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 17 genes and 10 molecular subtypes across 247 patients, 32 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'.

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

  • ATRX mutation correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • PTEN mutation correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • KRTAP5-5 mutation correlated to 'METHLYATION_CNMF' and 'RPPA_CHIERARCHICAL'.

  • TRAF7 mutation correlated to 'MIRSEQ_MATURE_CNMF'.

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

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

  • COL4A3 mutation correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 17 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, 32 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 85 (34%) 162 0.0003
(0.00527) 		1e-05
(0.00085) 		0.00547
(0.0595) 		0.0567
(0.284) 		0.00038
(0.00587) 		0.00013
(0.00316) 		0.00552
(0.0595) 		4e-05
(0.0017) 		0.00031
(0.00527) 		0.00615
(0.0615)
RB1 24 (10%) 223 0.00024
(0.0051) 		0.00261
(0.0341) 		0.0795
(0.323) 		0.382
(0.714) 		0.00052
(0.00737) 		0.00964
(0.0819) 		1e-05
(0.00085) 		6e-05
(0.0017) 		0.00679
(0.0641) 		4e-05
(0.0017)
NF1 9 (4%) 238 0.0908
(0.328) 		0.0444
(0.236) 		0.25
(0.599) 		0.0056
(0.0595) 		0.0888
(0.328) 		0.00792
(0.0709) 		1
(1.00) 		0.871
(1.00) 		0.037
(0.217) 		0.0127
(0.0978)
ATRX 36 (15%) 211 6e-05
(0.0017) 		0.361
(0.703) 		0.0599
(0.289) 		0.555
(0.858) 		0.399
(0.721) 		0.0926
(0.328) 		0.245
(0.596) 		0.444
(0.767) 		0.439
(0.767) 		0.0141
(0.1)
PTEN 7 (3%) 240 0.0189
(0.12) 		0.331
(0.678) 		1
(1.00) 		0.668
(0.896) 		0.132
(0.408) 		0.269
(0.618) 		0.219
(0.564) 		0.305
(0.64) 		0.578
(0.862) 		0.0389
(0.221)
KRTAP5-5 7 (3%) 240 1
(1.00) 		0.0119
(0.096) 		0.28
(0.618) 		0.0133
(0.0987) 		0.0625
(0.289) 		0.1
(0.341) 		0.0986
(0.341) 		0.0862
(0.328) 		0.0797
(0.323) 		0.0714
(0.316)
LOR 6 (2%) 241 0.0724
(0.316) 		0.132
(0.408) 		0.0191
(0.12) 		0.0352
(0.214) 		0.663
(0.896) 		0.458
(0.772) 		0.143
(0.436) 		0.15
(0.445)
TRAF7 4 (2%) 243 0.906
(1.00) 		0.669
(0.896) 		0.675
(0.896) 		0.152
(0.445) 		0.376
(0.711) 		0.166
(0.464) 		1
(1.00) 		1
(1.00) 		0.0169
(0.115) 		0.0511
(0.263)
COL4A3 4 (2%) 243 0.0425
(0.233) 		0.529
(0.842) 		0.339
(0.679) 		0.63
(0.885) 		0.587
(0.868) 		0.572
(0.862) 		0.533
(0.842) 		0.388
(0.717) 		1
(1.00) 		0.942
(1.00)
NUMBL 8 (3%) 239 0.957
(1.00) 		0.244
(0.596) 		0.953
(1.00) 		0.0824
(0.326) 		0.531
(0.842) 		0.289
(0.621) 		0.578
(0.862) 		0.273
(0.618) 		0.297
(0.631) 		0.121
(0.396)
MSH3 7 (3%) 240 0.766
(1.00) 		0.662
(0.896) 		1
(1.00) 		0.825
(1.00) 		0.886
(1.00) 		0.063
(0.289) 		0.75
(0.989) 		0.54
(0.842) 		0.492
(0.813) 		0.215
(0.564)
LTBP3 5 (2%) 242 0.13
(0.408) 		0.495
(0.813) 		0.284
(0.619) 		0.877
(1.00) 		0.219
(0.564) 		0.166
(0.464) 		0.0751
(0.319) 		0.18
(0.487) 		0.169
(0.464) 		0.091
(0.328)
EOMES 5 (2%) 242 0.924
(1.00) 		1
(1.00) 		0.885
(1.00) 		0.268
(0.618) 		1
(1.00) 		1
(1.00) 		0.28
(0.618) 		0.271
(0.618) 		0.839
(1.00) 		1
(1.00)
CABLES1 3 (1%) 244 1
(1.00) 		0.328
(0.678) 		0.339
(0.679) 		0.571
(0.862) 		0.167
(0.464) 		0.8
(1.00) 		0.61
(0.88) 		1
(1.00)
R3HDM1 4 (2%) 243 0.397
(0.721) 		0.668
(0.896) 		0.448
(0.767) 		0.415
(0.743) 		0.376
(0.711) 		0.236
(0.596) 		0.804
(1.00) 		0.364
(0.703)
MEGF9 3 (1%) 244 0.594
(0.87) 		0.627
(0.885) 		0.793
(1.00) 		0.932
(1.00) 		0.804
(1.00) 		0.807
(1.00) 		0.535
(0.842) 		1
(1.00)
SCAP 3 (1%) 244 0.115
(0.384) 		0.788
(1.00) 		0.451
(0.767) 		0.344
(0.68) 		0.613
(0.88) 		0.616
(0.88) 		0.426
(0.754) 		0.24
(0.596) 		0.497
(0.813) 		0.674
(0.896)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0053

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 58 38 57
TP53 MUTATED 31 8 16 28
TP53 WILD-TYPE 59 50 22 29

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 = 1e-05 (Fisher's exact test), Q value = 0.00085

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 68 72
TP53 MUTATED 13 6 38 28
TP53 WILD-TYPE 42 46 30 44

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 = 0.00547 (Fisher's exact test), Q value = 0.059

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 42 55 57
TP53 MUTATED 10 15 27 21
TP53 WILD-TYPE 46 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 = 0.0567 (Fisher's exact test), Q value = 0.28

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 23 34 47 62 22 22
TP53 MUTATED 3 11 18 29 5 7
TP53 WILD-TYPE 20 23 29 33 17 15
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0059

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 72 63
TP53 MUTATED 35 37 12
TP53 WILD-TYPE 75 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 = 0.00013 (Fisher's exact test), Q value = 0.0032

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 43 21 48 46 29 25 33
TP53 MUTATED 12 7 26 4 12 11 12
TP53 WILD-TYPE 31 14 22 42 17 14 21

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 = 0.00552 (Fisher's exact test), Q value = 0.059

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 50 96
TP53 MUTATED 27 13 45
TP53 WILD-TYPE 73 37 51

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 = 0.0017

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 36 110 21
TP53 MUTATED 25 5 53 2
TP53 WILD-TYPE 54 31 57 19

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 = 0.00031 (Fisher's exact test), Q value = 0.0053

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 56 26 44 23 39
TP53 MUTATED 11 3 24 10 16
TP53 WILD-TYPE 45 23 20 13 23

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 = 0.00615 (Fisher's exact test), Q value = 0.061

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
ALL 55 46 21 42 24
TP53 MUTATED 15 25 9 11 4
TP53 WILD-TYPE 40 21 12 31 20

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

'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0051

Table S11.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 58 38 57
RB1 MUTATED 5 1 3 14
RB1 WILD-TYPE 85 57 35 43

Figure S10.  Get High-res Image Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00261 (Fisher's exact test), Q value = 0.034

Table S12.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 68 72
RB1 MUTATED 3 3 15 3
RB1 WILD-TYPE 52 49 53 69

Figure S11.  Get High-res Image Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0795 (Fisher's exact test), Q value = 0.32

Table S13.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 42 55 57
RB1 MUTATED 3 1 9 6
RB1 WILD-TYPE 53 41 46 51
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.382 (Fisher's exact test), Q value = 0.71

Table S14.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 34 47 62 22 22
RB1 MUTATED 2 3 2 10 1 1
RB1 WILD-TYPE 21 31 45 52 21 21
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0074

Table S15.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 72 63
RB1 MUTATED 8 15 1
RB1 WILD-TYPE 102 57 62

Figure S12.  Get High-res Image Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00964 (Fisher's exact test), Q value = 0.082

Table S16.  Gene #2: '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 43 21 48 46 29 25 33
RB1 MUTATED 3 2 12 2 0 3 2
RB1 WILD-TYPE 40 19 36 44 29 22 31

Figure S13.  Get High-res Image Gene #2: '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 = 0.00085

Table S17.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 50 96
RB1 MUTATED 0 6 18
RB1 WILD-TYPE 100 44 78

Figure S14.  Get High-res Image Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.0017

Table S18.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 36 110 21
RB1 MUTATED 1 2 21 0
RB1 WILD-TYPE 78 34 89 21

Figure S15.  Get High-res Image Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00679 (Fisher's exact test), Q value = 0.064

Table S19.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 56 26 44 23 39
RB1 MUTATED 0 3 8 2 5
RB1 WILD-TYPE 56 23 36 21 34

Figure S16.  Get High-res Image Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.0017

Table S20.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 46 21 42 24
RB1 MUTATED 0 9 6 3 0
RB1 WILD-TYPE 55 37 15 39 24

Figure S17.  Get High-res Image Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0017

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 58 38 57
ATRX MUTATED 20 2 0 13
ATRX WILD-TYPE 70 56 38 44

Figure S18.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ATRX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.361 (Fisher's exact test), Q value = 0.7

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 68 72
ATRX MUTATED 7 7 7 15
ATRX WILD-TYPE 48 45 61 57
'ATRX MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0599 (Fisher's exact test), Q value = 0.29

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 42 55 57
ATRX MUTATED 9 11 4 6
ATRX WILD-TYPE 47 31 51 51
'ATRX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.555 (Fisher's exact test), Q value = 0.86

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 34 47 62 22 22
ATRX MUTATED 5 5 8 7 4 1
ATRX WILD-TYPE 18 29 39 55 18 21
'ATRX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.399 (Fisher's exact test), Q value = 0.72

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 72 63
ATRX MUTATED 20 8 8
ATRX WILD-TYPE 90 64 55
'ATRX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0926 (Fisher's exact test), Q value = 0.33

Table S26.  Gene #3: '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 43 21 48 46 29 25 33
ATRX MUTATED 10 2 2 5 5 6 6
ATRX WILD-TYPE 33 19 46 41 24 19 27
'ATRX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.245 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 50 96
ATRX MUTATED 16 10 10
ATRX WILD-TYPE 84 40 86
'ATRX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.444 (Fisher's exact test), Q value = 0.77

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 36 110 21
ATRX MUTATED 15 5 15 1
ATRX WILD-TYPE 64 31 95 20
'ATRX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.439 (Fisher's exact test), Q value = 0.77

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 56 26 44 23 39
ATRX MUTATED 10 5 3 4 7
ATRX WILD-TYPE 46 21 41 19 32
'ATRX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 46 21 42 24
ATRX MUTATED 14 4 5 6 0
ATRX WILD-TYPE 41 42 16 36 24

Figure S19.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NUMBL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.957 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 58 38 57
NUMBL MUTATED 4 2 1 1
NUMBL WILD-TYPE 86 56 37 56
'NUMBL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.244 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 68 72
NUMBL MUTATED 2 2 0 4
NUMBL WILD-TYPE 53 50 68 68
'NUMBL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.953 (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 56 42 55 57
NUMBL MUTATED 2 2 1 2
NUMBL WILD-TYPE 54 40 54 55
'NUMBL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0824 (Fisher's exact test), Q value = 0.33

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 23 34 47 62 22 22
NUMBL MUTATED 0 0 5 1 1 0
NUMBL WILD-TYPE 23 34 42 61 21 22
'NUMBL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.531 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 72 63
NUMBL MUTATED 4 1 3
NUMBL WILD-TYPE 106 71 60
'NUMBL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.289 (Fisher's exact test), Q value = 0.62

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 43 21 48 46 29 25 33
NUMBL MUTATED 1 0 0 2 3 1 1
NUMBL WILD-TYPE 42 21 48 44 26 24 32
'NUMBL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.578 (Fisher's exact test), Q value = 0.86

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 50 96
NUMBL MUTATED 5 1 2
NUMBL WILD-TYPE 95 49 94
'NUMBL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.273 (Fisher's exact test), Q value = 0.62

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 36 110 21
NUMBL MUTATED 3 0 3 2
NUMBL WILD-TYPE 76 36 107 19
'NUMBL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 0.63

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 56 26 44 23 39
NUMBL MUTATED 4 0 0 1 2
NUMBL WILD-TYPE 52 26 44 22 37
'NUMBL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.121 (Fisher's exact test), Q value = 0.4

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
ALL 55 46 21 42 24
NUMBL MUTATED 5 0 1 1 0
NUMBL WILD-TYPE 50 46 20 41 24
'MSH3 MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 58 38 57
MSH3 MUTATED 2 3 1 1
MSH3 WILD-TYPE 88 55 37 56
'MSH3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.662 (Fisher's exact test), Q value = 0.9

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 68 72
MSH3 MUTATED 3 1 1 2
MSH3 WILD-TYPE 52 51 67 70
'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 56 42 55 57
MSH3 MUTATED 2 1 1 2
MSH3 WILD-TYPE 54 41 54 55
'MSH3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.825 (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 23 34 47 62 22 22
MSH3 MUTATED 1 1 1 1 1 1
MSH3 WILD-TYPE 22 33 46 61 21 21
'MSH3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.886 (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 110 72 63
MSH3 MUTATED 4 2 1
MSH3 WILD-TYPE 106 70 62
'MSH3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.063 (Fisher's exact test), Q value = 0.29

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 43 21 48 46 29 25 33
MSH3 MUTATED 0 3 1 1 1 1 0
MSH3 WILD-TYPE 43 18 47 45 28 24 33
'MSH3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.75 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 50 96
MSH3 MUTATED 2 2 2
MSH3 WILD-TYPE 98 48 94
'MSH3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.54 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 36 110 21
MSH3 MUTATED 2 2 2 0
MSH3 WILD-TYPE 77 34 108 21
'MSH3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.492 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 56 26 44 23 39
MSH3 MUTATED 2 0 0 0 2
MSH3 WILD-TYPE 54 26 44 23 37
'MSH3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.215 (Fisher's exact test), Q value = 0.56

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
ALL 55 46 21 42 24
MSH3 MUTATED 1 0 0 3 0
MSH3 WILD-TYPE 54 46 21 39 24
'LTBP3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 0.41

Table S51.  Gene #6: 'LTBP3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 58 38 57
LTBP3 MUTATED 3 0 2 0
LTBP3 WILD-TYPE 87 58 36 57
'LTBP3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.495 (Fisher's exact test), Q value = 0.81

Table S52.  Gene #6: 'LTBP3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 68 72
LTBP3 MUTATED 1 0 3 1
LTBP3 WILD-TYPE 54 52 65 71
'LTBP3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.284 (Fisher's exact test), Q value = 0.62

Table S53.  Gene #6: 'LTBP3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 42 55 57
LTBP3 MUTATED 0 1 0 2
LTBP3 WILD-TYPE 56 41 55 55
'LTBP3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.877 (Fisher's exact test), Q value = 1

Table S54.  Gene #6: 'LTBP3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 34 47 62 22 22
LTBP3 MUTATED 0 0 2 1 0 0
LTBP3 WILD-TYPE 23 34 45 61 22 22
'LTBP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 0.56

Table S55.  Gene #6: 'LTBP3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 72 63
LTBP3 MUTATED 2 3 0
LTBP3 WILD-TYPE 108 69 63
'LTBP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.166 (Fisher's exact test), Q value = 0.46

Table S56.  Gene #6: '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 43 21 48 46 29 25 33
LTBP3 MUTATED 0 0 2 0 2 1 0
LTBP3 WILD-TYPE 43 21 46 46 27 24 33
'LTBP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0751 (Fisher's exact test), Q value = 0.32

Table S57.  Gene #6: 'LTBP3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 50 96
LTBP3 MUTATED 0 1 4
LTBP3 WILD-TYPE 100 49 92
'LTBP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.18 (Fisher's exact test), Q value = 0.49

Table S58.  Gene #6: 'LTBP3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 36 110 21
LTBP3 MUTATED 0 0 5 0
LTBP3 WILD-TYPE 79 36 105 21
'LTBP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.169 (Fisher's exact test), Q value = 0.46

Table S59.  Gene #6: 'LTBP3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 56 26 44 23 39
LTBP3 MUTATED 0 0 3 0 1
LTBP3 WILD-TYPE 56 26 41 23 38
'LTBP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.091 (Fisher's exact test), Q value = 0.33

Table S60.  Gene #6: 'LTBP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 46 21 42 24
LTBP3 MUTATED 0 3 1 0 0
LTBP3 WILD-TYPE 55 43 20 42 24
'EOMES MUTATION STATUS' versus 'CN_CNMF'

P value = 0.924 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 58 38 57
EOMES MUTATED 3 1 0 1
EOMES WILD-TYPE 87 57 38 56
'EOMES MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 68 72
EOMES MUTATED 1 1 1 2
EOMES WILD-TYPE 54 51 67 70
'EOMES MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.885 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 42 55 57
EOMES MUTATED 1 1 0 1
EOMES WILD-TYPE 55 41 55 56
'EOMES MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.268 (Fisher's exact test), Q value = 0.62

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 34 47 62 22 22
EOMES MUTATED 1 0 2 0 0 0
EOMES WILD-TYPE 22 34 45 62 22 22
'EOMES MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 72 63
EOMES MUTATED 3 1 1
EOMES WILD-TYPE 107 71 62
'EOMES MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S66.  Gene #7: '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 43 21 48 46 29 25 33
EOMES MUTATED 1 0 1 1 1 0 1
EOMES WILD-TYPE 42 21 47 45 28 25 32
'EOMES MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.28 (Fisher's exact test), Q value = 0.62

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 50 96
EOMES MUTATED 4 0 1
EOMES WILD-TYPE 96 50 95
'EOMES MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.271 (Fisher's exact test), Q value = 0.62

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 36 110 21
EOMES MUTATED 3 0 1 1
EOMES WILD-TYPE 76 36 109 20
'EOMES MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.839 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 56 26 44 23 39
EOMES MUTATED 2 0 1 0 2
EOMES WILD-TYPE 54 26 43 23 37
'EOMES MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 46 21 42 24
EOMES MUTATED 2 1 0 1 1
EOMES WILD-TYPE 53 45 21 41 23
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 58 38 57
PTEN MUTATED 0 1 3 3
PTEN WILD-TYPE 90 57 35 54

Figure S20.  Get High-res Image Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 68 72
PTEN MUTATED 0 1 4 2
PTEN WILD-TYPE 55 51 64 70
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 42 55 57
PTEN MUTATED 1 1 1 1
PTEN WILD-TYPE 55 41 54 56
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.668 (Fisher's exact test), Q value = 0.9

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 34 47 62 22 22
PTEN MUTATED 1 0 1 1 0 1
PTEN WILD-TYPE 22 34 46 61 22 21
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.132 (Fisher's exact test), Q value = 0.41

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 72 63
PTEN MUTATED 1 4 2
PTEN WILD-TYPE 109 68 61
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.269 (Fisher's exact test), Q value = 0.62

Table S76.  Gene #8: '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 43 21 48 46 29 25 33
PTEN MUTATED 0 0 4 2 0 0 1
PTEN WILD-TYPE 43 21 44 44 29 25 32
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 0.56

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 50 96
PTEN MUTATED 1 1 5
PTEN WILD-TYPE 99 49 91
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.305 (Fisher's exact test), Q value = 0.64

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 36 110 21
PTEN MUTATED 1 0 6 0
PTEN WILD-TYPE 78 36 104 21
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.578 (Fisher's exact test), Q value = 0.86

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 56 26 44 23 39
PTEN MUTATED 1 0 3 1 1
PTEN WILD-TYPE 55 26 41 22 38
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0389 (Fisher's exact test), Q value = 0.22

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 46 21 42 24
PTEN MUTATED 0 3 2 0 1
PTEN WILD-TYPE 55 43 19 42 23

Figure S21.  Get High-res Image Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KRTAP5-5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S81.  Gene #9: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 58 38 57
KRTAP5-5 MUTATED 3 2 1 1
KRTAP5-5 WILD-TYPE 87 56 37 56
'KRTAP5-5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.096

Table S82.  Gene #9: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 68 72
KRTAP5-5 MUTATED 1 5 0 1
KRTAP5-5 WILD-TYPE 54 47 68 71

Figure S22.  Get High-res Image Gene #9: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KRTAP5-5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.28 (Fisher's exact test), Q value = 0.62

Table S83.  Gene #9: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 42 55 57
KRTAP5-5 MUTATED 3 2 0 1
KRTAP5-5 WILD-TYPE 53 40 55 56
'KRTAP5-5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0133 (Fisher's exact test), Q value = 0.099

Table S84.  Gene #9: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 34 47 62 22 22
KRTAP5-5 MUTATED 1 3 0 0 0 2
KRTAP5-5 WILD-TYPE 22 31 47 62 22 20

Figure S23.  Get High-res Image Gene #9: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'KRTAP5-5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0625 (Fisher's exact test), Q value = 0.29

Table S85.  Gene #9: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 72 63
KRTAP5-5 MUTATED 3 0 4
KRTAP5-5 WILD-TYPE 107 72 59
'KRTAP5-5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.1 (Fisher's exact test), Q value = 0.34

Table S86.  Gene #9: '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 43 21 48 46 29 25 33
KRTAP5-5 MUTATED 2 1 0 4 0 0 0
KRTAP5-5 WILD-TYPE 41 20 48 42 29 25 33
'KRTAP5-5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0986 (Fisher's exact test), Q value = 0.34

Table S87.  Gene #9: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 50 96
KRTAP5-5 MUTATED 6 0 1
KRTAP5-5 WILD-TYPE 94 50 95
'KRTAP5-5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0862 (Fisher's exact test), Q value = 0.33

Table S88.  Gene #9: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 36 110 21
KRTAP5-5 MUTATED 5 0 1 1
KRTAP5-5 WILD-TYPE 74 36 109 20
'KRTAP5-5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0797 (Fisher's exact test), Q value = 0.32

Table S89.  Gene #9: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 56 26 44 23 39
KRTAP5-5 MUTATED 3 2 0 2 0
KRTAP5-5 WILD-TYPE 53 24 44 21 39
'KRTAP5-5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0714 (Fisher's exact test), Q value = 0.32

Table S90.  Gene #9: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 46 21 42 24
KRTAP5-5 MUTATED 4 0 1 0 2
KRTAP5-5 WILD-TYPE 51 46 20 42 22
'CABLES1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S91.  Gene #10: 'CABLES1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 58 38 57
CABLES1 MUTATED 1 1 0 1
CABLES1 WILD-TYPE 89 57 38 56
'CABLES1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.328 (Fisher's exact test), Q value = 0.68

Table S92.  Gene #10: 'CABLES1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 68 72
CABLES1 MUTATED 0 1 2 0
CABLES1 WILD-TYPE 55 51 66 72
'CABLES1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.339 (Fisher's exact test), Q value = 0.68

Table S93.  Gene #10: 'CABLES1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 42 55 57
CABLES1 MUTATED 1 0 2 0
CABLES1 WILD-TYPE 55 42 53 57
'CABLES1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.571 (Fisher's exact test), Q value = 0.86

Table S94.  Gene #10: 'CABLES1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 34 47 62 22 22
CABLES1 MUTATED 1 0 0 2 0 0
CABLES1 WILD-TYPE 22 34 47 60 22 22
'CABLES1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.167 (Fisher's exact test), Q value = 0.46

Table S95.  Gene #10: 'CABLES1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 72 63
CABLES1 MUTATED 0 2 1
CABLES1 WILD-TYPE 110 70 62
'CABLES1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S96.  Gene #10: '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 43 21 48 46 29 25 33
CABLES1 MUTATED 0 0 1 1 0 1 0
CABLES1 WILD-TYPE 43 21 47 45 29 24 33
'CABLES1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.61 (Fisher's exact test), Q value = 0.88

Table S97.  Gene #10: 'CABLES1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 50 96
CABLES1 MUTATED 1 0 2
CABLES1 WILD-TYPE 99 50 94
'CABLES1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S98.  Gene #10: 'CABLES1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 36 110 21
CABLES1 MUTATED 1 0 2 0
CABLES1 WILD-TYPE 78 36 108 21
'TRAF7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.906 (Fisher's exact test), Q value = 1

Table S99.  Gene #11: 'TRAF7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 58 38 57
TRAF7 MUTATED 1 1 1 1
TRAF7 WILD-TYPE 89 57 37 56
'TRAF7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.669 (Fisher's exact test), Q value = 0.9

Table S100.  Gene #11: 'TRAF7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 68 72
TRAF7 MUTATED 1 1 0 2
TRAF7 WILD-TYPE 54 51 68 70
'TRAF7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.675 (Fisher's exact test), Q value = 0.9

Table S101.  Gene #11: 'TRAF7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 42 55 57
TRAF7 MUTATED 2 1 0 1
TRAF7 WILD-TYPE 54 41 55 56
'TRAF7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.152 (Fisher's exact test), Q value = 0.45

Table S102.  Gene #11: 'TRAF7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 34 47 62 22 22
TRAF7 MUTATED 2 1 1 0 0 0
TRAF7 WILD-TYPE 21 33 46 62 22 22
'TRAF7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 0.71

Table S103.  Gene #11: 'TRAF7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 72 63
TRAF7 MUTATED 3 0 1
TRAF7 WILD-TYPE 107 72 62
'TRAF7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.166 (Fisher's exact test), Q value = 0.46

Table S104.  Gene #11: '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 43 21 48 46 29 25 33
TRAF7 MUTATED 2 0 0 0 0 0 2
TRAF7 WILD-TYPE 41 21 48 46 29 25 31
'TRAF7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S105.  Gene #11: 'TRAF7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 50 96
TRAF7 MUTATED 2 1 1
TRAF7 WILD-TYPE 98 49 95
'TRAF7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S106.  Gene #11: 'TRAF7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 36 110 21
TRAF7 MUTATED 2 0 2 0
TRAF7 WILD-TYPE 77 36 108 21
'TRAF7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.11

Table S107.  Gene #11: 'TRAF7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 56 26 44 23 39
TRAF7 MUTATED 0 2 0 1 0
TRAF7 WILD-TYPE 56 24 44 22 39

Figure S24.  Get High-res Image Gene #11: 'TRAF7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'TRAF7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0511 (Fisher's exact test), Q value = 0.26

Table S108.  Gene #11: 'TRAF7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 46 21 42 24
TRAF7 MUTATED 1 0 2 0 0
TRAF7 WILD-TYPE 54 46 19 42 24
'LOR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0724 (Fisher's exact test), Q value = 0.32

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 58 38 57
LOR MUTATED 1 4 1 0
LOR WILD-TYPE 89 54 37 57
'LOR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.132 (Fisher's exact test), Q value = 0.41

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 68 72
LOR MUTATED 2 3 0 1
LOR WILD-TYPE 53 49 68 71
'LOR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 42 55 57
LOR MUTATED 4 1 0 0
LOR WILD-TYPE 52 41 55 57

Figure S25.  Get High-res Image Gene #12: 'LOR MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'LOR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0352 (Fisher's exact test), Q value = 0.21

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 34 47 62 22 22
LOR MUTATED 1 3 0 0 0 1
LOR WILD-TYPE 22 31 47 62 22 21

Figure S26.  Get High-res Image Gene #12: '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 = 0.9

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 72 63
LOR MUTATED 4 1 1
LOR WILD-TYPE 106 71 62
'LOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.458 (Fisher's exact test), Q value = 0.77

Table S114.  Gene #12: '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 43 21 48 46 29 25 33
LOR MUTATED 1 1 0 1 0 1 2
LOR WILD-TYPE 42 20 48 45 29 24 31
'LOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.143 (Fisher's exact test), Q value = 0.44

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 50 96
LOR MUTATED 5 0 1
LOR WILD-TYPE 95 50 95
'LOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.15 (Fisher's exact test), Q value = 0.45

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 36 110 21
LOR MUTATED 4 0 1 1
LOR WILD-TYPE 75 36 109 20
'R3HDM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 0.72

Table S117.  Gene #13: 'R3HDM1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 58 38 57
R3HDM1 MUTATED 1 2 1 0
R3HDM1 WILD-TYPE 89 56 37 57
'R3HDM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.668 (Fisher's exact test), Q value = 0.9

Table S118.  Gene #13: 'R3HDM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 68 72
R3HDM1 MUTATED 1 1 0 2
R3HDM1 WILD-TYPE 54 51 68 70
'R3HDM1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.448 (Fisher's exact test), Q value = 0.77

Table S119.  Gene #13: 'R3HDM1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 42 55 57
R3HDM1 MUTATED 2 0 1 0
R3HDM1 WILD-TYPE 54 42 54 57
'R3HDM1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.415 (Fisher's exact test), Q value = 0.74

Table S120.  Gene #13: 'R3HDM1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 34 47 62 22 22
R3HDM1 MUTATED 0 1 1 0 0 1
R3HDM1 WILD-TYPE 23 33 46 62 22 21
'R3HDM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 0.71

Table S121.  Gene #13: 'R3HDM1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 72 63
R3HDM1 MUTATED 3 0 1
R3HDM1 WILD-TYPE 107 72 62
'R3HDM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.236 (Fisher's exact test), Q value = 0.6

Table S122.  Gene #13: 'R3HDM1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 21 48 46 29 25 33
R3HDM1 MUTATED 0 0 0 1 2 0 1
R3HDM1 WILD-TYPE 43 21 48 45 27 25 32
'R3HDM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.804 (Fisher's exact test), Q value = 1

Table S123.  Gene #13: 'R3HDM1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 50 96
R3HDM1 MUTATED 2 0 1
R3HDM1 WILD-TYPE 98 50 95
'R3HDM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.364 (Fisher's exact test), Q value = 0.7

Table S124.  Gene #13: 'R3HDM1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 36 110 21
R3HDM1 MUTATED 1 0 1 1
R3HDM1 WILD-TYPE 78 36 109 20
'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0908 (Fisher's exact test), Q value = 0.33

Table S125.  Gene #14: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 58 38 57
NF1 MUTATED 5 4 0 0
NF1 WILD-TYPE 85 54 38 57
'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0444 (Fisher's exact test), Q value = 0.24

Table S126.  Gene #14: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 68 72
NF1 MUTATED 5 2 0 2
NF1 WILD-TYPE 50 50 68 70

Figure S27.  Get High-res Image Gene #14: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.25 (Fisher's exact test), Q value = 0.6

Table S127.  Gene #14: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 42 55 57
NF1 MUTATED 2 2 0 4
NF1 WILD-TYPE 54 40 55 53
'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0056 (Fisher's exact test), Q value = 0.059

Table S128.  Gene #14: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 34 47 62 22 22
NF1 MUTATED 0 1 3 0 0 4
NF1 WILD-TYPE 23 33 44 62 22 18

Figure S28.  Get High-res Image Gene #14: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0888 (Fisher's exact test), Q value = 0.33

Table S129.  Gene #14: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 72 63
NF1 MUTATED 5 0 4
NF1 WILD-TYPE 105 72 59
'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00792 (Fisher's exact test), Q value = 0.071

Table S130.  Gene #14: '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 43 21 48 46 29 25 33
NF1 MUTATED 0 0 0 4 4 0 1
NF1 WILD-TYPE 43 21 48 42 25 25 32

Figure S29.  Get High-res Image Gene #14: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S131.  Gene #14: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 50 96
NF1 MUTATED 4 2 3
NF1 WILD-TYPE 96 48 93
'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.871 (Fisher's exact test), Q value = 1

Table S132.  Gene #14: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 36 110 21
NF1 MUTATED 3 2 4 0
NF1 WILD-TYPE 76 34 106 21
'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.22

Table S133.  Gene #14: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 56 26 44 23 39
NF1 MUTATED 1 0 0 2 4
NF1 WILD-TYPE 55 26 44 21 35

Figure S30.  Get High-res Image Gene #14: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.098

Table S134.  Gene #14: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 46 21 42 24
NF1 MUTATED 0 0 2 4 1
NF1 WILD-TYPE 55 46 19 38 23

Figure S31.  Get High-res Image Gene #14: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'COL4A3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0425 (Fisher's exact test), Q value = 0.23

Table S135.  Gene #15: 'COL4A3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 58 38 57
COL4A3 MUTATED 0 2 2 0
COL4A3 WILD-TYPE 90 56 36 57

Figure S32.  Get High-res Image Gene #15: 'COL4A3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'COL4A3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.529 (Fisher's exact test), Q value = 0.84

Table S136.  Gene #15: 'COL4A3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 68 72
COL4A3 MUTATED 0 2 1 1
COL4A3 WILD-TYPE 55 50 67 71
'COL4A3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.339 (Fisher's exact test), Q value = 0.68

Table S137.  Gene #15: 'COL4A3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 42 55 57
COL4A3 MUTATED 1 0 2 0
COL4A3 WILD-TYPE 55 42 53 57
'COL4A3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.63 (Fisher's exact test), Q value = 0.89

Table S138.  Gene #15: 'COL4A3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 34 47 62 22 22
COL4A3 MUTATED 0 1 0 1 0 1
COL4A3 WILD-TYPE 23 33 47 61 22 21
'COL4A3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.587 (Fisher's exact test), Q value = 0.87

Table S139.  Gene #15: 'COL4A3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 72 63
COL4A3 MUTATED 1 1 2
COL4A3 WILD-TYPE 109 71 61
'COL4A3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.572 (Fisher's exact test), Q value = 0.86

Table S140.  Gene #15: 'COL4A3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 21 48 46 29 25 33
COL4A3 MUTATED 0 0 1 1 0 0 2
COL4A3 WILD-TYPE 43 21 47 45 29 25 31
'COL4A3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.533 (Fisher's exact test), Q value = 0.84

Table S141.  Gene #15: 'COL4A3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 50 96
COL4A3 MUTATED 3 0 1
COL4A3 WILD-TYPE 97 50 95
'COL4A3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.388 (Fisher's exact test), Q value = 0.72

Table S142.  Gene #15: 'COL4A3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 36 110 21
COL4A3 MUTATED 2 0 1 1
COL4A3 WILD-TYPE 77 36 109 20
'COL4A3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S143.  Gene #15: 'COL4A3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 56 26 44 23 39
COL4A3 MUTATED 2 0 1 0 1
COL4A3 WILD-TYPE 54 26 43 23 38
'COL4A3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.942 (Fisher's exact test), Q value = 1

Table S144.  Gene #15: 'COL4A3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 46 21 42 24
COL4A3 MUTATED 1 1 0 1 1
COL4A3 WILD-TYPE 54 45 21 41 23
'MEGF9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.594 (Fisher's exact test), Q value = 0.87

Table S145.  Gene #16: 'MEGF9 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 58 38 57
MEGF9 MUTATED 1 0 1 1
MEGF9 WILD-TYPE 89 58 37 56
'MEGF9 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.627 (Fisher's exact test), Q value = 0.89

Table S146.  Gene #16: 'MEGF9 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 68 72
MEGF9 MUTATED 0 0 1 2
MEGF9 WILD-TYPE 55 52 67 70
'MEGF9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.793 (Fisher's exact test), Q value = 1

Table S147.  Gene #16: 'MEGF9 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 72 63
MEGF9 MUTATED 2 1 0
MEGF9 WILD-TYPE 108 71 63
'MEGF9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.932 (Fisher's exact test), Q value = 1

Table S148.  Gene #16: '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 43 21 48 46 29 25 33
MEGF9 MUTATED 1 0 1 0 0 0 1
MEGF9 WILD-TYPE 42 21 47 46 29 25 32
'MEGF9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.804 (Fisher's exact test), Q value = 1

Table S149.  Gene #16: 'MEGF9 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 50 96
MEGF9 MUTATED 2 0 1
MEGF9 WILD-TYPE 98 50 95
'MEGF9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.807 (Fisher's exact test), Q value = 1

Table S150.  Gene #16: 'MEGF9 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 36 110 21
MEGF9 MUTATED 2 0 1 0
MEGF9 WILD-TYPE 77 36 109 21
'MEGF9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.535 (Fisher's exact test), Q value = 0.84

Table S151.  Gene #16: 'MEGF9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 56 26 44 23 39
MEGF9 MUTATED 0 1 1 0 1
MEGF9 WILD-TYPE 56 25 43 23 38
'MEGF9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S152.  Gene #16: 'MEGF9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 46 21 42 24
MEGF9 MUTATED 1 1 0 1 0
MEGF9 WILD-TYPE 54 45 21 41 24
'SCAP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.115 (Fisher's exact test), Q value = 0.38

Table S153.  Gene #17: 'SCAP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 90 58 38 57
SCAP MUTATED 0 2 1 0
SCAP WILD-TYPE 90 56 37 57
'SCAP MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S154.  Gene #17: 'SCAP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 68 72
SCAP MUTATED 1 1 0 1
SCAP WILD-TYPE 54 51 68 71
'SCAP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.451 (Fisher's exact test), Q value = 0.77

Table S155.  Gene #17: 'SCAP MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 56 42 55 57
SCAP MUTATED 2 0 1 0
SCAP WILD-TYPE 54 42 54 57
'SCAP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.344 (Fisher's exact test), Q value = 0.68

Table S156.  Gene #17: 'SCAP MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 23 34 47 62 22 22
SCAP MUTATED 1 0 0 1 0 1
SCAP WILD-TYPE 22 34 47 61 22 21
'SCAP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.613 (Fisher's exact test), Q value = 0.88

Table S157.  Gene #17: 'SCAP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 110 72 63
SCAP MUTATED 2 0 1
SCAP WILD-TYPE 108 72 62
'SCAP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.616 (Fisher's exact test), Q value = 0.88

Table S158.  Gene #17: 'SCAP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 43 21 48 46 29 25 33
SCAP MUTATED 0 0 0 1 1 0 1
SCAP WILD-TYPE 43 21 48 45 28 25 32
'SCAP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.426 (Fisher's exact test), Q value = 0.75

Table S159.  Gene #17: 'SCAP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 50 96
SCAP MUTATED 2 1 0
SCAP WILD-TYPE 98 49 96
'SCAP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.24 (Fisher's exact test), Q value = 0.6

Table S160.  Gene #17: 'SCAP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 79 36 110 21
SCAP MUTATED 2 1 0 0
SCAP WILD-TYPE 77 35 110 21
'SCAP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.497 (Fisher's exact test), Q value = 0.81

Table S161.  Gene #17: 'SCAP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 56 26 44 23 39
SCAP MUTATED 1 0 0 0 2
SCAP WILD-TYPE 55 26 44 23 37
'SCAP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.674 (Fisher's exact test), Q value = 0.9

Table S162.  Gene #17: 'SCAP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 46 21 42 24
SCAP MUTATED 1 0 0 1 1
SCAP WILD-TYPE 54 46 21 41 23
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/22573933/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SARC-TP/22542442/SARC-TP.transferedmergedcluster.txt

  • Number of patients = 247

  • Number of significantly mutated genes = 17

  • 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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