This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
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.
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PTEN mutation correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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CTNNB1 mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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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'.
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CTCF mutation correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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ARID1A mutation correlated to 'CN_CNMF'.
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) |
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'
![](D1V1.png)
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'
![](D1V3.png)
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'
![](D1V4.png)
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'
![](D1V7.png)
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'
![](D1V8.png)
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'
![](D1V9.png)
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'
![](D1V10.png)
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'
![](D2V1.png)
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'
![](D2V2.png)
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'
![](D2V3.png)
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'
![](D2V5.png)
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'
![](D2V7.png)
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'
![](D2V8.png)
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'
![](D2V9.png)
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'
![](D2V10.png)
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'
![](D3V8.png)
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'
![](D4V8.png)
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'
![](D6V4.png)
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'
![](D6V7.png)
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'
![](D11V1.png)
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'
![](D11V2.png)
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'
![](D11V3.png)
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'
![](D11V4.png)
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'
![](D11V5.png)
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'
![](D11V7.png)
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'
![](D11V8.png)
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'
![](D11V9.png)
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'
![](D11V10.png)
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'
![](D12V3.png)
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'
![](D12V7.png)
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'
![](D12V8.png)
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'
![](D14V3.png)
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Mutation data file = UCEC-TP.mutsig.cluster.txt
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Molecular subtypes file = UCEC-TP.transferedmergedcluster.txt
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Number of patients = 248
-
Number of significantly mutated genes = 43
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Number of Molecular subtypes = 10
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Exclude genes that fewer than K tumors have mutations, K = 3
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
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
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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.