Correlation between gene mutation status and molecular subtypes
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1TX3CCF
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Uterine Corpus Endometrioid Carcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1TX3CCF
Overview
Introduction

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

Summary

Testing the association between mutation status of 43 genes and 10 molecular subtypes across 248 patients, 32 significant findings detected with P value < 0.05 and Q value < 0.25.

  • PTEN mutation correlated to 'MRNA_CNMF',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • FBXW7 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • KRAS mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

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

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

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

  • ARID1A mutation correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 43 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 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
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
TP53 69 (28%) 179 6.72e-06
(0.00254) 		5.02e-05
(0.0187) 		8.51e-31
(3.39e-28) 		3.54e-12
(1.36e-09) 		2.01e-05
(0.00752) 		0.0014
(0.51) 		5.76e-26
(2.27e-23) 		1.27e-27
(5.03e-25) 		9.81e-18
(3.84e-15) 		2.9e-22
(1.14e-19)
CTNNB1 74 (30%) 174 2.73e-06
(0.00104) 		1.57e-05
(0.00591) 		5.3e-06
(0.00201) 		0.00438
(1.00) 		1.29e-10
(4.94e-08) 		0.112
(1.00) 		1.18e-15
(4.58e-13) 		8.45e-30
(3.35e-27) 		2.12e-14
(8.17e-12) 		3.38e-07
(0.000129)
PTEN 161 (65%) 87 0.000274
(0.101) 		0.000718
(0.263) 		3.43e-21
(1.34e-18) 		3.44e-12
(1.33e-09) 		0.0257
(1.00) 		0.183
(1.00) 		7.04e-22
(2.77e-19) 		6.69e-16
(2.6e-13) 		1.54e-14
(5.97e-12) 		3.07e-16
(1.2e-13)
CTCF 45 (18%) 203 0.0367
(1.00) 		0.332
(1.00) 		9.19e-05
(0.0342) 		0.0632
(1.00) 		0.0784
(1.00) 		0.848
(1.00) 		0.000334
(0.123) 		0.000158
(0.0585) 		0.00555
(1.00) 		0.00862
(1.00)
PIK3R1 83 (33%) 165 0.0383
(1.00) 		0.043
(1.00) 		0.00177
(0.643) 		3.19e-05
(0.0119) 		0.649
(1.00) 		0.877
(1.00) 		1.15e-05
(0.00433) 		0.000937
(0.342) 		0.0251
(1.00) 		0.0225
(1.00)
FBXW7 39 (16%) 209 0.397
(1.00) 		0.0734
(1.00) 		0.201
(1.00) 		0.128
(1.00) 		0.106
(1.00) 		0.107
(1.00) 		0.068
(1.00) 		0.000124
(0.0459) 		0.761
(1.00) 		0.186
(1.00)
KRAS 53 (21%) 195 0.164
(1.00) 		0.00967
(1.00) 		0.00226
(0.813) 		0.116
(1.00) 		0.297
(1.00) 		0.855
(1.00) 		0.543
(1.00) 		0.000279
(0.103) 		0.117
(1.00) 		0.0326
(1.00)
ARID1A 83 (33%) 165 0.19
(1.00) 		0.0884
(1.00) 		3.81e-06
(0.00145) 		0.233
(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)
PIK3CA 132 (53%) 116 0.696
(1.00) 		0.256
(1.00) 		0.542
(1.00) 		0.569
(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)
PPP2R1A 27 (11%) 221 0.0514
(1.00) 		0.0266
(1.00) 		0.0215
(1.00) 		0.0217
(1.00) 		0.141
(1.00) 		0.313
(1.00) 		0.00251
(0.901) 		0.00215
(0.774) 		0.0139
(1.00) 		0.00194
(0.702)
PRKAR1B 4 (2%) 244 0.963
(1.00) 		0.513
(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)
RPL22 31 (12%) 217 0.0374
(1.00) 		0.0112
(1.00) 		0.0101
(1.00) 		0.00742
(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)
SPOP 21 (8%) 227 0.147
(1.00) 		0.838
(1.00) 		0.483
(1.00) 		0.323
(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)
FGFR2 31 (12%) 217 0.364
(1.00) 		0.316
(1.00) 		0.389
(1.00) 		0.949
(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)
P2RY11 7 (3%) 241 0.00993
(1.00) 		0.52
(1.00) 		0.724
(1.00) 		0.204
(1.00) 		0.0877
(1.00) 		0.527
(1.00) 		0.59
(1.00) 		0.367
(1.00)
CCND1 15 (6%) 233 0.333
(1.00) 		0.545
(1.00) 		0.0703
(1.00) 		0.561
(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)
CHD4 35 (14%) 213 0.0789
(1.00) 		0.53
(1.00) 		0.624
(1.00) 		0.865
(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)
NFE2L2 15 (6%) 233 0.167
(1.00) 		1
(1.00) 		0.00332
(1.00) 		0.705
(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)
SOX17 7 (3%) 241 0.00693
(1.00) 		0.2
(1.00) 		0.339
(1.00) 		0.41
(1.00) 		0.361
(1.00) 		0.401
(1.00) 		0.714
(1.00) 		0.184
(1.00)
FOXA2 12 (5%) 236 0.909
(1.00) 		0.889
(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)
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)
SMTNL2 9 (4%) 239 0.0498
(1.00) 		0.676
(1.00) 		0.603
(1.00) 		1
(1.00) 		0.776
(1.00) 		1
(1.00) 		0.916
(1.00) 		0.158
(1.00)
RBMX 13 (5%) 235 0.134
(1.00) 		0.0637
(1.00) 		0.145
(1.00) 		0.386
(1.00) 		0.0124
(1.00) 		1
(1.00) 		0.822
(1.00) 		0.022
(1.00) 		1
(1.00) 		0.132
(1.00)
MAX 11 (4%) 237 0.0313
(1.00) 		0.889
(1.00) 		0.568
(1.00) 		0.733
(1.00) 		0.593
(1.00) 		1
(1.00) 		1
(1.00) 		0.292
(1.00)
ING1 13 (5%) 235 0.0377
(1.00) 		0.541
(1.00) 		0.436
(1.00) 		0.083
(1.00) 		0.726
(1.00) 		0.659
(1.00) 		0.754
(1.00) 		0.0654
(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)
RPL14 7 (3%) 241 0.806
(1.00) 		0.873
(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)
DNER 18 (7%) 230 0.134
(1.00) 		0.022
(1.00) 		0.00316
(1.00) 		0.541
(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)
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)
HPD 7 (3%) 241 0.419
(1.00) 		0.775
(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)
RASA1 22 (9%) 226 0.364
(1.00) 		0.0751
(1.00) 		0.0846
(1.00) 		0.911
(1.00) 		0.331
(1.00) 		1
(1.00) 		0.742
(1.00) 		0.205
(1.00) 		0.603
(1.00) 		0.508
(1.00)
ZNF267 16 (6%) 232 0.324
(1.00) 		0.634
(1.00) 		0.509
(1.00) 		1
(1.00) 		0.0611
(1.00) 		0.248
(1.00) 		0.425
(1.00) 		0.466
(1.00) 		0.697
(1.00) 		0.207
(1.00)
SGK1 15 (6%) 233 0.305
(1.00) 		0.0137
(1.00) 		0.254
(1.00) 		0.624
(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)
ARID5B 29 (12%) 219 0.83
(1.00) 		0.185
(1.00) 		0.0344
(1.00) 		0.134
(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)
CYLC1 18 (7%) 230 0.134
(1.00) 		0.022
(1.00) 		0.344
(1.00) 		0.911
(1.00) 		0.282
(1.00) 		0.269
(1.00) 		0.511
(1.00) 		0.184
(1.00) 		0.319
(1.00) 		0.205
(1.00)
DYRK1A 12 (5%) 236 0.668
(1.00) 		0.463
(1.00) 		0.457
(1.00) 		0.252
(1.00) 		0.458
(1.00) 		0.306
(1.00) 		0.765
(1.00) 		0.0139
(1.00) 		0.532
(1.00) 		0.136
(1.00)
METTL14 10 (4%) 238 0.305
(1.00) 		0.249
(1.00) 		0.407
(1.00) 		0.676
(1.00) 		0.363
(1.00) 		0.509
(1.00) 		0.356
(1.00) 		0.00678
(1.00) 		0.0177
(1.00) 		0.414
(1.00)
TPTE 15 (6%) 233 0.00399
(1.00) 		0.541
(1.00) 		0.183
(1.00) 		0.769
(1.00) 		1
(1.00) 		0.213
(1.00) 		1
(1.00) 		0.424
(1.00)
UPF3B 16 (6%) 232 0.413
(1.00) 		0.285
(1.00) 		0.269
(1.00) 		0.464
(1.00) 		0.721
(1.00) 		0.269
(1.00) 		0.949
(1.00) 		0.481
(1.00) 		0.75
(1.00) 		0.805
(1.00)
UBE2QL1 5 (2%) 243 0.598
(1.00) 		0.735
(1.00) 		0.00875
(1.00) 		0.0201
(1.00) 		0.208
(1.00) 		0.0646
(1.00) 		0.631
(1.00) 		1
(1.00)
ZNF286A 12 (5%) 236 0.701
(1.00) 		0.376
(1.00) 		0.157
(1.00) 		0.322
(1.00) 		0.931
(1.00) 		0.153
(1.00) 		1
(1.00) 		0.924
(1.00)
ZNF263 8 (3%) 240 0.0106
(1.00) 		0.0137
(1.00) 		0.345
(1.00) 		0.386
(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)
TAB3 18 (7%) 230 0.0646
(1.00) 		0.0774
(1.00) 		0.0635
(1.00) 		0.728
(1.00) 		0.761
(1.00) 		1
(1.00) 		0.142
(1.00) 		0.0206
(1.00) 		0.455
(1.00) 		0.592
(1.00)
'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.000274 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 19 13 8
PTEN MUTATED 11 6 11 5
PTEN WILD-TYPE 0 13 2 3

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

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 3.43e-21 (Chi-square test), Q value = 1.3e-18

Table S2.  Gene #1: '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 S2.  Get High-res Image Gene #1: 'PTEN MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.44e-12 (Fisher's exact test), Q value = 1.3e-09

Table S3.  Gene #1: 'PTEN MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 42 50
PTEN MUTATED 7 31 43
PTEN WILD-TYPE 35 11 7

Figure S3.  Get High-res Image Gene #1: '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 S4.  Gene #1: '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 S4.  Get High-res Image Gene #1: '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 = 2.6e-13

Table S5.  Gene #1: '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 S5.  Get High-res Image Gene #1: '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 = 6e-12

Table S6.  Gene #1: '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 S6.  Get High-res Image Gene #1: '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 S7.  Gene #1: '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 S7.  Get High-res Image Gene #1: 'PTEN MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 2.73e-06 (Fisher's exact test), Q value = 0.001

Table S8.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 19 13 8
CTNNB1 MUTATED 0 3 6 8
CTNNB1 WILD-TYPE 11 16 7 0

Figure S8.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1.57e-05 (Fisher's exact test), Q value = 0.0059

Table S9.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 13 19
CTNNB1 MUTATED 14 1 2
CTNNB1 WILD-TYPE 5 12 17

Figure S9.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S10.  Gene #2: '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 S10.  Get High-res Image Gene #2: '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 = 4.9e-08

Table S11.  Gene #2: '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 S11.  Get High-res Image Gene #2: '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 = 4.6e-13

Table S12.  Gene #2: '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 S12.  Get High-res Image Gene #2: '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 S13.  Gene #2: '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 S13.  Get High-res Image Gene #2: '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 = 8.2e-12

Table S14.  Gene #2: '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 S14.  Get High-res Image Gene #2: '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 S15.  Gene #2: '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 S15.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000124 (Fisher's exact test), Q value = 0.046

Table S16.  Gene #3: '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 S16.  Get High-res Image Gene #3: 'FBXW7 MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S17.  Gene #4: '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 S17.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.19e-05 (Fisher's exact test), Q value = 0.012

Table S18.  Gene #6: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 42 50
PIK3R1 MUTATED 5 12 28
PIK3R1 WILD-TYPE 37 30 22

Figure S18.  Get High-res Image Gene #6: '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 = 0.0043

Table S19.  Gene #6: '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 S19.  Get High-res Image Gene #6: 'PIK3R1 MUTATION STATUS' versus Clinical Feature #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 6.72e-06 (Fisher's exact test), Q value = 0.0025

Table S20.  Gene #11: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 19 13 8
TP53 MUTATED 1 14 1 0
TP53 WILD-TYPE 10 5 12 8

Figure S20.  Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 5.02e-05 (Fisher's exact test), Q value = 0.019

Table S21.  Gene #11: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 19 13 19
TP53 MUTATED 1 2 13
TP53 WILD-TYPE 18 11 6

Figure S21.  Get High-res Image Gene #11: '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 = 3.4e-28

Table S22.  Gene #11: '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 #11: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.54e-12 (Fisher's exact test), Q value = 1.4e-09

Table S23.  Gene #11: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 42 50
TP53 MUTATED 30 4 5
TP53 WILD-TYPE 12 38 45

Figure S23.  Get High-res Image Gene #11: '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 = 0.0075

Table S24.  Gene #11: '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 #11: '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 #11: '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 #11: '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 = 5e-25

Table S26.  Gene #11: '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 #11: '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 = 3.8e-15

Table S27.  Gene #11: '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 #11: '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 = 1.1e-19

Table S28.  Gene #11: '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 #11: 'TP53 MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

'CTCF MUTATION STATUS' versus 'CN_CNMF'

P value = 9.19e-05 (Chi-square test), Q value = 0.034

Table S29.  Gene #12: '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 S29.  Get High-res Image Gene #12: '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 S30.  Gene #12: '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 S30.  Get High-res Image Gene #12: '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 S31.  Gene #12: '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 S31.  Get High-res Image Gene #12: '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 = 0.0014

Table S32.  Gene #14: '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 S32.  Get High-res Image Gene #14: 'ARID1A MUTATION STATUS' versus Clinical Feature #3: 'CN_CNMF'

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 = 43

  • 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

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.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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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