Correlation between gene mutation status and molecular subtypes
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C10Z72BP
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/C10Z72BP
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 10 (6%) 151 0.13
(0.639) 		9e-05
(0.0171) 		0.171
(0.703) 		0.38
(0.793) 		0.013
(0.413) 		0.00201
(0.14) 		0.0172
(0.413) 		0.02
(0.423) 		0.0725
(0.599) 		0.341
(0.793)
MET 15 (9%) 146 0.2
(0.703) 		0.0627
(0.599) 		0.296
(0.793) 		0.0891
(0.63) 		0.00221
(0.14) 		0.0813
(0.618) 		0.838
(0.964) 		0.817
(0.964) 		0.644
(0.904) 		0.138
(0.639)
HNRNPM 10 (6%) 151 0.0761
(0.602) 		0.22
(0.72) 		1
(1.00) 		0.471
(0.813) 		0.441
(0.793) 		0.627
(0.904) 		0.717
(0.941) 		0.317
(0.793) 		0.35
(0.793) 		0.513
(0.834)
NEFH 10 (6%) 151 0.436
(0.793) 		0.832
(0.964) 		0.381
(0.793) 		0.322
(0.793) 		0.131
(0.639) 		0.573
(0.85) 		0.0148
(0.413) 		0.0299
(0.431) 		0.196
(0.703) 		0.33
(0.793)
ZNF598 10 (6%) 151 0.517
(0.834) 		0.915
(0.994) 		0.744
(0.956) 		0.179
(0.703) 		0.157
(0.703) 		0.523
(0.834) 		0.391
(0.793) 		0.237
(0.757) 		0.101
(0.63) 		0.119
(0.639)
NF2 10 (6%) 151 0.133
(0.639) 		0.0223
(0.424) 		0.686
(0.913) 		0.407
(0.793) 		0.0957
(0.63) 		0.219
(0.72) 		0.654
(0.904) 		0.551
(0.85) 		0.492
(0.834) 		0.0382
(0.431)
TDG 5 (3%) 156 0.102
(0.63) 		0.0655
(0.599) 		0.848
(0.964) 		0.239
(0.757) 		0.862
(0.964) 		0.269
(0.793) 		0.443
(0.793) 		0.276
(0.793) 		0.44
(0.793) 		0.91
(0.994)
SKI 6 (4%) 155 0.109
(0.63) 		0.0723
(0.599) 		0.639
(0.904) 		0.718
(0.941) 		0.127
(0.639) 		1
(1.00) 		0.513
(0.834) 		0.46
(0.813) 		0.865
(0.964) 		0.375
(0.793)
MUC5B 14 (9%) 147 0.113
(0.63) 		0.665
(0.909) 		0.57
(0.85) 		0.423
(0.793) 		0.752
(0.959) 		0.0993
(0.63) 		0.882
(0.969) 		0.287
(0.793) 		0.442
(0.793) 		0.965
(1.00)
ZNF814 8 (5%) 153 0.686
(0.913) 		0.391
(0.793) 		1
(1.00) 		0.734
(0.949) 		0.763
(0.962) 		0.402
(0.793) 		0.433
(0.793) 		0.641
(0.904) 		0.193
(0.703) 		0.792
(0.962)
SMARCB1 4 (2%) 157 0.825
(0.964) 		0.184
(0.703) 		1
(1.00) 		0.797
(0.962) 		0.569
(0.85) 		0.526
(0.834) 		0.0362
(0.431) 		0.466
(0.813) 		0.108
(0.63) 		0.33
(0.793)
KDM6A 7 (4%) 154 1
(1.00) 		0.8
(0.962) 		0.848
(0.964) 		0.653
(0.904) 		0.0282
(0.431) 		0.315
(0.793) 		0.388
(0.793) 		0.165
(0.703) 		0.394
(0.793) 		0.22
(0.72)
AHNAK2 7 (4%) 154 0.951
(1.00) 		0.77
(0.962) 		0.656
(0.904) 		0.822
(0.964) 		0.568
(0.85) 		0.88
(0.969) 		0.294
(0.793) 		0.215
(0.72) 		0.256
(0.786) 		0.304
(0.793)
AHCY 4 (2%) 157 0.0575
(0.599) 		0.486
(0.831) 		0.687
(0.913) 		0.527
(0.834) 		0.261
(0.786) 		0.649
(0.904) 		0.197
(0.703) 		1
(1.00)
IDUA 5 (3%) 156 0.289
(0.793) 		0.388
(0.793) 		0.302
(0.793) 		0.532
(0.835) 		0.379
(0.793) 		0.412
(0.793) 		0.442
(0.793) 		0.0698
(0.599) 		0.83
(0.964) 		0.867
(0.964)
OR2L8 4 (2%) 157 0.389
(0.793) 		0.469
(0.813) 		0.676
(0.913) 		0.26
(0.786) 		0.0378
(0.431) 		0.187
(0.703) 		0.387
(0.793) 		0.508
(0.834) 		0.55
(0.85) 		0.866
(0.964)
HOXD8 4 (2%) 157 0.179
(0.703) 		0.78
(0.962) 		0.0385
(0.431) 		0.162
(0.703) 		0.341
(0.793) 		0.414
(0.793) 		0.32
(0.793) 		0.832
(0.964) 		0.0174
(0.413) 		0.0103
(0.413)
PAM 3 (2%) 158 0.588
(0.86) 		0.781
(0.962) 		0.113
(0.63) 		0.579
(0.853) 		0.173
(0.703) 		0.792
(0.962) 		0.388
(0.793) 		0.0294
(0.431)
CSGALNACT2 5 (3%) 156 0.136
(0.639) 		0.391
(0.793) 		1
(1.00) 		0.798
(0.962) 		0.57
(0.85) 		0.413
(0.793) 		0.525
(0.834) 		0.727
(0.946)
'HNRNPM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0761 (Fisher's exact test), Q value = 0.6

Table S1.  Gene #1: '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 = 0.22 (Fisher's exact test), Q value = 0.72

Table S2.  Gene #1: '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 = 1 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 46 32
HNRNPM MUTATED 4 4 2
HNRNPM WILD-TYPE 42 42 30
'HNRNPM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.471 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 21 23 16 25 16
HNRNPM MUTATED 3 1 1 2 1 1 1
HNRNPM WILD-TYPE 8 11 20 21 15 24 15
'HNRNPM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 0.79

Table S5.  Gene #1: '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 = 0.627 (Fisher's exact test), Q value = 0.9

Table S6.  Gene #1: '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 = 0.717 (Fisher's exact test), Q value = 0.94

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 54 60
HNRNPM MUTATED 2 3 5
HNRNPM WILD-TYPE 45 51 55
'HNRNPM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.317 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 35 39 57
HNRNPM MUTATED 0 4 2 4
HNRNPM WILD-TYPE 30 31 37 53
'HNRNPM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 39 46
HNRNPM MUTATED 3 1 5
HNRNPM WILD-TYPE 34 38 41
'HNRNPM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.513 (Fisher's exact test), Q value = 0.83

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 47 12 16
HNRNPM MUTATED 4 5 0 0
HNRNPM WILD-TYPE 43 42 12 16
'NEFH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.436 (Fisher's exact test), Q value = 0.79

Table S11.  Gene #2: '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 = 0.832 (Fisher's exact test), Q value = 0.96

Table S12.  Gene #2: '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 = 0.381 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 46 32
NEFH MUTATED 3 1 3
NEFH WILD-TYPE 43 45 29
'NEFH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.322 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 21 23 16 25 16
NEFH MUTATED 0 1 0 3 0 1 2
NEFH WILD-TYPE 11 11 21 20 16 24 14
'NEFH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.131 (Fisher's exact test), Q value = 0.64

Table S15.  Gene #2: '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 = 0.573 (Fisher's exact test), Q value = 0.85

Table S16.  Gene #2: '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 = 0.0148 (Fisher's exact test), Q value = 0.41

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 54 60
NEFH MUTATED 5 5 0
NEFH WILD-TYPE 42 49 60

Figure S1.  Get High-res Image Gene #2: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NEFH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0299 (Fisher's exact test), Q value = 0.43

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 35 39 57
NEFH MUTATED 3 4 3 0
NEFH WILD-TYPE 27 31 36 57

Figure S2.  Get High-res Image Gene #2: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.196 (Fisher's exact test), Q value = 0.7

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 39 46
NEFH MUTATED 2 1 0
NEFH WILD-TYPE 35 38 46
'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.33 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 47 12 16
NEFH MUTATED 3 0 0 0
NEFH WILD-TYPE 44 47 12 16
'ZNF598 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.517 (Fisher's exact test), Q value = 0.83

Table S21.  Gene #3: '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 = 0.915 (Fisher's exact test), Q value = 0.99

Table S22.  Gene #3: '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 = 0.744 (Fisher's exact test), Q value = 0.96

Table S23.  Gene #3: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 46 32
ZNF598 MUTATED 4 4 1
ZNF598 WILD-TYPE 42 42 31
'ZNF598 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.179 (Fisher's exact test), Q value = 0.7

Table S24.  Gene #3: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 21 23 16 25 16
ZNF598 MUTATED 2 1 1 1 3 0 1
ZNF598 WILD-TYPE 9 11 20 22 13 25 15
'ZNF598 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.157 (Fisher's exact test), Q value = 0.7

Table S25.  Gene #3: '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 = 0.523 (Fisher's exact test), Q value = 0.83

Table S26.  Gene #3: '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 = 0.391 (Fisher's exact test), Q value = 0.79

Table S27.  Gene #3: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 54 60
ZNF598 MUTATED 2 2 6
ZNF598 WILD-TYPE 45 52 54
'ZNF598 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.237 (Fisher's exact test), Q value = 0.76

Table S28.  Gene #3: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 35 39 57
ZNF598 MUTATED 2 0 2 6
ZNF598 WILD-TYPE 28 35 37 51
'ZNF598 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 0.63

Table S29.  Gene #3: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 39 46
ZNF598 MUTATED 2 1 7
ZNF598 WILD-TYPE 35 38 39
'ZNF598 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.119 (Fisher's exact test), Q value = 0.64

Table S30.  Gene #3: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 47 12 16
ZNF598 MUTATED 1 7 1 1
ZNF598 WILD-TYPE 46 40 11 15
'NF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.133 (Fisher's exact test), Q value = 0.64

Table S31.  Gene #4: '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 = 0.0223 (Fisher's exact test), Q value = 0.42

Table S32.  Gene #4: '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 #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NF2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 0.91

Table S33.  Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 46 32
NF2 MUTATED 2 4 3
NF2 WILD-TYPE 44 42 29
'NF2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.407 (Fisher's exact test), Q value = 0.79

Table S34.  Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 21 23 16 25 16
NF2 MUTATED 0 1 2 0 3 2 1
NF2 WILD-TYPE 11 11 19 23 13 23 15
'NF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0957 (Fisher's exact test), Q value = 0.63

Table S35.  Gene #4: '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 = 0.219 (Fisher's exact test), Q value = 0.72

Table S36.  Gene #4: '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 = 0.654 (Fisher's exact test), Q value = 0.9

Table S37.  Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 54 60
NF2 MUTATED 3 2 5
NF2 WILD-TYPE 44 52 55
'NF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.551 (Fisher's exact test), Q value = 0.85

Table S38.  Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 35 39 57
NF2 MUTATED 1 3 1 5
NF2 WILD-TYPE 29 32 38 52
'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.492 (Fisher's exact test), Q value = 0.83

Table S39.  Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 39 46
NF2 MUTATED 2 1 4
NF2 WILD-TYPE 35 38 42
'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0382 (Fisher's exact test), Q value = 0.43

Table S40.  Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 47 12 16
NF2 MUTATED 3 1 3 0
NF2 WILD-TYPE 44 46 9 16

Figure S4.  Get High-res Image Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TDG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.63

Table S41.  Gene #5: '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 = 0.0655 (Fisher's exact test), Q value = 0.6

Table S42.  Gene #5: '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 = 0.848 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 46 32
TDG MUTATED 1 2 2
TDG WILD-TYPE 45 44 30
'TDG MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.239 (Fisher's exact test), Q value = 0.76

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 21 23 16 25 16
TDG MUTATED 0 0 0 3 1 0 1
TDG WILD-TYPE 11 12 21 20 15 25 15
'TDG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.862 (Fisher's exact test), Q value = 0.96

Table S45.  Gene #5: '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 = 0.269 (Fisher's exact test), Q value = 0.79

Table S46.  Gene #5: '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 = 0.443 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 54 60
TDG MUTATED 3 1 1
TDG WILD-TYPE 44 53 59
'TDG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.276 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 35 39 57
TDG MUTATED 2 2 0 1
TDG WILD-TYPE 28 33 39 56
'TDG MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 39 46
TDG MUTATED 3 1 1
TDG WILD-TYPE 34 38 45
'TDG MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.91 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 47 12 16
TDG MUTATED 3 2 0 0
TDG WILD-TYPE 44 45 12 16
'SKI MUTATION STATUS' versus 'CN_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.63

Table S51.  Gene #6: '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 = 0.0723 (Fisher's exact test), Q value = 0.6

Table S52.  Gene #6: '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 = 0.639 (Fisher's exact test), Q value = 0.9

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 46 32
SKI MUTATED 3 1 1
SKI WILD-TYPE 43 45 31
'SKI MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.718 (Fisher's exact test), Q value = 0.94

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 21 23 16 25 16
SKI MUTATED 1 1 0 1 1 1 0
SKI WILD-TYPE 10 11 21 22 15 24 16
'SKI MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.127 (Fisher's exact test), Q value = 0.64

Table S55.  Gene #6: '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 S56.  Gene #6: '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 = 0.513 (Fisher's exact test), Q value = 0.83

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 54 60
SKI MUTATED 3 1 2
SKI WILD-TYPE 44 53 58
'SKI MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.46 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 35 39 57
SKI MUTATED 2 0 1 3
SKI WILD-TYPE 28 35 38 54
'SKI MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.865 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 39 46
SKI MUTATED 2 1 2
SKI WILD-TYPE 35 38 44
'SKI MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.375 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 47 12 16
SKI MUTATED 1 4 0 0
SKI WILD-TYPE 46 43 12 16
'MUC5B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.113 (Fisher's exact test), Q value = 0.63

Table S61.  Gene #7: '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 = 0.665 (Fisher's exact test), Q value = 0.91

Table S62.  Gene #7: '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 = 0.57 (Fisher's exact test), Q value = 0.85

Table S63.  Gene #7: 'MUC5B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 46 32
MUC5B MUTATED 2 5 2
MUC5B WILD-TYPE 44 41 30
'MUC5B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.423 (Fisher's exact test), Q value = 0.79

Table S64.  Gene #7: 'MUC5B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 21 23 16 25 16
MUC5B MUTATED 2 1 2 1 0 3 0
MUC5B WILD-TYPE 9 11 19 22 16 22 16
'MUC5B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.752 (Fisher's exact test), Q value = 0.96

Table S65.  Gene #7: '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 = 0.0993 (Fisher's exact test), Q value = 0.63

Table S66.  Gene #7: '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 = 0.882 (Fisher's exact test), Q value = 0.97

Table S67.  Gene #7: 'MUC5B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 54 60
MUC5B MUTATED 5 4 5
MUC5B WILD-TYPE 42 50 55
'MUC5B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.287 (Fisher's exact test), Q value = 0.79

Table S68.  Gene #7: 'MUC5B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 35 39 57
MUC5B MUTATED 4 4 4 2
MUC5B WILD-TYPE 26 31 35 55
'MUC5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.442 (Fisher's exact test), Q value = 0.79

Table S69.  Gene #7: 'MUC5B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 39 46
MUC5B MUTATED 5 2 5
MUC5B WILD-TYPE 32 37 41
'MUC5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.965 (Fisher's exact test), Q value = 1

Table S70.  Gene #7: 'MUC5B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 47 12 16
MUC5B MUTATED 4 5 1 2
MUC5B WILD-TYPE 43 42 11 14
'ZNF814 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 0.91

Table S71.  Gene #8: '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 = 0.391 (Fisher's exact test), Q value = 0.79

Table S72.  Gene #8: '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 S73.  Gene #8: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 46 32
ZNF814 MUTATED 3 2 2
ZNF814 WILD-TYPE 43 44 30
'ZNF814 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.734 (Fisher's exact test), Q value = 0.95

Table S74.  Gene #8: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 21 23 16 25 16
ZNF814 MUTATED 0 0 2 1 0 2 2
ZNF814 WILD-TYPE 11 12 19 22 16 23 14
'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.763 (Fisher's exact test), Q value = 0.96

Table S75.  Gene #8: '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 = 0.402 (Fisher's exact test), Q value = 0.79

Table S76.  Gene #8: '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 = 0.433 (Fisher's exact test), Q value = 0.79

Table S77.  Gene #8: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 54 60
ZNF814 MUTATED 3 1 4
ZNF814 WILD-TYPE 44 53 56
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.641 (Fisher's exact test), Q value = 0.9

Table S78.  Gene #8: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 35 39 57
ZNF814 MUTATED 2 3 1 2
ZNF814 WILD-TYPE 28 32 38 55
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S79.  Gene #8: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 39 46
ZNF814 MUTATED 0 3 4
ZNF814 WILD-TYPE 37 36 42
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.792 (Fisher's exact test), Q value = 0.96

Table S80.  Gene #8: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 47 12 16
ZNF814 MUTATED 2 4 0 1
ZNF814 WILD-TYPE 45 43 12 15
'MET MUTATION STATUS' versus 'CN_CNMF'

P value = 0.2 (Fisher's exact test), Q value = 0.7

Table S81.  Gene #9: '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 = 0.0627 (Fisher's exact test), Q value = 0.6

Table S82.  Gene #9: '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 = 0.296 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 46 32
MET MUTATED 7 5 1
MET WILD-TYPE 39 41 31
'MET MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0891 (Fisher's exact test), Q value = 0.63

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 21 23 16 25 16
MET MUTATED 3 0 4 2 2 0 2
MET WILD-TYPE 8 12 17 21 14 25 14
'MET MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00221 (Fisher's exact test), Q value = 0.14

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

'MET MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0813 (Fisher's exact test), Q value = 0.62

Table S86.  Gene #9: '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 = 0.838 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 54 60
MET MUTATED 5 4 6
MET WILD-TYPE 42 50 54
'MET MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.817 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 35 39 57
MET MUTATED 3 2 3 7
MET WILD-TYPE 27 33 36 50
'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.644 (Fisher's exact test), Q value = 0.9

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 39 46
MET MUTATED 4 5 3
MET WILD-TYPE 33 34 43
'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.138 (Fisher's exact test), Q value = 0.64

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 47 12 16
MET MUTATED 5 3 0 4
MET WILD-TYPE 42 44 12 12
'SMARCB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.825 (Fisher's exact test), Q value = 0.96

Table S91.  Gene #10: '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 S92.  Gene #10: '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 S93.  Gene #10: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 46 32
SMARCB1 MUTATED 1 1 1
SMARCB1 WILD-TYPE 45 45 31
'SMARCB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.797 (Fisher's exact test), Q value = 0.96

Table S94.  Gene #10: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 21 23 16 25 16
SMARCB1 MUTATED 0 1 0 1 0 1 0
SMARCB1 WILD-TYPE 11 11 21 22 16 24 16
'SMARCB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.569 (Fisher's exact test), Q value = 0.85

Table S95.  Gene #10: '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 = 0.526 (Fisher's exact test), Q value = 0.83

Table S96.  Gene #10: '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 = 0.0362 (Fisher's exact test), Q value = 0.43

Table S97.  Gene #10: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 54 60
SMARCB1 MUTATED 0 0 4
SMARCB1 WILD-TYPE 47 54 56

Figure S6.  Get High-res Image Gene #10: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.466 (Fisher's exact test), Q value = 0.81

Table S98.  Gene #10: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 35 39 57
SMARCB1 MUTATED 0 1 0 3
SMARCB1 WILD-TYPE 30 34 39 54
'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.108 (Fisher's exact test), Q value = 0.63

Table S99.  Gene #10: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 39 46
SMARCB1 MUTATED 0 0 3
SMARCB1 WILD-TYPE 37 39 43
'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.33 (Fisher's exact test), Q value = 0.79

Table S100.  Gene #10: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 47 12 16
SMARCB1 MUTATED 0 3 0 0
SMARCB1 WILD-TYPE 47 44 12 16
'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 = 0.8 (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 = 0.848 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 46 32
KDM6A MUTATED 1 2 2
KDM6A WILD-TYPE 45 44 30
'KDM6A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.653 (Fisher's exact test), Q value = 0.9

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 21 23 16 25 16
KDM6A MUTATED 0 0 1 1 0 3 0
KDM6A WILD-TYPE 11 12 20 22 16 22 16
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0282 (Fisher's exact test), Q value = 0.43

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 S7.  Get High-res Image Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.315 (Fisher's exact test), Q value = 0.79

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 = 0.388 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 54 60
KDM6A MUTATED 3 3 1
KDM6A WILD-TYPE 44 51 59
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 35 39 57
KDM6A MUTATED 1 4 1 1
KDM6A WILD-TYPE 29 31 38 56
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.394 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 39 46
KDM6A MUTATED 2 0 1
KDM6A WILD-TYPE 35 39 45
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.22 (Fisher's exact test), Q value = 0.72

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 47 12 16
KDM6A MUTATED 2 0 1 0
KDM6A WILD-TYPE 45 47 11 16
'SETD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 0.64

Table S111.  Gene #12: '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 4 1 0 5
SETD2 WILD-TYPE 57 38 25 31
'SETD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.017

Table S112.  Gene #12: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 45 60
SETD2 MUTATED 1 9 0
SETD2 WILD-TYPE 42 36 60

Figure S8.  Get High-res Image Gene #12: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'SETD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.171 (Fisher's exact test), Q value = 0.7

Table S113.  Gene #12: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 46 32
SETD2 MUTATED 1 2 4
SETD2 WILD-TYPE 45 44 28
'SETD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.38 (Fisher's exact test), Q value = 0.79

Table S114.  Gene #12: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 21 23 16 25 16
SETD2 MUTATED 0 0 0 1 1 4 1
SETD2 WILD-TYPE 11 12 21 22 15 21 15
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.41

Table S115.  Gene #12: '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 8
SETD2 WILD-TYPE 23 45 33 50

Figure S9.  Get High-res Image Gene #12: 'SETD2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00201 (Fisher's exact test), Q value = 0.14

Table S116.  Gene #12: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 64 30
SETD2 MUTATED 9 0 1
SETD2 WILD-TYPE 58 64 29

Figure S10.  Get High-res Image Gene #12: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0172 (Fisher's exact test), Q value = 0.41

Table S117.  Gene #12: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 54 60
SETD2 MUTATED 6 0 4
SETD2 WILD-TYPE 41 54 56

Figure S11.  Get High-res Image Gene #12: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.02 (Fisher's exact test), Q value = 0.42

Table S118.  Gene #12: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 35 39 57
SETD2 MUTATED 5 3 0 2
SETD2 WILD-TYPE 25 32 39 55

Figure S12.  Get High-res Image Gene #12: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0725 (Fisher's exact test), Q value = 0.6

Table S119.  Gene #12: 'SETD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 39 46
SETD2 MUTATED 4 0 5
SETD2 WILD-TYPE 33 39 41
'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.341 (Fisher's exact test), Q value = 0.79

Table S120.  Gene #12: 'SETD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 47 12 16
SETD2 MUTATED 3 6 0 0
SETD2 WILD-TYPE 44 41 12 16
'AHNAK2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S121.  Gene #13: '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 = 0.77 (Fisher's exact test), Q value = 0.96

Table S122.  Gene #13: '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 = 0.656 (Fisher's exact test), Q value = 0.9

Table S123.  Gene #13: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 46 32
AHNAK2 MUTATED 3 1 2
AHNAK2 WILD-TYPE 43 45 30
'AHNAK2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.822 (Fisher's exact test), Q value = 0.96

Table S124.  Gene #13: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 21 23 16 25 16
AHNAK2 MUTATED 0 1 1 0 1 2 1
AHNAK2 WILD-TYPE 11 11 20 23 15 23 15
'AHNAK2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.568 (Fisher's exact test), Q value = 0.85

Table S125.  Gene #13: '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 = 0.88 (Fisher's exact test), Q value = 0.97

Table S126.  Gene #13: '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 = 0.294 (Fisher's exact test), Q value = 0.79

Table S127.  Gene #13: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 54 60
AHNAK2 MUTATED 4 1 2
AHNAK2 WILD-TYPE 43 53 58
'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.215 (Fisher's exact test), Q value = 0.72

Table S128.  Gene #13: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 35 39 57
AHNAK2 MUTATED 2 3 0 2
AHNAK2 WILD-TYPE 28 32 39 55
'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.256 (Fisher's exact test), Q value = 0.79

Table S129.  Gene #13: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 39 46
AHNAK2 MUTATED 4 2 1
AHNAK2 WILD-TYPE 33 37 45
'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.304 (Fisher's exact test), Q value = 0.79

Table S130.  Gene #13: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 47 12 16
AHNAK2 MUTATED 5 1 0 1
AHNAK2 WILD-TYPE 42 46 12 15
'AHCY MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0575 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 39 25 36
AHCY MUTATED 0 1 0 3
AHCY WILD-TYPE 61 38 25 33
'AHCY MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.486 (Fisher's exact test), Q value = 0.83

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 45 60
AHCY MUTATED 0 2 1
AHCY WILD-TYPE 43 43 59
'AHCY MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.687 (Fisher's exact test), Q value = 0.91

Table S133.  Gene #14: 'AHCY MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 45 35 58
AHCY MUTATED 0 2 0 2
AHCY WILD-TYPE 23 43 35 56
'AHCY MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.527 (Fisher's exact test), Q value = 0.83

Table S134.  Gene #14: 'AHCY MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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

P value = 0.261 (Fisher's exact test), Q value = 0.79

Table S135.  Gene #14: 'AHCY MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 54 60
AHCY MUTATED 2 2 0
AHCY WILD-TYPE 45 52 60
'AHCY MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.649 (Fisher's exact test), Q value = 0.9

Table S136.  Gene #14: 'AHCY MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 35 39 57
AHCY MUTATED 0 2 1 1
AHCY WILD-TYPE 30 33 38 56
'AHCY MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.197 (Fisher's exact test), Q value = 0.7

Table S137.  Gene #14: 'AHCY MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 39 46
AHCY MUTATED 2 1 0
AHCY WILD-TYPE 35 38 46
'AHCY MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S138.  Gene #14: 'AHCY MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 47 12 16
AHCY MUTATED 2 1 0 0
AHCY WILD-TYPE 45 46 12 16
'IDUA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 0.79

Table S139.  Gene #15: '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 = 0.388 (Fisher's exact test), Q value = 0.79

Table S140.  Gene #15: '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 = 0.302 (Fisher's exact test), Q value = 0.79

Table S141.  Gene #15: 'IDUA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 46 32
IDUA MUTATED 1 1 3
IDUA WILD-TYPE 45 45 29
'IDUA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.532 (Fisher's exact test), Q value = 0.83

Table S142.  Gene #15: 'IDUA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 21 23 16 25 16
IDUA MUTATED 0 1 0 2 0 2 0
IDUA WILD-TYPE 11 11 21 21 16 23 16
'IDUA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.379 (Fisher's exact test), Q value = 0.79

Table S143.  Gene #15: '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 = 0.412 (Fisher's exact test), Q value = 0.79

Table S144.  Gene #15: '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 = 0.442 (Fisher's exact test), Q value = 0.79

Table S145.  Gene #15: 'IDUA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 54 60
IDUA MUTATED 3 1 1
IDUA WILD-TYPE 44 53 59
'IDUA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0698 (Fisher's exact test), Q value = 0.6

Table S146.  Gene #15: 'IDUA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 35 39 57
IDUA MUTATED 3 0 0 2
IDUA WILD-TYPE 27 35 39 55
'IDUA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.83 (Fisher's exact test), Q value = 0.96

Table S147.  Gene #15: 'IDUA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 39 46
IDUA MUTATED 1 2 1
IDUA WILD-TYPE 36 37 45
'IDUA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.867 (Fisher's exact test), Q value = 0.96

Table S148.  Gene #15: 'IDUA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 47 12 16
IDUA MUTATED 1 2 0 1
IDUA WILD-TYPE 46 45 12 15
'OR2L8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.389 (Fisher's exact test), Q value = 0.79

Table S149.  Gene #16: '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 = 0.469 (Fisher's exact test), Q value = 0.81

Table S150.  Gene #16: '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 = 0.676 (Fisher's exact test), Q value = 0.91

Table S151.  Gene #16: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 46 32
OR2L8 MUTATED 2 2 0
OR2L8 WILD-TYPE 44 44 32
'OR2L8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.26 (Fisher's exact test), Q value = 0.79

Table S152.  Gene #16: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 21 23 16 25 16
OR2L8 MUTATED 0 1 2 0 0 0 1
OR2L8 WILD-TYPE 11 11 19 23 16 25 15
'OR2L8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0378 (Fisher's exact test), Q value = 0.43

Table S153.  Gene #16: '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 S13.  Get High-res Image Gene #16: '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 S154.  Gene #16: '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 = 0.387 (Fisher's exact test), Q value = 0.79

Table S155.  Gene #16: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 54 60
OR2L8 MUTATED 0 1 3
OR2L8 WILD-TYPE 47 53 57
'OR2L8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.508 (Fisher's exact test), Q value = 0.83

Table S156.  Gene #16: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 35 39 57
OR2L8 MUTATED 0 0 1 3
OR2L8 WILD-TYPE 30 35 38 54
'OR2L8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.55 (Fisher's exact test), Q value = 0.85

Table S157.  Gene #16: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

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

P value = 0.866 (Fisher's exact test), Q value = 0.96

Table S158.  Gene #16: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 47 12 16
OR2L8 MUTATED 1 2 0 1
OR2L8 WILD-TYPE 46 45 12 15
'HOXD8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.179 (Fisher's exact test), Q value = 0.7

Table S159.  Gene #17: 'HOXD8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 61 39 25 36
HOXD8 MUTATED 1 3 0 0
HOXD8 WILD-TYPE 60 36 25 36
'HOXD8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.78 (Fisher's exact test), Q value = 0.96

Table S160.  Gene #17: 'HOXD8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 45 60
HOXD8 MUTATED 0 1 2
HOXD8 WILD-TYPE 43 44 58
'HOXD8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.43

Table S161.  Gene #17: 'HOXD8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 46 32
HOXD8 MUTATED 0 4 0
HOXD8 WILD-TYPE 46 42 32

Figure S14.  Get High-res Image Gene #17: 'HOXD8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'HOXD8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.162 (Fisher's exact test), Q value = 0.7

Table S162.  Gene #17: 'HOXD8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 21 23 16 25 16
HOXD8 MUTATED 0 0 3 1 0 0 0
HOXD8 WILD-TYPE 11 12 18 22 16 25 16
'HOXD8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.341 (Fisher's exact test), Q value = 0.79

Table S163.  Gene #17: 'HOXD8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 45 35 58
HOXD8 MUTATED 0 3 0 1
HOXD8 WILD-TYPE 23 42 35 57
'HOXD8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.414 (Fisher's exact test), Q value = 0.79

Table S164.  Gene #17: 'HOXD8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 64 30
HOXD8 MUTATED 1 3 0
HOXD8 WILD-TYPE 66 61 30
'HOXD8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.32 (Fisher's exact test), Q value = 0.79

Table S165.  Gene #17: 'HOXD8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 54 60
HOXD8 MUTATED 1 0 3
HOXD8 WILD-TYPE 46 54 57
'HOXD8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.832 (Fisher's exact test), Q value = 0.96

Table S166.  Gene #17: 'HOXD8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 35 39 57
HOXD8 MUTATED 1 0 1 2
HOXD8 WILD-TYPE 29 35 38 55
'HOXD8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.41

Table S167.  Gene #17: 'HOXD8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 39 46
HOXD8 MUTATED 0 4 0
HOXD8 WILD-TYPE 37 35 46

Figure S15.  Get High-res Image Gene #17: 'HOXD8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'HOXD8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.41

Table S168.  Gene #17: 'HOXD8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 47 12 16
HOXD8 MUTATED 1 0 0 3
HOXD8 WILD-TYPE 46 47 12 13

Figure S16.  Get High-res Image Gene #17: 'HOXD8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PAM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.588 (Fisher's exact test), Q value = 0.86

Table S169.  Gene #18: '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 = 0.96

Table S170.  Gene #18: '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 = 0.113 (Fisher's exact test), Q value = 0.63

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 46 32
PAM MUTATED 3 0 0
PAM WILD-TYPE 43 46 32
'PAM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.579 (Fisher's exact test), Q value = 0.85

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 21 23 16 25 16
PAM MUTATED 0 0 1 2 0 0 0
PAM WILD-TYPE 11 12 20 21 16 25 16
'PAM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.173 (Fisher's exact test), Q value = 0.7

Table S173.  Gene #18: '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 = 0.792 (Fisher's exact test), Q value = 0.96

Table S174.  Gene #18: '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 = 0.388 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 54 60
PAM MUTATED 1 2 0
PAM WILD-TYPE 46 52 60
'PAM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.43

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 35 39 57
PAM MUTATED 0 0 3 0
PAM WILD-TYPE 30 35 36 57

Figure S17.  Get High-res Image Gene #18: 'PAM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CSGALNACT2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.136 (Fisher's exact test), Q value = 0.64

Table S177.  Gene #19: '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 = 0.79

Table S178.  Gene #19: '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 = 1 (Fisher's exact test), Q value = 1

Table S179.  Gene #19: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 46 32
CSGALNACT2 MUTATED 1 2 1
CSGALNACT2 WILD-TYPE 45 44 31
'CSGALNACT2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.798 (Fisher's exact test), Q value = 0.96

Table S180.  Gene #19: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 12 21 23 16 25 16
CSGALNACT2 MUTATED 1 0 0 1 0 1 1
CSGALNACT2 WILD-TYPE 10 12 21 22 16 24 15
'CSGALNACT2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 0.85

Table S181.  Gene #19: '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 = 0.79

Table S182.  Gene #19: '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 = 0.525 (Fisher's exact test), Q value = 0.83

Table S183.  Gene #19: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 54 60
CSGALNACT2 MUTATED 1 3 1
CSGALNACT2 WILD-TYPE 46 51 59
'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.727 (Fisher's exact test), Q value = 0.95

Table S184.  Gene #19: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 35 39 57
CSGALNACT2 MUTATED 0 2 1 2
CSGALNACT2 WILD-TYPE 30 33 38 55
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/15174863/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRP-TP/15098835/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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