(primary solid tumor cohort)
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, 34 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', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
-
RPL22 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.
-
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'.
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 | Chi-square 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 (0.506) |
5.76e-26 (2.27e-23) |
1.27e-27 (5.03e-25) |
1.55e-16 (6.03e-14) |
4.21e-19 (1.65e-16) |
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 (4.55e-13) |
8.45e-30 (3.35e-27) |
9.76e-09 (3.73e-06) |
2.82e-17 (1.1e-14) |
PTEN | 161 (65%) | 87 |
0.000274 (0.101) |
0.000718 (0.261) |
3.43e-21 (1.35e-18) |
3.44e-12 (1.33e-09) |
0.0257 (1.00) |
0.183 (1.00) |
7.04e-22 (2.77e-19) |
6.69e-16 (2.59e-13) |
4.86e-19 (1.9e-16) |
4.77e-16 (1.85e-13) |
PIK3R1 | 83 (33%) | 165 |
0.0383 (1.00) |
0.043 (1.00) |
0.00177 (0.638) |
3.19e-05 (0.0119) |
0.649 (1.00) |
0.877 (1.00) |
1.15e-05 (0.00433) |
0.000937 (0.34) |
0.000304 (0.112) |
0.00892 (1.00) |
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 (0.122) |
0.000158 (0.0585) |
0.00221 (0.79) |
0.111 (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) |
0.397 (1.00) |
0.43 (1.00) |
KRAS | 53 (21%) | 195 |
0.164 (1.00) |
0.00967 (1.00) |
0.00226 (0.804) |
0.116 (1.00) |
0.297 (1.00) |
0.855 (1.00) |
0.543 (1.00) |
0.000279 (0.103) |
0.126 (1.00) |
0.0501 (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) |
0.557 (1.00) |
0.000644 (0.235) |
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) |
0.0432 (1.00) |
0.00409 (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) |
0.252 (1.00) |
0.572 (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 (0.891) |
0.00215 (0.768) |
0.00128 (0.465) |
0.00482 (1.00) |
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) |
0.833 (1.00) |
0.0625 (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) |
0.649 (1.00) |
0.867 (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) |
0.538 (1.00) |
0.005 (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) |
0.883 (1.00) |
0.319 (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) |
0.165 (1.00) |
0.153 (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) |
0.939 (1.00) |
0.709 (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) |
0.465 (1.00) |
0.271 (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) |
0.303 (1.00) |
0.332 (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) |
0.394 (1.00) |
0.441 (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) |
0.573 (1.00) |
0.0372 (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) |
0.577 (1.00) |
0.0627 (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) |
0.672 (1.00) |
0.00211 (0.759) |
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) |
0.795 (1.00) |
0.107 (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) |
0.365 (1.00) |
0.00372 (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) |
0.68 (1.00) |
0.607 (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) |
0.166 (1.00) |
0.877 (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) |
0.903 (1.00) |
0.044 (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) |
0.912 (1.00) |
0.318 (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) |
0.769 (1.00) |
0.86 (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) |
0.955 (1.00) |
0.613 (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) |
0.941 (1.00) |
0.6 (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) |
0.472 (1.00) |
0.875 (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) |
0.0549 (1.00) |
0.523 (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) |
0.332 (1.00) |
0.313 (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) |
0.811 (1.00) |
0.194 (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) |
0.0887 (1.00) |
0.155 (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) |
0.65 (1.00) |
0.224 (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) |
0.495 (1.00) |
0.313 (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) |
0.22 (1.00) |
0.863 (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) |
0.703 (1.00) |
0.597 (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) |
0.895 (1.00) |
0.571 (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) |
0.71 (1.00) |
0.413 (1.00) |
P value = 0.000274 (Fisher's exact test), Q value = 0.1
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 |
P value = 3.43e-21 (Chi-square test), Q value = 1.3e-18
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 |
P value = 3.44e-12 (Fisher's exact test), Q value = 1.3e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 42 | 50 |
PTEN MUTATED | 7 | 31 | 43 |
PTEN WILD-TYPE | 35 | 11 | 7 |
P value = 7.04e-22 (Fisher's exact test), Q value = 2.8e-19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 79 | 80 | 82 |
PTEN MUTATED | 18 | 74 | 63 |
PTEN WILD-TYPE | 61 | 6 | 19 |
P value = 6.69e-16 (Fisher's exact test), Q value = 2.6e-13
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 |
P value = 4.86e-19 (Fisher's exact test), Q value = 1.9e-16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 60 | 92 | 84 |
PTEN MUTATED | 11 | 81 | 63 |
PTEN WILD-TYPE | 49 | 11 | 21 |
P value = 4.77e-16 (Chi-square test), Q value = 1.8e-13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 19 | 51 | 58 | 9 | 16 | 83 |
PTEN MUTATED | 15 | 8 | 39 | 7 | 11 | 75 |
PTEN WILD-TYPE | 4 | 43 | 19 | 2 | 5 | 8 |
P value = 2.73e-06 (Fisher's exact test), Q value = 0.001
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 |
P value = 1.57e-05 (Fisher's exact test), Q value = 0.0059
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 19 | 13 | 19 |
CTNNB1 MUTATED | 14 | 1 | 2 |
CTNNB1 WILD-TYPE | 5 | 12 | 17 |
P value = 5.3e-06 (Chi-square test), Q value = 0.002
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 |
P value = 1.29e-10 (Chi-square test), Q value = 4.9e-08
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 |
P value = 1.18e-15 (Fisher's exact test), Q value = 4.6e-13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 79 | 80 | 82 |
CTNNB1 MUTATED | 6 | 14 | 52 |
CTNNB1 WILD-TYPE | 73 | 66 | 30 |
P value = 8.45e-30 (Fisher's exact test), Q value = 3.4e-27
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 |
P value = 9.76e-09 (Fisher's exact test), Q value = 3.7e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 60 | 92 | 84 |
CTNNB1 MUTATED | 5 | 21 | 44 |
CTNNB1 WILD-TYPE | 55 | 71 | 40 |
P value = 2.82e-17 (Chi-square test), Q value = 1.1e-14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 19 | 51 | 58 | 9 | 16 | 83 |
CTNNB1 MUTATED | 4 | 1 | 43 | 2 | 8 | 12 |
CTNNB1 WILD-TYPE | 15 | 50 | 15 | 7 | 8 | 71 |
P value = 0.000124 (Fisher's exact test), Q value = 0.046
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 |
P value = 0.000279 (Fisher's exact test), Q value = 0.1
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 |
P value = 3.19e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 42 | 50 |
PIK3R1 MUTATED | 5 | 12 | 28 |
PIK3R1 WILD-TYPE | 37 | 30 | 22 |
P value = 1.15e-05 (Fisher's exact test), Q value = 0.0043
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 79 | 80 | 82 |
PIK3R1 MUTATED | 10 | 33 | 35 |
PIK3R1 WILD-TYPE | 69 | 47 | 47 |
P value = 0.000304 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 60 | 92 | 84 |
PIK3R1 MUTATED | 8 | 36 | 35 |
PIK3R1 WILD-TYPE | 52 | 56 | 49 |
P value = 0.000644 (Chi-square test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 19 | 51 | 58 | 9 | 16 | 83 |
RPL22 MUTATED | 6 | 1 | 5 | 3 | 5 | 9 |
RPL22 WILD-TYPE | 13 | 50 | 53 | 6 | 11 | 74 |
P value = 6.72e-06 (Fisher's exact test), Q value = 0.0025
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 |
P value = 5.02e-05 (Fisher's exact test), Q value = 0.019
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 19 | 13 | 19 |
TP53 MUTATED | 1 | 2 | 13 |
TP53 WILD-TYPE | 18 | 11 | 6 |
P value = 8.51e-31 (Chi-square test), Q value = 3.4e-28
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 |
P value = 3.54e-12 (Fisher's exact test), Q value = 1.4e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 42 | 50 |
TP53 MUTATED | 30 | 4 | 5 |
TP53 WILD-TYPE | 12 | 38 | 45 |
P value = 2.01e-05 (Chi-square test), Q value = 0.0075
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 |
P value = 5.76e-26 (Fisher's exact test), Q value = 2.3e-23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 79 | 80 | 82 |
TP53 MUTATED | 57 | 3 | 8 |
TP53 WILD-TYPE | 22 | 77 | 74 |
P value = 1.27e-27 (Fisher's exact test), Q value = 5e-25
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 |
P value = 1.55e-16 (Fisher's exact test), Q value = 6e-14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 60 | 92 | 84 |
TP53 MUTATED | 42 | 8 | 14 |
TP53 WILD-TYPE | 18 | 84 | 70 |
P value = 4.21e-19 (Chi-square test), Q value = 1.6e-16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 19 | 51 | 58 | 9 | 16 | 83 |
TP53 MUTATED | 3 | 38 | 4 | 5 | 8 | 6 |
TP53 WILD-TYPE | 16 | 13 | 54 | 4 | 8 | 77 |
P value = 9.19e-05 (Chi-square test), Q value = 0.034
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 |
P value = 0.000334 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 79 | 80 | 82 |
CTCF MUTATED | 4 | 21 | 19 |
CTCF WILD-TYPE | 75 | 59 | 63 |
P value = 0.000158 (Fisher's exact test), Q value = 0.059
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 |
P value = 3.81e-06 (Chi-square test), Q value = 0.0014
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 |
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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
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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.