Correlation between gene mutation status and molecular subtypes
Liver Hepatocellular Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C17W6B86
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C17W6B86
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, 36 significant findings detected with P value < 0.05 and Q value < 0.25.

  • TP53 mutation correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • RB1 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

  • AXIN1 mutation correlated to 'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • BAP1 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • TSC2 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • ARID1A mutation correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CNMF'.

  • ALB mutation correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • HNF1A mutation correlated to 'MIRSEQ_MATURE_CNMF'.

  • APOB mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • GNAS mutation correlated to 'MRNASEQ_CNMF'.

  • HIST1H1C mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

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, 36 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 0.0377
(0.165) 		0.00087
(0.0114) 		1e-05
(0.000288) 		1e-05
(0.000288) 		0.0465
(0.186) 		1e-05
(0.000288) 		0.00038
(0.00684) 		1e-05
(0.000288)
BAP1 10 (5%) 188 0.706
(0.877) 		0.0075
(0.0635) 		0.00128
(0.0154) 		0.00036
(0.00684) 		5e-05
(0.0012) 		0.0106
(0.0779) 		0.0391
(0.166) 		0.0181
(0.105)
TP53 62 (31%) 136 0.00682
(0.0614) 		0.775
(0.905) 		1e-05
(0.000288) 		0.0205
(0.105) 		0.0197
(0.105) 		0.00054
(0.00864) 		0.232
(0.495) 		0.0115
(0.0787)
AXIN1 9 (5%) 189 0.279
(0.515) 		0.476
(0.711) 		0.0108
(0.0779) 		0.186
(0.438) 		0.00457
(0.0506) 		0.457
(0.7) 		0.00527
(0.0542) 		0.693
(0.876)
RB1 15 (8%) 183 0.727
(0.877) 		0.00081
(0.0114) 		0.00609
(0.0585) 		0.31
(0.531) 		0.213
(0.48) 		0.39
(0.624) 		0.213
(0.48) 		0.303
(0.525)
TSC2 9 (5%) 189 0.907
(0.953) 		0.0189
(0.105) 		0.102
(0.316) 		0.0194
(0.105) 		0.764
(0.901) 		0.567
(0.785) 		0.788
(0.905) 		0.11
(0.316)
ARID1A 16 (8%) 182 0.831
(0.907) 		0.29
(0.516) 		0.067
(0.254) 		0.0251
(0.117) 		0.109
(0.316) 		0.671
(0.863) 		0.016
(0.105) 		0.585
(0.795)
ALB 18 (9%) 180 0.0412
(0.17) 		0.0218
(0.105) 		0.408
(0.645) 		0.575
(0.788) 		0.824
(0.905) 		0.843
(0.913) 		0.505
(0.724) 		0.253
(0.501)
HNF1A 8 (4%) 190 0.162
(0.41) 		0.666
(0.863) 		0.0705
(0.254) 		0.526
(0.742) 		0.0944
(0.316) 		0.152
(0.399) 		0.0105
(0.0779) 		0.287
(0.516)
APOB 24 (12%) 174 1
(1.00) 		0.892
(0.944) 		0.132
(0.369) 		0.1
(0.316) 		0.276
(0.515) 		0.0693
(0.254) 		0.219
(0.484) 		0.0201
(0.105)
GNAS 7 (4%) 191 0.89
(0.944) 		0.238
(0.495) 		0.0293
(0.132) 		0.172
(0.419) 		0.0781
(0.274) 		0.45
(0.696) 		0.555
(0.777) 		0.725
(0.877)
HIST1H1C 5 (3%) 193 0.722
(0.877) 		0.737
(0.877) 		0.471
(0.711) 		0.347
(0.58) 		0.801
(0.905) 		0.247
(0.501) 		0.641
(0.839) 		0.0212
(0.105)
IL6ST 7 (4%) 191 0.491
(0.714) 		0.297
(0.521) 		0.17
(0.419) 		0.137
(0.373) 		0.441
(0.691) 		0.107
(0.316) 		0.479
(0.711) 		1
(1.00)
EEF1A1 5 (3%) 193 0.0555
(0.216) 		0.736
(0.877) 		0.254
(0.501) 		0.133
(0.369) 		0.611
(0.818) 		0.261
(0.505) 		0.241
(0.495) 		0.617
(0.818)
KIF19 10 (5%) 188 0.918
(0.958) 		0.104
(0.316) 		0.234
(0.495) 		0.238
(0.495) 		0.383
(0.62) 		0.81
(0.905) 		0.152
(0.399) 		0.1
(0.316)
F5 4 (2%) 194 0.817
(0.905) 		0.18
(0.432) 		0.798
(0.905) 		0.619
(0.818) 		0.102
(0.316) 		0.936
(0.963)
PTEN 7 (4%) 191 0.49
(0.714) 		0.263
(0.505) 		0.372
(0.615) 		0.508
(0.724) 		0.86
(0.924) 		0.275
(0.515) 		0.783
(0.905) 		0.285
(0.516)
DLK2 4 (2%) 194 0.818
(0.905) 		0.693
(0.876) 		0.735
(0.877) 		0.379
(0.62) 		0.333
(0.564) 		0.936
(0.963) 		0.189
(0.438) 		0.162
(0.41)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00682 (Fisher's exact test), Q value = 0.061

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 = 0.775 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
TP53 MUTATED 19 27 16
TP53 WILD-TYPE 38 56 42
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
TP53 MUTATED 30 16 3 5 7
TP53 WILD-TYPE 13 39 26 31 25

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 = 0.0205 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
TP53 MUTATED 18 10 20 6 7
TP53 WILD-TYPE 16 19 47 30 22

Figure S3.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.1

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 S4.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0086

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 S5.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.232 (Fisher's exact test), Q value = 0.49

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 = 0.0115 (Fisher's exact test), Q value = 0.079

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 S6.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.16

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 S7.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CTNNB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
CTNNB1 MUTATED 9 33 9
CTNNB1 WILD-TYPE 48 50 49

Figure S8.  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 = 0.00029

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
CTNNB1 MUTATED 9 8 1 5 28
CTNNB1 WILD-TYPE 34 47 28 31 4

Figure S9.  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 = 0.00029

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
CTNNB1 MUTATED 3 7 9 7 25
CTNNB1 WILD-TYPE 31 22 58 29 4

Figure S10.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0465 (Fisher's exact test), Q value = 0.19

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 S11.  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 = 0.00029

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 S12.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0068

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 S13.  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 = 0.00029

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 S14.  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 = 0.88

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 = 0.00081 (Fisher's exact test), Q value = 0.011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
RB1 MUTATED 1 3 11
RB1 WILD-TYPE 56 80 47

Figure S15.  Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00609 (Fisher's exact test), Q value = 0.058

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
RB1 MUTATED 3 6 6 0 0
RB1 WILD-TYPE 40 49 23 36 32

Figure S16.  Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.31 (Fisher's exact test), Q value = 0.53

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
RB1 MUTATED 3 1 8 3 0
RB1 WILD-TYPE 31 28 59 33 29
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.213 (Fisher's exact test), Q value = 0.48

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 = 0.39 (Fisher's exact test), Q value = 0.62

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 = 0.213 (Fisher's exact test), Q value = 0.48

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 = 0.303 (Fisher's exact test), Q value = 0.52

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 = 0.279 (Fisher's exact test), Q value = 0.51

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 = 0.476 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
AXIN1 MUTATED 1 4 4
AXIN1 WILD-TYPE 56 79 54
'AXIN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.078

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
AXIN1 MUTATED 1 3 5 0 0
AXIN1 WILD-TYPE 42 52 24 36 32

Figure S17.  Get High-res Image Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'AXIN1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.186 (Fisher's exact test), Q value = 0.44

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
AXIN1 MUTATED 1 0 4 4 0
AXIN1 WILD-TYPE 33 29 63 32 29
'AXIN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00457 (Fisher's exact test), Q value = 0.051

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 S18.  Get High-res Image Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'AXIN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.457 (Fisher's exact test), Q value = 0.7

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 = 0.00527 (Fisher's exact test), Q value = 0.054

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 S19.  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 = 0.693 (Fisher's exact test), Q value = 0.88

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 = 0.706 (Fisher's exact test), Q value = 0.88

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 = 0.0075 (Fisher's exact test), Q value = 0.064

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
BAP1 MUTATED 5 0 5
BAP1 WILD-TYPE 52 83 53

Figure S20.  Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00128 (Fisher's exact test), Q value = 0.015

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
BAP1 MUTATED 1 0 4 5 0
BAP1 WILD-TYPE 42 55 25 31 32

Figure S21.  Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0068

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
BAP1 MUTATED 5 0 0 5 0
BAP1 WILD-TYPE 29 29 67 31 29

Figure S22.  Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0012

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

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.078

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 S24.  Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.17

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 S25.  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 = 0.0181 (Fisher's exact test), Q value = 0.1

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 S26.  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 = 0.95

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 = 0.0189 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
TSC2 MUTATED 6 3 0
TSC2 WILD-TYPE 51 80 58

Figure S27.  Get High-res Image Gene #6: 'TSC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TSC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.32

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
TSC2 MUTATED 5 1 2 1 0
TSC2 WILD-TYPE 38 54 27 35 32
'TSC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
TSC2 MUTATED 5 0 4 0 0
TSC2 WILD-TYPE 29 29 63 36 29

Figure S28.  Get High-res Image Gene #6: 'TSC2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'TSC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.764 (Fisher's exact test), Q value = 0.9

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 = 0.567 (Fisher's exact test), Q value = 0.78

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 = 0.91

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 = 0.32

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 = 0.831 (Fisher's exact test), Q value = 0.91

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 = 0.29 (Fisher's exact test), Q value = 0.52

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
ARID1A MUTATED 5 4 7
ARID1A WILD-TYPE 52 79 51
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.067 (Fisher's exact test), Q value = 0.25

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
ARID1A MUTATED 2 2 6 2 4
ARID1A WILD-TYPE 41 53 23 34 28
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
ARID1A MUTATED 1 2 2 7 4
ARID1A WILD-TYPE 33 27 65 29 25

Figure S29.  Get High-res Image Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.32

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 = 0.671 (Fisher's exact test), Q value = 0.86

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 = 0.016 (Fisher's exact test), Q value = 0.1

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 S30.  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 = 0.585 (Fisher's exact test), Q value = 0.79

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 = 0.491 (Fisher's exact test), Q value = 0.71

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 = 0.297 (Fisher's exact test), Q value = 0.52

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
IL6ST MUTATED 3 1 3
IL6ST WILD-TYPE 54 82 55
'IL6ST MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 0.42

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
IL6ST MUTATED 1 1 2 0 3
IL6ST WILD-TYPE 42 54 27 36 29
'IL6ST MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.137 (Fisher's exact test), Q value = 0.37

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
IL6ST MUTATED 0 1 1 2 3
IL6ST WILD-TYPE 34 28 66 34 26
'IL6ST MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 0.69

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 = 0.107 (Fisher's exact test), Q value = 0.32

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 = 0.479 (Fisher's exact test), Q value = 0.71

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 = 0.0412 (Fisher's exact test), Q value = 0.17

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 S31.  Get High-res Image Gene #9: 'ALB MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ALB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
ALB MUTATED 5 12 1
ALB WILD-TYPE 52 71 57

Figure S32.  Get High-res Image Gene #9: 'ALB MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ALB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.408 (Fisher's exact test), Q value = 0.64

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
ALB MUTATED 4 6 0 4 3
ALB WILD-TYPE 39 49 29 32 29
'ALB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.575 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
ALB MUTATED 3 4 6 1 3
ALB WILD-TYPE 31 25 61 35 26
'ALB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.824 (Fisher's exact test), Q value = 0.91

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 = 0.843 (Fisher's exact test), Q value = 0.91

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 = 0.505 (Fisher's exact test), Q value = 0.72

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 = 0.5

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 = 0.162 (Fisher's exact test), Q value = 0.41

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 = 0.666 (Fisher's exact test), Q value = 0.86

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
HNF1A MUTATED 3 4 1
HNF1A WILD-TYPE 54 79 57
'HNF1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0705 (Fisher's exact test), Q value = 0.25

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
HNF1A MUTATED 1 6 0 0 1
HNF1A WILD-TYPE 42 49 29 36 31
'HNF1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.526 (Fisher's exact test), Q value = 0.74

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
HNF1A MUTATED 1 1 5 0 1
HNF1A WILD-TYPE 33 28 62 36 28
'HNF1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0944 (Fisher's exact test), Q value = 0.32

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 = 0.152 (Fisher's exact test), Q value = 0.4

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 = 0.0105 (Fisher's exact test), Q value = 0.078

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 S33.  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 = 0.287 (Fisher's exact test), Q value = 0.52

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 = 0.892 (Fisher's exact test), Q value = 0.94

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
APOB MUTATED 6 10 8
APOB WILD-TYPE 51 73 50
'APOB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.132 (Fisher's exact test), Q value = 0.37

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
APOB MUTATED 3 6 4 2 8
APOB WILD-TYPE 40 49 25 34 24
'APOB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.1 (Fisher's exact test), Q value = 0.32

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
APOB MUTATED 4 2 7 2 8
APOB WILD-TYPE 30 27 60 34 21
'APOB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.276 (Fisher's exact test), Q value = 0.51

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 = 0.0693 (Fisher's exact test), Q value = 0.25

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 = 0.219 (Fisher's exact test), Q value = 0.48

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 = 0.0201 (Fisher's exact test), Q value = 0.1

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 S34.  Get High-res Image Gene #11: 'APOB MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'EEF1A1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0555 (Fisher's exact test), Q value = 0.22

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 = 0.736 (Fisher's exact test), Q value = 0.88

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
EEF1A1 MUTATED 1 3 1
EEF1A1 WILD-TYPE 56 80 57
'EEF1A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.254 (Fisher's exact test), Q value = 0.5

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
EEF1A1 MUTATED 0 1 0 2 2
EEF1A1 WILD-TYPE 43 54 29 34 30
'EEF1A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.133 (Fisher's exact test), Q value = 0.37

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
EEF1A1 MUTATED 0 2 1 0 2
EEF1A1 WILD-TYPE 34 27 66 36 27
'EEF1A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.611 (Fisher's exact test), Q value = 0.82

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 = 0.5

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 = 0.241 (Fisher's exact test), Q value = 0.49

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 = 0.82

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 = 0.96

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 = 0.104 (Fisher's exact test), Q value = 0.32

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
KIF19 MUTATED 0 6 4
KIF19 WILD-TYPE 57 77 54
'KIF19 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.234 (Fisher's exact test), Q value = 0.49

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
KIF19 MUTATED 4 3 0 0 2
KIF19 WILD-TYPE 39 52 29 36 30
'KIF19 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.238 (Fisher's exact test), Q value = 0.49

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
KIF19 MUTATED 3 0 4 0 2
KIF19 WILD-TYPE 31 29 63 36 27
'KIF19 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.383 (Fisher's exact test), Q value = 0.62

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 = 0.81 (Fisher's exact test), Q value = 0.91

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 = 0.152 (Fisher's exact test), Q value = 0.4

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 = 0.1 (Fisher's exact test), Q value = 0.32

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 = 0.89 (Fisher's exact test), Q value = 0.94

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 = 0.238 (Fisher's exact test), Q value = 0.49

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
GNAS MUTATED 2 1 4
GNAS WILD-TYPE 55 82 54
'GNAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.13

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
GNAS MUTATED 0 1 2 4 0
GNAS WILD-TYPE 43 54 27 32 32

Figure S35.  Get High-res Image Gene #14: 'GNAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'GNAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.172 (Fisher's exact test), Q value = 0.42

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
GNAS MUTATED 1 3 1 2 0
GNAS WILD-TYPE 33 26 66 34 29
'GNAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0781 (Fisher's exact test), Q value = 0.27

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 = 0.45 (Fisher's exact test), Q value = 0.7

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 = 0.555 (Fisher's exact test), Q value = 0.78

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 = 0.725 (Fisher's exact test), Q value = 0.88

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 = 0.817 (Fisher's exact test), Q value = 0.91

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 = 0.18 (Fisher's exact test), Q value = 0.43

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
F5 MUTATED 0 1 3
F5 WILD-TYPE 57 82 55
'F5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.798 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
F5 MUTATED 1 2 1 0 0
F5 WILD-TYPE 42 53 28 36 32
'F5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.619 (Fisher's exact test), Q value = 0.82

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
F5 MUTATED 0 0 3 1 0
F5 WILD-TYPE 34 29 64 35 29
'F5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.32

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 = 0.936 (Fisher's exact test), Q value = 0.96

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 = 0.49 (Fisher's exact test), Q value = 0.71

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 = 0.263 (Fisher's exact test), Q value = 0.5

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
PTEN MUTATED 0 4 3
PTEN WILD-TYPE 57 79 55
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.372 (Fisher's exact test), Q value = 0.62

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
PTEN MUTATED 1 4 0 0 1
PTEN WILD-TYPE 42 51 29 36 31
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.508 (Fisher's exact test), Q value = 0.72

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
PTEN MUTATED 1 0 4 0 1
PTEN WILD-TYPE 33 29 63 36 28
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.86 (Fisher's exact test), Q value = 0.92

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 = 0.275 (Fisher's exact test), Q value = 0.51

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 = 0.783 (Fisher's exact test), Q value = 0.91

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 = 0.52

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 = 0.722 (Fisher's exact test), Q value = 0.88

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 = 0.737 (Fisher's exact test), Q value = 0.88

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
HIST1H1C MUTATED 1 3 1
HIST1H1C WILD-TYPE 56 80 57
'HIST1H1C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.471 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
HIST1H1C MUTATED 0 1 1 1 2
HIST1H1C WILD-TYPE 43 54 28 35 30
'HIST1H1C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.347 (Fisher's exact test), Q value = 0.58

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
HIST1H1C MUTATED 1 1 1 0 2
HIST1H1C WILD-TYPE 33 28 66 36 27
'HIST1H1C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.801 (Fisher's exact test), Q value = 0.91

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 = 0.247 (Fisher's exact test), Q value = 0.5

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 = 0.641 (Fisher's exact test), Q value = 0.84

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 = 0.0212 (Fisher's exact test), Q value = 0.1

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 S36.  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 = 0.91

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 = 0.88

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
DLK2 MUTATED 2 1 1
DLK2 WILD-TYPE 55 82 57
'DLK2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.735 (Fisher's exact test), Q value = 0.88

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
DLK2 MUTATED 2 1 0 1 0
DLK2 WILD-TYPE 41 54 29 35 32
'DLK2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.379 (Fisher's exact test), Q value = 0.62

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
DLK2 MUTATED 2 1 1 0 0
DLK2 WILD-TYPE 32 28 66 36 29
'DLK2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.333 (Fisher's exact test), Q value = 0.56

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 = 0.96

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 = 0.189 (Fisher's exact test), Q value = 0.44

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 = 0.41

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 = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/15165528/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LIHC-TP/15111045/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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