Correlation between gene mutation status and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between mutation status of 20 genes and 10 molecular subtypes across 194 patients, 39 significant findings detected with P value < 0.05 and Q value < 0.25.

  • PTEN mutation correlated to 'MRNASEQ_CNMF'.

  • HLA-B mutation correlated to 'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • HLA-A mutation correlated to 'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • EP300 mutation correlated to 'RPPA_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.

  • MAPK1 mutation correlated to 'CN_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • MLL3 mutation correlated to 'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • ARID1A mutation correlated to 'CN_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • NFE2L2 mutation correlated to 'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • PIK3CA mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • C3ORF70 mutation correlated to 'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • IFNGR1 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 20 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 39 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
KRAS 11 (6%) 183 0.01
(0.109) 		0.00029
(0.029) 		1
(1.00) 		0.218
(0.516) 		0.00613
(0.109) 		0.00146
(0.0584) 		0.00331
(0.109) 		0.00074
(0.037) 		0.00994
(0.109) 		8e-05
(0.016)
NFE2L2 12 (6%) 182 0.808
(0.951) 		0.0307
(0.213) 		0.496
(0.719) 		0.0486
(0.249) 		0.537
(0.749) 		0.0456
(0.241) 		0.0246
(0.183) 		0.0189
(0.157) 		0.033
(0.213) 		0.556
(0.753)
HLA-A 16 (8%) 178 0.603
(0.784) 		0.0104
(0.109) 		0.329
(0.611) 		0.018
(0.157) 		0.00518
(0.109) 		0.0657
(0.292) 		0.126
(0.432) 		0.00754
(0.109) 		0.217
(0.516) 		0.465
(0.695)
ARID1A 14 (7%) 180 0.0114
(0.114) 		0.0573
(0.267) 		0.853
(0.97) 		0.125
(0.432) 		0.205
(0.502) 		0.00072
(0.037) 		0.132
(0.441) 		0.00461
(0.109) 		0.231
(0.532) 		0.00935
(0.109)
HLA-B 11 (6%) 183 0.569
(0.758) 		0.396
(0.672) 		0.908
(1.00) 		0.328
(0.611) 		0.452
(0.695) 		0.0905
(0.342) 		0.0177
(0.157) 		0.136
(0.445) 		0.00737
(0.109) 		0.0353
(0.213)
MAPK1 9 (5%) 185 0.0403
(0.224) 		0.144
(0.462) 		0.335
(0.614) 		0.976
(1.00) 		0.0934
(0.346) 		0.0539
(0.263) 		0.0458
(0.241) 		0.082
(0.328) 		0.0362
(0.213) 		0.33
(0.611)
MLL3 29 (15%) 165 0.15
(0.462) 		0.0539
(0.263) 		0.495
(0.719) 		0.0209
(0.168) 		0.0351
(0.213) 		0.0223
(0.172) 		0.0724
(0.308) 		0.837
(0.97) 		0.32
(0.611) 		0.99
(1.00)
C3ORF70 4 (2%) 190 0.921
(1.00) 		0.0884
(0.342) 		0.469
(0.695) 		0.179
(0.496) 		0.656
(0.821) 		0.127
(0.432) 		0.0148
(0.141) 		0.298
(0.611) 		0.00816
(0.109) 		0.0086
(0.109)
EP300 21 (11%) 173 0.121
(0.431) 		0.201
(0.502) 		0.182
(0.496) 		0.0393
(0.224) 		0.148
(0.462) 		0.0727
(0.308) 		0.3
(0.611) 		0.0096
(0.109) 		1
(1.00) 		0.296
(0.611)
PTEN 15 (8%) 179 0.074
(0.308) 		0.747
(0.894) 		0.687
(0.836) 		0.591
(0.783) 		0.0334
(0.213) 		0.227
(0.528) 		0.184
(0.496) 		0.193
(0.496) 		0.387
(0.661) 		0.0906
(0.342)
PIK3CA 53 (27%) 141 0.0609
(0.277) 		0.455
(0.695) 		0.64
(0.806) 		0.297
(0.611) 		0.219
(0.516) 		0.00398
(0.109) 		0.29
(0.611) 		0.345
(0.618) 		0.196
(0.496) 		0.0552
(0.263)
IFNGR1 6 (3%) 188 0.147
(0.462) 		1
(1.00) 		0.469
(0.695) 		0.911
(1.00) 		0.846
(0.97) 		1
(1.00) 		0.325
(0.611) 		0.0333
(0.213) 		0.192
(0.496) 		0.174
(0.496)
MLL2 22 (11%) 172 0.434
(0.695) 		0.602
(0.784) 		0.368
(0.641) 		0.238
(0.542) 		0.52
(0.737) 		0.078
(0.318) 		0.715
(0.862) 		0.314
(0.611) 		0.69
(0.836) 		0.863
(0.975)
FBXW7 19 (10%) 175 0.555
(0.753) 		0.911
(1.00) 		0.849
(0.97) 		0.971
(1.00) 		0.286
(0.611) 		0.677
(0.836) 		0.181
(0.496) 		0.455
(0.695) 		0.42
(0.695) 		0.504
(0.724)
CASP8 9 (5%) 185 0.412
(0.692) 		0.524
(0.739) 		0.618
(0.798) 		0.169
(0.496) 		0.195
(0.496) 		0.463
(0.695) 		1
(1.00) 		0.451
(0.695) 		0.317
(0.611) 		0.784
(0.928)
FAT2 11 (6%) 183 0.843
(0.97) 		0.195
(0.496) 		1
(1.00) 		0.622
(0.798) 		0.349
(0.618) 		0.483
(0.71) 		0.539
(0.749) 		0.759
(0.904) 		0.424
(0.695) 		0.337
(0.614)
ZNF750 9 (5%) 185 0.187
(0.496) 		1
(1.00) 		1
(1.00) 		0.319
(0.611) 		0.559
(0.753) 		0.303
(0.611) 		0.288
(0.611) 		0.0963
(0.35) 		0.318
(0.611) 		0.351
(0.618)
C12ORF43 4 (2%) 190 0.851
(0.97) 		0.677
(0.836) 		0.912
(1.00) 		0.456
(0.695) 		0.386
(0.661) 		0.206
(0.502) 		0.517
(0.737) 		0.561
(0.753)
BAP1 4 (2%) 190 0.167
(0.496) 		0.453
(0.695) 		0.44
(0.695) 		0.456
(0.695) 		0.683
(0.836) 		0.352
(0.618) 		0.553
(0.753) 		0.629
(0.801)
USP28 4 (2%) 190 0.636
(0.805) 		0.251
(0.564) 		0.182
(0.496) 		0.909
(1.00) 		0.603
(0.784) 		1
(1.00) 		0.467
(0.695) 		0.937
(1.00) 		0.324
(0.611) 		0.274
(0.61)
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.074 (Fisher's exact test), Q value = 0.31

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 72 31 44 38
PTEN MUTATED 0 2 4 7 2
PTEN WILD-TYPE 6 70 27 37 36
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.747 (Fisher's exact test), Q value = 0.89

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 73 71
PTEN MUTATED 3 5 7
PTEN WILD-TYPE 47 68 64
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.687 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 33 55
PTEN MUTATED 2 2 5
PTEN WILD-TYPE 43 31 50
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.591 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
PTEN MUTATED 2 2 4 0 1
PTEN WILD-TYPE 25 38 28 18 15
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.21

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 64 49 41
PTEN MUTATED 5 8 2 0
PTEN WILD-TYPE 34 56 47 41

Figure S1.  Get High-res Image Gene #1: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.227 (Fisher's exact test), Q value = 0.53

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
PTEN MUTATED 6 9 0
PTEN WILD-TYPE 43 111 24
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.184 (Fisher's exact test), Q value = 0.5

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 55 78
PTEN MUTATED 8 3 4
PTEN WILD-TYPE 53 52 74
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.193 (Fisher's exact test), Q value = 0.5

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
PTEN MUTATED 4 6 3 2 0
PTEN WILD-TYPE 37 44 55 13 30
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.387 (Fisher's exact test), Q value = 0.66

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 60 68
PTEN MUTATED 7 4 4
PTEN WILD-TYPE 49 56 64
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0906 (Fisher's exact test), Q value = 0.34

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 19 62 59 22 22
PTEN MUTATED 4 6 5 0 0
PTEN WILD-TYPE 15 56 54 22 22
'HLA-B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.569 (Fisher's exact test), Q value = 0.76

Table S11.  Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 72 31 44 38
HLA-B MUTATED 1 5 2 2 1
HLA-B WILD-TYPE 5 67 29 42 37
'HLA-B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.396 (Fisher's exact test), Q value = 0.67

Table S12.  Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 73 71
HLA-B MUTATED 1 6 4
HLA-B WILD-TYPE 49 67 67
'HLA-B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.908 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 33 55
HLA-B MUTATED 4 2 3
HLA-B WILD-TYPE 41 31 52
'HLA-B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.328 (Fisher's exact test), Q value = 0.61

Table S14.  Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
HLA-B MUTATED 3 1 4 1 0
HLA-B WILD-TYPE 24 39 28 17 16
'HLA-B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.452 (Fisher's exact test), Q value = 0.7

Table S15.  Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 64 49 41
HLA-B MUTATED 2 4 1 4
HLA-B WILD-TYPE 37 60 48 37
'HLA-B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0905 (Fisher's exact test), Q value = 0.34

Table S16.  Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
HLA-B MUTATED 0 10 1
HLA-B WILD-TYPE 49 110 23
'HLA-B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.16

Table S17.  Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 55 78
HLA-B MUTATED 1 1 9
HLA-B WILD-TYPE 60 54 69

Figure S2.  Get High-res Image Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HLA-B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.136 (Fisher's exact test), Q value = 0.44

Table S18.  Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
HLA-B MUTATED 0 5 2 1 3
HLA-B WILD-TYPE 41 45 56 14 27
'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00737 (Fisher's exact test), Q value = 0.11

Table S19.  Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 60 68
HLA-B MUTATED 2 0 8
HLA-B WILD-TYPE 54 60 60

Figure S3.  Get High-res Image Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0353 (Fisher's exact test), Q value = 0.21

Table S20.  Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 19 62 59 22 22
HLA-B MUTATED 0 1 8 1 0
HLA-B WILD-TYPE 19 61 51 21 22

Figure S4.  Get High-res Image Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HLA-A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.603 (Fisher's exact test), Q value = 0.78

Table S21.  Gene #3: 'HLA-A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 72 31 44 38
HLA-A MUTATED 0 4 2 6 3
HLA-A WILD-TYPE 6 68 29 38 35
'HLA-A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.11

Table S22.  Gene #3: 'HLA-A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 73 71
HLA-A MUTATED 0 6 10
HLA-A WILD-TYPE 50 67 61

Figure S5.  Get High-res Image Gene #3: 'HLA-A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HLA-A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.329 (Fisher's exact test), Q value = 0.61

Table S23.  Gene #3: 'HLA-A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 33 55
HLA-A MUTATED 5 3 2
HLA-A WILD-TYPE 40 30 53
'HLA-A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.16

Table S24.  Gene #3: 'HLA-A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
HLA-A MUTATED 5 0 4 1 0
HLA-A WILD-TYPE 22 40 28 17 16

Figure S6.  Get High-res Image Gene #3: 'HLA-A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'HLA-A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00518 (Fisher's exact test), Q value = 0.11

Table S25.  Gene #3: 'HLA-A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 64 49 41
HLA-A MUTATED 2 6 0 8
HLA-A WILD-TYPE 37 58 49 33

Figure S7.  Get High-res Image Gene #3: 'HLA-A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HLA-A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0657 (Fisher's exact test), Q value = 0.29

Table S26.  Gene #3: 'HLA-A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
HLA-A MUTATED 1 11 4
HLA-A WILD-TYPE 48 109 20
'HLA-A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.126 (Fisher's exact test), Q value = 0.43

Table S27.  Gene #3: 'HLA-A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 55 78
HLA-A MUTATED 2 4 10
HLA-A WILD-TYPE 59 51 68
'HLA-A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00754 (Fisher's exact test), Q value = 0.11

Table S28.  Gene #3: 'HLA-A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
HLA-A MUTATED 0 4 3 3 6
HLA-A WILD-TYPE 41 46 55 12 24

Figure S8.  Get High-res Image Gene #3: 'HLA-A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.217 (Fisher's exact test), Q value = 0.52

Table S29.  Gene #3: 'HLA-A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 60 68
HLA-A MUTATED 2 4 8
HLA-A WILD-TYPE 54 56 60
'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.465 (Fisher's exact test), Q value = 0.7

Table S30.  Gene #3: 'HLA-A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 19 62 59 22 22
HLA-A MUTATED 1 4 6 3 0
HLA-A WILD-TYPE 18 58 53 19 22
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 72 31 44 38
KRAS MUTATED 1 1 1 7 1
KRAS WILD-TYPE 5 71 30 37 37

Figure S9.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.029

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 73 71
KRAS MUTATED 8 0 3
KRAS WILD-TYPE 42 73 68

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

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 33 55
KRAS MUTATED 3 2 3
KRAS WILD-TYPE 42 31 52
'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.218 (Fisher's exact test), Q value = 0.52

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
KRAS MUTATED 2 2 1 0 3
KRAS WILD-TYPE 25 38 31 18 13
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00613 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 64 49 41
KRAS MUTATED 4 0 6 1
KRAS WILD-TYPE 35 64 43 40

Figure S11.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00146 (Fisher's exact test), Q value = 0.058

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
KRAS MUTATED 8 2 1
KRAS WILD-TYPE 41 118 23

Figure S12.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00331 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 55 78
KRAS MUTATED 7 4 0
KRAS WILD-TYPE 54 51 78

Figure S13.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.037

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
KRAS MUTATED 8 0 2 1 0
KRAS WILD-TYPE 33 50 56 14 30

Figure S14.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00994 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 60 68
KRAS MUTATED 6 5 0
KRAS WILD-TYPE 50 55 68

Figure S15.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 19 62 59 22 22
KRAS MUTATED 4 2 0 0 5
KRAS WILD-TYPE 15 60 59 22 17

Figure S16.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MLL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.434 (Fisher's exact test), Q value = 0.7

Table S41.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 72 31 44 38
MLL2 MUTATED 0 5 5 7 5
MLL2 WILD-TYPE 6 67 26 37 33
'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.602 (Fisher's exact test), Q value = 0.78

Table S42.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 73 71
MLL2 MUTATED 6 10 6
MLL2 WILD-TYPE 44 63 65
'MLL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.368 (Fisher's exact test), Q value = 0.64

Table S43.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 33 55
MLL2 MUTATED 4 6 5
MLL2 WILD-TYPE 41 27 50
'MLL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.238 (Fisher's exact test), Q value = 0.54

Table S44.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
MLL2 MUTATED 2 2 7 2 2
MLL2 WILD-TYPE 25 38 25 16 14
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.52 (Fisher's exact test), Q value = 0.74

Table S45.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 64 49 41
MLL2 MUTATED 5 10 4 3
MLL2 WILD-TYPE 34 54 45 38
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.078 (Fisher's exact test), Q value = 0.32

Table S46.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
MLL2 MUTATED 4 18 0
MLL2 WILD-TYPE 45 102 24
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.715 (Fisher's exact test), Q value = 0.86

Table S47.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 55 78
MLL2 MUTATED 8 7 7
MLL2 WILD-TYPE 53 48 71
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.314 (Fisher's exact test), Q value = 0.61

Table S48.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
MLL2 MUTATED 3 8 9 0 2
MLL2 WILD-TYPE 38 42 49 15 28
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.69 (Fisher's exact test), Q value = 0.84

Table S49.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 60 68
MLL2 MUTATED 6 9 7
MLL2 WILD-TYPE 50 51 61
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.863 (Fisher's exact test), Q value = 0.98

Table S50.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 19 62 59 22 22
MLL2 MUTATED 1 7 9 2 3
MLL2 WILD-TYPE 18 55 50 20 19
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.555 (Fisher's exact test), Q value = 0.75

Table S51.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 72 31 44 38
FBXW7 MUTATED 0 5 2 5 6
FBXW7 WILD-TYPE 6 67 29 39 32
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.911 (Fisher's exact test), Q value = 1

Table S52.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 73 71
FBXW7 MUTATED 5 8 6
FBXW7 WILD-TYPE 45 65 65
'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.849 (Fisher's exact test), Q value = 0.97

Table S53.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 33 55
FBXW7 MUTATED 6 5 6
FBXW7 WILD-TYPE 39 28 49
'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.971 (Fisher's exact test), Q value = 1

Table S54.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
FBXW7 MUTATED 3 5 4 2 3
FBXW7 WILD-TYPE 24 35 28 16 13
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.286 (Fisher's exact test), Q value = 0.61

Table S55.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 64 49 41
FBXW7 MUTATED 1 9 5 4
FBXW7 WILD-TYPE 38 55 44 37
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.677 (Fisher's exact test), Q value = 0.84

Table S56.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
FBXW7 MUTATED 6 12 1
FBXW7 WILD-TYPE 43 108 23
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.181 (Fisher's exact test), Q value = 0.5

Table S57.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 55 78
FBXW7 MUTATED 7 2 10
FBXW7 WILD-TYPE 54 53 68
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.455 (Fisher's exact test), Q value = 0.7

Table S58.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
FBXW7 MUTATED 4 8 3 1 3
FBXW7 WILD-TYPE 37 42 55 14 27
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.42 (Fisher's exact test), Q value = 0.7

Table S59.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 60 68
FBXW7 MUTATED 8 4 7
FBXW7 WILD-TYPE 48 56 61
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.504 (Fisher's exact test), Q value = 0.72

Table S60.  Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 19 62 59 22 22
FBXW7 MUTATED 4 5 7 2 1
FBXW7 WILD-TYPE 15 57 52 20 21
'EP300 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.121 (Fisher's exact test), Q value = 0.43

Table S61.  Gene #7: 'EP300 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 72 31 44 38
EP300 MUTATED 1 6 7 2 4
EP300 WILD-TYPE 5 66 24 42 34
'EP300 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.201 (Fisher's exact test), Q value = 0.5

Table S62.  Gene #7: 'EP300 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 73 71
EP300 MUTATED 4 12 5
EP300 WILD-TYPE 46 61 66
'EP300 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 0.5

Table S63.  Gene #7: 'EP300 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 33 55
EP300 MUTATED 2 4 9
EP300 WILD-TYPE 43 29 46
'EP300 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0393 (Fisher's exact test), Q value = 0.22

Table S64.  Gene #7: 'EP300 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
EP300 MUTATED 2 5 8 0 0
EP300 WILD-TYPE 25 35 24 18 16

Figure S17.  Get High-res Image Gene #7: 'EP300 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'EP300 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.148 (Fisher's exact test), Q value = 0.46

Table S65.  Gene #7: 'EP300 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 64 49 41
EP300 MUTATED 6 10 2 3
EP300 WILD-TYPE 33 54 47 38
'EP300 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0727 (Fisher's exact test), Q value = 0.31

Table S66.  Gene #7: 'EP300 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
EP300 MUTATED 2 18 1
EP300 WILD-TYPE 47 102 23
'EP300 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.3 (Fisher's exact test), Q value = 0.61

Table S67.  Gene #7: 'EP300 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 55 78
EP300 MUTATED 7 3 11
EP300 WILD-TYPE 54 52 67
'EP300 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0096 (Fisher's exact test), Q value = 0.11

Table S68.  Gene #7: 'EP300 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
EP300 MUTATED 1 9 10 1 0
EP300 WILD-TYPE 40 41 48 14 30

Figure S18.  Get High-res Image Gene #7: 'EP300 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S69.  Gene #7: 'EP300 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 60 68
EP300 MUTATED 5 6 7
EP300 WILD-TYPE 51 54 61
'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.296 (Fisher's exact test), Q value = 0.61

Table S70.  Gene #7: 'EP300 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 19 62 59 22 22
EP300 MUTATED 2 6 9 1 0
EP300 WILD-TYPE 17 56 50 21 22
'MAPK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0403 (Fisher's exact test), Q value = 0.22

Table S71.  Gene #8: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 72 31 44 38
MAPK1 MUTATED 1 1 4 1 2
MAPK1 WILD-TYPE 5 71 27 43 36

Figure S19.  Get High-res Image Gene #8: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'MAPK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.144 (Fisher's exact test), Q value = 0.46

Table S72.  Gene #8: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 73 71
MAPK1 MUTATED 0 4 5
MAPK1 WILD-TYPE 50 69 66
'MAPK1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.335 (Fisher's exact test), Q value = 0.61

Table S73.  Gene #8: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 33 55
MAPK1 MUTATED 3 0 4
MAPK1 WILD-TYPE 42 33 51
'MAPK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.976 (Fisher's exact test), Q value = 1

Table S74.  Gene #8: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
MAPK1 MUTATED 2 2 1 1 1
MAPK1 WILD-TYPE 25 38 31 17 15
'MAPK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0934 (Fisher's exact test), Q value = 0.35

Table S75.  Gene #8: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 64 49 41
MAPK1 MUTATED 2 6 0 1
MAPK1 WILD-TYPE 37 58 49 40
'MAPK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0539 (Fisher's exact test), Q value = 0.26

Table S76.  Gene #8: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
MAPK1 MUTATED 0 9 0
MAPK1 WILD-TYPE 49 111 24
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0458 (Fisher's exact test), Q value = 0.24

Table S77.  Gene #8: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 55 78
MAPK1 MUTATED 0 5 4
MAPK1 WILD-TYPE 61 50 74

Figure S20.  Get High-res Image Gene #8: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'MAPK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.082 (Fisher's exact test), Q value = 0.33

Table S78.  Gene #8: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
MAPK1 MUTATED 0 2 6 1 0
MAPK1 WILD-TYPE 41 48 52 14 30
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 0.21

Table S79.  Gene #8: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 60 68
MAPK1 MUTATED 0 6 3
MAPK1 WILD-TYPE 56 54 65

Figure S21.  Get High-res Image Gene #8: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'MAPK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.33 (Fisher's exact test), Q value = 0.61

Table S80.  Gene #8: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 19 62 59 22 22
MAPK1 MUTATED 0 6 3 0 0
MAPK1 WILD-TYPE 19 56 56 22 22
'MLL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.15 (Fisher's exact test), Q value = 0.46

Table S81.  Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 72 31 44 38
MLL3 MUTATED 0 7 9 7 6
MLL3 WILD-TYPE 6 65 22 37 32
'MLL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0539 (Fisher's exact test), Q value = 0.26

Table S82.  Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 73 71
MLL3 MUTATED 5 17 7
MLL3 WILD-TYPE 45 56 64
'MLL3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.495 (Fisher's exact test), Q value = 0.72

Table S83.  Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 33 55
MLL3 MUTATED 4 6 8
MLL3 WILD-TYPE 41 27 47
'MLL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0209 (Fisher's exact test), Q value = 0.17

Table S84.  Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
MLL3 MUTATED 3 4 10 0 1
MLL3 WILD-TYPE 24 36 22 18 15

Figure S22.  Get High-res Image Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'MLL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0351 (Fisher's exact test), Q value = 0.21

Table S85.  Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 64 49 41
MLL3 MUTATED 1 14 6 7
MLL3 WILD-TYPE 38 50 43 34

Figure S23.  Get High-res Image Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'MLL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0223 (Fisher's exact test), Q value = 0.17

Table S86.  Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
MLL3 MUTATED 5 23 0
MLL3 WILD-TYPE 44 97 24

Figure S24.  Get High-res Image Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'MLL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0724 (Fisher's exact test), Q value = 0.31

Table S87.  Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 55 78
MLL3 MUTATED 4 10 15
MLL3 WILD-TYPE 57 45 63
'MLL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.837 (Fisher's exact test), Q value = 0.97

Table S88.  Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
MLL3 MUTATED 5 8 10 3 3
MLL3 WILD-TYPE 36 42 48 12 27
'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.32 (Fisher's exact test), Q value = 0.61

Table S89.  Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 60 68
MLL3 MUTATED 5 10 12
MLL3 WILD-TYPE 51 50 56
'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.99 (Fisher's exact test), Q value = 1

Table S90.  Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 19 62 59 22 22
MLL3 MUTATED 2 9 10 3 3
MLL3 WILD-TYPE 17 53 49 19 19
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.11

Table S91.  Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 72 31 44 38
ARID1A MUTATED 0 2 2 9 1
ARID1A WILD-TYPE 6 70 29 35 37

Figure S25.  Get High-res Image Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0573 (Fisher's exact test), Q value = 0.27

Table S92.  Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 73 71
ARID1A MUTATED 7 2 5
ARID1A WILD-TYPE 43 71 66
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.853 (Fisher's exact test), Q value = 0.97

Table S93.  Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 33 55
ARID1A MUTATED 3 3 5
ARID1A WILD-TYPE 42 30 50
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.125 (Fisher's exact test), Q value = 0.43

Table S94.  Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
ARID1A MUTATED 2 2 3 0 4
ARID1A WILD-TYPE 25 38 29 18 12
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.205 (Fisher's exact test), Q value = 0.5

Table S95.  Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 64 49 41
ARID1A MUTATED 5 2 5 2
ARID1A WILD-TYPE 34 62 44 39
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00072 (Fisher's exact test), Q value = 0.037

Table S96.  Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
ARID1A MUTATED 10 4 0
ARID1A WILD-TYPE 39 116 24

Figure S26.  Get High-res Image Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.132 (Fisher's exact test), Q value = 0.44

Table S97.  Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 55 78
ARID1A MUTATED 8 2 4
ARID1A WILD-TYPE 53 53 74
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00461 (Fisher's exact test), Q value = 0.11

Table S98.  Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
ARID1A MUTATED 7 1 1 3 2
ARID1A WILD-TYPE 34 49 57 12 28

Figure S27.  Get High-res Image Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.231 (Fisher's exact test), Q value = 0.53

Table S99.  Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 60 68
ARID1A MUTATED 6 4 2
ARID1A WILD-TYPE 50 56 66
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00935 (Fisher's exact test), Q value = 0.11

Table S100.  Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 19 62 59 22 22
ARID1A MUTATED 5 1 3 1 2
ARID1A WILD-TYPE 14 61 56 21 20

Figure S28.  Get High-res Image Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.808 (Fisher's exact test), Q value = 0.95

Table S101.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 72 31 44 38
NFE2L2 MUTATED 0 4 2 2 4
NFE2L2 WILD-TYPE 6 68 29 42 34
'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 0.21

Table S102.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 73 71
NFE2L2 MUTATED 0 8 4
NFE2L2 WILD-TYPE 50 65 67

Figure S29.  Get High-res Image Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.496 (Fisher's exact test), Q value = 0.72

Table S103.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 33 55
NFE2L2 MUTATED 4 3 2
NFE2L2 WILD-TYPE 41 30 53
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0486 (Fisher's exact test), Q value = 0.25

Table S104.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
NFE2L2 MUTATED 1 0 4 3 1
NFE2L2 WILD-TYPE 26 40 28 15 15

Figure S30.  Get High-res Image Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.537 (Fisher's exact test), Q value = 0.75

Table S105.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 64 49 41
NFE2L2 MUTATED 3 5 1 3
NFE2L2 WILD-TYPE 36 59 48 38
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0456 (Fisher's exact test), Q value = 0.24

Table S106.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
NFE2L2 MUTATED 0 11 1
NFE2L2 WILD-TYPE 49 109 23

Figure S31.  Get High-res Image Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.18

Table S107.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 55 78
NFE2L2 MUTATED 0 5 7
NFE2L2 WILD-TYPE 61 50 71

Figure S32.  Get High-res Image Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.16

Table S108.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
NFE2L2 MUTATED 0 1 6 3 2
NFE2L2 WILD-TYPE 41 49 52 12 28

Figure S33.  Get High-res Image Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.21

Table S109.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 60 68
NFE2L2 MUTATED 0 4 7
NFE2L2 WILD-TYPE 56 56 61

Figure S34.  Get High-res Image Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.556 (Fisher's exact test), Q value = 0.75

Table S110.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 19 62 59 22 22
NFE2L2 MUTATED 0 5 4 2 0
NFE2L2 WILD-TYPE 19 57 55 20 22
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0609 (Fisher's exact test), Q value = 0.28

Table S111.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 72 31 44 38
PIK3CA MUTATED 1 12 10 17 13
PIK3CA WILD-TYPE 5 60 21 27 25
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.455 (Fisher's exact test), Q value = 0.7

Table S112.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 73 71
PIK3CA MUTATED 17 19 17
PIK3CA WILD-TYPE 33 54 54
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.64 (Fisher's exact test), Q value = 0.81

Table S113.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 33 55
PIK3CA MUTATED 12 6 11
PIK3CA WILD-TYPE 33 27 44
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.297 (Fisher's exact test), Q value = 0.61

Table S114.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
PIK3CA MUTATED 9 8 4 3 5
PIK3CA WILD-TYPE 18 32 28 15 11
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 0.52

Table S115.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 64 49 41
PIK3CA MUTATED 11 19 16 6
PIK3CA WILD-TYPE 28 45 33 35
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00398 (Fisher's exact test), Q value = 0.11

Table S116.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
PIK3CA MUTATED 19 32 1
PIK3CA WILD-TYPE 30 88 23

Figure S35.  Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.29 (Fisher's exact test), Q value = 0.61

Table S117.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 55 78
PIK3CA MUTATED 21 12 20
PIK3CA WILD-TYPE 40 43 58
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.345 (Fisher's exact test), Q value = 0.62

Table S118.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
PIK3CA MUTATED 14 17 13 4 5
PIK3CA WILD-TYPE 27 33 45 11 25
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.196 (Fisher's exact test), Q value = 0.5

Table S119.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 60 68
PIK3CA MUTATED 20 14 15
PIK3CA WILD-TYPE 36 46 53
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0552 (Fisher's exact test), Q value = 0.26

Table S120.  Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 19 62 59 22 22
PIK3CA MUTATED 8 17 16 1 7
PIK3CA WILD-TYPE 11 45 43 21 15
'CASP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.412 (Fisher's exact test), Q value = 0.69

Table S121.  Gene #13: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 72 31 44 38
CASP8 MUTATED 0 4 3 2 0
CASP8 WILD-TYPE 6 68 28 42 38
'CASP8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.524 (Fisher's exact test), Q value = 0.74

Table S122.  Gene #13: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 73 71
CASP8 MUTATED 1 5 3
CASP8 WILD-TYPE 49 68 68
'CASP8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.618 (Fisher's exact test), Q value = 0.8

Table S123.  Gene #13: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 33 55
CASP8 MUTATED 2 2 1
CASP8 WILD-TYPE 43 31 54
'CASP8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.169 (Fisher's exact test), Q value = 0.5

Table S124.  Gene #13: 'CASP8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
CASP8 MUTATED 1 0 2 2 0
CASP8 WILD-TYPE 26 40 30 16 16
'CASP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.195 (Fisher's exact test), Q value = 0.5

Table S125.  Gene #13: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 64 49 41
CASP8 MUTATED 0 5 1 3
CASP8 WILD-TYPE 39 59 48 38
'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.463 (Fisher's exact test), Q value = 0.7

Table S126.  Gene #13: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
CASP8 MUTATED 1 6 2
CASP8 WILD-TYPE 48 114 22
'CASP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S127.  Gene #13: 'CASP8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 55 78
CASP8 MUTATED 3 2 4
CASP8 WILD-TYPE 58 53 74
'CASP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.451 (Fisher's exact test), Q value = 0.7

Table S128.  Gene #13: 'CASP8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
CASP8 MUTATED 0 3 3 1 2
CASP8 WILD-TYPE 41 47 55 14 28
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.317 (Fisher's exact test), Q value = 0.61

Table S129.  Gene #13: 'CASP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 60 68
CASP8 MUTATED 2 1 5
CASP8 WILD-TYPE 54 59 63
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.784 (Fisher's exact test), Q value = 0.93

Table S130.  Gene #13: 'CASP8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 19 62 59 22 22
CASP8 MUTATED 1 2 4 1 0
CASP8 WILD-TYPE 18 60 55 21 22
'FAT2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.843 (Fisher's exact test), Q value = 0.97

Table S131.  Gene #14: 'FAT2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 72 31 44 38
FAT2 MUTATED 0 4 1 4 2
FAT2 WILD-TYPE 6 68 30 40 36
'FAT2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.195 (Fisher's exact test), Q value = 0.5

Table S132.  Gene #14: 'FAT2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 73 71
FAT2 MUTATED 1 7 3
FAT2 WILD-TYPE 49 66 68
'FAT2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S133.  Gene #14: 'FAT2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 33 55
FAT2 MUTATED 3 2 3
FAT2 WILD-TYPE 42 31 52
'FAT2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.622 (Fisher's exact test), Q value = 0.8

Table S134.  Gene #14: 'FAT2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
FAT2 MUTATED 1 2 3 2 0
FAT2 WILD-TYPE 26 38 29 16 16
'FAT2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.349 (Fisher's exact test), Q value = 0.62

Table S135.  Gene #14: 'FAT2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 64 49 41
FAT2 MUTATED 1 5 1 4
FAT2 WILD-TYPE 38 59 48 37
'FAT2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.483 (Fisher's exact test), Q value = 0.71

Table S136.  Gene #14: 'FAT2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
FAT2 MUTATED 1 9 1
FAT2 WILD-TYPE 48 111 23
'FAT2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.539 (Fisher's exact test), Q value = 0.75

Table S137.  Gene #14: 'FAT2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 55 78
FAT2 MUTATED 2 3 6
FAT2 WILD-TYPE 59 52 72
'FAT2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.759 (Fisher's exact test), Q value = 0.9

Table S138.  Gene #14: 'FAT2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
FAT2 MUTATED 1 4 4 0 2
FAT2 WILD-TYPE 40 46 54 15 28
'FAT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.424 (Fisher's exact test), Q value = 0.7

Table S139.  Gene #14: 'FAT2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 60 68
FAT2 MUTATED 3 2 6
FAT2 WILD-TYPE 53 58 62
'FAT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.337 (Fisher's exact test), Q value = 0.61

Table S140.  Gene #14: 'FAT2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 19 62 59 22 22
FAT2 MUTATED 1 2 6 2 0
FAT2 WILD-TYPE 18 60 53 20 22
'ZNF750 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.187 (Fisher's exact test), Q value = 0.5

Table S141.  Gene #15: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 72 31 44 38
ZNF750 MUTATED 0 2 0 5 2
ZNF750 WILD-TYPE 6 70 31 39 36
'ZNF750 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S142.  Gene #15: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 73 71
ZNF750 MUTATED 2 4 3
ZNF750 WILD-TYPE 48 69 68
'ZNF750 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S143.  Gene #15: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 33 55
ZNF750 MUTATED 2 2 3
ZNF750 WILD-TYPE 43 31 52
'ZNF750 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.319 (Fisher's exact test), Q value = 0.61

Table S144.  Gene #15: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
ZNF750 MUTATED 3 1 3 0 0
ZNF750 WILD-TYPE 24 39 29 18 16
'ZNF750 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.559 (Fisher's exact test), Q value = 0.75

Table S145.  Gene #15: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 64 49 41
ZNF750 MUTATED 1 4 1 3
ZNF750 WILD-TYPE 38 60 48 38
'ZNF750 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.303 (Fisher's exact test), Q value = 0.61

Table S146.  Gene #15: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
ZNF750 MUTATED 1 8 0
ZNF750 WILD-TYPE 48 112 24
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.288 (Fisher's exact test), Q value = 0.61

Table S147.  Gene #15: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 55 78
ZNF750 MUTATED 2 1 6
ZNF750 WILD-TYPE 59 54 72
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0963 (Fisher's exact test), Q value = 0.35

Table S148.  Gene #15: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
ZNF750 MUTATED 0 5 1 1 2
ZNF750 WILD-TYPE 41 45 57 14 28
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.318 (Fisher's exact test), Q value = 0.61

Table S149.  Gene #15: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 60 68
ZNF750 MUTATED 2 1 5
ZNF750 WILD-TYPE 54 59 63
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.351 (Fisher's exact test), Q value = 0.62

Table S150.  Gene #15: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 19 62 59 22 22
ZNF750 MUTATED 0 1 5 1 1
ZNF750 WILD-TYPE 19 61 54 21 21
'C12ORF43 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.851 (Fisher's exact test), Q value = 0.97

Table S151.  Gene #16: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 72 31 44 38
C12ORF43 MUTATED 0 2 1 1 0
C12ORF43 WILD-TYPE 6 70 30 43 38
'C12ORF43 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.677 (Fisher's exact test), Q value = 0.84

Table S152.  Gene #16: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 73 71
C12ORF43 MUTATED 0 2 2
C12ORF43 WILD-TYPE 50 71 69
'C12ORF43 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.912 (Fisher's exact test), Q value = 1

Table S153.  Gene #16: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 64 49 41
C12ORF43 MUTATED 0 2 1 1
C12ORF43 WILD-TYPE 39 62 48 40
'C12ORF43 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.456 (Fisher's exact test), Q value = 0.7

Table S154.  Gene #16: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
C12ORF43 MUTATED 0 4 0
C12ORF43 WILD-TYPE 49 116 24
'C12ORF43 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.386 (Fisher's exact test), Q value = 0.66

Table S155.  Gene #16: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 55 78
C12ORF43 MUTATED 0 2 2
C12ORF43 WILD-TYPE 61 53 76
'C12ORF43 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.206 (Fisher's exact test), Q value = 0.5

Table S156.  Gene #16: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
C12ORF43 MUTATED 0 0 2 1 1
C12ORF43 WILD-TYPE 41 50 56 14 29
'C12ORF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.517 (Fisher's exact test), Q value = 0.74

Table S157.  Gene #16: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 60 68
C12ORF43 MUTATED 0 2 1
C12ORF43 WILD-TYPE 56 58 67
'C12ORF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.561 (Fisher's exact test), Q value = 0.75

Table S158.  Gene #16: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 19 62 59 22 22
C12ORF43 MUTATED 0 2 0 1 0
C12ORF43 WILD-TYPE 19 60 59 21 22
'C3ORF70 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.921 (Fisher's exact test), Q value = 1

Table S159.  Gene #17: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 72 31 44 38
C3ORF70 MUTATED 0 1 1 1 1
C3ORF70 WILD-TYPE 6 71 30 43 37
'C3ORF70 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0884 (Fisher's exact test), Q value = 0.34

Table S160.  Gene #17: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 73 71
C3ORF70 MUTATED 3 1 0
C3ORF70 WILD-TYPE 47 72 71
'C3ORF70 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.469 (Fisher's exact test), Q value = 0.7

Table S161.  Gene #17: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 33 55
C3ORF70 MUTATED 0 1 2
C3ORF70 WILD-TYPE 45 32 53
'C3ORF70 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.179 (Fisher's exact test), Q value = 0.5

Table S162.  Gene #17: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
C3ORF70 MUTATED 0 0 2 0 1
C3ORF70 WILD-TYPE 27 40 30 18 15
'C3ORF70 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.656 (Fisher's exact test), Q value = 0.82

Table S163.  Gene #17: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 64 49 41
C3ORF70 MUTATED 1 1 2 0
C3ORF70 WILD-TYPE 38 63 47 41
'C3ORF70 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.127 (Fisher's exact test), Q value = 0.43

Table S164.  Gene #17: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
C3ORF70 MUTATED 3 1 0
C3ORF70 WILD-TYPE 46 119 24
'C3ORF70 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.14

Table S165.  Gene #17: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 55 78
C3ORF70 MUTATED 4 0 0
C3ORF70 WILD-TYPE 57 55 78

Figure S36.  Get High-res Image Gene #17: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'C3ORF70 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.298 (Fisher's exact test), Q value = 0.61

Table S166.  Gene #17: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
C3ORF70 MUTATED 2 2 0 0 0
C3ORF70 WILD-TYPE 39 48 58 15 30
'C3ORF70 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00816 (Fisher's exact test), Q value = 0.11

Table S167.  Gene #17: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 60 68
C3ORF70 MUTATED 4 0 0
C3ORF70 WILD-TYPE 52 60 68

Figure S37.  Get High-res Image Gene #17: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'C3ORF70 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0086 (Fisher's exact test), Q value = 0.11

Table S168.  Gene #17: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 19 62 59 22 22
C3ORF70 MUTATED 3 0 1 0 0
C3ORF70 WILD-TYPE 16 62 58 22 22

Figure S38.  Get High-res Image Gene #17: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.167 (Fisher's exact test), Q value = 0.5

Table S169.  Gene #18: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 72 31 44 38
BAP1 MUTATED 0 1 0 0 3
BAP1 WILD-TYPE 6 71 31 44 35
'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.453 (Fisher's exact test), Q value = 0.7

Table S170.  Gene #18: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 73 71
BAP1 MUTATED 0 3 1
BAP1 WILD-TYPE 50 70 70
'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 0.7

Table S171.  Gene #18: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 64 49 41
BAP1 MUTATED 0 3 1 0
BAP1 WILD-TYPE 39 61 48 41
'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.456 (Fisher's exact test), Q value = 0.7

Table S172.  Gene #18: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
BAP1 MUTATED 0 4 0
BAP1 WILD-TYPE 49 116 24
'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.683 (Fisher's exact test), Q value = 0.84

Table S173.  Gene #18: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 55 78
BAP1 MUTATED 1 2 1
BAP1 WILD-TYPE 60 53 77
'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.352 (Fisher's exact test), Q value = 0.62

Table S174.  Gene #18: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
BAP1 MUTATED 0 2 1 1 0
BAP1 WILD-TYPE 41 48 57 14 30
'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.553 (Fisher's exact test), Q value = 0.75

Table S175.  Gene #18: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 60 68
BAP1 MUTATED 0 2 2
BAP1 WILD-TYPE 56 58 66
'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.629 (Fisher's exact test), Q value = 0.8

Table S176.  Gene #18: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 19 62 59 22 22
BAP1 MUTATED 0 1 3 0 0
BAP1 WILD-TYPE 19 61 56 22 22
'USP28 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.636 (Fisher's exact test), Q value = 0.81

Table S177.  Gene #19: 'USP28 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 72 31 44 38
USP28 MUTATED 0 2 0 2 0
USP28 WILD-TYPE 6 70 31 42 38
'USP28 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.251 (Fisher's exact test), Q value = 0.56

Table S178.  Gene #19: 'USP28 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 73 71
USP28 MUTATED 1 3 0
USP28 WILD-TYPE 49 70 71
'USP28 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 0.5

Table S179.  Gene #19: 'USP28 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 33 55
USP28 MUTATED 0 0 3
USP28 WILD-TYPE 45 33 52
'USP28 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.909 (Fisher's exact test), Q value = 1

Table S180.  Gene #19: 'USP28 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
USP28 MUTATED 0 2 1 0 0
USP28 WILD-TYPE 27 38 31 18 16
'USP28 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.603 (Fisher's exact test), Q value = 0.78

Table S181.  Gene #19: 'USP28 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 64 49 41
USP28 MUTATED 0 1 1 2
USP28 WILD-TYPE 39 63 48 39
'USP28 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S182.  Gene #19: 'USP28 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
USP28 MUTATED 1 3 0
USP28 WILD-TYPE 48 117 24
'USP28 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 0.7

Table S183.  Gene #19: 'USP28 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 55 78
USP28 MUTATED 1 0 3
USP28 WILD-TYPE 60 55 75
'USP28 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S184.  Gene #19: 'USP28 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
USP28 MUTATED 1 1 2 0 0
USP28 WILD-TYPE 40 49 56 15 30
'USP28 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 0.61

Table S185.  Gene #19: 'USP28 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 60 68
USP28 MUTATED 1 0 3
USP28 WILD-TYPE 55 60 65
'USP28 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.274 (Fisher's exact test), Q value = 0.61

Table S186.  Gene #19: 'USP28 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 19 62 59 22 22
USP28 MUTATED 1 0 2 1 0
USP28 WILD-TYPE 18 62 57 21 22
'IFNGR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.147 (Fisher's exact test), Q value = 0.46

Table S187.  Gene #20: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 72 31 44 38
IFNGR1 MUTATED 0 0 1 3 2
IFNGR1 WILD-TYPE 6 72 30 41 36
'IFNGR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S188.  Gene #20: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 73 71
IFNGR1 MUTATED 2 2 2
IFNGR1 WILD-TYPE 48 71 69
'IFNGR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.469 (Fisher's exact test), Q value = 0.7

Table S189.  Gene #20: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 33 55
IFNGR1 MUTATED 0 1 2
IFNGR1 WILD-TYPE 45 32 53
'IFNGR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.911 (Fisher's exact test), Q value = 1

Table S190.  Gene #20: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 27 40 32 18 16
IFNGR1 MUTATED 0 2 1 0 0
IFNGR1 WILD-TYPE 27 38 31 18 16
'IFNGR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.846 (Fisher's exact test), Q value = 0.97

Table S191.  Gene #20: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 64 49 41
IFNGR1 MUTATED 2 2 1 1
IFNGR1 WILD-TYPE 37 62 48 40
'IFNGR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S192.  Gene #20: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 120 24
IFNGR1 MUTATED 2 4 0
IFNGR1 WILD-TYPE 47 116 24
'IFNGR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.325 (Fisher's exact test), Q value = 0.61

Table S193.  Gene #20: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 55 78
IFNGR1 MUTATED 3 0 3
IFNGR1 WILD-TYPE 58 55 75
'IFNGR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0333 (Fisher's exact test), Q value = 0.21

Table S194.  Gene #20: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 41 50 58 15 30
IFNGR1 MUTATED 1 3 0 2 0
IFNGR1 WILD-TYPE 40 47 58 13 30

Figure S39.  Get High-res Image Gene #20: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'IFNGR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.192 (Fisher's exact test), Q value = 0.5

Table S195.  Gene #20: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 60 68
IFNGR1 MUTATED 3 0 3
IFNGR1 WILD-TYPE 53 60 65
'IFNGR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.174 (Fisher's exact test), Q value = 0.5

Table S196.  Gene #20: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 19 62 59 22 22
IFNGR1 MUTATED 1 0 4 0 1
IFNGR1 WILD-TYPE 18 62 55 22 21
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/CESC-TP/22574677/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CESC-TP/22541064/CESC-TP.transferedmergedcluster.txt

  • Number of patients = 194

  • Number of significantly mutated genes = 20

  • Number of Molecular subtypes = 10

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

Fisher's exact test

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

Q value calculation

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

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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