Correlation between gene mutation status and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between mutation status of 28 genes and 8 molecular subtypes across 168 patients, 2 significant findings detected with P value < 0.05 and Q value < 0.25.

  • SETD2 mutation correlated to 'METHLYATION_CNMF'.

  • MET mutation correlated to 'MRNASEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 28 genes and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 2 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		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
SETD2 15 (9%) 153 0.105
(1.00) 		0.00103
(0.23) 		0.0715
(1.00) 		0.226
(1.00) 		0.888
(1.00) 		0.718
(1.00) 		0.943
(1.00) 		0.091
(1.00)
MET 15 (9%) 153 0.696
(1.00) 		0.072
(1.00) 		0.00056
(0.125) 		0.0113
(1.00) 		0.745
(1.00) 		0.633
(1.00) 		0.747
(1.00) 		0.069
(1.00)
HNRNPM 11 (7%) 157 1
(1.00) 		0.382
(1.00) 		0.594
(1.00) 		0.497
(1.00) 		0.579
(1.00) 		0.541
(1.00) 		0.924
(1.00) 		0.411
(1.00)
NF2 12 (7%) 156 0.0695
(1.00) 		0.0148
(1.00) 		0.034
(1.00) 		0.932
(1.00) 		0.933
(1.00) 		0.676
(1.00) 		1
(1.00) 		0.697
(1.00)
NEFH 10 (6%) 158 0.238
(1.00) 		0.911
(1.00) 		0.115
(1.00) 		0.227
(1.00) 		0.0128
(1.00) 		0.00291
(0.646) 		0.00303
(0.67) 		0.0982
(1.00)
TDG 5 (3%) 163 0.324
(1.00) 		0.277
(1.00) 		0.866
(1.00) 		0.325
(1.00) 		0.0766
(1.00) 		0.584
(1.00) 		0.16
(1.00) 		0.683
(1.00)
ZNF598 13 (8%) 155 0.194
(1.00) 		0.444
(1.00) 		0.112
(1.00) 		0.62
(1.00) 		0.179
(1.00) 		0.145
(1.00) 		0.441
(1.00) 		0.00565
(1.00)
SKI 6 (4%) 162 0.86
(1.00) 		0.0624
(1.00) 		0.162
(1.00) 		0.876
(1.00) 		0.775
(1.00) 		1
(1.00) 		0.879
(1.00) 		0.665
(1.00)
CSGALNACT2 7 (4%) 161 0.0647
(1.00) 		0.295
(1.00) 		0.505
(1.00) 		0.889
(1.00) 		0.0813
(1.00) 		0.764
(1.00) 		0.207
(1.00) 		0.979
(1.00)
MUC5B 18 (11%) 150 0.881
(1.00) 		0.849
(1.00) 		0.746
(1.00) 		0.606
(1.00) 		0.492
(1.00) 		0.186
(1.00) 		0.155
(1.00) 		0.651
(1.00)
KDM6A 9 (5%) 159 0.449
(1.00) 		0.831
(1.00) 		0.108
(1.00) 		0.39
(1.00) 		0.689
(1.00) 		0.732
(1.00) 		0.258
(1.00) 		0.208
(1.00)
ZNF814 8 (5%) 160 0.46
(1.00) 		0.483
(1.00) 		0.713
(1.00) 		0.314
(1.00) 		0.597
(1.00) 		0.553
(1.00) 		0.6
(1.00) 		0.662
(1.00)
OR2L8 4 (2%) 164 0.458
(1.00) 		0.301
(1.00) 		0.481
(1.00) 		0.108
(1.00) 		0.322
(1.00) 		0.313
(1.00) 		0.2
(1.00) 		0.704
(1.00)
MYH6 8 (5%) 160 0.297
(1.00) 		0.294
(1.00) 		0.409
(1.00) 		0.599
(1.00) 		0.905
(1.00) 		0.235
(1.00) 		0.823
(1.00) 		0.313
(1.00)
UNC13A 9 (5%) 159 0.0753
(1.00) 		0.834
(1.00) 		0.186
(1.00) 		0.833
(1.00) 		0.913
(1.00) 		0.483
(1.00) 		1
(1.00) 		0.525
(1.00)
MED16 4 (2%) 164 0.0867
(1.00) 		0.0965
(1.00) 		0.638
(1.00) 		0.198
(1.00) 		1
(1.00) 		0.315
(1.00) 		1
(1.00) 		0.29
(1.00)
GLUD2 11 (7%) 157 1
(1.00) 		0.924
(1.00) 		0.464
(1.00) 		0.127
(1.00) 		0.28
(1.00) 		0.448
(1.00) 		0.0432
(1.00) 		0.728
(1.00)
BMS1 13 (8%) 155 0.784
(1.00) 		0.672
(1.00) 		0.427
(1.00) 		0.716
(1.00) 		0.936
(1.00) 		0.052
(1.00) 		0.633
(1.00) 		0.0989
(1.00)
FUS 3 (2%) 165 1
(1.00) 		0.262
(1.00) 		0.44
(1.00) 		0.778
(1.00) 		0.64
(1.00) 		1
(1.00) 		0.633
(1.00) 		0.839
(1.00)
TP53 7 (4%) 161 0.201
(1.00) 		0.0507
(1.00) 		0.353
(1.00) 		0.178
(1.00) 		0.707
(1.00) 		0.291
(1.00) 		0.792
(1.00) 		0.161
(1.00)
ACADL 4 (2%) 164 0.35
(1.00) 		0.48
(1.00) 		1
(1.00) 		0.463
(1.00) 		0.0181
(1.00) 		0.394
(1.00) 		0.146
(1.00) 		0.352
(1.00)
AHNAK2 10 (6%) 158 0.435
(1.00) 		0.317
(1.00) 		0.0217
(1.00) 		0.249
(1.00) 		0.229
(1.00) 		0.104
(1.00) 		0.715
(1.00) 		0.0327
(1.00)
SMARCB1 5 (3%) 163 1
(1.00) 		0.0606
(1.00) 		0.316
(1.00) 		0.322
(1.00) 		0.012
(1.00) 		0.493
(1.00) 		0.0122
(1.00) 		0.918
(1.00)
TEKT1 4 (2%) 164 0.607
(1.00) 		0.686
(1.00) 		0.906
(1.00) 		0.831
(1.00) 		0.463
(1.00) 		0.514
(1.00) 		1
(1.00) 		0.362
(1.00)
MKL1 9 (5%) 159 0.0773
(1.00) 		0.717
(1.00) 		0.142
(1.00) 		0.472
(1.00) 		0.913
(1.00) 		0.278
(1.00) 		1
(1.00) 		0.996
(1.00)
MYH7 6 (4%) 162 0.606
(1.00) 		1
(1.00) 		0.376
(1.00) 		0.383
(1.00) 		0.774
(1.00) 		0.0372
(1.00) 		0.88
(1.00) 		0.251
(1.00)
MAP4K3 5 (3%) 163 0.827
(1.00) 		0.379
(1.00) 		0.274
(1.00) 		0.228
(1.00) 		0.133
(1.00) 		0.203
(1.00) 		0.104
(1.00) 		0.759
(1.00)
NEK2 3 (2%) 165 1
(1.00) 		0.784
(1.00) 		0.515
(1.00) 		0.196
(1.00) 		0.296
(1.00) 		0.182
(1.00) 		0.273
(1.00) 		0.696
(1.00)
'HNRNPM MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
HNRNPM MUTATED 4 6 1
HNRNPM WILD-TYPE 57 79 21
'HNRNPM MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
HNRNPM MUTATED 5 3 3
HNRNPM WILD-TYPE 37 44 61
'HNRNPM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.594 (Fisher's exact test), Q value = 1

Table S3.  Gene #1: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
HNRNPM MUTATED 1 4 3 3
HNRNPM WILD-TYPE 36 57 41 23
'HNRNPM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.497 (Fisher's exact test), Q value = 1

Table S4.  Gene #1: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
HNRNPM MUTATED 3 3 5
HNRNPM WILD-TYPE 61 51 45
'HNRNPM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.579 (Fisher's exact test), Q value = 1

Table S5.  Gene #1: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
HNRNPM MUTATED 2 4 5
HNRNPM WILD-TYPE 54 46 57
'HNRNPM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.541 (Fisher's exact test), Q value = 1

Table S6.  Gene #1: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
HNRNPM MUTATED 4 3 4
HNRNPM WILD-TYPE 77 27 53
'HNRNPM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.924 (Fisher's exact test), Q value = 1

Table S7.  Gene #1: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
HNRNPM MUTATED 3 3 5
HNRNPM WILD-TYPE 57 43 57
'HNRNPM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.411 (Fisher's exact test), Q value = 1

Table S8.  Gene #1: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
HNRNPM MUTATED 2 0 1 1 4 3 0
HNRNPM WILD-TYPE 18 27 22 19 27 28 16
'NF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0695 (Fisher's exact test), Q value = 1

Table S9.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
NF2 MUTATED 1 9 2
NF2 WILD-TYPE 60 76 20
'NF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 1

Table S10.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
NF2 MUTATED 0 7 4
NF2 WILD-TYPE 42 40 60

Figure S1.  Get High-res Image Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 1

Table S11.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
NF2 MUTATED 0 7 5 0
NF2 WILD-TYPE 37 54 39 26

Figure S2.  Get High-res Image Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'NF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.932 (Fisher's exact test), Q value = 1

Table S12.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
NF2 MUTATED 4 4 4
NF2 WILD-TYPE 60 50 46
'NF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S13.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
NF2 MUTATED 4 3 5
NF2 WILD-TYPE 52 47 57
'NF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.676 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
NF2 MUTATED 6 1 5
NF2 WILD-TYPE 75 29 52
'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S15.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
NF2 MUTATED 4 3 5
NF2 WILD-TYPE 56 43 57
'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.697 (Fisher's exact test), Q value = 1

Table S16.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
NF2 MUTATED 1 2 2 1 1 2 3
NF2 WILD-TYPE 19 25 21 19 30 29 13
'NEFH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.238 (Fisher's exact test), Q value = 1

Table S17.  Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
NEFH MUTATED 3 4 3
NEFH WILD-TYPE 58 81 19
'NEFH MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S18.  Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
NEFH MUTATED 3 2 4
NEFH WILD-TYPE 39 45 60
'NEFH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.115 (Fisher's exact test), Q value = 1

Table S19.  Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
NEFH MUTATED 5 2 3 0
NEFH WILD-TYPE 32 59 41 26
'NEFH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.227 (Fisher's exact test), Q value = 1

Table S20.  Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
NEFH MUTATED 6 1 3
NEFH WILD-TYPE 58 53 47
'NEFH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 1

Table S21.  Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
NEFH MUTATED 6 4 0
NEFH WILD-TYPE 50 46 62

Figure S3.  Get High-res Image Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'NEFH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00291 (Fisher's exact test), Q value = 0.65

Table S22.  Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
NEFH MUTATED 10 0 0
NEFH WILD-TYPE 71 30 57

Figure S4.  Get High-res Image Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00303 (Fisher's exact test), Q value = 0.67

Table S23.  Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
NEFH MUTATED 8 2 0
NEFH WILD-TYPE 52 44 62

Figure S5.  Get High-res Image Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0982 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
NEFH MUTATED 2 2 4 0 0 2 0
NEFH WILD-TYPE 18 25 19 20 31 29 16
'TDG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 1

Table S25.  Gene #4: 'TDG MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
TDG MUTATED 3 1 1
TDG WILD-TYPE 58 84 21
'TDG MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.277 (Fisher's exact test), Q value = 1

Table S26.  Gene #4: 'TDG MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
TDG MUTATED 0 3 2
TDG WILD-TYPE 42 44 62
'TDG MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S27.  Gene #4: 'TDG MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
TDG MUTATED 1 3 1 0
TDG WILD-TYPE 36 58 43 26
'TDG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S28.  Gene #4: 'TDG MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
TDG MUTATED 3 0 2
TDG WILD-TYPE 61 54 48
'TDG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0766 (Fisher's exact test), Q value = 1

Table S29.  Gene #4: 'TDG MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
TDG MUTATED 4 0 1
TDG WILD-TYPE 52 50 61
'TDG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.584 (Fisher's exact test), Q value = 1

Table S30.  Gene #4: 'TDG MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
TDG MUTATED 4 0 1
TDG WILD-TYPE 77 30 56
'TDG MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.16 (Fisher's exact test), Q value = 1

Table S31.  Gene #4: 'TDG MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
TDG MUTATED 4 0 1
TDG WILD-TYPE 56 46 61
'TDG MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S32.  Gene #4: 'TDG MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
TDG MUTATED 1 2 1 0 1 0 0
TDG WILD-TYPE 19 25 22 20 30 31 16
'ZNF598 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.194 (Fisher's exact test), Q value = 1

Table S33.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
ZNF598 MUTATED 2 8 3
ZNF598 WILD-TYPE 59 77 19
'ZNF598 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 1

Table S34.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
ZNF598 MUTATED 4 5 3
ZNF598 WILD-TYPE 38 42 61
'ZNF598 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 1

Table S35.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
ZNF598 MUTATED 1 5 2 5
ZNF598 WILD-TYPE 36 56 42 21
'ZNF598 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S36.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
ZNF598 MUTATED 4 6 3
ZNF598 WILD-TYPE 60 48 47
'ZNF598 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.179 (Fisher's exact test), Q value = 1

Table S37.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
ZNF598 MUTATED 2 3 8
ZNF598 WILD-TYPE 54 47 54
'ZNF598 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 1

Table S38.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
ZNF598 MUTATED 3 3 7
ZNF598 WILD-TYPE 78 27 50
'ZNF598 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 1

Table S39.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
ZNF598 MUTATED 3 3 7
ZNF598 WILD-TYPE 57 43 55
'ZNF598 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00565 (Fisher's exact test), Q value = 1

Table S40.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
ZNF598 MUTATED 0 3 0 1 7 0 2
ZNF598 WILD-TYPE 20 24 23 19 24 31 14

Figure S6.  Get High-res Image Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SKI MUTATION STATUS' versus 'CN_CNMF'

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

Table S41.  Gene #6: 'SKI MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
SKI MUTATED 2 4 0
SKI WILD-TYPE 59 81 22
'SKI MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0624 (Fisher's exact test), Q value = 1

Table S42.  Gene #6: 'SKI MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
SKI MUTATED 4 0 2
SKI WILD-TYPE 38 47 62
'SKI MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.162 (Fisher's exact test), Q value = 1

Table S43.  Gene #6: 'SKI MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
SKI MUTATED 1 1 1 3
SKI WILD-TYPE 36 60 43 23
'SKI MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.876 (Fisher's exact test), Q value = 1

Table S44.  Gene #6: 'SKI MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
SKI MUTATED 3 2 1
SKI WILD-TYPE 61 52 49
'SKI MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.775 (Fisher's exact test), Q value = 1

Table S45.  Gene #6: 'SKI MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
SKI MUTATED 3 1 2
SKI WILD-TYPE 53 49 60
'SKI MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S46.  Gene #6: 'SKI MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
SKI MUTATED 3 1 2
SKI WILD-TYPE 78 29 55
'SKI MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.879 (Fisher's exact test), Q value = 1

Table S47.  Gene #6: 'SKI MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
SKI MUTATED 2 1 3
SKI WILD-TYPE 58 45 59
'SKI MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.665 (Fisher's exact test), Q value = 1

Table S48.  Gene #6: 'SKI MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
SKI MUTATED 0 2 0 0 2 2 0
SKI WILD-TYPE 20 25 23 20 29 29 16
'CSGALNACT2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0647 (Fisher's exact test), Q value = 1

Table S49.  Gene #7: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
CSGALNACT2 MUTATED 1 3 3
CSGALNACT2 WILD-TYPE 60 82 19
'CSGALNACT2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.295 (Fisher's exact test), Q value = 1

Table S50.  Gene #7: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
CSGALNACT2 MUTATED 4 1 2
CSGALNACT2 WILD-TYPE 38 46 62
'CSGALNACT2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.505 (Fisher's exact test), Q value = 1

Table S51.  Gene #7: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
CSGALNACT2 MUTATED 0 4 2 1
CSGALNACT2 WILD-TYPE 37 57 42 25
'CSGALNACT2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.889 (Fisher's exact test), Q value = 1

Table S52.  Gene #7: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
CSGALNACT2 MUTATED 2 3 2
CSGALNACT2 WILD-TYPE 62 51 48
'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0813 (Fisher's exact test), Q value = 1

Table S53.  Gene #7: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
CSGALNACT2 MUTATED 1 5 1
CSGALNACT2 WILD-TYPE 55 45 61
'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S54.  Gene #7: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
CSGALNACT2 MUTATED 3 2 2
CSGALNACT2 WILD-TYPE 78 28 55
'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.207 (Fisher's exact test), Q value = 1

Table S55.  Gene #7: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
CSGALNACT2 MUTATED 2 4 1
CSGALNACT2 WILD-TYPE 58 42 61
'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.979 (Fisher's exact test), Q value = 1

Table S56.  Gene #7: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
CSGALNACT2 MUTATED 0 1 1 1 2 1 1
CSGALNACT2 WILD-TYPE 20 26 22 19 29 30 15
'SETD2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S57.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
SETD2 MUTATED 2 10 3
SETD2 WILD-TYPE 59 75 19
'SETD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.23

Table S58.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
SETD2 MUTATED 1 11 3
SETD2 WILD-TYPE 41 36 61

Figure S7.  Get High-res Image Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0715 (Fisher's exact test), Q value = 1

Table S59.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
SETD2 MUTATED 2 10 3 0
SETD2 WILD-TYPE 35 51 41 26
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.226 (Fisher's exact test), Q value = 1

Table S60.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
SETD2 MUTATED 9 3 3
SETD2 WILD-TYPE 55 51 47
'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.888 (Fisher's exact test), Q value = 1

Table S61.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
SETD2 MUTATED 6 4 5
SETD2 WILD-TYPE 50 46 57
'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.718 (Fisher's exact test), Q value = 1

Table S62.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
SETD2 MUTATED 9 2 4
SETD2 WILD-TYPE 72 28 53
'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.943 (Fisher's exact test), Q value = 1

Table S63.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
SETD2 MUTATED 6 4 5
SETD2 WILD-TYPE 54 42 57
'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.091 (Fisher's exact test), Q value = 1

Table S64.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
SETD2 MUTATED 1 6 0 0 3 4 1
SETD2 WILD-TYPE 19 21 23 20 28 27 15
'MET MUTATION STATUS' versus 'CN_CNMF'

P value = 0.696 (Fisher's exact test), Q value = 1

Table S65.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
MET MUTATED 7 7 1
MET WILD-TYPE 54 78 21
'MET MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.072 (Fisher's exact test), Q value = 1

Table S66.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
MET MUTATED 3 1 9
MET WILD-TYPE 39 46 55
'MET MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.13

Table S67.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
MET MUTATED 1 1 6 7
MET WILD-TYPE 36 60 38 19

Figure S8.  Get High-res Image Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'MET MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 1

Table S68.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
MET MUTATED 4 10 1
MET WILD-TYPE 60 44 49

Figure S9.  Get High-res Image Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'MET MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.745 (Fisher's exact test), Q value = 1

Table S69.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
MET MUTATED 6 3 6
MET WILD-TYPE 50 47 56
'MET MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.633 (Fisher's exact test), Q value = 1

Table S70.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
MET MUTATED 6 2 7
MET WILD-TYPE 75 28 50
'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.747 (Fisher's exact test), Q value = 1

Table S71.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
MET MUTATED 5 3 7
MET WILD-TYPE 55 43 55
'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.069 (Fisher's exact test), Q value = 1

Table S72.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
MET MUTATED 4 1 1 5 2 2 0
MET WILD-TYPE 16 26 22 15 29 29 16
'MUC5B MUTATION STATUS' versus 'CN_CNMF'

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

Table S73.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
MUC5B MUTATED 6 9 3
MUC5B WILD-TYPE 55 76 19
'MUC5B MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S74.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
MUC5B MUTATED 5 6 6
MUC5B WILD-TYPE 37 41 58
'MUC5B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.746 (Fisher's exact test), Q value = 1

Table S75.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
MUC5B MUTATED 3 9 4 2
MUC5B WILD-TYPE 34 52 40 24
'MUC5B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.606 (Fisher's exact test), Q value = 1

Table S76.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
MUC5B MUTATED 9 5 4
MUC5B WILD-TYPE 55 49 46
'MUC5B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.492 (Fisher's exact test), Q value = 1

Table S77.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
MUC5B MUTATED 5 4 9
MUC5B WILD-TYPE 51 46 53
'MUC5B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S78.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
MUC5B MUTATED 10 5 3
MUC5B WILD-TYPE 71 25 54
'MUC5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.155 (Fisher's exact test), Q value = 1

Table S79.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
MUC5B MUTATED 6 2 10
MUC5B WILD-TYPE 54 44 52
'MUC5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S80.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
MUC5B MUTATED 2 6 1 2 3 3 1
MUC5B WILD-TYPE 18 21 22 18 28 28 15
'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.449 (Fisher's exact test), Q value = 1

Table S81.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
KDM6A MUTATED 5 3 1
KDM6A WILD-TYPE 56 82 21
'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S82.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
KDM6A MUTATED 3 3 3
KDM6A WILD-TYPE 39 44 61
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.108 (Fisher's exact test), Q value = 1

Table S83.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
KDM6A MUTATED 5 2 2 0
KDM6A WILD-TYPE 32 59 42 26
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.39 (Fisher's exact test), Q value = 1

Table S84.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
KDM6A MUTATED 5 1 3
KDM6A WILD-TYPE 59 53 47
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.689 (Fisher's exact test), Q value = 1

Table S85.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
KDM6A MUTATED 4 3 2
KDM6A WILD-TYPE 52 47 60
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S86.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
KDM6A MUTATED 5 2 2
KDM6A WILD-TYPE 76 28 55
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S87.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
KDM6A MUTATED 5 3 1
KDM6A WILD-TYPE 55 43 61
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S88.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
KDM6A MUTATED 3 1 1 0 0 3 1
KDM6A WILD-TYPE 17 26 22 20 31 28 15
'ZNF814 MUTATION STATUS' versus 'CN_CNMF'

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

Table S89.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
ZNF814 MUTATED 3 3 2
ZNF814 WILD-TYPE 58 82 20
'ZNF814 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 1

Table S90.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
ZNF814 MUTATED 1 4 3
ZNF814 WILD-TYPE 41 43 61
'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.713 (Fisher's exact test), Q value = 1

Table S91.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
ZNF814 MUTATED 2 4 2 0
ZNF814 WILD-TYPE 35 57 42 26
'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.314 (Fisher's exact test), Q value = 1

Table S92.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
ZNF814 MUTATED 5 1 2
ZNF814 WILD-TYPE 59 53 48
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S93.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
ZNF814 MUTATED 3 1 4
ZNF814 WILD-TYPE 53 49 58
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S94.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
ZNF814 MUTATED 5 0 3
ZNF814 WILD-TYPE 76 30 54
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S95.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
ZNF814 MUTATED 3 1 4
ZNF814 WILD-TYPE 57 45 58
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.662 (Fisher's exact test), Q value = 1

Table S96.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
ZNF814 MUTATED 0 3 1 0 2 1 1
ZNF814 WILD-TYPE 20 24 22 20 29 30 15
'OR2L8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.458 (Fisher's exact test), Q value = 1

Table S97.  Gene #13: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
OR2L8 MUTATED 2 1 1
OR2L8 WILD-TYPE 59 84 21
'OR2L8 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S98.  Gene #13: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
OR2L8 MUTATED 2 0 2
OR2L8 WILD-TYPE 40 47 62
'OR2L8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.481 (Fisher's exact test), Q value = 1

Table S99.  Gene #13: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
OR2L8 MUTATED 0 1 2 1
OR2L8 WILD-TYPE 37 60 42 25
'OR2L8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.108 (Fisher's exact test), Q value = 1

Table S100.  Gene #13: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
OR2L8 MUTATED 0 3 1
OR2L8 WILD-TYPE 64 51 49
'OR2L8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S101.  Gene #13: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
OR2L8 MUTATED 0 1 3
OR2L8 WILD-TYPE 56 49 59
'OR2L8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.313 (Fisher's exact test), Q value = 1

Table S102.  Gene #13: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
OR2L8 MUTATED 1 0 3
OR2L8 WILD-TYPE 80 30 54
'OR2L8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.2 (Fisher's exact test), Q value = 1

Table S103.  Gene #13: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
OR2L8 MUTATED 0 1 3
OR2L8 WILD-TYPE 60 45 59
'OR2L8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S104.  Gene #13: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
OR2L8 MUTATED 0 0 0 1 2 1 0
OR2L8 WILD-TYPE 20 27 23 19 29 30 16
'MYH6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 1

Table S105.  Gene #14: 'MYH6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
MYH6 MUTATED 1 6 1
MYH6 WILD-TYPE 60 79 21
'MYH6 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S106.  Gene #14: 'MYH6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
MYH6 MUTATED 4 1 3
MYH6 WILD-TYPE 38 46 61
'MYH6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.409 (Fisher's exact test), Q value = 1

Table S107.  Gene #14: 'MYH6 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
MYH6 MUTATED 1 2 2 3
MYH6 WILD-TYPE 36 59 42 23
'MYH6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.599 (Fisher's exact test), Q value = 1

Table S108.  Gene #14: 'MYH6 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
MYH6 MUTATED 2 4 2
MYH6 WILD-TYPE 62 50 48
'MYH6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.905 (Fisher's exact test), Q value = 1

Table S109.  Gene #14: 'MYH6 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
MYH6 MUTATED 2 3 3
MYH6 WILD-TYPE 54 47 59
'MYH6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.235 (Fisher's exact test), Q value = 1

Table S110.  Gene #14: 'MYH6 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
MYH6 MUTATED 2 1 5
MYH6 WILD-TYPE 79 29 52
'MYH6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.823 (Fisher's exact test), Q value = 1

Table S111.  Gene #14: 'MYH6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
MYH6 MUTATED 2 3 3
MYH6 WILD-TYPE 58 43 59
'MYH6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.313 (Fisher's exact test), Q value = 1

Table S112.  Gene #14: 'MYH6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
MYH6 MUTATED 2 0 0 1 2 1 2
MYH6 WILD-TYPE 18 27 23 19 29 30 14
'UNC13A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0753 (Fisher's exact test), Q value = 1

Table S113.  Gene #15: 'UNC13A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
UNC13A MUTATED 1 8 0
UNC13A WILD-TYPE 60 77 22
'UNC13A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S114.  Gene #15: 'UNC13A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
UNC13A MUTATED 3 3 3
UNC13A WILD-TYPE 39 44 61
'UNC13A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S115.  Gene #15: 'UNC13A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
UNC13A MUTATED 0 4 2 3
UNC13A WILD-TYPE 37 57 42 23
'UNC13A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.833 (Fisher's exact test), Q value = 1

Table S116.  Gene #15: 'UNC13A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
UNC13A MUTATED 4 2 3
UNC13A WILD-TYPE 60 52 47
'UNC13A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S117.  Gene #15: 'UNC13A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
UNC13A MUTATED 3 2 4
UNC13A WILD-TYPE 53 48 58
'UNC13A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.483 (Fisher's exact test), Q value = 1

Table S118.  Gene #15: 'UNC13A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
UNC13A MUTATED 3 1 5
UNC13A WILD-TYPE 78 29 52
'UNC13A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S119.  Gene #15: 'UNC13A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
UNC13A MUTATED 3 2 4
UNC13A WILD-TYPE 57 44 58
'UNC13A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.525 (Fisher's exact test), Q value = 1

Table S120.  Gene #15: 'UNC13A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
UNC13A MUTATED 1 2 0 1 4 1 0
UNC13A WILD-TYPE 19 25 23 19 27 30 16
'MED16 MUTATION STATUS' versus 'CN_CNMF'

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

Table S121.  Gene #16: 'MED16 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
MED16 MUTATED 0 2 2
MED16 WILD-TYPE 61 83 20
'MED16 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0965 (Fisher's exact test), Q value = 1

Table S122.  Gene #16: 'MED16 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
MED16 MUTATED 1 3 0
MED16 WILD-TYPE 41 44 64
'MED16 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.638 (Fisher's exact test), Q value = 1

Table S123.  Gene #16: 'MED16 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
MED16 MUTATED 1 2 0 1
MED16 WILD-TYPE 36 59 44 25
'MED16 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.198 (Fisher's exact test), Q value = 1

Table S124.  Gene #16: 'MED16 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
MED16 MUTATED 1 3 0
MED16 WILD-TYPE 63 51 50
'MED16 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S125.  Gene #16: 'MED16 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
MED16 MUTATED 1 1 2
MED16 WILD-TYPE 55 49 60
'MED16 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S126.  Gene #16: 'MED16 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
MED16 MUTATED 1 0 3
MED16 WILD-TYPE 80 30 54
'MED16 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S127.  Gene #16: 'MED16 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
MED16 MUTATED 1 1 2
MED16 WILD-TYPE 59 45 60
'MED16 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.29 (Fisher's exact test), Q value = 1

Table S128.  Gene #16: 'MED16 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
MED16 MUTATED 1 0 0 0 2 0 1
MED16 WILD-TYPE 19 27 23 20 29 31 15
'GLUD2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S129.  Gene #17: 'GLUD2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
GLUD2 MUTATED 4 6 1
GLUD2 WILD-TYPE 57 79 21
'GLUD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.924 (Fisher's exact test), Q value = 1

Table S130.  Gene #17: 'GLUD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
GLUD2 MUTATED 3 4 4
GLUD2 WILD-TYPE 39 43 60
'GLUD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.464 (Fisher's exact test), Q value = 1

Table S131.  Gene #17: 'GLUD2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
GLUD2 MUTATED 4 4 1 2
GLUD2 WILD-TYPE 33 57 43 24
'GLUD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.127 (Fisher's exact test), Q value = 1

Table S132.  Gene #17: 'GLUD2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
GLUD2 MUTATED 7 1 3
GLUD2 WILD-TYPE 57 53 47
'GLUD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.28 (Fisher's exact test), Q value = 1

Table S133.  Gene #17: 'GLUD2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
GLUD2 MUTATED 6 3 2
GLUD2 WILD-TYPE 50 47 60
'GLUD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S134.  Gene #17: 'GLUD2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
GLUD2 MUTATED 6 3 2
GLUD2 WILD-TYPE 75 27 55
'GLUD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 1

Table S135.  Gene #17: 'GLUD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
GLUD2 MUTATED 8 1 2
GLUD2 WILD-TYPE 52 45 60

Figure S10.  Get High-res Image Gene #17: 'GLUD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'GLUD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.728 (Fisher's exact test), Q value = 1

Table S136.  Gene #17: 'GLUD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
GLUD2 MUTATED 2 3 2 0 2 2 0
GLUD2 WILD-TYPE 18 24 21 20 29 29 16
'BMS1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S137.  Gene #18: 'BMS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
BMS1 MUTATED 4 8 1
BMS1 WILD-TYPE 57 77 21
'BMS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.672 (Fisher's exact test), Q value = 1

Table S138.  Gene #18: 'BMS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
BMS1 MUTATED 3 2 6
BMS1 WILD-TYPE 39 45 58
'BMS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.427 (Fisher's exact test), Q value = 1

Table S139.  Gene #18: 'BMS1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
BMS1 MUTATED 3 3 3 4
BMS1 WILD-TYPE 34 58 41 22
'BMS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.716 (Fisher's exact test), Q value = 1

Table S140.  Gene #18: 'BMS1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
BMS1 MUTATED 4 4 5
BMS1 WILD-TYPE 60 50 45
'BMS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S141.  Gene #18: 'BMS1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
BMS1 MUTATED 5 4 4
BMS1 WILD-TYPE 51 46 58
'BMS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.052 (Fisher's exact test), Q value = 1

Table S142.  Gene #18: 'BMS1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
BMS1 MUTATED 10 2 1
BMS1 WILD-TYPE 71 28 56
'BMS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.633 (Fisher's exact test), Q value = 1

Table S143.  Gene #18: 'BMS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
BMS1 MUTATED 3 4 6
BMS1 WILD-TYPE 57 42 56
'BMS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0989 (Fisher's exact test), Q value = 1

Table S144.  Gene #18: 'BMS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
BMS1 MUTATED 1 0 4 0 2 5 1
BMS1 WILD-TYPE 19 27 19 20 29 26 15
'FUS MUTATION STATUS' versus 'CN_CNMF'

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

Table S145.  Gene #19: 'FUS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
FUS MUTATED 1 2 0
FUS WILD-TYPE 60 83 22
'FUS MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S146.  Gene #19: 'FUS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
FUS MUTATED 1 2 0
FUS WILD-TYPE 41 45 64
'FUS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 1

Table S147.  Gene #19: 'FUS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
FUS MUTATED 0 2 0 1
FUS WILD-TYPE 37 59 44 25
'FUS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.778 (Fisher's exact test), Q value = 1

Table S148.  Gene #19: 'FUS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
FUS MUTATED 2 1 0
FUS WILD-TYPE 62 53 50
'FUS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.64 (Fisher's exact test), Q value = 1

Table S149.  Gene #19: 'FUS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
FUS MUTATED 2 0 1
FUS WILD-TYPE 54 50 61
'FUS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S150.  Gene #19: 'FUS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
FUS MUTATED 2 0 1
FUS WILD-TYPE 79 30 56
'FUS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.633 (Fisher's exact test), Q value = 1

Table S151.  Gene #19: 'FUS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
FUS MUTATED 2 0 1
FUS WILD-TYPE 58 46 61
'FUS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.839 (Fisher's exact test), Q value = 1

Table S152.  Gene #19: 'FUS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
FUS MUTATED 1 1 0 0 1 0 0
FUS WILD-TYPE 19 26 23 20 30 31 16
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.201 (Fisher's exact test), Q value = 1

Table S153.  Gene #20: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
TP53 MUTATED 1 6 0
TP53 WILD-TYPE 60 79 22
'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0507 (Fisher's exact test), Q value = 1

Table S154.  Gene #20: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
TP53 MUTATED 3 3 0
TP53 WILD-TYPE 39 44 64
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.353 (Fisher's exact test), Q value = 1

Table S155.  Gene #20: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
TP53 MUTATED 2 4 0 1
TP53 WILD-TYPE 35 57 44 25
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.178 (Fisher's exact test), Q value = 1

Table S156.  Gene #20: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
TP53 MUTATED 3 4 0
TP53 WILD-TYPE 61 50 50
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.707 (Fisher's exact test), Q value = 1

Table S157.  Gene #20: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
TP53 MUTATED 3 1 3
TP53 WILD-TYPE 53 49 59
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.291 (Fisher's exact test), Q value = 1

Table S158.  Gene #20: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
TP53 MUTATED 3 0 4
TP53 WILD-TYPE 78 30 53
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S159.  Gene #20: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
TP53 MUTATED 3 1 3
TP53 WILD-TYPE 57 45 59
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.161 (Fisher's exact test), Q value = 1

Table S160.  Gene #20: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
TP53 MUTATED 1 1 0 0 1 1 3
TP53 WILD-TYPE 19 26 23 20 30 30 13
'ACADL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 1

Table S161.  Gene #21: 'ACADL MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
ACADL MUTATED 3 1 0
ACADL WILD-TYPE 58 84 22
'ACADL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.48 (Fisher's exact test), Q value = 1

Table S162.  Gene #21: 'ACADL MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
ACADL MUTATED 0 2 1
ACADL WILD-TYPE 42 45 63
'ACADL MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S163.  Gene #21: 'ACADL MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
ACADL MUTATED 1 2 1 0
ACADL WILD-TYPE 36 59 43 26
'ACADL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.463 (Fisher's exact test), Q value = 1

Table S164.  Gene #21: 'ACADL MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
ACADL MUTATED 2 0 2
ACADL WILD-TYPE 62 54 48
'ACADL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 1

Table S165.  Gene #21: 'ACADL MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
ACADL MUTATED 4 0 0
ACADL WILD-TYPE 52 50 62

Figure S11.  Get High-res Image Gene #21: 'ACADL MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'ACADL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.394 (Fisher's exact test), Q value = 1

Table S166.  Gene #21: 'ACADL MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
ACADL MUTATED 3 1 0
ACADL WILD-TYPE 78 29 57
'ACADL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.146 (Fisher's exact test), Q value = 1

Table S167.  Gene #21: 'ACADL MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
ACADL MUTATED 3 1 0
ACADL WILD-TYPE 57 45 62
'ACADL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.352 (Fisher's exact test), Q value = 1

Table S168.  Gene #21: 'ACADL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
ACADL MUTATED 0 2 0 0 0 2 0
ACADL WILD-TYPE 20 25 23 20 31 29 16
'AHNAK2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.435 (Fisher's exact test), Q value = 1

Table S169.  Gene #22: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
AHNAK2 MUTATED 2 6 2
AHNAK2 WILD-TYPE 59 79 20
'AHNAK2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S170.  Gene #22: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
AHNAK2 MUTATED 4 1 4
AHNAK2 WILD-TYPE 38 46 60
'AHNAK2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 1

Table S171.  Gene #22: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
AHNAK2 MUTATED 2 1 2 5
AHNAK2 WILD-TYPE 35 60 42 21

Figure S12.  Get High-res Image Gene #22: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'AHNAK2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S172.  Gene #22: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
AHNAK2 MUTATED 6 3 1
AHNAK2 WILD-TYPE 58 51 49
'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.229 (Fisher's exact test), Q value = 1

Table S173.  Gene #22: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
AHNAK2 MUTATED 6 2 2
AHNAK2 WILD-TYPE 50 48 60
'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S174.  Gene #22: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
AHNAK2 MUTATED 8 0 2
AHNAK2 WILD-TYPE 73 30 55
'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.715 (Fisher's exact test), Q value = 1

Table S175.  Gene #22: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
AHNAK2 MUTATED 5 2 3
AHNAK2 WILD-TYPE 55 44 59
'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 1

Table S176.  Gene #22: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
AHNAK2 MUTATED 4 1 0 2 0 3 0
AHNAK2 WILD-TYPE 16 26 23 18 31 28 16

Figure S13.  Get High-res Image Gene #22: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SMARCB1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S177.  Gene #23: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
SMARCB1 MUTATED 2 3 0
SMARCB1 WILD-TYPE 59 82 22
'SMARCB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0606 (Fisher's exact test), Q value = 1

Table S178.  Gene #23: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
SMARCB1 MUTATED 0 4 1
SMARCB1 WILD-TYPE 42 43 63
'SMARCB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S179.  Gene #23: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
SMARCB1 MUTATED 0 4 1 0
SMARCB1 WILD-TYPE 37 57 43 26
'SMARCB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S180.  Gene #23: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
SMARCB1 MUTATED 3 0 2
SMARCB1 WILD-TYPE 61 54 48
'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 1

Table S181.  Gene #23: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
SMARCB1 MUTATED 0 0 5
SMARCB1 WILD-TYPE 56 50 57

Figure S14.  Get High-res Image Gene #23: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S182.  Gene #23: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
SMARCB1 MUTATED 2 0 3
SMARCB1 WILD-TYPE 79 30 54
'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 1

Table S183.  Gene #23: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
SMARCB1 MUTATED 0 0 5
SMARCB1 WILD-TYPE 60 46 57

Figure S15.  Get High-res Image Gene #23: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.918 (Fisher's exact test), Q value = 1

Table S184.  Gene #23: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
SMARCB1 MUTATED 0 1 0 1 2 1 0
SMARCB1 WILD-TYPE 20 26 23 19 29 30 16
'TEKT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.607 (Fisher's exact test), Q value = 1

Table S185.  Gene #24: 'TEKT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
TEKT1 MUTATED 1 2 1
TEKT1 WILD-TYPE 60 83 21
'TEKT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S186.  Gene #24: 'TEKT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
TEKT1 MUTATED 2 1 1
TEKT1 WILD-TYPE 40 46 63
'TEKT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.906 (Fisher's exact test), Q value = 1

Table S187.  Gene #24: 'TEKT1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
TEKT1 MUTATED 1 1 1 1
TEKT1 WILD-TYPE 36 60 43 25
'TEKT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S188.  Gene #24: 'TEKT1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
TEKT1 MUTATED 1 2 1
TEKT1 WILD-TYPE 63 52 49
'TEKT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.463 (Fisher's exact test), Q value = 1

Table S189.  Gene #24: 'TEKT1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
TEKT1 MUTATED 0 2 2
TEKT1 WILD-TYPE 56 48 60
'TEKT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.514 (Fisher's exact test), Q value = 1

Table S190.  Gene #24: 'TEKT1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
TEKT1 MUTATED 1 1 2
TEKT1 WILD-TYPE 80 29 55
'TEKT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S191.  Gene #24: 'TEKT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
TEKT1 MUTATED 1 1 2
TEKT1 WILD-TYPE 59 45 60
'TEKT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.362 (Fisher's exact test), Q value = 1

Table S192.  Gene #24: 'TEKT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
TEKT1 MUTATED 0 0 1 0 2 0 1
TEKT1 WILD-TYPE 20 27 22 20 29 31 15
'MKL1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0773 (Fisher's exact test), Q value = 1

Table S193.  Gene #25: 'MKL1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
MKL1 MUTATED 1 8 0
MKL1 WILD-TYPE 60 77 22
'MKL1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.717 (Fisher's exact test), Q value = 1

Table S194.  Gene #25: 'MKL1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
MKL1 MUTATED 2 3 2
MKL1 WILD-TYPE 40 44 62
'MKL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 1

Table S195.  Gene #25: 'MKL1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
MKL1 MUTATED 2 4 0 3
MKL1 WILD-TYPE 35 57 44 23
'MKL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.472 (Fisher's exact test), Q value = 1

Table S196.  Gene #25: 'MKL1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
MKL1 MUTATED 4 4 1
MKL1 WILD-TYPE 60 50 49
'MKL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S197.  Gene #25: 'MKL1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
MKL1 MUTATED 3 2 4
MKL1 WILD-TYPE 53 48 58
'MKL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.278 (Fisher's exact test), Q value = 1

Table S198.  Gene #25: 'MKL1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
MKL1 MUTATED 4 0 5
MKL1 WILD-TYPE 77 30 52
'MKL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S199.  Gene #25: 'MKL1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
MKL1 MUTATED 3 2 4
MKL1 WILD-TYPE 57 44 58
'MKL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.996 (Fisher's exact test), Q value = 1

Table S200.  Gene #25: 'MKL1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
MKL1 MUTATED 1 2 1 1 2 1 1
MKL1 WILD-TYPE 19 25 22 19 29 30 15
'MYH7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.606 (Fisher's exact test), Q value = 1

Table S201.  Gene #26: 'MYH7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
MYH7 MUTATED 3 2 1
MYH7 WILD-TYPE 58 83 21
'MYH7 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S202.  Gene #26: 'MYH7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
MYH7 MUTATED 1 2 2
MYH7 WILD-TYPE 41 45 62
'MYH7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S203.  Gene #26: 'MYH7 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
MYH7 MUTATED 3 1 1 1
MYH7 WILD-TYPE 34 60 43 25
'MYH7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S204.  Gene #26: 'MYH7 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
MYH7 MUTATED 4 1 1
MYH7 WILD-TYPE 60 53 49
'MYH7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.774 (Fisher's exact test), Q value = 1

Table S205.  Gene #26: 'MYH7 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
MYH7 MUTATED 3 1 2
MYH7 WILD-TYPE 53 49 60
'MYH7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0372 (Fisher's exact test), Q value = 1

Table S206.  Gene #26: 'MYH7 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
MYH7 MUTATED 6 0 0
MYH7 WILD-TYPE 75 30 57

Figure S16.  Get High-res Image Gene #26: 'MYH7 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'MYH7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S207.  Gene #26: 'MYH7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
MYH7 MUTATED 2 1 3
MYH7 WILD-TYPE 58 45 59
'MYH7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.251 (Fisher's exact test), Q value = 1

Table S208.  Gene #26: 'MYH7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
MYH7 MUTATED 2 2 0 0 0 2 0
MYH7 WILD-TYPE 18 25 23 20 31 29 16
'MAP4K3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.827 (Fisher's exact test), Q value = 1

Table S209.  Gene #27: 'MAP4K3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
MAP4K3 MUTATED 2 2 1
MAP4K3 WILD-TYPE 59 83 21
'MAP4K3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.379 (Fisher's exact test), Q value = 1

Table S210.  Gene #27: 'MAP4K3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
MAP4K3 MUTATED 1 0 3
MAP4K3 WILD-TYPE 41 47 61
'MAP4K3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S211.  Gene #27: 'MAP4K3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
MAP4K3 MUTATED 0 1 3 1
MAP4K3 WILD-TYPE 37 60 41 25
'MAP4K3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.228 (Fisher's exact test), Q value = 1

Table S212.  Gene #27: 'MAP4K3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
MAP4K3 MUTATED 2 0 3
MAP4K3 WILD-TYPE 62 54 47
'MAP4K3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.133 (Fisher's exact test), Q value = 1

Table S213.  Gene #27: 'MAP4K3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
MAP4K3 MUTATED 2 3 0
MAP4K3 WILD-TYPE 54 47 62
'MAP4K3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.203 (Fisher's exact test), Q value = 1

Table S214.  Gene #27: 'MAP4K3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
MAP4K3 MUTATED 4 1 0
MAP4K3 WILD-TYPE 77 29 57
'MAP4K3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S215.  Gene #27: 'MAP4K3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
MAP4K3 MUTATED 2 3 0
MAP4K3 WILD-TYPE 58 43 62
'MAP4K3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S216.  Gene #27: 'MAP4K3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
MAP4K3 MUTATED 1 1 1 0 0 2 0
MAP4K3 WILD-TYPE 19 26 22 20 31 29 16
'NEK2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S217.  Gene #28: 'NEK2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
NEK2 MUTATED 1 2 0
NEK2 WILD-TYPE 60 83 22
'NEK2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S218.  Gene #28: 'NEK2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
NEK2 MUTATED 0 1 2
NEK2 WILD-TYPE 42 46 62
'NEK2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.515 (Fisher's exact test), Q value = 1

Table S219.  Gene #28: 'NEK2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
NEK2 MUTATED 0 1 2 0
NEK2 WILD-TYPE 37 60 42 26
'NEK2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.196 (Fisher's exact test), Q value = 1

Table S220.  Gene #28: 'NEK2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
NEK2 MUTATED 0 1 2
NEK2 WILD-TYPE 64 53 48
'NEK2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.296 (Fisher's exact test), Q value = 1

Table S221.  Gene #28: 'NEK2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
NEK2 MUTATED 0 2 1
NEK2 WILD-TYPE 56 48 61
'NEK2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.182 (Fisher's exact test), Q value = 1

Table S222.  Gene #28: 'NEK2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
NEK2 MUTATED 0 1 2
NEK2 WILD-TYPE 81 29 55
'NEK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 1

Table S223.  Gene #28: 'NEK2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
NEK2 MUTATED 0 2 1
NEK2 WILD-TYPE 60 44 61
'NEK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.696 (Fisher's exact test), Q value = 1

Table S224.  Gene #28: 'NEK2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
NEK2 MUTATED 0 0 1 1 1 0 0
NEK2 WILD-TYPE 20 27 22 19 30 31 16
Methods & Data
Input

  • Mutation data file = transformed.cor.cli.txt

  • Molecular subtypes file = KIRP-TP.transferedmergedcluster.txt

  • Number of patients = 168

  • Number of significantly mutated genes = 28

  • Number of Molecular subtypes = 8

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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