Correlation between gene mutation status and molecular subtypes
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1DN447N
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1DN447N
Overview
Introduction

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

Summary

Testing the association between mutation status of 20 genes and 10 molecular subtypes across 194 patients, 32 significant findings detected with P value < 0.05 and Q value < 0.25.

  • PTEN mutation correlated to 'MRNASEQ_CNMF'.

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

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

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

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

  • MAPK1 mutation correlated to 'MIRSEQ_MATURE_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • MLL3 mutation correlated to 'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

  • NFE2L2 mutation correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • PIK3CA mutation correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • IFNGR1 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 20 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 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
KRAS 11 (6%) 183 0.566
(0.745) 		0.00408
(0.0792) 		0.4
(0.668) 		0.219
(0.537) 		0.00451
(0.0792) 		0.00158
(0.0632) 		0.00319
(0.0792) 		0.00092
(0.046) 		0.0363
(0.234) 		0.00016
(0.032)
ARID1A 14 (7%) 180 0.00629
(0.0968) 		0.00427
(0.0792) 		0.654
(0.798) 		0.125
(0.413) 		0.167
(0.479) 		0.00063
(0.046) 		0.101
(0.354) 		0.00431
(0.0792) 		0.702
(0.821) 		0.00475
(0.0792)
MLL3 29 (15%) 165 0.964
(1.00) 		0.0453
(0.268) 		0.00969
(0.121) 		0.0208
(0.186) 		0.0511
(0.268) 		0.0222
(0.186) 		0.0244
(0.195) 		0.836
(0.937) 		0.629
(0.777) 		0.614
(0.773)
HLA-A 16 (8%) 178 0.259
(0.558) 		0.0938
(0.348) 		0.344
(0.611) 		0.0171
(0.186) 		0.00086
(0.046) 		0.0676
(0.314) 		0.43
(0.681) 		0.0077
(0.11) 		0.692
(0.815) 		0.418
(0.681)
EP300 21 (11%) 173 1
(1.00) 		0.0266
(0.197) 		0.764
(0.874) 		0.0387
(0.242) 		0.136
(0.426) 		0.0729
(0.317) 		0.839
(0.937) 		0.00956
(0.121) 		1
(1.00) 		0.247
(0.55)
HLA-B 11 (6%) 183 0.519
(0.729) 		0.164
(0.479) 		0.428
(0.681) 		0.326
(0.611) 		0.238
(0.544) 		0.0924
(0.348) 		0.0188
(0.186) 		0.135
(0.426) 		0.0124
(0.146) 		0.0482
(0.268)
MAPK1 9 (5%) 185 0.55
(0.739) 		0.228
(0.537) 		0.275
(0.585) 		0.976
(1.00) 		0.0925
(0.348) 		0.0534
(0.268) 		0.185
(0.495) 		0.0832
(0.34) 		0.0218
(0.186) 		0.0223
(0.186)
NFE2L2 12 (6%) 182 0.926
(0.996) 		0.099
(0.354) 		0.463
(0.685) 		0.0494
(0.268) 		0.455
(0.685) 		0.0465
(0.268) 		0.0357
(0.234) 		0.0184
(0.186) 		0.384
(0.656) 		0.0726
(0.317)
PIK3CA 53 (27%) 141 0.0345
(0.234) 		0.282
(0.594) 		0.304
(0.611) 		0.298
(0.61) 		0.351
(0.615) 		0.004
(0.0792) 		0.331
(0.611) 		0.345
(0.611) 		0.481
(0.692) 		0.232
(0.539)
PTEN 15 (8%) 179 0.568
(0.745) 		0.342
(0.611) 		0.62
(0.775) 		0.59
(0.761) 		0.0263
(0.197) 		0.228
(0.537) 		0.432
(0.681) 		0.193
(0.508) 		1
(1.00) 		0.421
(0.681)
IFNGR1 6 (3%) 188 1
(1.00) 		0.743
(0.859) 		0.453
(0.685) 		0.911
(0.986) 		0.843
(0.937) 		1
(1.00) 		0.327
(0.611) 		0.0329
(0.234) 		0.0535
(0.268) 		0.786
(0.894)
MLL2 22 (11%) 172 0.672
(0.808) 		0.242
(0.544) 		0.894
(0.983) 		0.24
(0.544) 		0.521
(0.729) 		0.0797
(0.335) 		0.882
(0.975) 		0.313
(0.611) 		0.0904
(0.348) 		0.736
(0.856)
FBXW7 19 (10%) 175 0.496
(0.709) 		0.258
(0.558) 		0.329
(0.611) 		0.972
(1.00) 		0.342
(0.611) 		0.678
(0.808) 		0.401
(0.668) 		0.455
(0.685) 		0.224
(0.537) 		0.539
(0.739)
CASP8 9 (5%) 185 0.677
(0.808) 		0.476
(0.692) 		0.186
(0.495) 		0.168
(0.479) 		0.221
(0.537) 		0.459
(0.685) 		0.57
(0.745) 		0.451
(0.685) 		0.125
(0.413) 		0.433
(0.681)
FAT2 11 (6%) 183 0.615
(0.773) 		0.0519
(0.268) 		0.539
(0.739) 		0.627
(0.777) 		0.064
(0.305) 		0.48
(0.692) 		0.586
(0.76) 		0.762
(0.874) 		0.0694
(0.315) 		0.0915
(0.348)
ZNF750 9 (5%) 185 0.132
(0.426) 		0.561
(0.745) 		0.42
(0.681) 		0.321
(0.611) 		0.603
(0.773) 		0.307
(0.611) 		0.32
(0.611) 		0.096
(0.349) 		0.549
(0.739) 		0.0804
(0.335)
C12ORF43 4 (2%) 190 0.199
(0.509) 		0.145
(0.438) 		0.912
(0.986) 		0.452
(0.685) 		0.473
(0.692) 		0.206
(0.514) 		0.292
(0.609) 		0.162
(0.479)
C3ORF70 4 (2%) 190 0.55
(0.739) 		0.342
(0.611) 		0.377
(0.651) 		0.178
(0.495) 		0.653
(0.798) 		0.126
(0.413) 		0.184
(0.495) 		0.299
(0.61) 		0.321
(0.611) 		0.126
(0.413)
BAP1 4 (2%) 190 0.14
(0.431) 		0.059
(0.288) 		0.51
(0.724) 		0.454
(0.685) 		0.689
(0.815) 		0.354
(0.615) 		0.259
(0.558) 		0.172
(0.485)
USP28 4 (2%) 190 0.199
(0.509) 		0.543
(0.739) 		0.661
(0.801) 		0.911
(0.986) 		0.607
(0.773) 		1
(1.00) 		0.389
(0.659) 		0.937
(1.00) 		0.201
(0.509) 		0.818
(0.925)
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.568 (Fisher's exact test), Q value = 0.74

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
PTEN MUTATED 9 3 3
PTEN WILD-TYPE 81 37 58
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.342 (Fisher's exact test), Q value = 0.61

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
PTEN MUTATED 5 2 3 1 2 2
PTEN WILD-TYPE 45 30 33 35 5 31
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.62 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 23 17 17 14 28 22 3 9
PTEN MUTATED 3 0 0 1 3 1 0 1
PTEN WILD-TYPE 20 17 17 13 25 21 3 8
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.59 (Fisher's exact test), Q value = 0.76

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

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

P value = 0.0263 (Fisher's exact test), Q value = 0.2

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
PTEN MUTATED 5 8 2 0
PTEN WILD-TYPE 32 57 47 42

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

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.228 (Fisher's exact test), Q value = 0.54

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

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

P value = 0.432 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
PTEN MUTATED 7 3 5
PTEN WILD-TYPE 52 53 74
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.193 (Fisher's exact test), Q value = 0.51

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

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

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
PTEN MUTATED 6 4 5
PTEN WILD-TYPE 63 53 53
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.421 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
PTEN MUTATED 4 4 3 4
PTEN WILD-TYPE 38 28 25 78
'HLA-B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.519 (Fisher's exact test), Q value = 0.73

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
HLA-B MUTATED 7 2 2
HLA-B WILD-TYPE 83 38 59
'HLA-B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.48

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
HLA-B MUTATED 0 4 3 2 0 2
HLA-B WILD-TYPE 50 28 33 34 7 31
'HLA-B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.428 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 23 17 17 14 28 22 3 9
HLA-B MUTATED 1 2 2 1 0 3 0 0
HLA-B WILD-TYPE 22 15 15 13 28 19 3 9
'HLA-B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.326 (Fisher's exact test), Q value = 0.61

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

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

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
HLA-B MUTATED 1 4 1 5
HLA-B WILD-TYPE 36 61 48 37
'HLA-B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0924 (Fisher's exact test), Q value = 0.35

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

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

P value = 0.0188 (Fisher's exact test), Q value = 0.19

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
HLA-B MUTATED 1 1 9
HLA-B WILD-TYPE 58 55 70

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

'HLA-B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.135 (Fisher's exact test), Q value = 0.43

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

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

P value = 0.0124 (Fisher's exact test), Q value = 0.15

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
HLA-B MUTATED 3 0 7
HLA-B WILD-TYPE 66 57 51

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

'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0482 (Fisher's exact test), Q value = 0.27

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
HLA-B MUTATED 0 0 2 8
HLA-B WILD-TYPE 42 32 26 74

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

'HLA-A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.259 (Fisher's exact test), Q value = 0.56

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
HLA-A MUTATED 9 4 2
HLA-A WILD-TYPE 81 36 59
'HLA-A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0938 (Fisher's exact test), Q value = 0.35

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
HLA-A MUTATED 1 3 5 6 0 1
HLA-A WILD-TYPE 49 29 31 30 7 32
'HLA-A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.344 (Fisher's exact test), Q value = 0.61

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 23 17 17 14 28 22 3 9
HLA-A MUTATED 4 1 0 0 1 3 0 1
HLA-A WILD-TYPE 19 16 17 14 27 19 3 8
'HLA-A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 0.19

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

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

Figure S5.  Get High-res Image Gene #3: 'HLA-A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'HLA-A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.046

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
HLA-A MUTATED 1 6 0 9
HLA-A WILD-TYPE 36 59 49 33

Figure S6.  Get High-res Image Gene #3: 'HLA-A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HLA-A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0676 (Fisher's exact test), Q value = 0.31

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

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

P value = 0.43 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
HLA-A MUTATED 3 4 9
HLA-A WILD-TYPE 56 52 70
'HLA-A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0077 (Fisher's exact test), Q value = 0.11

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

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

Figure S7.  Get High-res Image Gene #3: 'HLA-A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.692 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
HLA-A MUTATED 4 4 6
HLA-A WILD-TYPE 65 53 52
'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.418 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
HLA-A MUTATED 1 2 2 9
HLA-A WILD-TYPE 41 30 26 73
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.566 (Fisher's exact test), Q value = 0.74

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
KRAS MUTATED 7 1 3
KRAS WILD-TYPE 83 39 58
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00408 (Fisher's exact test), Q value = 0.079

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
KRAS MUTATED 9 0 1 0 0 1
KRAS WILD-TYPE 41 32 35 36 7 32

Figure S8.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.4 (Fisher's exact test), Q value = 0.67

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 23 17 17 14 28 22 3 9
KRAS MUTATED 1 0 2 1 4 0 0 0
KRAS WILD-TYPE 22 17 15 13 24 22 3 9
'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.219 (Fisher's exact test), Q value = 0.54

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

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

P value = 0.00451 (Fisher's exact test), Q value = 0.079

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
KRAS MUTATED 4 0 6 1
KRAS WILD-TYPE 33 65 43 41

Figure S9.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00158 (Fisher's exact test), Q value = 0.063

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

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

Figure S10.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00319 (Fisher's exact test), Q value = 0.079

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
KRAS MUTATED 7 4 0
KRAS WILD-TYPE 52 52 79

Figure S11.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.046

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

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

Figure S12.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.23

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
KRAS MUTATED 6 5 0
KRAS WILD-TYPE 63 52 58

Figure S13.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.032

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
KRAS MUTATED 9 1 0 1
KRAS WILD-TYPE 33 31 28 81

Figure S14.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MLL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.672 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
MLL2 MUTATED 12 3 7
MLL2 WILD-TYPE 78 37 54
'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 0.54

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
MLL2 MUTATED 4 6 5 1 1 5
MLL2 WILD-TYPE 46 26 31 35 6 28
'MLL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.894 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 23 17 17 14 28 22 3 9
MLL2 MUTATED 2 1 1 3 4 3 0 1
MLL2 WILD-TYPE 21 16 16 11 24 19 3 8
'MLL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.24 (Fisher's exact test), Q value = 0.54

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

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

P value = 0.521 (Fisher's exact test), Q value = 0.73

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
MLL2 MUTATED 5 10 4 3
MLL2 WILD-TYPE 32 55 45 39
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0797 (Fisher's exact test), Q value = 0.34

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

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

P value = 0.882 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
MLL2 MUTATED 7 7 8
MLL2 WILD-TYPE 52 49 71
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.313 (Fisher's exact test), Q value = 0.61

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

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

P value = 0.0904 (Fisher's exact test), Q value = 0.35

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
MLL2 MUTATED 4 10 8
MLL2 WILD-TYPE 65 47 50
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.736 (Fisher's exact test), Q value = 0.86

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
MLL2 MUTATED 3 4 4 11
MLL2 WILD-TYPE 39 28 24 71
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.496 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
FBXW7 MUTATED 11 3 4
FBXW7 WILD-TYPE 79 37 57
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.258 (Fisher's exact test), Q value = 0.56

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
FBXW7 MUTATED 6 4 4 5 0 0
FBXW7 WILD-TYPE 44 28 32 31 7 33
'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 23 17 17 14 28 22 3 9
FBXW7 MUTATED 2 3 4 3 1 4 0 0
FBXW7 WILD-TYPE 21 14 13 11 27 18 3 9
'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.972 (Fisher's exact test), Q value = 1

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

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

P value = 0.342 (Fisher's exact test), Q value = 0.61

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
FBXW7 MUTATED 1 9 5 4
FBXW7 WILD-TYPE 36 56 44 38
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.678 (Fisher's exact test), Q value = 0.81

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

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

P value = 0.401 (Fisher's exact test), Q value = 0.67

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
FBXW7 MUTATED 6 3 10
FBXW7 WILD-TYPE 53 53 69
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.455 (Fisher's exact test), Q value = 0.68

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

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

P value = 0.224 (Fisher's exact test), Q value = 0.54

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
FBXW7 MUTATED 10 3 6
FBXW7 WILD-TYPE 59 54 52
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.539 (Fisher's exact test), Q value = 0.74

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
FBXW7 MUTATED 5 1 3 10
FBXW7 WILD-TYPE 37 31 25 72
'EP300 MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
EP300 MUTATED 10 4 6
EP300 WILD-TYPE 80 36 55
'EP300 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 0.2

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
EP300 MUTATED 2 7 5 1 2 4
EP300 WILD-TYPE 48 25 31 35 5 29

Figure S15.  Get High-res Image Gene #7: 'EP300 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EP300 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.764 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 23 17 17 14 28 22 3 9
EP300 MUTATED 3 1 1 3 3 4 0 0
EP300 WILD-TYPE 20 16 16 11 25 18 3 9
'EP300 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0387 (Fisher's exact test), Q value = 0.24

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

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

Figure S16.  Get High-res Image Gene #7: 'EP300 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'EP300 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.136 (Fisher's exact test), Q value = 0.43

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
EP300 MUTATED 6 10 2 3
EP300 WILD-TYPE 31 55 47 39
'EP300 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0729 (Fisher's exact test), Q value = 0.32

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

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

P value = 0.839 (Fisher's exact test), Q value = 0.94

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
EP300 MUTATED 6 5 10
EP300 WILD-TYPE 53 51 69
'EP300 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00956 (Fisher's exact test), Q value = 0.12

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

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

Figure S17.  Get High-res Image Gene #7: 'EP300 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
EP300 MUTATED 7 5 6
EP300 WILD-TYPE 62 52 52
'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.247 (Fisher's exact test), Q value = 0.55

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
EP300 MUTATED 2 3 1 12
EP300 WILD-TYPE 40 29 27 70
'MAPK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.55 (Fisher's exact test), Q value = 0.74

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
MAPK1 MUTATED 6 1 2
MAPK1 WILD-TYPE 84 39 59
'MAPK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.228 (Fisher's exact test), Q value = 0.54

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
MAPK1 MUTATED 0 2 3 1 0 3
MAPK1 WILD-TYPE 50 30 33 35 7 30
'MAPK1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.275 (Fisher's exact test), Q value = 0.59

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 23 17 17 14 28 22 3 9
MAPK1 MUTATED 2 0 1 0 0 3 0 1
MAPK1 WILD-TYPE 21 17 16 14 28 19 3 8
'MAPK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

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

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

P value = 0.0925 (Fisher's exact test), Q value = 0.35

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
MAPK1 MUTATED 2 6 0 1
MAPK1 WILD-TYPE 35 59 49 41
'MAPK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0534 (Fisher's exact test), Q value = 0.27

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

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

P value = 0.185 (Fisher's exact test), Q value = 0.5

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
MAPK1 MUTATED 1 5 3
MAPK1 WILD-TYPE 58 51 76
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0832 (Fisher's exact test), Q value = 0.34

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

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

P value = 0.0218 (Fisher's exact test), Q value = 0.19

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
MAPK1 MUTATED 0 5 4
MAPK1 WILD-TYPE 69 52 54

Figure S18.  Get High-res Image Gene #8: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'MAPK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0223 (Fisher's exact test), Q value = 0.19

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
MAPK1 MUTATED 0 5 1 3
MAPK1 WILD-TYPE 42 27 27 79

Figure S19.  Get High-res Image Gene #8: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MLL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.964 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
MLL3 MUTATED 13 6 10
MLL3 WILD-TYPE 77 34 51
'MLL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0453 (Fisher's exact test), Q value = 0.27

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
MLL3 MUTATED 5 11 6 3 1 3
MLL3 WILD-TYPE 45 21 30 33 6 30

Figure S20.  Get High-res Image Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'MLL3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00969 (Fisher's exact test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 23 17 17 14 28 22 3 9
MLL3 MUTATED 2 1 2 5 0 5 0 3
MLL3 WILD-TYPE 21 16 15 9 28 17 3 6

Figure S21.  Get High-res Image Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'MLL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0208 (Fisher's exact test), Q value = 0.19

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

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

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

'MLL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0511 (Fisher's exact test), Q value = 0.27

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
MLL3 MUTATED 1 14 6 7
MLL3 WILD-TYPE 36 51 43 35
'MLL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.19

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

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

Figure S23.  Get High-res Image Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'MLL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.2

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
MLL3 MUTATED 3 10 16
MLL3 WILD-TYPE 56 46 63

Figure S24.  Get High-res Image Gene #9: 'MLL3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'MLL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.836 (Fisher's exact test), Q value = 0.94

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

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

P value = 0.629 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
MLL3 MUTATED 8 10 9
MLL3 WILD-TYPE 61 47 49
'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.614 (Fisher's exact test), Q value = 0.77

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
MLL3 MUTATED 5 7 3 12
MLL3 WILD-TYPE 37 25 25 70
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00629 (Fisher's exact test), Q value = 0.097

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
ARID1A MUTATED 11 3 0
ARID1A WILD-TYPE 79 37 61

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

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00427 (Fisher's exact test), Q value = 0.079

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
ARID1A MUTATED 10 2 2 0 0 0
ARID1A WILD-TYPE 40 30 34 36 7 33

Figure S26.  Get High-res Image Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.654 (Fisher's exact test), Q value = 0.8

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 23 17 17 14 28 22 3 9
ARID1A MUTATED 3 1 0 0 4 2 0 1
ARID1A WILD-TYPE 20 16 17 14 24 20 3 8
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.125 (Fisher's exact test), Q value = 0.41

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

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

P value = 0.167 (Fisher's exact test), Q value = 0.48

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
ARID1A MUTATED 5 2 5 2
ARID1A WILD-TYPE 32 63 44 40
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.046

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

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

Figure S27.  Get High-res Image Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 0.35

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
ARID1A MUTATED 8 2 4
ARID1A WILD-TYPE 51 54 75
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00431 (Fisher's exact test), Q value = 0.079

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

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

Figure S28.  Get High-res Image Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.702 (Fisher's exact test), Q value = 0.82

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
ARID1A MUTATED 6 3 3
ARID1A WILD-TYPE 63 54 55
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00475 (Fisher's exact test), Q value = 0.079

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
ARID1A MUTATED 7 0 3 2
ARID1A WILD-TYPE 35 32 25 80

Figure S29.  Get High-res Image Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.926 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
NFE2L2 MUTATED 5 3 4
NFE2L2 WILD-TYPE 85 37 57
'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.099 (Fisher's exact test), Q value = 0.35

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
NFE2L2 MUTATED 0 4 2 2 0 4
NFE2L2 WILD-TYPE 50 28 34 34 7 29
'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.463 (Fisher's exact test), Q value = 0.69

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 23 17 17 14 28 22 3 9
NFE2L2 MUTATED 1 2 1 2 0 2 0 1
NFE2L2 WILD-TYPE 22 15 16 12 28 20 3 8
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0494 (Fisher's exact test), Q value = 0.27

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

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

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

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.455 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
NFE2L2 MUTATED 2 5 1 4
NFE2L2 WILD-TYPE 35 60 48 38
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0465 (Fisher's exact test), Q value = 0.27

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

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

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

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.23

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
NFE2L2 MUTATED 0 5 7
NFE2L2 WILD-TYPE 59 51 72

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

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0184 (Fisher's exact test), Q value = 0.19

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

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

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

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 0.66

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
NFE2L2 MUTATED 2 4 5
NFE2L2 WILD-TYPE 67 53 53
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0726 (Fisher's exact test), Q value = 0.32

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
NFE2L2 MUTATED 0 2 4 5
NFE2L2 WILD-TYPE 42 30 24 77
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.23

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
PIK3CA MUTATED 33 7 13
PIK3CA WILD-TYPE 57 33 48

Figure S34.  Get High-res Image Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.282 (Fisher's exact test), Q value = 0.59

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
PIK3CA MUTATED 18 8 11 5 1 10
PIK3CA WILD-TYPE 32 24 25 31 6 23
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.304 (Fisher's exact test), Q value = 0.61

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 23 17 17 14 28 22 3 9
PIK3CA MUTATED 7 3 3 2 4 5 0 5
PIK3CA WILD-TYPE 16 14 14 12 24 17 3 4
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

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

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

P value = 0.351 (Fisher's exact test), Q value = 0.61

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
PIK3CA MUTATED 10 19 16 7
PIK3CA WILD-TYPE 27 46 33 35
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.004 (Fisher's exact test), Q value = 0.079

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

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

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

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 0.61

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
PIK3CA MUTATED 20 12 21
PIK3CA WILD-TYPE 39 44 58
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.345 (Fisher's exact test), Q value = 0.61

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

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

P value = 0.481 (Fisher's exact test), Q value = 0.69

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
PIK3CA MUTATED 22 13 14
PIK3CA WILD-TYPE 47 44 44
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.232 (Fisher's exact test), Q value = 0.54

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
PIK3CA MUTATED 16 9 7 17
PIK3CA WILD-TYPE 26 23 21 65
'CASP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.677 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
CASP8 MUTATED 3 2 4
CASP8 WILD-TYPE 87 38 57
'CASP8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.476 (Fisher's exact test), Q value = 0.69

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
CASP8 MUTATED 1 1 3 2 1 1
CASP8 WILD-TYPE 49 31 33 34 6 32
'CASP8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.186 (Fisher's exact test), Q value = 0.5

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 23 17 17 14 28 22 3 9
CASP8 MUTATED 1 1 0 1 0 1 1 0
CASP8 WILD-TYPE 22 16 17 13 28 21 2 9
'CASP8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.168 (Fisher's exact test), Q value = 0.48

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

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

P value = 0.221 (Fisher's exact test), Q value = 0.54

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
CASP8 MUTATED 0 5 1 3
CASP8 WILD-TYPE 37 60 48 39
'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.459 (Fisher's exact test), Q value = 0.69

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

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

P value = 0.57 (Fisher's exact test), Q value = 0.74

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
CASP8 MUTATED 3 1 5
CASP8 WILD-TYPE 56 55 74
'CASP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.451 (Fisher's exact test), Q value = 0.68

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

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

P value = 0.125 (Fisher's exact test), Q value = 0.41

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
CASP8 MUTATED 4 0 4
CASP8 WILD-TYPE 65 57 54
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.433 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
CASP8 MUTATED 1 0 1 6
CASP8 WILD-TYPE 41 32 27 76
'FAT2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.615 (Fisher's exact test), Q value = 0.77

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
FAT2 MUTATED 6 3 2
FAT2 WILD-TYPE 84 37 59
'FAT2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0519 (Fisher's exact test), Q value = 0.27

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
FAT2 MUTATED 1 5 2 2 1 0
FAT2 WILD-TYPE 49 27 34 34 6 33
'FAT2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.539 (Fisher's exact test), Q value = 0.74

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 23 17 17 14 28 22 3 9
FAT2 MUTATED 1 3 0 0 2 2 0 0
FAT2 WILD-TYPE 22 14 17 14 26 20 3 9
'FAT2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.627 (Fisher's exact test), Q value = 0.78

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

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

P value = 0.064 (Fisher's exact test), Q value = 0.3

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
FAT2 MUTATED 0 5 1 5
FAT2 WILD-TYPE 37 60 48 37
'FAT2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.48 (Fisher's exact test), Q value = 0.69

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

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

P value = 0.586 (Fisher's exact test), Q value = 0.76

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
FAT2 MUTATED 2 3 6
FAT2 WILD-TYPE 57 53 73
'FAT2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.762 (Fisher's exact test), Q value = 0.87

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

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

P value = 0.0694 (Fisher's exact test), Q value = 0.32

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
FAT2 MUTATED 3 1 7
FAT2 WILD-TYPE 66 56 51
'FAT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0915 (Fisher's exact test), Q value = 0.35

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
FAT2 MUTATED 1 0 1 9
FAT2 WILD-TYPE 41 32 27 73
'ZNF750 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.132 (Fisher's exact test), Q value = 0.43

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
ZNF750 MUTATED 7 0 2
ZNF750 WILD-TYPE 83 40 59
'ZNF750 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.561 (Fisher's exact test), Q value = 0.74

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
ZNF750 MUTATED 1 3 3 1 0 1
ZNF750 WILD-TYPE 49 29 33 35 7 32
'ZNF750 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.42 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 23 17 17 14 28 22 3 9
ZNF750 MUTATED 2 0 0 0 1 3 0 1
ZNF750 WILD-TYPE 21 17 17 14 27 19 3 8
'ZNF750 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.321 (Fisher's exact test), Q value = 0.61

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

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

P value = 0.603 (Fisher's exact test), Q value = 0.77

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
ZNF750 MUTATED 1 4 1 3
ZNF750 WILD-TYPE 36 61 48 39
'ZNF750 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.307 (Fisher's exact test), Q value = 0.61

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

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

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
ZNF750 MUTATED 2 1 6
ZNF750 WILD-TYPE 57 55 73
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.096 (Fisher's exact test), Q value = 0.35

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

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

P value = 0.549 (Fisher's exact test), Q value = 0.74

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
ZNF750 MUTATED 4 1 3
ZNF750 WILD-TYPE 65 56 55
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0804 (Fisher's exact test), Q value = 0.34

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
ZNF750 MUTATED 0 0 1 7
ZNF750 WILD-TYPE 42 32 27 75
'C12ORF43 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 0.51

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
C12ORF43 MUTATED 2 2 0
C12ORF43 WILD-TYPE 88 38 61
'C12ORF43 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.145 (Fisher's exact test), Q value = 0.44

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
C12ORF43 MUTATED 0 1 1 1 1 0
C12ORF43 WILD-TYPE 50 31 35 35 6 33
'C12ORF43 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.912 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
C12ORF43 MUTATED 0 2 1 1
C12ORF43 WILD-TYPE 37 63 48 41
'C12ORF43 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.452 (Fisher's exact test), Q value = 0.68

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

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

P value = 0.473 (Fisher's exact test), Q value = 0.69

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
C12ORF43 MUTATED 0 2 2
C12ORF43 WILD-TYPE 59 54 77
'C12ORF43 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.206 (Fisher's exact test), Q value = 0.51

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

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

P value = 0.292 (Fisher's exact test), Q value = 0.61

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
C12ORF43 MUTATED 0 1 2
C12ORF43 WILD-TYPE 69 56 56
'C12ORF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.162 (Fisher's exact test), Q value = 0.48

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
C12ORF43 MUTATED 0 0 2 1
C12ORF43 WILD-TYPE 42 32 26 81
'C3ORF70 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.55 (Fisher's exact test), Q value = 0.74

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
C3ORF70 MUTATED 1 1 2
C3ORF70 WILD-TYPE 89 39 59
'C3ORF70 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.342 (Fisher's exact test), Q value = 0.61

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
C3ORF70 MUTATED 3 0 0 0 0 1
C3ORF70 WILD-TYPE 47 32 36 36 7 32
'C3ORF70 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.377 (Fisher's exact test), Q value = 0.65

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 23 17 17 14 28 22 3 9
C3ORF70 MUTATED 0 0 1 0 1 0 0 1
C3ORF70 WILD-TYPE 23 17 16 14 27 22 3 8
'C3ORF70 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.178 (Fisher's exact test), Q value = 0.5

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

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

P value = 0.653 (Fisher's exact test), Q value = 0.8

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
C3ORF70 MUTATED 1 1 2 0
C3ORF70 WILD-TYPE 36 64 47 42
'C3ORF70 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.126 (Fisher's exact test), Q value = 0.41

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

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

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
C3ORF70 MUTATED 3 0 1
C3ORF70 WILD-TYPE 56 56 78
'C3ORF70 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.299 (Fisher's exact test), Q value = 0.61

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

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

P value = 0.321 (Fisher's exact test), Q value = 0.61

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
C3ORF70 MUTATED 3 1 0
C3ORF70 WILD-TYPE 66 56 58
'C3ORF70 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.126 (Fisher's exact test), Q value = 0.41

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
C3ORF70 MUTATED 3 0 0 1
C3ORF70 WILD-TYPE 39 32 28 81
'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.14 (Fisher's exact test), Q value = 0.43

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
BAP1 MUTATED 4 0 0
BAP1 WILD-TYPE 86 40 61
'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.059 (Fisher's exact test), Q value = 0.29

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
BAP1 MUTATED 0 3 1 0 0 0
BAP1 WILD-TYPE 50 29 35 36 7 33
'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.51 (Fisher's exact test), Q value = 0.72

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
BAP1 MUTATED 0 3 1 0
BAP1 WILD-TYPE 37 62 48 42
'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.454 (Fisher's exact test), Q value = 0.68

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

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

P value = 0.689 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
BAP1 MUTATED 1 2 1
BAP1 WILD-TYPE 58 54 78
'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.354 (Fisher's exact test), Q value = 0.61

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

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

P value = 0.259 (Fisher's exact test), Q value = 0.56

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
BAP1 MUTATED 0 2 2
BAP1 WILD-TYPE 69 55 56
'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.172 (Fisher's exact test), Q value = 0.49

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
BAP1 MUTATED 0 2 1 1
BAP1 WILD-TYPE 42 30 27 81
'USP28 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 0.51

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
USP28 MUTATED 2 2 0
USP28 WILD-TYPE 88 38 61
'USP28 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.543 (Fisher's exact test), Q value = 0.74

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
USP28 MUTATED 1 2 1 0 0 0
USP28 WILD-TYPE 49 30 35 36 7 33
'USP28 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.661 (Fisher's exact test), Q value = 0.8

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 23 17 17 14 28 22 3 9
USP28 MUTATED 0 1 0 1 1 0 0 0
USP28 WILD-TYPE 23 16 17 13 27 22 3 9
'USP28 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.911 (Fisher's exact test), Q value = 0.99

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

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

P value = 0.607 (Fisher's exact test), Q value = 0.77

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
USP28 MUTATED 0 1 1 2
USP28 WILD-TYPE 37 64 48 40
'USP28 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

P value = 0.389 (Fisher's exact test), Q value = 0.66

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
USP28 MUTATED 1 0 3
USP28 WILD-TYPE 58 56 76
'USP28 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

P value = 0.201 (Fisher's exact test), Q value = 0.51

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
USP28 MUTATED 1 0 3
USP28 WILD-TYPE 68 57 55
'USP28 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.818 (Fisher's exact test), Q value = 0.92

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
USP28 MUTATED 1 0 0 3
USP28 WILD-TYPE 41 32 28 79
'IFNGR1 MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 40 61
IFNGR1 MUTATED 3 1 2
IFNGR1 WILD-TYPE 87 39 59
'IFNGR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.743 (Fisher's exact test), Q value = 0.86

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 50 32 36 36 7 33
IFNGR1 MUTATED 2 2 0 1 0 1
IFNGR1 WILD-TYPE 48 30 36 35 7 32
'IFNGR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.453 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 23 17 17 14 28 22 3 9
IFNGR1 MUTATED 0 0 0 1 2 0 0 0
IFNGR1 WILD-TYPE 23 17 17 13 26 22 3 9
'IFNGR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.911 (Fisher's exact test), Q value = 0.99

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

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

P value = 0.843 (Fisher's exact test), Q value = 0.94

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 65 49 42
IFNGR1 MUTATED 2 2 1 1
IFNGR1 WILD-TYPE 35 63 48 41
'IFNGR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

P value = 0.327 (Fisher's exact test), Q value = 0.61

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 56 79
IFNGR1 MUTATED 3 0 3
IFNGR1 WILD-TYPE 56 56 76
'IFNGR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0329 (Fisher's exact test), Q value = 0.23

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

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

Figure S36.  Get High-res Image Gene #20: 'IFNGR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'IFNGR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0535 (Fisher's exact test), Q value = 0.27

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 69 57 58
IFNGR1 MUTATED 5 0 1
IFNGR1 WILD-TYPE 64 57 57
'IFNGR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.786 (Fisher's exact test), Q value = 0.89

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 32 28 82
IFNGR1 MUTATED 2 0 1 3
IFNGR1 WILD-TYPE 40 32 27 79
Methods & Data
Input

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CESC-TP/20063384/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CESC-TP/20124378/CESC-TP.transferedmergedcluster.txt

  • Number of patients = 194

  • Number of significantly mutated genes = 20

  • Number of Molecular subtypes = 10

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

Fisher's exact test

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

Q value calculation

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

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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