Correlation between gene mutation status and molecular subtypes
Lung Squamous Cell Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C10000J7
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C10000J7
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 12 molecular subtypes across 177 patients, 7 significant findings detected with P value < 0.05 and Q value < 0.25.

  • TP53 mutation correlated to 'CN_CNMF'.

  • NFE2L2 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • KEAP1 mutation correlated to 'MRNA_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 17 genes and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 7 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		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 Fisher's exact test Fisher's exact test
NFE2L2 27 (15%) 150 0.000356
(0.0663) 		0.00115
(0.211) 		0.0185
(1.00) 		0.0334
(1.00) 		0.261
(1.00) 		0.149
(1.00) 		6.26e-06
(0.00118) 		2.46e-06
(0.000465) 		0.0296
(1.00) 		2.36e-06
(0.000449) 		0.589
(1.00) 		0.14
(1.00)
TP53 141 (80%) 36 0.0846
(1.00) 		0.0524
(1.00) 		0.00018
(0.0338) 		0.00153
(0.28) 		1
(1.00) 		0.894
(1.00) 		0.0021
(0.378) 		0.0183
(1.00) 		0.119
(1.00) 		0.565
(1.00) 		0.824
(1.00) 		0.726
(1.00)
KEAP1 22 (12%) 155 0.00196
(0.354) 		0.000403
(0.0746) 		0.17
(1.00) 		0.0758
(1.00) 		0.204
(1.00) 		0.0963
(1.00) 		0.159
(1.00) 		0.0428
(1.00) 		0.701
(1.00) 		0.824
(1.00) 		0.00504
(0.903) 		0.61
(1.00)
CDKN2A 26 (15%) 151 0.00177
(0.323) 		0.0627
(1.00) 		0.0183
(1.00) 		0.668
(1.00) 		0.34
(1.00) 		0.203
(1.00) 		0.331
(1.00) 		0.646
(1.00) 		0.751
(1.00) 		1
(1.00) 		1
(1.00) 		0.0993
(1.00)
PIK3CA 27 (15%) 150 0.64
(1.00) 		0.578
(1.00) 		0.448
(1.00) 		0.545
(1.00) 		1
(1.00) 		0.702
(1.00) 		0.39
(1.00) 		0.916
(1.00) 		0.615
(1.00) 		0.671
(1.00) 		0.456
(1.00) 		0.726
(1.00)
PTEN 14 (8%) 163 0.376
(1.00) 		0.427
(1.00) 		0.439
(1.00) 		0.134
(1.00) 		0.721
(1.00) 		0.473
(1.00) 		0.613
(1.00) 		0.158
(1.00) 		0.575
(1.00) 		0.431
(1.00) 		0.357
(1.00) 		1
(1.00)
MLL2 35 (20%) 142 0.146
(1.00) 		0.809
(1.00) 		0.253
(1.00) 		0.315
(1.00) 		0.696
(1.00) 		0.221
(1.00) 		0.248
(1.00) 		0.611
(1.00) 		0.948
(1.00) 		0.638
(1.00) 		0.614
(1.00) 		1
(1.00)
CSMD3 81 (46%) 96 0.24
(1.00) 		0.878
(1.00) 		0.746
(1.00) 		0.479
(1.00) 		0.275
(1.00) 		0.765
(1.00) 		0.429
(1.00) 		0.769
(1.00) 		0.642
(1.00) 		1
(1.00) 		0.389
(1.00) 		0.164
(1.00)
RB1 12 (7%) 165 0.343
(1.00) 		0.198
(1.00) 		0.418
(1.00) 		0.108
(1.00) 		0.657
(1.00) 		0.433
(1.00) 		1
(1.00) 		0.355
(1.00) 		0.575
(1.00) 		0.911
(1.00) 		1
(1.00)
HS6ST1 5 (3%) 172 0.269
(1.00) 		0.295
(1.00) 		0.53
(1.00) 		0.568
(1.00) 		0.101
(1.00) 		1
(1.00) 		1
(1.00)
FBXW7 10 (6%) 167 0.458
(1.00) 		1
(1.00) 		0.508
(1.00) 		0.621
(1.00) 		0.785
(1.00) 		0.834
(1.00) 		0.574
(1.00) 		0.935
(1.00) 		0.772
(1.00) 		1
(1.00)
ZNF567 3 (2%) 174 0.364
(1.00) 		0.359
(1.00) 		0.424
(1.00) 		0.389
(1.00) 		0.427
(1.00) 		0.253
(1.00) 		0.19
(1.00) 		1
(1.00)
ELTD1 18 (10%) 159 0.0295
(1.00) 		0.303
(1.00) 		0.0533
(1.00) 		0.6
(1.00) 		0.341
(1.00) 		0.648
(1.00) 		0.554
(1.00) 		0.42
(1.00) 		0.0887
(1.00) 		0.722
(1.00) 		0.305
(1.00) 		0.419
(1.00)
ASCL4 6 (3%) 171 0.0924
(1.00) 		0.534
(1.00) 		0.882
(1.00) 		0.783
(1.00) 		0.817
(1.00) 		0.835
(1.00) 		0.348
(1.00) 		0.247
(1.00) 		0.91
(1.00) 		0.219
(1.00)
OR2G6 16 (9%) 161 0.366
(1.00) 		0.211
(1.00) 		0.909
(1.00) 		1
(1.00) 		1
(1.00) 		0.717
(1.00) 		0.199
(1.00) 		0.0466
(1.00) 		0.428
(1.00) 		0.245
(1.00) 		0.668
(1.00) 		0.61
(1.00)
HLA-A 6 (3%) 171 0.0391
(1.00) 		0.33
(1.00) 		0.446
(1.00) 		0.178
(1.00) 		1
(1.00) 		0.513
(1.00) 		0.128
(1.00) 		0.114
(1.00) 		0.471
(1.00) 		0.73
(1.00) 		0.381
(1.00) 		1
(1.00)
NOTCH1 14 (8%) 163 0.812
(1.00) 		0.921
(1.00) 		0.543
(1.00) 		0.0342
(1.00) 		0.591
(1.00) 		0.824
(1.00) 		0.686
(1.00) 		0.401
(1.00) 		0.185
(1.00) 		0.844
(1.00) 		0.483
(1.00) 		0.668
(1.00)
'CDKN2A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.32

Table S1.  Gene #1: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 16 19
CDKN2A MUTATED 0 13 3 2
CDKN2A WILD-TYPE 37 35 13 17

Figure S1.  Get High-res Image Gene #1: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CDKN2A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0627 (Fisher's exact test), Q value = 1

Table S2.  Gene #1: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 52 20 41
CDKN2A MUTATED 1 13 1 3
CDKN2A WILD-TYPE 6 39 19 38
'CDKN2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 1

Table S3.  Gene #1: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 69 47
CDKN2A MUTATED 3 14 9
CDKN2A WILD-TYPE 58 55 38

Figure S2.  Get High-res Image Gene #1: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CDKN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.668 (Fisher's exact test), Q value = 1

Table S4.  Gene #1: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
CDKN2A MUTATED 2 4 3
CDKN2A WILD-TYPE 25 25 15
'CDKN2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.34 (Fisher's exact test), Q value = 1

Table S5.  Gene #1: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
CDKN2A MUTATED 2 8 3
CDKN2A WILD-TYPE 32 39 28
'CDKN2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.203 (Fisher's exact test), Q value = 1

Table S6.  Gene #1: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 27 33 21
CDKN2A MUTATED 3 1 4 5
CDKN2A WILD-TYPE 28 26 29 16
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 1

Table S7.  Gene #1: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 61 49 25
CDKN2A MUTATED 4 12 5 5
CDKN2A WILD-TYPE 38 49 44 20
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.646 (Fisher's exact test), Q value = 1

Table S8.  Gene #1: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 60 83
CDKN2A MUTATED 4 11 11
CDKN2A WILD-TYPE 30 49 72
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.751 (Fisher's exact test), Q value = 1

Table S9.  Gene #1: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 16 23 23
CDKN2A MUTATED 15 3 2 4
CDKN2A WILD-TYPE 84 13 21 19
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S10.  Gene #1: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 32 99
CDKN2A MUTATED 4 5 15
CDKN2A WILD-TYPE 26 27 84
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S11.  Gene #1: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
CDKN2A MUTATED 2 2 3
CDKN2A WILD-TYPE 13 16 16
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0993 (Fisher's exact test), Q value = 1

Table S12.  Gene #1: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 26 26
CDKN2A MUTATED 1 6
CDKN2A WILD-TYPE 25 20
'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0846 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 16 19
TP53 MUTATED 29 43 10 14
TP53 WILD-TYPE 8 5 6 5
'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0524 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 52 20 41
TP53 MUTATED 6 47 14 29
TP53 WILD-TYPE 1 5 6 12
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.034

Table S15.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 69 47
TP53 MUTATED 38 63 40
TP53 WILD-TYPE 23 6 7

Figure S3.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00153 (Fisher's exact test), Q value = 0.28

Table S16.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
TP53 MUTATED 16 28 15
TP53 WILD-TYPE 11 1 3

Figure S4.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S17.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
TP53 MUTATED 26 37 24
TP53 WILD-TYPE 8 10 7
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.894 (Fisher's exact test), Q value = 1

Table S18.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 27 33 21
TP53 MUTATED 23 21 27 16
TP53 WILD-TYPE 8 6 6 5
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0021 (Fisher's exact test), Q value = 0.38

Table S19.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 61 49 25
TP53 MUTATED 33 55 40 13
TP53 WILD-TYPE 9 6 9 12

Figure S5.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0183 (Fisher's exact test), Q value = 1

Table S20.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 60 83
TP53 MUTATED 28 54 59
TP53 WILD-TYPE 6 6 24

Figure S6.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 1

Table S21.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 16 23 23
TP53 MUTATED 83 14 15 21
TP53 WILD-TYPE 16 2 8 2
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.565 (Fisher's exact test), Q value = 1

Table S22.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 32 99
TP53 MUTATED 26 28 79
TP53 WILD-TYPE 4 4 20
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.824 (Fisher's exact test), Q value = 1

Table S23.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
TP53 MUTATED 13 14 15
TP53 WILD-TYPE 2 4 4
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S24.  Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 26 26
TP53 MUTATED 20 22
TP53 WILD-TYPE 6 4
'NFE2L2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.000356 (Fisher's exact test), Q value = 0.066

Table S25.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 16 19
NFE2L2 MUTATED 0 14 1 1
NFE2L2 WILD-TYPE 37 34 15 18

Figure S7.  Get High-res Image Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00115 (Fisher's exact test), Q value = 0.21

Table S26.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 52 20 41
NFE2L2 MUTATED 1 14 0 1
NFE2L2 WILD-TYPE 6 38 20 40

Figure S8.  Get High-res Image Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 1

Table S27.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 69 47
NFE2L2 MUTATED 7 17 3
NFE2L2 WILD-TYPE 54 52 44

Figure S9.  Get High-res Image Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 1

Table S28.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
NFE2L2 MUTATED 4 8 0
NFE2L2 WILD-TYPE 23 21 18

Figure S10.  Get High-res Image Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.261 (Fisher's exact test), Q value = 1

Table S29.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
NFE2L2 MUTATED 8 5 6
NFE2L2 WILD-TYPE 26 42 25
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.149 (Fisher's exact test), Q value = 1

Table S30.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 27 33 21
NFE2L2 MUTATED 6 5 2 6
NFE2L2 WILD-TYPE 25 22 31 15
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 6.26e-06 (Fisher's exact test), Q value = 0.0012

Table S31.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 61 49 25
NFE2L2 MUTATED 2 21 1 3
NFE2L2 WILD-TYPE 40 40 48 22

Figure S11.  Get High-res Image Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.46e-06 (Fisher's exact test), Q value = 0.00046

Table S32.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 60 83
NFE2L2 MUTATED 1 21 5
NFE2L2 WILD-TYPE 33 39 78

Figure S12.  Get High-res Image Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 1

Table S33.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 16 23 23
NFE2L2 MUTATED 15 0 3 8
NFE2L2 WILD-TYPE 84 16 20 15

Figure S13.  Get High-res Image Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.36e-06 (Fisher's exact test), Q value = 0.00045

Table S34.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 32 99
NFE2L2 MUTATED 14 0 12
NFE2L2 WILD-TYPE 16 32 87

Figure S14.  Get High-res Image Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.589 (Fisher's exact test), Q value = 1

Table S35.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
NFE2L2 MUTATED 4 2 3
NFE2L2 WILD-TYPE 11 16 16
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.14 (Fisher's exact test), Q value = 1

Table S36.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 26 26
NFE2L2 MUTATED 2 7
NFE2L2 WILD-TYPE 24 19
'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.64 (Fisher's exact test), Q value = 1

Table S37.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 16 19
PIK3CA MUTATED 4 6 3 4
PIK3CA WILD-TYPE 33 42 13 15
'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.578 (Fisher's exact test), Q value = 1

Table S38.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 52 20 41
PIK3CA MUTATED 0 6 4 7
PIK3CA WILD-TYPE 7 46 16 34
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.448 (Fisher's exact test), Q value = 1

Table S39.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 69 47
PIK3CA MUTATED 12 8 7
PIK3CA WILD-TYPE 49 61 40
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.545 (Fisher's exact test), Q value = 1

Table S40.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
PIK3CA MUTATED 4 3 4
PIK3CA WILD-TYPE 23 26 14
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S41.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
PIK3CA MUTATED 5 7 5
PIK3CA WILD-TYPE 29 40 26
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.702 (Fisher's exact test), Q value = 1

Table S42.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 27 33 21
PIK3CA MUTATED 4 4 7 2
PIK3CA WILD-TYPE 27 23 26 19
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.39 (Fisher's exact test), Q value = 1

Table S43.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 61 49 25
PIK3CA MUTATED 8 7 10 2
PIK3CA WILD-TYPE 34 54 39 23
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.916 (Fisher's exact test), Q value = 1

Table S44.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 60 83
PIK3CA MUTATED 6 9 12
PIK3CA WILD-TYPE 28 51 71
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.615 (Fisher's exact test), Q value = 1

Table S45.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 16 23 23
PIK3CA MUTATED 18 2 2 2
PIK3CA WILD-TYPE 81 14 21 21
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.671 (Fisher's exact test), Q value = 1

Table S46.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 32 99
PIK3CA MUTATED 3 4 17
PIK3CA WILD-TYPE 27 28 82
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.456 (Fisher's exact test), Q value = 1

Table S47.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
PIK3CA MUTATED 4 4 2
PIK3CA WILD-TYPE 11 14 17
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S48.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 26 26
PIK3CA MUTATED 6 4
PIK3CA WILD-TYPE 20 22
'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 1

Table S49.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 16 19
PTEN MUTATED 4 2 0 2
PTEN WILD-TYPE 33 46 16 17
'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.427 (Fisher's exact test), Q value = 1

Table S50.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 52 20 41
PTEN MUTATED 1 2 1 4
PTEN WILD-TYPE 6 50 19 37
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.439 (Fisher's exact test), Q value = 1

Table S51.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 69 47
PTEN MUTATED 7 4 3
PTEN WILD-TYPE 54 65 44
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 1

Table S52.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
PTEN MUTATED 5 3 0
PTEN WILD-TYPE 22 26 18
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S53.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
PTEN MUTATED 3 4 1
PTEN WILD-TYPE 31 43 30
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.473 (Fisher's exact test), Q value = 1

Table S54.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 27 33 21
PTEN MUTATED 2 2 1 3
PTEN WILD-TYPE 29 25 32 18
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.613 (Fisher's exact test), Q value = 1

Table S55.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 61 49 25
PTEN MUTATED 4 3 4 3
PTEN WILD-TYPE 38 58 45 22
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.158 (Fisher's exact test), Q value = 1

Table S56.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 60 83
PTEN MUTATED 5 2 7
PTEN WILD-TYPE 29 58 76
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.575 (Fisher's exact test), Q value = 1

Table S57.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 16 23 23
PTEN MUTATED 9 1 2 0
PTEN WILD-TYPE 90 15 21 23
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.431 (Fisher's exact test), Q value = 1

Table S58.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 32 99
PTEN MUTATED 1 4 7
PTEN WILD-TYPE 29 28 92
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.357 (Fisher's exact test), Q value = 1

Table S59.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
PTEN MUTATED 0 2 3
PTEN WILD-TYPE 15 16 16
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S60.  Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 26 26
PTEN MUTATED 3 2
PTEN WILD-TYPE 23 24
'KEAP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00196 (Fisher's exact test), Q value = 0.35

Table S61.  Gene #6: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 16 19
KEAP1 MUTATED 0 12 1 4
KEAP1 WILD-TYPE 37 36 15 15

Figure S15.  Get High-res Image Gene #6: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'KEAP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.000403 (Fisher's exact test), Q value = 0.075

Table S62.  Gene #6: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 52 20 41
KEAP1 MUTATED 3 13 0 1
KEAP1 WILD-TYPE 4 39 20 40

Figure S16.  Get High-res Image Gene #6: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 1

Table S63.  Gene #6: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 69 47
KEAP1 MUTATED 4 12 6
KEAP1 WILD-TYPE 57 57 41
'KEAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0758 (Fisher's exact test), Q value = 1

Table S64.  Gene #6: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
KEAP1 MUTATED 0 4 3
KEAP1 WILD-TYPE 27 25 15
'KEAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.204 (Fisher's exact test), Q value = 1

Table S65.  Gene #6: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
KEAP1 MUTATED 5 2 4
KEAP1 WILD-TYPE 29 45 27
'KEAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0963 (Fisher's exact test), Q value = 1

Table S66.  Gene #6: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 27 33 21
KEAP1 MUTATED 3 6 1 1
KEAP1 WILD-TYPE 28 21 32 20
'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.159 (Fisher's exact test), Q value = 1

Table S67.  Gene #6: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 61 49 25
KEAP1 MUTATED 2 12 5 3
KEAP1 WILD-TYPE 40 49 44 22
'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0428 (Fisher's exact test), Q value = 1

Table S68.  Gene #6: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 60 83
KEAP1 MUTATED 6 11 5
KEAP1 WILD-TYPE 28 49 78

Figure S17.  Get High-res Image Gene #6: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.701 (Fisher's exact test), Q value = 1

Table S69.  Gene #6: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 16 23 23
KEAP1 MUTATED 13 1 1 3
KEAP1 WILD-TYPE 86 15 22 20
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.824 (Fisher's exact test), Q value = 1

Table S70.  Gene #6: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 32 99
KEAP1 MUTATED 4 4 10
KEAP1 WILD-TYPE 26 28 89
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00504 (Fisher's exact test), Q value = 0.9

Table S71.  Gene #6: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
KEAP1 MUTATED 4 0 0
KEAP1 WILD-TYPE 11 18 19

Figure S18.  Get High-res Image Gene #6: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.61 (Fisher's exact test), Q value = 1

Table S72.  Gene #6: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 26 26
KEAP1 MUTATED 1 3
KEAP1 WILD-TYPE 25 23
'MLL2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.146 (Fisher's exact test), Q value = 1

Table S73.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 16 19
MLL2 MUTATED 4 10 6 5
MLL2 WILD-TYPE 33 38 10 14
'MLL2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.809 (Fisher's exact test), Q value = 1

Table S74.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 52 20 41
MLL2 MUTATED 1 13 3 8
MLL2 WILD-TYPE 6 39 17 33
'MLL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.253 (Fisher's exact test), Q value = 1

Table S75.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 69 47
MLL2 MUTATED 8 16 11
MLL2 WILD-TYPE 53 53 36
'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.315 (Fisher's exact test), Q value = 1

Table S76.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
MLL2 MUTATED 6 6 1
MLL2 WILD-TYPE 21 23 17
'MLL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.696 (Fisher's exact test), Q value = 1

Table S77.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
MLL2 MUTATED 6 9 8
MLL2 WILD-TYPE 28 38 23
'MLL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.221 (Fisher's exact test), Q value = 1

Table S78.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 27 33 21
MLL2 MUTATED 5 4 6 8
MLL2 WILD-TYPE 26 23 27 13
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.248 (Fisher's exact test), Q value = 1

Table S79.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 61 49 25
MLL2 MUTATED 4 15 11 5
MLL2 WILD-TYPE 38 46 38 20
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.611 (Fisher's exact test), Q value = 1

Table S80.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 60 83
MLL2 MUTATED 5 14 16
MLL2 WILD-TYPE 29 46 67
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.948 (Fisher's exact test), Q value = 1

Table S81.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 16 23 23
MLL2 MUTATED 17 3 4 5
MLL2 WILD-TYPE 82 13 19 18
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.638 (Fisher's exact test), Q value = 1

Table S82.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 32 99
MLL2 MUTATED 5 4 20
MLL2 WILD-TYPE 25 28 79
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S83.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
MLL2 MUTATED 2 5 3
MLL2 WILD-TYPE 13 13 16
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S84.  Gene #7: 'MLL2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 26 26
MLL2 MUTATED 5 5
MLL2 WILD-TYPE 21 21
'CSMD3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.24 (Fisher's exact test), Q value = 1

Table S85.  Gene #8: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 16 19
CSMD3 MUTATED 16 17 10 10
CSMD3 WILD-TYPE 21 31 6 9
'CSMD3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S86.  Gene #8: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 52 20 41
CSMD3 MUTATED 3 21 9 20
CSMD3 WILD-TYPE 4 31 11 21
'CSMD3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.746 (Fisher's exact test), Q value = 1

Table S87.  Gene #8: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 69 47
CSMD3 MUTATED 26 34 21
CSMD3 WILD-TYPE 35 35 26
'CSMD3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.479 (Fisher's exact test), Q value = 1

Table S88.  Gene #8: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
CSMD3 MUTATED 14 14 6
CSMD3 WILD-TYPE 13 15 12
'CSMD3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.275 (Fisher's exact test), Q value = 1

Table S89.  Gene #8: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
CSMD3 MUTATED 17 23 10
CSMD3 WILD-TYPE 17 24 21
'CSMD3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.765 (Fisher's exact test), Q value = 1

Table S90.  Gene #8: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 27 33 21
CSMD3 MUTATED 16 11 15 8
CSMD3 WILD-TYPE 15 16 18 13
'CSMD3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.429 (Fisher's exact test), Q value = 1

Table S91.  Gene #8: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 61 49 25
CSMD3 MUTATED 17 26 23 15
CSMD3 WILD-TYPE 25 35 26 10
'CSMD3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S92.  Gene #8: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 60 83
CSMD3 MUTATED 14 27 40
CSMD3 WILD-TYPE 20 33 43
'CSMD3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 1

Table S93.  Gene #8: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 16 23 23
CSMD3 MUTATED 44 6 12 8
CSMD3 WILD-TYPE 55 10 11 15
'CSMD3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S94.  Gene #8: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 32 99
CSMD3 MUTATED 13 14 43
CSMD3 WILD-TYPE 17 18 56
'CSMD3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.389 (Fisher's exact test), Q value = 1

Table S95.  Gene #8: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
CSMD3 MUTATED 9 8 7
CSMD3 WILD-TYPE 6 10 12
'CSMD3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.164 (Fisher's exact test), Q value = 1

Table S96.  Gene #8: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 26 26
CSMD3 MUTATED 9 15
CSMD3 WILD-TYPE 17 11
'RB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.343 (Fisher's exact test), Q value = 1

Table S97.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 16 19
RB1 MUTATED 2 5 0 3
RB1 WILD-TYPE 35 43 16 16
'RB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.198 (Fisher's exact test), Q value = 1

Table S98.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 52 20 41
RB1 MUTATED 2 5 1 2
RB1 WILD-TYPE 5 47 19 39
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.418 (Fisher's exact test), Q value = 1

Table S99.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 69 47
RB1 MUTATED 4 3 5
RB1 WILD-TYPE 57 66 42
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.108 (Fisher's exact test), Q value = 1

Table S100.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
RB1 MUTATED 0 4 1
RB1 WILD-TYPE 27 25 17
'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.657 (Fisher's exact test), Q value = 1

Table S101.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
RB1 MUTATED 3 2 1
RB1 WILD-TYPE 31 45 30
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.433 (Fisher's exact test), Q value = 1

Table S102.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 27 33 21
RB1 MUTATED 1 3 2 0
RB1 WILD-TYPE 30 24 31 21
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S103.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 61 49 25
RB1 MUTATED 3 4 3 2
RB1 WILD-TYPE 39 57 46 23
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.355 (Fisher's exact test), Q value = 1

Table S104.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 60 83
RB1 MUTATED 4 4 4
RB1 WILD-TYPE 30 56 79
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.575 (Fisher's exact test), Q value = 1

Table S105.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 16 23 23
RB1 MUTATED 9 1 0 2
RB1 WILD-TYPE 90 15 23 21
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S106.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 32 99
RB1 MUTATED 2 3 7
RB1 WILD-TYPE 28 29 92
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S107.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 26 26
RB1 MUTATED 0 1
RB1 WILD-TYPE 26 25
'HS6ST1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.269 (Fisher's exact test), Q value = 1

Table S108.  Gene #10: 'HS6ST1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 16 19
HS6ST1 MUTATED 1 1 2 1
HS6ST1 WILD-TYPE 36 47 14 18
'HS6ST1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.295 (Fisher's exact test), Q value = 1

Table S109.  Gene #10: 'HS6ST1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 52 20 41
HS6ST1 MUTATED 1 1 1 2
HS6ST1 WILD-TYPE 6 51 19 39
'HS6ST1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.53 (Fisher's exact test), Q value = 1

Table S110.  Gene #10: 'HS6ST1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 69 47
HS6ST1 MUTATED 3 1 1
HS6ST1 WILD-TYPE 58 68 46
'HS6ST1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.568 (Fisher's exact test), Q value = 1

Table S111.  Gene #10: 'HS6ST1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 61 49 25
HS6ST1 MUTATED 1 1 3 0
HS6ST1 WILD-TYPE 41 60 46 25
'HS6ST1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.101 (Fisher's exact test), Q value = 1

Table S112.  Gene #10: 'HS6ST1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 60 83
HS6ST1 MUTATED 3 1 1
HS6ST1 WILD-TYPE 31 59 82
'HS6ST1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S113.  Gene #10: 'HS6ST1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 16 23 23
HS6ST1 MUTATED 3 0 0 0
HS6ST1 WILD-TYPE 96 16 23 23
'HS6ST1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S114.  Gene #10: 'HS6ST1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 32 99
HS6ST1 MUTATED 0 0 3
HS6ST1 WILD-TYPE 30 32 96
'FBXW7 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.458 (Fisher's exact test), Q value = 1

Table S115.  Gene #11: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 16 19
FBXW7 MUTATED 1 4 2 2
FBXW7 WILD-TYPE 36 44 14 17
'FBXW7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S116.  Gene #11: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 52 20 41
FBXW7 MUTATED 0 5 1 3
FBXW7 WILD-TYPE 7 47 19 38
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.508 (Fisher's exact test), Q value = 1

Table S117.  Gene #11: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 69 47
FBXW7 MUTATED 4 5 1
FBXW7 WILD-TYPE 57 64 46
'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.621 (Fisher's exact test), Q value = 1

Table S118.  Gene #11: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
FBXW7 MUTATED 0 2 1
FBXW7 WILD-TYPE 34 45 30
'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.785 (Fisher's exact test), Q value = 1

Table S119.  Gene #11: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 27 33 21
FBXW7 MUTATED 0 1 1 1
FBXW7 WILD-TYPE 31 26 32 20
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.834 (Fisher's exact test), Q value = 1

Table S120.  Gene #11: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 61 49 25
FBXW7 MUTATED 2 5 2 1
FBXW7 WILD-TYPE 40 56 47 24
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.574 (Fisher's exact test), Q value = 1

Table S121.  Gene #11: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 60 83
FBXW7 MUTATED 1 5 4
FBXW7 WILD-TYPE 33 55 79
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S122.  Gene #11: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 16 23 23
FBXW7 MUTATED 6 0 1 1
FBXW7 WILD-TYPE 93 16 22 22
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.772 (Fisher's exact test), Q value = 1

Table S123.  Gene #11: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 32 99
FBXW7 MUTATED 2 1 5
FBXW7 WILD-TYPE 28 31 94
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S124.  Gene #11: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 26 26
FBXW7 MUTATED 0 1
FBXW7 WILD-TYPE 26 25
'ZNF567 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.364 (Fisher's exact test), Q value = 1

Table S125.  Gene #12: 'ZNF567 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 69 47
ZNF567 MUTATED 2 0 1
ZNF567 WILD-TYPE 59 69 46
'ZNF567 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.359 (Fisher's exact test), Q value = 1

Table S126.  Gene #12: 'ZNF567 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
ZNF567 MUTATED 0 1 2
ZNF567 WILD-TYPE 34 46 29
'ZNF567 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.424 (Fisher's exact test), Q value = 1

Table S127.  Gene #12: 'ZNF567 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 27 33 21
ZNF567 MUTATED 2 1 0 0
ZNF567 WILD-TYPE 29 26 33 21
'ZNF567 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.389 (Fisher's exact test), Q value = 1

Table S128.  Gene #12: 'ZNF567 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 61 49 25
ZNF567 MUTATED 1 0 1 1
ZNF567 WILD-TYPE 41 61 48 24
'ZNF567 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.427 (Fisher's exact test), Q value = 1

Table S129.  Gene #12: 'ZNF567 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 60 83
ZNF567 MUTATED 1 0 2
ZNF567 WILD-TYPE 33 60 81
'ZNF567 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.253 (Fisher's exact test), Q value = 1

Table S130.  Gene #12: 'ZNF567 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 16 23 23
ZNF567 MUTATED 1 1 1 0
ZNF567 WILD-TYPE 98 15 22 23
'ZNF567 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.19 (Fisher's exact test), Q value = 1

Table S131.  Gene #12: 'ZNF567 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 32 99
ZNF567 MUTATED 0 2 1
ZNF567 WILD-TYPE 30 30 98
'ZNF567 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S132.  Gene #12: 'ZNF567 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 26 26
ZNF567 MUTATED 0 1
ZNF567 WILD-TYPE 26 25
'ELTD1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 1

Table S133.  Gene #13: 'ELTD1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 16 19
ELTD1 MUTATED 3 2 5 2
ELTD1 WILD-TYPE 34 46 11 17

Figure S19.  Get High-res Image Gene #13: 'ELTD1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'ELTD1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.303 (Fisher's exact test), Q value = 1

Table S134.  Gene #13: 'ELTD1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 52 20 41
ELTD1 MUTATED 0 3 2 7
ELTD1 WILD-TYPE 7 49 18 34
'ELTD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0533 (Fisher's exact test), Q value = 1

Table S135.  Gene #13: 'ELTD1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 69 47
ELTD1 MUTATED 11 4 3
ELTD1 WILD-TYPE 50 65 44
'ELTD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.6 (Fisher's exact test), Q value = 1

Table S136.  Gene #13: 'ELTD1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
ELTD1 MUTATED 4 2 1
ELTD1 WILD-TYPE 23 27 17
'ELTD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.341 (Fisher's exact test), Q value = 1

Table S137.  Gene #13: 'ELTD1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
ELTD1 MUTATED 4 6 1
ELTD1 WILD-TYPE 30 41 30
'ELTD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.648 (Fisher's exact test), Q value = 1

Table S138.  Gene #13: 'ELTD1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 27 33 21
ELTD1 MUTATED 4 1 4 2
ELTD1 WILD-TYPE 27 26 29 19
'ELTD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.554 (Fisher's exact test), Q value = 1

Table S139.  Gene #13: 'ELTD1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 61 49 25
ELTD1 MUTATED 4 4 7 3
ELTD1 WILD-TYPE 38 57 42 22
'ELTD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.42 (Fisher's exact test), Q value = 1

Table S140.  Gene #13: 'ELTD1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 60 83
ELTD1 MUTATED 5 4 9
ELTD1 WILD-TYPE 29 56 74
'ELTD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0887 (Fisher's exact test), Q value = 1

Table S141.  Gene #13: 'ELTD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 16 23 23
ELTD1 MUTATED 7 0 5 2
ELTD1 WILD-TYPE 92 16 18 21
'ELTD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.722 (Fisher's exact test), Q value = 1

Table S142.  Gene #13: 'ELTD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 32 99
ELTD1 MUTATED 2 4 8
ELTD1 WILD-TYPE 28 28 91
'ELTD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.305 (Fisher's exact test), Q value = 1

Table S143.  Gene #13: 'ELTD1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
ELTD1 MUTATED 2 4 1
ELTD1 WILD-TYPE 13 14 18
'ELTD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.419 (Fisher's exact test), Q value = 1

Table S144.  Gene #13: 'ELTD1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 26 26
ELTD1 MUTATED 5 2
ELTD1 WILD-TYPE 21 24
'ASCL4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0924 (Fisher's exact test), Q value = 1

Table S145.  Gene #14: 'ASCL4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 16 19
ASCL4 MUTATED 0 2 2 2
ASCL4 WILD-TYPE 37 46 14 17
'ASCL4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.534 (Fisher's exact test), Q value = 1

Table S146.  Gene #14: 'ASCL4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 52 20 41
ASCL4 MUTATED 1 2 1 2
ASCL4 WILD-TYPE 6 50 19 39
'ASCL4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S147.  Gene #14: 'ASCL4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 69 47
ASCL4 MUTATED 2 3 1
ASCL4 WILD-TYPE 59 66 46
'ASCL4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.783 (Fisher's exact test), Q value = 1

Table S148.  Gene #14: 'ASCL4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
ASCL4 MUTATED 1 2 0
ASCL4 WILD-TYPE 26 27 18
'ASCL4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.817 (Fisher's exact test), Q value = 1

Table S149.  Gene #14: 'ASCL4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
ASCL4 MUTATED 2 1 1
ASCL4 WILD-TYPE 32 46 30
'ASCL4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.835 (Fisher's exact test), Q value = 1

Table S150.  Gene #14: 'ASCL4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 27 33 21
ASCL4 MUTATED 2 1 1 0
ASCL4 WILD-TYPE 29 26 32 21
'ASCL4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 1

Table S151.  Gene #14: 'ASCL4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 61 49 25
ASCL4 MUTATED 0 3 3 0
ASCL4 WILD-TYPE 42 58 46 25
'ASCL4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.247 (Fisher's exact test), Q value = 1

Table S152.  Gene #14: 'ASCL4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 60 83
ASCL4 MUTATED 2 3 1
ASCL4 WILD-TYPE 32 57 82
'ASCL4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.91 (Fisher's exact test), Q value = 1

Table S153.  Gene #14: 'ASCL4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 16 23 23
ASCL4 MUTATED 5 0 0 1
ASCL4 WILD-TYPE 94 16 23 22
'ASCL4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.219 (Fisher's exact test), Q value = 1

Table S154.  Gene #14: 'ASCL4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 32 99
ASCL4 MUTATED 2 2 2
ASCL4 WILD-TYPE 28 30 97
'OR2G6 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.366 (Fisher's exact test), Q value = 1

Table S155.  Gene #15: 'OR2G6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 16 19
OR2G6 MUTATED 5 2 2 2
OR2G6 WILD-TYPE 32 46 14 17
'OR2G6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.211 (Fisher's exact test), Q value = 1

Table S156.  Gene #15: 'OR2G6 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 52 20 41
OR2G6 MUTATED 1 2 2 6
OR2G6 WILD-TYPE 6 50 18 35
'OR2G6 MUTATION STATUS' versus 'CN_CNMF'

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

Table S157.  Gene #15: 'OR2G6 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 69 47
OR2G6 MUTATED 5 6 5
OR2G6 WILD-TYPE 56 63 42
'OR2G6 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S158.  Gene #15: 'OR2G6 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
OR2G6 MUTATED 2 3 1
OR2G6 WILD-TYPE 25 26 17
'OR2G6 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S159.  Gene #15: 'OR2G6 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
OR2G6 MUTATED 2 4 2
OR2G6 WILD-TYPE 32 43 29
'OR2G6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.717 (Fisher's exact test), Q value = 1

Table S160.  Gene #15: 'OR2G6 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 27 33 21
OR2G6 MUTATED 2 1 4 1
OR2G6 WILD-TYPE 29 26 29 20
'OR2G6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 1

Table S161.  Gene #15: 'OR2G6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 61 49 25
OR2G6 MUTATED 4 3 8 1
OR2G6 WILD-TYPE 38 58 41 24
'OR2G6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0466 (Fisher's exact test), Q value = 1

Table S162.  Gene #15: 'OR2G6 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 60 83
OR2G6 MUTATED 7 3 6
OR2G6 WILD-TYPE 27 57 77

Figure S20.  Get High-res Image Gene #15: 'OR2G6 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'OR2G6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.428 (Fisher's exact test), Q value = 1

Table S163.  Gene #15: 'OR2G6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 16 23 23
OR2G6 MUTATED 9 3 1 1
OR2G6 WILD-TYPE 90 13 22 22
'OR2G6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.245 (Fisher's exact test), Q value = 1

Table S164.  Gene #15: 'OR2G6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 32 99
OR2G6 MUTATED 1 5 8
OR2G6 WILD-TYPE 29 27 91
'OR2G6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.668 (Fisher's exact test), Q value = 1

Table S165.  Gene #15: 'OR2G6 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
OR2G6 MUTATED 2 1 1
OR2G6 WILD-TYPE 13 17 18
'OR2G6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.61 (Fisher's exact test), Q value = 1

Table S166.  Gene #15: 'OR2G6 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 26 26
OR2G6 MUTATED 1 3
OR2G6 WILD-TYPE 25 23
'HLA-A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 1

Table S167.  Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 16 19
HLA-A MUTATED 1 0 2 0
HLA-A WILD-TYPE 36 48 14 19

Figure S21.  Get High-res Image Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'HLA-A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.33 (Fisher's exact test), Q value = 1

Table S168.  Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 52 20 41
HLA-A MUTATED 0 0 1 2
HLA-A WILD-TYPE 7 52 19 39
'HLA-A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.446 (Fisher's exact test), Q value = 1

Table S169.  Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 69 47
HLA-A MUTATED 1 2 3
HLA-A WILD-TYPE 60 67 44
'HLA-A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.178 (Fisher's exact test), Q value = 1

Table S170.  Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
HLA-A MUTATED 1 0 2
HLA-A WILD-TYPE 26 29 16
'HLA-A MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S171.  Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
HLA-A MUTATED 1 2 1
HLA-A WILD-TYPE 33 45 30
'HLA-A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.513 (Fisher's exact test), Q value = 1

Table S172.  Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 27 33 21
HLA-A MUTATED 2 0 2 0
HLA-A WILD-TYPE 29 27 31 21
'HLA-A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.128 (Fisher's exact test), Q value = 1

Table S173.  Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 61 49 25
HLA-A MUTATED 2 0 2 2
HLA-A WILD-TYPE 40 61 47 23
'HLA-A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.114 (Fisher's exact test), Q value = 1

Table S174.  Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 60 83
HLA-A MUTATED 1 0 5
HLA-A WILD-TYPE 33 60 78
'HLA-A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.471 (Fisher's exact test), Q value = 1

Table S175.  Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 16 23 23
HLA-A MUTATED 4 0 2 0
HLA-A WILD-TYPE 95 16 21 23
'HLA-A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.73 (Fisher's exact test), Q value = 1

Table S176.  Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 32 99
HLA-A MUTATED 0 1 5
HLA-A WILD-TYPE 30 31 94
'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 1

Table S177.  Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
HLA-A MUTATED 1 2 0
HLA-A WILD-TYPE 14 16 19
'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S178.  Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 26 26
HLA-A MUTATED 1 2
HLA-A WILD-TYPE 25 24
'NOTCH1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.812 (Fisher's exact test), Q value = 1

Table S179.  Gene #17: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 16 19
NOTCH1 MUTATED 1 4 1 1
NOTCH1 WILD-TYPE 36 44 15 18
'NOTCH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S180.  Gene #17: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 7 52 20 41
NOTCH1 MUTATED 0 4 1 2
NOTCH1 WILD-TYPE 7 48 19 39
'NOTCH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.543 (Fisher's exact test), Q value = 1

Table S181.  Gene #17: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 69 47
NOTCH1 MUTATED 3 7 4
NOTCH1 WILD-TYPE 58 62 43
'NOTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 1

Table S182.  Gene #17: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 29 18
NOTCH1 MUTATED 0 4 4
NOTCH1 WILD-TYPE 27 25 14

Figure S22.  Get High-res Image Gene #17: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'NOTCH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.591 (Fisher's exact test), Q value = 1

Table S183.  Gene #17: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 47 31
NOTCH1 MUTATED 1 4 3
NOTCH1 WILD-TYPE 33 43 28
'NOTCH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.824 (Fisher's exact test), Q value = 1

Table S184.  Gene #17: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 31 27 33 21
NOTCH1 MUTATED 3 1 3 1
NOTCH1 WILD-TYPE 28 26 30 20
'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 1

Table S185.  Gene #17: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 61 49 25
NOTCH1 MUTATED 2 6 5 1
NOTCH1 WILD-TYPE 40 55 44 24
'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.401 (Fisher's exact test), Q value = 1

Table S186.  Gene #17: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 60 83
NOTCH1 MUTATED 2 7 5
NOTCH1 WILD-TYPE 32 53 78
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 1

Table S187.  Gene #17: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 16 23 23
NOTCH1 MUTATED 8 3 0 2
NOTCH1 WILD-TYPE 91 13 23 21
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S188.  Gene #17: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 32 99
NOTCH1 MUTATED 3 2 8
NOTCH1 WILD-TYPE 27 30 91
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 1

Table S189.  Gene #17: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 18 19
NOTCH1 MUTATED 3 1 2
NOTCH1 WILD-TYPE 12 17 17
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.668 (Fisher's exact test), Q value = 1

Table S190.  Gene #17: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 26 26
NOTCH1 MUTATED 2 4
NOTCH1 WILD-TYPE 24 22
Methods & Data
Input

  • Mutation data file = transformed.cor.cli.txt

  • Molecular subtypes file = LUSC-TP.transferedmergedcluster.txt

  • Number of patients = 177

  • Number of significantly mutated genes = 17

  • Number of Molecular subtypes = 12

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

Fisher's exact test

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

Q value calculation

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

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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