Correlation between gene mutation status and molecular subtypes
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C19C6WN6
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C19C6WN6
Overview
Introduction

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

Summary

Testing the association between mutation status of 19 genes and 10 molecular subtypes across 161 patients, 3 significant findings detected with P value < 0.05 and Q value < 0.25.

  • MET mutation correlated to 'MRNASEQ_CNMF'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 19 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, 3 significant findings 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
SETD2 11 (7%) 150 0.136
(0.616) 		4e-05
(0.0076) 		0.118
(0.604) 		0.0319
(0.46) 		0.00574
(0.273) 		0.00125
(0.119) 		0.0124
(0.369) 		0.0136
(0.369) 		0.0539
(0.569) 		0.0912
(0.604)
MET 15 (9%) 146 0.202
(0.697) 		0.0611
(0.58) 		0.193
(0.697) 		0.218
(0.724) 		0.00195
(0.123) 		0.0826
(0.604) 		0.835
(0.964) 		0.785
(0.953) 		0.642
(0.912) 		0.096
(0.604)
FAM18B2 35 (22%) 126 0.85
(0.967) 		0.476
(0.873) 		0.372
(0.873) 		0.885
(0.973) 		0.48
(0.873) 		0.679
(0.929) 		0.0573
(0.573) 		0.451
(0.873) 		0.648
(0.912) 		0.323
(0.873)
HNRNPM 10 (6%) 151 0.074
(0.586) 		0.219
(0.724) 		0.918
(0.985) 		0.398
(0.873) 		0.445
(0.873) 		0.626
(0.912) 		0.842
(0.964) 		1
(1.00) 		0.351
(0.873) 		0.626
(0.912)
NEFH 10 (6%) 151 0.433
(0.873) 		0.833
(0.964) 		0.491
(0.873) 		0.728
(0.953) 		0.13
(0.616) 		0.572
(0.893) 		0.028
(0.444) 		0.0215
(0.444) 		0.0715
(0.586) 		0.114
(0.604)
ZNF598 10 (6%) 151 0.515
(0.873) 		0.914
(0.985) 		0.468
(0.873) 		0.295
(0.836) 		0.159
(0.697) 		0.525
(0.882) 		0.714
(0.949) 		0.255
(0.795) 		0.0915
(0.604) 		0.534
(0.882)
NF2 10 (6%) 151 0.132
(0.616) 		0.0228
(0.444) 		0.57
(0.893) 		0.903
(0.98) 		0.0955
(0.604) 		0.221
(0.724) 		0.51
(0.873) 		0.595
(0.905) 		0.495
(0.873) 		0.0387
(0.46)
TDG 5 (3%) 156 0.101
(0.604) 		0.0658
(0.586) 		0.622
(0.912) 		0.458
(0.873) 		0.861
(0.973) 		0.267
(0.82) 		0.441
(0.873) 		0.292
(0.836) 		0.444
(0.873) 		1
(1.00)
SKI 6 (4%) 155 0.108
(0.604) 		0.0724
(0.586) 		0.733
(0.953) 		0.674
(0.929) 		0.127
(0.616) 		1
(1.00) 		0.511
(0.873) 		0.88
(0.973) 		0.866
(0.973) 		0.498
(0.873)
MUC5B 14 (9%) 147 0.115
(0.604) 		0.664
(0.927) 		0.38
(0.873) 		0.0532
(0.569) 		0.753
(0.953) 		0.102
(0.604) 		0.838
(0.964) 		0.456
(0.873) 		0.444
(0.873) 		0.902
(0.98)
KDM6A 7 (4%) 154 1
(1.00) 		0.801
(0.957) 		0.378
(0.873) 		0.199
(0.697) 		0.028
(0.444) 		0.313
(0.873) 		0.502
(0.873) 		0.226
(0.726) 		0.397
(0.873) 		0.165
(0.697)
ZNF814 8 (5%) 153 0.684
(0.929) 		0.392
(0.873) 		1
(1.00) 		0.7
(0.936) 		0.764
(0.953) 		0.404
(0.873) 		0.43
(0.873) 		0.195
(0.697) 		0.194
(0.697) 		0.836
(0.964)
SMARCB1 4 (2%) 157 0.824
(0.964) 		0.184
(0.697) 		1
(1.00) 		0.4
(0.873) 		0.569
(0.893) 		0.53
(0.882) 		0.036
(0.46) 		0.365
(0.873) 		0.107
(0.604) 		0.438
(0.873)
AHNAK2 7 (4%) 154 0.951
(1.00) 		0.768
(0.953) 		0.764
(0.953) 		0.886
(0.973) 		0.566
(0.893) 		0.879
(0.973) 		0.293
(0.836) 		0.167
(0.697) 		0.255
(0.795) 		0.643
(0.912)
OR2L8 4 (2%) 157 0.391
(0.873) 		0.471
(0.873) 		0.555
(0.893) 		0.698
(0.936) 		0.0375
(0.46) 		0.187
(0.697) 		0.329
(0.873) 		0.177
(0.697) 		0.55
(0.893) 		0.765
(0.953)
PAM 3 (2%) 158 0.585
(0.904) 		0.781
(0.953) 		0.111
(0.604) 		0.777
(0.953) 		0.178
(0.697) 		0.793
(0.954) 		0.511
(0.873) 		0.0132
(0.369)
IDUA 5 (3%) 156 0.289
(0.836) 		0.39
(0.873) 		0.375
(0.873) 		0.761
(0.953) 		0.377
(0.873) 		0.41
(0.873) 		0.441
(0.873) 		0.446
(0.873) 		0.834
(0.964) 		0.764
(0.953)
CSGALNACT2 5 (3%) 156 0.136
(0.616) 		0.391
(0.873) 		0.681
(0.929) 		0.642
(0.912) 		0.573
(0.893) 		0.413
(0.873) 		0.627
(0.912) 		0.637
(0.912)
RPL7A 3 (2%) 158 0.771
(0.953) 		0.189
(0.697) 		0.63
(0.912) 		0.463
(0.873) 		0.026
(0.444) 		0.594
(0.905) 		0.289
(0.836) 		0.788
(0.953)
'FAM18B2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.85 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 39 25 36
FAM18B2 MUTATED 13 10 4 8
FAM18B2 WILD-TYPE 48 29 21 28
'FAM18B2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.476 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 45 60
FAM18B2 MUTATED 7 12 12
FAM18B2 WILD-TYPE 36 33 48
'FAM18B2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.372 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 41 35
FAM18B2 MUTATED 8 7 10
FAM18B2 WILD-TYPE 40 34 25
'FAM18B2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.885 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 34 42 25
FAM18B2 MUTATED 5 8 7 5
FAM18B2 WILD-TYPE 18 26 35 20
'FAM18B2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.48 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 45 35 58
FAM18B2 MUTATED 7 9 5 14
FAM18B2 WILD-TYPE 16 36 30 44
'FAM18B2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.679 (Fisher's exact test), Q value = 0.93

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 64 30
FAM18B2 MUTATED 14 16 5
FAM18B2 WILD-TYPE 53 48 25
'FAM18B2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0573 (Fisher's exact test), Q value = 0.57

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 57 57
FAM18B2 MUTATED 16 10 9
FAM18B2 WILD-TYPE 31 47 48
'FAM18B2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.451 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 39 59
FAM18B2 MUTATED 17 7 11
FAM18B2 WILD-TYPE 46 32 48
'FAM18B2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.648 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 46
FAM18B2 MUTATED 9 11 9
FAM18B2 WILD-TYPE 29 28 37
'FAM18B2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.323 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 49 12 15
FAM18B2 MUTATED 14 11 3 1
FAM18B2 WILD-TYPE 33 38 9 14
'HNRNPM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.074 (Fisher's exact test), Q value = 0.59

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 39 25 36
HNRNPM MUTATED 7 0 2 1
HNRNPM WILD-TYPE 54 39 23 35
'HNRNPM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 0.72

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 45 60
HNRNPM MUTATED 5 3 2
HNRNPM WILD-TYPE 38 42 58
'HNRNPM MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.918 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 41 35
HNRNPM MUTATED 4 4 2
HNRNPM WILD-TYPE 44 37 33
'HNRNPM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.398 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 34 42 25
HNRNPM MUTATED 4 2 3 1
HNRNPM WILD-TYPE 19 32 39 24
'HNRNPM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.445 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 45 35 58
HNRNPM MUTATED 3 2 1 4
HNRNPM WILD-TYPE 20 43 34 54
'HNRNPM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.626 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 64 30
HNRNPM MUTATED 4 3 3
HNRNPM WILD-TYPE 63 61 27
'HNRNPM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.842 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 57 57
HNRNPM MUTATED 2 4 4
HNRNPM WILD-TYPE 45 53 53
'HNRNPM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 39 59
HNRNPM MUTATED 4 2 4
HNRNPM WILD-TYPE 59 37 55
'HNRNPM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.351 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 46
HNRNPM MUTATED 3 1 5
HNRNPM WILD-TYPE 35 38 41
'HNRNPM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.626 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 49 12 15
HNRNPM MUTATED 4 5 0 0
HNRNPM WILD-TYPE 43 44 12 15
'NEFH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.433 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 39 25 36
NEFH MUTATED 3 1 2 4
NEFH WILD-TYPE 58 38 23 32
'NEFH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.833 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 45 60
NEFH MUTATED 3 2 4
NEFH WILD-TYPE 40 43 56
'NEFH MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.491 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 41 35
NEFH MUTATED 3 1 3
NEFH WILD-TYPE 45 40 32
'NEFH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.728 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 34 42 25
NEFH MUTATED 1 1 4 1
NEFH WILD-TYPE 22 33 38 24
'NEFH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 0.62

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 45 35 58
NEFH MUTATED 0 3 5 2
NEFH WILD-TYPE 23 42 30 56
'NEFH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.572 (Fisher's exact test), Q value = 0.89

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 64 30
NEFH MUTATED 6 3 1
NEFH WILD-TYPE 61 61 29
'NEFH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.44

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 57 57
NEFH MUTATED 5 5 0
NEFH WILD-TYPE 42 52 57

Figure S1.  Get High-res Image Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NEFH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0215 (Fisher's exact test), Q value = 0.44

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 39 59
NEFH MUTATED 6 4 0
NEFH WILD-TYPE 57 35 59

Figure S2.  Get High-res Image Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0715 (Fisher's exact test), Q value = 0.59

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 46
NEFH MUTATED 3 1 0
NEFH WILD-TYPE 35 38 46
'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.114 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 49 12 15
NEFH MUTATED 4 0 0 0
NEFH WILD-TYPE 43 49 12 15
'ZNF598 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.515 (Fisher's exact test), Q value = 0.87

Table S31.  Gene #4: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 39 25 36
ZNF598 MUTATED 4 1 1 4
ZNF598 WILD-TYPE 57 38 24 32
'ZNF598 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.914 (Fisher's exact test), Q value = 0.99

Table S32.  Gene #4: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 45 60
ZNF598 MUTATED 3 3 3
ZNF598 WILD-TYPE 40 42 57
'ZNF598 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.468 (Fisher's exact test), Q value = 0.87

Table S33.  Gene #4: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 41 35
ZNF598 MUTATED 5 3 1
ZNF598 WILD-TYPE 43 38 34
'ZNF598 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.295 (Fisher's exact test), Q value = 0.84

Table S34.  Gene #4: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 34 42 25
ZNF598 MUTATED 3 2 4 0
ZNF598 WILD-TYPE 20 32 38 25
'ZNF598 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.159 (Fisher's exact test), Q value = 0.7

Table S35.  Gene #4: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 45 35 58
ZNF598 MUTATED 4 2 1 3
ZNF598 WILD-TYPE 19 43 34 55
'ZNF598 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.525 (Fisher's exact test), Q value = 0.88

Table S36.  Gene #4: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 64 30
ZNF598 MUTATED 3 4 3
ZNF598 WILD-TYPE 64 60 27
'ZNF598 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.714 (Fisher's exact test), Q value = 0.95

Table S37.  Gene #4: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 57 57
ZNF598 MUTATED 2 3 5
ZNF598 WILD-TYPE 45 54 52
'ZNF598 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.255 (Fisher's exact test), Q value = 0.8

Table S38.  Gene #4: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 39 59
ZNF598 MUTATED 2 2 6
ZNF598 WILD-TYPE 61 37 53
'ZNF598 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0915 (Fisher's exact test), Q value = 0.6

Table S39.  Gene #4: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 46
ZNF598 MUTATED 2 1 7
ZNF598 WILD-TYPE 36 38 39
'ZNF598 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.534 (Fisher's exact test), Q value = 0.88

Table S40.  Gene #4: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 49 12 15
ZNF598 MUTATED 2 6 1 1
ZNF598 WILD-TYPE 45 43 11 14
'NF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.132 (Fisher's exact test), Q value = 0.62

Table S41.  Gene #5: 'NF2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 39 25 36
NF2 MUTATED 4 1 0 5
NF2 WILD-TYPE 57 38 25 31
'NF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.44

Table S42.  Gene #5: 'NF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 45 60
NF2 MUTATED 0 6 3
NF2 WILD-TYPE 43 39 57

Figure S3.  Get High-res Image Gene #5: 'NF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NF2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 0.89

Table S43.  Gene #5: 'NF2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 41 35
NF2 MUTATED 3 2 4
NF2 WILD-TYPE 45 39 31
'NF2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.903 (Fisher's exact test), Q value = 0.98

Table S44.  Gene #5: 'NF2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 34 42 25
NF2 MUTATED 1 2 4 2
NF2 WILD-TYPE 22 32 38 23
'NF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0955 (Fisher's exact test), Q value = 0.6

Table S45.  Gene #5: 'NF2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 45 35 58
NF2 MUTATED 0 4 0 6
NF2 WILD-TYPE 23 41 35 52
'NF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.221 (Fisher's exact test), Q value = 0.72

Table S46.  Gene #5: 'NF2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 64 30
NF2 MUTATED 3 3 4
NF2 WILD-TYPE 64 61 26
'NF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.51 (Fisher's exact test), Q value = 0.87

Table S47.  Gene #5: 'NF2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 57 57
NF2 MUTATED 3 2 5
NF2 WILD-TYPE 44 55 52
'NF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.595 (Fisher's exact test), Q value = 0.9

Table S48.  Gene #5: 'NF2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 39 59
NF2 MUTATED 4 1 5
NF2 WILD-TYPE 59 38 54
'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S49.  Gene #5: 'NF2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 46
NF2 MUTATED 2 1 4
NF2 WILD-TYPE 36 38 42
'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0387 (Fisher's exact test), Q value = 0.46

Table S50.  Gene #5: 'NF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 49 12 15
NF2 MUTATED 3 1 3 0
NF2 WILD-TYPE 44 48 9 15

Figure S4.  Get High-res Image Gene #5: 'NF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TDG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 39 25 36
TDG MUTATED 0 2 2 1
TDG WILD-TYPE 61 37 23 35
'TDG MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0658 (Fisher's exact test), Q value = 0.59

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 45 60
TDG MUTATED 0 4 1
TDG WILD-TYPE 43 41 59
'TDG MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 41 35
TDG MUTATED 1 2 2
TDG WILD-TYPE 47 39 33
'TDG MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.458 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 34 42 25
TDG MUTATED 0 2 3 0
TDG WILD-TYPE 23 32 39 25
'TDG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.861 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 45 35 58
TDG MUTATED 0 1 1 3
TDG WILD-TYPE 23 44 34 55
'TDG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.267 (Fisher's exact test), Q value = 0.82

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 64 30
TDG MUTATED 4 1 0
TDG WILD-TYPE 63 63 30
'TDG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 57 57
TDG MUTATED 3 1 1
TDG WILD-TYPE 44 56 56
'TDG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.292 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 39 59
TDG MUTATED 4 0 1
TDG WILD-TYPE 59 39 58
'TDG MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 46
TDG MUTATED 3 1 1
TDG WILD-TYPE 35 38 45
'TDG MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 49 12 15
TDG MUTATED 2 3 0 0
TDG WILD-TYPE 45 46 12 15
'MET MUTATION STATUS' versus 'CN_CNMF'

P value = 0.202 (Fisher's exact test), Q value = 0.7

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 39 25 36
MET MUTATED 5 6 0 4
MET WILD-TYPE 56 33 25 32
'MET MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0611 (Fisher's exact test), Q value = 0.58

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 45 60
MET MUTATED 3 1 9
MET WILD-TYPE 40 44 51
'MET MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.193 (Fisher's exact test), Q value = 0.7

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 41 35
MET MUTATED 7 5 1
MET WILD-TYPE 41 36 34
'MET MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.218 (Fisher's exact test), Q value = 0.72

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 34 42 25
MET MUTATED 3 5 5 0
MET WILD-TYPE 20 29 37 25
'MET MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00195 (Fisher's exact test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 45 35 58
MET MUTATED 5 8 1 1
MET WILD-TYPE 18 37 34 57

Figure S5.  Get High-res Image Gene #7: 'MET MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'MET MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0826 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 64 30
MET MUTATED 3 10 2
MET WILD-TYPE 64 54 28
'MET MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.835 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 57 57
MET MUTATED 5 4 6
MET WILD-TYPE 42 53 51
'MET MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.785 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 39 59
MET MUTATED 5 3 7
MET WILD-TYPE 58 36 52
'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 46
MET MUTATED 4 5 3
MET WILD-TYPE 34 34 43
'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.096 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 49 12 15
MET MUTATED 5 3 0 4
MET WILD-TYPE 42 46 12 11
'SETD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.136 (Fisher's exact test), Q value = 0.62

Table S71.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 39 25 36
SETD2 MUTATED 5 1 0 5
SETD2 WILD-TYPE 56 38 25 31
'SETD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0076

Table S72.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 45 60
SETD2 MUTATED 1 10 0
SETD2 WILD-TYPE 42 35 60

Figure S6.  Get High-res Image Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'SETD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.118 (Fisher's exact test), Q value = 0.6

Table S73.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 41 35
SETD2 MUTATED 2 1 5
SETD2 WILD-TYPE 46 40 30
'SETD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0319 (Fisher's exact test), Q value = 0.46

Table S74.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 34 42 25
SETD2 MUTATED 0 1 2 5
SETD2 WILD-TYPE 23 33 40 20

Figure S7.  Get High-res Image Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00574 (Fisher's exact test), Q value = 0.27

Table S75.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 45 35 58
SETD2 MUTATED 0 0 2 9
SETD2 WILD-TYPE 23 45 33 49

Figure S8.  Get High-res Image Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00125 (Fisher's exact test), Q value = 0.12

Table S76.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 64 30
SETD2 MUTATED 10 0 1
SETD2 WILD-TYPE 57 64 29

Figure S9.  Get High-res Image Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.37

Table S77.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 57 57
SETD2 MUTATED 6 0 5
SETD2 WILD-TYPE 41 57 52

Figure S10.  Get High-res Image Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.37

Table S78.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 39 59
SETD2 MUTATED 9 0 2
SETD2 WILD-TYPE 54 39 57

Figure S11.  Get High-res Image Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0539 (Fisher's exact test), Q value = 0.57

Table S79.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 46
SETD2 MUTATED 4 0 6
SETD2 WILD-TYPE 34 39 40
'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0912 (Fisher's exact test), Q value = 0.6

Table S80.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 49 12 15
SETD2 MUTATED 2 8 0 0
SETD2 WILD-TYPE 45 41 12 15
'SKI MUTATION STATUS' versus 'CN_CNMF'

P value = 0.108 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 39 25 36
SKI MUTATED 5 0 1 0
SKI WILD-TYPE 56 39 24 36
'SKI MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0724 (Fisher's exact test), Q value = 0.59

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 45 60
SKI MUTATED 4 0 2
SKI WILD-TYPE 39 45 58
'SKI MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.733 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 41 35
SKI MUTATED 3 1 1
SKI WILD-TYPE 45 40 34
'SKI MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.674 (Fisher's exact test), Q value = 0.93

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 34 42 25
SKI MUTATED 2 1 1 1
SKI WILD-TYPE 21 33 41 24
'SKI MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.127 (Fisher's exact test), Q value = 0.62

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 45 35 58
SKI MUTATED 3 1 1 1
SKI WILD-TYPE 20 44 34 57
'SKI MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 64 30
SKI MUTATED 3 2 1
SKI WILD-TYPE 64 62 29
'SKI MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.511 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 57 57
SKI MUTATED 3 1 2
SKI WILD-TYPE 44 56 55
'SKI MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.88 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 39 59
SKI MUTATED 2 1 3
SKI WILD-TYPE 61 38 56
'SKI MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.866 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 46
SKI MUTATED 2 1 2
SKI WILD-TYPE 36 38 44
'SKI MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.498 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 49 12 15
SKI MUTATED 1 4 0 0
SKI WILD-TYPE 46 45 12 15
'MUC5B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.115 (Fisher's exact test), Q value = 0.6

Table S91.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 39 25 36
MUC5B MUTATED 2 3 4 5
MUC5B WILD-TYPE 59 36 21 31
'MUC5B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.664 (Fisher's exact test), Q value = 0.93

Table S92.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 45 60
MUC5B MUTATED 5 4 4
MUC5B WILD-TYPE 38 41 56
'MUC5B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.38 (Fisher's exact test), Q value = 0.87

Table S93.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 41 35
MUC5B MUTATED 2 5 2
MUC5B WILD-TYPE 46 36 33
'MUC5B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0532 (Fisher's exact test), Q value = 0.57

Table S94.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 34 42 25
MUC5B MUTATED 3 3 0 3
MUC5B WILD-TYPE 20 31 42 22
'MUC5B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.753 (Fisher's exact test), Q value = 0.95

Table S95.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 45 35 58
MUC5B MUTATED 1 3 3 7
MUC5B WILD-TYPE 22 42 32 51
'MUC5B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.102 (Fisher's exact test), Q value = 0.6

Table S96.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 64 30
MUC5B MUTATED 9 2 3
MUC5B WILD-TYPE 58 62 27
'MUC5B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.838 (Fisher's exact test), Q value = 0.96

Table S97.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 57 57
MUC5B MUTATED 5 4 5
MUC5B WILD-TYPE 42 53 52
'MUC5B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.456 (Fisher's exact test), Q value = 0.87

Table S98.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 39 59
MUC5B MUTATED 7 4 3
MUC5B WILD-TYPE 56 35 56
'MUC5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 0.87

Table S99.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 46
MUC5B MUTATED 5 2 5
MUC5B WILD-TYPE 33 37 41
'MUC5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.902 (Fisher's exact test), Q value = 0.98

Table S100.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 49 12 15
MUC5B MUTATED 5 4 1 2
MUC5B WILD-TYPE 42 45 11 13
'KDM6A MUTATION STATUS' versus 'CN_CNMF'

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

Table S101.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 39 25 36
KDM6A MUTATED 3 2 1 1
KDM6A WILD-TYPE 58 37 24 35
'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.801 (Fisher's exact test), Q value = 0.96

Table S102.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 45 60
KDM6A MUTATED 3 2 2
KDM6A WILD-TYPE 40 43 58
'KDM6A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 0.87

Table S103.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 41 35
KDM6A MUTATED 1 1 3
KDM6A WILD-TYPE 47 40 32
'KDM6A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.199 (Fisher's exact test), Q value = 0.7

Table S104.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 34 42 25
KDM6A MUTATED 0 1 1 3
KDM6A WILD-TYPE 23 33 41 22
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.44

Table S105.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 45 35 58
KDM6A MUTATED 0 1 5 1
KDM6A WILD-TYPE 23 44 30 57

Figure S12.  Get High-res Image Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.313 (Fisher's exact test), Q value = 0.87

Table S106.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 64 30
KDM6A MUTATED 5 1 1
KDM6A WILD-TYPE 62 63 29
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.502 (Fisher's exact test), Q value = 0.87

Table S107.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 57 57
KDM6A MUTATED 3 3 1
KDM6A WILD-TYPE 44 54 56
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.226 (Fisher's exact test), Q value = 0.73

Table S108.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 39 59
KDM6A MUTATED 5 1 1
KDM6A WILD-TYPE 58 38 58
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 0.87

Table S109.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 46
KDM6A MUTATED 2 0 1
KDM6A WILD-TYPE 36 39 45
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.165 (Fisher's exact test), Q value = 0.7

Table S110.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 49 12 15
KDM6A MUTATED 2 0 1 0
KDM6A WILD-TYPE 45 49 11 15
'ZNF814 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.684 (Fisher's exact test), Q value = 0.93

Table S111.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 39 25 36
ZNF814 MUTATED 2 2 1 3
ZNF814 WILD-TYPE 59 37 24 33
'ZNF814 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.392 (Fisher's exact test), Q value = 0.87

Table S112.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 45 60
ZNF814 MUTATED 1 4 3
ZNF814 WILD-TYPE 42 41 57
'ZNF814 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S113.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 41 35
ZNF814 MUTATED 3 2 2
ZNF814 WILD-TYPE 45 39 33
'ZNF814 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.7 (Fisher's exact test), Q value = 0.94

Table S114.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 34 42 25
ZNF814 MUTATED 0 2 3 2
ZNF814 WILD-TYPE 23 32 39 23
'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.764 (Fisher's exact test), Q value = 0.95

Table S115.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 45 35 58
ZNF814 MUTATED 0 2 2 4
ZNF814 WILD-TYPE 23 43 33 54
'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.404 (Fisher's exact test), Q value = 0.87

Table S116.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 64 30
ZNF814 MUTATED 5 3 0
ZNF814 WILD-TYPE 62 61 30
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.43 (Fisher's exact test), Q value = 0.87

Table S117.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 57 57
ZNF814 MUTATED 3 1 4
ZNF814 WILD-TYPE 44 56 53
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 0.7

Table S118.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 39 59
ZNF814 MUTATED 5 0 3
ZNF814 WILD-TYPE 58 39 56
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.194 (Fisher's exact test), Q value = 0.7

Table S119.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 46
ZNF814 MUTATED 0 3 4
ZNF814 WILD-TYPE 38 36 42
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.836 (Fisher's exact test), Q value = 0.96

Table S120.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 49 12 15
ZNF814 MUTATED 2 4 0 1
ZNF814 WILD-TYPE 45 45 12 14
'SMARCB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.824 (Fisher's exact test), Q value = 0.96

Table S121.  Gene #13: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 39 25 36
SMARCB1 MUTATED 2 1 1 0
SMARCB1 WILD-TYPE 59 38 24 36
'SMARCB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.184 (Fisher's exact test), Q value = 0.7

Table S122.  Gene #13: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 45 60
SMARCB1 MUTATED 0 3 1
SMARCB1 WILD-TYPE 43 42 59
'SMARCB1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S123.  Gene #13: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 41 35
SMARCB1 MUTATED 1 1 1
SMARCB1 WILD-TYPE 47 40 34
'SMARCB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.4 (Fisher's exact test), Q value = 0.87

Table S124.  Gene #13: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 34 42 25
SMARCB1 MUTATED 1 1 0 1
SMARCB1 WILD-TYPE 22 33 42 24
'SMARCB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.569 (Fisher's exact test), Q value = 0.89

Table S125.  Gene #13: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 45 35 58
SMARCB1 MUTATED 0 1 0 3
SMARCB1 WILD-TYPE 23 44 35 55
'SMARCB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.53 (Fisher's exact test), Q value = 0.88

Table S126.  Gene #13: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 64 30
SMARCB1 MUTATED 3 1 0
SMARCB1 WILD-TYPE 64 63 30
'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.46

Table S127.  Gene #13: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 57 57
SMARCB1 MUTATED 0 0 4
SMARCB1 WILD-TYPE 47 57 53

Figure S13.  Get High-res Image Gene #13: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.365 (Fisher's exact test), Q value = 0.87

Table S128.  Gene #13: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 39 59
SMARCB1 MUTATED 1 0 3
SMARCB1 WILD-TYPE 62 39 56
'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 0.6

Table S129.  Gene #13: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 46
SMARCB1 MUTATED 0 0 3
SMARCB1 WILD-TYPE 38 39 43
'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.438 (Fisher's exact test), Q value = 0.87

Table S130.  Gene #13: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 49 12 15
SMARCB1 MUTATED 0 3 0 0
SMARCB1 WILD-TYPE 47 46 12 15
'AHNAK2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.951 (Fisher's exact test), Q value = 1

Table S131.  Gene #14: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 39 25 36
AHNAK2 MUTATED 3 1 1 2
AHNAK2 WILD-TYPE 58 38 24 34
'AHNAK2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.768 (Fisher's exact test), Q value = 0.95

Table S132.  Gene #14: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 45 60
AHNAK2 MUTATED 2 1 3
AHNAK2 WILD-TYPE 41 44 57
'AHNAK2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.764 (Fisher's exact test), Q value = 0.95

Table S133.  Gene #14: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 41 35
AHNAK2 MUTATED 3 1 2
AHNAK2 WILD-TYPE 45 40 33
'AHNAK2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.886 (Fisher's exact test), Q value = 0.97

Table S134.  Gene #14: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 34 42 25
AHNAK2 MUTATED 1 1 2 2
AHNAK2 WILD-TYPE 22 33 40 23
'AHNAK2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.566 (Fisher's exact test), Q value = 0.89

Table S135.  Gene #14: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 45 35 58
AHNAK2 MUTATED 2 1 2 2
AHNAK2 WILD-TYPE 21 44 33 56
'AHNAK2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.879 (Fisher's exact test), Q value = 0.97

Table S136.  Gene #14: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 64 30
AHNAK2 MUTATED 4 2 1
AHNAK2 WILD-TYPE 63 62 29
'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 0.84

Table S137.  Gene #14: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 57 57
AHNAK2 MUTATED 4 1 2
AHNAK2 WILD-TYPE 43 56 55
'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.167 (Fisher's exact test), Q value = 0.7

Table S138.  Gene #14: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 39 59
AHNAK2 MUTATED 5 0 2
AHNAK2 WILD-TYPE 58 39 57
'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.255 (Fisher's exact test), Q value = 0.8

Table S139.  Gene #14: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 46
AHNAK2 MUTATED 4 2 1
AHNAK2 WILD-TYPE 34 37 45
'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.643 (Fisher's exact test), Q value = 0.91

Table S140.  Gene #14: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 49 12 15
AHNAK2 MUTATED 4 2 0 1
AHNAK2 WILD-TYPE 43 47 12 14
'OR2L8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.391 (Fisher's exact test), Q value = 0.87

Table S141.  Gene #15: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 39 25 36
OR2L8 MUTATED 1 2 1 0
OR2L8 WILD-TYPE 60 37 24 36
'OR2L8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.471 (Fisher's exact test), Q value = 0.87

Table S142.  Gene #15: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 45 60
OR2L8 MUTATED 2 0 2
OR2L8 WILD-TYPE 41 45 58
'OR2L8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.555 (Fisher's exact test), Q value = 0.89

Table S143.  Gene #15: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 41 35
OR2L8 MUTATED 2 2 0
OR2L8 WILD-TYPE 46 39 35
'OR2L8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.698 (Fisher's exact test), Q value = 0.94

Table S144.  Gene #15: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 34 42 25
OR2L8 MUTATED 1 2 1 0
OR2L8 WILD-TYPE 22 32 41 25
'OR2L8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0375 (Fisher's exact test), Q value = 0.46

Table S145.  Gene #15: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 45 35 58
OR2L8 MUTATED 2 2 0 0
OR2L8 WILD-TYPE 21 43 35 58

Figure S14.  Get High-res Image Gene #15: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'OR2L8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.187 (Fisher's exact test), Q value = 0.7

Table S146.  Gene #15: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 64 30
OR2L8 MUTATED 0 3 1
OR2L8 WILD-TYPE 67 61 29
'OR2L8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.329 (Fisher's exact test), Q value = 0.87

Table S147.  Gene #15: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 57 57
OR2L8 MUTATED 0 1 3
OR2L8 WILD-TYPE 47 56 54
'OR2L8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.177 (Fisher's exact test), Q value = 0.7

Table S148.  Gene #15: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 39 59
OR2L8 MUTATED 0 1 3
OR2L8 WILD-TYPE 63 38 56
'OR2L8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.55 (Fisher's exact test), Q value = 0.89

Table S149.  Gene #15: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 46
OR2L8 MUTATED 0 2 2
OR2L8 WILD-TYPE 38 37 44
'OR2L8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.765 (Fisher's exact test), Q value = 0.95

Table S150.  Gene #15: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 49 12 15
OR2L8 MUTATED 1 2 0 1
OR2L8 WILD-TYPE 46 47 12 14
'PAM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.585 (Fisher's exact test), Q value = 0.9

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 39 25 36
PAM MUTATED 1 0 1 1
PAM WILD-TYPE 60 39 24 35
'PAM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.781 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 45 60
PAM MUTATED 0 1 2
PAM WILD-TYPE 43 44 58
'PAM MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.111 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 41 35
PAM MUTATED 3 0 0
PAM WILD-TYPE 45 41 35
'PAM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.777 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 34 42 25
PAM MUTATED 0 1 2 0
PAM WILD-TYPE 23 33 40 25
'PAM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.178 (Fisher's exact test), Q value = 0.7

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 45 35 58
PAM MUTATED 0 1 2 0
PAM WILD-TYPE 23 44 33 58
'PAM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.793 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 64 30
PAM MUTATED 1 2 0
PAM WILD-TYPE 66 62 30
'PAM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.511 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 57 57
PAM MUTATED 1 2 0
PAM WILD-TYPE 46 55 57
'PAM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.37

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 39 59
PAM MUTATED 0 3 0
PAM WILD-TYPE 63 36 59

Figure S15.  Get High-res Image Gene #16: 'PAM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'IDUA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 0.84

Table S159.  Gene #17: 'IDUA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 39 25 36
IDUA MUTATED 4 0 0 1
IDUA WILD-TYPE 57 39 25 35
'IDUA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.39 (Fisher's exact test), Q value = 0.87

Table S160.  Gene #17: 'IDUA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 45 60
IDUA MUTATED 3 1 1
IDUA WILD-TYPE 40 44 59
'IDUA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.375 (Fisher's exact test), Q value = 0.87

Table S161.  Gene #17: 'IDUA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 41 35
IDUA MUTATED 1 1 3
IDUA WILD-TYPE 47 40 32
'IDUA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.761 (Fisher's exact test), Q value = 0.95

Table S162.  Gene #17: 'IDUA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 34 42 25
IDUA MUTATED 1 1 1 2
IDUA WILD-TYPE 22 33 41 23
'IDUA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.377 (Fisher's exact test), Q value = 0.87

Table S163.  Gene #17: 'IDUA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 45 35 58
IDUA MUTATED 1 0 2 2
IDUA WILD-TYPE 22 45 33 56
'IDUA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.41 (Fisher's exact test), Q value = 0.87

Table S164.  Gene #17: 'IDUA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 64 30
IDUA MUTATED 2 1 2
IDUA WILD-TYPE 65 63 28
'IDUA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 0.87

Table S165.  Gene #17: 'IDUA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 57 57
IDUA MUTATED 3 1 1
IDUA WILD-TYPE 44 56 56
'IDUA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.446 (Fisher's exact test), Q value = 0.87

Table S166.  Gene #17: 'IDUA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 39 59
IDUA MUTATED 3 0 2
IDUA WILD-TYPE 60 39 57
'IDUA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.834 (Fisher's exact test), Q value = 0.96

Table S167.  Gene #17: 'IDUA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 39 46
IDUA MUTATED 1 2 1
IDUA WILD-TYPE 37 37 45
'IDUA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.764 (Fisher's exact test), Q value = 0.95

Table S168.  Gene #17: 'IDUA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 49 12 15
IDUA MUTATED 1 2 0 1
IDUA WILD-TYPE 46 47 12 14
'CSGALNACT2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.136 (Fisher's exact test), Q value = 0.62

Table S169.  Gene #18: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 39 25 36
CSGALNACT2 MUTATED 1 0 1 3
CSGALNACT2 WILD-TYPE 60 39 24 33
'CSGALNACT2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.391 (Fisher's exact test), Q value = 0.87

Table S170.  Gene #18: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 45 60
CSGALNACT2 MUTATED 3 1 1
CSGALNACT2 WILD-TYPE 40 44 59
'CSGALNACT2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.681 (Fisher's exact test), Q value = 0.93

Table S171.  Gene #18: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 41 35
CSGALNACT2 MUTATED 1 1 2
CSGALNACT2 WILD-TYPE 47 40 33
'CSGALNACT2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.642 (Fisher's exact test), Q value = 0.91

Table S172.  Gene #18: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 34 42 25
CSGALNACT2 MUTATED 1 0 2 1
CSGALNACT2 WILD-TYPE 22 34 40 24
'CSGALNACT2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.573 (Fisher's exact test), Q value = 0.89

Table S173.  Gene #18: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 45 35 58
CSGALNACT2 MUTATED 1 1 0 3
CSGALNACT2 WILD-TYPE 22 44 35 55
'CSGALNACT2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.413 (Fisher's exact test), Q value = 0.87

Table S174.  Gene #18: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 64 30
CSGALNACT2 MUTATED 2 1 2
CSGALNACT2 WILD-TYPE 65 63 28
'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.627 (Fisher's exact test), Q value = 0.91

Table S175.  Gene #18: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 57 57
CSGALNACT2 MUTATED 1 3 1
CSGALNACT2 WILD-TYPE 46 54 56
'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.637 (Fisher's exact test), Q value = 0.91

Table S176.  Gene #18: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 39 59
CSGALNACT2 MUTATED 1 2 2
CSGALNACT2 WILD-TYPE 62 37 57
'RPL7A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.771 (Fisher's exact test), Q value = 0.95

Table S177.  Gene #19: 'RPL7A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 39 25 36
RPL7A MUTATED 2 0 0 1
RPL7A WILD-TYPE 59 39 25 35
'RPL7A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.189 (Fisher's exact test), Q value = 0.7

Table S178.  Gene #19: 'RPL7A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 45 60
RPL7A MUTATED 2 1 0
RPL7A WILD-TYPE 41 44 60
'RPL7A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.63 (Fisher's exact test), Q value = 0.91

Table S179.  Gene #19: 'RPL7A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 48 41 35
RPL7A MUTATED 2 0 1
RPL7A WILD-TYPE 46 41 34
'RPL7A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.463 (Fisher's exact test), Q value = 0.87

Table S180.  Gene #19: 'RPL7A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 34 42 25
RPL7A MUTATED 1 0 2 0
RPL7A WILD-TYPE 22 34 40 25
'RPL7A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.44

Table S181.  Gene #19: 'RPL7A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 45 35 58
RPL7A MUTATED 2 0 1 0
RPL7A WILD-TYPE 21 45 34 58

Figure S16.  Get High-res Image Gene #19: 'RPL7A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'RPL7A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.594 (Fisher's exact test), Q value = 0.9

Table S182.  Gene #19: 'RPL7A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 64 30
RPL7A MUTATED 1 1 1
RPL7A WILD-TYPE 66 63 29
'RPL7A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 0.84

Table S183.  Gene #19: 'RPL7A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 57 57
RPL7A MUTATED 2 0 1
RPL7A WILD-TYPE 45 57 56
'RPL7A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.788 (Fisher's exact test), Q value = 0.95

Table S184.  Gene #19: 'RPL7A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 63 39 59
RPL7A MUTATED 2 0 1
RPL7A WILD-TYPE 61 39 58
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/KIRP-TP/19898020/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRP-TP/20139337/KIRP-TP.transferedmergedcluster.txt

  • Number of patients = 161

  • Number of significantly mutated genes = 19

  • 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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