This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.
Testing the association between copy number variation 68 focal events and 14 molecular subtypes across 569 patients, 74 significant findings detected with P value < 0.05 and Q value < 0.25.
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amp_1p34.3 cnv correlated to 'CN_CNMF'.
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amp_1q21.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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amp_1q42.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
amp_2p23.2 cnv correlated to 'CN_CNMF'.
-
amp_2q31.2 cnv correlated to 'CN_CNMF'.
-
amp_3q26.2 cnv correlated to 'CN_CNMF'.
-
amp_5p15.33 cnv correlated to 'CN_CNMF'.
-
amp_6p22.3 cnv correlated to 'CN_CNMF'.
-
amp_7q36.3 cnv correlated to 'CN_CNMF'.
-
amp_8p11.21 cnv correlated to 'CN_CNMF'.
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amp_8q24.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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amp_10p15.3 cnv correlated to 'CN_CNMF'.
-
amp_11q14.1 cnv correlated to 'CN_CNMF'.
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amp_12p13.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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amp_12p12.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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amp_14q32.33 cnv correlated to 'CN_CNMF'.
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amp_15q26.3 cnv correlated to 'CN_CNMF'.
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amp_18q11.2 cnv correlated to 'CN_CNMF'.
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amp_19p13.12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
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amp_19q12 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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amp_19q13.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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amp_20p13 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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amp_20q11.21 cnv correlated to 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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amp_20q13.33 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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amp_xp11.23 cnv correlated to 'CN_CNMF'.
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del_1p36.11 cnv correlated to 'CN_CNMF'.
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del_1q41 cnv correlated to 'CN_CNMF'.
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del_2q37.3 cnv correlated to 'CN_CNMF'.
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del_3p26.2 cnv correlated to 'CN_CNMF'.
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del_5q11.2 cnv correlated to 'CN_CNMF'.
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del_5q13.2 cnv correlated to 'CN_CNMF'.
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del_6q27 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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del_7p22.1 cnv correlated to 'CN_CNMF'.
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del_8p23.3 cnv correlated to 'CN_CNMF'.
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del_8p21.2 cnv correlated to 'CN_CNMF'.
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del_9p24.3 cnv correlated to 'MRNA_CNMF' and 'METHLYATION_CNMF'.
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del_9q34.13 cnv correlated to 'CN_CNMF'.
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del_10q24.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'RPPA_CHIERARCHICAL'.
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del_11p15.5 cnv correlated to 'CN_CNMF'.
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del_12q24.33 cnv correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
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del_13q14.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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del_14q23.3 cnv correlated to 'CN_CNMF'.
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del_15q15.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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del_16q22.1 cnv correlated to 'CN_CNMF'.
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del_16q23.1 cnv correlated to 'CN_CNMF'.
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del_19q13.33 cnv correlated to 'MRNA_CNMF' and 'MRNA_CHIERARCHICAL'.
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del_19q13.43 cnv correlated to 'METHLYATION_CNMF'.
Clinical Features |
MRNA CNMF |
MRNA CHIERARCHICAL |
MIR CNMF |
MIR CHIERARCHICAL |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Fisher's exact test | 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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
amp 8q24 21 | 451 (79%) | 118 |
1.32e-07 (0.000122) |
2.3e-05 (0.0208) |
0.251 (1.00) |
0.00244 (1.00) |
1.96e-16 (1.87e-13) |
0.00445 (1.00) |
0.982 (1.00) |
0.658 (1.00) |
4.18e-07 (0.000385) |
2.63e-05 (0.0237) |
0.161 (1.00) |
0.0377 (1.00) |
0.0613 (1.00) |
0.0711 (1.00) |
amp 19p13 12 | 308 (54%) | 261 |
0.000229 (0.202) |
2.01e-07 (0.000185) |
0.0377 (1.00) |
0.025 (1.00) |
1.27e-11 (1.2e-08) |
2.36e-06 (0.00215) |
0.000312 (0.274) |
0.00164 (1.00) |
0.241 (1.00) |
0.314 (1.00) |
0.576 (1.00) |
0.598 (1.00) |
0.981 (1.00) |
0.763 (1.00) |
amp 20q11 21 | 340 (60%) | 229 |
0.00267 (1.00) |
0.00246 (1.00) |
0.111 (1.00) |
0.000258 (0.227) |
4.34e-22 (4.13e-19) |
8.58e-12 (8.1e-09) |
0.131 (1.00) |
0.0221 (1.00) |
0.000256 (0.226) |
0.506 (1.00) |
0.289 (1.00) |
0.173 (1.00) |
0.734 (1.00) |
0.485 (1.00) |
del 6q27 | 381 (67%) | 188 |
0.168 (1.00) |
0.0407 (1.00) |
0.257 (1.00) |
0.0174 (1.00) |
4.09e-10 (3.83e-07) |
2.58e-05 (0.0232) |
0.459 (1.00) |
0.868 (1.00) |
1.75e-05 (0.0159) |
0.342 (1.00) |
0.366 (1.00) |
0.906 (1.00) |
0.336 (1.00) |
0.0851 (1.00) |
del 10q24 2 | 246 (43%) | 323 |
0.00197 (1.00) |
0.000124 (0.11) |
0.00622 (1.00) |
0.0681 (1.00) |
2.37e-05 (0.0213) |
0.00156 (1.00) |
0.0115 (1.00) |
9.21e-05 (0.0823) |
0.437 (1.00) |
0.439 (1.00) |
0.00187 (1.00) |
0.351 (1.00) |
0.0106 (1.00) |
0.00898 (1.00) |
amp 1q21 3 | 361 (63%) | 208 |
0.266 (1.00) |
0.342 (1.00) |
0.633 (1.00) |
0.154 (1.00) |
3.7e-11 (3.47e-08) |
0.000123 (0.11) |
0.075 (1.00) |
0.0208 (1.00) |
0.658 (1.00) |
0.35 (1.00) |
0.84 (1.00) |
0.888 (1.00) |
0.737 (1.00) |
0.827 (1.00) |
amp 1q42 2 | 314 (55%) | 255 |
0.0232 (1.00) |
0.0288 (1.00) |
0.873 (1.00) |
0.00718 (1.00) |
1.17e-09 (1.09e-06) |
5.42e-05 (0.0485) |
0.252 (1.00) |
0.216 (1.00) |
0.501 (1.00) |
0.374 (1.00) |
0.267 (1.00) |
0.351 (1.00) |
0.357 (1.00) |
0.264 (1.00) |
amp 12p13 33 | 323 (57%) | 246 |
0.0235 (1.00) |
0.122 (1.00) |
0.263 (1.00) |
0.00801 (1.00) |
1.13e-08 (1.05e-05) |
0.000213 (0.189) |
0.19 (1.00) |
0.472 (1.00) |
0.0148 (1.00) |
0.164 (1.00) |
0.531 (1.00) |
1 (1.00) |
0.828 (1.00) |
0.482 (1.00) |
amp 12p12 1 | 306 (54%) | 263 |
0.129 (1.00) |
0.11 (1.00) |
0.899 (1.00) |
0.0636 (1.00) |
5.63e-12 (5.32e-09) |
3.22e-05 (0.0289) |
0.624 (1.00) |
0.216 (1.00) |
0.0123 (1.00) |
0.108 (1.00) |
0.447 (1.00) |
0.944 (1.00) |
0.72 (1.00) |
0.897 (1.00) |
amp 19q12 | 319 (56%) | 250 |
0.124 (1.00) |
0.00514 (1.00) |
0.0292 (1.00) |
0.0624 (1.00) |
1.38e-27 (1.32e-24) |
4.56e-10 (4.26e-07) |
0.0468 (1.00) |
0.691 (1.00) |
0.53 (1.00) |
0.843 (1.00) |
0.346 (1.00) |
0.676 (1.00) |
0.827 (1.00) |
0.494 (1.00) |
amp 19q13 2 | 241 (42%) | 328 |
0.938 (1.00) |
0.844 (1.00) |
0.658 (1.00) |
0.193 (1.00) |
1.26e-11 (1.18e-08) |
9.84e-05 (0.0878) |
0.444 (1.00) |
0.468 (1.00) |
0.371 (1.00) |
1 (1.00) |
0.97 (1.00) |
0.433 (1.00) |
0.707 (1.00) |
0.433 (1.00) |
amp 20p13 | 313 (55%) | 256 |
0.468 (1.00) |
0.0608 (1.00) |
0.14 (1.00) |
0.0357 (1.00) |
5.49e-11 (5.15e-08) |
2.29e-05 (0.0207) |
0.195 (1.00) |
0.983 (1.00) |
0.0816 (1.00) |
0.718 (1.00) |
0.19 (1.00) |
0.841 (1.00) |
0.658 (1.00) |
0.279 (1.00) |
amp 20q13 33 | 393 (69%) | 176 |
0.0104 (1.00) |
0.0201 (1.00) |
0.684 (1.00) |
0.00375 (1.00) |
4.81e-16 (4.56e-13) |
2.08e-06 (0.00191) |
0.843 (1.00) |
0.494 (1.00) |
0.00804 (1.00) |
0.809 (1.00) |
0.47 (1.00) |
0.595 (1.00) |
0.694 (1.00) |
0.308 (1.00) |
del 9p24 3 | 257 (45%) | 312 |
0.000237 (0.209) |
0.0119 (1.00) |
0.612 (1.00) |
0.00911 (1.00) |
0.0386 (1.00) |
7.5e-05 (0.067) |
0.318 (1.00) |
0.448 (1.00) |
0.0712 (1.00) |
0.0723 (1.00) |
0.0864 (1.00) |
0.168 (1.00) |
0.0631 (1.00) |
0.157 (1.00) |
del 12q24 33 | 217 (38%) | 352 |
0.00104 (0.902) |
0.000202 (0.179) |
0.163 (1.00) |
0.0891 (1.00) |
3.95e-09 (3.68e-06) |
0.0195 (1.00) |
0.299 (1.00) |
0.335 (1.00) |
0.0514 (1.00) |
0.00198 (1.00) |
0.0152 (1.00) |
0.00695 (1.00) |
0.0185 (1.00) |
0.0116 (1.00) |
del 13q14 2 | 358 (63%) | 211 |
0.0102 (1.00) |
0.0204 (1.00) |
0.621 (1.00) |
0.616 (1.00) |
1.44e-06 (0.00132) |
2.34e-05 (0.0211) |
0.00192 (1.00) |
0.00125 (1.00) |
0.0994 (1.00) |
0.236 (1.00) |
0.366 (1.00) |
0.868 (1.00) |
0.446 (1.00) |
0.634 (1.00) |
del 15q15 1 | 360 (63%) | 209 |
0.0265 (1.00) |
0.0097 (1.00) |
0.0213 (1.00) |
0.00604 (1.00) |
1.1e-11 (1.04e-08) |
7.06e-06 (0.00644) |
0.16 (1.00) |
0.0714 (1.00) |
0.0107 (1.00) |
0.844 (1.00) |
0.397 (1.00) |
0.636 (1.00) |
0.2 (1.00) |
0.191 (1.00) |
del 19q13 33 | 295 (52%) | 274 |
0.000217 (0.192) |
0.00015 (0.133) |
0.0445 (1.00) |
0.188 (1.00) |
0.0978 (1.00) |
0.00269 (1.00) |
0.0289 (1.00) |
0.181 (1.00) |
0.00687 (1.00) |
0.0584 (1.00) |
0.322 (1.00) |
0.159 (1.00) |
0.297 (1.00) |
0.469 (1.00) |
amp 1p34 3 | 287 (50%) | 282 |
0.427 (1.00) |
0.485 (1.00) |
0.123 (1.00) |
0.079 (1.00) |
9.72e-07 (0.000892) |
0.194 (1.00) |
0.112 (1.00) |
0.808 (1.00) |
0.549 (1.00) |
0.0547 (1.00) |
0.0838 (1.00) |
0.102 (1.00) |
0.0652 (1.00) |
0.6 (1.00) |
amp 2p23 2 | 245 (43%) | 324 |
0.327 (1.00) |
0.441 (1.00) |
0.75 (1.00) |
0.0106 (1.00) |
1.19e-08 (1.11e-05) |
0.00438 (1.00) |
0.144 (1.00) |
0.444 (1.00) |
0.0318 (1.00) |
0.814 (1.00) |
0.919 (1.00) |
0.127 (1.00) |
0.93 (1.00) |
0.71 (1.00) |
amp 2q31 2 | 259 (46%) | 310 |
0.113 (1.00) |
0.0942 (1.00) |
0.033 (1.00) |
0.0604 (1.00) |
4.18e-09 (3.89e-06) |
0.00784 (1.00) |
0.0486 (1.00) |
0.317 (1.00) |
0.152 (1.00) |
0.425 (1.00) |
0.287 (1.00) |
0.397 (1.00) |
0.0821 (1.00) |
0.0744 (1.00) |
amp 3q26 2 | 476 (84%) | 93 |
0.00909 (1.00) |
0.00489 (1.00) |
0.809 (1.00) |
0.348 (1.00) |
1.85e-10 (1.73e-07) |
0.0347 (1.00) |
0.408 (1.00) |
0.445 (1.00) |
0.00759 (1.00) |
0.0147 (1.00) |
0.125 (1.00) |
0.393 (1.00) |
0.476 (1.00) |
0.643 (1.00) |
amp 5p15 33 | 304 (53%) | 265 |
1 (1.00) |
0.965 (1.00) |
0.625 (1.00) |
0.606 (1.00) |
8.67e-07 (0.000797) |
0.099 (1.00) |
0.976 (1.00) |
0.287 (1.00) |
0.249 (1.00) |
0.963 (1.00) |
0.0246 (1.00) |
0.544 (1.00) |
0.105 (1.00) |
0.5 (1.00) |
amp 6p22 3 | 300 (53%) | 269 |
0.173 (1.00) |
0.0462 (1.00) |
0.275 (1.00) |
0.109 (1.00) |
1.07e-06 (0.000979) |
0.0123 (1.00) |
0.0723 (1.00) |
0.0499 (1.00) |
0.852 (1.00) |
0.0934 (1.00) |
0.373 (1.00) |
0.444 (1.00) |
0.17 (1.00) |
0.277 (1.00) |
amp 7q36 3 | 311 (55%) | 258 |
0.105 (1.00) |
0.091 (1.00) |
0.352 (1.00) |
0.731 (1.00) |
2.82e-05 (0.0253) |
0.457 (1.00) |
0.0314 (1.00) |
0.155 (1.00) |
0.837 (1.00) |
0.556 (1.00) |
0.213 (1.00) |
0.174 (1.00) |
0.0227 (1.00) |
0.264 (1.00) |
amp 8p11 21 | 207 (36%) | 362 |
0.108 (1.00) |
0.0235 (1.00) |
0.1 (1.00) |
0.133 (1.00) |
1.91e-05 (0.0173) |
0.0159 (1.00) |
0.0108 (1.00) |
0.282 (1.00) |
0.281 (1.00) |
0.167 (1.00) |
0.763 (1.00) |
0.758 (1.00) |
0.674 (1.00) |
0.869 (1.00) |
amp 10p15 3 | 246 (43%) | 323 |
0.821 (1.00) |
0.71 (1.00) |
0.0551 (1.00) |
0.241 (1.00) |
2.06e-12 (1.95e-09) |
0.000533 (0.466) |
0.491 (1.00) |
0.337 (1.00) |
0.233 (1.00) |
0.421 (1.00) |
0.373 (1.00) |
0.883 (1.00) |
0.6 (1.00) |
0.633 (1.00) |
amp 11q14 1 | 253 (44%) | 316 |
0.00523 (1.00) |
0.0454 (1.00) |
0.767 (1.00) |
0.467 (1.00) |
6.61e-07 (0.000608) |
0.00245 (1.00) |
0.382 (1.00) |
0.25 (1.00) |
0.00422 (1.00) |
0.00764 (1.00) |
0.133 (1.00) |
0.722 (1.00) |
0.215 (1.00) |
1 (1.00) |
amp 14q32 33 | 153 (27%) | 416 |
0.443 (1.00) |
0.497 (1.00) |
0.197 (1.00) |
0.764 (1.00) |
0.000263 (0.231) |
0.281 (1.00) |
1 (1.00) |
0.537 (1.00) |
0.163 (1.00) |
0.658 (1.00) |
0.372 (1.00) |
0.625 (1.00) |
0.484 (1.00) |
0.589 (1.00) |
amp 15q26 3 | 161 (28%) | 408 |
0.0857 (1.00) |
0.301 (1.00) |
0.504 (1.00) |
0.826 (1.00) |
3.28e-09 (3.05e-06) |
0.788 (1.00) |
0.979 (1.00) |
0.308 (1.00) |
0.209 (1.00) |
0.977 (1.00) |
0.154 (1.00) |
0.463 (1.00) |
0.162 (1.00) |
0.49 (1.00) |
amp 18q11 2 | 142 (25%) | 427 |
0.819 (1.00) |
0.985 (1.00) |
0.953 (1.00) |
0.493 (1.00) |
1.83e-05 (0.0166) |
0.00379 (1.00) |
0.15 (1.00) |
0.258 (1.00) |
0.0419 (1.00) |
0.0914 (1.00) |
0.146 (1.00) |
0.54 (1.00) |
0.169 (1.00) |
0.276 (1.00) |
amp xp11 23 | 154 (27%) | 415 |
0.662 (1.00) |
0.322 (1.00) |
0.425 (1.00) |
0.349 (1.00) |
2.11e-05 (0.0191) |
0.00171 (1.00) |
0.716 (1.00) |
0.252 (1.00) |
0.442 (1.00) |
0.341 (1.00) |
0.273 (1.00) |
1 (1.00) |
0.448 (1.00) |
0.917 (1.00) |
del 1p36 11 | 267 (47%) | 302 |
0.739 (1.00) |
0.517 (1.00) |
0.0292 (1.00) |
0.393 (1.00) |
9.81e-06 (0.00895) |
0.089 (1.00) |
0.124 (1.00) |
0.214 (1.00) |
0.836 (1.00) |
0.871 (1.00) |
0.222 (1.00) |
0.148 (1.00) |
0.338 (1.00) |
0.154 (1.00) |
del 1q41 | 95 (17%) | 474 |
0.0866 (1.00) |
0.589 (1.00) |
0.303 (1.00) |
0.419 (1.00) |
3.23e-07 (0.000298) |
0.132 (1.00) |
0.475 (1.00) |
0.097 (1.00) |
0.268 (1.00) |
0.538 (1.00) |
0.913 (1.00) |
0.657 (1.00) |
0.763 (1.00) |
0.884 (1.00) |
del 2q37 3 | 173 (30%) | 396 |
0.0163 (1.00) |
0.0393 (1.00) |
0.758 (1.00) |
0.00149 (1.00) |
1.14e-05 (0.0104) |
0.0653 (1.00) |
0.798 (1.00) |
0.994 (1.00) |
0.0158 (1.00) |
0.0209 (1.00) |
0.0133 (1.00) |
0.0109 (1.00) |
0.052 (1.00) |
0.0218 (1.00) |
del 3p26 2 | 209 (37%) | 360 |
0.15 (1.00) |
0.13 (1.00) |
0.00575 (1.00) |
0.0341 (1.00) |
1.78e-05 (0.0161) |
0.000565 (0.493) |
0.955 (1.00) |
0.0949 (1.00) |
0.00318 (1.00) |
0.665 (1.00) |
0.622 (1.00) |
0.628 (1.00) |
0.971 (1.00) |
0.0265 (1.00) |
del 5q11 2 | 347 (61%) | 222 |
0.929 (1.00) |
0.635 (1.00) |
0.644 (1.00) |
0.206 (1.00) |
1.56e-08 (1.45e-05) |
0.000329 (0.288) |
0.731 (1.00) |
0.8 (1.00) |
0.207 (1.00) |
0.171 (1.00) |
0.0905 (1.00) |
0.00191 (1.00) |
0.0652 (1.00) |
0.0633 (1.00) |
del 5q13 2 | 412 (72%) | 157 |
0.745 (1.00) |
0.633 (1.00) |
0.896 (1.00) |
0.76 (1.00) |
3.57e-11 (3.35e-08) |
0.103 (1.00) |
0.773 (1.00) |
0.816 (1.00) |
0.519 (1.00) |
0.00563 (1.00) |
0.154 (1.00) |
0.0119 (1.00) |
0.21 (1.00) |
0.17 (1.00) |
del 7p22 1 | 248 (44%) | 321 |
0.391 (1.00) |
0.611 (1.00) |
0.766 (1.00) |
0.677 (1.00) |
1.69e-13 (1.6e-10) |
0.631 (1.00) |
0.803 (1.00) |
0.717 (1.00) |
0.35 (1.00) |
0.131 (1.00) |
0.354 (1.00) |
0.643 (1.00) |
0.702 (1.00) |
0.593 (1.00) |
del 8p23 3 | 382 (67%) | 187 |
0.0446 (1.00) |
0.242 (1.00) |
0.572 (1.00) |
0.0137 (1.00) |
6.56e-12 (6.2e-09) |
0.0506 (1.00) |
0.888 (1.00) |
0.52 (1.00) |
0.883 (1.00) |
0.597 (1.00) |
0.239 (1.00) |
0.145 (1.00) |
0.167 (1.00) |
0.366 (1.00) |
del 8p21 2 | 400 (70%) | 169 |
0.043 (1.00) |
0.44 (1.00) |
0.178 (1.00) |
0.00887 (1.00) |
3.95e-09 (3.68e-06) |
0.145 (1.00) |
0.871 (1.00) |
0.899 (1.00) |
0.458 (1.00) |
0.207 (1.00) |
0.575 (1.00) |
0.497 (1.00) |
0.908 (1.00) |
1 (1.00) |
del 9q34 13 | 337 (59%) | 232 |
0.0283 (1.00) |
0.0369 (1.00) |
0.968 (1.00) |
0.0165 (1.00) |
6.04e-07 (0.000556) |
0.0576 (1.00) |
0.421 (1.00) |
0.379 (1.00) |
0.208 (1.00) |
1 (1.00) |
0.0345 (1.00) |
0.128 (1.00) |
0.131 (1.00) |
0.0798 (1.00) |
del 11p15 5 | 338 (59%) | 231 |
0.108 (1.00) |
0.442 (1.00) |
0.602 (1.00) |
0.0314 (1.00) |
5.22e-10 (4.88e-07) |
0.00741 (1.00) |
0.937 (1.00) |
0.616 (1.00) |
0.704 (1.00) |
0.25 (1.00) |
0.107 (1.00) |
0.0299 (1.00) |
0.155 (1.00) |
0.33 (1.00) |
del 14q23 3 | 299 (53%) | 270 |
0.0643 (1.00) |
0.526 (1.00) |
0.651 (1.00) |
0.768 (1.00) |
0.000123 (0.109) |
0.732 (1.00) |
0.222 (1.00) |
0.285 (1.00) |
0.855 (1.00) |
0.196 (1.00) |
0.891 (1.00) |
0.654 (1.00) |
0.708 (1.00) |
0.482 (1.00) |
del 16q22 1 | 453 (80%) | 116 |
0.496 (1.00) |
0.73 (1.00) |
0.0316 (1.00) |
0.892 (1.00) |
0.000193 (0.172) |
0.637 (1.00) |
0.69 (1.00) |
0.331 (1.00) |
0.218 (1.00) |
0.186 (1.00) |
0.312 (1.00) |
0.0976 (1.00) |
0.0603 (1.00) |
0.12 (1.00) |
del 16q23 1 | 444 (78%) | 125 |
0.11 (1.00) |
0.229 (1.00) |
0.101 (1.00) |
0.394 (1.00) |
1.07e-05 (0.00975) |
0.536 (1.00) |
0.805 (1.00) |
0.86 (1.00) |
0.278 (1.00) |
0.298 (1.00) |
0.0577 (1.00) |
0.0249 (1.00) |
0.0405 (1.00) |
0.0301 (1.00) |
del 19q13 43 | 279 (49%) | 290 |
0.0114 (1.00) |
0.00146 (1.00) |
0.0966 (1.00) |
0.163 (1.00) |
0.00279 (1.00) |
2.76e-05 (0.0247) |
0.174 (1.00) |
0.356 (1.00) |
0.478 (1.00) |
0.13 (1.00) |
0.52 (1.00) |
0.505 (1.00) |
0.365 (1.00) |
0.682 (1.00) |
amp 4p16 3 | 157 (28%) | 412 |
1 (1.00) |
0.279 (1.00) |
0.0293 (1.00) |
0.607 (1.00) |
0.000292 (0.257) |
0.0274 (1.00) |
0.276 (1.00) |
0.747 (1.00) |
0.69 (1.00) |
0.402 (1.00) |
0.624 (1.00) |
0.621 (1.00) |
0.743 (1.00) |
0.456 (1.00) |
amp 4q13 3 | 110 (19%) | 459 |
0.945 (1.00) |
0.905 (1.00) |
0.344 (1.00) |
0.106 (1.00) |
0.000322 (0.282) |
0.528 (1.00) |
0.525 (1.00) |
0.225 (1.00) |
0.13 (1.00) |
0.895 (1.00) |
1 (1.00) |
0.104 (1.00) |
0.866 (1.00) |
0.524 (1.00) |
amp 10q22 3 | 181 (32%) | 388 |
0.472 (1.00) |
0.645 (1.00) |
0.541 (1.00) |
0.16 (1.00) |
0.215 (1.00) |
0.751 (1.00) |
0.636 (1.00) |
0.962 (1.00) |
0.201 (1.00) |
0.57 (1.00) |
0.266 (1.00) |
0.236 (1.00) |
0.905 (1.00) |
0.406 (1.00) |
amp 14q11 2 | 146 (26%) | 423 |
0.0171 (1.00) |
0.0368 (1.00) |
0.287 (1.00) |
0.00102 (0.885) |
0.0388 (1.00) |
0.194 (1.00) |
0.529 (1.00) |
0.398 (1.00) |
0.34 (1.00) |
0.27 (1.00) |
0.295 (1.00) |
0.438 (1.00) |
0.221 (1.00) |
0.262 (1.00) |
amp 17q25 3 | 212 (37%) | 357 |
0.468 (1.00) |
0.726 (1.00) |
0.98 (1.00) |
0.174 (1.00) |
0.00225 (1.00) |
0.78 (1.00) |
0.0734 (1.00) |
0.0652 (1.00) |
0.0123 (1.00) |
0.0187 (1.00) |
0.325 (1.00) |
0.125 (1.00) |
0.295 (1.00) |
0.11 (1.00) |
amp 22q12 2 | 89 (16%) | 480 |
0.615 (1.00) |
0.577 (1.00) |
0.0697 (1.00) |
0.259 (1.00) |
0.00155 (1.00) |
0.00069 (0.601) |
0.974 (1.00) |
0.036 (1.00) |
0.063 (1.00) |
0.123 (1.00) |
0.105 (1.00) |
0.00958 (1.00) |
0.0374 (1.00) |
0.0299 (1.00) |
amp xq28 | 217 (38%) | 352 |
0.244 (1.00) |
0.31 (1.00) |
0.561 (1.00) |
0.0511 (1.00) |
0.00117 (1.00) |
0.175 (1.00) |
0.45 (1.00) |
0.727 (1.00) |
0.62 (1.00) |
0.758 (1.00) |
0.871 (1.00) |
0.0152 (1.00) |
0.868 (1.00) |
1 (1.00) |
del 2p25 3 | 120 (21%) | 449 |
0.883 (1.00) |
1 (1.00) |
0.409 (1.00) |
0.279 (1.00) |
0.245 (1.00) |
0.64 (1.00) |
0.264 (1.00) |
0.137 (1.00) |
0.0625 (1.00) |
0.518 (1.00) |
0.877 (1.00) |
0.512 (1.00) |
0.893 (1.00) |
0.608 (1.00) |
del 2q22 1 | 136 (24%) | 433 |
0.105 (1.00) |
0.143 (1.00) |
0.568 (1.00) |
0.151 (1.00) |
0.0867 (1.00) |
0.672 (1.00) |
0.603 (1.00) |
0.844 (1.00) |
0.894 (1.00) |
0.314 (1.00) |
0.479 (1.00) |
0.369 (1.00) |
0.418 (1.00) |
0.108 (1.00) |
del 4q22 1 | 388 (68%) | 181 |
0.0527 (1.00) |
0.123 (1.00) |
1 (1.00) |
0.00771 (1.00) |
0.0204 (1.00) |
0.221 (1.00) |
0.191 (1.00) |
0.0264 (1.00) |
0.0722 (1.00) |
0.508 (1.00) |
0.299 (1.00) |
0.00977 (1.00) |
0.0292 (1.00) |
0.154 (1.00) |
del 4q34 3 | 415 (73%) | 154 |
0.0541 (1.00) |
0.0397 (1.00) |
0.0629 (1.00) |
0.0242 (1.00) |
0.15 (1.00) |
0.596 (1.00) |
0.667 (1.00) |
0.314 (1.00) |
0.0886 (1.00) |
0.0291 (1.00) |
0.418 (1.00) |
0.199 (1.00) |
0.161 (1.00) |
0.269 (1.00) |
del 10p15 3 | 120 (21%) | 449 |
0.18 (1.00) |
0.0467 (1.00) |
0.0874 (1.00) |
0.092 (1.00) |
0.149 (1.00) |
0.347 (1.00) |
0.284 (1.00) |
0.0454 (1.00) |
0.0154 (1.00) |
0.0572 (1.00) |
0.246 (1.00) |
0.327 (1.00) |
0.114 (1.00) |
0.269 (1.00) |
del 11q25 | 195 (34%) | 374 |
0.709 (1.00) |
0.647 (1.00) |
0.173 (1.00) |
0.356 (1.00) |
0.148 (1.00) |
0.444 (1.00) |
0.32 (1.00) |
0.176 (1.00) |
0.928 (1.00) |
0.866 (1.00) |
0.635 (1.00) |
0.188 (1.00) |
0.676 (1.00) |
0.298 (1.00) |
del 16p13 3 | 307 (54%) | 262 |
0.602 (1.00) |
0.12 (1.00) |
0.276 (1.00) |
0.615 (1.00) |
0.0535 (1.00) |
0.418 (1.00) |
0.825 (1.00) |
0.251 (1.00) |
0.357 (1.00) |
0.556 (1.00) |
0.221 (1.00) |
0.863 (1.00) |
0.11 (1.00) |
0.829 (1.00) |
del 17p12 | 483 (85%) | 86 |
0.144 (1.00) |
0.244 (1.00) |
0.587 (1.00) |
0.607 (1.00) |
0.737 (1.00) |
0.319 (1.00) |
0.902 (1.00) |
0.269 (1.00) |
0.15 (1.00) |
0.403 (1.00) |
0.51 (1.00) |
0.511 (1.00) |
0.471 (1.00) |
0.775 (1.00) |
del 17q11 2 | 466 (82%) | 103 |
0.923 (1.00) |
0.216 (1.00) |
0.722 (1.00) |
0.471 (1.00) |
0.000581 (0.507) |
0.00286 (1.00) |
0.763 (1.00) |
0.067 (1.00) |
0.368 (1.00) |
0.444 (1.00) |
0.146 (1.00) |
0.495 (1.00) |
0.0264 (1.00) |
0.377 (1.00) |
del 18q23 | 377 (66%) | 192 |
0.98 (1.00) |
0.992 (1.00) |
0.148 (1.00) |
0.406 (1.00) |
0.0155 (1.00) |
0.396 (1.00) |
0.33 (1.00) |
0.17 (1.00) |
0.128 (1.00) |
0.435 (1.00) |
0.474 (1.00) |
0.544 (1.00) |
0.0754 (1.00) |
0.538 (1.00) |
del 19p13 3 | 502 (88%) | 67 |
0.156 (1.00) |
0.00917 (1.00) |
0.823 (1.00) |
0.462 (1.00) |
0.000634 (0.552) |
0.0174 (1.00) |
0.616 (1.00) |
0.278 (1.00) |
0.321 (1.00) |
0.0163 (1.00) |
0.478 (1.00) |
0.805 (1.00) |
0.435 (1.00) |
0.909 (1.00) |
del 21q22 3 | 224 (39%) | 345 |
0.365 (1.00) |
0.472 (1.00) |
0.697 (1.00) |
0.246 (1.00) |
0.808 (1.00) |
0.263 (1.00) |
0.651 (1.00) |
0.642 (1.00) |
0.249 (1.00) |
0.373 (1.00) |
0.819 (1.00) |
0.712 (1.00) |
0.197 (1.00) |
0.502 (1.00) |
del 22q13 32 | 495 (87%) | 74 |
0.159 (1.00) |
0.0764 (1.00) |
0.0226 (1.00) |
0.07 (1.00) |
0.00533 (1.00) |
0.101 (1.00) |
0.102 (1.00) |
0.411 (1.00) |
0.103 (1.00) |
0.27 (1.00) |
0.031 (1.00) |
0.351 (1.00) |
0.0274 (1.00) |
0.635 (1.00) |
del xp21 1 | 350 (62%) | 219 |
0.398 (1.00) |
0.66 (1.00) |
0.0971 (1.00) |
0.802 (1.00) |
0.124 (1.00) |
0.0205 (1.00) |
0.454 (1.00) |
0.0605 (1.00) |
0.873 (1.00) |
0.377 (1.00) |
0.974 (1.00) |
0.685 (1.00) |
0.854 (1.00) |
0.726 (1.00) |
P value = 9.72e-07 (Fisher's exact test), Q value = 0.00089
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 1(1P34.3) MUTATED | 59 | 120 | 108 |
AMP PEAK 1(1P34.3) WILD-TYPE | 115 | 86 | 81 |
P value = 3.7e-11 (Fisher's exact test), Q value = 3.5e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 2(1Q21.3) MUTATED | 90 | 115 | 156 |
AMP PEAK 2(1Q21.3) WILD-TYPE | 84 | 91 | 33 |
P value = 0.000123 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
AMP PEAK 2(1Q21.3) MUTATED | 128 | 92 | 141 |
AMP PEAK 2(1Q21.3) WILD-TYPE | 44 | 83 | 80 |
P value = 1.17e-09 (Fisher's exact test), Q value = 1.1e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 3(1Q42.2) MUTATED | 90 | 86 | 138 |
AMP PEAK 3(1Q42.2) WILD-TYPE | 84 | 120 | 51 |
P value = 5.42e-05 (Fisher's exact test), Q value = 0.048
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
AMP PEAK 3(1Q42.2) MUTATED | 119 | 87 | 108 |
AMP PEAK 3(1Q42.2) WILD-TYPE | 53 | 88 | 113 |
P value = 1.19e-08 (Fisher's exact test), Q value = 1.1e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 4(2P23.2) MUTATED | 48 | 86 | 111 |
AMP PEAK 4(2P23.2) WILD-TYPE | 126 | 120 | 78 |
P value = 4.18e-09 (Fisher's exact test), Q value = 3.9e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 5(2Q31.2) MUTATED | 47 | 102 | 110 |
AMP PEAK 5(2Q31.2) WILD-TYPE | 127 | 104 | 79 |
P value = 1.85e-10 (Fisher's exact test), Q value = 1.7e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 6(3Q26.2) MUTATED | 118 | 182 | 176 |
AMP PEAK 6(3Q26.2) WILD-TYPE | 56 | 24 | 13 |
P value = 8.67e-07 (Fisher's exact test), Q value = 8e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 9(5P15.33) MUTATED | 64 | 125 | 115 |
AMP PEAK 9(5P15.33) WILD-TYPE | 110 | 81 | 74 |
P value = 1.07e-06 (Fisher's exact test), Q value = 0.00098
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 10(6P22.3) MUTATED | 63 | 124 | 113 |
AMP PEAK 10(6P22.3) WILD-TYPE | 111 | 82 | 76 |
P value = 2.82e-05 (Fisher's exact test), Q value = 0.025
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 11(7Q36.3) MUTATED | 70 | 125 | 116 |
AMP PEAK 11(7Q36.3) WILD-TYPE | 104 | 81 | 73 |
P value = 1.91e-05 (Fisher's exact test), Q value = 0.017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 12(8P11.21) MUTATED | 43 | 73 | 91 |
AMP PEAK 12(8P11.21) WILD-TYPE | 131 | 133 | 98 |
P value = 1.32e-07 (Fisher's exact test), Q value = 0.00012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 215 | 216 | 126 |
AMP PEAK 13(8Q24.21) MUTATED | 144 | 188 | 110 |
AMP PEAK 13(8Q24.21) WILD-TYPE | 71 | 28 | 16 |
P value = 2.3e-05 (Fisher's exact test), Q value = 0.021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 128 | 210 | 219 |
AMP PEAK 13(8Q24.21) MUTATED | 114 | 146 | 182 |
AMP PEAK 13(8Q24.21) WILD-TYPE | 14 | 64 | 37 |
P value = 1.96e-16 (Fisher's exact test), Q value = 1.9e-13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 13(8Q24.21) MUTATED | 118 | 199 | 134 |
AMP PEAK 13(8Q24.21) WILD-TYPE | 56 | 7 | 55 |
P value = 4.18e-07 (Fisher's exact test), Q value = 0.00039
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 100 | 67 | 91 |
AMP PEAK 13(8Q24.21) MUTATED | 90 | 61 | 56 |
AMP PEAK 13(8Q24.21) WILD-TYPE | 10 | 6 | 35 |
P value = 2.63e-05 (Fisher's exact test), Q value = 0.024
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 110 | 110 | 38 |
AMP PEAK 13(8Q24.21) MUTATED | 74 | 97 | 36 |
AMP PEAK 13(8Q24.21) WILD-TYPE | 36 | 13 | 2 |
P value = 2.06e-12 (Fisher's exact test), Q value = 2e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 14(10P15.3) MUTATED | 46 | 80 | 120 |
AMP PEAK 14(10P15.3) WILD-TYPE | 128 | 126 | 69 |
P value = 6.61e-07 (Fisher's exact test), Q value = 0.00061
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 16(11Q14.1) MUTATED | 57 | 121 | 75 |
AMP PEAK 16(11Q14.1) WILD-TYPE | 117 | 85 | 114 |
P value = 1.13e-08 (Fisher's exact test), Q value = 1.1e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 17(12P13.33) MUTATED | 72 | 114 | 137 |
AMP PEAK 17(12P13.33) WILD-TYPE | 102 | 92 | 52 |
P value = 0.000213 (Fisher's exact test), Q value = 0.19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
AMP PEAK 17(12P13.33) MUTATED | 119 | 96 | 108 |
AMP PEAK 17(12P13.33) WILD-TYPE | 53 | 79 | 113 |
P value = 5.63e-12 (Fisher's exact test), Q value = 5.3e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 18(12P12.1) MUTATED | 67 | 99 | 140 |
AMP PEAK 18(12P12.1) WILD-TYPE | 107 | 107 | 49 |
P value = 3.22e-05 (Fisher's exact test), Q value = 0.029
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
AMP PEAK 18(12P12.1) MUTATED | 117 | 87 | 102 |
AMP PEAK 18(12P12.1) WILD-TYPE | 55 | 88 | 119 |
P value = 0.000263 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 20(14Q32.33) MUTATED | 43 | 75 | 35 |
AMP PEAK 20(14Q32.33) WILD-TYPE | 131 | 131 | 154 |
P value = 3.28e-09 (Fisher's exact test), Q value = 3.1e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 21(15Q26.3) MUTATED | 35 | 91 | 35 |
AMP PEAK 21(15Q26.3) WILD-TYPE | 139 | 115 | 154 |
P value = 1.83e-05 (Fisher's exact test), Q value = 0.017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 23(18Q11.2) MUTATED | 26 | 48 | 68 |
AMP PEAK 23(18Q11.2) WILD-TYPE | 148 | 158 | 121 |
P value = 0.000229 (Fisher's exact test), Q value = 0.2
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 215 | 216 | 126 |
AMP PEAK 24(19P13.12) MUTATED | 136 | 115 | 51 |
AMP PEAK 24(19P13.12) WILD-TYPE | 79 | 101 | 75 |
P value = 2.01e-07 (Fisher's exact test), Q value = 0.00019
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 128 | 210 | 219 |
AMP PEAK 24(19P13.12) MUTATED | 44 | 137 | 121 |
AMP PEAK 24(19P13.12) WILD-TYPE | 84 | 73 | 98 |
P value = 1.27e-11 (Fisher's exact test), Q value = 1.2e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 24(19P13.12) MUTATED | 72 | 95 | 141 |
AMP PEAK 24(19P13.12) WILD-TYPE | 102 | 111 | 48 |
P value = 2.36e-06 (Fisher's exact test), Q value = 0.0022
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
AMP PEAK 24(19P13.12) MUTATED | 118 | 73 | 116 |
AMP PEAK 24(19P13.12) WILD-TYPE | 54 | 102 | 105 |
P value = 1.38e-27 (Fisher's exact test), Q value = 1.3e-24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 25(19Q12) MUTATED | 66 | 88 | 165 |
AMP PEAK 25(19Q12) WILD-TYPE | 108 | 118 | 24 |
P value = 4.56e-10 (Fisher's exact test), Q value = 4.3e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
AMP PEAK 25(19Q12) MUTATED | 128 | 70 | 121 |
AMP PEAK 25(19Q12) WILD-TYPE | 44 | 105 | 100 |
P value = 1.26e-11 (Fisher's exact test), Q value = 1.2e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 26(19Q13.2) MUTATED | 51 | 71 | 119 |
AMP PEAK 26(19Q13.2) WILD-TYPE | 123 | 135 | 70 |
P value = 9.84e-05 (Fisher's exact test), Q value = 0.088
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
AMP PEAK 26(19Q13.2) MUTATED | 94 | 56 | 91 |
AMP PEAK 26(19Q13.2) WILD-TYPE | 78 | 119 | 130 |
P value = 5.49e-11 (Fisher's exact test), Q value = 5.2e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 27(20P13) MUTATED | 72 | 100 | 141 |
AMP PEAK 27(20P13) WILD-TYPE | 102 | 106 | 48 |
P value = 2.29e-05 (Fisher's exact test), Q value = 0.021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
AMP PEAK 27(20P13) MUTATED | 119 | 81 | 112 |
AMP PEAK 27(20P13) WILD-TYPE | 53 | 94 | 109 |
P value = 0.000258 (Chi-square test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 65 | 115 | 125 | 99 | 57 | 94 |
AMP PEAK 28(20Q11.21) MUTATED | 37 | 56 | 73 | 53 | 39 | 74 |
AMP PEAK 28(20Q11.21) WILD-TYPE | 28 | 59 | 52 | 46 | 18 | 20 |
P value = 4.34e-22 (Fisher's exact test), Q value = 4.1e-19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 28(20Q11.21) MUTATED | 78 | 97 | 165 |
AMP PEAK 28(20Q11.21) WILD-TYPE | 96 | 109 | 24 |
P value = 8.58e-12 (Fisher's exact test), Q value = 8.1e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
AMP PEAK 28(20Q11.21) MUTATED | 140 | 91 | 109 |
AMP PEAK 28(20Q11.21) WILD-TYPE | 32 | 84 | 112 |
P value = 0.000256 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 100 | 67 | 91 |
AMP PEAK 28(20Q11.21) MUTATED | 63 | 28 | 67 |
AMP PEAK 28(20Q11.21) WILD-TYPE | 37 | 39 | 24 |
P value = 4.81e-16 (Fisher's exact test), Q value = 4.6e-13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 29(20Q13.33) MUTATED | 88 | 136 | 169 |
AMP PEAK 29(20Q13.33) WILD-TYPE | 86 | 70 | 20 |
P value = 2.08e-06 (Fisher's exact test), Q value = 0.0019
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
AMP PEAK 29(20Q13.33) MUTATED | 144 | 109 | 140 |
AMP PEAK 29(20Q13.33) WILD-TYPE | 28 | 66 | 81 |
P value = 2.11e-05 (Fisher's exact test), Q value = 0.019
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
AMP PEAK 31(XP11.23) MUTATED | 28 | 55 | 71 |
AMP PEAK 31(XP11.23) WILD-TYPE | 146 | 151 | 118 |
P value = 9.81e-06 (Fisher's exact test), Q value = 0.0089
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
DEL PEAK 1(1P36.11) MUTATED | 92 | 113 | 62 |
DEL PEAK 1(1P36.11) WILD-TYPE | 82 | 93 | 127 |
P value = 3.23e-07 (Fisher's exact test), Q value = 3e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
DEL PEAK 2(1Q41) MUTATED | 15 | 58 | 22 |
DEL PEAK 2(1Q41) WILD-TYPE | 159 | 148 | 167 |
P value = 1.14e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
DEL PEAK 5(2Q37.3) MUTATED | 39 | 88 | 46 |
DEL PEAK 5(2Q37.3) WILD-TYPE | 135 | 118 | 143 |
P value = 1.78e-05 (Fisher's exact test), Q value = 0.016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
DEL PEAK 6(3P26.2) MUTATED | 45 | 71 | 93 |
DEL PEAK 6(3P26.2) WILD-TYPE | 129 | 135 | 96 |
P value = 1.56e-08 (Fisher's exact test), Q value = 1.4e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
DEL PEAK 9(5Q11.2) MUTATED | 74 | 146 | 127 |
DEL PEAK 9(5Q11.2) WILD-TYPE | 100 | 60 | 62 |
P value = 3.57e-11 (Fisher's exact test), Q value = 3.4e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
DEL PEAK 10(5Q13.2) MUTATED | 95 | 178 | 139 |
DEL PEAK 10(5Q13.2) WILD-TYPE | 79 | 28 | 50 |
P value = 4.09e-10 (Fisher's exact test), Q value = 3.8e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
DEL PEAK 11(6Q27) MUTATED | 127 | 162 | 92 |
DEL PEAK 11(6Q27) WILD-TYPE | 47 | 44 | 97 |
P value = 2.58e-05 (Fisher's exact test), Q value = 0.023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
DEL PEAK 11(6Q27) MUTATED | 92 | 133 | 155 |
DEL PEAK 11(6Q27) WILD-TYPE | 80 | 42 | 66 |
P value = 1.75e-05 (Fisher's exact test), Q value = 0.016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 100 | 67 | 91 |
DEL PEAK 11(6Q27) MUTATED | 67 | 52 | 39 |
DEL PEAK 11(6Q27) WILD-TYPE | 33 | 15 | 52 |
P value = 1.69e-13 (Fisher's exact test), Q value = 1.6e-10
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
DEL PEAK 12(7P22.1) MUTATED | 51 | 133 | 64 |
DEL PEAK 12(7P22.1) WILD-TYPE | 123 | 73 | 125 |
P value = 6.56e-12 (Fisher's exact test), Q value = 6.2e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
DEL PEAK 13(8P23.3) MUTATED | 80 | 164 | 138 |
DEL PEAK 13(8P23.3) WILD-TYPE | 94 | 42 | 51 |
P value = 3.95e-09 (Fisher's exact test), Q value = 3.7e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
DEL PEAK 14(8P21.2) MUTATED | 91 | 166 | 143 |
DEL PEAK 14(8P21.2) WILD-TYPE | 83 | 40 | 46 |
P value = 0.000237 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 215 | 216 | 126 |
DEL PEAK 15(9P24.3) MUTATED | 109 | 73 | 66 |
DEL PEAK 15(9P24.3) WILD-TYPE | 106 | 143 | 60 |
P value = 7.5e-05 (Fisher's exact test), Q value = 0.067
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
DEL PEAK 15(9P24.3) MUTATED | 92 | 90 | 75 |
DEL PEAK 15(9P24.3) WILD-TYPE | 80 | 85 | 146 |
P value = 6.04e-07 (Fisher's exact test), Q value = 0.00056
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
DEL PEAK 16(9Q34.13) MUTATED | 91 | 105 | 141 |
DEL PEAK 16(9Q34.13) WILD-TYPE | 83 | 101 | 48 |
P value = 0.000124 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 128 | 210 | 219 |
DEL PEAK 18(10Q24.2) MUTATED | 40 | 83 | 117 |
DEL PEAK 18(10Q24.2) WILD-TYPE | 88 | 127 | 102 |
P value = 2.37e-05 (Fisher's exact test), Q value = 0.021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
DEL PEAK 18(10Q24.2) MUTATED | 55 | 113 | 78 |
DEL PEAK 18(10Q24.2) WILD-TYPE | 119 | 93 | 111 |
P value = 9.21e-05 (Fisher's exact test), Q value = 0.082
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 57 | 84 | 108 | 149 |
DEL PEAK 18(10Q24.2) MUTATED | 39 | 41 | 46 | 50 |
DEL PEAK 18(10Q24.2) WILD-TYPE | 18 | 43 | 62 | 99 |
P value = 5.22e-10 (Fisher's exact test), Q value = 4.9e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
DEL PEAK 19(11P15.5) MUTATED | 81 | 158 | 99 |
DEL PEAK 19(11P15.5) WILD-TYPE | 93 | 48 | 90 |
P value = 0.000202 (Fisher's exact test), Q value = 0.18
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 128 | 210 | 219 |
DEL PEAK 21(12Q24.33) MUTATED | 52 | 58 | 102 |
DEL PEAK 21(12Q24.33) WILD-TYPE | 76 | 152 | 117 |
P value = 3.95e-09 (Fisher's exact test), Q value = 3.7e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
DEL PEAK 21(12Q24.33) MUTATED | 58 | 112 | 47 |
DEL PEAK 21(12Q24.33) WILD-TYPE | 116 | 94 | 142 |
P value = 1.44e-06 (Fisher's exact test), Q value = 0.0013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
DEL PEAK 22(13Q14.2) MUTATED | 88 | 156 | 114 |
DEL PEAK 22(13Q14.2) WILD-TYPE | 86 | 50 | 75 |
P value = 2.34e-05 (Fisher's exact test), Q value = 0.021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
DEL PEAK 22(13Q14.2) MUTATED | 109 | 88 | 161 |
DEL PEAK 22(13Q14.2) WILD-TYPE | 63 | 87 | 60 |
P value = 0.000123 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
DEL PEAK 23(14Q23.3) MUTATED | 75 | 102 | 122 |
DEL PEAK 23(14Q23.3) WILD-TYPE | 99 | 104 | 67 |
P value = 1.1e-11 (Fisher's exact test), Q value = 1e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
DEL PEAK 24(15Q15.1) MUTATED | 83 | 122 | 155 |
DEL PEAK 24(15Q15.1) WILD-TYPE | 91 | 84 | 34 |
P value = 7.06e-06 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
DEL PEAK 24(15Q15.1) MUTATED | 134 | 97 | 129 |
DEL PEAK 24(15Q15.1) WILD-TYPE | 38 | 78 | 92 |
P value = 0.000193 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
DEL PEAK 26(16Q22.1) MUTATED | 120 | 171 | 162 |
DEL PEAK 26(16Q22.1) WILD-TYPE | 54 | 35 | 27 |
P value = 1.07e-05 (Fisher's exact test), Q value = 0.0097
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 174 | 206 | 189 |
DEL PEAK 27(16Q23.1) MUTATED | 114 | 168 | 162 |
DEL PEAK 27(16Q23.1) WILD-TYPE | 60 | 38 | 27 |
P value = 0.000217 (Fisher's exact test), Q value = 0.19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 215 | 216 | 126 |
DEL PEAK 32(19Q13.33) MUTATED | 127 | 117 | 46 |
DEL PEAK 32(19Q13.33) WILD-TYPE | 88 | 99 | 80 |
P value = 0.00015 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 128 | 210 | 219 |
DEL PEAK 32(19Q13.33) MUTATED | 47 | 126 | 117 |
DEL PEAK 32(19Q13.33) WILD-TYPE | 81 | 84 | 102 |
P value = 2.76e-05 (Fisher's exact test), Q value = 0.025
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 172 | 175 | 221 |
DEL PEAK 33(19Q13.43) MUTATED | 105 | 64 | 110 |
DEL PEAK 33(19Q13.43) WILD-TYPE | 67 | 111 | 111 |
-
Copy number data file = transformed.cor.cli.txt
-
Molecular subtype file = OV-TP.transferedmergedcluster.txt
-
Number of patients = 569
-
Number of significantly focal cnvs = 68
-
Number of molecular subtypes = 14
-
Exclude genes that fewer than K tumors have alterations, 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.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.