This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 45 genes and 10 molecular subtypes across 306 patients, 19 significant findings detected with P value < 0.05 and Q value < 0.25.
-
NSD1 mutation correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
HRAS mutation correlated to 'CN_CNMF'.
-
TP53 mutation correlated to 'CN_CNMF'.
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NOTCH1 mutation correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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CASP8 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
-
EPHA2 mutation correlated to 'MIRSEQ_MATURE_CNMF'.
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CSMD3 mutation correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
Table 1. Get Full Table Overview of the association between mutation status of 45 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, 19 significant findings detected.
|
Clinical Features |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
| nMutated (%) | nWild-Type | 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 | Fisher's exact test | Fisher's exact test | |
| CASP8 | 27 (9%) | 279 |
1.62e-05 (0.00695) |
0.000335 (0.142) |
0.699 (1.00) |
0.739 (1.00) |
3e-07 (0.000131) |
5.28e-07 (0.00023) |
0.377 (1.00) |
0.564 (1.00) |
0.000302 (0.128) |
0.0244 (1.00) |
| NOTCH1 | 57 (19%) | 249 |
0.88 (1.00) |
0.000562 (0.236) |
0.0187 (1.00) |
0.279 (1.00) |
0.000428 (0.181) |
2.54e-06 (0.0011) |
0.000112 (0.0481) |
0.292 (1.00) |
0.000786 (0.329) |
0.0017 (0.703) |
| CSMD3 | 70 (23%) | 236 |
0.0549 (1.00) |
0.00234 (0.965) |
0.00973 (1.00) |
0.463 (1.00) |
1.35e-05 (0.00583) |
6.66e-07 (0.00029) |
0.000542 (0.228) |
0.00103 (0.429) |
0.000137 (0.0586) |
0.00299 (1.00) |
| NSD1 | 33 (11%) | 273 |
0.302 (1.00) |
1.27e-05 (0.0055) |
0.244 (1.00) |
0.73 (1.00) |
0.000411 (0.174) |
6.41e-06 (0.00277) |
0.00974 (1.00) |
0.0355 (1.00) |
0.0297 (1.00) |
0.0072 (1.00) |
| HRAS | 10 (3%) | 296 |
8.17e-05 (0.0351) |
0.0261 (1.00) |
0.168 (1.00) |
0.599 (1.00) |
0.00339 (1.00) |
0.0011 (0.457) |
0.0991 (1.00) |
0.188 (1.00) |
0.0484 (1.00) |
0.21 (1.00) |
| TP53 | 214 (70%) | 92 |
1.7e-12 (7.44e-10) |
0.00948 (1.00) |
0.11 (1.00) |
0.776 (1.00) |
0.0113 (1.00) |
0.00143 (0.592) |
0.0611 (1.00) |
0.0008 (0.334) |
0.0417 (1.00) |
0.00811 (1.00) |
| EPHA2 | 14 (5%) | 292 |
0.111 (1.00) |
0.00794 (1.00) |
0.811 (1.00) |
0.906 (1.00) |
0.499 (1.00) |
0.57 (1.00) |
0.775 (1.00) |
0.184 (1.00) |
0.000357 (0.151) |
0.0592 (1.00) |
| PIK3CA | 64 (21%) | 242 |
0.0654 (1.00) |
0.0334 (1.00) |
0.0948 (1.00) |
0.928 (1.00) |
0.119 (1.00) |
0.398 (1.00) |
0.038 (1.00) |
0.0446 (1.00) |
0.0942 (1.00) |
0.304 (1.00) |
| CDKN2A | 65 (21%) | 241 |
0.022 (1.00) |
0.494 (1.00) |
0.0349 (1.00) |
0.583 (1.00) |
0.201 (1.00) |
0.206 (1.00) |
0.418 (1.00) |
0.113 (1.00) |
0.191 (1.00) |
0.15 (1.00) |
| NFE2L2 | 17 (6%) | 289 |
0.807 (1.00) |
0.267 (1.00) |
0.125 (1.00) |
0.765 (1.00) |
1 (1.00) |
0.464 (1.00) |
0.248 (1.00) |
0.0736 (1.00) |
0.357 (1.00) |
0.471 (1.00) |
| FAT1 | 72 (24%) | 234 |
0.24 (1.00) |
0.621 (1.00) |
0.794 (1.00) |
0.487 (1.00) |
0.152 (1.00) |
0.288 (1.00) |
0.885 (1.00) |
0.317 (1.00) |
0.162 (1.00) |
0.151 (1.00) |
| JUB | 18 (6%) | 288 |
0.201 (1.00) |
0.181 (1.00) |
0.0646 (1.00) |
0.0816 (1.00) |
0.305 (1.00) |
0.221 (1.00) |
0.328 (1.00) |
1 (1.00) |
0.0121 (1.00) |
0.706 (1.00) |
| MLL2 | 56 (18%) | 250 |
0.0727 (1.00) |
0.00657 (1.00) |
0.687 (1.00) |
0.521 (1.00) |
0.0532 (1.00) |
0.00795 (1.00) |
0.0529 (1.00) |
0.0102 (1.00) |
0.225 (1.00) |
0.0303 (1.00) |
| FBXW7 | 15 (5%) | 291 |
0.76 (1.00) |
0.851 (1.00) |
0.092 (1.00) |
0.303 (1.00) |
0.881 (1.00) |
0.636 (1.00) |
0.945 (1.00) |
0.854 (1.00) |
0.872 (1.00) |
0.804 (1.00) |
| ZNF750 | 13 (4%) | 293 |
0.396 (1.00) |
0.00628 (1.00) |
0.946 (1.00) |
0.353 (1.00) |
0.119 (1.00) |
0.128 (1.00) |
0.632 (1.00) |
1 (1.00) |
0.29 (1.00) |
0.692 (1.00) |
| FLG | 48 (16%) | 258 |
0.733 (1.00) |
0.0404 (1.00) |
0.532 (1.00) |
0.575 (1.00) |
0.139 (1.00) |
0.223 (1.00) |
0.0631 (1.00) |
0.163 (1.00) |
0.0672 (1.00) |
0.275 (1.00) |
| B2M | 7 (2%) | 299 |
0.241 (1.00) |
0.225 (1.00) |
0.515 (1.00) |
0.517 (1.00) |
0.141 (1.00) |
0.756 (1.00) |
0.157 (1.00) |
0.499 (1.00) |
||
| IL32 | 4 (1%) | 302 |
0.0451 (1.00) |
0.129 (1.00) |
0.561 (1.00) |
1 (1.00) |
0.561 (1.00) |
0.669 (1.00) |
0.828 (1.00) |
1 (1.00) |
||
| EP300 | 25 (8%) | 281 |
0.0376 (1.00) |
0.728 (1.00) |
0.769 (1.00) |
0.264 (1.00) |
0.00955 (1.00) |
0.00467 (1.00) |
0.352 (1.00) |
0.335 (1.00) |
0.232 (1.00) |
0.026 (1.00) |
| RHOA | 4 (1%) | 302 |
0.724 (1.00) |
0.177 (1.00) |
0.379 (1.00) |
0.444 (1.00) |
0.245 (1.00) |
0.141 (1.00) |
0.246 (1.00) |
0.231 (1.00) |
0.139 (1.00) |
0.361 (1.00) |
| HLA-A | 9 (3%) | 297 |
0.916 (1.00) |
0.711 (1.00) |
1 (1.00) |
1 (1.00) |
0.072 (1.00) |
0.0311 (1.00) |
0.634 (1.00) |
0.588 (1.00) |
0.175 (1.00) |
0.337 (1.00) |
| CTCF | 11 (4%) | 295 |
0.248 (1.00) |
0.122 (1.00) |
0.393 (1.00) |
0.541 (1.00) |
0.636 (1.00) |
0.632 (1.00) |
0.861 (1.00) |
0.81 (1.00) |
0.66 (1.00) |
0.722 (1.00) |
| RB1 | 10 (3%) | 296 |
0.0297 (1.00) |
0.00888 (1.00) |
0.282 (1.00) |
0.129 (1.00) |
0.00607 (1.00) |
0.00838 (1.00) |
0.0561 (1.00) |
1 (1.00) |
0.263 (1.00) |
0.0707 (1.00) |
| TGFBR2 | 10 (3%) | 296 |
0.0814 (1.00) |
0.483 (1.00) |
0.469 (1.00) |
1 (1.00) |
0.313 (1.00) |
0.785 (1.00) |
0.919 (1.00) |
1 (1.00) |
0.159 (1.00) |
0.46 (1.00) |
| NECAB1 | 6 (2%) | 300 |
0.0438 (1.00) |
1 (1.00) |
0.856 (1.00) |
0.672 (1.00) |
0.114 (1.00) |
0.0622 (1.00) |
0.773 (1.00) |
0.49 (1.00) |
0.769 (1.00) |
0.45 (1.00) |
| KRTAP1-5 | 3 (1%) | 303 |
0.927 (1.00) |
1 (1.00) |
0.78 (1.00) |
0.63 (1.00) |
0.0245 (1.00) |
1 (1.00) |
0.37 (1.00) |
0.794 (1.00) |
||
| MAPK1 | 4 (1%) | 302 |
0.808 (1.00) |
0.698 (1.00) |
0.569 (1.00) |
1 (1.00) |
0.691 (1.00) |
0.686 (1.00) |
0.69 (1.00) |
0.669 (1.00) |
0.685 (1.00) |
0.713 (1.00) |
| PLSCR1 | 5 (2%) | 301 |
0.329 (1.00) |
0.291 (1.00) |
1 (1.00) |
1 (1.00) |
0.524 (1.00) |
0.526 (1.00) |
0.157 (1.00) |
0.442 (1.00) |
0.739 (1.00) |
0.761 (1.00) |
| CNPY3 | 3 (1%) | 303 |
0.443 (1.00) |
0.66 (1.00) |
0.5 (1.00) |
0.499 (1.00) |
0.501 (1.00) |
0.59 (1.00) |
0.498 (1.00) |
0.794 (1.00) |
||
| EPB41L3 | 16 (5%) | 290 |
0.815 (1.00) |
0.308 (1.00) |
0.253 (1.00) |
0.0152 (1.00) |
0.0509 (1.00) |
0.0132 (1.00) |
0.154 (1.00) |
0.202 (1.00) |
0.161 (1.00) |
0.185 (1.00) |
| RAC1 | 9 (3%) | 297 |
0.302 (1.00) |
1 (1.00) |
1 (1.00) |
0.519 (1.00) |
0.195 (1.00) |
0.192 (1.00) |
0.218 (1.00) |
0.321 (1.00) |
0.496 (1.00) |
0.332 (1.00) |
| CUL3 | 10 (3%) | 296 |
0.82 (1.00) |
0.336 (1.00) |
0.737 (1.00) |
0.636 (1.00) |
0.403 (1.00) |
0.852 (1.00) |
0.79 (1.00) |
0.359 (1.00) |
0.904 (1.00) |
0.567 (1.00) |
| TRPV4 | 7 (2%) | 299 |
0.302 (1.00) |
0.412 (1.00) |
0.796 (1.00) |
0.27 (1.00) |
0.571 (1.00) |
0.0634 (1.00) |
0.569 (1.00) |
0.371 (1.00) |
0.714 (1.00) |
0.332 (1.00) |
| PRB2 | 10 (3%) | 296 |
0.499 (1.00) |
0.0801 (1.00) |
0.888 (1.00) |
1 (1.00) |
0.669 (1.00) |
0.231 (1.00) |
0.667 (1.00) |
0.15 (1.00) |
0.235 (1.00) |
0.164 (1.00) |
| PRB1 | 7 (2%) | 299 |
0.568 (1.00) |
0.639 (1.00) |
0.757 (1.00) |
0.672 (1.00) |
0.89 (1.00) |
0.639 (1.00) |
0.106 (1.00) |
1 (1.00) |
0.157 (1.00) |
0.797 (1.00) |
| WHSC1 | 10 (3%) | 296 |
0.0792 (1.00) |
0.112 (1.00) |
0.284 (1.00) |
0.622 (1.00) |
0.855 (1.00) |
0.852 (1.00) |
0.174 (1.00) |
1 (1.00) |
0.0832 (1.00) |
0.93 (1.00) |
| STEAP4 | 10 (3%) | 296 |
0.292 (1.00) |
0.0801 (1.00) |
0.175 (1.00) |
0.656 (1.00) |
0.0813 (1.00) |
0.0997 (1.00) |
0.0817 (1.00) |
1 (1.00) |
0.109 (1.00) |
0.137 (1.00) |
| HIST1H1B | 7 (2%) | 299 |
0.0466 (1.00) |
0.152 (1.00) |
0.705 (1.00) |
0.822 (1.00) |
0.802 (1.00) |
0.717 (1.00) |
0.569 (1.00) |
0.108 (1.00) |
0.89 (1.00) |
0.131 (1.00) |
| KCNA3 | 8 (3%) | 298 |
0.855 (1.00) |
0.105 (1.00) |
0.802 (1.00) |
0.0518 (1.00) |
0.606 (1.00) |
0.491 (1.00) |
0.907 (1.00) |
0.306 (1.00) |
0.582 (1.00) |
0.503 (1.00) |
| EPDR1 | 6 (2%) | 300 |
0.45 (1.00) |
1 (1.00) |
0.561 (1.00) |
0.779 (1.00) |
0.327 (1.00) |
0.675 (1.00) |
0.88 (1.00) |
1 (1.00) |
1 (1.00) |
0.705 (1.00) |
| SLC26A7 | 8 (3%) | 298 |
0.646 (1.00) |
0.606 (1.00) |
0.569 (1.00) |
0.209 (1.00) |
0.2 (1.00) |
0.311 (1.00) |
0.907 (1.00) |
0.764 (1.00) |
1 (1.00) |
0.828 (1.00) |
| OR8D4 | 6 (2%) | 300 |
0.927 (1.00) |
0.618 (1.00) |
0.894 (1.00) |
0.438 (1.00) |
0.387 (1.00) |
1 (1.00) |
0.387 (1.00) |
0.72 (1.00) |
0.328 (1.00) |
0.264 (1.00) |
| POU4F2 | 7 (2%) | 299 |
0.671 (1.00) |
0.802 (1.00) |
0.428 (1.00) |
0.404 (1.00) |
0.571 (1.00) |
0.563 (1.00) |
0.344 (1.00) |
0.756 (1.00) |
0.304 (1.00) |
0.332 (1.00) |
| FCRL4 | 13 (4%) | 293 |
0.677 (1.00) |
0.406 (1.00) |
0.788 (1.00) |
1 (1.00) |
0.405 (1.00) |
0.106 (1.00) |
0.377 (1.00) |
0.833 (1.00) |
0.43 (1.00) |
0.572 (1.00) |
| TXK | 3 (1%) | 303 |
0.417 (1.00) |
0.547 (1.00) |
0.78 (1.00) |
0.782 (1.00) |
0.114 (1.00) |
1 (1.00) |
P value = 1.27e-05 (Fisher's exact test), Q value = 0.0055
Table S1. Gene #1: 'NSD1 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 100 | 104 | 102 |
| NSD1 MUTATED | 22 | 9 | 2 |
| NSD1 WILD-TYPE | 78 | 95 | 100 |
Figure S1. Get High-res Image Gene #1: 'NSD1 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'
P value = 0.000411 (Fisher's exact test), Q value = 0.17
Table S2. Gene #1: 'NSD1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 93 | 89 |
| NSD1 MUTATED | 23 | 3 | 7 |
| NSD1 WILD-TYPE | 94 | 90 | 82 |
Figure S2. Get High-res Image Gene #1: 'NSD1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'
P value = 6.41e-06 (Fisher's exact test), Q value = 0.0028
Table S3. Gene #1: 'NSD1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 97 | 84 | 118 |
| NSD1 MUTATED | 3 | 4 | 26 |
| NSD1 WILD-TYPE | 94 | 80 | 92 |
Figure S3. Get High-res Image Gene #1: 'NSD1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'
P value = 8.17e-05 (Chi-square test), Q value = 0.035
Table S4. Gene #4: 'HRAS MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
|---|---|---|---|---|---|---|---|---|
| ALL | 70 | 47 | 63 | 26 | 58 | 17 | 6 | 15 |
| HRAS MUTATED | 0 | 0 | 9 | 0 | 1 | 0 | 0 | 0 |
| HRAS WILD-TYPE | 70 | 47 | 54 | 26 | 57 | 17 | 6 | 15 |
Figure S4. Get High-res Image Gene #4: 'HRAS MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'
P value = 1.7e-12 (Chi-square test), Q value = 7.4e-10
Table S5. Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
|---|---|---|---|---|---|---|---|---|
| ALL | 70 | 47 | 63 | 26 | 58 | 17 | 6 | 15 |
| TP53 MUTATED | 59 | 36 | 20 | 14 | 47 | 16 | 6 | 14 |
| TP53 WILD-TYPE | 11 | 11 | 43 | 12 | 11 | 1 | 0 | 1 |
Figure S5. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'
P value = 0.000562 (Fisher's exact test), Q value = 0.24
Table S6. Gene #7: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 100 | 104 | 102 |
| NOTCH1 MUTATED | 18 | 9 | 30 |
| NOTCH1 WILD-TYPE | 82 | 95 | 72 |
Figure S6. Get High-res Image Gene #7: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'
P value = 0.000428 (Fisher's exact test), Q value = 0.18
Table S7. Gene #7: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 93 | 89 |
| NOTCH1 MUTATED | 10 | 22 | 25 |
| NOTCH1 WILD-TYPE | 107 | 71 | 64 |
Figure S7. Get High-res Image Gene #7: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'
P value = 2.54e-06 (Fisher's exact test), Q value = 0.0011
Table S8. Gene #7: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 97 | 84 | 118 |
| NOTCH1 MUTATED | 20 | 29 | 8 |
| NOTCH1 WILD-TYPE | 77 | 55 | 110 |
Figure S8. Get High-res Image Gene #7: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.000112 (Fisher's exact test), Q value = 0.048
Table S9. Gene #7: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 89 | 119 | 96 |
| NOTCH1 MUTATED | 26 | 9 | 21 |
| NOTCH1 WILD-TYPE | 63 | 110 | 75 |
Figure S9. Get High-res Image Gene #7: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'
P value = 1.62e-05 (Chi-square test), Q value = 0.0069
Table S10. Gene #9: 'CASP8 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
|---|---|---|---|---|---|---|---|---|
| ALL | 70 | 47 | 63 | 26 | 58 | 17 | 6 | 15 |
| CASP8 MUTATED | 1 | 0 | 16 | 3 | 4 | 1 | 1 | 0 |
| CASP8 WILD-TYPE | 69 | 47 | 47 | 23 | 54 | 16 | 5 | 15 |
Figure S10. Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'
P value = 0.000335 (Fisher's exact test), Q value = 0.14
Table S11. Gene #9: 'CASP8 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 100 | 104 | 102 |
| CASP8 MUTATED | 11 | 1 | 15 |
| CASP8 WILD-TYPE | 89 | 103 | 87 |
Figure S11. Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'
P value = 3e-07 (Fisher's exact test), Q value = 0.00013
Table S12. Gene #9: 'CASP8 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 93 | 89 |
| CASP8 MUTATED | 1 | 5 | 19 |
| CASP8 WILD-TYPE | 116 | 88 | 70 |
Figure S12. Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'
P value = 5.28e-07 (Fisher's exact test), Q value = 0.00023
Table S13. Gene #9: 'CASP8 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 97 | 84 | 118 |
| CASP8 MUTATED | 6 | 18 | 1 |
| CASP8 WILD-TYPE | 91 | 66 | 117 |
Figure S13. Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.000302 (Fisher's exact test), Q value = 0.13
Table S14. Gene #9: 'CASP8 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 74 | 106 | 88 |
| CASP8 MUTATED | 14 | 2 | 8 |
| CASP8 WILD-TYPE | 60 | 104 | 80 |
Figure S14. Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'
P value = 0.000357 (Fisher's exact test), Q value = 0.15
Table S15. Gene #13: 'EPHA2 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 74 | 106 | 88 |
| EPHA2 MUTATED | 8 | 0 | 2 |
| EPHA2 WILD-TYPE | 66 | 106 | 86 |
Figure S15. Get High-res Image Gene #13: 'EPHA2 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'
P value = 1.35e-05 (Fisher's exact test), Q value = 0.0058
Table S16. Gene #24: 'CSMD3 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 117 | 93 | 89 |
| CSMD3 MUTATED | 43 | 9 | 18 |
| CSMD3 WILD-TYPE | 74 | 84 | 71 |
Figure S16. Get High-res Image Gene #24: 'CSMD3 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'
P value = 6.66e-07 (Fisher's exact test), Q value = 0.00029
Table S17. Gene #24: 'CSMD3 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 97 | 84 | 118 |
| CSMD3 MUTATED | 9 | 15 | 46 |
| CSMD3 WILD-TYPE | 88 | 69 | 72 |
Figure S17. Get High-res Image Gene #24: 'CSMD3 MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'
P value = 0.000542 (Fisher's exact test), Q value = 0.23
Table S18. Gene #24: 'CSMD3 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 89 | 119 | 96 |
| CSMD3 MUTATED | 22 | 38 | 10 |
| CSMD3 WILD-TYPE | 67 | 81 | 86 |
Figure S18. Get High-res Image Gene #24: 'CSMD3 MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'
P value = 0.000137 (Fisher's exact test), Q value = 0.059
Table S19. Gene #24: 'CSMD3 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 74 | 106 | 88 |
| CSMD3 MUTATED | 16 | 34 | 7 |
| CSMD3 WILD-TYPE | 58 | 72 | 81 |
Figure S19. Get High-res Image Gene #24: 'CSMD3 MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'
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Mutation data file = HNSC-TP.mutsig.cluster.txt
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Molecular subtypes file = HNSC-TP.transferedmergedcluster.txt
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Number of patients = 306
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Number of significantly mutated genes = 45
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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 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 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 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.