
(1.00)
0.365
(1.00)
0.25
(1.00)
0.817
(1.00)
0.91
(1.00)
0.399
(1.00)
0.484
(1.00)
0.454
(1.00)
PSIP1 7 (5%) 123 0.371
(1.00)
0.625
(1.00)
0.138
(1.00)
0.385
(1.00)
0.884
(1.00)
0.509
(1.00)
0.483
(1.00)
0.847
(1.00)
0.536
(1.00)
0.191
(1.00)
ZNF513 7 (5%) 123 0.16
(1.00)
0.704
(1.00)
0.206
(1.00)
0.414
(1.00)
0.48
(1.00)
0.335
(1.00)
0.89
(1.00)
0.761
(1.00)
1
(1.00)
1
(1.00)
FOXA1 7 (5%) 123 0.611
(1.00)
0.91
(1.00)
0.539
(1.00)
0.694
(1.00)
0.257
(1.00)
0.908
(1.00)
0.888
(1.00)
0.647
(1.00)
0.675
(1.00)
0.661
(1.00)
TRIP11 5 (4%) 125 0.822
(1.00)
0.531
(1.00)
0.804
(1.00)
0.288
(1.00)
0.731
(1.00)
0.869
(1.00)
0.316
(1.00)
0.0933
(1.00)
0.34
(1.00)
0.368
(1.00)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 1

Table S1.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
TP53 MUTATED 20 21 22
TP53 WILD-TYPE 11 21 32
'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.148 (Fisher's exact test), Q value = 1

Table S2.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
TP53 MUTATED 21 19 16 8
TP53 WILD-TYPE 21 11 17 17
'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.04 (Fisher's exact test), Q value = 1

Table S3.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
TP53 MUTATED 14 11 23 1 9
TP53 WILD-TYPE 22 17 10 4 8

Figure S1.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00663 (Fisher's exact test), Q value = 1

Table S4.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
TP53 MUTATED 16 15 17 10
TP53 WILD-TYPE 27 21 4 9

Figure S2.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.244 (Fisher's exact test), Q value = 1

Table S5.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
TP53 MUTATED 22 20 22
TP53 WILD-TYPE 32 15 18
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.299 (Fisher's exact test), Q value = 1

Table S6.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
TP53 MUTATED 16 14 18 16
TP53 WILD-TYPE 23 7 20 15
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.453 (Fisher's exact test), Q value = 1

Table S7.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
TP53 MUTATED 14 27 23
TP53 WILD-TYPE 21 25 20
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S8.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
TP53 MUTATED 9 6 8 9 15 10 7
TP53 WILD-TYPE 15 7 5 5 12 7 15
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.46 (Fisher's exact test), Q value = 1

Table S9.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
TP53 MUTATED 9 31 24
TP53 WILD-TYPE 15 29 22
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.316 (Fisher's exact test), Q value = 1

Table S10.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
TP53 MUTATED 8 38 18
TP53 WILD-TYPE 15 36 15
'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.154 (Fisher's exact test), Q value = 1

Table S11.  Gene #2: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
KDM6A MUTATED 10 6 15
KDM6A WILD-TYPE 21 36 39
'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.824 (Fisher's exact test), Q value = 1

Table S12.  Gene #2: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
KDM6A MUTATED 9 9 8 5
KDM6A WILD-TYPE 33 21 25 20
'KDM6A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.34 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
KDM6A MUTATED 9 4 10 2 2
KDM6A WILD-TYPE 27 24 23 3 15
'KDM6A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.136 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
KDM6A MUTATED 9 6 9 3
KDM6A WILD-TYPE 34 30 12 16
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.608 (Fisher's exact test), Q value = 1

Table S15.  Gene #2: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
KDM6A MUTATED 12 7 12
KDM6A WILD-TYPE 42 28 28
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.668 (Fisher's exact test), Q value = 1

Table S16.  Gene #2: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
KDM6A MUTATED 9 3 10 9
KDM6A WILD-TYPE 30 18 28 22
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.121 (Fisher's exact test), Q value = 1

Table S17.  Gene #2: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
KDM6A MUTATED 4 15 12
KDM6A WILD-TYPE 31 37 31
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.501 (Fisher's exact test), Q value = 1

Table S18.  Gene #2: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
KDM6A MUTATED 3 2 3 3 8 7 5
KDM6A WILD-TYPE 21 11 10 11 19 10 17
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.658 (Fisher's exact test), Q value = 1

Table S19.  Gene #2: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
KDM6A MUTATED 4 16 11
KDM6A WILD-TYPE 20 44 35
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.326 (Fisher's exact test), Q value = 1

Table S20.  Gene #2: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
KDM6A MUTATED 3 18 10
KDM6A WILD-TYPE 20 56 23
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00472 (Fisher's exact test), Q value = 1

Table S21.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
RB1 MUTATED 4 11 2
RB1 WILD-TYPE 27 31 52

Figure S3.  Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S22.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
RB1 MUTATED 7 3 5 2
RB1 WILD-TYPE 35 27 28 23
'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.592 (Fisher's exact test), Q value = 1

Table S23.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
RB1 MUTATED 3 6 5 0 2
RB1 WILD-TYPE 33 22 28 5 15
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.316 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
RB1 MUTATED 3 7 4 2
RB1 WILD-TYPE 40 29 17 17
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.605 (Fisher's exact test), Q value = 1

Table S25.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
RB1 MUTATED 6 4 7
RB1 WILD-TYPE 48 31 33
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.54 (Fisher's exact test), Q value = 1

Table S26.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
RB1 MUTATED 3 3 5 6
RB1 WILD-TYPE 36 18 33 25
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S27.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
RB1 MUTATED 4 7 6
RB1 WILD-TYPE 31 45 37
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.346 (Fisher's exact test), Q value = 1

Table S28.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
RB1 MUTATED 1 3 3 1 3 4 2
RB1 WILD-TYPE 23 10 10 13 24 13 20
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.217 (Fisher's exact test), Q value = 1

Table S29.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
RB1 MUTATED 1 11 5
RB1 WILD-TYPE 23 49 41
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.432 (Fisher's exact test), Q value = 1

Table S30.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
RB1 MUTATED 1 12 4
RB1 WILD-TYPE 22 62 29
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.68 (Fisher's exact test), Q value = 1

Table S31.  Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
ARID1A MUTATED 6 12 14
ARID1A WILD-TYPE 25 30 40
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.828 (Fisher's exact test), Q value = 1

Table S32.  Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
ARID1A MUTATED 11 9 7 5
ARID1A WILD-TYPE 31 21 26 20
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.589 (Fisher's exact test), Q value = 1

Table S33.  Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
ARID1A MUTATED 11 8 6 2 3
ARID1A WILD-TYPE 25 20 27 3 14
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0803 (Fisher's exact test), Q value = 1

Table S34.  Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
ARID1A MUTATED 11 14 3 2
ARID1A WILD-TYPE 32 22 18 17
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 1

Table S35.  Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
ARID1A MUTATED 14 11 7
ARID1A WILD-TYPE 40 24 33
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.564 (Fisher's exact test), Q value = 1

Table S36.  Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
ARID1A MUTATED 8 7 11 6
ARID1A WILD-TYPE 31 14 27 25
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 1

Table S37.  Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
ARID1A MUTATED 10 8 14
ARID1A WILD-TYPE 25 44 29
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0926 (Fisher's exact test), Q value = 1

Table S38.  Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
ARID1A MUTATED 8 3 2 2 12 3 2
ARID1A WILD-TYPE 16 10 11 12 15 14 20
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 1

Table S39.  Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
ARID1A MUTATED 7 17 8
ARID1A WILD-TYPE 17 43 38
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.282 (Fisher's exact test), Q value = 1

Table S40.  Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
ARID1A MUTATED 7 20 5
ARID1A WILD-TYPE 16 54 28
'CDKN1A MUTATION STATUS' versus 'CN_CNMF'

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

Table S41.  Gene #5: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
CDKN1A MUTATED 5 5 8
CDKN1A WILD-TYPE 26 37 46
'CDKN1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0785 (Fisher's exact test), Q value = 1

Table S42.  Gene #5: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
CDKN1A MUTATED 7 1 8 2
CDKN1A WILD-TYPE 35 29 25 23
'CDKN1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.831 (Fisher's exact test), Q value = 1

Table S43.  Gene #5: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
CDKN1A MUTATED 6 4 5 1 1
CDKN1A WILD-TYPE 30 24 28 4 16
'CDKN1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.824 (Fisher's exact test), Q value = 1

Table S44.  Gene #5: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
CDKN1A MUTATED 7 4 4 2
CDKN1A WILD-TYPE 36 32 17 17
'CDKN1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.73 (Fisher's exact test), Q value = 1

Table S45.  Gene #5: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
CDKN1A MUTATED 6 6 6
CDKN1A WILD-TYPE 48 29 34
'CDKN1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.498 (Fisher's exact test), Q value = 1

Table S46.  Gene #5: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
CDKN1A MUTATED 7 4 3 4
CDKN1A WILD-TYPE 32 17 35 27
'CDKN1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S47.  Gene #5: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
CDKN1A MUTATED 7 5 6
CDKN1A WILD-TYPE 28 47 37
'CDKN1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.91 (Fisher's exact test), Q value = 1

Table S48.  Gene #5: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
CDKN1A MUTATED 5 2 2 2 3 1 3
CDKN1A WILD-TYPE 19 11 11 12 24 16 19
'CDKN1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.842 (Fisher's exact test), Q value = 1

Table S49.  Gene #5: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
CDKN1A MUTATED 4 7 7
CDKN1A WILD-TYPE 20 53 39
'CDKN1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.53 (Fisher's exact test), Q value = 1

Table S50.  Gene #5: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
CDKN1A MUTATED 5 9 4
CDKN1A WILD-TYPE 18 65 29
'MLL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 1

Table S51.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
MLL2 MUTATED 11 11 12
MLL2 WILD-TYPE 20 31 42
'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.814 (Fisher's exact test), Q value = 1

Table S52.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
MLL2 MUTATED 13 9 7 7
MLL2 WILD-TYPE 29 21 26 18
'MLL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.366 (Fisher's exact test), Q value = 1

Table S53.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
MLL2 MUTATED 9 5 12 1 7
MLL2 WILD-TYPE 27 23 21 4 10
'MLL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.328 (Fisher's exact test), Q value = 1

Table S54.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
MLL2 MUTATED 12 7 7 8
MLL2 WILD-TYPE 31 29 14 11
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 1

Table S55.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
MLL2 MUTATED 12 8 15
MLL2 WILD-TYPE 42 27 25
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.308 (Fisher's exact test), Q value = 1

Table S56.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
MLL2 MUTATED 8 4 11 12
MLL2 WILD-TYPE 31 17 27 19
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.326 (Fisher's exact test), Q value = 1

Table S57.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
MLL2 MUTATED 9 18 9
MLL2 WILD-TYPE 26 34 34
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.292 (Fisher's exact test), Q value = 1

Table S58.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
MLL2 MUTATED 6 3 7 3 6 7 4
MLL2 WILD-TYPE 18 10 6 11 21 10 18
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.71 (Fisher's exact test), Q value = 1

Table S59.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
MLL2 MUTATED 5 17 14
MLL2 WILD-TYPE 19 43 32
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.589 (Fisher's exact test), Q value = 1

Table S60.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
MLL2 MUTATED 6 23 7
MLL2 WILD-TYPE 17 51 26
'ELF3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.784 (Fisher's exact test), Q value = 1

Table S61.  Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
ELF3 MUTATED 2 3 6
ELF3 WILD-TYPE 29 39 48
'ELF3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.208 (Fisher's exact test), Q value = 1

Table S62.  Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
ELF3 MUTATED 2 2 2 5
ELF3 WILD-TYPE 40 28 31 20
'ELF3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.759 (Fisher's exact test), Q value = 1

Table S63.  Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
ELF3 MUTATED 4 3 3 0 0
ELF3 WILD-TYPE 32 25 30 5 17
'ELF3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.383 (Fisher's exact test), Q value = 1

Table S64.  Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
ELF3 MUTATED 3 4 3 0
ELF3 WILD-TYPE 40 32 18 19
'ELF3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S65.  Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
ELF3 MUTATED 6 3 2
ELF3 WILD-TYPE 48 32 38
'ELF3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.222 (Fisher's exact test), Q value = 1

Table S66.  Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
ELF3 MUTATED 3 0 6 2
ELF3 WILD-TYPE 36 21 32 29
'ELF3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.569 (Fisher's exact test), Q value = 1

Table S67.  Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
ELF3 MUTATED 3 3 5
ELF3 WILD-TYPE 32 49 38
'ELF3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.847 (Fisher's exact test), Q value = 1

Table S68.  Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
ELF3 MUTATED 2 2 0 1 3 2 1
ELF3 WILD-TYPE 22 11 13 13 24 15 21
'ELF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.916 (Fisher's exact test), Q value = 1

Table S69.  Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
ELF3 MUTATED 2 6 3
ELF3 WILD-TYPE 22 54 43
'ELF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.456 (Fisher's exact test), Q value = 1

Table S70.  Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
ELF3 MUTATED 2 8 1
ELF3 WILD-TYPE 21 66 32
'FGFR3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 1

Table S71.  Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
FGFR3 MUTATED 1 3 12
FGFR3 WILD-TYPE 30 39 42

Figure S4.  Get High-res Image Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'FGFR3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.232 (Fisher's exact test), Q value = 1

Table S72.  Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
FGFR3 MUTATED 3 2 6 5
FGFR3 WILD-TYPE 39 28 27 20
'FGFR3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0924 (Fisher's exact test), Q value = 1

Table S73.  Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
FGFR3 MUTATED 9 2 4 0 0
FGFR3 WILD-TYPE 27 26 29 5 17
'FGFR3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00986 (Fisher's exact test), Q value = 1

Table S74.  Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
FGFR3 MUTATED 9 0 4 2
FGFR3 WILD-TYPE 34 36 17 17

Figure S5.  Get High-res Image Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'FGFR3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.186 (Fisher's exact test), Q value = 1

Table S75.  Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
FGFR3 MUTATED 10 2 4
FGFR3 WILD-TYPE 44 33 36
'FGFR3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0473 (Fisher's exact test), Q value = 1

Table S76.  Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
FGFR3 MUTATED 10 1 3 2
FGFR3 WILD-TYPE 29 20 35 29

Figure S6.  Get High-res Image Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.197 (Fisher's exact test), Q value = 1

Table S77.  Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
FGFR3 MUTATED 3 10 3
FGFR3 WILD-TYPE 32 42 40
'FGFR3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00929 (Fisher's exact test), Q value = 1

Table S78.  Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
FGFR3 MUTATED 3 0 0 4 1 1 7
FGFR3 WILD-TYPE 21 13 13 10 26 16 15

Figure S7.  Get High-res Image Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 1

Table S79.  Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
FGFR3 MUTATED 2 3 11
FGFR3 WILD-TYPE 22 57 35

Figure S8.  Get High-res Image Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0414 (Fisher's exact test), Q value = 1

Table S80.  Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
FGFR3 MUTATED 3 5 8
FGFR3 WILD-TYPE 20 69 25

Figure S9.  Get High-res Image Gene #8: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CDKN2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 1

Table S81.  Gene #9: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
CDKN2A MUTATED 2 0 5
CDKN2A WILD-TYPE 29 42 49
'CDKN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.563 (Fisher's exact test), Q value = 1

Table S82.  Gene #9: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
CDKN2A MUTATED 2 2 3 0
CDKN2A WILD-TYPE 40 28 30 25
'CDKN2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.389 (Fisher's exact test), Q value = 1

Table S83.  Gene #9: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
CDKN2A MUTATED 2 0 4 0 1
CDKN2A WILD-TYPE 34 28 29 5 16
'CDKN2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.183 (Fisher's exact test), Q value = 1

Table S84.  Gene #9: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
CDKN2A MUTATED 3 0 2 2
CDKN2A WILD-TYPE 40 36 19 17
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.799 (Fisher's exact test), Q value = 1

Table S85.  Gene #9: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
CDKN2A MUTATED 3 1 3
CDKN2A WILD-TYPE 51 34 37
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.866 (Fisher's exact test), Q value = 1

Table S86.  Gene #9: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
CDKN2A MUTATED 2 2 2 1
CDKN2A WILD-TYPE 37 19 36 30
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 1

Table S87.  Gene #9: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
CDKN2A MUTATED 1 5 1
CDKN2A WILD-TYPE 34 47 42
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.283 (Fisher's exact test), Q value = 1

Table S88.  Gene #9: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
CDKN2A MUTATED 1 0 2 1 0 2 1
CDKN2A WILD-TYPE 23 13 11 13 27 15 21
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.301 (Fisher's exact test), Q value = 1

Table S89.  Gene #9: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
CDKN2A MUTATED 0 3 4
CDKN2A WILD-TYPE 24 57 42
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S90.  Gene #9: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
CDKN2A MUTATED 1 4 2
CDKN2A WILD-TYPE 22 70 31
'STAG2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S91.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
STAG2 MUTATED 2 3 9
STAG2 WILD-TYPE 29 39 45
'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.183 (Fisher's exact test), Q value = 1

Table S92.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
STAG2 MUTATED 3 2 3 6
STAG2 WILD-TYPE 39 28 30 19
'STAG2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.301 (Fisher's exact test), Q value = 1

Table S93.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
STAG2 MUTATED 7 3 3 0 0
STAG2 WILD-TYPE 29 25 30 5 17
'STAG2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.553 (Fisher's exact test), Q value = 1

Table S94.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
STAG2 MUTATED 7 3 1 2
STAG2 WILD-TYPE 36 33 20 17
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S95.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
STAG2 MUTATED 8 4 2
STAG2 WILD-TYPE 46 31 38
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.144 (Fisher's exact test), Q value = 1

Table S96.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
STAG2 MUTATED 7 0 5 2
STAG2 WILD-TYPE 32 21 33 29
'STAG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.19 (Fisher's exact test), Q value = 1

Table S97.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
STAG2 MUTATED 2 9 3
STAG2 WILD-TYPE 33 43 40
'STAG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.26 (Fisher's exact test), Q value = 1

Table S98.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
STAG2 MUTATED 2 1 0 2 2 1 6
STAG2 WILD-TYPE 22 12 13 12 25 16 16
'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.249 (Fisher's exact test), Q value = 1

Table S99.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
STAG2 MUTATED 2 4 8
STAG2 WILD-TYPE 22 56 38
'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0177 (Fisher's exact test), Q value = 1

Table S100.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
STAG2 MUTATED 2 4 8
STAG2 WILD-TYPE 21 70 25

Figure S10.  Get High-res Image Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.117 (Fisher's exact test), Q value = 1

Table S101.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
NFE2L2 MUTATED 0 5 6
NFE2L2 WILD-TYPE 31 37 48
'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.655 (Fisher's exact test), Q value = 1

Table S102.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
NFE2L2 MUTATED 5 1 3 2
NFE2L2 WILD-TYPE 37 29 30 23
'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.307 (Fisher's exact test), Q value = 1

Table S103.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
NFE2L2 MUTATED 1 4 3 1 2
NFE2L2 WILD-TYPE 35 24 30 4 15
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.725 (Fisher's exact test), Q value = 1

Table S104.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
NFE2L2 MUTATED 3 4 3 1
NFE2L2 WILD-TYPE 40 32 18 18
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0957 (Fisher's exact test), Q value = 1

Table S105.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
NFE2L2 MUTATED 1 4 5
NFE2L2 WILD-TYPE 53 31 35
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0416 (Fisher's exact test), Q value = 1

Table S106.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
NFE2L2 MUTATED 0 1 4 5
NFE2L2 WILD-TYPE 39 20 34 26

Figure S11.  Get High-res Image Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S107.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
NFE2L2 MUTATED 3 4 4
NFE2L2 WILD-TYPE 32 48 39
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0163 (Fisher's exact test), Q value = 1

Table S108.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
NFE2L2 MUTATED 1 3 1 4 0 1 1
NFE2L2 WILD-TYPE 23 10 12 10 27 16 21

Figure S12.  Get High-res Image Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.843 (Fisher's exact test), Q value = 1

Table S109.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
NFE2L2 MUTATED 1 6 4
NFE2L2 WILD-TYPE 23 54 42
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S110.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
NFE2L2 MUTATED 1 8 2
NFE2L2 WILD-TYPE 22 66 31
'ERCC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.618 (Fisher's exact test), Q value = 1

Table S111.  Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
ERCC2 MUTATED 5 6 5
ERCC2 WILD-TYPE 26 36 49
'ERCC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.448 (Fisher's exact test), Q value = 1

Table S112.  Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
ERCC2 MUTATED 5 4 6 1
ERCC2 WILD-TYPE 37 26 27 24
'ERCC2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0867 (Fisher's exact test), Q value = 1

Table S113.  Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
ERCC2 MUTATED 3 0 6 1 1
ERCC2 WILD-TYPE 33 28 27 4 16
'ERCC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0178 (Fisher's exact test), Q value = 1

Table S114.  Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
ERCC2 MUTATED 3 1 6 1
ERCC2 WILD-TYPE 40 35 15 18

Figure S13.  Get High-res Image Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'ERCC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 1

Table S115.  Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
ERCC2 MUTATED 4 4 8
ERCC2 WILD-TYPE 50 31 32
'ERCC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.123 (Fisher's exact test), Q value = 1

Table S116.  Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
ERCC2 MUTATED 3 2 3 8
ERCC2 WILD-TYPE 36 19 35 23
'ERCC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.395 (Fisher's exact test), Q value = 1

Table S117.  Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
ERCC2 MUTATED 6 7 3
ERCC2 WILD-TYPE 29 45 40
'ERCC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.105 (Fisher's exact test), Q value = 1

Table S118.  Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
ERCC2 MUTATED 2 5 1 2 1 3 2
ERCC2 WILD-TYPE 22 8 12 12 26 14 20
'ERCC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.78 (Fisher's exact test), Q value = 1

Table S119.  Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
ERCC2 MUTATED 4 7 5
ERCC2 WILD-TYPE 20 53 41
'ERCC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.933 (Fisher's exact test), Q value = 1

Table S120.  Gene #12: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
ERCC2 MUTATED 2 10 4
ERCC2 WILD-TYPE 21 64 29
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.288 (Fisher's exact test), Q value = 1

Table S121.  Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
FBXW7 MUTATED 1 6 5
FBXW7 WILD-TYPE 30 36 49
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 1

Table S122.  Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
FBXW7 MUTATED 9 2 1 1
FBXW7 WILD-TYPE 33 28 32 24

Figure S14.  Get High-res Image Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 1

Table S123.  Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
FBXW7 MUTATED 1 3 5 1 1
FBXW7 WILD-TYPE 35 25 28 4 16
'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.532 (Fisher's exact test), Q value = 1

Table S124.  Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
FBXW7 MUTATED 2 4 3 2
FBXW7 WILD-TYPE 41 32 18 17
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.104 (Fisher's exact test), Q value = 1

Table S125.  Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
FBXW7 MUTATED 2 5 6
FBXW7 WILD-TYPE 52 30 34
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0904 (Fisher's exact test), Q value = 1

Table S126.  Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
FBXW7 MUTATED 1 3 3 6
FBXW7 WILD-TYPE 38 18 35 25
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 1

Table S127.  Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
FBXW7 MUTATED 6 3 4
FBXW7 WILD-TYPE 29 49 39
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0284 (Fisher's exact test), Q value = 1

Table S128.  Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
FBXW7 MUTATED 4 2 1 2 0 4 0
FBXW7 WILD-TYPE 20 11 12 12 27 13 22

Figure S15.  Get High-res Image Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0264 (Fisher's exact test), Q value = 1

Table S129.  Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
FBXW7 MUTATED 5 7 1
FBXW7 WILD-TYPE 19 53 45

Figure S16.  Get High-res Image Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.187 (Fisher's exact test), Q value = 1

Table S130.  Gene #13: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
FBXW7 MUTATED 4 8 1
FBXW7 WILD-TYPE 19 66 32
'RHOB MUTATION STATUS' versus 'CN_CNMF'

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

Table S131.  Gene #14: 'RHOB MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
RHOB MUTATED 2 2 3
RHOB WILD-TYPE 29 40 51
'RHOB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.705 (Fisher's exact test), Q value = 1

Table S132.  Gene #14: 'RHOB MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
RHOB MUTATED 2 3 1 1
RHOB WILD-TYPE 40 27 32 24
'RHOB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.564 (Fisher's exact test), Q value = 1

Table S133.  Gene #14: 'RHOB MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
RHOB MUTATED 2 1 4 0 0
RHOB WILD-TYPE 34 27 29 5 17
'RHOB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.317 (Fisher's exact test), Q value = 1

Table S134.  Gene #14: 'RHOB MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
RHOB MUTATED 2 2 3 0
RHOB WILD-TYPE 41 34 18 19
'RHOB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S135.  Gene #14: 'RHOB MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
RHOB MUTATED 3 1 3
RHOB WILD-TYPE 51 34 37
'RHOB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.345 (Fisher's exact test), Q value = 1

Table S136.  Gene #14: 'RHOB MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
RHOB MUTATED 1 0 4 2
RHOB WILD-TYPE 38 21 34 29
'RHOB MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S137.  Gene #14: 'RHOB MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
RHOB MUTATED 1 4 2
RHOB WILD-TYPE 34 48 41
'RHOB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.544 (Fisher's exact test), Q value = 1

Table S138.  Gene #14: 'RHOB MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
RHOB MUTATED 1 0 2 1 2 1 0
RHOB WILD-TYPE 23 13 11 13 25 16 22
'RHOB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.299 (Fisher's exact test), Q value = 1

Table S139.  Gene #14: 'RHOB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
RHOB MUTATED 0 3 4
RHOB WILD-TYPE 24 57 42
'RHOB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.498 (Fisher's exact test), Q value = 1

Table S140.  Gene #14: 'RHOB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
RHOB MUTATED 1 3 3
RHOB WILD-TYPE 22 71 30
'TSC1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S141.  Gene #15: 'TSC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
TSC1 MUTATED 3 1 7
TSC1 WILD-TYPE 28 41 47
'TSC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.699 (Fisher's exact test), Q value = 1

Table S142.  Gene #15: 'TSC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
TSC1 MUTATED 2 3 4 2
TSC1 WILD-TYPE 40 27 29 23
'TSC1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.416 (Fisher's exact test), Q value = 1

Table S143.  Gene #15: 'TSC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
TSC1 MUTATED 6 1 2 0 2
TSC1 WILD-TYPE 30 27 31 5 15
'TSC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.569 (Fisher's exact test), Q value = 1

Table S144.  Gene #15: 'TSC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
TSC1 MUTATED 6 2 1 2
TSC1 WILD-TYPE 37 34 20 17
'TSC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.244 (Fisher's exact test), Q value = 1

Table S145.  Gene #15: 'TSC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
TSC1 MUTATED 6 4 1
TSC1 WILD-TYPE 48 31 39
'TSC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.141 (Fisher's exact test), Q value = 1

Table S146.  Gene #15: 'TSC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
TSC1 MUTATED 4 0 6 1
TSC1 WILD-TYPE 35 21 32 30
'TSC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.621 (Fisher's exact test), Q value = 1

Table S147.  Gene #15: 'TSC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
TSC1 MUTATED 4 3 4
TSC1 WILD-TYPE 31 49 39
'TSC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.496 (Fisher's exact test), Q value = 1

Table S148.  Gene #15: 'TSC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
TSC1 MUTATED 3 1 0 2 3 2 0
TSC1 WILD-TYPE 21 12 13 12 24 15 22
'TSC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.413 (Fisher's exact test), Q value = 1

Table S149.  Gene #15: 'TSC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
TSC1 MUTATED 3 6 2
TSC1 WILD-TYPE 21 54 44
'TSC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0855 (Fisher's exact test), Q value = 1

Table S150.  Gene #15: 'TSC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
TSC1 MUTATED 3 8 0
TSC1 WILD-TYPE 20 66 33
'FOXQ1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.423 (Fisher's exact test), Q value = 1

Table S151.  Gene #16: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
FOXQ1 MUTATED 3 1 3
FOXQ1 WILD-TYPE 28 41 51
'FOXQ1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 1

Table S152.  Gene #16: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
FOXQ1 MUTATED 3 2 0 2
FOXQ1 WILD-TYPE 39 28 33 23
'FOXQ1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 1

Table S153.  Gene #16: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
FOXQ1 MUTATED 2 0 2 0 2
FOXQ1 WILD-TYPE 34 28 31 5 15
'FOXQ1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.366 (Fisher's exact test), Q value = 1

Table S154.  Gene #16: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
FOXQ1 MUTATED 3 1 0 2
FOXQ1 WILD-TYPE 40 35 21 17
'FOXQ1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.884 (Fisher's exact test), Q value = 1

Table S155.  Gene #16: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
FOXQ1 MUTATED 4 1 2
FOXQ1 WILD-TYPE 50 34 38
'FOXQ1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S156.  Gene #16: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
FOXQ1 MUTATED 2 1 2 2
FOXQ1 WILD-TYPE 37 20 36 29
'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.152 (Fisher's exact test), Q value = 1

Table S157.  Gene #16: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
FOXQ1 MUTATED 0 5 2
FOXQ1 WILD-TYPE 35 47 41
'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.294 (Fisher's exact test), Q value = 1

Table S158.  Gene #16: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
FOXQ1 MUTATED 0 0 2 0 2 2 1
FOXQ1 WILD-TYPE 24 13 11 14 25 15 21
'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.299 (Fisher's exact test), Q value = 1

Table S159.  Gene #16: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
FOXQ1 MUTATED 0 3 4
FOXQ1 WILD-TYPE 24 57 42
'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.422 (Fisher's exact test), Q value = 1

Table S160.  Gene #16: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
FOXQ1 MUTATED 0 4 3
FOXQ1 WILD-TYPE 23 70 30
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.407 (Fisher's exact test), Q value = 1

Table S161.  Gene #17: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
PIK3CA MUTATED 4 11 11
PIK3CA WILD-TYPE 27 31 43
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.961 (Fisher's exact test), Q value = 1

Table S162.  Gene #17: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
PIK3CA MUTATED 8 7 6 5
PIK3CA WILD-TYPE 34 23 27 20
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.224 (Fisher's exact test), Q value = 1

Table S163.  Gene #17: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
PIK3CA MUTATED 5 6 11 0 2
PIK3CA WILD-TYPE 31 22 22 5 15
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S164.  Gene #17: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
PIK3CA MUTATED 8 9 5 2
PIK3CA WILD-TYPE 35 27 16 17
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.432 (Fisher's exact test), Q value = 1

Table S165.  Gene #17: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
PIK3CA MUTATED 8 9 9
PIK3CA WILD-TYPE 46 26 31
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.166 (Fisher's exact test), Q value = 1

Table S166.  Gene #17: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
PIK3CA MUTATED 5 2 11 8
PIK3CA WILD-TYPE 34 19 27 23
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.789 (Fisher's exact test), Q value = 1

Table S167.  Gene #17: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
PIK3CA MUTATED 6 12 8
PIK3CA WILD-TYPE 29 40 35
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.537 (Fisher's exact test), Q value = 1

Table S168.  Gene #17: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
PIK3CA MUTATED 3 4 2 2 6 6 3
PIK3CA WILD-TYPE 21 9 11 12 21 11 19
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.419 (Fisher's exact test), Q value = 1

Table S169.  Gene #17: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
PIK3CA MUTATED 3 15 8
PIK3CA WILD-TYPE 21 45 38
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.6 (Fisher's exact test), Q value = 1

Table S170.  Gene #17: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
PIK3CA MUTATED 3 17 6
PIK3CA WILD-TYPE 20 57 27
'RXRA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 1

Table S171.  Gene #18: 'RXRA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
RXRA MUTATED 6 2 4
RXRA WILD-TYPE 25 40 50
'RXRA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.193 (Fisher's exact test), Q value = 1

Table S172.  Gene #18: 'RXRA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
RXRA MUTATED 4 5 3 0
RXRA WILD-TYPE 38 25 30 25
'RXRA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.168 (Fisher's exact test), Q value = 1

Table S173.  Gene #18: 'RXRA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
RXRA MUTATED 7 1 2 1 1
RXRA WILD-TYPE 29 27 31 4 16
'RXRA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.923 (Fisher's exact test), Q value = 1

Table S174.  Gene #18: 'RXRA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
RXRA MUTATED 5 4 1 2
RXRA WILD-TYPE 38 32 20 17
'RXRA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.591 (Fisher's exact test), Q value = 1

Table S175.  Gene #18: 'RXRA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
RXRA MUTATED 6 4 2
RXRA WILD-TYPE 48 31 38
'RXRA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.321 (Fisher's exact test), Q value = 1

Table S176.  Gene #18: 'RXRA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
RXRA MUTATED 5 0 5 2
RXRA WILD-TYPE 34 21 33 29
'RXRA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.549 (Fisher's exact test), Q value = 1

Table S177.  Gene #18: 'RXRA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
RXRA MUTATED 5 4 3
RXRA WILD-TYPE 30 48 40
'RXRA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.336 (Fisher's exact test), Q value = 1

Table S178.  Gene #18: 'RXRA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
RXRA MUTATED 4 1 2 0 3 2 0
RXRA WILD-TYPE 20 12 11 14 24 15 22
'RXRA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.674 (Fisher's exact test), Q value = 1

Table S179.  Gene #18: 'RXRA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
RXRA MUTATED 3 6 3
RXRA WILD-TYPE 21 54 43
'RXRA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S180.  Gene #18: 'RXRA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
RXRA MUTATED 4 6 2
RXRA WILD-TYPE 19 68 31
'CREBBP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.299 (Fisher's exact test), Q value = 1

Table S181.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
CREBBP MUTATED 5 7 4
CREBBP WILD-TYPE 26 35 50
'CREBBP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.849 (Fisher's exact test), Q value = 1

Table S182.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
CREBBP MUTATED 7 4 3 3
CREBBP WILD-TYPE 35 26 30 22
'CREBBP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.921 (Fisher's exact test), Q value = 1

Table S183.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
CREBBP MUTATED 4 4 5 0 1
CREBBP WILD-TYPE 32 24 28 5 16
'CREBBP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.546 (Fisher's exact test), Q value = 1

Table S184.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
CREBBP MUTATED 6 3 4 1
CREBBP WILD-TYPE 37 33 17 18
'CREBBP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.213 (Fisher's exact test), Q value = 1

Table S185.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
CREBBP MUTATED 4 7 6
CREBBP WILD-TYPE 50 28 34
'CREBBP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.288 (Fisher's exact test), Q value = 1

Table S186.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
CREBBP MUTATED 2 3 7 5
CREBBP WILD-TYPE 37 18 31 26
'CREBBP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.193 (Fisher's exact test), Q value = 1

Table S187.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
CREBBP MUTATED 3 5 9
CREBBP WILD-TYPE 32 47 34
'CREBBP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.911 (Fisher's exact test), Q value = 1

Table S188.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
CREBBP MUTATED 2 1 2 2 5 3 2
CREBBP WILD-TYPE 22 12 11 12 22 14 20
'CREBBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.651 (Fisher's exact test), Q value = 1

Table S189.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
CREBBP MUTATED 2 10 5
CREBBP WILD-TYPE 22 50 41
'CREBBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.247 (Fisher's exact test), Q value = 1

Table S190.  Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
CREBBP MUTATED 2 13 2
CREBBP WILD-TYPE 21 61 31
'ERBB3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.936 (Fisher's exact test), Q value = 1

Table S191.  Gene #20: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
ERBB3 MUTATED 4 4 6
ERBB3 WILD-TYPE 27 38 48
'ERBB3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.593 (Fisher's exact test), Q value = 1

Table S192.  Gene #20: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
ERBB3 MUTATED 3 5 4 2
ERBB3 WILD-TYPE 39 25 29 23
'ERBB3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S193.  Gene #20: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
ERBB3 MUTATED 6 3 3 1 1
ERBB3 WILD-TYPE 30 25 30 4 16
'ERBB3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.493 (Fisher's exact test), Q value = 1

Table S194.  Gene #20: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
ERBB3 MUTATED 6 6 1 1
ERBB3 WILD-TYPE 37 30 20 18
'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.675 (Fisher's exact test), Q value = 1

Table S195.  Gene #20: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
ERBB3 MUTATED 6 5 3
ERBB3 WILD-TYPE 48 30 37
'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.842 (Fisher's exact test), Q value = 1

Table S196.  Gene #20: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
ERBB3 MUTATED 5 2 5 2
ERBB3 WILD-TYPE 34 19 33 29
'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.821 (Fisher's exact test), Q value = 1

Table S197.  Gene #20: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
ERBB3 MUTATED 3 7 4
ERBB3 WILD-TYPE 32 45 39
'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.731 (Fisher's exact test), Q value = 1

Table S198.  Gene #20: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
ERBB3 MUTATED 2 1 0 1 3 3 4
ERBB3 WILD-TYPE 22 12 13 13 24 14 18
'ERBB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.573 (Fisher's exact test), Q value = 1

Table S199.  Gene #20: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
ERBB3 MUTATED 1 8 5
ERBB3 WILD-TYPE 23 52 41
'ERBB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S200.  Gene #20: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
ERBB3 MUTATED 2 8 4
ERBB3 WILD-TYPE 21 66 29
'FAT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.205 (Fisher's exact test), Q value = 1

Table S201.  Gene #21: 'FAT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
FAT1 MUTATED 1 7 7
FAT1 WILD-TYPE 30 35 47
'FAT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 1

Table S202.  Gene #21: 'FAT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
FAT1 MUTATED 7 1 4 3
FAT1 WILD-TYPE 35 29 29 22
'FAT1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.22 (Fisher's exact test), Q value = 1

Table S203.  Gene #21: 'FAT1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
FAT1 MUTATED 3 2 6 2 2
FAT1 WILD-TYPE 33 26 27 3 15
'FAT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.436 (Fisher's exact test), Q value = 1

Table S204.  Gene #21: 'FAT1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
FAT1 MUTATED 4 4 5 2
FAT1 WILD-TYPE 39 32 16 17
'FAT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.37 (Fisher's exact test), Q value = 1

Table S205.  Gene #21: 'FAT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
FAT1 MUTATED 4 6 4
FAT1 WILD-TYPE 50 29 36
'FAT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S206.  Gene #21: 'FAT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
FAT1 MUTATED 4 2 4 4
FAT1 WILD-TYPE 35 19 34 27
'FAT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.453 (Fisher's exact test), Q value = 1

Table S207.  Gene #21: 'FAT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
FAT1 MUTATED 2 7 6
FAT1 WILD-TYPE 33 45 37
'FAT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.288 (Fisher's exact test), Q value = 1

Table S208.  Gene #21: 'FAT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
FAT1 MUTATED 0 3 1 2 3 3 3
FAT1 WILD-TYPE 24 10 12 12 24 14 19
'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0884 (Fisher's exact test), Q value = 1

Table S209.  Gene #21: 'FAT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
FAT1 MUTATED 0 10 5
FAT1 WILD-TYPE 24 50 41
'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0737 (Fisher's exact test), Q value = 1

Table S210.  Gene #21: 'FAT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
FAT1 MUTATED 0 12 3
FAT1 WILD-TYPE 23 62 30
'MLL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.845 (Fisher's exact test), Q value = 1

Table S211.  Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
MLL MUTATED 3 6 8
MLL WILD-TYPE 28 36 46
'MLL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.984 (Fisher's exact test), Q value = 1

Table S212.  Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
MLL MUTATED 6 4 4 4
MLL WILD-TYPE 36 26 29 21
'MLL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 1

Table S213.  Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
MLL MUTATED 5 1 7 2 0
MLL WILD-TYPE 31 27 26 3 17

Figure S17.  Get High-res Image Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'MLL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00499 (Fisher's exact test), Q value = 1

Table S214.  Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
MLL MUTATED 8 1 6 0
MLL WILD-TYPE 35 35 15 19

Figure S18.  Get High-res Image Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'MLL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.325 (Fisher's exact test), Q value = 1

Table S215.  Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
MLL MUTATED 5 5 8
MLL WILD-TYPE 49 30 32
'MLL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.532 (Fisher's exact test), Q value = 1

Table S216.  Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
MLL MUTATED 3 4 6 5
MLL WILD-TYPE 36 17 32 26
'MLL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.813 (Fisher's exact test), Q value = 1

Table S217.  Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
MLL MUTATED 5 6 7
MLL WILD-TYPE 30 46 36
'MLL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.705 (Fisher's exact test), Q value = 1

Table S218.  Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
MLL MUTATED 4 2 3 1 5 2 1
MLL WILD-TYPE 20 11 10 13 22 15 21
'MLL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.891 (Fisher's exact test), Q value = 1

Table S219.  Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
MLL MUTATED 4 8 6
MLL WILD-TYPE 20 52 40
'MLL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.881 (Fisher's exact test), Q value = 1

Table S220.  Gene #22: 'MLL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
MLL MUTATED 4 10 4
MLL WILD-TYPE 19 64 29
'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 1

Table S221.  Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
HRAS MUTATED 1 1 4
HRAS WILD-TYPE 30 41 50
'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.799 (Fisher's exact test), Q value = 1

Table S222.  Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
HRAS MUTATED 1 2 2 1
HRAS WILD-TYPE 41 28 31 24
'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 1

Table S223.  Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
HRAS MUTATED 2 0 1 2 0
HRAS WILD-TYPE 34 28 32 3 17

Figure S19.  Get High-res Image Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.339 (Fisher's exact test), Q value = 1

Table S224.  Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
HRAS MUTATED 3 0 1 1
HRAS WILD-TYPE 40 36 20 18
'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.88 (Fisher's exact test), Q value = 1

Table S225.  Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
HRAS MUTATED 2 2 2
HRAS WILD-TYPE 52 33 38
'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.439 (Fisher's exact test), Q value = 1

Table S226.  Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
HRAS MUTATED 2 0 1 3
HRAS WILD-TYPE 37 21 37 28
'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 1

Table S227.  Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
HRAS MUTATED 1 4 1
HRAS WILD-TYPE 34 48 42
'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S228.  Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
HRAS MUTATED 1 0 0 0 1 1 3
HRAS WILD-TYPE 23 13 13 14 26 16 19
'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.197 (Fisher's exact test), Q value = 1

Table S229.  Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
HRAS MUTATED 1 1 4
HRAS WILD-TYPE 23 59 42
'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.258 (Fisher's exact test), Q value = 1

Table S230.  Gene #23: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
HRAS MUTATED 1 2 3
HRAS WILD-TYPE 22 72 30
'ACRC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.281 (Fisher's exact test), Q value = 1

Table S231.  Gene #24: 'ACRC MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
ACRC MUTATED 2 0 2
ACRC WILD-TYPE 29 42 52
'ACRC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 1

Table S232.  Gene #24: 'ACRC MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
ACRC MUTATED 0 1 3 0
ACRC WILD-TYPE 42 29 30 25
'ACRC MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S233.  Gene #24: 'ACRC MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
ACRC MUTATED 1 1 2 0 0
ACRC WILD-TYPE 35 27 31 5 17
'ACRC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.76 (Fisher's exact test), Q value = 1

Table S234.  Gene #24: 'ACRC MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
ACRC MUTATED 1 2 1 0
ACRC WILD-TYPE 42 34 20 19
'ACRC MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S235.  Gene #24: 'ACRC MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
ACRC MUTATED 2 1 1
ACRC WILD-TYPE 52 34 39
'ACRC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.912 (Fisher's exact test), Q value = 1

Table S236.  Gene #24: 'ACRC MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
ACRC MUTATED 2 0 1 1
ACRC WILD-TYPE 37 21 37 30
'ACRC MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S237.  Gene #24: 'ACRC MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
ACRC MUTATED 1 2 1
ACRC WILD-TYPE 34 50 42
'ACRC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.87 (Fisher's exact test), Q value = 1

Table S238.  Gene #24: 'ACRC MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
ACRC MUTATED 1 0 1 0 1 1 0
ACRC WILD-TYPE 23 13 12 14 26 16 22
'ACRC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S239.  Gene #24: 'ACRC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
ACRC MUTATED 1 2 1
ACRC WILD-TYPE 23 58 45
'ACRC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.812 (Fisher's exact test), Q value = 1

Table S240.  Gene #24: 'ACRC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
ACRC MUTATED 1 2 1
ACRC WILD-TYPE 22 72 32
'TXNIP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.588 (Fisher's exact test), Q value = 1

Table S241.  Gene #25: 'TXNIP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
TXNIP MUTATED 1 2 5
TXNIP WILD-TYPE 30 40 49
'TXNIP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.274 (Fisher's exact test), Q value = 1

Table S242.  Gene #25: 'TXNIP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
TXNIP MUTATED 3 0 4 2
TXNIP WILD-TYPE 39 30 29 23
'TXNIP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.872 (Fisher's exact test), Q value = 1

Table S243.  Gene #25: 'TXNIP MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
TXNIP MUTATED 2 2 4 0 1
TXNIP WILD-TYPE 34 26 29 5 16
'TXNIP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.703 (Fisher's exact test), Q value = 1

Table S244.  Gene #25: 'TXNIP MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
TXNIP MUTATED 3 2 3 1
TXNIP WILD-TYPE 40 34 18 18
'TXNIP MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S245.  Gene #25: 'TXNIP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
TXNIP MUTATED 4 2 3
TXNIP WILD-TYPE 50 33 37
'TXNIP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0801 (Fisher's exact test), Q value = 1

Table S246.  Gene #25: 'TXNIP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
TXNIP MUTATED 1 0 6 2
TXNIP WILD-TYPE 38 21 32 29
'TXNIP MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S247.  Gene #25: 'TXNIP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
TXNIP MUTATED 3 3 3
TXNIP WILD-TYPE 32 49 40
'TXNIP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.983 (Fisher's exact test), Q value = 1

Table S248.  Gene #25: 'TXNIP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
TXNIP MUTATED 2 1 1 0 2 1 2
TXNIP WILD-TYPE 22 12 12 14 25 16 20
'TXNIP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.732 (Fisher's exact test), Q value = 1

Table S249.  Gene #25: 'TXNIP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
TXNIP MUTATED 2 5 2
TXNIP WILD-TYPE 22 55 44
'TXNIP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.897 (Fisher's exact test), Q value = 1

Table S250.  Gene #25: 'TXNIP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
TXNIP MUTATED 2 5 2
TXNIP WILD-TYPE 21 69 31
'ECM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0794 (Fisher's exact test), Q value = 1

Table S251.  Gene #26: 'ECM1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
ECM1 MUTATED 2 3 0
ECM1 WILD-TYPE 29 39 54
'ECM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S252.  Gene #26: 'ECM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
ECM1 MUTATED 3 2 0 0
ECM1 WILD-TYPE 39 28 33 25
'ECM1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S253.  Gene #26: 'ECM1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
ECM1 MUTATED 2 1 2 0 0
ECM1 WILD-TYPE 34 27 31 5 17
'ECM1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.181 (Fisher's exact test), Q value = 1

Table S254.  Gene #26: 'ECM1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
ECM1 MUTATED 1 4 0 0
ECM1 WILD-TYPE 42 32 21 19
'ECM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.733 (Fisher's exact test), Q value = 1

Table S255.  Gene #26: 'ECM1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
ECM1 MUTATED 2 2 1
ECM1 WILD-TYPE 52 33 39
'ECM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.55 (Fisher's exact test), Q value = 1

Table S256.  Gene #26: 'ECM1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
ECM1 MUTATED 1 2 1 1
ECM1 WILD-TYPE 38 19 37 30
'ECM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.52 (Fisher's exact test), Q value = 1

Table S257.  Gene #26: 'ECM1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
ECM1 MUTATED 1 1 3
ECM1 WILD-TYPE 34 51 40
'ECM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.186 (Fisher's exact test), Q value = 1

Table S258.  Gene #26: 'ECM1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
ECM1 MUTATED 0 1 1 0 3 0 0
ECM1 WILD-TYPE 24 12 12 14 24 17 22
'ECM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.416 (Fisher's exact test), Q value = 1

Table S259.  Gene #26: 'ECM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
ECM1 MUTATED 0 4 1
ECM1 WILD-TYPE 24 56 45
'ECM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.698 (Fisher's exact test), Q value = 1

Table S260.  Gene #26: 'ECM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
ECM1 MUTATED 0 3 2
ECM1 WILD-TYPE 23 71 31
'KLF5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0917 (Fisher's exact test), Q value = 1

Table S261.  Gene #27: 'KLF5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
KLF5 MUTATED 0 3 7
KLF5 WILD-TYPE 31 39 47
'KLF5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.778 (Fisher's exact test), Q value = 1

Table S262.  Gene #27: 'KLF5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
KLF5 MUTATED 3 2 4 1
KLF5 WILD-TYPE 39 28 29 24
'KLF5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.303 (Fisher's exact test), Q value = 1

Table S263.  Gene #27: 'KLF5 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
KLF5 MUTATED 4 1 4 1 0
KLF5 WILD-TYPE 32 27 29 4 17
'KLF5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.31 (Fisher's exact test), Q value = 1

Table S264.  Gene #27: 'KLF5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
KLF5 MUTATED 6 2 2 0
KLF5 WILD-TYPE 37 34 19 19
'KLF5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.915 (Fisher's exact test), Q value = 1

Table S265.  Gene #27: 'KLF5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
KLF5 MUTATED 5 2 3
KLF5 WILD-TYPE 49 33 37
'KLF5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.679 (Fisher's exact test), Q value = 1

Table S266.  Gene #27: 'KLF5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
KLF5 MUTATED 3 3 2 2
KLF5 WILD-TYPE 36 18 36 29
'KLF5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.706 (Fisher's exact test), Q value = 1

Table S267.  Gene #27: 'KLF5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
KLF5 MUTATED 3 5 2
KLF5 WILD-TYPE 32 47 41
'KLF5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.23 (Fisher's exact test), Q value = 1

Table S268.  Gene #27: 'KLF5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
KLF5 MUTATED 3 0 3 0 2 0 2
KLF5 WILD-TYPE 21 13 10 14 25 17 20
'KLF5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.192 (Fisher's exact test), Q value = 1

Table S269.  Gene #27: 'KLF5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
KLF5 MUTATED 3 2 5
KLF5 WILD-TYPE 21 58 41
'KLF5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0234 (Fisher's exact test), Q value = 1

Table S270.  Gene #27: 'KLF5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
KLF5 MUTATED 3 2 5
KLF5 WILD-TYPE 20 72 28

Figure S20.  Get High-res Image Gene #27: 'KLF5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RBM26 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.619 (Fisher's exact test), Q value = 1

Table S271.  Gene #28: 'RBM26 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
RBM26 MUTATED 1 3 5
RBM26 WILD-TYPE 30 39 49
'RBM26 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.964 (Fisher's exact test), Q value = 1

Table S272.  Gene #28: 'RBM26 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
RBM26 MUTATED 3 2 3 1
RBM26 WILD-TYPE 39 28 30 24
'RBM26 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.255 (Fisher's exact test), Q value = 1

Table S273.  Gene #28: 'RBM26 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
RBM26 MUTATED 1 2 5 0 0
RBM26 WILD-TYPE 35 26 28 5 17
'RBM26 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.725 (Fisher's exact test), Q value = 1

Table S274.  Gene #28: 'RBM26 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
RBM26 MUTATED 3 3 2 0
RBM26 WILD-TYPE 40 33 19 19
'RBM26 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S275.  Gene #28: 'RBM26 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
RBM26 MUTATED 2 4 3
RBM26 WILD-TYPE 52 31 37
'RBM26 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.566 (Fisher's exact test), Q value = 1

Table S276.  Gene #28: 'RBM26 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
RBM26 MUTATED 1 2 3 3
RBM26 WILD-TYPE 38 19 35 28
'RBM26 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0938 (Fisher's exact test), Q value = 1

Table S277.  Gene #28: 'RBM26 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
RBM26 MUTATED 0 6 3
RBM26 WILD-TYPE 35 46 40
'RBM26 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.288 (Fisher's exact test), Q value = 1

Table S278.  Gene #28: 'RBM26 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
RBM26 MUTATED 0 0 2 0 3 2 2
RBM26 WILD-TYPE 24 13 11 14 24 15 20
'RBM26 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.389 (Fisher's exact test), Q value = 1

Table S279.  Gene #28: 'RBM26 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
RBM26 MUTATED 0 5 4
RBM26 WILD-TYPE 24 55 42
'RBM26 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.246 (Fisher's exact test), Q value = 1

Table S280.  Gene #28: 'RBM26 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
RBM26 MUTATED 0 5 4
RBM26 WILD-TYPE 23 69 29
'RAD51C MUTATION STATUS' versus 'CN_CNMF'

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

Table S281.  Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
RAD51C MUTATED 1 1 2
RAD51C WILD-TYPE 30 41 52
'RAD51C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.165 (Fisher's exact test), Q value = 1

Table S282.  Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
RAD51C MUTATED 0 2 2 0
RAD51C WILD-TYPE 42 28 31 25
'RAD51C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 1

Table S283.  Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
RAD51C MUTATED 1 0 2 1 0
RAD51C WILD-TYPE 35 28 31 4 17
'RAD51C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S284.  Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
RAD51C MUTATED 2 1 1 0
RAD51C WILD-TYPE 41 35 20 19
'RAD51C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 1

Table S285.  Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
RAD51C MUTATED 0 3 1
RAD51C WILD-TYPE 54 32 39

Figure S21.  Get High-res Image Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'RAD51C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.21 (Fisher's exact test), Q value = 1

Table S286.  Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
RAD51C MUTATED 0 0 3 1
RAD51C WILD-TYPE 39 21 35 30
'RAD51C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 1

Table S287.  Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
RAD51C MUTATED 1 0 3
RAD51C WILD-TYPE 34 52 40
'RAD51C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.449 (Fisher's exact test), Q value = 1

Table S288.  Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
RAD51C MUTATED 0 1 0 0 2 1 0
RAD51C WILD-TYPE 24 12 13 14 25 16 22
'RAD51C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 1

Table S289.  Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
RAD51C MUTATED 0 4 0
RAD51C WILD-TYPE 24 56 46
'RAD51C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.375 (Fisher's exact test), Q value = 1

Table S290.  Gene #29: 'RAD51C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
RAD51C MUTATED 0 4 0
RAD51C WILD-TYPE 23 70 33
'CEP192 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.85 (Fisher's exact test), Q value = 1

Table S291.  Gene #30: 'CEP192 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
CEP192 MUTATED 1 1 3
CEP192 WILD-TYPE 30 41 51
'CEP192 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.725 (Fisher's exact test), Q value = 1

Table S292.  Gene #30: 'CEP192 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
CEP192 MUTATED 2 2 1 0
CEP192 WILD-TYPE 40 28 32 25
'CEP192 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.895 (Fisher's exact test), Q value = 1

Table S293.  Gene #30: 'CEP192 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
CEP192 MUTATED 1 1 2 0 1
CEP192 WILD-TYPE 35 27 31 5 16
'CEP192 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.696 (Fisher's exact test), Q value = 1

Table S294.  Gene #30: 'CEP192 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
CEP192 MUTATED 3 1 0 1
CEP192 WILD-TYPE 40 35 21 18
'CEP192 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.733 (Fisher's exact test), Q value = 1

Table S295.  Gene #30: 'CEP192 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
CEP192 MUTATED 2 2 1
CEP192 WILD-TYPE 52 33 39
'CEP192 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.587 (Fisher's exact test), Q value = 1

Table S296.  Gene #30: 'CEP192 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
CEP192 MUTATED 1 0 3 1
CEP192 WILD-TYPE 38 21 35 30
'CEP192 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.734 (Fisher's exact test), Q value = 1

Table S297.  Gene #30: 'CEP192 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
CEP192 MUTATED 1 3 1
CEP192 WILD-TYPE 34 49 42
'CEP192 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0615 (Fisher's exact test), Q value = 1

Table S298.  Gene #30: 'CEP192 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
CEP192 MUTATED 0 1 2 1 0 1 0
CEP192 WILD-TYPE 24 12 11 13 27 16 22
'CEP192 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.591 (Fisher's exact test), Q value = 1

Table S299.  Gene #30: 'CEP192 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
CEP192 MUTATED 0 2 3
CEP192 WILD-TYPE 24 58 43
'CEP192 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.699 (Fisher's exact test), Q value = 1

Table S300.  Gene #30: 'CEP192 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
CEP192 MUTATED 0 3 2
CEP192 WILD-TYPE 23 71 31
'ASXL2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S301.  Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
ASXL2 MUTATED 3 0 6
ASXL2 WILD-TYPE 28 42 48

Figure S22.  Get High-res Image Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ASXL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.508 (Fisher's exact test), Q value = 1

Table S302.  Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
ASXL2 MUTATED 1 3 3 2
ASXL2 WILD-TYPE 41 27 30 23
'ASXL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 1

Table S303.  Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
ASXL2 MUTATED 4 1 3 1 0
ASXL2 WILD-TYPE 32 27 30 4 17
'ASXL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.365 (Fisher's exact test), Q value = 1

Table S304.  Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
ASXL2 MUTATED 4 2 3 0
ASXL2 WILD-TYPE 39 34 18 19
'ASXL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.25 (Fisher's exact test), Q value = 1

Table S305.  Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
ASXL2 MUTATED 3 1 5
ASXL2 WILD-TYPE 51 34 35
'ASXL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.817 (Fisher's exact test), Q value = 1

Table S306.  Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
ASXL2 MUTATED 2 1 4 2
ASXL2 WILD-TYPE 37 20 34 29
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.91 (Fisher's exact test), Q value = 1

Table S307.  Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
ASXL2 MUTATED 3 3 3
ASXL2 WILD-TYPE 32 49 40
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.399 (Fisher's exact test), Q value = 1

Table S308.  Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
ASXL2 MUTATED 3 0 2 0 3 0 1
ASXL2 WILD-TYPE 21 13 11 14 24 17 21
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.484 (Fisher's exact test), Q value = 1

Table S309.  Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
ASXL2 MUTATED 3 3 3
ASXL2 WILD-TYPE 21 57 43
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.454 (Fisher's exact test), Q value = 1

Table S310.  Gene #31: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
ASXL2 MUTATED 3 4 2
ASXL2 WILD-TYPE 20 70 31
'PSIP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.371 (Fisher's exact test), Q value = 1

Table S311.  Gene #32: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
PSIP1 MUTATED 1 1 5
PSIP1 WILD-TYPE 30 41 49
'PSIP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.625 (Fisher's exact test), Q value = 1

Table S312.  Gene #32: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
PSIP1 MUTATED 1 2 3 1
PSIP1 WILD-TYPE 41 28 30 24
'PSIP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.138 (Fisher's exact test), Q value = 1

Table S313.  Gene #32: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
PSIP1 MUTATED 3 2 0 1 0
PSIP1 WILD-TYPE 33 26 33 4 17
'PSIP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.385 (Fisher's exact test), Q value = 1

Table S314.  Gene #32: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
PSIP1 MUTATED 4 2 0 0
PSIP1 WILD-TYPE 39 34 21 19
'PSIP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.884 (Fisher's exact test), Q value = 1

Table S315.  Gene #32: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
PSIP1 MUTATED 4 1 2
PSIP1 WILD-TYPE 50 34 38
'PSIP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.509 (Fisher's exact test), Q value = 1

Table S316.  Gene #32: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
PSIP1 MUTATED 4 1 1 1
PSIP1 WILD-TYPE 35 20 37 30
'PSIP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 1

Table S317.  Gene #32: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
PSIP1 MUTATED 3 3 1
PSIP1 WILD-TYPE 32 49 42
'PSIP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.847 (Fisher's exact test), Q value = 1

Table S318.  Gene #32: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
PSIP1 MUTATED 2 1 0 1 1 0 2
PSIP1 WILD-TYPE 22 12 13 13 26 17 20
'PSIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.536 (Fisher's exact test), Q value = 1

Table S319.  Gene #32: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
PSIP1 MUTATED 1 2 4
PSIP1 WILD-TYPE 23 58 42
'PSIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S320.  Gene #32: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
PSIP1 MUTATED 2 2 3
PSIP1 WILD-TYPE 21 72 30
'ZNF513 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.16 (Fisher's exact test), Q value = 1

Table S321.  Gene #33: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
ZNF513 MUTATED 4 1 2
ZNF513 WILD-TYPE 27 41 52
'ZNF513 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S322.  Gene #33: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
ZNF513 MUTATED 2 3 1 1
ZNF513 WILD-TYPE 40 27 32 24
'ZNF513 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.206 (Fisher's exact test), Q value = 1

Table S323.  Gene #33: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
ZNF513 MUTATED 3 0 1 1 1
ZNF513 WILD-TYPE 33 28 32 4 16
'ZNF513 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.414 (Fisher's exact test), Q value = 1

Table S324.  Gene #33: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
ZNF513 MUTATED 4 1 0 1
ZNF513 WILD-TYPE 39 35 21 18
'ZNF513 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.48 (Fisher's exact test), Q value = 1

Table S325.  Gene #33: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
ZNF513 MUTATED 3 3 1
ZNF513 WILD-TYPE 51 32 39
'ZNF513 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.335 (Fisher's exact test), Q value = 1

Table S326.  Gene #33: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
ZNF513 MUTATED 2 2 3 0
ZNF513 WILD-TYPE 37 19 35 31
'ZNF513 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.89 (Fisher's exact test), Q value = 1

Table S327.  Gene #33: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
ZNF513 MUTATED 2 2 3
ZNF513 WILD-TYPE 33 50 40
'ZNF513 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.761 (Fisher's exact test), Q value = 1

Table S328.  Gene #33: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
ZNF513 MUTATED 1 1 1 0 3 0 1
ZNF513 WILD-TYPE 23 12 12 14 24 17 21
'ZNF513 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S329.  Gene #33: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
ZNF513 MUTATED 1 3 3
ZNF513 WILD-TYPE 23 57 43
'ZNF513 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S330.  Gene #33: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
ZNF513 MUTATED 1 4 2
ZNF513 WILD-TYPE 22 70 31
'FOXA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.611 (Fisher's exact test), Q value = 1

Table S331.  Gene #34: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
FOXA1 MUTATED 2 1 4
FOXA1 WILD-TYPE 29 41 50
'FOXA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.91 (Fisher's exact test), Q value = 1

Table S332.  Gene #34: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
FOXA1 MUTATED 3 2 1 1
FOXA1 WILD-TYPE 39 28 32 24
'FOXA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.539 (Fisher's exact test), Q value = 1

Table S333.  Gene #34: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
FOXA1 MUTATED 2 2 1 1 1
FOXA1 WILD-TYPE 34 26 32 4 16
'FOXA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.694 (Fisher's exact test), Q value = 1

Table S334.  Gene #34: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
FOXA1 MUTATED 4 2 1 0
FOXA1 WILD-TYPE 39 34 20 19
'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S335.  Gene #34: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
FOXA1 MUTATED 2 4 1
FOXA1 WILD-TYPE 52 31 39
'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.908 (Fisher's exact test), Q value = 1

Table S336.  Gene #34: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
FOXA1 MUTATED 2 1 3 1
FOXA1 WILD-TYPE 37 20 35 30
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.888 (Fisher's exact test), Q value = 1

Table S337.  Gene #34: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
FOXA1 MUTATED 2 2 3
FOXA1 WILD-TYPE 33 50 40
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.647 (Fisher's exact test), Q value = 1

Table S338.  Gene #34: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
FOXA1 MUTATED 2 0 0 2 2 0 1
FOXA1 WILD-TYPE 22 13 13 12 25 17 21
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.675 (Fisher's exact test), Q value = 1

Table S339.  Gene #34: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
FOXA1 MUTATED 2 2 3
FOXA1 WILD-TYPE 22 58 43
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.661 (Fisher's exact test), Q value = 1

Table S340.  Gene #34: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
FOXA1 MUTATED 2 3 2
FOXA1 WILD-TYPE 21 71 31
'TRIP11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.822 (Fisher's exact test), Q value = 1

Table S341.  Gene #35: 'TRIP11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 42 54
TRIP11 MUTATED 1 2 1
TRIP11 WILD-TYPE 30 40 53
'TRIP11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.531 (Fisher's exact test), Q value = 1

Table S342.  Gene #35: 'TRIP11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 33 25
TRIP11 MUTATED 2 2 0 1
TRIP11 WILD-TYPE 40 28 33 24
'TRIP11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.804 (Fisher's exact test), Q value = 1

Table S343.  Gene #35: 'TRIP11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 28 33 5 17
TRIP11 MUTATED 1 2 1 0 1
TRIP11 WILD-TYPE 35 26 32 5 16
'TRIP11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.288 (Fisher's exact test), Q value = 1

Table S344.  Gene #35: 'TRIP11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 36 21 19
TRIP11 MUTATED 4 1 0 0
TRIP11 WILD-TYPE 39 35 21 19
'TRIP11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.731 (Fisher's exact test), Q value = 1

Table S345.  Gene #35: 'TRIP11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 35 40
TRIP11 MUTATED 2 2 1
TRIP11 WILD-TYPE 52 33 39
'TRIP11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S346.  Gene #35: 'TRIP11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 21 38 31
TRIP11 MUTATED 2 0 2 1
TRIP11 WILD-TYPE 37 21 36 30
'TRIP11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.316 (Fisher's exact test), Q value = 1

Table S347.  Gene #35: 'TRIP11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 52 43
TRIP11 MUTATED 3 1 1
TRIP11 WILD-TYPE 32 51 42
'TRIP11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0933 (Fisher's exact test), Q value = 1

Table S348.  Gene #35: 'TRIP11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 24 13 13 14 27 17 22
TRIP11 MUTATED 2 1 0 2 0 0 0
TRIP11 WILD-TYPE 22 12 13 12 27 17 22
'TRIP11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.34 (Fisher's exact test), Q value = 1

Table S349.  Gene #35: 'TRIP11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 24 60 46
TRIP11 MUTATED 1 1 3
TRIP11 WILD-TYPE 23 59 43
'TRIP11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.368 (Fisher's exact test), Q value = 1

Table S350.  Gene #35: 'TRIP11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 74 33
TRIP11 MUTATED 2 2 1
TRIP11 WILD-TYPE 21 72 32
Methods & Data
Input
  • Mutation data file = transformed.cor.cli.txt

  • Molecular subtypes file = BLCA-TP.transferedmergedcluster.txt

  • Number of patients = 130

  • Number of significantly mutated genes = 35

  • Number of Molecular subtypes = 10

  • 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)