This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.
Testing the association between copy number variation 78 arm-level results and 8 molecular subtypes across 306 patients, 112 significant findings detected with Q value < 0.25.
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1q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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2p gain cnv correlated to 'CN_CNMF'.
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5p gain cnv correlated to 'CN_CNMF'.
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6p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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6q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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7p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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7q gain cnv correlated to 'CN_CNMF'.
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8p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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8q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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10p gain cnv correlated to 'CN_CNMF'.
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10q gain cnv correlated to 'CN_CNMF'.
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13q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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18p gain cnv correlated to 'METHLYATION_CNMF'.
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20p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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20q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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1p loss cnv correlated to 'CN_CNMF'.
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3p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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3q loss cnv correlated to 'CN_CNMF'.
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4p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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4q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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5p loss cnv correlated to 'CN_CNMF'.
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5q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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7q loss cnv correlated to 'CN_CNMF'.
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8p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
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9p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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9q loss cnv correlated to 'CN_CNMF'.
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10p loss cnv correlated to 'CN_CNMF'.
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10q loss cnv correlated to 'CN_CNMF'.
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11p loss cnv correlated to 'METHLYATION_CNMF'.
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11q loss cnv correlated to 'CN_CNMF'.
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12p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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14q loss cnv correlated to 'CN_CNMF'.
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15q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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16p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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16q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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17p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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17q loss cnv correlated to 'CN_CNMF'.
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18q loss cnv correlated to 'CN_CNMF'.
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19p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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19q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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20p loss cnv correlated to 'MRNASEQ_CNMF'.
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21q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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22q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
Molecular subtypes |
CN CNMF |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
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nCNV (%) | nWild-Type | Fisher's exact 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 | |
20q gain | 0 (0%) | 149 |
1.47e-24 (8.98e-22) |
7.34e-14 (4.44e-11) |
1.98e-08 (1.16e-05) |
1.23e-06 (0.000706) |
2.11e-09 (1.25e-06) |
2.63e-11 (1.56e-08) |
6.8e-05 (0.0364) |
1.39e-11 (8.32e-09) |
4q loss | 0 (0%) | 253 |
3.37e-14 (2.04e-11) |
4.26e-05 (0.0231) |
0.00341 (1.00) |
0.000371 (0.188) |
1.87e-06 (0.00107) |
0.000246 (0.127) |
9.24e-05 (0.0491) |
0.000452 (0.226) |
19p loss | 0 (0%) | 273 |
1.37e-11 (8.22e-09) |
4.4e-06 (0.00248) |
4.05e-06 (0.00229) |
0.000158 (0.0826) |
4.86e-08 (2.85e-05) |
4.21e-06 (0.00237) |
0.0188 (1.00) |
5e-05 (0.027) |
20p gain | 0 (0%) | 178 |
1.86e-17 (1.13e-14) |
5.66e-09 (3.33e-06) |
2.44e-07 (0.000142) |
0.000895 (0.434) |
2.71e-06 (0.00154) |
1.61e-06 (0.000924) |
0.00126 (0.595) |
9.62e-07 (0.000555) |
4p loss | 0 (0%) | 251 |
4.58e-12 (2.75e-09) |
0.000389 (0.197) |
0.00464 (1.00) |
0.000778 (0.381) |
3.22e-05 (0.0177) |
0.000232 (0.12) |
0.000193 (0.1) |
0.000418 (0.211) |
5q loss | 0 (0%) | 271 |
1.59e-12 (9.54e-10) |
2.47e-06 (0.00141) |
3.87e-05 (0.0211) |
0.00182 (0.842) |
7.98e-05 (0.0427) |
0.000173 (0.0901) |
0.000612 (0.301) |
7.43e-07 (0.00043) |
8q gain | 0 (0%) | 184 |
4.29e-10 (2.54e-07) |
3.99e-07 (0.000232) |
0.00634 (1.00) |
0.00132 (0.625) |
0.000314 (0.161) |
0.0289 (1.00) |
0.0003 (0.154) |
5.46e-05 (0.0295) |
16p loss | 0 (0%) | 277 |
2.1e-11 (1.25e-08) |
1.89e-05 (0.0105) |
0.000186 (0.0971) |
0.00104 (0.498) |
0.0055 (1.00) |
0.0261 (1.00) |
8.48e-06 (0.00474) |
8.07e-05 (0.043) |
19q loss | 0 (0%) | 283 |
2.73e-07 (0.000159) |
1.26e-05 (0.00702) |
0.000109 (0.0575) |
0.0135 (1.00) |
3.91e-06 (0.00221) |
8.88e-05 (0.0473) |
0.0559 (1.00) |
0.00222 (1.00) |
17p loss | 0 (0%) | 242 |
6.31e-12 (3.78e-09) |
8.72e-07 (0.000504) |
0.000595 (0.294) |
0.0021 (0.962) |
0.000245 (0.126) |
0.0034 (1.00) |
0.00109 (0.519) |
0.000205 (0.106) |
1q gain | 0 (0%) | 263 |
1.99e-07 (0.000116) |
0.000395 (0.2) |
0.00139 (0.652) |
0.0688 (1.00) |
0.00163 (0.759) |
0.00137 (0.643) |
0.000467 (0.233) |
0.00376 (1.00) |
6p gain | 0 (0%) | 279 |
3.37e-05 (0.0185) |
5.54e-05 (0.0298) |
0.00808 (1.00) |
0.0195 (1.00) |
0.00972 (1.00) |
0.0221 (1.00) |
9.29e-05 (0.0492) |
0.00128 (0.605) |
6q gain | 0 (0%) | 284 |
9.53e-05 (0.0504) |
0.000353 (0.179) |
0.0399 (1.00) |
0.0415 (1.00) |
0.057 (1.00) |
0.0722 (1.00) |
8.06e-05 (0.043) |
0.00524 (1.00) |
12p loss | 0 (0%) | 285 |
4.38e-05 (0.0237) |
0.000447 (0.225) |
0.00234 (1.00) |
0.00436 (1.00) |
0.00286 (1.00) |
0.0117 (1.00) |
0.141 (1.00) |
0.000323 (0.165) |
15q loss | 0 (0%) | 281 |
1.45e-07 (8.49e-05) |
2.34e-05 (0.013) |
0.0183 (1.00) |
0.0178 (1.00) |
0.0014 (0.656) |
0.00423 (1.00) |
0.00234 (1.00) |
6.2e-05 (0.0333) |
22q loss | 0 (0%) | 266 |
7.2e-15 (4.37e-12) |
1.9e-06 (0.00109) |
0.00199 (0.919) |
0.0207 (1.00) |
3.76e-05 (0.0206) |
0.000558 (0.277) |
0.00731 (1.00) |
0.0101 (1.00) |
7p gain | 0 (0%) | 210 |
7.19e-14 (4.35e-11) |
3.79e-05 (0.0207) |
0.107 (1.00) |
0.229 (1.00) |
0.0749 (1.00) |
0.0183 (1.00) |
0.00438 (1.00) |
0.000599 (0.296) |
8p gain | 0 (0%) | 216 |
2.76e-10 (1.64e-07) |
0.00046 (0.23) |
0.276 (1.00) |
0.00862 (1.00) |
0.00249 (1.00) |
0.491 (1.00) |
0.0116 (1.00) |
0.0379 (1.00) |
13q gain | 0 (0%) | 241 |
1.2e-06 (0.000693) |
0.000325 (0.165) |
0.114 (1.00) |
0.975 (1.00) |
0.0226 (1.00) |
0.0093 (1.00) |
0.0289 (1.00) |
0.0165 (1.00) |
3p loss | 0 (0%) | 281 |
5.51e-07 (0.000319) |
0.000954 (0.46) |
0.000874 (0.426) |
0.0102 (1.00) |
0.00104 (0.498) |
0.0106 (1.00) |
0.0188 (1.00) |
0.000146 (0.0764) |
8p loss | 0 (0%) | 275 |
5.9e-06 (0.00332) |
0.0246 (1.00) |
0.0597 (1.00) |
0.281 (1.00) |
0.0248 (1.00) |
0.0564 (1.00) |
2.84e-05 (0.0157) |
0.00487 (1.00) |
9p loss | 0 (0%) | 255 |
1.45e-11 (8.65e-09) |
2.64e-05 (0.0146) |
0.00233 (1.00) |
0.0106 (1.00) |
0.00156 (0.726) |
0.00117 (0.558) |
0.0553 (1.00) |
0.0351 (1.00) |
16q loss | 0 (0%) | 274 |
3.96e-11 (2.35e-08) |
3.51e-06 (0.00199) |
0.0062 (1.00) |
0.003 (1.00) |
0.0126 (1.00) |
0.16 (1.00) |
0.00427 (1.00) |
0.00341 (1.00) |
21q loss | 0 (0%) | 244 |
4.08e-09 (2.4e-06) |
6.83e-06 (0.00383) |
0.0492 (1.00) |
0.00568 (1.00) |
0.178 (1.00) |
0.0489 (1.00) |
0.259 (1.00) |
0.326 (1.00) |
2p gain | 0 (0%) | 282 |
0.000434 (0.218) |
0.00148 (0.693) |
0.0406 (1.00) |
0.0199 (1.00) |
0.0325 (1.00) |
0.00938 (1.00) |
0.000993 (0.478) |
0.00214 (0.98) |
5p gain | 0 (0%) | 264 |
1.92e-06 (0.0011) |
0.00442 (1.00) |
0.00536 (1.00) |
0.0207 (1.00) |
0.101 (1.00) |
0.0226 (1.00) |
0.00688 (1.00) |
0.00469 (1.00) |
7q gain | 0 (0%) | 229 |
2.11e-13 (1.27e-10) |
0.000562 (0.279) |
0.376 (1.00) |
0.494 (1.00) |
0.494 (1.00) |
0.481 (1.00) |
0.133 (1.00) |
0.045 (1.00) |
10p gain | 0 (0%) | 261 |
3.76e-09 (2.22e-06) |
0.00204 (0.94) |
0.000804 (0.392) |
0.000773 (0.379) |
0.024 (1.00) |
0.00111 (0.529) |
0.173 (1.00) |
0.0281 (1.00) |
10q gain | 0 (0%) | 280 |
2.63e-05 (0.0145) |
0.0481 (1.00) |
0.224 (1.00) |
0.237 (1.00) |
0.575 (1.00) |
0.141 (1.00) |
0.115 (1.00) |
0.173 (1.00) |
18p gain | 0 (0%) | 281 |
0.00377 (1.00) |
3.87e-05 (0.0211) |
0.067 (1.00) |
0.577 (1.00) |
0.0404 (1.00) |
0.243 (1.00) |
0.455 (1.00) |
0.175 (1.00) |
1p loss | 0 (0%) | 292 |
1.5e-05 (0.00833) |
0.0945 (1.00) |
0.0459 (1.00) |
0.0304 (1.00) |
0.122 (1.00) |
0.73 (1.00) |
0.682 (1.00) |
0.832 (1.00) |
3q loss | 0 (0%) | 292 |
5.76e-05 (0.031) |
0.0197 (1.00) |
0.0392 (1.00) |
0.143 (1.00) |
0.00743 (1.00) |
0.0612 (1.00) |
0.0154 (1.00) |
0.00401 (1.00) |
5p loss | 0 (0%) | 289 |
2.12e-05 (0.0117) |
0.00392 (1.00) |
0.0182 (1.00) |
0.0363 (1.00) |
0.0107 (1.00) |
0.046 (1.00) |
0.0793 (1.00) |
0.00761 (1.00) |
7q loss | 0 (0%) | 293 |
0.0002 (0.104) |
0.0414 (1.00) |
0.321 (1.00) |
1 (1.00) |
0.0144 (1.00) |
0.22 (1.00) |
0.00528 (1.00) |
0.212 (1.00) |
9q loss | 0 (0%) | 281 |
3.06e-05 (0.0168) |
0.00415 (1.00) |
0.0237 (1.00) |
0.0463 (1.00) |
0.032 (1.00) |
0.118 (1.00) |
0.0933 (1.00) |
0.193 (1.00) |
10p loss | 0 (0%) | 289 |
0.000261 (0.134) |
0.00808 (1.00) |
0.0731 (1.00) |
0.115 (1.00) |
0.016 (1.00) |
0.363 (1.00) |
0.0305 (1.00) |
0.0469 (1.00) |
10q loss | 0 (0%) | 290 |
0.000133 (0.0702) |
0.00307 (1.00) |
0.106 (1.00) |
0.256 (1.00) |
0.0115 (1.00) |
0.046 (1.00) |
0.0175 (1.00) |
0.00234 (1.00) |
11p loss | 0 (0%) | 288 |
0.000611 (0.301) |
0.000168 (0.0878) |
0.745 (1.00) |
0.171 (1.00) |
0.0518 (1.00) |
0.0326 (1.00) |
0.0437 (1.00) |
0.0469 (1.00) |
11q loss | 0 (0%) | 290 |
0.000269 (0.138) |
0.00892 (1.00) |
0.892 (1.00) |
0.892 (1.00) |
0.2 (1.00) |
0.416 (1.00) |
0.0656 (1.00) |
0.386 (1.00) |
14q loss | 0 (0%) | 278 |
8.18e-06 (0.00458) |
0.000905 (0.438) |
0.00142 (0.667) |
0.0183 (1.00) |
0.0214 (1.00) |
0.0175 (1.00) |
0.0095 (1.00) |
0.00254 (1.00) |
17q loss | 0 (0%) | 286 |
0.000103 (0.0542) |
0.0245 (1.00) |
0.0808 (1.00) |
0.0906 (1.00) |
0.0729 (1.00) |
0.0599 (1.00) |
0.0549 (1.00) |
0.0529 (1.00) |
18q loss | 0 (0%) | 254 |
2.74e-06 (0.00155) |
0.0206 (1.00) |
0.0212 (1.00) |
0.00674 (1.00) |
0.00777 (1.00) |
0.0651 (1.00) |
0.0619 (1.00) |
0.0561 (1.00) |
20p loss | 0 (0%) | 297 |
0.00451 (1.00) |
0.017 (1.00) |
0.000492 (0.245) |
0.00196 (0.903) |
0.0695 (1.00) |
0.812 (1.00) |
0.177 (1.00) |
1 (1.00) |
1p gain | 0 (0%) | 291 |
0.00429 (1.00) |
0.507 (1.00) |
0.269 (1.00) |
0.588 (1.00) |
0.0806 (1.00) |
0.153 (1.00) |
0.0175 (1.00) |
0.109 (1.00) |
2q gain | 0 (0%) | 283 |
0.00439 (1.00) |
0.0108 (1.00) |
0.00102 (0.49) |
0.0033 (1.00) |
0.0623 (1.00) |
0.0428 (1.00) |
0.00942 (1.00) |
0.0198 (1.00) |
3p gain | 0 (0%) | 295 |
0.248 (1.00) |
0.086 (1.00) |
0.629 (1.00) |
0.773 (1.00) |
0.547 (1.00) |
0.427 (1.00) |
0.887 (1.00) |
0.431 (1.00) |
3q gain | 0 (0%) | 277 |
0.000666 (0.327) |
0.174 (1.00) |
0.363 (1.00) |
0.249 (1.00) |
0.643 (1.00) |
0.0588 (1.00) |
0.193 (1.00) |
0.134 (1.00) |
4p gain | 0 (0%) | 301 |
0.0903 (1.00) |
0.286 (1.00) |
0.332 (1.00) |
0.346 (1.00) |
0.872 (1.00) |
1 (1.00) |
0.789 (1.00) |
0.346 (1.00) |
5q gain | 0 (0%) | 296 |
0.26 (1.00) |
0.95 (1.00) |
0.826 (1.00) |
0.516 (1.00) |
0.651 (1.00) |
0.464 (1.00) |
0.266 (1.00) |
0.554 (1.00) |
9p gain | 0 (0%) | 284 |
0.0258 (1.00) |
0.139 (1.00) |
0.243 (1.00) |
0.333 (1.00) |
0.466 (1.00) |
0.204 (1.00) |
0.577 (1.00) |
0.0373 (1.00) |
9q gain | 0 (0%) | 277 |
0.00579 (1.00) |
0.113 (1.00) |
0.379 (1.00) |
0.7 (1.00) |
0.702 (1.00) |
0.867 (1.00) |
0.218 (1.00) |
0.0741 (1.00) |
11p gain | 0 (0%) | 294 |
0.845 (1.00) |
0.115 (1.00) |
0.741 (1.00) |
0.161 (1.00) |
0.0561 (1.00) |
0.203 (1.00) |
0.601 (1.00) |
0.199 (1.00) |
11q gain | 0 (0%) | 286 |
0.137 (1.00) |
0.0338 (1.00) |
0.937 (1.00) |
0.721 (1.00) |
0.0872 (1.00) |
0.446 (1.00) |
0.0871 (1.00) |
0.0274 (1.00) |
12p gain | 0 (0%) | 271 |
0.00368 (1.00) |
0.178 (1.00) |
0.0645 (1.00) |
0.378 (1.00) |
0.0363 (1.00) |
0.583 (1.00) |
0.00174 (0.807) |
0.0735 (1.00) |
12q gain | 0 (0%) | 278 |
0.329 (1.00) |
0.168 (1.00) |
0.435 (1.00) |
0.483 (1.00) |
0.0923 (1.00) |
0.381 (1.00) |
0.00956 (1.00) |
0.0725 (1.00) |
14q gain | 0 (0%) | 301 |
0.0438 (1.00) |
0.283 (1.00) |
0.0569 (1.00) |
0.104 (1.00) |
||||
15q gain | 0 (0%) | 296 |
0.0326 (1.00) |
0.543 (1.00) |
0.0774 (1.00) |
0.0101 (1.00) |
0.0296 (1.00) |
0.0574 (1.00) |
0.0346 (1.00) |
0.0147 (1.00) |
16p gain | 0 (0%) | 293 |
0.0238 (1.00) |
0.116 (1.00) |
0.29 (1.00) |
0.319 (1.00) |
0.98 (1.00) |
0.0112 (1.00) |
0.755 (1.00) |
0.695 (1.00) |
16q gain | 0 (0%) | 294 |
0.117 (1.00) |
0.826 (1.00) |
0.848 (1.00) |
0.493 (1.00) |
0.859 (1.00) |
0.121 (1.00) |
0.601 (1.00) |
0.901 (1.00) |
17p gain | 0 (0%) | 299 |
0.0216 (1.00) |
0.457 (1.00) |
0.756 (1.00) |
0.868 (1.00) |
0.3 (1.00) |
0.875 (1.00) |
0.181 (1.00) |
0.302 (1.00) |
17q gain | 0 (0%) | 291 |
0.00983 (1.00) |
0.664 (1.00) |
0.314 (1.00) |
0.185 (1.00) |
0.0404 (1.00) |
0.701 (1.00) |
0.126 (1.00) |
0.301 (1.00) |
18q gain | 0 (0%) | 292 |
0.221 (1.00) |
0.0615 (1.00) |
0.141 (1.00) |
0.486 (1.00) |
0.00679 (1.00) |
0.119 (1.00) |
0.126 (1.00) |
0.282 (1.00) |
19p gain | 0 (0%) | 293 |
0.261 (1.00) |
0.0219 (1.00) |
0.917 (1.00) |
0.313 (1.00) |
0.841 (1.00) |
1 (1.00) |
0.482 (1.00) |
0.597 (1.00) |
19q gain | 0 (0%) | 274 |
0.431 (1.00) |
0.382 (1.00) |
0.727 (1.00) |
0.246 (1.00) |
0.524 (1.00) |
0.534 (1.00) |
0.177 (1.00) |
0.244 (1.00) |
21q gain | 0 (0%) | 303 |
0.212 (1.00) |
0.86 (1.00) |
0.3 (1.00) |
0.259 (1.00) |
0.26 (1.00) |
0.256 (1.00) |
||
22q gain | 0 (0%) | 300 |
0.0244 (1.00) |
0.181 (1.00) |
0.747 (1.00) |
0.146 (1.00) |
0.451 (1.00) |
0.768 (1.00) |
0.177 (1.00) |
0.164 (1.00) |
Xq gain | 0 (0%) | 301 |
0.345 (1.00) |
0.223 (1.00) |
0.114 (1.00) |
0.104 (1.00) |
||||
1q loss | 0 (0%) | 302 |
0.154 (1.00) |
1 (1.00) |
0.147 (1.00) |
0.793 (1.00) |
1 (1.00) |
0.789 (1.00) |
||
2p loss | 0 (0%) | 300 |
0.0268 (1.00) |
0.4 (1.00) |
0.308 (1.00) |
0.231 (1.00) |
0.451 (1.00) |
0.334 (1.00) |
0.28 (1.00) |
0.256 (1.00) |
2q loss | 0 (0%) | 301 |
0.0438 (1.00) |
0.68 (1.00) |
0.563 (1.00) |
0.43 (1.00) |
0.472 (1.00) |
0.0785 (1.00) |
0.578 (1.00) |
0.56 (1.00) |
6p loss | 0 (0%) | 291 |
0.0368 (1.00) |
0.29 (1.00) |
0.157 (1.00) |
0.18 (1.00) |
0.228 (1.00) |
0.482 (1.00) |
0.92 (1.00) |
0.17 (1.00) |
6q loss | 0 (0%) | 287 |
0.0114 (1.00) |
0.107 (1.00) |
0.00564 (1.00) |
0.0727 (1.00) |
0.553 (1.00) |
0.813 (1.00) |
0.514 (1.00) |
0.318 (1.00) |
7p loss | 0 (0%) | 302 |
0.118 (1.00) |
0.344 (1.00) |
0.615 (1.00) |
0.403 (1.00) |
0.286 (1.00) |
|||
8q loss | 0 (0%) | 298 |
0.0115 (1.00) |
0.268 (1.00) |
0.756 (1.00) |
0.392 (1.00) |
0.338 (1.00) |
0.13 (1.00) |
0.28 (1.00) |
0.0876 (1.00) |
12q loss | 0 (0%) | 294 |
0.00807 (1.00) |
0.00679 (1.00) |
0.0606 (1.00) |
0.294 (1.00) |
0.117 (1.00) |
0.165 (1.00) |
0.832 (1.00) |
0.00813 (1.00) |
13q loss | 0 (0%) | 295 |
0.000884 (0.43) |
0.106 (1.00) |
0.221 (1.00) |
0.236 (1.00) |
0.386 (1.00) |
0.536 (1.00) |
0.263 (1.00) |
0.475 (1.00) |
18p loss | 0 (0%) | 266 |
0.000932 (0.45) |
0.013 (1.00) |
0.0366 (1.00) |
0.0768 (1.00) |
0.0247 (1.00) |
0.591 (1.00) |
0.0479 (1.00) |
0.175 (1.00) |
Xq loss | 0 (0%) | 292 |
0.0116 (1.00) |
0.11 (1.00) |
0.527 (1.00) |
0.298 (1.00) |
0.164 (1.00) |
0.14 (1.00) |
0.00451 (1.00) |
0.0502 (1.00) |
P value = 1.99e-07 (Fisher's exact test), Q value = 0.00012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
1Q GAIN CNV | 4 | 6 | 3 | 30 |
1Q GAIN WILD-TYPE | 133 | 22 | 25 | 83 |
P value = 0.000395 (Fisher's exact test), Q value = 0.2
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
1Q GAIN CNV | 2 | 14 | 2 | 19 |
1Q GAIN WILD-TYPE | 35 | 66 | 63 | 57 |
P value = 0.000467 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 67 | 103 |
1Q GAIN CNV | 5 | 4 | 26 |
1Q GAIN WILD-TYPE | 62 | 63 | 77 |
P value = 0.000434 (Fisher's exact test), Q value = 0.22
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
2P GAIN CNV | 2 | 4 | 4 | 14 |
2P GAIN WILD-TYPE | 135 | 24 | 24 | 99 |
P value = 1.92e-06 (Fisher's exact test), Q value = 0.0011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
5P GAIN CNV | 6 | 3 | 2 | 31 |
5P GAIN WILD-TYPE | 131 | 25 | 26 | 82 |
P value = 3.37e-05 (Fisher's exact test), Q value = 0.018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
6P GAIN CNV | 2 | 2 | 3 | 20 |
6P GAIN WILD-TYPE | 135 | 26 | 25 | 93 |
P value = 5.54e-05 (Fisher's exact test), Q value = 0.03
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
6P GAIN CNV | 0 | 8 | 0 | 14 |
6P GAIN WILD-TYPE | 37 | 72 | 65 | 62 |
P value = 9.29e-05 (Fisher's exact test), Q value = 0.049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 67 | 103 |
6P GAIN CNV | 1 | 2 | 19 |
6P GAIN WILD-TYPE | 66 | 65 | 84 |
P value = 9.53e-05 (Fisher's exact test), Q value = 0.05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
6Q GAIN CNV | 2 | 0 | 3 | 17 |
6Q GAIN WILD-TYPE | 135 | 28 | 25 | 96 |
P value = 0.000353 (Fisher's exact test), Q value = 0.18
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
6Q GAIN CNV | 0 | 6 | 0 | 12 |
6Q GAIN WILD-TYPE | 37 | 74 | 65 | 64 |
P value = 8.06e-05 (Fisher's exact test), Q value = 0.043
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 67 | 103 |
6Q GAIN CNV | 0 | 2 | 16 |
6Q GAIN WILD-TYPE | 67 | 65 | 87 |
P value = 7.19e-14 (Fisher's exact test), Q value = 4.4e-11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
7P GAIN CNV | 21 | 25 | 6 | 44 |
7P GAIN WILD-TYPE | 116 | 3 | 22 | 69 |
P value = 3.79e-05 (Fisher's exact test), Q value = 0.021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
7P GAIN CNV | 12 | 30 | 6 | 32 |
7P GAIN WILD-TYPE | 25 | 50 | 59 | 44 |
P value = 2.11e-13 (Fisher's exact test), Q value = 1.3e-10
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
7Q GAIN CNV | 20 | 25 | 5 | 27 |
7Q GAIN WILD-TYPE | 117 | 3 | 23 | 86 |
P value = 2.76e-10 (Fisher's exact test), Q value = 1.6e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
8P GAIN CNV | 29 | 11 | 24 | 26 |
8P GAIN WILD-TYPE | 108 | 17 | 4 | 87 |
P value = 0.00046 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
8P GAIN CNV | 13 | 30 | 6 | 21 |
8P GAIN WILD-TYPE | 24 | 50 | 59 | 55 |
P value = 4.29e-10 (Fisher's exact test), Q value = 2.5e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
8Q GAIN CNV | 36 | 12 | 26 | 48 |
8Q GAIN WILD-TYPE | 101 | 16 | 2 | 65 |
P value = 3.99e-07 (Fisher's exact test), Q value = 0.00023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
8Q GAIN CNV | 13 | 39 | 7 | 38 |
8Q GAIN WILD-TYPE | 24 | 41 | 58 | 38 |
P value = 0.000314 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 61 | 69 | 97 | 57 |
8Q GAIN CNV | 31 | 14 | 40 | 30 |
8Q GAIN WILD-TYPE | 30 | 55 | 57 | 27 |
P value = 3e-04 (Fisher's exact test), Q value = 0.15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 67 | 103 |
8Q GAIN CNV | 26 | 13 | 51 |
8Q GAIN WILD-TYPE | 41 | 54 | 52 |
P value = 5.46e-05 (Fisher's exact test), Q value = 0.029
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 83 | 96 |
8Q GAIN CNV | 32 | 17 | 41 |
8Q GAIN WILD-TYPE | 26 | 66 | 55 |
P value = 3.76e-09 (Fisher's exact test), Q value = 2.2e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
10P GAIN CNV | 3 | 7 | 3 | 32 |
10P GAIN WILD-TYPE | 134 | 21 | 25 | 81 |
P value = 2.63e-05 (Fisher's exact test), Q value = 0.015
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
10Q GAIN CNV | 2 | 1 | 3 | 20 |
10Q GAIN WILD-TYPE | 135 | 27 | 25 | 93 |
P value = 1.2e-06 (Fisher's exact test), Q value = 0.00069
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
13Q GAIN CNV | 16 | 15 | 2 | 32 |
13Q GAIN WILD-TYPE | 121 | 13 | 26 | 81 |
P value = 0.000325 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
13Q GAIN CNV | 7 | 15 | 5 | 28 |
13Q GAIN WILD-TYPE | 30 | 65 | 60 | 48 |
P value = 3.87e-05 (Fisher's exact test), Q value = 0.021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
18P GAIN CNV | 0 | 5 | 0 | 14 |
18P GAIN WILD-TYPE | 37 | 75 | 65 | 62 |
P value = 1.86e-17 (Fisher's exact test), Q value = 1.1e-14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
20P GAIN CNV | 23 | 25 | 15 | 65 |
20P GAIN WILD-TYPE | 114 | 3 | 13 | 48 |
P value = 5.66e-09 (Fisher's exact test), Q value = 3.3e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
20P GAIN CNV | 21 | 30 | 8 | 46 |
20P GAIN WILD-TYPE | 16 | 50 | 57 | 30 |
P value = 2.44e-07 (Chi-square test), Q value = 0.00014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 45 | 41 | 35 | 37 | 50 |
20P GAIN CNV | 13 | 7 | 6 | 20 | 33 |
20P GAIN WILD-TYPE | 32 | 34 | 29 | 17 | 17 |
P value = 2.71e-06 (Fisher's exact test), Q value = 0.0015
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 61 | 69 | 97 | 57 |
20P GAIN CNV | 22 | 17 | 37 | 40 |
20P GAIN WILD-TYPE | 39 | 52 | 60 | 17 |
P value = 1.61e-06 (Fisher's exact test), Q value = 0.00092
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 71 | 89 | 124 |
20P GAIN CNV | 46 | 22 | 48 |
20P GAIN WILD-TYPE | 25 | 67 | 76 |
P value = 9.62e-07 (Fisher's exact test), Q value = 0.00056
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 83 | 96 |
20P GAIN CNV | 38 | 18 | 37 |
20P GAIN WILD-TYPE | 20 | 65 | 59 |
P value = 1.47e-24 (Fisher's exact test), Q value = 9e-22
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
20Q GAIN CNV | 27 | 26 | 18 | 86 |
20Q GAIN WILD-TYPE | 110 | 2 | 10 | 27 |
P value = 7.34e-14 (Fisher's exact test), Q value = 4.4e-11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
20Q GAIN CNV | 21 | 37 | 12 | 63 |
20Q GAIN WILD-TYPE | 16 | 43 | 53 | 13 |
P value = 1.98e-08 (Chi-square test), Q value = 1.2e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 45 | 41 | 35 | 37 | 50 |
20Q GAIN CNV | 15 | 11 | 12 | 22 | 42 |
20Q GAIN WILD-TYPE | 30 | 30 | 23 | 15 | 8 |
P value = 1.23e-06 (Fisher's exact test), Q value = 0.00071
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 42 | 42 | 55 | 69 |
20Q GAIN CNV | 10 | 22 | 42 | 28 |
20Q GAIN WILD-TYPE | 32 | 20 | 13 | 41 |
P value = 2.11e-09 (Fisher's exact test), Q value = 1.2e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 61 | 69 | 97 | 57 |
20Q GAIN CNV | 25 | 22 | 49 | 49 |
20Q GAIN WILD-TYPE | 36 | 47 | 48 | 8 |
P value = 2.63e-11 (Fisher's exact test), Q value = 1.6e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 71 | 89 | 124 |
20Q GAIN CNV | 60 | 29 | 56 |
20Q GAIN WILD-TYPE | 11 | 60 | 68 |
P value = 6.8e-05 (Fisher's exact test), Q value = 0.036
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 67 | 103 |
20Q GAIN CNV | 28 | 24 | 69 |
20Q GAIN WILD-TYPE | 39 | 43 | 34 |
P value = 1.39e-11 (Fisher's exact test), Q value = 8.3e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 83 | 96 |
20Q GAIN CNV | 50 | 23 | 48 |
20Q GAIN WILD-TYPE | 8 | 60 | 48 |
P value = 1.5e-05 (Fisher's exact test), Q value = 0.0083
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
1P LOSS CNV | 0 | 0 | 0 | 14 |
1P LOSS WILD-TYPE | 137 | 28 | 28 | 99 |
P value = 5.51e-07 (Fisher's exact test), Q value = 0.00032
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
3P LOSS CNV | 1 | 1 | 1 | 22 |
3P LOSS WILD-TYPE | 136 | 27 | 27 | 91 |
P value = 0.000146 (Fisher's exact test), Q value = 0.076
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 83 | 96 |
3P LOSS CNV | 10 | 0 | 8 |
3P LOSS WILD-TYPE | 48 | 83 | 88 |
P value = 5.76e-05 (Fisher's exact test), Q value = 0.031
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
3Q LOSS CNV | 0 | 1 | 0 | 13 |
3Q LOSS WILD-TYPE | 137 | 27 | 28 | 100 |
P value = 4.58e-12 (Fisher's exact test), Q value = 2.8e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
4P LOSS CNV | 6 | 4 | 1 | 44 |
4P LOSS WILD-TYPE | 131 | 24 | 27 | 69 |
P value = 0.000389 (Fisher's exact test), Q value = 0.2
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
4P LOSS CNV | 1 | 16 | 6 | 23 |
4P LOSS WILD-TYPE | 36 | 64 | 59 | 53 |
P value = 3.22e-05 (Fisher's exact test), Q value = 0.018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 61 | 69 | 97 | 57 |
4P LOSS CNV | 6 | 4 | 20 | 21 |
4P LOSS WILD-TYPE | 55 | 65 | 77 | 36 |
P value = 0.000232 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 71 | 89 | 124 |
4P LOSS CNV | 24 | 8 | 19 |
4P LOSS WILD-TYPE | 47 | 81 | 105 |
P value = 0.000193 (Fisher's exact test), Q value = 0.1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 67 | 103 |
4P LOSS CNV | 5 | 7 | 31 |
4P LOSS WILD-TYPE | 62 | 60 | 72 |
P value = 0.000418 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 83 | 96 |
4P LOSS CNV | 21 | 9 | 13 |
4P LOSS WILD-TYPE | 37 | 74 | 83 |
P value = 3.37e-14 (Fisher's exact test), Q value = 2e-11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
4Q LOSS CNV | 4 | 3 | 1 | 45 |
4Q LOSS WILD-TYPE | 133 | 25 | 27 | 68 |
P value = 4.26e-05 (Fisher's exact test), Q value = 0.023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
4Q LOSS CNV | 1 | 18 | 4 | 23 |
4Q LOSS WILD-TYPE | 36 | 62 | 61 | 53 |
P value = 0.000371 (Fisher's exact test), Q value = 0.19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 42 | 42 | 55 | 69 |
4Q LOSS CNV | 1 | 6 | 18 | 8 |
4Q LOSS WILD-TYPE | 41 | 36 | 37 | 61 |
P value = 1.87e-06 (Fisher's exact test), Q value = 0.0011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 61 | 69 | 97 | 57 |
4Q LOSS CNV | 5 | 3 | 18 | 22 |
4Q LOSS WILD-TYPE | 56 | 66 | 79 | 35 |
P value = 0.000246 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 71 | 89 | 124 |
4Q LOSS CNV | 23 | 7 | 18 |
4Q LOSS WILD-TYPE | 48 | 82 | 106 |
P value = 9.24e-05 (Fisher's exact test), Q value = 0.049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 67 | 103 |
4Q LOSS CNV | 5 | 6 | 31 |
4Q LOSS WILD-TYPE | 62 | 61 | 72 |
P value = 0.000452 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 83 | 96 |
4Q LOSS CNV | 20 | 7 | 15 |
4Q LOSS WILD-TYPE | 38 | 76 | 81 |
P value = 2.12e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
5P LOSS CNV | 0 | 1 | 1 | 15 |
5P LOSS WILD-TYPE | 137 | 27 | 27 | 98 |
P value = 1.59e-12 (Fisher's exact test), Q value = 9.5e-10
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
5Q LOSS CNV | 0 | 2 | 1 | 32 |
5Q LOSS WILD-TYPE | 137 | 26 | 27 | 81 |
P value = 2.47e-06 (Fisher's exact test), Q value = 0.0014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
5Q LOSS CNV | 0 | 11 | 1 | 20 |
5Q LOSS WILD-TYPE | 37 | 69 | 64 | 56 |
P value = 3.87e-05 (Chi-square test), Q value = 0.021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 45 | 41 | 35 | 37 | 50 |
5Q LOSS CNV | 3 | 0 | 2 | 3 | 15 |
5Q LOSS WILD-TYPE | 42 | 41 | 33 | 34 | 35 |
P value = 7.98e-05 (Fisher's exact test), Q value = 0.043
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 61 | 69 | 97 | 57 |
5Q LOSS CNV | 3 | 2 | 11 | 16 |
5Q LOSS WILD-TYPE | 58 | 67 | 86 | 41 |
P value = 0.000173 (Fisher's exact test), Q value = 0.09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 71 | 89 | 124 |
5Q LOSS CNV | 18 | 4 | 10 |
5Q LOSS WILD-TYPE | 53 | 85 | 114 |
P value = 7.43e-07 (Fisher's exact test), Q value = 0.00043
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 83 | 96 |
5Q LOSS CNV | 19 | 2 | 9 |
5Q LOSS WILD-TYPE | 39 | 81 | 87 |
P value = 2e-04 (Fisher's exact test), Q value = 0.1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
7Q LOSS CNV | 0 | 0 | 1 | 12 |
7Q LOSS WILD-TYPE | 137 | 28 | 27 | 101 |
P value = 5.9e-06 (Fisher's exact test), Q value = 0.0033
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
8P LOSS CNV | 4 | 3 | 0 | 24 |
8P LOSS WILD-TYPE | 133 | 25 | 28 | 89 |
P value = 2.84e-05 (Fisher's exact test), Q value = 0.016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 67 | 103 |
8P LOSS CNV | 4 | 0 | 20 |
8P LOSS WILD-TYPE | 63 | 67 | 83 |
P value = 1.45e-11 (Fisher's exact test), Q value = 8.6e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
9P LOSS CNV | 4 | 3 | 3 | 41 |
9P LOSS WILD-TYPE | 133 | 25 | 25 | 72 |
P value = 2.64e-05 (Fisher's exact test), Q value = 0.015
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
9P LOSS CNV | 0 | 13 | 6 | 24 |
9P LOSS WILD-TYPE | 37 | 67 | 59 | 52 |
P value = 3.06e-05 (Fisher's exact test), Q value = 0.017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
9Q LOSS CNV | 2 | 1 | 2 | 20 |
9Q LOSS WILD-TYPE | 135 | 27 | 26 | 93 |
P value = 0.000261 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
10P LOSS CNV | 1 | 2 | 0 | 14 |
10P LOSS WILD-TYPE | 136 | 26 | 28 | 99 |
P value = 0.000133 (Fisher's exact test), Q value = 0.07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
10Q LOSS CNV | 0 | 3 | 1 | 12 |
10Q LOSS WILD-TYPE | 137 | 25 | 27 | 101 |
P value = 0.000168 (Fisher's exact test), Q value = 0.088
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
11P LOSS CNV | 0 | 2 | 0 | 11 |
11P LOSS WILD-TYPE | 37 | 78 | 65 | 65 |
P value = 0.000269 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
11Q LOSS CNV | 1 | 0 | 1 | 14 |
11Q LOSS WILD-TYPE | 136 | 28 | 27 | 99 |
P value = 4.38e-05 (Fisher's exact test), Q value = 0.024
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
12P LOSS CNV | 2 | 1 | 0 | 18 |
12P LOSS WILD-TYPE | 135 | 27 | 28 | 95 |
P value = 0.000447 (Fisher's exact test), Q value = 0.22
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
12P LOSS CNV | 0 | 2 | 2 | 13 |
12P LOSS WILD-TYPE | 37 | 78 | 63 | 63 |
P value = 0.000323 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 83 | 96 |
12P LOSS CNV | 11 | 3 | 2 |
12P LOSS WILD-TYPE | 47 | 80 | 94 |
P value = 8.18e-06 (Fisher's exact test), Q value = 0.0046
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
14Q LOSS CNV | 3 | 1 | 1 | 23 |
14Q LOSS WILD-TYPE | 134 | 27 | 27 | 90 |
P value = 1.45e-07 (Fisher's exact test), Q value = 8.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
15Q LOSS CNV | 0 | 2 | 2 | 21 |
15Q LOSS WILD-TYPE | 137 | 26 | 26 | 92 |
P value = 2.34e-05 (Fisher's exact test), Q value = 0.013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
15Q LOSS CNV | 0 | 7 | 0 | 15 |
15Q LOSS WILD-TYPE | 37 | 73 | 65 | 61 |
P value = 6.2e-05 (Fisher's exact test), Q value = 0.033
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 83 | 96 |
15Q LOSS CNV | 11 | 0 | 9 |
15Q LOSS WILD-TYPE | 47 | 83 | 87 |
P value = 2.1e-11 (Fisher's exact test), Q value = 1.3e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
16P LOSS CNV | 0 | 0 | 1 | 28 |
16P LOSS WILD-TYPE | 137 | 28 | 27 | 85 |
P value = 1.89e-05 (Fisher's exact test), Q value = 0.011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
16P LOSS CNV | 0 | 10 | 0 | 15 |
16P LOSS WILD-TYPE | 37 | 70 | 65 | 61 |
P value = 0.000186 (Chi-square test), Q value = 0.097
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 45 | 41 | 35 | 37 | 50 |
16P LOSS CNV | 2 | 0 | 1 | 1 | 11 |
16P LOSS WILD-TYPE | 43 | 41 | 34 | 36 | 39 |
P value = 8.48e-06 (Fisher's exact test), Q value = 0.0047
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 67 | 103 |
16P LOSS CNV | 1 | 1 | 20 |
16P LOSS WILD-TYPE | 66 | 66 | 83 |
P value = 8.07e-05 (Fisher's exact test), Q value = 0.043
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 83 | 96 |
16P LOSS CNV | 13 | 1 | 8 |
16P LOSS WILD-TYPE | 45 | 82 | 88 |
P value = 3.96e-11 (Fisher's exact test), Q value = 2.4e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
16Q LOSS CNV | 1 | 0 | 1 | 30 |
16Q LOSS WILD-TYPE | 136 | 28 | 27 | 83 |
P value = 3.51e-06 (Fisher's exact test), Q value = 0.002
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
16Q LOSS CNV | 0 | 9 | 0 | 17 |
16Q LOSS WILD-TYPE | 37 | 71 | 65 | 59 |
P value = 6.31e-12 (Fisher's exact test), Q value = 3.8e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
17P LOSS CNV | 6 | 9 | 4 | 45 |
17P LOSS WILD-TYPE | 131 | 19 | 24 | 68 |
P value = 8.72e-07 (Fisher's exact test), Q value = 5e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
17P LOSS CNV | 2 | 18 | 4 | 30 |
17P LOSS WILD-TYPE | 35 | 62 | 61 | 46 |
P value = 0.000245 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 61 | 69 | 97 | 57 |
17P LOSS CNV | 10 | 6 | 20 | 23 |
17P LOSS WILD-TYPE | 51 | 63 | 77 | 34 |
P value = 0.000205 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 83 | 96 |
17P LOSS CNV | 23 | 9 | 17 |
17P LOSS WILD-TYPE | 35 | 74 | 79 |
P value = 0.000103 (Fisher's exact test), Q value = 0.054
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
17Q LOSS CNV | 1 | 2 | 1 | 16 |
17Q LOSS WILD-TYPE | 136 | 26 | 27 | 97 |
P value = 2.74e-06 (Fisher's exact test), Q value = 0.0016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
18Q LOSS CNV | 10 | 8 | 1 | 33 |
18Q LOSS WILD-TYPE | 127 | 20 | 27 | 80 |
P value = 1.37e-11 (Fisher's exact test), Q value = 8.2e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
19P LOSS CNV | 0 | 2 | 1 | 30 |
19P LOSS WILD-TYPE | 137 | 26 | 27 | 83 |
P value = 4.4e-06 (Fisher's exact test), Q value = 0.0025
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
19P LOSS CNV | 0 | 7 | 1 | 19 |
19P LOSS WILD-TYPE | 37 | 73 | 64 | 57 |
P value = 4.05e-06 (Chi-square test), Q value = 0.0023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 45 | 41 | 35 | 37 | 50 |
19P LOSS CNV | 1 | 0 | 2 | 3 | 15 |
19P LOSS WILD-TYPE | 44 | 41 | 33 | 34 | 35 |
P value = 0.000158 (Fisher's exact test), Q value = 0.083
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 42 | 42 | 55 | 69 |
19P LOSS CNV | 0 | 2 | 14 | 5 |
19P LOSS WILD-TYPE | 42 | 40 | 41 | 64 |
P value = 4.86e-08 (Fisher's exact test), Q value = 2.8e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 61 | 69 | 97 | 57 |
19P LOSS CNV | 4 | 1 | 7 | 20 |
19P LOSS WILD-TYPE | 57 | 68 | 90 | 37 |
P value = 4.21e-06 (Fisher's exact test), Q value = 0.0024
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 71 | 89 | 124 |
19P LOSS CNV | 20 | 3 | 9 |
19P LOSS WILD-TYPE | 51 | 86 | 115 |
P value = 5e-05 (Fisher's exact test), Q value = 0.027
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 83 | 96 |
19P LOSS CNV | 16 | 3 | 7 |
19P LOSS WILD-TYPE | 42 | 80 | 89 |
P value = 2.73e-07 (Fisher's exact test), Q value = 0.00016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
19Q LOSS CNV | 0 | 2 | 1 | 20 |
19Q LOSS WILD-TYPE | 137 | 26 | 27 | 93 |
P value = 1.26e-05 (Fisher's exact test), Q value = 0.007
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
19Q LOSS CNV | 0 | 2 | 1 | 15 |
19Q LOSS WILD-TYPE | 37 | 78 | 64 | 61 |
P value = 0.000109 (Chi-square test), Q value = 0.058
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 45 | 41 | 35 | 37 | 50 |
19Q LOSS CNV | 0 | 0 | 2 | 2 | 11 |
19Q LOSS WILD-TYPE | 45 | 41 | 33 | 35 | 39 |
P value = 3.91e-06 (Fisher's exact test), Q value = 0.0022
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 61 | 69 | 97 | 57 |
19Q LOSS CNV | 2 | 1 | 5 | 15 |
19Q LOSS WILD-TYPE | 59 | 68 | 92 | 42 |
P value = 8.88e-05 (Fisher's exact test), Q value = 0.047
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 71 | 89 | 124 |
19Q LOSS CNV | 15 | 3 | 5 |
19Q LOSS WILD-TYPE | 56 | 86 | 119 |
P value = 0.000492 (Chi-square test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 45 | 41 | 35 | 37 | 50 |
20P LOSS CNV | 0 | 0 | 5 | 0 | 1 |
20P LOSS WILD-TYPE | 45 | 41 | 30 | 37 | 49 |
P value = 4.08e-09 (Fisher's exact test), Q value = 2.4e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
21Q LOSS CNV | 8 | 4 | 10 | 40 |
21Q LOSS WILD-TYPE | 129 | 24 | 18 | 73 |
P value = 6.83e-06 (Fisher's exact test), Q value = 0.0038
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
21Q LOSS CNV | 1 | 28 | 5 | 18 |
21Q LOSS WILD-TYPE | 36 | 52 | 60 | 58 |
P value = 7.2e-15 (Fisher's exact test), Q value = 4.4e-12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
22Q LOSS CNV | 0 | 2 | 1 | 37 |
22Q LOSS WILD-TYPE | 137 | 26 | 27 | 76 |
P value = 1.9e-06 (Fisher's exact test), Q value = 0.0011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 80 | 65 | 76 |
22Q LOSS CNV | 0 | 9 | 2 | 22 |
22Q LOSS WILD-TYPE | 37 | 71 | 63 | 54 |
P value = 3.76e-05 (Fisher's exact test), Q value = 0.021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 61 | 69 | 97 | 57 |
22Q LOSS CNV | 6 | 2 | 10 | 18 |
22Q LOSS WILD-TYPE | 55 | 67 | 87 | 39 |
-
Mutation data file = broad_values_by_arm.mutsig.cluster.txt
-
Molecular subtypes file = STAD-TP.transferedmergedcluster.txt
-
Number of patients = 306
-
Number of significantly arm-level cnvs = 78
-
Number of molecular subtypes = 8
-
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.