Correlation between gene mutation status and molecular subtypes
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C19886C2
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C19886C2
Overview
Introduction

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

Summary

Testing the association between mutation status of 36 genes and 10 molecular subtypes across 48 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 36 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
B2M 10 (21%) 38 0.032
(0.54) 		0.154
(0.852) 		0.513
(0.963) 		0.86
(1.00) 		0.0851
(0.666) 		0.159
(0.869) 		0.378
(0.895) 		0.456
(0.928) 		0.208
(0.895) 		0.698
(1.00)
MYD88 3 (6%) 45 0.759
(1.00) 		0.329
(0.895) 		0.0711
(0.659) 		0.77
(1.00) 		0.389
(0.895) 		0.0238
(0.506) 		0.303
(0.895) 		0.85
(1.00) 		0.0823
(0.659) 		0.231
(0.895)
MLL2 14 (29%) 34 0.0281
(0.506) 		0.0614
(0.659) 		0.56
(0.984) 		0.893
(1.00) 		0.549
(0.983) 		0.812
(1.00) 		0.922
(1.00) 		0.81
(1.00) 		0.66
(1.00) 		0.0524
(0.614)
HLA-C 7 (15%) 41 0.132
(0.81) 		0.505
(0.963) 		0.874
(1.00) 		0.825
(1.00) 		0.954
(1.00) 		0.521
(0.964) 		0.183
(0.895) 		0.208
(0.895) 		0.378
(0.895) 		0.149
(0.852)
ZNF814 7 (15%) 41 0.331
(0.895) 		0.652
(1.00) 		0.0164
(0.506) 		0.276
(0.895) 		0.203
(0.895) 		0.0122
(0.506) 		0.268
(0.895) 		0.00476
(0.506) 		0.183
(0.895) 		0.0252
(0.506)
CD79B 5 (10%) 43 0.345
(0.895) 		0.428
(0.924) 		0.417
(0.924) 		0.0771
(0.659) 		0.264
(0.895) 		0.511
(0.963) 		0.181
(0.895) 		0.523
(0.964) 		0.0814
(0.659) 		0.0377
(0.54)
TP53 5 (10%) 43 0.342
(0.895) 		0.135
(0.81) 		0.0261
(0.506) 		0.365
(0.895) 		0.345
(0.895) 		0.402
(0.899) 		0.311
(0.895) 		0.198
(0.895)
TNFAIP3 7 (15%) 41 0.28
(0.895) 		0.508
(0.963) 		0.0788
(0.659) 		0.439
(0.924) 		0.507
(0.963) 		0.709
(1.00) 		0.0775
(0.659) 		0.567
(0.991) 		0.656
(1.00) 		0.279
(0.895)
TMSB4X 6 (12%) 42 0.0556
(0.625) 		0.198
(0.895) 		0.229
(0.895) 		0.56
(0.984) 		0.49
(0.963) 		0.624
(1.00) 		0.86
(1.00) 		0.632
(1.00) 		0.154
(0.852) 		0.927
(1.00)
APLF 3 (6%) 45 0.119
(0.779) 		0.189
(0.895) 		0.39
(0.895) 		0.443
(0.924)
RHPN2 7 (15%) 41 0.748
(1.00) 		0.131
(0.81) 		0.395
(0.895) 		0.275
(0.895) 		0.379
(0.895) 		0.354
(0.895) 		0.86
(1.00) 		0.34
(0.895) 		0.289
(0.895) 		0.299
(0.895)
CIITA 5 (10%) 43 0.272
(0.895) 		0.238
(0.895) 		0.961
(1.00) 		1
(1.00) 		0.28
(0.895) 		0.231
(0.895) 		0.304
(0.895) 		0.389
(0.895) 		0.335
(0.895) 		0.605
(1.00)
KDR 4 (8%) 44 0.645
(1.00) 		0.739
(1.00) 		0.835
(1.00) 		0.802
(1.00) 		1
(1.00) 		0.623
(1.00) 		0.686
(1.00) 		0.316
(0.895)
CARD11 10 (21%) 38 1
(1.00) 		0.55
(0.983) 		0.62
(1.00) 		0.439
(0.924) 		0.463
(0.934) 		0.426
(0.924) 		0.894
(1.00) 		0.362
(0.895) 		0.134
(0.81) 		0.77
(1.00)
EZH2 3 (6%) 45 0.271
(0.895) 		0.742
(1.00) 		0.0966
(0.69) 		0.444
(0.924) 		0.0976
(0.69) 		0.0254
(0.506) 		0.682
(1.00) 		0.726
(1.00)
NFKBIE 4 (8%) 44 1
(1.00) 		0.0643
(0.659) 		0.893
(1.00) 		0.804
(1.00) 		0.302
(0.895) 		0.261
(0.895) 		0.348
(0.895) 		0.796
(1.00)
MLH1 3 (6%) 45 0.117
(0.779) 		1
(1.00) 		0.237
(0.895) 		0.442
(0.924)
FAS 5 (10%) 43 1
(1.00) 		0.34
(0.895) 		0.0141
(0.506) 		0.394
(0.895) 		0.595
(1.00) 		1
(1.00) 		0.658
(1.00) 		0.514
(0.963)
ENOX1 4 (8%) 44 0.365
(0.895) 		1
(1.00) 		0.394
(0.895) 		0.277
(0.895) 		0.616
(1.00) 		1
(1.00) 		1
(1.00) 		0.261
(0.895) 		0.175
(0.895) 		0.724
(1.00)
SGK1 4 (8%) 44 0.0755
(0.659) 		0.00079
(0.284) 		0.102
(0.709) 		0.302
(0.895) 		0.762
(1.00) 		0.51
(0.963) 		0.604
(1.00) 		0.151
(0.852)
IFITM3 3 (6%) 45 0.757
(1.00) 		0.0469
(0.603) 		0.54
(0.977) 		1
(1.00) 		0.0969
(0.69) 		0.592
(1.00) 		0.602
(1.00) 		0.724
(1.00)
APOB 3 (6%) 45 0.268
(0.895) 		0.274
(0.895) 		0.834
(1.00) 		0.854
(1.00) 		0.764
(1.00) 		0.92
(1.00) 		1
(1.00) 		0.516
(0.963)
MCM8 3 (6%) 45 0.271
(0.895) 		0.554
(0.983) 		0.835
(1.00) 		1
(1.00) 		0.762
(1.00) 		0.3
(0.895) 		0.683
(1.00) 		0.854
(1.00)
ARID1A 5 (10%) 43 0.69
(1.00) 		0.782
(1.00) 		0.482
(0.959) 		0.468
(0.937) 		0.597
(1.00) 		0.885
(1.00) 		0.345
(0.895) 		0.799
(1.00)
PCDHA10 6 (12%) 42 0.0803
(0.659) 		0.0101
(0.506) 		0.227
(0.895) 		0.374
(0.895) 		0.86
(1.00) 		0.661
(1.00) 		0.319
(0.895) 		0.864
(1.00)
LRRC16B 4 (8%) 44 0.0036
(0.506) 		0.0186
(0.506) 		0.169
(0.895) 		0.306
(0.895) 		0.762
(1.00) 		0.0178
(0.506) 		0.605
(1.00) 		0.443
(0.924)
PNPLA7 3 (6%) 45 0.27
(0.895) 		0.744
(1.00) 		0.393
(0.895) 		1
(1.00) 		0.238
(0.895) 		0.438
(0.924) 		0.763
(1.00) 		0.132
(0.81) 		1
(1.00) 		1
(1.00)
SLC16A8 3 (6%) 45 0.0263
(0.506) 		0.27
(0.895) 		0.0975
(0.69) 		0.443
(0.924) 		0.0977
(0.69) 		0.0256
(0.506) 		0.682
(1.00) 		0.726
(1.00)
PKHD1L1 5 (10%) 43 0.0528
(0.614) 		0.0359
(0.54) 		0.105
(0.71) 		0.916
(1.00) 		0.0715
(0.659) 		0.00863
(0.506) 		0.0403
(0.54) 		0.797
(1.00)
HRCT1 4 (8%) 44 0.361
(0.895) 		0.242
(0.895) 		0.392
(0.895) 		0.275
(0.895) 		0.537
(0.977) 		0.803
(1.00) 		0.526
(0.964) 		0.0628
(0.659) 		0.311
(0.895) 		0.402
(0.899)
TYRO3 4 (8%) 44 0.148
(0.852) 		0.898
(1.00) 		0.629
(1.00) 		0.503
(0.963) 		0.454
(0.928) 		0.455
(0.928) 		1
(1.00) 		0.0352
(0.54) 		1
(1.00) 		0.895
(1.00)
GSTZ1 3 (6%) 45 0.0268
(0.506) 		0.0491
(0.609) 		0.513
(0.963) 		0.444
(0.924) 		0.761
(1.00) 		0.302
(0.895) 		1
(1.00) 		1
(1.00)
STAT3 7 (15%) 41 0.746
(1.00) 		0.253
(0.895) 		0.552
(0.983) 		1
(1.00) 		0.339
(0.895) 		0.494
(0.963) 		0.0362
(0.54) 		0.0163
(0.506) 		0.0405
(0.54) 		0.229
(0.895)
IRF8 5 (10%) 43 0.275
(0.895) 		0.236
(0.895) 		0.296
(0.895) 		0.387
(0.895) 		0.239
(0.895) 		0.658
(1.00) 		1
(1.00) 		0.343
(0.895) 		0.602
(1.00) 		0.727
(1.00)
TMEM30A 4 (8%) 44 0.0747
(0.659) 		0.898
(1.00) 		0.394
(0.895) 		0.275
(0.895) 		0.691
(1.00) 		1
(1.00) 		0.678
(1.00) 		0.259
(0.895) 		1
(1.00) 		0.724
(1.00)
UBE2A 4 (8%) 44 0.365
(0.895) 		0.381
(0.895) 		0.961
(1.00) 		1
(1.00) 		0.464
(0.934) 		0.303
(0.895) 		0.528
(0.964) 		0.0102
(0.506) 		0.312
(0.895) 		0.453
(0.928)
'B2M MUTATION STATUS' versus 'CN_CNMF'

P value = 0.032 (Fisher's exact test), Q value = 0.54

Table S1.  Gene #1: 'B2M MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
B2M MUTATED 7 2 1
B2M WILD-TYPE 13 5 20

Figure S1.  Get High-res Image Gene #1: 'B2M MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'B2M MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.154 (Fisher's exact test), Q value = 0.85

Table S2.  Gene #1: 'B2M MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
B2M MUTATED 4 1 3 2
B2M WILD-TYPE 5 12 16 5
'B2M MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.513 (Fisher's exact test), Q value = 0.96

Table S3.  Gene #1: 'B2M MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 5 5 6 6 5
B2M MUTATED 0 1 1 1 3 1
B2M WILD-TYPE 6 4 4 5 3 4
'B2M MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.86 (Fisher's exact test), Q value = 1

Table S4.  Gene #1: 'B2M MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 15 12
B2M MUTATED 1 4 2
B2M WILD-TYPE 5 11 10
'B2M MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0851 (Fisher's exact test), Q value = 0.67

Table S5.  Gene #1: 'B2M MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
B2M MUTATED 4 0 1 0 3 2
B2M WILD-TYPE 6 12 8 3 5 4
'B2M MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.159 (Fisher's exact test), Q value = 0.87

Table S6.  Gene #1: 'B2M MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
B2M MUTATED 6 0 1 3
B2M WILD-TYPE 16 11 6 5
'B2M MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 0.9

Table S7.  Gene #1: 'B2M MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
B2M MUTATED 4 4 1
B2M WILD-TYPE 12 12 14
'B2M MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.456 (Fisher's exact test), Q value = 0.93

Table S8.  Gene #1: 'B2M MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
B2M MUTATED 1 2 1 2 3
B2M WILD-TYPE 8 10 7 10 3
'B2M MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.208 (Fisher's exact test), Q value = 0.9

Table S9.  Gene #1: 'B2M MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
B2M MUTATED 1 2 0 5
B2M WILD-TYPE 8 8 9 9
'B2M MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.698 (Fisher's exact test), Q value = 1

Table S10.  Gene #1: 'B2M MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
B2M MUTATED 1 3 0 4
B2M WILD-TYPE 7 12 5 10
'MYD88 MUTATION STATUS' versus 'CN_CNMF'

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

Table S11.  Gene #2: 'MYD88 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
MYD88 MUTATED 2 0 1
MYD88 WILD-TYPE 18 7 20
'MYD88 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.329 (Fisher's exact test), Q value = 0.9

Table S12.  Gene #2: 'MYD88 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
MYD88 MUTATED 0 0 3 0
MYD88 WILD-TYPE 9 13 16 7
'MYD88 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0711 (Fisher's exact test), Q value = 0.66

Table S13.  Gene #2: 'MYD88 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 5 5 6 6 5
MYD88 MUTATED 0 1 0 0 0 2
MYD88 WILD-TYPE 6 4 5 6 6 3
'MYD88 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S14.  Gene #2: 'MYD88 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 15 12
MYD88 MUTATED 1 1 1
MYD88 WILD-TYPE 5 14 11
'MYD88 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.389 (Fisher's exact test), Q value = 0.9

Table S15.  Gene #2: 'MYD88 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
MYD88 MUTATED 1 0 2 0 0 0
MYD88 WILD-TYPE 9 12 7 3 8 6
'MYD88 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0238 (Fisher's exact test), Q value = 0.51

Table S16.  Gene #2: 'MYD88 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
MYD88 MUTATED 0 0 2 1
MYD88 WILD-TYPE 22 11 5 7

Figure S2.  Get High-res Image Gene #2: 'MYD88 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'MYD88 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.303 (Fisher's exact test), Q value = 0.9

Table S17.  Gene #2: 'MYD88 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
MYD88 MUTATED 1 0 2
MYD88 WILD-TYPE 15 16 13
'MYD88 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.85 (Fisher's exact test), Q value = 1

Table S18.  Gene #2: 'MYD88 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
MYD88 MUTATED 1 0 1 1 0
MYD88 WILD-TYPE 8 12 7 11 6
'MYD88 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0823 (Fisher's exact test), Q value = 0.66

Table S19.  Gene #2: 'MYD88 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
MYD88 MUTATED 1 0 2 0
MYD88 WILD-TYPE 8 10 7 14
'MYD88 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.231 (Fisher's exact test), Q value = 0.9

Table S20.  Gene #2: 'MYD88 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
MYD88 MUTATED 0 0 1 2
MYD88 WILD-TYPE 8 15 4 12
'MLL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0281 (Fisher's exact test), Q value = 0.51

Table S21.  Gene #3: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
MLL2 MUTATED 2 2 10
MLL2 WILD-TYPE 18 5 11

Figure S3.  Get High-res Image Gene #3: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0614 (Fisher's exact test), Q value = 0.66

Table S22.  Gene #3: 'MLL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
MLL2 MUTATED 0 3 9 2
MLL2 WILD-TYPE 9 10 10 5
'MLL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.56 (Fisher's exact test), Q value = 0.98

Table S23.  Gene #3: 'MLL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 5 5 6 6 5
MLL2 MUTATED 3 2 2 3 2 0
MLL2 WILD-TYPE 3 3 3 3 4 5
'MLL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.893 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'MLL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 15 12
MLL2 MUTATED 2 5 5
MLL2 WILD-TYPE 4 10 7
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.549 (Fisher's exact test), Q value = 0.98

Table S25.  Gene #3: 'MLL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
MLL2 MUTATED 3 3 4 1 3 0
MLL2 WILD-TYPE 7 9 5 2 5 6
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S26.  Gene #3: 'MLL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
MLL2 MUTATED 8 3 1 2
MLL2 WILD-TYPE 14 8 6 6
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S27.  Gene #3: 'MLL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
MLL2 MUTATED 4 5 5
MLL2 WILD-TYPE 12 11 10
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.81 (Fisher's exact test), Q value = 1

Table S28.  Gene #3: 'MLL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
MLL2 MUTATED 2 3 2 4 3
MLL2 WILD-TYPE 7 9 6 8 3
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.66 (Fisher's exact test), Q value = 1

Table S29.  Gene #3: 'MLL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
MLL2 MUTATED 2 2 4 5
MLL2 WILD-TYPE 7 8 5 9
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0524 (Fisher's exact test), Q value = 0.61

Table S30.  Gene #3: 'MLL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
MLL2 MUTATED 2 2 4 5
MLL2 WILD-TYPE 6 13 1 9
'HLA-C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.132 (Fisher's exact test), Q value = 0.81

Table S31.  Gene #4: 'HLA-C MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
HLA-C MUTATED 4 2 1
HLA-C WILD-TYPE 16 5 20
'HLA-C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.505 (Fisher's exact test), Q value = 0.96

Table S32.  Gene #4: 'HLA-C MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
HLA-C MUTATED 2 3 2 0
HLA-C WILD-TYPE 7 10 17 7
'HLA-C MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S33.  Gene #4: 'HLA-C MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 5 5 6 6 5
HLA-C MUTATED 1 1 0 1 2 0
HLA-C WILD-TYPE 5 4 5 5 4 5
'HLA-C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.825 (Fisher's exact test), Q value = 1

Table S34.  Gene #4: 'HLA-C MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 15 12
HLA-C MUTATED 1 3 1
HLA-C WILD-TYPE 5 12 11
'HLA-C MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S35.  Gene #4: 'HLA-C MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
HLA-C MUTATED 1 3 1 0 1 1
HLA-C WILD-TYPE 9 9 8 3 7 5
'HLA-C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.521 (Fisher's exact test), Q value = 0.96

Table S36.  Gene #4: 'HLA-C MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
HLA-C MUTATED 3 3 0 1
HLA-C WILD-TYPE 19 8 7 7
'HLA-C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.183 (Fisher's exact test), Q value = 0.9

Table S37.  Gene #4: 'HLA-C MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
HLA-C MUTATED 1 5 1
HLA-C WILD-TYPE 15 11 14
'HLA-C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.208 (Fisher's exact test), Q value = 0.9

Table S38.  Gene #4: 'HLA-C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
HLA-C MUTATED 2 4 0 1 0
HLA-C WILD-TYPE 7 8 8 11 6
'HLA-C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 0.9

Table S39.  Gene #4: 'HLA-C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
HLA-C MUTATED 0 3 1 3
HLA-C WILD-TYPE 9 7 8 11
'HLA-C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.149 (Fisher's exact test), Q value = 0.85

Table S40.  Gene #4: 'HLA-C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
HLA-C MUTATED 0 5 1 1
HLA-C WILD-TYPE 8 10 4 13
'ZNF814 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 0.9

Table S41.  Gene #5: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
ZNF814 MUTATED 2 0 5
ZNF814 WILD-TYPE 18 7 16
'ZNF814 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.652 (Fisher's exact test), Q value = 1

Table S42.  Gene #5: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
ZNF814 MUTATED 1 3 3 0
ZNF814 WILD-TYPE 8 10 16 7
'ZNF814 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.51

Table S43.  Gene #5: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 5 5 6 6 5
ZNF814 MUTATED 0 0 0 3 0 0
ZNF814 WILD-TYPE 6 5 5 3 6 5

Figure S4.  Get High-res Image Gene #5: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'ZNF814 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.276 (Fisher's exact test), Q value = 0.9

Table S44.  Gene #5: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 15 12
ZNF814 MUTATED 0 3 0
ZNF814 WILD-TYPE 6 12 12
'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.203 (Fisher's exact test), Q value = 0.9

Table S45.  Gene #5: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
ZNF814 MUTATED 0 3 3 0 0 1
ZNF814 WILD-TYPE 10 9 6 3 8 5
'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0122 (Fisher's exact test), Q value = 0.51

Table S46.  Gene #5: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
ZNF814 MUTATED 0 3 1 3
ZNF814 WILD-TYPE 22 8 6 5

Figure S5.  Get High-res Image Gene #5: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.268 (Fisher's exact test), Q value = 0.9

Table S47.  Gene #5: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
ZNF814 MUTATED 2 1 4
ZNF814 WILD-TYPE 14 15 11
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00476 (Fisher's exact test), Q value = 0.51

Table S48.  Gene #5: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
ZNF814 MUTATED 0 1 0 6 0
ZNF814 WILD-TYPE 9 11 8 6 6

Figure S6.  Get High-res Image Gene #5: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.183 (Fisher's exact test), Q value = 0.9

Table S49.  Gene #5: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
ZNF814 MUTATED 0 2 3 1
ZNF814 WILD-TYPE 9 8 6 13
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0252 (Fisher's exact test), Q value = 0.51

Table S50.  Gene #5: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
ZNF814 MUTATED 0 4 2 0
ZNF814 WILD-TYPE 8 11 3 14

Figure S7.  Get High-res Image Gene #5: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CD79B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.345 (Fisher's exact test), Q value = 0.9

Table S51.  Gene #6: 'CD79B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
CD79B MUTATED 1 0 4
CD79B WILD-TYPE 19 7 17
'CD79B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.428 (Fisher's exact test), Q value = 0.92

Table S52.  Gene #6: 'CD79B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
CD79B MUTATED 0 1 4 0
CD79B WILD-TYPE 9 12 15 7
'CD79B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.417 (Fisher's exact test), Q value = 0.92

Table S53.  Gene #6: 'CD79B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 5 5 6 6 5
CD79B MUTATED 0 1 1 0 0 1
CD79B WILD-TYPE 6 4 4 6 6 4
'CD79B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0771 (Fisher's exact test), Q value = 0.66

Table S54.  Gene #6: 'CD79B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 15 12
CD79B MUTATED 0 0 3
CD79B WILD-TYPE 6 15 9
'CD79B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.264 (Fisher's exact test), Q value = 0.9

Table S55.  Gene #6: 'CD79B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
CD79B MUTATED 0 1 3 0 1 0
CD79B WILD-TYPE 10 11 6 3 7 6
'CD79B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.511 (Fisher's exact test), Q value = 0.96

Table S56.  Gene #6: 'CD79B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
CD79B MUTATED 2 1 0 2
CD79B WILD-TYPE 20 10 7 6
'CD79B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.181 (Fisher's exact test), Q value = 0.9

Table S57.  Gene #6: 'CD79B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
CD79B MUTATED 2 0 3
CD79B WILD-TYPE 14 16 12
'CD79B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.523 (Fisher's exact test), Q value = 0.96

Table S58.  Gene #6: 'CD79B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
CD79B MUTATED 0 1 2 2 0
CD79B WILD-TYPE 9 11 6 10 6
'CD79B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0814 (Fisher's exact test), Q value = 0.66

Table S59.  Gene #6: 'CD79B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
CD79B MUTATED 2 0 1 0
CD79B WILD-TYPE 7 10 8 14
'CD79B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0377 (Fisher's exact test), Q value = 0.54

Table S60.  Gene #6: 'CD79B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
CD79B MUTATED 2 0 1 0
CD79B WILD-TYPE 6 15 4 14

Figure S8.  Get High-res Image Gene #6: 'CD79B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.342 (Fisher's exact test), Q value = 0.9

Table S61.  Gene #7: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
TP53 MUTATED 1 0 4
TP53 WILD-TYPE 19 7 17
'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.81

Table S62.  Gene #7: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
TP53 MUTATED 0 0 3 2
TP53 WILD-TYPE 9 13 16 5
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0261 (Fisher's exact test), Q value = 0.51

Table S63.  Gene #7: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
TP53 MUTATED 0 0 1 1 3 0
TP53 WILD-TYPE 10 12 8 2 5 6

Figure S9.  Get High-res Image Gene #7: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.365 (Fisher's exact test), Q value = 0.9

Table S64.  Gene #7: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
TP53 MUTATED 4 0 1 0
TP53 WILD-TYPE 18 11 6 8
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.345 (Fisher's exact test), Q value = 0.9

Table S65.  Gene #7: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
TP53 MUTATED 2 3 0
TP53 WILD-TYPE 14 13 15
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.402 (Fisher's exact test), Q value = 0.9

Table S66.  Gene #7: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
TP53 MUTATED 1 1 2 0 1
TP53 WILD-TYPE 8 11 6 12 5
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.311 (Fisher's exact test), Q value = 0.9

Table S67.  Gene #7: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
TP53 MUTATED 2 0 0 2
TP53 WILD-TYPE 7 10 9 12
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.198 (Fisher's exact test), Q value = 0.9

Table S68.  Gene #7: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
TP53 MUTATED 2 0 0 2
TP53 WILD-TYPE 6 15 5 12
'TNFAIP3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.28 (Fisher's exact test), Q value = 0.9

Table S69.  Gene #8: 'TNFAIP3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
TNFAIP3 MUTATED 5 0 2
TNFAIP3 WILD-TYPE 15 7 19
'TNFAIP3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.508 (Fisher's exact test), Q value = 0.96

Table S70.  Gene #8: 'TNFAIP3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
TNFAIP3 MUTATED 2 3 2 0
TNFAIP3 WILD-TYPE 7 10 17 7
'TNFAIP3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0788 (Fisher's exact test), Q value = 0.66

Table S71.  Gene #8: 'TNFAIP3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 5 5 6 6 5
TNFAIP3 MUTATED 0 2 0 0 3 1
TNFAIP3 WILD-TYPE 6 3 5 6 3 4
'TNFAIP3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.439 (Fisher's exact test), Q value = 0.92

Table S72.  Gene #8: 'TNFAIP3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 15 12
TNFAIP3 MUTATED 0 4 2
TNFAIP3 WILD-TYPE 6 11 10
'TNFAIP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.507 (Fisher's exact test), Q value = 0.96

Table S73.  Gene #8: 'TNFAIP3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
TNFAIP3 MUTATED 0 2 2 0 1 2
TNFAIP3 WILD-TYPE 10 10 7 3 7 4
'TNFAIP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.709 (Fisher's exact test), Q value = 1

Table S74.  Gene #8: 'TNFAIP3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
TNFAIP3 MUTATED 2 2 1 2
TNFAIP3 WILD-TYPE 20 9 6 6
'TNFAIP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0775 (Fisher's exact test), Q value = 0.66

Table S75.  Gene #8: 'TNFAIP3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
TNFAIP3 MUTATED 0 3 4
TNFAIP3 WILD-TYPE 16 13 11
'TNFAIP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.567 (Fisher's exact test), Q value = 0.99

Table S76.  Gene #8: 'TNFAIP3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
TNFAIP3 MUTATED 2 3 0 1 1
TNFAIP3 WILD-TYPE 7 9 8 11 5
'TNFAIP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.656 (Fisher's exact test), Q value = 1

Table S77.  Gene #8: 'TNFAIP3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
TNFAIP3 MUTATED 0 2 2 2
TNFAIP3 WILD-TYPE 9 8 7 12
'TNFAIP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.279 (Fisher's exact test), Q value = 0.9

Table S78.  Gene #8: 'TNFAIP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
TNFAIP3 MUTATED 0 4 1 1
TNFAIP3 WILD-TYPE 8 11 4 13
'TMSB4X MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0556 (Fisher's exact test), Q value = 0.63

Table S79.  Gene #9: 'TMSB4X MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
TMSB4X MUTATED 2 3 1
TMSB4X WILD-TYPE 18 4 20
'TMSB4X MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 0.9

Table S80.  Gene #9: 'TMSB4X MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
TMSB4X MUTATED 3 1 1 1
TMSB4X WILD-TYPE 6 12 18 6
'TMSB4X MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.229 (Fisher's exact test), Q value = 0.9

Table S81.  Gene #9: 'TMSB4X MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 5 5 6 6 5
TMSB4X MUTATED 0 2 1 2 0 0
TMSB4X WILD-TYPE 6 3 4 4 6 5
'TMSB4X MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.56 (Fisher's exact test), Q value = 0.98

Table S82.  Gene #9: 'TMSB4X MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 15 12
TMSB4X MUTATED 0 2 3
TMSB4X WILD-TYPE 6 13 9
'TMSB4X MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.49 (Fisher's exact test), Q value = 0.96

Table S83.  Gene #9: 'TMSB4X MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
TMSB4X MUTATED 2 1 0 0 1 2
TMSB4X WILD-TYPE 8 11 9 3 7 4
'TMSB4X MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.624 (Fisher's exact test), Q value = 1

Table S84.  Gene #9: 'TMSB4X MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
TMSB4X MUTATED 3 1 0 2
TMSB4X WILD-TYPE 19 10 7 6
'TMSB4X MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.86 (Fisher's exact test), Q value = 1

Table S85.  Gene #9: 'TMSB4X MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
TMSB4X MUTATED 2 3 1
TMSB4X WILD-TYPE 14 13 14
'TMSB4X MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.632 (Fisher's exact test), Q value = 1

Table S86.  Gene #9: 'TMSB4X MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
TMSB4X MUTATED 1 3 0 1 1
TMSB4X WILD-TYPE 8 9 8 11 5
'TMSB4X MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.154 (Fisher's exact test), Q value = 0.85

Table S87.  Gene #9: 'TMSB4X MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
TMSB4X MUTATED 0 3 0 3
TMSB4X WILD-TYPE 9 7 9 11
'TMSB4X MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.927 (Fisher's exact test), Q value = 1

Table S88.  Gene #9: 'TMSB4X MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
TMSB4X MUTATED 1 3 0 2
TMSB4X WILD-TYPE 7 12 5 12
'APLF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 0.78

Table S89.  Gene #10: 'APLF MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
APLF MUTATED 3 0 0
APLF WILD-TYPE 17 7 21
'APLF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.189 (Fisher's exact test), Q value = 0.9

Table S90.  Gene #10: 'APLF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
APLF MUTATED 2 0 1 0
APLF WILD-TYPE 7 13 18 7
'APLF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.39 (Fisher's exact test), Q value = 0.9

Table S91.  Gene #10: 'APLF MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
APLF MUTATED 2 0 0 0 1 0
APLF WILD-TYPE 8 12 9 3 7 6
'APLF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.443 (Fisher's exact test), Q value = 0.92

Table S92.  Gene #10: 'APLF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
APLF MUTATED 3 0 0 0
APLF WILD-TYPE 19 11 7 8
'RHPN2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.748 (Fisher's exact test), Q value = 1

Table S93.  Gene #11: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
RHPN2 MUTATED 4 1 2
RHPN2 WILD-TYPE 16 6 19
'RHPN2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.131 (Fisher's exact test), Q value = 0.81

Table S94.  Gene #11: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
RHPN2 MUTATED 1 2 1 3
RHPN2 WILD-TYPE 8 11 18 4
'RHPN2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.395 (Fisher's exact test), Q value = 0.9

Table S95.  Gene #11: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 5 5 6 6 5
RHPN2 MUTATED 0 0 0 1 2 0
RHPN2 WILD-TYPE 6 5 5 5 4 5
'RHPN2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 0.9

Table S96.  Gene #11: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 15 12
RHPN2 MUTATED 0 3 0
RHPN2 WILD-TYPE 6 12 12
'RHPN2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.379 (Fisher's exact test), Q value = 0.9

Table S97.  Gene #11: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
RHPN2 MUTATED 3 3 0 0 1 0
RHPN2 WILD-TYPE 7 9 9 3 7 6
'RHPN2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.354 (Fisher's exact test), Q value = 0.9

Table S98.  Gene #11: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
RHPN2 MUTATED 5 2 0 0
RHPN2 WILD-TYPE 17 9 7 8
'RHPN2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.86 (Fisher's exact test), Q value = 1

Table S99.  Gene #11: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
RHPN2 MUTATED 2 3 1
RHPN2 WILD-TYPE 14 13 14
'RHPN2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.34 (Fisher's exact test), Q value = 0.9

Table S100.  Gene #11: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
RHPN2 MUTATED 3 1 0 1 1
RHPN2 WILD-TYPE 6 11 8 11 5
'RHPN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 0.9

Table S101.  Gene #11: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
RHPN2 MUTATED 1 0 1 4
RHPN2 WILD-TYPE 8 10 8 10
'RHPN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.299 (Fisher's exact test), Q value = 0.9

Table S102.  Gene #11: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
RHPN2 MUTATED 0 2 0 4
RHPN2 WILD-TYPE 8 13 5 10
'CIITA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.272 (Fisher's exact test), Q value = 0.9

Table S103.  Gene #12: 'CIITA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
CIITA MUTATED 4 0 1
CIITA WILD-TYPE 16 7 20
'CIITA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.238 (Fisher's exact test), Q value = 0.9

Table S104.  Gene #12: 'CIITA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
CIITA MUTATED 2 0 3 0
CIITA WILD-TYPE 7 13 16 7
'CIITA MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S105.  Gene #12: 'CIITA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 5 5 6 6 5
CIITA MUTATED 0 0 1 1 1 0
CIITA WILD-TYPE 6 5 4 5 5 5
'CIITA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S106.  Gene #12: 'CIITA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 15 12
CIITA MUTATED 0 2 1
CIITA WILD-TYPE 6 13 11
'CIITA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.28 (Fisher's exact test), Q value = 0.9

Table S107.  Gene #12: 'CIITA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
CIITA MUTATED 1 0 2 1 1 0
CIITA WILD-TYPE 9 12 7 2 7 6
'CIITA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.231 (Fisher's exact test), Q value = 0.9

Table S108.  Gene #12: 'CIITA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
CIITA MUTATED 2 0 2 1
CIITA WILD-TYPE 20 11 5 7
'CIITA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.304 (Fisher's exact test), Q value = 0.9

Table S109.  Gene #12: 'CIITA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
CIITA MUTATED 3 1 0
CIITA WILD-TYPE 13 15 15
'CIITA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.389 (Fisher's exact test), Q value = 0.9

Table S110.  Gene #12: 'CIITA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
CIITA MUTATED 0 0 1 2 1
CIITA WILD-TYPE 9 12 7 10 5
'CIITA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.335 (Fisher's exact test), Q value = 0.9

Table S111.  Gene #12: 'CIITA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
CIITA MUTATED 0 0 2 1
CIITA WILD-TYPE 9 10 7 13
'CIITA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S112.  Gene #12: 'CIITA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
CIITA MUTATED 0 1 1 1
CIITA WILD-TYPE 8 14 4 13
'KDR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.645 (Fisher's exact test), Q value = 1

Table S113.  Gene #13: 'KDR MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
KDR MUTATED 2 1 1
KDR WILD-TYPE 18 6 20
'KDR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.739 (Fisher's exact test), Q value = 1

Table S114.  Gene #13: 'KDR MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
KDR MUTATED 1 2 1 0
KDR WILD-TYPE 8 11 18 7
'KDR MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S115.  Gene #13: 'KDR MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
KDR MUTATED 0 1 1 0 1 1
KDR WILD-TYPE 10 11 8 3 7 5
'KDR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.802 (Fisher's exact test), Q value = 1

Table S116.  Gene #13: 'KDR MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
KDR MUTATED 3 1 0 0
KDR WILD-TYPE 19 10 7 8
'KDR MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S117.  Gene #13: 'KDR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
KDR MUTATED 2 1 1
KDR WILD-TYPE 14 15 14
'KDR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.623 (Fisher's exact test), Q value = 1

Table S118.  Gene #13: 'KDR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
KDR MUTATED 1 2 1 0 0
KDR WILD-TYPE 8 10 7 12 6
'KDR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 1

Table S119.  Gene #13: 'KDR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
KDR MUTATED 1 2 0 1
KDR WILD-TYPE 8 8 9 13
'KDR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.316 (Fisher's exact test), Q value = 0.9

Table S120.  Gene #13: 'KDR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
KDR MUTATED 1 3 0 0
KDR WILD-TYPE 7 12 5 14
'CARD11 MUTATION STATUS' versus 'CN_CNMF'

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

Table S121.  Gene #14: 'CARD11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
CARD11 MUTATED 4 1 5
CARD11 WILD-TYPE 16 6 16
'CARD11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.55 (Fisher's exact test), Q value = 0.98

Table S122.  Gene #14: 'CARD11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
CARD11 MUTATED 2 2 3 3
CARD11 WILD-TYPE 7 11 16 4
'CARD11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.62 (Fisher's exact test), Q value = 1

Table S123.  Gene #14: 'CARD11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 5 5 6 6 5
CARD11 MUTATED 0 0 1 2 2 1
CARD11 WILD-TYPE 6 5 4 4 4 4
'CARD11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.439 (Fisher's exact test), Q value = 0.92

Table S124.  Gene #14: 'CARD11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 15 12
CARD11 MUTATED 0 4 2
CARD11 WILD-TYPE 6 11 10
'CARD11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.463 (Fisher's exact test), Q value = 0.93

Table S125.  Gene #14: 'CARD11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
CARD11 MUTATED 4 2 1 1 2 0
CARD11 WILD-TYPE 6 10 8 2 6 6
'CARD11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.426 (Fisher's exact test), Q value = 0.92

Table S126.  Gene #14: 'CARD11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
CARD11 MUTATED 6 2 2 0
CARD11 WILD-TYPE 16 9 5 8
'CARD11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S127.  Gene #14: 'CARD11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
CARD11 MUTATED 3 4 2
CARD11 WILD-TYPE 13 12 13
'CARD11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.362 (Fisher's exact test), Q value = 0.9

Table S128.  Gene #14: 'CARD11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
CARD11 MUTATED 4 2 1 1 1
CARD11 WILD-TYPE 5 10 7 11 5
'CARD11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 0.81

Table S129.  Gene #14: 'CARD11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
CARD11 MUTATED 1 0 2 5
CARD11 WILD-TYPE 8 10 7 9
'CARD11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S130.  Gene #14: 'CARD11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
CARD11 MUTATED 1 2 1 4
CARD11 WILD-TYPE 7 13 4 10
'EZH2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.271 (Fisher's exact test), Q value = 0.9

Table S131.  Gene #15: 'EZH2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
EZH2 MUTATED 2 1 0
EZH2 WILD-TYPE 18 6 21
'EZH2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.742 (Fisher's exact test), Q value = 1

Table S132.  Gene #15: 'EZH2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
EZH2 MUTATED 0 1 1 1
EZH2 WILD-TYPE 9 12 18 6
'EZH2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0966 (Fisher's exact test), Q value = 0.69

Table S133.  Gene #15: 'EZH2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
EZH2 MUTATED 0 0 0 0 2 1
EZH2 WILD-TYPE 10 12 9 3 6 5
'EZH2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.444 (Fisher's exact test), Q value = 0.92

Table S134.  Gene #15: 'EZH2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
EZH2 MUTATED 3 0 0 0
EZH2 WILD-TYPE 19 11 7 8
'EZH2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0976 (Fisher's exact test), Q value = 0.69

Table S135.  Gene #15: 'EZH2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
EZH2 MUTATED 0 3 0
EZH2 WILD-TYPE 16 13 15
'EZH2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0254 (Fisher's exact test), Q value = 0.51

Table S136.  Gene #15: 'EZH2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
EZH2 MUTATED 1 0 0 0 2
EZH2 WILD-TYPE 8 12 8 12 4

Figure S10.  Get High-res Image Gene #15: 'EZH2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'EZH2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.682 (Fisher's exact test), Q value = 1

Table S137.  Gene #15: 'EZH2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
EZH2 MUTATED 0 1 0 2
EZH2 WILD-TYPE 9 9 9 12
'EZH2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.726 (Fisher's exact test), Q value = 1

Table S138.  Gene #15: 'EZH2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
EZH2 MUTATED 0 1 0 2
EZH2 WILD-TYPE 8 14 5 12
'NFKBIE MUTATION STATUS' versus 'CN_CNMF'

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

Table S139.  Gene #16: 'NFKBIE MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
NFKBIE MUTATED 2 0 2
NFKBIE WILD-TYPE 18 7 19
'NFKBIE MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0643 (Fisher's exact test), Q value = 0.66

Table S140.  Gene #16: 'NFKBIE MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
NFKBIE MUTATED 1 1 0 2
NFKBIE WILD-TYPE 8 12 19 5
'NFKBIE MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.893 (Fisher's exact test), Q value = 1

Table S141.  Gene #16: 'NFKBIE MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
NFKBIE MUTATED 1 1 0 0 1 1
NFKBIE WILD-TYPE 9 11 9 3 7 5
'NFKBIE MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.804 (Fisher's exact test), Q value = 1

Table S142.  Gene #16: 'NFKBIE MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
NFKBIE MUTATED 3 1 0 0
NFKBIE WILD-TYPE 19 10 7 8
'NFKBIE MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.302 (Fisher's exact test), Q value = 0.9

Table S143.  Gene #16: 'NFKBIE MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
NFKBIE MUTATED 1 3 0
NFKBIE WILD-TYPE 15 13 15
'NFKBIE MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 0.9

Table S144.  Gene #16: 'NFKBIE MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
NFKBIE MUTATED 2 2 0 0 0
NFKBIE WILD-TYPE 7 10 8 12 6
'NFKBIE MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 0.9

Table S145.  Gene #16: 'NFKBIE MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
NFKBIE MUTATED 0 1 0 3
NFKBIE WILD-TYPE 9 9 9 11
'NFKBIE MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S146.  Gene #16: 'NFKBIE MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
NFKBIE MUTATED 0 2 0 2
NFKBIE WILD-TYPE 8 13 5 12
'MLH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.117 (Fisher's exact test), Q value = 0.78

Table S147.  Gene #17: 'MLH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
MLH1 MUTATED 3 0 0
MLH1 WILD-TYPE 17 7 21
'MLH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S148.  Gene #17: 'MLH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
MLH1 MUTATED 1 1 1 0
MLH1 WILD-TYPE 8 12 18 7
'MLH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.237 (Fisher's exact test), Q value = 0.9

Table S149.  Gene #17: 'MLH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
MLH1 MUTATED 2 0 0 0 0 1
MLH1 WILD-TYPE 8 12 9 3 8 5
'MLH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.442 (Fisher's exact test), Q value = 0.92

Table S150.  Gene #17: 'MLH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
MLH1 MUTATED 3 0 0 0
MLH1 WILD-TYPE 19 11 7 8
'FAS MUTATION STATUS' versus 'CN_CNMF'

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

Table S151.  Gene #18: 'FAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
FAS MUTATED 2 1 2
FAS WILD-TYPE 18 6 19
'FAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.34 (Fisher's exact test), Q value = 0.9

Table S152.  Gene #18: 'FAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
FAS MUTATED 1 1 1 2
FAS WILD-TYPE 8 12 18 5
'FAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.51

Table S153.  Gene #18: 'FAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
FAS MUTATED 0 1 0 2 2 0
FAS WILD-TYPE 10 11 9 1 6 6

Figure S11.  Get High-res Image Gene #18: 'FAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'FAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.394 (Fisher's exact test), Q value = 0.9

Table S154.  Gene #18: 'FAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
FAS MUTATED 2 1 2 0
FAS WILD-TYPE 20 10 5 8
'FAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.595 (Fisher's exact test), Q value = 1

Table S155.  Gene #18: 'FAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
FAS MUTATED 1 3 1
FAS WILD-TYPE 15 13 14
'FAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S156.  Gene #18: 'FAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
FAS MUTATED 1 1 1 1 1
FAS WILD-TYPE 8 11 7 11 5
'FAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S157.  Gene #18: 'FAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
FAS MUTATED 0 1 1 3
FAS WILD-TYPE 9 9 8 11
'FAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.514 (Fisher's exact test), Q value = 0.96

Table S158.  Gene #18: 'FAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
FAS MUTATED 0 2 0 3
FAS WILD-TYPE 8 13 5 11
'ENOX1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 0.9

Table S159.  Gene #19: 'ENOX1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
ENOX1 MUTATED 3 0 1
ENOX1 WILD-TYPE 17 7 20
'ENOX1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S160.  Gene #19: 'ENOX1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
ENOX1 MUTATED 1 1 2 0
ENOX1 WILD-TYPE 8 12 17 7
'ENOX1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.394 (Fisher's exact test), Q value = 0.9

Table S161.  Gene #19: 'ENOX1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 5 5 6 6 5
ENOX1 MUTATED 0 0 0 1 2 0
ENOX1 WILD-TYPE 6 5 5 5 4 5
'ENOX1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.277 (Fisher's exact test), Q value = 0.9

Table S162.  Gene #19: 'ENOX1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 15 12
ENOX1 MUTATED 0 3 0
ENOX1 WILD-TYPE 6 12 12
'ENOX1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.616 (Fisher's exact test), Q value = 1

Table S163.  Gene #19: 'ENOX1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
ENOX1 MUTATED 2 1 0 0 0 1
ENOX1 WILD-TYPE 8 11 9 3 8 5
'ENOX1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S164.  Gene #19: 'ENOX1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
ENOX1 MUTATED 2 1 0 1
ENOX1 WILD-TYPE 20 10 7 7
'ENOX1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S165.  Gene #19: 'ENOX1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
ENOX1 MUTATED 2 1 1
ENOX1 WILD-TYPE 14 15 14
'ENOX1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 0.9

Table S166.  Gene #19: 'ENOX1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
ENOX1 MUTATED 2 2 0 0 0
ENOX1 WILD-TYPE 7 10 8 12 6
'ENOX1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.175 (Fisher's exact test), Q value = 0.9

Table S167.  Gene #19: 'ENOX1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
ENOX1 MUTATED 0 0 0 3
ENOX1 WILD-TYPE 9 10 9 11
'ENOX1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S168.  Gene #19: 'ENOX1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
ENOX1 MUTATED 0 1 0 2
ENOX1 WILD-TYPE 8 14 5 12
'SGK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0755 (Fisher's exact test), Q value = 0.66

Table S169.  Gene #20: 'SGK1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
SGK1 MUTATED 4 0 0
SGK1 WILD-TYPE 16 7 21
'SGK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.28

Table S170.  Gene #20: 'SGK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
SGK1 MUTATED 4 0 0 0
SGK1 WILD-TYPE 5 13 19 7

Figure S12.  Get High-res Image Gene #20: 'SGK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'SGK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.71

Table S171.  Gene #20: 'SGK1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
SGK1 MUTATED 3 0 0 0 1 0
SGK1 WILD-TYPE 7 12 9 3 7 6
'SGK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.302 (Fisher's exact test), Q value = 0.9

Table S172.  Gene #20: 'SGK1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
SGK1 MUTATED 4 0 0 0
SGK1 WILD-TYPE 18 11 7 8
'SGK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.762 (Fisher's exact test), Q value = 1

Table S173.  Gene #20: 'SGK1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
SGK1 MUTATED 1 2 0
SGK1 WILD-TYPE 15 14 15
'SGK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.51 (Fisher's exact test), Q value = 0.96

Table S174.  Gene #20: 'SGK1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
SGK1 MUTATED 1 2 0 0 0
SGK1 WILD-TYPE 8 10 8 12 6
'SGK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.604 (Fisher's exact test), Q value = 1

Table S175.  Gene #20: 'SGK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
SGK1 MUTATED 1 0 0 2
SGK1 WILD-TYPE 8 10 9 12
'SGK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.151 (Fisher's exact test), Q value = 0.85

Table S176.  Gene #20: 'SGK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
SGK1 MUTATED 2 1 0 0
SGK1 WILD-TYPE 6 14 5 14
'IFITM3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.757 (Fisher's exact test), Q value = 1

Table S177.  Gene #21: 'IFITM3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
IFITM3 MUTATED 2 0 1
IFITM3 WILD-TYPE 18 7 20
'IFITM3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0469 (Fisher's exact test), Q value = 0.6

Table S178.  Gene #21: 'IFITM3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
IFITM3 MUTATED 0 1 0 2
IFITM3 WILD-TYPE 9 12 19 5

Figure S13.  Get High-res Image Gene #21: 'IFITM3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'IFITM3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.54 (Fisher's exact test), Q value = 0.98

Table S179.  Gene #21: 'IFITM3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
IFITM3 MUTATED 0 2 0 0 1 0
IFITM3 WILD-TYPE 10 10 9 3 7 6
'IFITM3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S180.  Gene #21: 'IFITM3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
IFITM3 MUTATED 2 1 0 0
IFITM3 WILD-TYPE 20 10 7 8
'IFITM3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0969 (Fisher's exact test), Q value = 0.69

Table S181.  Gene #21: 'IFITM3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
IFITM3 MUTATED 0 3 0
IFITM3 WILD-TYPE 16 13 15
'IFITM3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S182.  Gene #21: 'IFITM3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
IFITM3 MUTATED 1 1 0 0 1
IFITM3 WILD-TYPE 8 11 8 12 5
'IFITM3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.602 (Fisher's exact test), Q value = 1

Table S183.  Gene #21: 'IFITM3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
IFITM3 MUTATED 1 0 0 2
IFITM3 WILD-TYPE 8 10 9 12
'IFITM3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S184.  Gene #21: 'IFITM3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
IFITM3 MUTATED 0 1 0 2
IFITM3 WILD-TYPE 8 14 5 12
'APOB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.268 (Fisher's exact test), Q value = 0.9

Table S185.  Gene #22: 'APOB MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
APOB MUTATED 2 1 0
APOB WILD-TYPE 18 6 21
'APOB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.274 (Fisher's exact test), Q value = 0.9

Table S186.  Gene #22: 'APOB MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
APOB MUTATED 1 1 0 1
APOB WILD-TYPE 8 12 19 6
'APOB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.834 (Fisher's exact test), Q value = 1

Table S187.  Gene #22: 'APOB MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
APOB MUTATED 1 1 0 0 0 1
APOB WILD-TYPE 9 11 9 3 8 5
'APOB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.854 (Fisher's exact test), Q value = 1

Table S188.  Gene #22: 'APOB MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
APOB MUTATED 1 1 0 1
APOB WILD-TYPE 21 10 7 7
'APOB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.764 (Fisher's exact test), Q value = 1

Table S189.  Gene #22: 'APOB MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
APOB MUTATED 2 1 0
APOB WILD-TYPE 14 15 15
'APOB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S190.  Gene #22: 'APOB MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
APOB MUTATED 0 1 1 1 0
APOB WILD-TYPE 9 11 7 11 6
'APOB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S191.  Gene #22: 'APOB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
APOB MUTATED 1 1 0 1
APOB WILD-TYPE 8 9 9 13
'APOB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.516 (Fisher's exact test), Q value = 0.96

Table S192.  Gene #22: 'APOB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
APOB MUTATED 1 2 0 0
APOB WILD-TYPE 7 13 5 14
'MCM8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.271 (Fisher's exact test), Q value = 0.9

Table S193.  Gene #23: 'MCM8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
MCM8 MUTATED 2 1 0
MCM8 WILD-TYPE 18 6 21
'MCM8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.554 (Fisher's exact test), Q value = 0.98

Table S194.  Gene #23: 'MCM8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
MCM8 MUTATED 0 2 1 0
MCM8 WILD-TYPE 9 11 18 7
'MCM8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S195.  Gene #23: 'MCM8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
MCM8 MUTATED 1 1 0 0 0 1
MCM8 WILD-TYPE 9 11 9 3 8 5
'MCM8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S196.  Gene #23: 'MCM8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
MCM8 MUTATED 2 1 0 0
MCM8 WILD-TYPE 20 10 7 8
'MCM8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.762 (Fisher's exact test), Q value = 1

Table S197.  Gene #23: 'MCM8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
MCM8 MUTATED 2 1 0
MCM8 WILD-TYPE 14 15 15
'MCM8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.3 (Fisher's exact test), Q value = 0.9

Table S198.  Gene #23: 'MCM8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
MCM8 MUTATED 2 1 0 0 0
MCM8 WILD-TYPE 7 11 8 12 6
'MCM8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.683 (Fisher's exact test), Q value = 1

Table S199.  Gene #23: 'MCM8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
MCM8 MUTATED 0 1 0 2
MCM8 WILD-TYPE 9 9 9 12
'MCM8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.854 (Fisher's exact test), Q value = 1

Table S200.  Gene #23: 'MCM8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
MCM8 MUTATED 0 2 0 1
MCM8 WILD-TYPE 8 13 5 13
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.69 (Fisher's exact test), Q value = 1

Table S201.  Gene #24: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
ARID1A MUTATED 3 0 2
ARID1A WILD-TYPE 17 7 19
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.782 (Fisher's exact test), Q value = 1

Table S202.  Gene #24: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
ARID1A MUTATED 0 2 2 1
ARID1A WILD-TYPE 9 11 17 6
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.482 (Fisher's exact test), Q value = 0.96

Table S203.  Gene #24: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
ARID1A MUTATED 0 2 1 1 1 0
ARID1A WILD-TYPE 10 10 8 2 7 6
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.468 (Fisher's exact test), Q value = 0.94

Table S204.  Gene #24: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
ARID1A MUTATED 1 2 1 1
ARID1A WILD-TYPE 21 9 6 7
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S205.  Gene #24: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
ARID1A MUTATED 1 3 1
ARID1A WILD-TYPE 15 13 14
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.885 (Fisher's exact test), Q value = 1

Table S206.  Gene #24: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
ARID1A MUTATED 1 2 0 1 1
ARID1A WILD-TYPE 8 10 8 11 5
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.345 (Fisher's exact test), Q value = 0.9

Table S207.  Gene #24: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
ARID1A MUTATED 0 1 0 3
ARID1A WILD-TYPE 9 9 9 11
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S208.  Gene #24: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
ARID1A MUTATED 0 2 0 2
ARID1A WILD-TYPE 8 13 5 12
'PCDHA10 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0803 (Fisher's exact test), Q value = 0.66

Table S209.  Gene #25: 'PCDHA10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
PCDHA10 MUTATED 1 3 2
PCDHA10 WILD-TYPE 19 4 19
'PCDHA10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.51

Table S210.  Gene #25: 'PCDHA10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
PCDHA10 MUTATED 2 1 0 3
PCDHA10 WILD-TYPE 7 12 19 4

Figure S14.  Get High-res Image Gene #25: 'PCDHA10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PCDHA10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.227 (Fisher's exact test), Q value = 0.9

Table S211.  Gene #25: 'PCDHA10 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
PCDHA10 MUTATED 2 1 0 0 3 0
PCDHA10 WILD-TYPE 8 11 9 3 5 6
'PCDHA10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.374 (Fisher's exact test), Q value = 0.9

Table S212.  Gene #25: 'PCDHA10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
PCDHA10 MUTATED 5 1 0 0
PCDHA10 WILD-TYPE 17 10 7 8
'PCDHA10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.86 (Fisher's exact test), Q value = 1

Table S213.  Gene #25: 'PCDHA10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
PCDHA10 MUTATED 2 3 1
PCDHA10 WILD-TYPE 14 13 14
'PCDHA10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.661 (Fisher's exact test), Q value = 1

Table S214.  Gene #25: 'PCDHA10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
PCDHA10 MUTATED 1 1 1 1 2
PCDHA10 WILD-TYPE 8 11 7 11 4
'PCDHA10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.319 (Fisher's exact test), Q value = 0.9

Table S215.  Gene #25: 'PCDHA10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
PCDHA10 MUTATED 1 1 0 4
PCDHA10 WILD-TYPE 8 9 9 10
'PCDHA10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.864 (Fisher's exact test), Q value = 1

Table S216.  Gene #25: 'PCDHA10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
PCDHA10 MUTATED 1 2 0 3
PCDHA10 WILD-TYPE 7 13 5 11
'LRRC16B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0036 (Fisher's exact test), Q value = 0.51

Table S217.  Gene #26: 'LRRC16B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
LRRC16B MUTATED 1 3 0
LRRC16B WILD-TYPE 19 4 21

Figure S15.  Get High-res Image Gene #26: 'LRRC16B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'LRRC16B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.51

Table S218.  Gene #26: 'LRRC16B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
LRRC16B MUTATED 2 0 0 2
LRRC16B WILD-TYPE 7 13 19 5

Figure S16.  Get High-res Image Gene #26: 'LRRC16B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'LRRC16B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.169 (Fisher's exact test), Q value = 0.9

Table S219.  Gene #26: 'LRRC16B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
LRRC16B MUTATED 2 0 0 0 2 0
LRRC16B WILD-TYPE 8 12 9 3 6 6
'LRRC16B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.306 (Fisher's exact test), Q value = 0.9

Table S220.  Gene #26: 'LRRC16B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
LRRC16B MUTATED 4 0 0 0
LRRC16B WILD-TYPE 18 11 7 8
'LRRC16B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.762 (Fisher's exact test), Q value = 1

Table S221.  Gene #26: 'LRRC16B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
LRRC16B MUTATED 1 2 0
LRRC16B WILD-TYPE 15 14 15
'LRRC16B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0178 (Fisher's exact test), Q value = 0.51

Table S222.  Gene #26: 'LRRC16B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
LRRC16B MUTATED 0 0 1 0 2
LRRC16B WILD-TYPE 9 12 7 12 4

Figure S17.  Get High-res Image Gene #26: 'LRRC16B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'LRRC16B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S223.  Gene #26: 'LRRC16B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
LRRC16B MUTATED 1 0 0 2
LRRC16B WILD-TYPE 8 10 9 12
'LRRC16B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.443 (Fisher's exact test), Q value = 0.92

Table S224.  Gene #26: 'LRRC16B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
LRRC16B MUTATED 1 0 0 2
LRRC16B WILD-TYPE 7 15 5 12
'PNPLA7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.27 (Fisher's exact test), Q value = 0.9

Table S225.  Gene #27: 'PNPLA7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
PNPLA7 MUTATED 2 1 0
PNPLA7 WILD-TYPE 18 6 21
'PNPLA7 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S226.  Gene #27: 'PNPLA7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
PNPLA7 MUTATED 0 1 1 1
PNPLA7 WILD-TYPE 9 12 18 6
'PNPLA7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.393 (Fisher's exact test), Q value = 0.9

Table S227.  Gene #27: 'PNPLA7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 5 5 6 6 5
PNPLA7 MUTATED 0 0 0 1 2 0
PNPLA7 WILD-TYPE 6 5 5 5 4 5
'PNPLA7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S228.  Gene #27: 'PNPLA7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 15 12
PNPLA7 MUTATED 0 2 1
PNPLA7 WILD-TYPE 6 13 11
'PNPLA7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.238 (Fisher's exact test), Q value = 0.9

Table S229.  Gene #27: 'PNPLA7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
PNPLA7 MUTATED 2 0 0 0 0 1
PNPLA7 WILD-TYPE 8 12 9 3 8 5
'PNPLA7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.438 (Fisher's exact test), Q value = 0.92

Table S230.  Gene #27: 'PNPLA7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
PNPLA7 MUTATED 3 0 0 0
PNPLA7 WILD-TYPE 19 11 7 8
'PNPLA7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S231.  Gene #27: 'PNPLA7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
PNPLA7 MUTATED 2 1 0
PNPLA7 WILD-TYPE 14 15 15
'PNPLA7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.132 (Fisher's exact test), Q value = 0.81

Table S232.  Gene #27: 'PNPLA7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
PNPLA7 MUTATED 2 0 1 0 0
PNPLA7 WILD-TYPE 7 12 7 12 6
'PNPLA7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S233.  Gene #27: 'PNPLA7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
PNPLA7 MUTATED 1 1 0 1
PNPLA7 WILD-TYPE 8 9 9 13
'PNPLA7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S234.  Gene #27: 'PNPLA7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
PNPLA7 MUTATED 1 1 0 1
PNPLA7 WILD-TYPE 7 14 5 13
'SLC16A8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.51

Table S235.  Gene #28: 'SLC16A8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
SLC16A8 MUTATED 1 2 0
SLC16A8 WILD-TYPE 19 5 21

Figure S18.  Get High-res Image Gene #28: 'SLC16A8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'SLC16A8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.27 (Fisher's exact test), Q value = 0.9

Table S236.  Gene #28: 'SLC16A8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
SLC16A8 MUTATED 1 1 0 1
SLC16A8 WILD-TYPE 8 12 19 6
'SLC16A8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0975 (Fisher's exact test), Q value = 0.69

Table S237.  Gene #28: 'SLC16A8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
SLC16A8 MUTATED 0 0 0 0 2 1
SLC16A8 WILD-TYPE 10 12 9 3 6 5
'SLC16A8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.443 (Fisher's exact test), Q value = 0.92

Table S238.  Gene #28: 'SLC16A8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
SLC16A8 MUTATED 3 0 0 0
SLC16A8 WILD-TYPE 19 11 7 8
'SLC16A8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0977 (Fisher's exact test), Q value = 0.69

Table S239.  Gene #28: 'SLC16A8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
SLC16A8 MUTATED 0 3 0
SLC16A8 WILD-TYPE 16 13 15
'SLC16A8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0256 (Fisher's exact test), Q value = 0.51

Table S240.  Gene #28: 'SLC16A8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
SLC16A8 MUTATED 1 0 0 0 2
SLC16A8 WILD-TYPE 8 12 8 12 4

Figure S19.  Get High-res Image Gene #28: 'SLC16A8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'SLC16A8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.682 (Fisher's exact test), Q value = 1

Table S241.  Gene #28: 'SLC16A8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
SLC16A8 MUTATED 0 1 0 2
SLC16A8 WILD-TYPE 9 9 9 12
'SLC16A8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.726 (Fisher's exact test), Q value = 1

Table S242.  Gene #28: 'SLC16A8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
SLC16A8 MUTATED 0 1 0 2
SLC16A8 WILD-TYPE 8 14 5 12
'PKHD1L1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0528 (Fisher's exact test), Q value = 0.61

Table S243.  Gene #29: 'PKHD1L1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
PKHD1L1 MUTATED 3 2 0
PKHD1L1 WILD-TYPE 17 5 21
'PKHD1L1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.54

Table S244.  Gene #29: 'PKHD1L1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
PKHD1L1 MUTATED 3 1 0 1
PKHD1L1 WILD-TYPE 6 12 19 6

Figure S20.  Get High-res Image Gene #29: 'PKHD1L1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PKHD1L1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.105 (Fisher's exact test), Q value = 0.71

Table S245.  Gene #29: 'PKHD1L1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
PKHD1L1 MUTATED 0 1 0 0 3 1
PKHD1L1 WILD-TYPE 10 11 9 3 5 5
'PKHD1L1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S246.  Gene #29: 'PKHD1L1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
PKHD1L1 MUTATED 3 1 0 1
PKHD1L1 WILD-TYPE 19 10 7 7
'PKHD1L1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0715 (Fisher's exact test), Q value = 0.66

Table S247.  Gene #29: 'PKHD1L1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
PKHD1L1 MUTATED 0 4 1
PKHD1L1 WILD-TYPE 16 12 14
'PKHD1L1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00863 (Fisher's exact test), Q value = 0.51

Table S248.  Gene #29: 'PKHD1L1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
PKHD1L1 MUTATED 0 2 0 0 3
PKHD1L1 WILD-TYPE 9 10 8 12 3

Figure S21.  Get High-res Image Gene #29: 'PKHD1L1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PKHD1L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0403 (Fisher's exact test), Q value = 0.54

Table S249.  Gene #29: 'PKHD1L1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
PKHD1L1 MUTATED 0 0 0 4
PKHD1L1 WILD-TYPE 9 10 9 10

Figure S22.  Get High-res Image Gene #29: 'PKHD1L1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'PKHD1L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S250.  Gene #29: 'PKHD1L1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
PKHD1L1 MUTATED 0 2 0 2
PKHD1L1 WILD-TYPE 8 13 5 12
'HRCT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.361 (Fisher's exact test), Q value = 0.9

Table S251.  Gene #30: 'HRCT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
HRCT1 MUTATED 3 0 1
HRCT1 WILD-TYPE 17 7 20
'HRCT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 0.9

Table S252.  Gene #30: 'HRCT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
HRCT1 MUTATED 0 1 1 2
HRCT1 WILD-TYPE 9 12 18 5
'HRCT1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.392 (Fisher's exact test), Q value = 0.9

Table S253.  Gene #30: 'HRCT1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 5 5 6 6 5
HRCT1 MUTATED 0 0 0 1 2 0
HRCT1 WILD-TYPE 6 5 5 5 4 5
'HRCT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 0.9

Table S254.  Gene #30: 'HRCT1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 15 12
HRCT1 MUTATED 0 3 0
HRCT1 WILD-TYPE 6 12 12
'HRCT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.537 (Fisher's exact test), Q value = 0.98

Table S255.  Gene #30: 'HRCT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
HRCT1 MUTATED 2 2 0 0 0 0
HRCT1 WILD-TYPE 8 10 9 3 8 6
'HRCT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.803 (Fisher's exact test), Q value = 1

Table S256.  Gene #30: 'HRCT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
HRCT1 MUTATED 3 1 0 0
HRCT1 WILD-TYPE 19 10 7 8
'HRCT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.526 (Fisher's exact test), Q value = 0.96

Table S257.  Gene #30: 'HRCT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
HRCT1 MUTATED 2 2 0
HRCT1 WILD-TYPE 14 14 15
'HRCT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0628 (Fisher's exact test), Q value = 0.66

Table S258.  Gene #30: 'HRCT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
HRCT1 MUTATED 3 1 0 0 0
HRCT1 WILD-TYPE 6 11 8 12 6
'HRCT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.311 (Fisher's exact test), Q value = 0.9

Table S259.  Gene #30: 'HRCT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
HRCT1 MUTATED 1 0 0 3
HRCT1 WILD-TYPE 8 10 9 11
'HRCT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.402 (Fisher's exact test), Q value = 0.9

Table S260.  Gene #30: 'HRCT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
HRCT1 MUTATED 0 1 0 3
HRCT1 WILD-TYPE 8 14 5 11
'TYRO3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.148 (Fisher's exact test), Q value = 0.85

Table S261.  Gene #31: 'TYRO3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
TYRO3 MUTATED 3 1 0
TYRO3 WILD-TYPE 17 6 21
'TYRO3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.898 (Fisher's exact test), Q value = 1

Table S262.  Gene #31: 'TYRO3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
TYRO3 MUTATED 0 1 2 1
TYRO3 WILD-TYPE 9 12 17 6
'TYRO3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.629 (Fisher's exact test), Q value = 1

Table S263.  Gene #31: 'TYRO3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 5 5 6 6 5
TYRO3 MUTATED 0 0 0 1 2 1
TYRO3 WILD-TYPE 6 5 5 5 4 4
'TYRO3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.503 (Fisher's exact test), Q value = 0.96

Table S264.  Gene #31: 'TYRO3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 15 12
TYRO3 MUTATED 0 3 1
TYRO3 WILD-TYPE 6 12 11
'TYRO3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.454 (Fisher's exact test), Q value = 0.93

Table S265.  Gene #31: 'TYRO3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
TYRO3 MUTATED 2 0 1 0 0 1
TYRO3 WILD-TYPE 8 12 8 3 8 5
'TYRO3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.455 (Fisher's exact test), Q value = 0.93

Table S266.  Gene #31: 'TYRO3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
TYRO3 MUTATED 3 0 1 0
TYRO3 WILD-TYPE 19 11 6 8
'TYRO3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S267.  Gene #31: 'TYRO3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
TYRO3 MUTATED 2 1 1
TYRO3 WILD-TYPE 14 15 14
'TYRO3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0352 (Fisher's exact test), Q value = 0.54

Table S268.  Gene #31: 'TYRO3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
TYRO3 MUTATED 3 0 1 0 0
TYRO3 WILD-TYPE 6 12 7 12 6

Figure S23.  Get High-res Image Gene #31: 'TYRO3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TYRO3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S269.  Gene #31: 'TYRO3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
TYRO3 MUTATED 1 1 1 1
TYRO3 WILD-TYPE 8 9 8 13
'TYRO3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.895 (Fisher's exact test), Q value = 1

Table S270.  Gene #31: 'TYRO3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
TYRO3 MUTATED 1 1 0 2
TYRO3 WILD-TYPE 7 14 5 12
'GSTZ1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0268 (Fisher's exact test), Q value = 0.51

Table S271.  Gene #32: 'GSTZ1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
GSTZ1 MUTATED 1 2 0
GSTZ1 WILD-TYPE 19 5 21

Figure S24.  Get High-res Image Gene #32: 'GSTZ1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'GSTZ1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.61

Table S272.  Gene #32: 'GSTZ1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
GSTZ1 MUTATED 0 1 0 2
GSTZ1 WILD-TYPE 9 12 19 5

Figure S25.  Get High-res Image Gene #32: 'GSTZ1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'GSTZ1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.513 (Fisher's exact test), Q value = 0.96

Table S273.  Gene #32: 'GSTZ1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
GSTZ1 MUTATED 1 0 0 0 1 1
GSTZ1 WILD-TYPE 9 12 9 3 7 5
'GSTZ1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.444 (Fisher's exact test), Q value = 0.92

Table S274.  Gene #32: 'GSTZ1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
GSTZ1 MUTATED 3 0 0 0
GSTZ1 WILD-TYPE 19 11 7 8
'GSTZ1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.761 (Fisher's exact test), Q value = 1

Table S275.  Gene #32: 'GSTZ1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
GSTZ1 MUTATED 1 2 0
GSTZ1 WILD-TYPE 15 14 15
'GSTZ1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.302 (Fisher's exact test), Q value = 0.9

Table S276.  Gene #32: 'GSTZ1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
GSTZ1 MUTATED 1 0 1 0 1
GSTZ1 WILD-TYPE 8 12 7 12 5
'GSTZ1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S277.  Gene #32: 'GSTZ1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
GSTZ1 MUTATED 1 1 0 1
GSTZ1 WILD-TYPE 8 9 9 13
'GSTZ1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S278.  Gene #32: 'GSTZ1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
GSTZ1 MUTATED 1 1 0 1
GSTZ1 WILD-TYPE 7 14 5 13
'STAT3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.746 (Fisher's exact test), Q value = 1

Table S279.  Gene #33: 'STAT3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
STAT3 MUTATED 4 1 2
STAT3 WILD-TYPE 16 6 19
'STAT3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.253 (Fisher's exact test), Q value = 0.9

Table S280.  Gene #33: 'STAT3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
STAT3 MUTATED 2 0 4 1
STAT3 WILD-TYPE 7 13 15 6
'STAT3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.552 (Fisher's exact test), Q value = 0.98

Table S281.  Gene #33: 'STAT3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 5 5 6 6 5
STAT3 MUTATED 1 1 0 0 1 2
STAT3 WILD-TYPE 5 4 5 6 5 3
'STAT3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S282.  Gene #33: 'STAT3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 15 12
STAT3 MUTATED 1 2 2
STAT3 WILD-TYPE 5 13 10
'STAT3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.339 (Fisher's exact test), Q value = 0.9

Table S283.  Gene #33: 'STAT3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
STAT3 MUTATED 4 1 1 0 1 0
STAT3 WILD-TYPE 6 11 8 3 7 6
'STAT3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 0.96

Table S284.  Gene #33: 'STAT3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
STAT3 MUTATED 5 1 1 0
STAT3 WILD-TYPE 17 10 6 8
'STAT3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 0.54

Table S285.  Gene #33: 'STAT3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
STAT3 MUTATED 5 1 0
STAT3 WILD-TYPE 11 15 15

Figure S26.  Get High-res Image Gene #33: 'STAT3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'STAT3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0163 (Fisher's exact test), Q value = 0.51

Table S286.  Gene #33: 'STAT3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
STAT3 MUTATED 1 1 4 0 0
STAT3 WILD-TYPE 8 11 4 12 6

Figure S27.  Get High-res Image Gene #33: 'STAT3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'STAT3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.54

Table S287.  Gene #33: 'STAT3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
STAT3 MUTATED 4 1 0 1
STAT3 WILD-TYPE 5 9 9 13

Figure S28.  Get High-res Image Gene #33: 'STAT3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'STAT3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.229 (Fisher's exact test), Q value = 0.9

Table S288.  Gene #33: 'STAT3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
STAT3 MUTATED 3 1 0 2
STAT3 WILD-TYPE 5 14 5 12
'IRF8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.275 (Fisher's exact test), Q value = 0.9

Table S289.  Gene #34: 'IRF8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
IRF8 MUTATED 4 0 1
IRF8 WILD-TYPE 16 7 20
'IRF8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.236 (Fisher's exact test), Q value = 0.9

Table S290.  Gene #34: 'IRF8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
IRF8 MUTATED 2 0 3 0
IRF8 WILD-TYPE 7 13 16 7
'IRF8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.296 (Fisher's exact test), Q value = 0.9

Table S291.  Gene #34: 'IRF8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 5 5 6 6 5
IRF8 MUTATED 0 0 0 0 2 1
IRF8 WILD-TYPE 6 5 5 6 4 4
'IRF8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.387 (Fisher's exact test), Q value = 0.9

Table S292.  Gene #34: 'IRF8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 15 12
IRF8 MUTATED 1 2 0
IRF8 WILD-TYPE 5 13 12
'IRF8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.239 (Fisher's exact test), Q value = 0.9

Table S293.  Gene #34: 'IRF8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
IRF8 MUTATED 2 0 0 0 2 1
IRF8 WILD-TYPE 8 12 9 3 6 5
'IRF8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S294.  Gene #34: 'IRF8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
IRF8 MUTATED 3 0 1 1
IRF8 WILD-TYPE 19 11 6 7
'IRF8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S295.  Gene #34: 'IRF8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
IRF8 MUTATED 2 2 1
IRF8 WILD-TYPE 14 14 14
'IRF8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.343 (Fisher's exact test), Q value = 0.9

Table S296.  Gene #34: 'IRF8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
IRF8 MUTATED 1 3 1 0 0
IRF8 WILD-TYPE 8 9 7 12 6
'IRF8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.602 (Fisher's exact test), Q value = 1

Table S297.  Gene #34: 'IRF8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
IRF8 MUTATED 1 0 0 2
IRF8 WILD-TYPE 8 10 9 12
'IRF8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.727 (Fisher's exact test), Q value = 1

Table S298.  Gene #34: 'IRF8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
IRF8 MUTATED 0 1 0 2
IRF8 WILD-TYPE 8 14 5 12
'TMEM30A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0747 (Fisher's exact test), Q value = 0.66

Table S299.  Gene #35: 'TMEM30A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
TMEM30A MUTATED 4 0 0
TMEM30A WILD-TYPE 16 7 21
'TMEM30A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.898 (Fisher's exact test), Q value = 1

Table S300.  Gene #35: 'TMEM30A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
TMEM30A MUTATED 1 1 1 1
TMEM30A WILD-TYPE 8 12 18 6
'TMEM30A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.394 (Fisher's exact test), Q value = 0.9

Table S301.  Gene #35: 'TMEM30A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 5 5 6 6 5
TMEM30A MUTATED 0 0 0 1 2 0
TMEM30A WILD-TYPE 6 5 5 5 4 5
'TMEM30A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 0.9

Table S302.  Gene #35: 'TMEM30A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 15 12
TMEM30A MUTATED 0 3 0
TMEM30A WILD-TYPE 6 12 12
'TMEM30A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.691 (Fisher's exact test), Q value = 1

Table S303.  Gene #35: 'TMEM30A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
TMEM30A MUTATED 1 2 0 0 0 1
TMEM30A WILD-TYPE 9 10 9 3 8 5
'TMEM30A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S304.  Gene #35: 'TMEM30A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
TMEM30A MUTATED 2 1 0 1
TMEM30A WILD-TYPE 20 10 7 7
'TMEM30A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.678 (Fisher's exact test), Q value = 1

Table S305.  Gene #35: 'TMEM30A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
TMEM30A MUTATED 1 1 2
TMEM30A WILD-TYPE 15 15 13
'TMEM30A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.259 (Fisher's exact test), Q value = 0.9

Table S306.  Gene #35: 'TMEM30A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
TMEM30A MUTATED 2 2 0 0 0
TMEM30A WILD-TYPE 7 10 8 12 6
'TMEM30A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S307.  Gene #35: 'TMEM30A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
TMEM30A MUTATED 1 1 0 1
TMEM30A WILD-TYPE 8 9 9 13
'TMEM30A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S308.  Gene #35: 'TMEM30A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
TMEM30A MUTATED 0 1 0 2
TMEM30A WILD-TYPE 8 14 5 12
'UBE2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 0.9

Table S309.  Gene #36: 'UBE2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 7 21
UBE2A MUTATED 3 0 1
UBE2A WILD-TYPE 17 7 20
'UBE2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 0.9

Table S310.  Gene #36: 'UBE2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 13 19 7
UBE2A MUTATED 1 0 3 0
UBE2A WILD-TYPE 8 13 16 7
'UBE2A MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S311.  Gene #36: 'UBE2A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 5 5 6 6 5
UBE2A MUTATED 1 0 1 0 1 0
UBE2A WILD-TYPE 5 5 4 6 5 5
'UBE2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S312.  Gene #36: 'UBE2A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 15 12
UBE2A MUTATED 0 2 1
UBE2A WILD-TYPE 6 13 11
'UBE2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.464 (Fisher's exact test), Q value = 0.93

Table S313.  Gene #36: 'UBE2A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 12 9 3 8 6
UBE2A MUTATED 1 0 1 0 2 0
UBE2A WILD-TYPE 9 12 8 3 6 6
'UBE2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.303 (Fisher's exact test), Q value = 0.9

Table S314.  Gene #36: 'UBE2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 11 7 8
UBE2A MUTATED 4 0 0 0
UBE2A WILD-TYPE 18 11 7 8
'UBE2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.528 (Fisher's exact test), Q value = 0.96

Table S315.  Gene #36: 'UBE2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 16 15
UBE2A MUTATED 2 2 0
UBE2A WILD-TYPE 14 14 15
'UBE2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.51

Table S316.  Gene #36: 'UBE2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 9 12 8 12 6
UBE2A MUTATED 0 0 2 0 2
UBE2A WILD-TYPE 9 12 6 12 4

Figure S29.  Get High-res Image Gene #36: 'UBE2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'UBE2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.312 (Fisher's exact test), Q value = 0.9

Table S317.  Gene #36: 'UBE2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 10 9 14
UBE2A MUTATED 2 0 0 2
UBE2A WILD-TYPE 7 10 9 12
'UBE2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.453 (Fisher's exact test), Q value = 0.93

Table S318.  Gene #36: 'UBE2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 15 5 14
UBE2A MUTATED 2 1 0 1
UBE2A WILD-TYPE 6 14 5 13
Methods & Data
Input

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/DLBC-TP/22573826/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/DLBC-TP/22541055/DLBC-TP.transferedmergedcluster.txt

  • Number of patients = 48

  • Number of significantly mutated genes = 36

  • 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)
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