Correlation between gene mutation status and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between mutation status of 36 genes and 12 molecular subtypes across 248 patients, 36 significant findings detected with P value < 0.05 and Q value < 0.25.

  • CTNNB1 mutation correlated to 'MRNA_CNMF',  'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • PIK3R1 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

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

  • KRAS mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

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

  • FBXW7 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • CTCF mutation correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • ARID1A mutation correlated to 'CN_CNMF'.

  • RNF43 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 36 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, 36 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 Chi-square test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
TP53 69 (28%) 179 3.88e-05
(0.0147) 		1.72e-07
(6.67e-05) 		8.51e-31
(3.47e-28) 		3.61e-12
(1.42e-09) 		2.01e-05
(0.00766) 		0.0014
(0.517) 		5.76e-26
(2.33e-23) 		1.27e-27
(5.16e-25) 		9.81e-18
(3.93e-15) 		2.9e-22
(1.17e-19) 		2.24e-09
(8.75e-07) 		2.08e-08
(8.1e-06)
PTEN 161 (65%) 87 0.00428
(1.00) 		0.000357
(0.133) 		3.43e-21
(1.38e-18) 		3.35e-12
(1.32e-09) 		0.0257
(1.00) 		0.183
(1.00) 		7.04e-22
(2.84e-19) 		6.69e-16
(2.67e-13) 		1.54e-14
(6.12e-12) 		3.07e-16
(1.23e-13) 		1.49e-08
(5.82e-06) 		3.96e-11
(1.56e-08)
CTNNB1 74 (30%) 174 4.9e-07
(0.000189) 		0.00115
(0.426) 		5.3e-06
(0.00204) 		0.00416
(1.00) 		1.29e-10
(5.05e-08) 		0.112
(1.00) 		1.18e-15
(4.69e-13) 		8.45e-30
(3.44e-27) 		2.12e-14
(8.38e-12) 		3.38e-07
(0.000131) 		0.0619
(1.00) 		0.39
(1.00)
CTCF 45 (18%) 203 0.149
(1.00) 		0.421
(1.00) 		9.19e-05
(0.0348) 		0.0528
(1.00) 		0.0784
(1.00) 		0.848
(1.00) 		0.000334
(0.125) 		0.000158
(0.0595) 		0.00555
(1.00) 		0.00862
(1.00) 		0.00901
(1.00) 		0.0352
(1.00)
PIK3R1 83 (33%) 165 0.0667
(1.00) 		0.0221
(1.00) 		0.00177
(0.651) 		3.99e-05
(0.0151) 		0.649
(1.00) 		0.877
(1.00) 		1.15e-05
(0.0044) 		0.000937
(0.348) 		0.0251
(1.00) 		0.0225
(1.00) 		0.153
(1.00) 		0.0274
(1.00)
KRAS 53 (21%) 195 0.203
(1.00) 		0.000742
(0.276) 		0.00226
(0.822) 		0.143
(1.00) 		0.297
(1.00) 		0.855
(1.00) 		0.543
(1.00) 		0.000279
(0.105) 		0.117
(1.00) 		0.0326
(1.00) 		0.123
(1.00) 		0.417
(1.00)
FBXW7 39 (16%) 209 0.225
(1.00) 		0.692
(1.00) 		0.201
(1.00) 		0.132
(1.00) 		0.106
(1.00) 		0.107
(1.00) 		0.068
(1.00) 		0.000124
(0.0466) 		0.761
(1.00) 		0.186
(1.00) 		0.144
(1.00) 		0.115
(1.00)
ARID1A 83 (33%) 165 0.265
(1.00) 		0.0115
(1.00) 		3.81e-06
(0.00147) 		0.225
(1.00) 		0.0271
(1.00) 		1
(1.00) 		0.0421
(1.00) 		0.0836
(1.00) 		0.0357
(1.00) 		0.0125
(1.00) 		0.0465
(1.00) 		0.00528
(1.00)
RNF43 12 (5%) 236 0.133
(1.00) 		0.151
(1.00) 		0.359
(1.00) 		0.378
(1.00) 		0.296
(1.00) 		1
(1.00) 		0.0429
(1.00) 		2.64e-05
(0.0101) 		0.0546
(1.00) 		0.0166
(1.00) 		0.0643
(1.00) 		0.0574
(1.00)
PPP2R1A 27 (11%) 221 0.076
(1.00) 		0.0518
(1.00) 		0.0215
(1.00) 		0.0213
(1.00) 		0.141
(1.00) 		0.313
(1.00) 		0.00251
(0.911) 		0.00215
(0.783) 		0.0139
(1.00) 		0.00194
(0.709) 		0.225
(1.00) 		0.0448
(1.00)
PIK3CA 132 (53%) 116 0.859
(1.00) 		0.203
(1.00) 		0.542
(1.00) 		0.692
(1.00) 		0.366
(1.00) 		0.365
(1.00) 		0.772
(1.00) 		0.766
(1.00) 		0.195
(1.00) 		0.44
(1.00) 		0.293
(1.00) 		0.331
(1.00)
PRKAR1B 4 (2%) 244 0.963
(1.00) 		0.506
(1.00) 		0.887
(1.00) 		1
(1.00) 		0.698
(1.00) 		0.417
(1.00) 		0.832
(1.00) 		0.199
(1.00) 		0.786
(1.00) 		0.303
(1.00)
RPL22 31 (12%) 217 0.0531
(1.00) 		0.16
(1.00) 		0.0101
(1.00) 		0.00913
(1.00) 		0.0153
(1.00) 		0.26
(1.00) 		0.407
(1.00) 		0.121
(1.00) 		0.342
(1.00) 		0.0101
(1.00) 		0.584
(1.00) 		0.438
(1.00)
SPOP 21 (8%) 227 0.349
(1.00) 		1
(1.00) 		0.483
(1.00) 		0.326
(1.00) 		0.834
(1.00) 		0.415
(1.00) 		0.742
(1.00) 		1
(1.00) 		0.958
(1.00) 		0.732
(1.00) 		0.666
(1.00) 		0.876
(1.00)
ARID5B 29 (12%) 219 0.961
(1.00) 		0.459
(1.00) 		0.0344
(1.00) 		0.137
(1.00) 		0.164
(1.00) 		0.182
(1.00) 		0.326
(1.00) 		0.0574
(1.00) 		0.333
(1.00) 		0.206
(1.00) 		0.859
(1.00) 		0.25
(1.00)
FGFR2 31 (12%) 217 0.385
(1.00) 		0.293
(1.00) 		0.389
(1.00) 		0.898
(1.00) 		0.97
(1.00) 		0.829
(1.00) 		0.912
(1.00) 		0.0685
(1.00) 		0.457
(1.00) 		0.235
(1.00) 		0.732
(1.00) 		1
(1.00)
CCND1 15 (6%) 233 0.631
(1.00) 		0.833
(1.00) 		0.0703
(1.00) 		0.494
(1.00) 		0.374
(1.00) 		0.338
(1.00) 		0.48
(1.00) 		0.331
(1.00) 		0.169
(1.00) 		0.126
(1.00) 		0.421
(1.00) 		0.726
(1.00)
SMTNL2 9 (4%) 239 0.0498
(1.00) 		0.589
(1.00) 		0.603
(1.00) 		1
(1.00) 		0.776
(1.00) 		1
(1.00) 		0.916
(1.00) 		0.158
(1.00) 		0.786
(1.00) 		1
(1.00)
NFE2L2 15 (6%) 233 0.0905
(1.00) 		0.833
(1.00) 		0.00332
(1.00) 		0.633
(1.00) 		0.248
(1.00) 		1
(1.00) 		0.0291
(1.00) 		0.00347
(1.00) 		0.474
(1.00) 		0.85
(1.00) 		0.338
(1.00) 		0.313
(1.00)
CHD4 35 (14%) 213 0.0986
(1.00) 		0.284
(1.00) 		0.624
(1.00) 		0.863
(1.00) 		0.97
(1.00) 		0.287
(1.00) 		0.63
(1.00) 		0.524
(1.00) 		0.367
(1.00) 		0.607
(1.00) 		0.78
(1.00) 		0.659
(1.00)
RBMX 13 (5%) 235 0.191
(1.00) 		0.18
(1.00) 		0.145
(1.00) 		0.385
(1.00) 		0.0124
(1.00) 		1
(1.00) 		0.822
(1.00) 		0.022
(1.00) 		1
(1.00) 		0.132
(1.00) 		0.678
(1.00) 		0.726
(1.00)
FAM9A 14 (6%) 234 0.75
(1.00) 		0.269
(1.00) 		0.178
(1.00) 		0.0227
(1.00) 		0.309
(1.00) 		0.174
(1.00) 		0.784
(1.00) 		0.11
(1.00) 		0.0218
(1.00) 		0.0708
(1.00)
HPD 7 (3%) 241 0.419
(1.00) 		0.776
(1.00) 		0.447
(1.00) 		0.651
(1.00) 		0.374
(1.00) 		0.0103
(1.00) 		0.44
(1.00) 		0.221
(1.00) 		0.816
(1.00) 		1
(1.00)
MORC4 20 (8%) 228 0.583
(1.00) 		0.18
(1.00) 		0.3
(1.00) 		0.279
(1.00) 		0.212
(1.00) 		0.0332
(1.00) 		0.0835
(1.00) 		0.304
(1.00) 		0.0191
(1.00) 		0.283
(1.00) 		0.233
(1.00) 		0.876
(1.00)
CASP8 17 (7%) 231 0.381
(1.00) 		0.0595
(1.00) 		0.0946
(1.00) 		0.626
(1.00) 		0.154
(1.00) 		0.269
(1.00) 		0.777
(1.00) 		0.263
(1.00) 		0.468
(1.00) 		0.0232
(1.00) 		0.885
(1.00) 		0.688
(1.00)
ABI1 4 (2%) 244 0.699
(1.00) 		0.64
(1.00) 		0.637
(1.00) 		0.55
(1.00) 		0.702
(1.00) 		0.557
(1.00) 		0.606
(1.00)
FOXA2 12 (5%) 236 0.909
(1.00) 		0.797
(1.00) 		0.0719
(1.00) 		0.744
(1.00) 		0.82
(1.00) 		0.371
(1.00) 		0.193
(1.00) 		0.916
(1.00) 		0.467
(1.00) 		0.475
(1.00)
BRS3 15 (6%) 233 0.536
(1.00) 		0.151
(1.00) 		0.254
(1.00) 		0.518
(1.00) 		0.392
(1.00) 		0.54
(1.00) 		0.0576
(1.00) 		0.00305
(1.00) 		0.31
(1.00) 		0.0478
(1.00) 		0.546
(1.00) 		0.533
(1.00)
NRAS 9 (4%) 239 0.56
(1.00) 		0.316
(1.00) 		1
(1.00) 		0.843
(1.00) 		0.966
(1.00) 		0.58
(1.00) 		0.68
(1.00)
DNER 18 (7%) 230 0.191
(1.00) 		0.0515
(1.00) 		0.00316
(1.00) 		0.655
(1.00) 		0.0217
(1.00) 		0.581
(1.00) 		0.635
(1.00) 		0.013
(1.00) 		0.666
(1.00) 		0.128
(1.00) 		0.675
(1.00) 		1
(1.00)
TIAL1 11 (4%) 237 0.381
(1.00) 		0.405
(1.00) 		0.221
(1.00) 		0.0766
(1.00) 		0.564
(1.00) 		0.744
(1.00) 		0.132
(1.00) 		0.0469
(1.00) 		0.74
(1.00) 		0.809
(1.00) 		0.859
(1.00) 		0.25
(1.00)
RPL14 7 (3%) 241 0.806
(1.00) 		0.875
(1.00) 		0.479
(1.00) 		1
(1.00) 		0.9
(1.00) 		0.591
(1.00) 		0.385
(1.00) 		0.903
(1.00) 		0.851
(1.00) 		1
(1.00)
SGK1 15 (6%) 233 0.381
(1.00) 		0.0595
(1.00) 		0.254
(1.00) 		0.626
(1.00) 		0.226
(1.00) 		0.0954
(1.00) 		0.848
(1.00) 		0.811
(1.00) 		0.291
(1.00) 		0.446
(1.00) 		0.678
(1.00) 		0.726
(1.00)
SLC48A1 5 (2%) 243 0.598
(1.00) 		0.639
(1.00) 		0.803
(1.00) 		0.372
(1.00) 		0.624
(1.00) 		1
(1.00) 		0.526
(1.00) 		0.6
(1.00) 		0.786
(1.00) 		0.693
(1.00)
BCOR 30 (12%) 218 0.687
(1.00) 		0.405
(1.00) 		0.00159
(0.585) 		0.0251
(1.00) 		0.512
(1.00) 		0.5
(1.00) 		0.107
(1.00) 		0.24
(1.00) 		0.908
(1.00) 		0.213
(1.00) 		0.594
(1.00) 		0.302
(1.00)
ZNF263 8 (3%) 240 0.0242
(1.00) 		0.0595
(1.00) 		0.345
(1.00) 		0.385
(1.00) 		0.611
(1.00) 		1
(1.00) 		0.284
(1.00) 		0.0929
(1.00) 		0.159
(1.00) 		0.0598
(1.00) 		0.421
(1.00) 		0.367
(1.00)
'CTNNB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 4.9e-07 (Fisher's exact test), Q value = 0.00019

Table S1.  Gene #3: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
CTNNB1 MUTATED 0 3 4 10
CTNNB1 WILD-TYPE 12 15 7 0

Figure S1.  Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 5.3e-06 (Chi-square test), Q value = 0.002

Table S2.  Gene #3: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 157 19 54 9 3
CTNNB1 MUTATED 60 9 1 1 1
CTNNB1 WILD-TYPE 97 10 53 8 2

Figure S2.  Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'CTNNB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1.29e-10 (Chi-square test), Q value = 5.1e-08

Table S3.  Gene #3: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
CTNNB1 MUTATED 6 10 6 0 32 10
CTNNB1 WILD-TYPE 33 26 31 10 8 14

Figure S3.  Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.18e-15 (Fisher's exact test), Q value = 4.7e-13

Table S4.  Gene #3: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 80 82
CTNNB1 MUTATED 6 14 52
CTNNB1 WILD-TYPE 73 66 30

Figure S4.  Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.45e-30 (Fisher's exact test), Q value = 3.4e-27

Table S5.  Gene #3: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 70 42 78
CTNNB1 MUTATED 49 8 6 9
CTNNB1 WILD-TYPE 2 62 36 69

Figure S5.  Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2.12e-14 (Fisher's exact test), Q value = 8.4e-12

Table S6.  Gene #3: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 91 78
CTNNB1 MUTATED 4 19 48
CTNNB1 WILD-TYPE 67 72 30

Figure S6.  Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.38e-07 (Fisher's exact test), Q value = 0.00013

Table S7.  Gene #3: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 41 13 63
CTNNB1 MUTATED 44 19 5 3
CTNNB1 WILD-TYPE 79 22 8 60

Figure S7.  Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.99e-05 (Fisher's exact test), Q value = 0.015

Table S8.  Gene #4: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 41 51
PIK3R1 MUTATED 5 12 28
PIK3R1 WILD-TYPE 37 29 23

Figure S8.  Get High-res Image Gene #4: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.15e-05 (Fisher's exact test), Q value = 0.0044

Table S9.  Gene #4: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 80 82
PIK3R1 MUTATED 10 33 35
PIK3R1 WILD-TYPE 69 47 47

Figure S9.  Get High-res Image Gene #4: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.000357 (Fisher's exact test), Q value = 0.13

Table S10.  Gene #6: 'PTEN MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
PTEN MUTATED 15 14 4
PTEN WILD-TYPE 2 4 12

Figure S10.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 3.43e-21 (Chi-square test), Q value = 1.4e-18

Table S11.  Gene #6: 'PTEN MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 157 19 54 9 3
PTEN MUTATED 130 12 4 8 2
PTEN WILD-TYPE 27 7 50 1 1

Figure S11.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.35e-12 (Fisher's exact test), Q value = 1.3e-09

Table S12.  Gene #6: 'PTEN MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 41 51
PTEN MUTATED 7 30 44
PTEN WILD-TYPE 35 11 7

Figure S12.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 7.04e-22 (Fisher's exact test), Q value = 2.8e-19

Table S13.  Gene #6: 'PTEN MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 80 82
PTEN MUTATED 18 74 63
PTEN WILD-TYPE 61 6 19

Figure S13.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.69e-16 (Fisher's exact test), Q value = 2.7e-13

Table S14.  Gene #6: 'PTEN MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 70 42 78
PTEN MUTATED 38 64 31 22
PTEN WILD-TYPE 13 6 11 56

Figure S14.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.54e-14 (Fisher's exact test), Q value = 6.1e-12

Table S15.  Gene #6: 'PTEN MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 91 78
PTEN MUTATED 21 80 57
PTEN WILD-TYPE 50 11 21

Figure S15.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.07e-16 (Fisher's exact test), Q value = 1.2e-13

Table S16.  Gene #6: 'PTEN MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 41 13 63
PTEN MUTATED 106 27 10 15
PTEN WILD-TYPE 17 14 3 48

Figure S16.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.49e-08 (Fisher's exact test), Q value = 5.8e-06

Table S17.  Gene #6: 'PTEN MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 54 24
PTEN MUTATED 13 48 9
PTEN WILD-TYPE 24 6 15

Figure S17.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.96e-11 (Fisher's exact test), Q value = 1.6e-08

Table S18.  Gene #6: 'PTEN MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 51 9
PTEN MUTATED 50 15 5
PTEN WILD-TYPE 5 36 4

Figure S18.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000279 (Fisher's exact test), Q value = 0.1

Table S19.  Gene #8: 'KRAS MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 70 42 78
KRAS MUTATED 3 20 16 12
KRAS WILD-TYPE 48 50 26 66

Figure S19.  Get High-res Image Gene #8: 'KRAS MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 3.88e-05 (Fisher's exact test), Q value = 0.015

Table S20.  Gene #9: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
TP53 MUTATED 2 13 1 0
TP53 WILD-TYPE 10 5 10 10

Figure S20.  Get High-res Image Gene #9: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1.72e-07 (Fisher's exact test), Q value = 6.7e-05

Table S21.  Gene #9: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
TP53 MUTATED 3 0 13
TP53 WILD-TYPE 14 18 3

Figure S21.  Get High-res Image Gene #9: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 8.51e-31 (Chi-square test), Q value = 3.5e-28

Table S22.  Gene #9: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 157 19 54 9 3
TP53 MUTATED 11 5 50 2 0
TP53 WILD-TYPE 146 14 4 7 3

Figure S22.  Get High-res Image Gene #9: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.61e-12 (Fisher's exact test), Q value = 1.4e-09

Table S23.  Gene #9: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 41 51
TP53 MUTATED 30 4 5
TP53 WILD-TYPE 12 37 46

Figure S23.  Get High-res Image Gene #9: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 2.01e-05 (Chi-square test), Q value = 0.0077

Table S24.  Gene #9: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
TP53 MUTATED 9 19 4 2 2 8
TP53 WILD-TYPE 30 17 33 8 38 16

Figure S24.  Get High-res Image Gene #9: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 5.76e-26 (Fisher's exact test), Q value = 2.3e-23

Table S25.  Gene #9: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 80 82
TP53 MUTATED 57 3 8
TP53 WILD-TYPE 22 77 74

Figure S25.  Get High-res Image Gene #9: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.27e-27 (Fisher's exact test), Q value = 5.2e-25

Table S26.  Gene #9: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 70 42 78
TP53 MUTATED 0 2 10 56
TP53 WILD-TYPE 51 68 32 22

Figure S26.  Get High-res Image Gene #9: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 9.81e-18 (Fisher's exact test), Q value = 3.9e-15

Table S27.  Gene #9: 'TP53 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 71 91 78
TP53 MUTATED 47 8 9
TP53 WILD-TYPE 24 83 69

Figure S27.  Get High-res Image Gene #9: 'TP53 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.9e-22 (Fisher's exact test), Q value = 1.2e-19

Table S28.  Gene #9: 'TP53 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 41 13 63
TP53 MUTATED 7 5 7 45
TP53 WILD-TYPE 116 36 6 18

Figure S28.  Get High-res Image Gene #9: 'TP53 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.24e-09 (Fisher's exact test), Q value = 8.7e-07

Table S29.  Gene #9: 'TP53 MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 54 24
TP53 MUTATED 24 3 8
TP53 WILD-TYPE 13 51 16

Figure S29.  Get High-res Image Gene #9: 'TP53 MUTATION STATUS' versus Clinical Feature #11: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.08e-08 (Fisher's exact test), Q value = 8.1e-06

Table S30.  Gene #9: 'TP53 MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 51 9
TP53 MUTATED 3 28 4
TP53 WILD-TYPE 52 23 5

Figure S30.  Get High-res Image Gene #9: 'TP53 MUTATION STATUS' versus Clinical Feature #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000124 (Fisher's exact test), Q value = 0.047

Table S31.  Gene #10: 'FBXW7 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 70 42 78
FBXW7 MUTATED 0 10 10 19
FBXW7 WILD-TYPE 51 60 32 59

Figure S31.  Get High-res Image Gene #10: 'FBXW7 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'CTCF MUTATION STATUS' versus 'CN_CNMF'

P value = 9.19e-05 (Chi-square test), Q value = 0.035

Table S32.  Gene #11: 'CTCF MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 157 19 54 9 3
CTCF MUTATED 39 0 0 3 0
CTCF WILD-TYPE 118 19 54 6 3

Figure S32.  Get High-res Image Gene #11: 'CTCF MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'CTCF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000334 (Fisher's exact test), Q value = 0.12

Table S33.  Gene #11: 'CTCF MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 80 82
CTCF MUTATED 4 21 19
CTCF WILD-TYPE 75 59 63

Figure S33.  Get High-res Image Gene #11: 'CTCF MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'CTCF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000158 (Fisher's exact test), Q value = 0.059

Table S34.  Gene #11: 'CTCF MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 70 42 78
CTCF MUTATED 11 19 11 3
CTCF WILD-TYPE 40 51 31 75

Figure S34.  Get High-res Image Gene #11: 'CTCF MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 3.81e-06 (Chi-square test), Q value = 0.0015

Table S35.  Gene #12: 'ARID1A MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 157 19 54 9 3
ARID1A MUTATED 68 3 3 5 1
ARID1A WILD-TYPE 89 16 51 4 2

Figure S35.  Get High-res Image Gene #12: 'ARID1A MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'RNF43 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.64e-05 (Fisher's exact test), Q value = 0.01

Table S36.  Gene #36: 'RNF43 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 51 70 42 78
RNF43 MUTATED 1 1 9 1
RNF43 WILD-TYPE 50 69 33 77

Figure S36.  Get High-res Image Gene #36: 'RNF43 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

Methods & Data
Input

  • Mutation data file = UCEC-TP.mutsig.cluster.txt

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

  • Number of patients = 248

  • Number of significantly mutated genes = 36

  • 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

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

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] 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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