Correlation between gene mutation status and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between mutation status of 18 genes and 8 molecular subtypes across 198 patients, 11 significant findings detected with P value < 0.05 and Q value < 0.25.

  • TP53 mutation correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • CTNNB1 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • RB1 mutation correlated to 'METHLYATION_CNMF'.

  • BAP1 mutation correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 18 genes and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 11 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
CTNNB1 51 (26%) 147 0.0382
(1.00) 		0.00029
(0.0394) 		1e-05
(0.00142) 		1e-05
(0.00142) 		0.0449
(1.00) 		1e-05
(0.00142) 		0.00047
(0.0634) 		1e-05
(0.00142)
TP53 62 (31%) 136 0.00681
(0.865) 		0.48
(1.00) 		0.00171
(0.226) 		0.447
(1.00) 		0.0194
(1.00) 		0.00063
(0.0844) 		0.234
(1.00) 		0.0119
(1.00)
BAP1 10 (5%) 188 0.705
(1.00) 		0.00374
(0.486) 		0.00025
(0.0342) 		0.00193
(0.253) 		3e-05
(0.00414) 		0.0107
(1.00) 		0.0393
(1.00) 		0.0171
(1.00)
RB1 15 (8%) 183 0.727
(1.00) 		0.00074
(0.0984) 		0.0247
(1.00) 		0.149
(1.00) 		0.215
(1.00) 		0.389
(1.00) 		0.214
(1.00) 		0.299
(1.00)
AXIN1 9 (5%) 189 0.277
(1.00) 		0.47
(1.00) 		0.18
(1.00) 		0.358
(1.00) 		0.0047
(0.606) 		0.456
(1.00) 		0.00548
(0.701) 		0.694
(1.00)
TSC2 9 (5%) 189 0.907
(1.00) 		0.0406
(1.00) 		0.139
(1.00) 		0.359
(1.00) 		0.768
(1.00) 		0.565
(1.00) 		0.788
(1.00) 		0.11
(1.00)
ARID1A 16 (8%) 182 0.834
(1.00) 		0.24
(1.00) 		0.0169
(1.00) 		0.322
(1.00) 		0.109
(1.00) 		0.672
(1.00) 		0.0167
(1.00) 		0.586
(1.00)
IL6ST 7 (4%) 191 0.489
(1.00) 		0.265
(1.00) 		0.313
(1.00) 		0.0344
(1.00) 		0.439
(1.00) 		0.11
(1.00) 		0.477
(1.00) 		1
(1.00)
ALB 18 (9%) 180 0.0409
(1.00) 		0.0192
(1.00) 		0.088
(1.00) 		0.297
(1.00) 		0.822
(1.00) 		0.842
(1.00) 		0.504
(1.00) 		0.253
(1.00)
HNF1A 8 (4%) 190 0.163
(1.00) 		0.598
(1.00) 		0.108
(1.00) 		0.142
(1.00) 		0.0944
(1.00) 		0.153
(1.00) 		0.0104
(1.00) 		0.284
(1.00)
APOB 24 (12%) 174 1
(1.00) 		1
(1.00) 		0.0922
(1.00) 		0.0172
(1.00) 		0.278
(1.00) 		0.0716
(1.00) 		0.22
(1.00) 		0.0198
(1.00)
EEF1A1 5 (3%) 193 0.055
(1.00) 		0.865
(1.00) 		0.13
(1.00) 		0.0734
(1.00) 		0.612
(1.00) 		0.261
(1.00) 		0.239
(1.00) 		0.617
(1.00)
KIF19 10 (5%) 188 0.918
(1.00) 		0.13
(1.00) 		0.228
(1.00) 		0.457
(1.00) 		0.383
(1.00) 		0.814
(1.00) 		0.155
(1.00) 		0.101
(1.00)
GNAS 7 (4%) 191 0.891
(1.00) 		0.158
(1.00) 		0.237
(1.00) 		0.759
(1.00) 		0.0781
(1.00) 		0.452
(1.00) 		0.556
(1.00) 		0.723
(1.00)
F5 4 (2%) 194 0.819
(1.00) 		0.208
(1.00) 		0.7
(1.00) 		1
(1.00) 		0.0988
(1.00) 		0.937
(1.00)
PTEN 7 (4%) 191 0.488
(1.00) 		0.326
(1.00) 		0.867
(1.00) 		0.625
(1.00) 		0.858
(1.00) 		0.278
(1.00) 		0.781
(1.00) 		0.285
(1.00)
HIST1H1C 5 (3%) 193 0.72
(1.00) 		0.864
(1.00) 		0.822
(1.00) 		0.28
(1.00) 		0.802
(1.00) 		0.25
(1.00) 		0.639
(1.00) 		0.0204
(1.00)
DLK2 4 (2%) 194 0.818
(1.00) 		0.693
(1.00) 		0.442
(1.00) 		1
(1.00) 		0.336
(1.00) 		0.936
(1.00) 		0.19
(1.00) 		0.162
(1.00)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00681 (Fisher's exact test), Q value = 0.86

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
TP53 MUTATED 9 29 24
TP53 WILD-TYPE 37 33 61

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

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 87 58
TP53 MUTATED 16 31 15
TP53 WILD-TYPE 37 56 43
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00171 (Fisher's exact test), Q value = 0.23

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 51 29 21 35 32
TP53 MUTATED 18 15 6 6 8 8
TP53 WILD-TYPE 8 36 23 15 27 24

Figure S2.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.447 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 99 28
TP53 MUTATED 25 28 8
TP53 WILD-TYPE 42 71 20
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
TP53 MUTATED 16 25 10 10
TP53 WILD-TYPE 22 43 17 50

Figure S3.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.084

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
TP53 MUTATED 14 25 6 14 2
TP53 WILD-TYPE 10 33 18 52 19

Figure S4.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.234 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
TP53 MUTATED 22 10 17 10
TP53 WILD-TYPE 35 31 39 11
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0119 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
TP53 MUTATED 13 23 10 10 3
TP53 WILD-TYPE 19 30 40 10 17

Figure S5.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0382 (Fisher's exact test), Q value = 1

Table S9.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
CTNNB1 MUTATED 19 13 19
CTNNB1 WILD-TYPE 27 49 66

Figure S6.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CTNNB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.039

Table S10.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 87 58
CTNNB1 MUTATED 7 35 9
CTNNB1 WILD-TYPE 46 52 49

Figure S7.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

Table S11.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 51 29 21 35 32
CTNNB1 MUTATED 5 7 3 8 0 28
CTNNB1 WILD-TYPE 21 44 26 13 35 4

Figure S8.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

Table S12.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 99 28
CTNNB1 MUTATED 7 19 25
CTNNB1 WILD-TYPE 60 80 3

Figure S9.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0449 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
CTNNB1 MUTATED 9 25 7 9
CTNNB1 WILD-TYPE 29 43 20 51

Figure S10.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

Table S14.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
CTNNB1 MUTATED 8 11 2 11 18
CTNNB1 WILD-TYPE 16 47 22 55 3

Figure S11.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.063

Table S15.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
CTNNB1 MUTATED 8 5 25 5
CTNNB1 WILD-TYPE 49 36 31 16

Figure S12.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

Table S16.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
CTNNB1 MUTATED 3 10 7 7 16
CTNNB1 WILD-TYPE 29 43 43 13 4

Figure S13.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.727 (Fisher's exact test), Q value = 1

Table S17.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
RB1 MUTATED 3 6 5
RB1 WILD-TYPE 43 56 80
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.098

Table S18.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 87 58
RB1 MUTATED 1 3 11
RB1 WILD-TYPE 52 84 47

Figure S14.  Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 1

Table S19.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 51 29 21 35 32
RB1 MUTATED 1 6 6 0 2 0
RB1 WILD-TYPE 25 45 23 21 33 32

Figure S15.  Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.149 (Fisher's exact test), Q value = 1

Table S20.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 99 28
RB1 MUTATED 8 7 0
RB1 WILD-TYPE 59 92 28
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.215 (Fisher's exact test), Q value = 1

Table S21.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
RB1 MUTATED 0 6 2 6
RB1 WILD-TYPE 38 62 25 54
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S22.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
RB1 MUTATED 1 3 2 8 0
RB1 WILD-TYPE 23 55 22 58 21
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S23.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
RB1 MUTATED 6 4 1 1
RB1 WILD-TYPE 51 37 55 20
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S24.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
RB1 MUTATED 5 3 3 1 0
RB1 WILD-TYPE 27 50 47 19 20
'AXIN1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S25.  Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
AXIN1 MUTATED 2 5 2
AXIN1 WILD-TYPE 44 57 83
'AXIN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.47 (Fisher's exact test), Q value = 1

Table S26.  Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 87 58
AXIN1 MUTATED 1 4 4
AXIN1 WILD-TYPE 52 83 54
'AXIN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.18 (Fisher's exact test), Q value = 1

Table S27.  Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 51 29 21 35 32
AXIN1 MUTATED 1 3 4 0 1 0
AXIN1 WILD-TYPE 25 48 25 21 34 32
'AXIN1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.358 (Fisher's exact test), Q value = 1

Table S28.  Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 99 28
AXIN1 MUTATED 5 4 0
AXIN1 WILD-TYPE 62 95 28
'AXIN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0047 (Fisher's exact test), Q value = 0.61

Table S29.  Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
AXIN1 MUTATED 0 4 4 0
AXIN1 WILD-TYPE 38 64 23 60

Figure S16.  Get High-res Image Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'AXIN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S30.  Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
AXIN1 MUTATED 1 1 2 4 0
AXIN1 WILD-TYPE 23 57 22 62 21
'AXIN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00548 (Fisher's exact test), Q value = 0.7

Table S31.  Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
AXIN1 MUTATED 1 0 2 4
AXIN1 WILD-TYPE 56 41 54 17

Figure S17.  Get High-res Image Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'AXIN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.694 (Fisher's exact test), Q value = 1

Table S32.  Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
AXIN1 MUTATED 0 2 3 1 1
AXIN1 WILD-TYPE 32 51 47 19 19
'BAP1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S33.  Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
BAP1 MUTATED 2 2 6
BAP1 WILD-TYPE 44 60 79
'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00374 (Fisher's exact test), Q value = 0.49

Table S34.  Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 87 58
BAP1 MUTATED 5 0 5
BAP1 WILD-TYPE 48 87 53

Figure S18.  Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.034

Table S35.  Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 51 29 21 35 32
BAP1 MUTATED 0 0 4 0 6 0
BAP1 WILD-TYPE 26 51 25 21 29 32

Figure S19.  Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00193 (Fisher's exact test), Q value = 0.25

Table S36.  Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 99 28
BAP1 MUTATED 9 1 0
BAP1 WILD-TYPE 58 98 28

Figure S20.  Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0041

Table S37.  Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
BAP1 MUTATED 0 0 0 10
BAP1 WILD-TYPE 38 68 27 50

Figure S21.  Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 1

Table S38.  Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
BAP1 MUTATED 0 0 2 8 0
BAP1 WILD-TYPE 24 58 22 58 21

Figure S22.  Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0393 (Fisher's exact test), Q value = 1

Table S39.  Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
BAP1 MUTATED 4 5 0 1
BAP1 WILD-TYPE 53 36 56 20

Figure S23.  Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 1

Table S40.  Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
BAP1 MUTATED 1 1 8 0 0
BAP1 WILD-TYPE 31 52 42 20 20

Figure S24.  Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TSC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.907 (Fisher's exact test), Q value = 1

Table S41.  Gene #6: 'TSC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
TSC2 MUTATED 2 2 5
TSC2 WILD-TYPE 44 60 80
'TSC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0406 (Fisher's exact test), Q value = 1

Table S42.  Gene #6: 'TSC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 87 58
TSC2 MUTATED 5 4 0
TSC2 WILD-TYPE 48 83 58

Figure S25.  Get High-res Image Gene #6: 'TSC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TSC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.139 (Fisher's exact test), Q value = 1

Table S43.  Gene #6: 'TSC2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 51 29 21 35 32
TSC2 MUTATED 3 1 2 0 3 0
TSC2 WILD-TYPE 23 50 27 21 32 32
'TSC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.359 (Fisher's exact test), Q value = 1

Table S44.  Gene #6: 'TSC2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 99 28
TSC2 MUTATED 5 4 0
TSC2 WILD-TYPE 62 95 28
'TSC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.768 (Fisher's exact test), Q value = 1

Table S45.  Gene #6: 'TSC2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
TSC2 MUTATED 2 4 0 3
TSC2 WILD-TYPE 36 64 27 57
'TSC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.565 (Fisher's exact test), Q value = 1

Table S46.  Gene #6: 'TSC2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
TSC2 MUTATED 2 2 2 2 1
TSC2 WILD-TYPE 22 56 22 64 20
'TSC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.788 (Fisher's exact test), Q value = 1

Table S47.  Gene #6: 'TSC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
TSC2 MUTATED 4 2 3 0
TSC2 WILD-TYPE 53 39 53 21
'TSC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S48.  Gene #6: 'TSC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
TSC2 MUTATED 4 1 1 1 2
TSC2 WILD-TYPE 28 52 49 19 18
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

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

Table S49.  Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
ARID1A MUTATED 3 6 6
ARID1A WILD-TYPE 43 56 79
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.24 (Fisher's exact test), Q value = 1

Table S50.  Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 87 58
ARID1A MUTATED 6 4 6
ARID1A WILD-TYPE 47 83 52
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 1

Table S51.  Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 51 29 21 35 32
ARID1A MUTATED 2 1 5 3 0 4
ARID1A WILD-TYPE 24 50 24 18 35 28

Figure S26.  Get High-res Image Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S52.  Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 99 28
ARID1A MUTATED 7 5 3
ARID1A WILD-TYPE 60 94 25
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S53.  Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
ARID1A MUTATED 4 5 5 2
ARID1A WILD-TYPE 34 63 22 58
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S54.  Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
ARID1A MUTATED 3 3 3 6 1
ARID1A WILD-TYPE 21 55 21 60 20
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0167 (Fisher's exact test), Q value = 1

Table S55.  Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
ARID1A MUTATED 4 3 2 6
ARID1A WILD-TYPE 53 38 54 15

Figure S27.  Get High-res Image Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.586 (Fisher's exact test), Q value = 1

Table S56.  Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
ARID1A MUTATED 2 3 6 3 1
ARID1A WILD-TYPE 30 50 44 17 19
'IL6ST MUTATION STATUS' versus 'CN_CNMF'

P value = 0.489 (Fisher's exact test), Q value = 1

Table S57.  Gene #8: 'IL6ST MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
IL6ST MUTATED 0 2 4
IL6ST WILD-TYPE 46 60 81
'IL6ST MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.265 (Fisher's exact test), Q value = 1

Table S58.  Gene #8: 'IL6ST MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 87 58
IL6ST MUTATED 3 1 3
IL6ST WILD-TYPE 50 86 55
'IL6ST MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S59.  Gene #8: 'IL6ST MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 51 29 21 35 32
IL6ST MUTATED 1 1 1 0 0 3
IL6ST WILD-TYPE 25 50 28 21 35 29
'IL6ST MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0344 (Fisher's exact test), Q value = 1

Table S60.  Gene #8: 'IL6ST MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 99 28
IL6ST MUTATED 2 1 3
IL6ST WILD-TYPE 65 98 25

Figure S28.  Get High-res Image Gene #8: 'IL6ST MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'IL6ST MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S61.  Gene #8: 'IL6ST MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
IL6ST MUTATED 0 3 2 2
IL6ST WILD-TYPE 38 65 25 58
'IL6ST MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S62.  Gene #8: 'IL6ST MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
IL6ST MUTATED 0 0 1 4 2
IL6ST WILD-TYPE 24 58 23 62 19
'IL6ST MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.477 (Fisher's exact test), Q value = 1

Table S63.  Gene #8: 'IL6ST MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
IL6ST MUTATED 2 0 3 1
IL6ST WILD-TYPE 55 41 53 20
'IL6ST MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S64.  Gene #8: 'IL6ST MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
IL6ST MUTATED 1 2 2 0 1
IL6ST WILD-TYPE 31 51 48 20 19
'ALB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
ALB MUTATED 8 2 7
ALB WILD-TYPE 38 60 78

Figure S29.  Get High-res Image Gene #9: 'ALB MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ALB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 87 58
ALB MUTATED 4 13 1
ALB WILD-TYPE 49 74 57

Figure S30.  Get High-res Image Gene #9: 'ALB MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ALB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.088 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 51 29 21 35 32
ALB MUTATED 4 5 0 4 1 3
ALB WILD-TYPE 22 46 29 17 34 29
'ALB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 99 28
ALB MUTATED 3 11 3
ALB WILD-TYPE 64 88 25
'ALB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.822 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
ALB MUTATED 4 6 1 5
ALB WILD-TYPE 34 62 26 55
'ALB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
ALB MUTATED 3 5 2 4 2
ALB WILD-TYPE 21 53 22 62 19
'ALB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.504 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
ALB MUTATED 4 4 6 0
ALB WILD-TYPE 53 37 50 21
'ALB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.253 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
ALB MUTATED 1 5 2 3 3
ALB WILD-TYPE 31 48 48 17 17
'HNF1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.163 (Fisher's exact test), Q value = 1

Table S73.  Gene #10: 'HNF1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
HNF1A MUTATED 0 2 6
HNF1A WILD-TYPE 46 60 79
'HNF1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.598 (Fisher's exact test), Q value = 1

Table S74.  Gene #10: 'HNF1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 87 58
HNF1A MUTATED 3 4 1
HNF1A WILD-TYPE 50 83 57
'HNF1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S75.  Gene #10: 'HNF1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 51 29 21 35 32
HNF1A MUTATED 0 6 0 0 1 1
HNF1A WILD-TYPE 26 45 29 21 34 31
'HNF1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S76.  Gene #10: 'HNF1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 99 28
HNF1A MUTATED 1 7 0
HNF1A WILD-TYPE 66 92 28
'HNF1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0944 (Fisher's exact test), Q value = 1

Table S77.  Gene #10: 'HNF1A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
HNF1A MUTATED 1 5 2 0
HNF1A WILD-TYPE 37 63 25 60
'HNF1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.153 (Fisher's exact test), Q value = 1

Table S78.  Gene #10: 'HNF1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
HNF1A MUTATED 0 6 0 2 0
HNF1A WILD-TYPE 24 52 24 64 21
'HNF1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 1

Table S79.  Gene #10: 'HNF1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
HNF1A MUTATED 0 0 5 2
HNF1A WILD-TYPE 57 41 51 19

Figure S31.  Get High-res Image Gene #10: 'HNF1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'HNF1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.284 (Fisher's exact test), Q value = 1

Table S80.  Gene #10: 'HNF1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
HNF1A MUTATED 1 5 1 0 0
HNF1A WILD-TYPE 31 48 49 20 20
'APOB MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
APOB MUTATED 5 7 10
APOB WILD-TYPE 41 55 75
'APOB MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 87 58
APOB MUTATED 6 11 7
APOB WILD-TYPE 47 76 51
'APOB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0922 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 51 29 21 35 32
APOB MUTATED 0 6 4 2 3 8
APOB WILD-TYPE 26 45 25 19 32 24
'APOB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 99 28
APOB MUTATED 7 8 8
APOB WILD-TYPE 60 91 20

Figure S32.  Get High-res Image Gene #11: 'APOB MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'APOB MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
APOB MUTATED 8 6 4 6
APOB WILD-TYPE 30 62 23 54
'APOB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0716 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
APOB MUTATED 3 7 0 8 6
APOB WILD-TYPE 21 51 24 58 15
'APOB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
APOB MUTATED 6 3 11 1
APOB WILD-TYPE 51 38 45 20
'APOB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0198 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
APOB MUTATED 1 5 5 3 7
APOB WILD-TYPE 31 48 45 17 13

Figure S33.  Get High-res Image Gene #11: 'APOB MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'EEF1A1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.055 (Fisher's exact test), Q value = 1

Table S89.  Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
EEF1A1 MUTATED 0 0 5
EEF1A1 WILD-TYPE 46 62 80
'EEF1A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.865 (Fisher's exact test), Q value = 1

Table S90.  Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 87 58
EEF1A1 MUTATED 1 3 1
EEF1A1 WILD-TYPE 52 84 57
'EEF1A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 1

Table S91.  Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 51 29 21 35 32
EEF1A1 MUTATED 0 1 0 2 0 2
EEF1A1 WILD-TYPE 26 50 29 19 35 30
'EEF1A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0734 (Fisher's exact test), Q value = 1

Table S92.  Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 99 28
EEF1A1 MUTATED 0 3 2
EEF1A1 WILD-TYPE 67 96 26
'EEF1A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.612 (Fisher's exact test), Q value = 1

Table S93.  Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
EEF1A1 MUTATED 1 1 0 3
EEF1A1 WILD-TYPE 37 67 27 57
'EEF1A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 1

Table S94.  Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
EEF1A1 MUTATED 1 2 1 0 1
EEF1A1 WILD-TYPE 23 56 23 66 20
'EEF1A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.239 (Fisher's exact test), Q value = 1

Table S95.  Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
EEF1A1 MUTATED 0 2 3 0
EEF1A1 WILD-TYPE 57 39 53 21
'EEF1A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.617 (Fisher's exact test), Q value = 1

Table S96.  Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
EEF1A1 MUTATED 0 2 1 1 1
EEF1A1 WILD-TYPE 32 51 49 19 19
'KIF19 MUTATION STATUS' versus 'CN_CNMF'

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

Table S97.  Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
KIF19 MUTATED 2 4 4
KIF19 WILD-TYPE 44 58 81
'KIF19 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 1

Table S98.  Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 87 58
KIF19 MUTATED 0 6 4
KIF19 WILD-TYPE 53 81 54
'KIF19 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S99.  Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 51 29 21 35 32
KIF19 MUTATED 3 3 0 1 0 2
KIF19 WILD-TYPE 23 48 29 20 35 30
'KIF19 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.457 (Fisher's exact test), Q value = 1

Table S100.  Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 99 28
KIF19 MUTATED 4 3 2
KIF19 WILD-TYPE 63 96 26
'KIF19 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S101.  Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
KIF19 MUTATED 1 6 0 3
KIF19 WILD-TYPE 37 62 27 57
'KIF19 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S102.  Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
KIF19 MUTATED 2 3 0 4 1
KIF19 WILD-TYPE 22 55 24 62 20
'KIF19 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S103.  Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
KIF19 MUTATED 5 0 4 0
KIF19 WILD-TYPE 52 41 52 21
'KIF19 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.101 (Fisher's exact test), Q value = 1

Table S104.  Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
KIF19 MUTATED 4 3 0 1 1
KIF19 WILD-TYPE 28 50 50 19 19
'GNAS MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
GNAS MUTATED 1 2 4
GNAS WILD-TYPE 45 60 81
'GNAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.158 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 87 58
GNAS MUTATED 2 1 4
GNAS WILD-TYPE 51 86 54
'GNAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.237 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 51 29 21 35 32
GNAS MUTATED 0 1 2 2 2 0
GNAS WILD-TYPE 26 50 27 19 33 32
'GNAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 99 28
GNAS MUTATED 3 4 0
GNAS WILD-TYPE 64 95 28
'GNAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0781 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
GNAS MUTATED 0 1 0 5
GNAS WILD-TYPE 38 67 27 55
'GNAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.452 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
GNAS MUTATED 0 1 2 3 0
GNAS WILD-TYPE 24 57 22 63 21
'GNAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.556 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
GNAS MUTATED 2 3 1 0
GNAS WILD-TYPE 55 38 55 21
'GNAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.723 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
GNAS MUTATED 1 1 3 0 1
GNAS WILD-TYPE 31 52 47 20 19
'F5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.819 (Fisher's exact test), Q value = 1

Table S113.  Gene #15: 'F5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
F5 MUTATED 1 2 1
F5 WILD-TYPE 45 60 84
'F5 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S114.  Gene #15: 'F5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 87 58
F5 MUTATED 0 1 3
F5 WILD-TYPE 53 86 55
'F5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.7 (Fisher's exact test), Q value = 1

Table S115.  Gene #15: 'F5 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 51 29 21 35 32
F5 MUTATED 1 2 1 0 0 0
F5 WILD-TYPE 25 49 28 21 35 32
'F5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S116.  Gene #15: 'F5 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 99 28
F5 MUTATED 2 2 0
F5 WILD-TYPE 65 97 28
'F5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0988 (Fisher's exact test), Q value = 1

Table S117.  Gene #15: 'F5 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
F5 MUTATED 0 4 0 0
F5 WILD-TYPE 38 64 27 60
'F5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.937 (Fisher's exact test), Q value = 1

Table S118.  Gene #15: 'F5 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
F5 MUTATED 0 1 1 2 0
F5 WILD-TYPE 24 57 23 64 21
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.488 (Fisher's exact test), Q value = 1

Table S119.  Gene #16: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
PTEN MUTATED 0 2 4
PTEN WILD-TYPE 46 60 81
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S120.  Gene #16: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 87 58
PTEN MUTATED 0 4 3
PTEN WILD-TYPE 53 83 55
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.867 (Fisher's exact test), Q value = 1

Table S121.  Gene #16: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 51 29 21 35 32
PTEN MUTATED 1 3 0 0 1 1
PTEN WILD-TYPE 25 48 29 21 34 31
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.625 (Fisher's exact test), Q value = 1

Table S122.  Gene #16: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 99 28
PTEN MUTATED 1 4 1
PTEN WILD-TYPE 66 95 27
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.858 (Fisher's exact test), Q value = 1

Table S123.  Gene #16: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
PTEN MUTATED 1 3 0 3
PTEN WILD-TYPE 37 65 27 57
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S124.  Gene #16: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
PTEN MUTATED 0 5 0 2 0
PTEN WILD-TYPE 24 53 24 64 21
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.781 (Fisher's exact test), Q value = 1

Table S125.  Gene #16: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
PTEN MUTATED 3 1 3 0
PTEN WILD-TYPE 54 40 53 21
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.285 (Fisher's exact test), Q value = 1

Table S126.  Gene #16: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
PTEN MUTATED 1 5 1 0 0
PTEN WILD-TYPE 31 48 49 20 20
'HIST1H1C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.72 (Fisher's exact test), Q value = 1

Table S127.  Gene #17: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
HIST1H1C MUTATED 2 1 2
HIST1H1C WILD-TYPE 44 61 83
'HIST1H1C MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S128.  Gene #17: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 87 58
HIST1H1C MUTATED 1 3 1
HIST1H1C WILD-TYPE 52 84 57
'HIST1H1C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.822 (Fisher's exact test), Q value = 1

Table S129.  Gene #17: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 51 29 21 35 32
HIST1H1C MUTATED 0 1 1 0 1 2
HIST1H1C WILD-TYPE 26 50 28 21 34 30
'HIST1H1C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S130.  Gene #17: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 99 28
HIST1H1C MUTATED 1 2 2
HIST1H1C WILD-TYPE 66 97 26
'HIST1H1C MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S131.  Gene #17: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
HIST1H1C MUTATED 1 3 0 1
HIST1H1C WILD-TYPE 37 65 27 59
'HIST1H1C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.25 (Fisher's exact test), Q value = 1

Table S132.  Gene #17: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
HIST1H1C MUTATED 0 1 1 1 2
HIST1H1C WILD-TYPE 24 57 23 65 19
'HIST1H1C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.639 (Fisher's exact test), Q value = 1

Table S133.  Gene #17: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
HIST1H1C MUTATED 1 1 3 0
HIST1H1C WILD-TYPE 56 40 53 21
'HIST1H1C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 1

Table S134.  Gene #17: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
HIST1H1C MUTATED 1 0 1 0 3
HIST1H1C WILD-TYPE 31 53 49 20 17

Figure S34.  Get High-res Image Gene #17: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'DLK2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.818 (Fisher's exact test), Q value = 1

Table S135.  Gene #18: 'DLK2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
DLK2 MUTATED 1 2 1
DLK2 WILD-TYPE 45 60 84
'DLK2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S136.  Gene #18: 'DLK2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 87 58
DLK2 MUTATED 2 1 1
DLK2 WILD-TYPE 51 86 57
'DLK2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.442 (Fisher's exact test), Q value = 1

Table S137.  Gene #18: 'DLK2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 51 29 21 35 32
DLK2 MUTATED 0 1 0 1 2 0
DLK2 WILD-TYPE 26 50 29 20 33 32
'DLK2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S138.  Gene #18: 'DLK2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 99 28
DLK2 MUTATED 2 2 0
DLK2 WILD-TYPE 65 97 28
'DLK2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S139.  Gene #18: 'DLK2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
DLK2 MUTATED 1 0 1 2
DLK2 WILD-TYPE 37 68 26 58
'DLK2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S140.  Gene #18: 'DLK2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
DLK2 MUTATED 1 1 0 2 0
DLK2 WILD-TYPE 23 57 24 64 21
'DLK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S141.  Gene #18: 'DLK2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
DLK2 MUTATED 0 2 1 1
DLK2 WILD-TYPE 57 39 55 20
'DLK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S142.  Gene #18: 'DLK2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
DLK2 MUTATED 0 0 3 1 0
DLK2 WILD-TYPE 32 53 47 19 20
Methods & Data
Input

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

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

  • Number of patients = 198

  • Number of significantly mutated genes = 18

  • Number of Molecular subtypes = 8

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

Fisher's exact test

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

Q value calculation

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

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