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 23 genes and 10 molecular subtypes across 244 patients, 25 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • ATRX mutation correlated to 'CN_CNMF'.

  • RB1 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • NUMBL mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • KRTAP5-5 mutation correlated to 'RPPA_CHIERARCHICAL'.

  • LOR mutation correlated to 'CN_CNMF' and 'RPPA_CNMF'.

  • LHCGR mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • NF1 mutation correlated to 'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 23 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, 25 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
TP53 84 (34%) 160 0.00047
(0.00958) 		0.00016
(0.00652) 		0.0206
(0.21) 		0.156
(0.552) 		0.00023
(0.00661) 		0.00022
(0.00661) 		0.00045
(0.00958) 		4e-05
(0.00287) 		0.00345
(0.061) 		0.00833
(0.12)
RB1 24 (10%) 220 0.104
(0.499) 		0.0137
(0.166) 		0.0755
(0.457) 		0.404
(0.787) 		0.0005
(0.00958) 		0.0101
(0.137) 		1e-05
(0.0023) 		0.00017
(0.00652) 		4e-05
(0.00287) 		0.00038
(0.00958)
NF1 10 (4%) 234 0.445
(0.831) 		0.162
(0.559) 		0.236
(0.651) 		0.0128
(0.163) 		0.081
(0.466) 		0.0219
(0.21) 		0.647
(1.00) 		0.739
(1.00) 		0.0467
(0.357) 		0.00507
(0.0833)
LOR 6 (2%) 238 0.0226
(0.21) 		0.436
(0.823) 		0.0191
(0.21) 		0.0434
(0.357) 		0.663
(1.00) 		0.365
(0.777) 		0.146
(0.552) 		0.141
(0.551)
ATRX 37 (15%) 207 5e-05
(0.00287) 		0.0481
(0.357) 		0.112
(0.525) 		0.618
(1.00) 		0.328
(0.746) 		0.155
(0.552) 		0.5
(0.889) 		0.0595
(0.411) 		0.766
(1.00) 		0.222
(0.651)
NUMBL 9 (4%) 235 0.411
(0.789) 		0.266
(0.672) 		1
(1.00) 		0.141
(0.551) 		0.832
(1.00) 		0.55
(0.959) 		0.745
(1.00) 		0.735
(1.00) 		0.146
(0.552) 		0.00798
(0.12)
KRTAP5-5 7 (3%) 237 0.949
(1.00) 		0.101
(0.494) 		0.28
(0.692) 		0.0181
(0.208) 		0.0608
(0.411) 		0.121
(0.539) 		0.0987
(0.494) 		0.0565
(0.406) 		0.0648
(0.426) 		0.292
(0.693)
LHCGR 6 (2%) 238 0.39
(0.786) 		0.189
(0.613) 		0.0475
(0.357) 		0.0989
(0.494) 		0.287
(0.692) 		0.0228
(0.21) 		0.658
(1.00) 		0.251
(0.651) 		0.726
(1.00) 		0.137
(0.551)
MSH3 7 (3%) 237 0.286
(0.692) 		0.116
(0.531) 		1
(1.00) 		0.714
(1.00) 		0.889
(1.00) 		0.0865
(0.485) 		0.75
(1.00) 		0.867
(1.00) 		0.284
(0.692) 		0.318
(0.732)
EOMES 6 (2%) 238 0.938
(1.00) 		0.796
(1.00) 		0.721
(1.00) 		0.726
(1.00) 		1
(1.00) 		1
(1.00) 		0.575
(0.987) 		0.401
(0.787) 		1
(1.00) 		0.796
(1.00)
PKD2 6 (2%) 238 0.781
(1.00) 		0.86
(1.00) 		1
(1.00) 		0.725
(1.00) 		1
(1.00) 		0.344
(0.754) 		0.369
(0.78) 		0.22
(0.651) 		0.212
(0.651) 		0.599
(1.00)
LTBP3 5 (2%) 239 0.134
(0.551) 		0.636
(1.00) 		0.289
(0.692) 		0.827
(1.00) 		0.219
(0.651) 		0.128
(0.551) 		0.0723
(0.457) 		0.0735
(0.457) 		0.122
(0.539) 		0.244
(0.651)
SHROOM4 8 (3%) 236 0.405
(0.787) 		0.665
(1.00) 		0.384
(0.784) 		0.517
(0.909) 		0.427
(0.813) 		0.938
(1.00) 		0.468
(0.861) 		0.377
(0.783) 		0.874
(1.00) 		0.833
(1.00)
WNK1 6 (2%) 238 0.352
(0.763) 		0.86
(1.00) 		0.355
(0.763) 		0.682
(1.00) 		0.769
(1.00) 		0.882
(1.00) 		0.867
(1.00) 		0.664
(1.00) 		1
(1.00) 		0.988
(1.00)
ANP32E 4 (2%) 240 0.8
(1.00) 		0.0476
(0.357) 		0.396
(0.787) 		0.935
(1.00) 		0.204
(0.642) 		0.245
(0.651) 		0.198
(0.632) 		0.449
(0.832)
PTEN 7 (3%) 237 0.581
(0.99) 		0.249
(0.651) 		1
(1.00) 		0.663
(1.00) 		0.132
(0.551) 		0.262
(0.67) 		0.154
(0.552) 		0.502
(0.889) 		0.239
(0.651) 		0.31
(0.728)
TRAF7 4 (2%) 240 0.407
(0.787) 		0.596
(1.00) 		0.677
(1.00) 		0.171
(0.571) 		0.378
(0.783) 		0.151
(0.552) 		1
(1.00) 		1
(1.00) 		0.476
(0.863) 		0.317
(0.732)
MEGF9 3 (1%) 241 1
(1.00) 		0.901
(1.00) 		0.794
(1.00) 		0.93
(1.00) 		0.8
(1.00) 		0.704
(1.00) 		1
(1.00) 		0.935
(1.00)
CABLES1 3 (1%) 241 1
(1.00) 		0.239
(0.651) 		0.341
(0.754) 		0.629
(1.00) 		0.165
(0.559) 		0.852
(1.00) 		0.606
(1.00) 		0.847
(1.00)
COL18A1 7 (3%) 237 0.903
(1.00) 		0.689
(1.00) 		0.477
(0.863) 		0.67
(1.00) 		0.878
(1.00) 		0.614
(1.00) 		0.79
(1.00) 		0.557
(0.963) 		0.724
(1.00) 		0.223
(0.651)
FOXD2 3 (1%) 241 0.844
(1.00) 		0.775
(1.00) 		1
(1.00) 		0.385
(0.784) 		0.798
(1.00) 		0.494
(0.888) 		1
(1.00) 		0.0992
(0.494)
MMP17 3 (1%) 241 0.841
(1.00) 		0.163
(0.559) 		0.242
(0.651) 		0.745
(1.00) 		0.252
(0.651) 		0.805
(1.00) 		0.23
(0.651) 		0.133
(0.551)
ASTE1 3 (1%) 241 0.0901
(0.494) 		0.0785
(0.463) 		0.344
(0.754) 		0.0453
(0.357) 		0.233
(0.651) 		0.0972
(0.494) 		0.183
(0.6) 		0.334
(0.752)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0096

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
TP53 MUTATED 27 24 30 1
TP53 WILD-TYPE 35 59 40 24

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 = 0.00016 (Fisher's exact test), Q value = 0.0065

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
TP53 MUTATED 9 14 33 6 19 2 1
TP53 WILD-TYPE 36 32 24 29 26 11 2

Figure S2.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.21

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 42 54 56
TP53 MUTATED 11 15 26 20
TP53 WILD-TYPE 44 27 28 36

Figure S3.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.156 (Fisher's exact test), Q value = 0.55

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 25 34 46 61 19 22
TP53 MUTATED 5 10 18 28 4 7
TP53 WILD-TYPE 20 24 28 33 15 15
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0066

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
TP53 MUTATED 36 36 11
TP53 WILD-TYPE 73 35 51

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

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.0066

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
TP53 MUTATED 12 8 25 4 9 11 14
TP53 WILD-TYPE 30 15 22 42 17 14 19

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

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0096

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
TP53 MUTATED 26 12 46
TP53 WILD-TYPE 76 37 46

Figure S6.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.0029

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
TP53 MUTATED 23 8 49 4
TP53 WILD-TYPE 53 42 46 18

Figure S7.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00345 (Fisher's exact test), Q value = 0.061

Table S9.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 60 46
TP53 MUTATED 18 30 15
TP53 WILD-TYPE 61 30 31

Figure S8.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00833 (Fisher's exact test), Q value = 0.12

Table S10.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 29 33 24 11 21 21 22
TP53 MUTATED 4 6 17 12 6 9 5 4
TP53 WILD-TYPE 20 23 16 12 5 12 16 18

Figure S9.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0029

Table S11.  Gene #2: 'ATRX MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
ATRX MUTATED 15 2 17 2
ATRX WILD-TYPE 47 81 53 23

Figure S10.  Get High-res Image Gene #2: 'ATRX MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ATRX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0481 (Fisher's exact test), Q value = 0.36

Table S12.  Gene #2: 'ATRX MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
ATRX MUTATED 13 4 7 2 10 1 0
ATRX WILD-TYPE 32 42 50 33 35 12 3

Figure S11.  Get High-res Image Gene #2: 'ATRX MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ATRX MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 0.52

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 42 54 56
ATRX MUTATED 9 11 5 6
ATRX WILD-TYPE 46 31 49 50
'ATRX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.618 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 25 34 46 61 19 22
ATRX MUTATED 5 5 8 8 4 1
ATRX WILD-TYPE 20 29 38 53 15 21
'ATRX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.328 (Fisher's exact test), Q value = 0.75

Table S15.  Gene #2: 'ATRX MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
ATRX MUTATED 21 9 7
ATRX WILD-TYPE 88 62 55
'ATRX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.155 (Fisher's exact test), Q value = 0.55

Table S16.  Gene #2: 'ATRX MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
ATRX MUTATED 10 2 3 5 4 6 7
ATRX WILD-TYPE 32 21 44 41 22 19 26
'ATRX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.5 (Fisher's exact test), Q value = 0.89

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
ATRX MUTATED 17 9 11
ATRX WILD-TYPE 85 40 81
'ATRX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0595 (Fisher's exact test), Q value = 0.41

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
ATRX MUTATED 16 9 12 0
ATRX WILD-TYPE 60 41 83 22
'ATRX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.766 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 60 46
ATRX MUTATED 14 8 8
ATRX WILD-TYPE 65 52 38
'ATRX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.222 (Fisher's exact test), Q value = 0.65

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 29 33 24 11 21 21 22
ATRX MUTATED 5 7 4 5 1 5 3 0
ATRX WILD-TYPE 19 22 29 19 10 16 18 22
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.104 (Fisher's exact test), Q value = 0.5

Table S21.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
RB1 MUTATED 11 7 4 1
RB1 WILD-TYPE 51 76 66 24
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.17

Table S22.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
RB1 MUTATED 3 3 13 1 2 1 1
RB1 WILD-TYPE 42 43 44 34 43 12 2

Figure S12.  Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0755 (Fisher's exact test), Q value = 0.46

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 42 54 56
RB1 MUTATED 3 1 9 6
RB1 WILD-TYPE 52 41 45 50
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.404 (Fisher's exact test), Q value = 0.79

Table S24.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 25 34 46 61 19 22
RB1 MUTATED 2 3 2 10 1 1
RB1 WILD-TYPE 23 31 44 51 18 21
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0096

Table S25.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
RB1 MUTATED 8 15 1
RB1 WILD-TYPE 101 56 61

Figure S13.  Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.14

Table S26.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
RB1 MUTATED 3 2 12 2 0 3 2
RB1 WILD-TYPE 39 21 35 44 26 22 31

Figure S14.  Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0023

Table S27.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
RB1 MUTATED 0 6 18
RB1 WILD-TYPE 102 43 74

Figure S15.  Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.0065

Table S28.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
RB1 MUTATED 1 4 19 0
RB1 WILD-TYPE 75 46 76 22

Figure S16.  Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0029

Table S29.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 60 46
RB1 MUTATED 0 11 7
RB1 WILD-TYPE 79 49 39

Figure S17.  Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.0096

Table S30.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 29 33 24 11 21 21 22
RB1 MUTATED 3 0 6 7 2 0 0 0
RB1 WILD-TYPE 21 29 27 17 9 21 21 22

Figure S18.  Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NUMBL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.411 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
NUMBL MUTATED 2 2 5 0
NUMBL WILD-TYPE 60 81 65 25
'NUMBL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.266 (Fisher's exact test), Q value = 0.67

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
NUMBL MUTATED 0 2 1 1 4 1 0
NUMBL WILD-TYPE 45 44 56 34 41 12 3
'NUMBL MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 42 54 56
NUMBL MUTATED 2 2 2 2
NUMBL WILD-TYPE 53 40 52 54
'NUMBL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.141 (Fisher's exact test), Q value = 0.55

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 25 34 46 61 19 22
NUMBL MUTATED 0 0 5 2 1 0
NUMBL WILD-TYPE 25 34 41 59 18 22
'NUMBL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.832 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
NUMBL MUTATED 4 2 3
NUMBL WILD-TYPE 105 69 59
'NUMBL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.55 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
NUMBL MUTATED 1 0 1 2 3 1 1
NUMBL WILD-TYPE 41 23 46 44 23 24 32
'NUMBL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.745 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
NUMBL MUTATED 5 1 3
NUMBL WILD-TYPE 97 48 89
'NUMBL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.735 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
NUMBL MUTATED 4 1 3 1
NUMBL WILD-TYPE 72 49 92 21
'NUMBL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.146 (Fisher's exact test), Q value = 0.55

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 60 46
NUMBL MUTATED 5 0 2
NUMBL WILD-TYPE 74 60 44
'NUMBL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00798 (Fisher's exact test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 29 33 24 11 21 21 22
NUMBL MUTATED 1 0 0 2 0 4 0 0
NUMBL WILD-TYPE 23 29 33 22 11 17 21 22

Figure S19.  Get High-res Image Gene #4: 'NUMBL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MSH3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.286 (Fisher's exact test), Q value = 0.69

Table S41.  Gene #5: 'MSH3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
MSH3 MUTATED 0 4 2 1
MSH3 WILD-TYPE 62 79 68 24
'MSH3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.116 (Fisher's exact test), Q value = 0.53

Table S42.  Gene #5: 'MSH3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
MSH3 MUTATED 1 2 1 0 1 1 1
MSH3 WILD-TYPE 44 44 56 35 44 12 2
'MSH3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S43.  Gene #5: 'MSH3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 42 54 56
MSH3 MUTATED 2 1 1 2
MSH3 WILD-TYPE 53 41 53 54
'MSH3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.714 (Fisher's exact test), Q value = 1

Table S44.  Gene #5: 'MSH3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 25 34 46 61 19 22
MSH3 MUTATED 1 2 1 1 0 1
MSH3 WILD-TYPE 24 32 45 60 19 21
'MSH3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.889 (Fisher's exact test), Q value = 1

Table S45.  Gene #5: 'MSH3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
MSH3 MUTATED 4 2 1
MSH3 WILD-TYPE 105 69 61
'MSH3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0865 (Fisher's exact test), Q value = 0.49

Table S46.  Gene #5: 'MSH3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
MSH3 MUTATED 0 3 1 1 1 1 0
MSH3 WILD-TYPE 42 20 46 45 25 24 33
'MSH3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.75 (Fisher's exact test), Q value = 1

Table S47.  Gene #5: 'MSH3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
MSH3 MUTATED 2 2 2
MSH3 WILD-TYPE 100 47 90
'MSH3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S48.  Gene #5: 'MSH3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
MSH3 MUTATED 2 2 2 0
MSH3 WILD-TYPE 74 48 93 22
'MSH3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.284 (Fisher's exact test), Q value = 0.69

Table S49.  Gene #5: 'MSH3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 60 46
MSH3 MUTATED 2 0 2
MSH3 WILD-TYPE 77 60 44
'MSH3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.318 (Fisher's exact test), Q value = 0.73

Table S50.  Gene #5: 'MSH3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 29 33 24 11 21 21 22
MSH3 MUTATED 1 1 0 0 0 0 2 0
MSH3 WILD-TYPE 23 28 33 24 11 21 19 22
'EOMES MUTATION STATUS' versus 'CN_CNMF'

P value = 0.938 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
EOMES MUTATED 1 3 2 0
EOMES WILD-TYPE 61 80 68 25
'EOMES MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.796 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
EOMES MUTATED 1 1 1 1 1 1 0
EOMES WILD-TYPE 44 45 56 34 44 12 3
'EOMES MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.721 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 42 54 56
EOMES MUTATED 1 1 0 2
EOMES WILD-TYPE 54 41 54 54
'EOMES MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.726 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 25 34 46 61 19 22
EOMES MUTATED 1 0 2 1 0 0
EOMES WILD-TYPE 24 34 44 60 19 22
'EOMES MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
EOMES MUTATED 3 2 1
EOMES WILD-TYPE 106 69 61
'EOMES MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
EOMES MUTATED 1 0 1 1 1 1 1
EOMES WILD-TYPE 41 23 46 45 25 24 32
'EOMES MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.575 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
EOMES MUTATED 4 1 1
EOMES WILD-TYPE 98 48 91
'EOMES MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.401 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
EOMES MUTATED 3 0 2 1
EOMES WILD-TYPE 73 50 93 21
'EOMES MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 60 46
EOMES MUTATED 3 2 1
EOMES WILD-TYPE 76 58 45
'EOMES MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.796 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 29 33 24 11 21 21 22
EOMES MUTATED 0 1 1 0 1 1 1 1
EOMES WILD-TYPE 24 28 32 24 10 20 20 21
'PKD2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S61.  Gene #7: 'PKD2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
PKD2 MUTATED 1 2 3 0
PKD2 WILD-TYPE 61 81 67 25
'PKD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.86 (Fisher's exact test), Q value = 1

Table S62.  Gene #7: 'PKD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
PKD2 MUTATED 0 2 2 1 1 0 0
PKD2 WILD-TYPE 45 44 55 34 44 13 3
'PKD2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S63.  Gene #7: 'PKD2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 42 54 56
PKD2 MUTATED 1 1 1 1
PKD2 WILD-TYPE 54 41 53 55
'PKD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.725 (Fisher's exact test), Q value = 1

Table S64.  Gene #7: 'PKD2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 25 34 46 61 19 22
PKD2 MUTATED 1 0 2 1 0 0
PKD2 WILD-TYPE 24 34 44 60 19 22
'PKD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S65.  Gene #7: 'PKD2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
PKD2 MUTATED 3 2 1
PKD2 WILD-TYPE 106 69 61
'PKD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.344 (Fisher's exact test), Q value = 0.75

Table S66.  Gene #7: 'PKD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
PKD2 MUTATED 0 1 2 1 2 0 0
PKD2 WILD-TYPE 42 22 45 45 24 25 33
'PKD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.369 (Fisher's exact test), Q value = 0.78

Table S67.  Gene #7: 'PKD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
PKD2 MUTATED 1 2 3
PKD2 WILD-TYPE 101 47 89
'PKD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.22 (Fisher's exact test), Q value = 0.65

Table S68.  Gene #7: 'PKD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
PKD2 MUTATED 0 2 3 1
PKD2 WILD-TYPE 76 48 92 21
'PKD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.212 (Fisher's exact test), Q value = 0.65

Table S69.  Gene #7: 'PKD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 60 46
PKD2 MUTATED 1 1 3
PKD2 WILD-TYPE 78 59 43
'PKD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.599 (Fisher's exact test), Q value = 1

Table S70.  Gene #7: 'PKD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 29 33 24 11 21 21 22
PKD2 MUTATED 0 0 1 2 0 0 1 1
PKD2 WILD-TYPE 24 29 32 22 11 21 20 21
'LTBP3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 0.55

Table S71.  Gene #8: 'LTBP3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
LTBP3 MUTATED 0 1 4 0
LTBP3 WILD-TYPE 62 82 66 25
'LTBP3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.636 (Fisher's exact test), Q value = 1

Table S72.  Gene #8: 'LTBP3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
LTBP3 MUTATED 0 1 3 0 1 0 0
LTBP3 WILD-TYPE 45 45 54 35 44 13 3
'LTBP3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 0.69

Table S73.  Gene #8: 'LTBP3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 42 54 56
LTBP3 MUTATED 0 1 0 2
LTBP3 WILD-TYPE 55 41 54 54
'LTBP3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.827 (Fisher's exact test), Q value = 1

Table S74.  Gene #8: 'LTBP3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 25 34 46 61 19 22
LTBP3 MUTATED 0 0 2 1 0 0
LTBP3 WILD-TYPE 25 34 44 60 19 22
'LTBP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 0.65

Table S75.  Gene #8: 'LTBP3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
LTBP3 MUTATED 2 3 0
LTBP3 WILD-TYPE 107 68 62
'LTBP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.128 (Fisher's exact test), Q value = 0.55

Table S76.  Gene #8: 'LTBP3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
LTBP3 MUTATED 0 0 2 0 2 1 0
LTBP3 WILD-TYPE 42 23 45 46 24 24 33
'LTBP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0723 (Fisher's exact test), Q value = 0.46

Table S77.  Gene #8: 'LTBP3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
LTBP3 MUTATED 0 1 4
LTBP3 WILD-TYPE 102 48 88
'LTBP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0735 (Fisher's exact test), Q value = 0.46

Table S78.  Gene #8: 'LTBP3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
LTBP3 MUTATED 0 0 5 0
LTBP3 WILD-TYPE 76 50 90 22
'LTBP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.122 (Fisher's exact test), Q value = 0.54

Table S79.  Gene #8: 'LTBP3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 60 46
LTBP3 MUTATED 0 3 1
LTBP3 WILD-TYPE 79 57 45
'LTBP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.244 (Fisher's exact test), Q value = 0.65

Table S80.  Gene #8: 'LTBP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 29 33 24 11 21 21 22
LTBP3 MUTATED 0 0 3 1 0 0 0 0
LTBP3 WILD-TYPE 24 29 30 23 11 21 21 22
'SHROOM4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.405 (Fisher's exact test), Q value = 0.79

Table S81.  Gene #9: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
SHROOM4 MUTATED 2 1 4 1
SHROOM4 WILD-TYPE 60 82 66 24
'SHROOM4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.665 (Fisher's exact test), Q value = 1

Table S82.  Gene #9: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
SHROOM4 MUTATED 1 2 3 0 1 1 0
SHROOM4 WILD-TYPE 44 44 54 35 44 12 3
'SHROOM4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 0.78

Table S83.  Gene #9: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 42 54 56
SHROOM4 MUTATED 1 2 4 1
SHROOM4 WILD-TYPE 54 40 50 55
'SHROOM4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.517 (Fisher's exact test), Q value = 0.91

Table S84.  Gene #9: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 25 34 46 61 19 22
SHROOM4 MUTATED 1 0 3 4 0 0
SHROOM4 WILD-TYPE 24 34 43 57 19 22
'SHROOM4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.427 (Fisher's exact test), Q value = 0.81

Table S85.  Gene #9: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
SHROOM4 MUTATED 3 4 1
SHROOM4 WILD-TYPE 106 67 61
'SHROOM4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.938 (Fisher's exact test), Q value = 1

Table S86.  Gene #9: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
SHROOM4 MUTATED 1 0 3 1 1 1 1
SHROOM4 WILD-TYPE 41 23 44 45 25 24 32
'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.468 (Fisher's exact test), Q value = 0.86

Table S87.  Gene #9: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
SHROOM4 MUTATED 2 1 5
SHROOM4 WILD-TYPE 100 48 87
'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.377 (Fisher's exact test), Q value = 0.78

Table S88.  Gene #9: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
SHROOM4 MUTATED 3 0 5 0
SHROOM4 WILD-TYPE 73 50 90 22
'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.874 (Fisher's exact test), Q value = 1

Table S89.  Gene #9: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 60 46
SHROOM4 MUTATED 2 2 2
SHROOM4 WILD-TYPE 77 58 44
'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.833 (Fisher's exact test), Q value = 1

Table S90.  Gene #9: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 29 33 24 11 21 21 22
SHROOM4 MUTATED 0 1 1 1 1 1 1 0
SHROOM4 WILD-TYPE 24 28 32 23 10 20 20 22
'WNK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.352 (Fisher's exact test), Q value = 0.76

Table S91.  Gene #10: 'WNK1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
WNK1 MUTATED 0 4 2 0
WNK1 WILD-TYPE 62 79 68 25
'WNK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.86 (Fisher's exact test), Q value = 1

Table S92.  Gene #10: 'WNK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
WNK1 MUTATED 1 2 2 1 0 0 0
WNK1 WILD-TYPE 44 44 55 34 45 13 3
'WNK1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.355 (Fisher's exact test), Q value = 0.76

Table S93.  Gene #10: 'WNK1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 42 54 56
WNK1 MUTATED 0 1 3 2
WNK1 WILD-TYPE 55 41 51 54
'WNK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.682 (Fisher's exact test), Q value = 1

Table S94.  Gene #10: 'WNK1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 25 34 46 61 19 22
WNK1 MUTATED 0 0 2 2 1 1
WNK1 WILD-TYPE 25 34 44 59 18 21
'WNK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.769 (Fisher's exact test), Q value = 1

Table S95.  Gene #10: 'WNK1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
WNK1 MUTATED 2 2 2
WNK1 WILD-TYPE 107 69 60
'WNK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.882 (Fisher's exact test), Q value = 1

Table S96.  Gene #10: 'WNK1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
WNK1 MUTATED 1 0 2 2 1 0 0
WNK1 WILD-TYPE 41 23 45 44 25 25 33
'WNK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S97.  Gene #10: 'WNK1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
WNK1 MUTATED 2 1 3
WNK1 WILD-TYPE 100 48 89
'WNK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.664 (Fisher's exact test), Q value = 1

Table S98.  Gene #10: 'WNK1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
WNK1 MUTATED 1 1 3 1
WNK1 WILD-TYPE 75 49 92 21
'WNK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S99.  Gene #10: 'WNK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 60 46
WNK1 MUTATED 2 1 1
WNK1 WILD-TYPE 77 59 45
'WNK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.988 (Fisher's exact test), Q value = 1

Table S100.  Gene #10: 'WNK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 29 33 24 11 21 21 22
WNK1 MUTATED 0 1 1 1 0 0 0 1
WNK1 WILD-TYPE 24 28 32 23 11 21 21 21
'ANP32E MUTATION STATUS' versus 'CN_CNMF'

P value = 0.8 (Fisher's exact test), Q value = 1

Table S101.  Gene #11: 'ANP32E MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
ANP32E MUTATED 2 1 1 0
ANP32E WILD-TYPE 60 82 69 25
'ANP32E MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0476 (Fisher's exact test), Q value = 0.36

Table S102.  Gene #11: 'ANP32E MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
ANP32E MUTATED 0 1 1 0 0 2 0
ANP32E WILD-TYPE 45 45 56 35 45 11 3

Figure S20.  Get High-res Image Gene #11: 'ANP32E MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ANP32E MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.396 (Fisher's exact test), Q value = 0.79

Table S103.  Gene #11: 'ANP32E MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 42 54 56
ANP32E MUTATED 0 0 2 1
ANP32E WILD-TYPE 55 42 52 55
'ANP32E MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.935 (Fisher's exact test), Q value = 1

Table S104.  Gene #11: 'ANP32E MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 25 34 46 61 19 22
ANP32E MUTATED 0 0 1 2 0 0
ANP32E WILD-TYPE 25 34 45 59 19 22
'ANP32E MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.204 (Fisher's exact test), Q value = 0.64

Table S105.  Gene #11: 'ANP32E MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
ANP32E MUTATED 1 3 0
ANP32E WILD-TYPE 108 68 62
'ANP32E MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.245 (Fisher's exact test), Q value = 0.65

Table S106.  Gene #11: 'ANP32E MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
ANP32E MUTATED 1 0 1 0 0 2 0
ANP32E WILD-TYPE 41 23 46 46 26 23 33
'ANP32E MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 0.63

Table S107.  Gene #11: 'ANP32E MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
ANP32E MUTATED 0 1 3
ANP32E WILD-TYPE 102 48 89
'ANP32E MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.449 (Fisher's exact test), Q value = 0.83

Table S108.  Gene #11: 'ANP32E MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
ANP32E MUTATED 0 1 3 0
ANP32E WILD-TYPE 76 49 92 22
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.581 (Fisher's exact test), Q value = 0.99

Table S109.  Gene #12: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
PTEN MUTATED 3 2 1 1
PTEN WILD-TYPE 59 81 69 24
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.249 (Fisher's exact test), Q value = 0.65

Table S110.  Gene #12: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
PTEN MUTATED 0 0 4 2 1 0 0
PTEN WILD-TYPE 45 46 53 33 44 13 3
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S111.  Gene #12: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 42 54 56
PTEN MUTATED 1 1 1 1
PTEN WILD-TYPE 54 41 53 55
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.663 (Fisher's exact test), Q value = 1

Table S112.  Gene #12: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 25 34 46 61 19 22
PTEN MUTATED 1 0 1 1 0 1
PTEN WILD-TYPE 24 34 45 60 19 21
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.132 (Fisher's exact test), Q value = 0.55

Table S113.  Gene #12: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
PTEN MUTATED 1 4 2
PTEN WILD-TYPE 108 67 60
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.262 (Fisher's exact test), Q value = 0.67

Table S114.  Gene #12: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
PTEN MUTATED 0 0 4 2 0 0 1
PTEN WILD-TYPE 42 23 43 44 26 25 32
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.154 (Fisher's exact test), Q value = 0.55

Table S115.  Gene #12: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
PTEN MUTATED 1 1 5
PTEN WILD-TYPE 101 48 87
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.502 (Fisher's exact test), Q value = 0.89

Table S116.  Gene #12: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
PTEN MUTATED 1 1 5 0
PTEN WILD-TYPE 75 49 90 22
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.239 (Fisher's exact test), Q value = 0.65

Table S117.  Gene #12: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 60 46
PTEN MUTATED 1 4 1
PTEN WILD-TYPE 78 56 45
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.31 (Fisher's exact test), Q value = 0.73

Table S118.  Gene #12: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 29 33 24 11 21 21 22
PTEN MUTATED 1 0 3 2 0 0 0 0
PTEN WILD-TYPE 23 29 30 22 11 21 21 22
'KRTAP5-5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.949 (Fisher's exact test), Q value = 1

Table S119.  Gene #13: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
KRTAP5-5 MUTATED 2 2 2 1
KRTAP5-5 WILD-TYPE 60 81 68 24
'KRTAP5-5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 0.49

Table S120.  Gene #13: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
KRTAP5-5 MUTATED 3 1 0 3 0 0 0
KRTAP5-5 WILD-TYPE 42 45 57 32 45 13 3
'KRTAP5-5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.28 (Fisher's exact test), Q value = 0.69

Table S121.  Gene #13: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 42 54 56
KRTAP5-5 MUTATED 3 2 0 1
KRTAP5-5 WILD-TYPE 52 40 54 55
'KRTAP5-5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.21

Table S122.  Gene #13: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 25 34 46 61 19 22
KRTAP5-5 MUTATED 1 3 0 0 0 2
KRTAP5-5 WILD-TYPE 24 31 46 61 19 20

Figure S21.  Get High-res Image Gene #13: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'KRTAP5-5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0608 (Fisher's exact test), Q value = 0.41

Table S123.  Gene #13: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
KRTAP5-5 MUTATED 3 0 4
KRTAP5-5 WILD-TYPE 106 71 58
'KRTAP5-5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.121 (Fisher's exact test), Q value = 0.54

Table S124.  Gene #13: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
KRTAP5-5 MUTATED 2 1 0 4 0 0 0
KRTAP5-5 WILD-TYPE 40 22 47 42 26 25 33
'KRTAP5-5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0987 (Fisher's exact test), Q value = 0.49

Table S125.  Gene #13: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
KRTAP5-5 MUTATED 6 0 1
KRTAP5-5 WILD-TYPE 96 49 91
'KRTAP5-5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0565 (Fisher's exact test), Q value = 0.41

Table S126.  Gene #13: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
KRTAP5-5 MUTATED 4 0 1 2
KRTAP5-5 WILD-TYPE 72 50 94 20
'KRTAP5-5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0648 (Fisher's exact test), Q value = 0.43

Table S127.  Gene #13: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 60 46
KRTAP5-5 MUTATED 6 1 0
KRTAP5-5 WILD-TYPE 73 59 46
'KRTAP5-5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.292 (Fisher's exact test), Q value = 0.69

Table S128.  Gene #13: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 29 33 24 11 21 21 22
KRTAP5-5 MUTATED 1 3 0 1 0 0 0 2
KRTAP5-5 WILD-TYPE 23 26 33 23 11 21 21 20
'TRAF7 MUTATION STATUS' versus 'CN_CNMF'

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

Table S129.  Gene #14: 'TRAF7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
TRAF7 MUTATED 1 2 0 1
TRAF7 WILD-TYPE 61 81 70 24
'TRAF7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.596 (Fisher's exact test), Q value = 1

Table S130.  Gene #14: 'TRAF7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
TRAF7 MUTATED 2 1 0 0 1 0 0
TRAF7 WILD-TYPE 43 45 57 35 44 13 3
'TRAF7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.677 (Fisher's exact test), Q value = 1

Table S131.  Gene #14: 'TRAF7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 42 54 56
TRAF7 MUTATED 2 1 0 1
TRAF7 WILD-TYPE 53 41 54 55
'TRAF7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.171 (Fisher's exact test), Q value = 0.57

Table S132.  Gene #14: 'TRAF7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 25 34 46 61 19 22
TRAF7 MUTATED 2 1 1 0 0 0
TRAF7 WILD-TYPE 23 33 45 61 19 22
'TRAF7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 0.78

Table S133.  Gene #14: 'TRAF7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
TRAF7 MUTATED 3 0 1
TRAF7 WILD-TYPE 106 71 61
'TRAF7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.151 (Fisher's exact test), Q value = 0.55

Table S134.  Gene #14: 'TRAF7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
TRAF7 MUTATED 2 0 0 0 0 0 2
TRAF7 WILD-TYPE 40 23 47 46 26 25 31
'TRAF7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S135.  Gene #14: 'TRAF7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
TRAF7 MUTATED 2 1 1
TRAF7 WILD-TYPE 100 48 91
'TRAF7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S136.  Gene #14: 'TRAF7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
TRAF7 MUTATED 1 1 2 0
TRAF7 WILD-TYPE 75 49 93 22
'TRAF7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.476 (Fisher's exact test), Q value = 0.86

Table S137.  Gene #14: 'TRAF7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 60 46
TRAF7 MUTATED 1 2 0
TRAF7 WILD-TYPE 78 58 46
'TRAF7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.317 (Fisher's exact test), Q value = 0.73

Table S138.  Gene #14: 'TRAF7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 29 33 24 11 21 21 22
TRAF7 MUTATED 0 1 0 2 0 0 0 0
TRAF7 WILD-TYPE 24 28 33 22 11 21 21 22
'MEGF9 MUTATION STATUS' versus 'CN_CNMF'

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

Table S139.  Gene #15: 'MEGF9 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
MEGF9 MUTATED 1 1 1 0
MEGF9 WILD-TYPE 61 82 69 25
'MEGF9 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.901 (Fisher's exact test), Q value = 1

Table S140.  Gene #15: 'MEGF9 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
MEGF9 MUTATED 1 0 1 0 1 0 0
MEGF9 WILD-TYPE 44 46 56 35 44 13 3
'MEGF9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.794 (Fisher's exact test), Q value = 1

Table S141.  Gene #15: 'MEGF9 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
MEGF9 MUTATED 2 1 0
MEGF9 WILD-TYPE 107 70 62
'MEGF9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.93 (Fisher's exact test), Q value = 1

Table S142.  Gene #15: 'MEGF9 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
MEGF9 MUTATED 1 0 1 0 0 0 1
MEGF9 WILD-TYPE 41 23 46 46 26 25 32
'MEGF9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.8 (Fisher's exact test), Q value = 1

Table S143.  Gene #15: 'MEGF9 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
MEGF9 MUTATED 1 1 1
MEGF9 WILD-TYPE 101 48 91
'MEGF9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.704 (Fisher's exact test), Q value = 1

Table S144.  Gene #15: 'MEGF9 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
MEGF9 MUTATED 2 0 1 0
MEGF9 WILD-TYPE 74 50 94 22
'MEGF9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S145.  Gene #15: 'MEGF9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 60 46
MEGF9 MUTATED 1 1 1
MEGF9 WILD-TYPE 78 59 45
'MEGF9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.935 (Fisher's exact test), Q value = 1

Table S146.  Gene #15: 'MEGF9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 29 33 24 11 21 21 22
MEGF9 MUTATED 0 1 1 0 0 0 1 0
MEGF9 WILD-TYPE 24 28 32 24 11 21 20 22
'LOR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0226 (Fisher's exact test), Q value = 0.21

Table S147.  Gene #16: 'LOR MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
LOR MUTATED 0 2 1 3
LOR WILD-TYPE 62 81 69 22

Figure S22.  Get High-res Image Gene #16: 'LOR MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'LOR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.436 (Fisher's exact test), Q value = 0.82

Table S148.  Gene #16: 'LOR MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
LOR MUTATED 1 2 0 1 1 1 0
LOR WILD-TYPE 44 44 57 34 44 12 3
'LOR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.21

Table S149.  Gene #16: 'LOR MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 42 54 56
LOR MUTATED 4 1 0 0
LOR WILD-TYPE 51 41 54 56

Figure S23.  Get High-res Image Gene #16: 'LOR MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'LOR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0434 (Fisher's exact test), Q value = 0.36

Table S150.  Gene #16: 'LOR MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 25 34 46 61 19 22
LOR MUTATED 1 3 0 0 0 1
LOR WILD-TYPE 24 31 46 61 19 21

Figure S24.  Get High-res Image Gene #16: 'LOR MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'LOR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.663 (Fisher's exact test), Q value = 1

Table S151.  Gene #16: 'LOR MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
LOR MUTATED 4 1 1
LOR WILD-TYPE 105 70 61
'LOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.365 (Fisher's exact test), Q value = 0.78

Table S152.  Gene #16: 'LOR MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
LOR MUTATED 1 2 0 1 0 1 1
LOR WILD-TYPE 41 21 47 45 26 24 32
'LOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.146 (Fisher's exact test), Q value = 0.55

Table S153.  Gene #16: 'LOR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
LOR MUTATED 5 0 1
LOR WILD-TYPE 97 49 91
'LOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.141 (Fisher's exact test), Q value = 0.55

Table S154.  Gene #16: 'LOR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
LOR MUTATED 4 0 1 1
LOR WILD-TYPE 72 50 94 21
'CABLES1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S155.  Gene #17: 'CABLES1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
CABLES1 MUTATED 1 1 1 0
CABLES1 WILD-TYPE 61 82 69 25
'CABLES1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.239 (Fisher's exact test), Q value = 0.65

Table S156.  Gene #17: 'CABLES1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
CABLES1 MUTATED 1 0 1 0 0 1 0
CABLES1 WILD-TYPE 44 46 56 35 45 12 3
'CABLES1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.341 (Fisher's exact test), Q value = 0.75

Table S157.  Gene #17: 'CABLES1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 42 54 56
CABLES1 MUTATED 1 0 2 0
CABLES1 WILD-TYPE 54 42 52 56
'CABLES1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.629 (Fisher's exact test), Q value = 1

Table S158.  Gene #17: 'CABLES1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 25 34 46 61 19 22
CABLES1 MUTATED 1 0 0 2 0 0
CABLES1 WILD-TYPE 24 34 46 59 19 22
'CABLES1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.165 (Fisher's exact test), Q value = 0.56

Table S159.  Gene #17: 'CABLES1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
CABLES1 MUTATED 0 2 1
CABLES1 WILD-TYPE 109 69 61
'CABLES1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.852 (Fisher's exact test), Q value = 1

Table S160.  Gene #17: 'CABLES1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
CABLES1 MUTATED 0 0 1 1 0 1 0
CABLES1 WILD-TYPE 42 23 46 45 26 24 33
'CABLES1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.606 (Fisher's exact test), Q value = 1

Table S161.  Gene #17: 'CABLES1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
CABLES1 MUTATED 1 0 2
CABLES1 WILD-TYPE 101 49 90
'CABLES1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.847 (Fisher's exact test), Q value = 1

Table S162.  Gene #17: 'CABLES1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
CABLES1 MUTATED 1 0 2 0
CABLES1 WILD-TYPE 75 50 93 22
'COL18A1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.903 (Fisher's exact test), Q value = 1

Table S163.  Gene #18: 'COL18A1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
COL18A1 MUTATED 2 2 3 0
COL18A1 WILD-TYPE 60 81 67 25
'COL18A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.689 (Fisher's exact test), Q value = 1

Table S164.  Gene #18: 'COL18A1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
COL18A1 MUTATED 2 3 1 0 1 0 0
COL18A1 WILD-TYPE 43 43 56 35 44 13 3
'COL18A1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.477 (Fisher's exact test), Q value = 0.86

Table S165.  Gene #18: 'COL18A1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 42 54 56
COL18A1 MUTATED 1 1 1 4
COL18A1 WILD-TYPE 54 41 53 52
'COL18A1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.67 (Fisher's exact test), Q value = 1

Table S166.  Gene #18: 'COL18A1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 25 34 46 61 19 22
COL18A1 MUTATED 1 1 3 1 1 0
COL18A1 WILD-TYPE 24 33 43 60 18 22
'COL18A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.878 (Fisher's exact test), Q value = 1

Table S167.  Gene #18: 'COL18A1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
COL18A1 MUTATED 3 1 2
COL18A1 WILD-TYPE 106 70 60
'COL18A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.614 (Fisher's exact test), Q value = 1

Table S168.  Gene #18: 'COL18A1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
COL18A1 MUTATED 1 0 1 2 2 0 0
COL18A1 WILD-TYPE 41 23 46 44 24 25 33
'COL18A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.79 (Fisher's exact test), Q value = 1

Table S169.  Gene #18: 'COL18A1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
COL18A1 MUTATED 3 2 2
COL18A1 WILD-TYPE 99 47 90
'COL18A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.557 (Fisher's exact test), Q value = 0.96

Table S170.  Gene #18: 'COL18A1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
COL18A1 MUTATED 2 3 2 0
COL18A1 WILD-TYPE 74 47 93 22
'COL18A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S171.  Gene #18: 'COL18A1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 60 46
COL18A1 MUTATED 2 1 2
COL18A1 WILD-TYPE 77 59 44
'COL18A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.223 (Fisher's exact test), Q value = 0.65

Table S172.  Gene #18: 'COL18A1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 29 33 24 11 21 21 22
COL18A1 MUTATED 2 0 1 0 0 0 2 0
COL18A1 WILD-TYPE 22 29 32 24 11 21 19 22
'LHCGR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.39 (Fisher's exact test), Q value = 0.79

Table S173.  Gene #19: 'LHCGR MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
LHCGR MUTATED 1 1 4 0
LHCGR WILD-TYPE 61 82 66 25
'LHCGR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.189 (Fisher's exact test), Q value = 0.61

Table S174.  Gene #19: 'LHCGR MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
LHCGR MUTATED 1 0 0 2 3 0 0
LHCGR WILD-TYPE 44 46 57 33 42 13 3
'LHCGR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0475 (Fisher's exact test), Q value = 0.36

Table S175.  Gene #19: 'LHCGR MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 42 54 56
LHCGR MUTATED 0 3 0 2
LHCGR WILD-TYPE 55 39 54 54

Figure S25.  Get High-res Image Gene #19: 'LHCGR MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'LHCGR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0989 (Fisher's exact test), Q value = 0.49

Table S176.  Gene #19: 'LHCGR MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 25 34 46 61 19 22
LHCGR MUTATED 0 0 3 0 1 1
LHCGR WILD-TYPE 25 34 43 61 18 21
'LHCGR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.287 (Fisher's exact test), Q value = 0.69

Table S177.  Gene #19: 'LHCGR MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
LHCGR MUTATED 4 0 2
LHCGR WILD-TYPE 105 71 60
'LHCGR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0228 (Fisher's exact test), Q value = 0.21

Table S178.  Gene #19: 'LHCGR MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
LHCGR MUTATED 0 1 0 2 3 0 0
LHCGR WILD-TYPE 42 22 47 44 23 25 33

Figure S26.  Get High-res Image Gene #19: 'LHCGR MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'LHCGR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.658 (Fisher's exact test), Q value = 1

Table S179.  Gene #19: 'LHCGR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
LHCGR MUTATED 3 0 3
LHCGR WILD-TYPE 99 49 89
'LHCGR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.251 (Fisher's exact test), Q value = 0.65

Table S180.  Gene #19: 'LHCGR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
LHCGR MUTATED 1 1 2 2
LHCGR WILD-TYPE 75 49 93 20
'LHCGR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.726 (Fisher's exact test), Q value = 1

Table S181.  Gene #19: 'LHCGR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 60 46
LHCGR MUTATED 2 1 2
LHCGR WILD-TYPE 77 59 44
'LHCGR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.137 (Fisher's exact test), Q value = 0.55

Table S182.  Gene #19: 'LHCGR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 29 33 24 11 21 21 22
LHCGR MUTATED 0 0 0 2 0 0 1 2
LHCGR WILD-TYPE 24 29 33 22 11 21 20 20
'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.445 (Fisher's exact test), Q value = 0.83

Table S183.  Gene #20: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
NF1 MUTATED 1 3 5 1
NF1 WILD-TYPE 61 80 65 24
'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.162 (Fisher's exact test), Q value = 0.56

Table S184.  Gene #20: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
NF1 MUTATED 1 5 0 2 2 0 0
NF1 WILD-TYPE 44 41 57 33 43 13 3
'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.236 (Fisher's exact test), Q value = 0.65

Table S185.  Gene #20: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 42 54 56
NF1 MUTATED 3 2 0 4
NF1 WILD-TYPE 52 40 54 52
'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.16

Table S186.  Gene #20: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 25 34 46 61 19 22
NF1 MUTATED 1 1 3 0 0 4
NF1 WILD-TYPE 24 33 43 61 19 18

Figure S27.  Get High-res Image Gene #20: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.081 (Fisher's exact test), Q value = 0.47

Table S187.  Gene #20: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
NF1 MUTATED 6 0 4
NF1 WILD-TYPE 103 71 58
'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.21

Table S188.  Gene #20: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
NF1 MUTATED 1 0 0 4 4 0 1
NF1 WILD-TYPE 41 23 47 42 22 25 32

Figure S28.  Get High-res Image Gene #20: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.647 (Fisher's exact test), Q value = 1

Table S189.  Gene #20: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
NF1 MUTATED 4 3 3
NF1 WILD-TYPE 98 46 89
'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.739 (Fisher's exact test), Q value = 1

Table S190.  Gene #20: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
NF1 MUTATED 2 3 4 1
NF1 WILD-TYPE 74 47 91 21
'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0467 (Fisher's exact test), Q value = 0.36

Table S191.  Gene #20: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 60 46
NF1 MUTATED 1 2 5
NF1 WILD-TYPE 78 58 41

Figure S29.  Get High-res Image Gene #20: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00507 (Fisher's exact test), Q value = 0.083

Table S192.  Gene #20: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 29 33 24 11 21 21 22
NF1 MUTATED 0 0 0 4 0 0 3 1
NF1 WILD-TYPE 24 29 33 20 11 21 18 21

Figure S30.  Get High-res Image Gene #20: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'FOXD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.844 (Fisher's exact test), Q value = 1

Table S193.  Gene #21: 'FOXD2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
FOXD2 MUTATED 0 2 1 0
FOXD2 WILD-TYPE 62 81 69 25
'FOXD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.775 (Fisher's exact test), Q value = 1

Table S194.  Gene #21: 'FOXD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
FOXD2 MUTATED 0 0 1 1 1 0 0
FOXD2 WILD-TYPE 45 46 56 34 44 13 3
'FOXD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S195.  Gene #21: 'FOXD2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
FOXD2 MUTATED 1 1 1
FOXD2 WILD-TYPE 108 70 61
'FOXD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.385 (Fisher's exact test), Q value = 0.78

Table S196.  Gene #21: 'FOXD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
FOXD2 MUTATED 0 0 0 1 1 1 0
FOXD2 WILD-TYPE 42 23 47 45 25 24 33
'FOXD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.798 (Fisher's exact test), Q value = 1

Table S197.  Gene #21: 'FOXD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
FOXD2 MUTATED 1 1 1
FOXD2 WILD-TYPE 101 48 91
'FOXD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 0.89

Table S198.  Gene #21: 'FOXD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
FOXD2 MUTATED 1 0 1 1
FOXD2 WILD-TYPE 75 50 94 21
'FOXD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S199.  Gene #21: 'FOXD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 60 46
FOXD2 MUTATED 1 1 1
FOXD2 WILD-TYPE 78 59 45
'FOXD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0992 (Fisher's exact test), Q value = 0.49

Table S200.  Gene #21: 'FOXD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 29 33 24 11 21 21 22
FOXD2 MUTATED 0 0 0 0 1 0 1 1
FOXD2 WILD-TYPE 24 29 33 24 10 21 20 21
'MMP17 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.841 (Fisher's exact test), Q value = 1

Table S201.  Gene #22: 'MMP17 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
MMP17 MUTATED 0 2 1 0
MMP17 WILD-TYPE 62 81 69 25
'MMP17 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.163 (Fisher's exact test), Q value = 0.56

Table S202.  Gene #22: 'MMP17 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
MMP17 MUTATED 1 0 0 2 0 0 0
MMP17 WILD-TYPE 44 46 57 33 45 13 3
'MMP17 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 0.65

Table S203.  Gene #22: 'MMP17 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 42 54 56
MMP17 MUTATED 2 1 0 0
MMP17 WILD-TYPE 53 41 54 56
'MMP17 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.745 (Fisher's exact test), Q value = 1

Table S204.  Gene #22: 'MMP17 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 25 34 46 61 19 22
MMP17 MUTATED 0 0 1 1 0 1
MMP17 WILD-TYPE 25 34 45 60 19 21
'MMP17 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.252 (Fisher's exact test), Q value = 0.65

Table S205.  Gene #22: 'MMP17 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
MMP17 MUTATED 1 0 2
MMP17 WILD-TYPE 108 71 60
'MMP17 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.805 (Fisher's exact test), Q value = 1

Table S206.  Gene #22: 'MMP17 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
MMP17 MUTATED 1 0 0 1 1 0 0
MMP17 WILD-TYPE 41 23 47 45 25 25 33
'MMP17 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.23 (Fisher's exact test), Q value = 0.65

Table S207.  Gene #22: 'MMP17 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
MMP17 MUTATED 3 0 0
MMP17 WILD-TYPE 99 49 92
'MMP17 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.133 (Fisher's exact test), Q value = 0.55

Table S208.  Gene #22: 'MMP17 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
MMP17 MUTATED 1 1 0 1
MMP17 WILD-TYPE 75 49 95 21
'ASTE1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0901 (Fisher's exact test), Q value = 0.49

Table S209.  Gene #23: 'ASTE1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 62 83 70 25
ASTE1 MUTATED 0 0 3 0
ASTE1 WILD-TYPE 62 83 67 25
'ASTE1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0785 (Fisher's exact test), Q value = 0.46

Table S210.  Gene #23: 'ASTE1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 45 46 57 35 45 13 3
ASTE1 MUTATED 3 0 0 0 0 0 0
ASTE1 WILD-TYPE 42 46 57 35 45 13 3
'ASTE1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.344 (Fisher's exact test), Q value = 0.75

Table S211.  Gene #23: 'ASTE1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 109 71 62
ASTE1 MUTATED 3 0 0
ASTE1 WILD-TYPE 106 71 62
'ASTE1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0453 (Fisher's exact test), Q value = 0.36

Table S212.  Gene #23: 'ASTE1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 23 47 46 26 25 33
ASTE1 MUTATED 3 0 0 0 0 0 0
ASTE1 WILD-TYPE 39 23 47 46 26 25 33

Figure S31.  Get High-res Image Gene #23: 'ASTE1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ASTE1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.233 (Fisher's exact test), Q value = 0.65

Table S213.  Gene #23: 'ASTE1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 102 49 92
ASTE1 MUTATED 3 0 0
ASTE1 WILD-TYPE 99 49 92
'ASTE1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0972 (Fisher's exact test), Q value = 0.49

Table S214.  Gene #23: 'ASTE1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 50 95 22
ASTE1 MUTATED 3 0 0 0
ASTE1 WILD-TYPE 73 50 95 22
'ASTE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.183 (Fisher's exact test), Q value = 0.6

Table S215.  Gene #23: 'ASTE1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 60 46
ASTE1 MUTATED 3 0 0
ASTE1 WILD-TYPE 76 60 46
'ASTE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.334 (Fisher's exact test), Q value = 0.75

Table S216.  Gene #23: 'ASTE1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 24 29 33 24 11 21 21 22
ASTE1 MUTATED 0 2 0 0 0 1 0 0
ASTE1 WILD-TYPE 24 27 33 24 11 20 21 22
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/SARC-TP/19898602/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SARC-TP/20140640/SARC-TP.transferedmergedcluster.txt

  • Number of patients = 244

  • Number of significantly mutated genes = 23

  • 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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