Correlation between gene mutation status and molecular subtypes
Liver Hepatocellular Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1DN43X6
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1DN43X6
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.

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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