This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.
Testing the association between copy number variation 55 focal events and 10 molecular subtypes across 331 patients, 109 significant findings detected with P value < 0.05 and Q value < 0.25.
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amp_1q21.3 cnv correlated to 'CN_CNMF'.
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amp_3q22.1 cnv correlated to 'CN_CNMF'.
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amp_3q26.2 cnv correlated to 'CN_CNMF'.
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amp_4p16.3 cnv correlated to 'CN_CNMF'.
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amp_5q35.3 cnv correlated to 'CN_CNMF'.
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amp_7p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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amp_8p11.23 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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amp_9q34.3 cnv correlated to 'CN_CNMF'.
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amp_11q13.3 cnv correlated to 'CN_CNMF'.
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amp_12q24.32 cnv correlated to 'CN_CNMF'.
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amp_14q21.1 cnv correlated to 'CN_CNMF'.
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amp_19q13.43 cnv correlated to 'CN_CNMF'.
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amp_20q13.31 cnv correlated to 'CN_CNMF'.
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del_1p31.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_1q42.2 cnv correlated to 'METHLYATION_CNMF'.
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del_2q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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del_2q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_3p13 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_4q28.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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del_5q11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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del_5q21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_6q14.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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del_8p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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del_8p11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_9p23 cnv correlated to 'CN_CNMF'.
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del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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del_12p13.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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del_12q24.31 cnv correlated to 'CN_CNMF'.
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del_13q14.12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_13q22.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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del_15q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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del_16q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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del_16q23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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del_17p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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del_17q21.31 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_18q22.1 cnv correlated to 'CN_CNMF'.
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del_21q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Clinical Features |
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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Chi-square test | Fisher's exact test | |
del 16q22 3 | 119 (36%) | 212 |
1.38e-16 (7.49e-14) |
1.87e-07 (9.38e-05) |
0.405 (1.00) |
0.207 (1.00) |
2.27e-05 (0.0109) |
1.46e-06 (0.000725) |
1.18e-05 (0.00571) |
4.51e-08 (2.31e-05) |
4.29e-05 (0.0201) |
0.00229 (0.952) |
del 6q14 3 | 105 (32%) | 226 |
5.25e-17 (2.86e-14) |
5.25e-23 (2.87e-20) |
0.00716 (1.00) |
0.0375 (1.00) |
6.65e-08 (3.36e-05) |
1.19e-09 (6.18e-07) |
0.000543 (0.239) |
0.0318 (1.00) |
2.52e-05 (0.0121) |
0.462 (1.00) |
del 8p21 3 | 182 (55%) | 149 |
4.19e-09 (2.17e-06) |
5.51e-09 (2.84e-06) |
0.0304 (1.00) |
0.0834 (1.00) |
3.08e-07 (0.000154) |
8.41e-06 (0.00409) |
4.48e-10 (2.34e-07) |
0.0301 (1.00) |
3.79e-07 (0.000189) |
0.0971 (1.00) |
del 10q23 31 | 101 (31%) | 230 |
2.31e-10 (1.21e-07) |
5.23e-11 (2.77e-08) |
0.0687 (1.00) |
0.306 (1.00) |
1.32e-14 (7.08e-12) |
5.67e-12 (3.02e-09) |
0.000226 (0.103) |
0.0157 (1.00) |
4.05e-05 (0.019) |
0.00253 (1.00) |
del 17p13 1 | 90 (27%) | 241 |
3.37e-14 (1.81e-11) |
5.85e-08 (2.97e-05) |
0.029 (1.00) |
0.0385 (1.00) |
4.65e-10 (2.43e-07) |
3.31e-10 (1.73e-07) |
0.00475 (1.00) |
8.68e-07 (0.000431) |
0.000282 (0.126) |
0.012 (1.00) |
del 21q22 3 | 99 (30%) | 232 |
5.08e-09 (2.62e-06) |
9.18e-22 (5.02e-19) |
0.123 (1.00) |
0.235 (1.00) |
4.08e-20 (2.23e-17) |
5.83e-16 (3.16e-13) |
0.00763 (1.00) |
0.000124 (0.057) |
0.00184 (0.772) |
0.000554 (0.244) |
del 2q22 1 | 50 (15%) | 281 |
4.56e-15 (2.45e-12) |
6.62e-11 (3.5e-08) |
0.015 (1.00) |
0.0897 (1.00) |
9.14e-05 (0.0422) |
2.34e-05 (0.0112) |
0.0859 (1.00) |
0.0608 (1.00) |
0.00013 (0.0594) |
0.000657 (0.287) |
del 15q21 3 | 38 (11%) | 293 |
1.04e-08 (5.35e-06) |
0.000148 (0.0678) |
0.00162 (0.685) |
0.0793 (1.00) |
0.000517 (0.229) |
0.000159 (0.0723) |
0.0208 (1.00) |
8.43e-05 (0.0391) |
0.00419 (1.00) |
0.127 (1.00) |
del 16q23 3 | 130 (39%) | 201 |
3.78e-18 (2.06e-15) |
5.76e-08 (2.92e-05) |
0.784 (1.00) |
0.703 (1.00) |
0.000181 (0.0823) |
4.52e-05 (0.0211) |
0.000595 (0.261) |
4.46e-06 (0.00218) |
0.00704 (1.00) |
0.0471 (1.00) |
del 1p31 3 | 38 (11%) | 293 |
0.000375 (0.167) |
2.32e-05 (0.0112) |
0.312 (1.00) |
0.714 (1.00) |
3.18e-05 (0.0151) |
2.41e-06 (0.00119) |
0.0394 (1.00) |
0.0375 (1.00) |
0.0199 (1.00) |
0.103 (1.00) |
del 2q22 3 | 44 (13%) | 287 |
1.18e-15 (6.36e-13) |
3.58e-08 (1.83e-05) |
0.129 (1.00) |
0.0412 (1.00) |
0.000272 (0.122) |
2.71e-05 (0.013) |
0.395 (1.00) |
0.0474 (1.00) |
0.0566 (1.00) |
0.0621 (1.00) |
del 5q21 1 | 57 (17%) | 274 |
1.45e-15 (7.83e-13) |
2.28e-10 (1.2e-07) |
0.118 (1.00) |
0.228 (1.00) |
0.000459 (0.204) |
6.6e-05 (0.0308) |
0.0457 (1.00) |
0.125 (1.00) |
0.0325 (1.00) |
0.0768 (1.00) |
del 8p11 21 | 105 (32%) | 226 |
9.84e-07 (0.000488) |
8.55e-10 (4.45e-07) |
0.846 (1.00) |
0.59 (1.00) |
1.18e-05 (0.00573) |
0.00026 (0.117) |
0.00142 (0.603) |
0.00398 (1.00) |
0.00316 (1.00) |
0.204 (1.00) |
del 13q14 12 | 139 (42%) | 192 |
4.88e-12 (2.6e-09) |
4.96e-08 (2.53e-05) |
0.0747 (1.00) |
0.207 (1.00) |
8.3e-06 (0.00404) |
7.12e-06 (0.00347) |
0.00107 (0.458) |
0.0244 (1.00) |
0.00257 (1.00) |
0.0865 (1.00) |
amp 7p15 3 | 61 (18%) | 270 |
2.48e-10 (1.3e-07) |
8.74e-08 (4.41e-05) |
0.309 (1.00) |
0.462 (1.00) |
7.08e-05 (0.033) |
0.00489 (1.00) |
0.154 (1.00) |
0.283 (1.00) |
0.195 (1.00) |
0.853 (1.00) |
amp 8q24 21 | 84 (25%) | 247 |
1.48e-16 (8e-14) |
1.96e-05 (0.00949) |
0.00642 (1.00) |
0.0247 (1.00) |
0.000311 (0.139) |
0.000786 (0.34) |
0.00156 (0.663) |
0.0229 (1.00) |
0.00124 (0.529) |
0.477 (1.00) |
del 3p13 | 54 (16%) | 277 |
0.066 (1.00) |
1.37e-07 (6.91e-05) |
0.803 (1.00) |
0.855 (1.00) |
0.000137 (0.0625) |
1.36e-07 (6.85e-05) |
0.0491 (1.00) |
0.0573 (1.00) |
0.00992 (1.00) |
0.0175 (1.00) |
del 17q21 31 | 65 (20%) | 266 |
0.0397 (1.00) |
9.14e-09 (4.7e-06) |
0.529 (1.00) |
0.846 (1.00) |
3.3e-09 (1.71e-06) |
2.87e-05 (0.0137) |
0.0341 (1.00) |
0.00544 (1.00) |
0.0938 (1.00) |
0.144 (1.00) |
amp 8p11 23 | 32 (10%) | 299 |
5e-08 (2.54e-05) |
7.44e-05 (0.0346) |
0.0844 (1.00) |
0.31 (1.00) |
0.0476 (1.00) |
0.0995 (1.00) |
0.142 (1.00) |
0.233 (1.00) |
0.101 (1.00) |
0.274 (1.00) |
del 4q28 2 | 25 (8%) | 306 |
8.45e-05 (0.0391) |
2.78e-05 (0.0133) |
0.138 (1.00) |
0.359 (1.00) |
0.0608 (1.00) |
0.02 (1.00) |
0.193 (1.00) |
0.335 (1.00) |
0.176 (1.00) |
0.167 (1.00) |
del 5q11 2 | 52 (16%) | 279 |
1.09e-10 (5.75e-08) |
2.56e-06 (0.00126) |
0.00457 (1.00) |
0.024 (1.00) |
0.0115 (1.00) |
0.00206 (0.864) |
0.0353 (1.00) |
0.00687 (1.00) |
0.02 (1.00) |
0.0639 (1.00) |
del 12p13 1 | 71 (21%) | 260 |
3.68e-05 (0.0174) |
0.000159 (0.0723) |
0.125 (1.00) |
0.429 (1.00) |
0.00148 (0.628) |
0.00584 (1.00) |
0.0163 (1.00) |
0.0103 (1.00) |
0.0468 (1.00) |
0.247 (1.00) |
del 13q22 1 | 107 (32%) | 224 |
4.69e-14 (2.51e-11) |
3.82e-05 (0.018) |
0.00886 (1.00) |
0.0609 (1.00) |
0.000919 (0.397) |
0.00241 (1.00) |
0.00164 (0.693) |
0.0483 (1.00) |
0.00633 (1.00) |
0.329 (1.00) |
amp 1q21 3 | 22 (7%) | 309 |
2.87e-06 (0.00141) |
0.00482 (1.00) |
0.00369 (1.00) |
0.16 (1.00) |
0.0029 (1.00) |
0.00108 (0.461) |
0.0548 (1.00) |
0.0838 (1.00) |
0.186 (1.00) |
0.655 (1.00) |
amp 3q22 1 | 40 (12%) | 291 |
4.34e-11 (2.3e-08) |
0.00447 (1.00) |
0.174 (1.00) |
0.406 (1.00) |
0.00642 (1.00) |
0.0154 (1.00) |
0.388 (1.00) |
0.862 (1.00) |
0.319 (1.00) |
0.619 (1.00) |
amp 3q26 2 | 47 (14%) | 284 |
3.46e-09 (1.79e-06) |
0.156 (1.00) |
0.142 (1.00) |
0.506 (1.00) |
0.0454 (1.00) |
0.135 (1.00) |
0.335 (1.00) |
0.588 (1.00) |
0.246 (1.00) |
0.509 (1.00) |
amp 4p16 3 | 13 (4%) | 318 |
0.000244 (0.11) |
0.01 (1.00) |
0.505 (1.00) |
0.188 (1.00) |
0.0151 (1.00) |
0.119 (1.00) |
0.786 (1.00) |
0.528 (1.00) |
0.448 (1.00) |
0.671 (1.00) |
amp 5q35 3 | 16 (5%) | 315 |
6.03e-07 (3e-04) |
0.0453 (1.00) |
0.112 (1.00) |
0.158 (1.00) |
0.0881 (1.00) |
0.0819 (1.00) |
0.102 (1.00) |
0.0857 (1.00) |
0.79 (1.00) |
0.694 (1.00) |
amp 9q34 3 | 35 (11%) | 296 |
4.93e-14 (2.63e-11) |
0.0362 (1.00) |
0.0541 (1.00) |
0.0411 (1.00) |
0.00217 (0.906) |
0.00518 (1.00) |
0.0853 (1.00) |
0.0264 (1.00) |
0.225 (1.00) |
0.546 (1.00) |
amp 11q13 3 | 20 (6%) | 311 |
1.7e-06 (0.000841) |
0.0581 (1.00) |
0.521 (1.00) |
0.39 (1.00) |
0.0226 (1.00) |
0.16 (1.00) |
0.789 (1.00) |
0.198 (1.00) |
0.163 (1.00) |
0.6 (1.00) |
amp 12q24 32 | 12 (4%) | 319 |
9.15e-05 (0.0422) |
0.317 (1.00) |
0.228 (1.00) |
0.264 (1.00) |
0.872 (1.00) |
0.0614 (1.00) |
0.256 (1.00) |
0.621 (1.00) |
0.2 (1.00) |
0.396 (1.00) |
amp 14q21 1 | 17 (5%) | 314 |
2.9e-05 (0.0138) |
0.0108 (1.00) |
0.166 (1.00) |
0.139 (1.00) |
0.182 (1.00) |
0.279 (1.00) |
0.417 (1.00) |
0.144 (1.00) |
0.439 (1.00) |
0.984 (1.00) |
amp 19q13 43 | 8 (2%) | 323 |
0.00023 (0.104) |
0.101 (1.00) |
0.452 (1.00) |
0.314 (1.00) |
0.101 (1.00) |
0.0118 (1.00) |
0.471 (1.00) |
0.0993 (1.00) |
0.462 (1.00) |
0.366 (1.00) |
amp 20q13 31 | 21 (6%) | 310 |
0.000309 (0.138) |
0.00104 (0.446) |
0.303 (1.00) |
0.304 (1.00) |
0.0837 (1.00) |
0.126 (1.00) |
0.56 (1.00) |
0.458 (1.00) |
0.284 (1.00) |
0.324 (1.00) |
del 1q42 2 | 27 (8%) | 304 |
0.00077 (0.334) |
0.000471 (0.209) |
0.933 (1.00) |
0.391 (1.00) |
0.464 (1.00) |
0.266 (1.00) |
0.38 (1.00) |
0.819 (1.00) |
0.395 (1.00) |
0.805 (1.00) |
del 9p23 | 26 (8%) | 305 |
3.41e-05 (0.0161) |
0.219 (1.00) |
0.00358 (1.00) |
0.071 (1.00) |
0.0204 (1.00) |
0.0228 (1.00) |
0.408 (1.00) |
0.756 (1.00) |
0.146 (1.00) |
0.74 (1.00) |
del 12q24 31 | 28 (8%) | 303 |
3.8e-06 (0.00186) |
0.0887 (1.00) |
1 (1.00) |
1 (1.00) |
0.0521 (1.00) |
0.116 (1.00) |
0.13 (1.00) |
0.248 (1.00) |
0.304 (1.00) |
0.83 (1.00) |
del 18q22 1 | 83 (25%) | 248 |
1.71e-07 (8.56e-05) |
0.109 (1.00) |
0.319 (1.00) |
0.0644 (1.00) |
0.00845 (1.00) |
0.0141 (1.00) |
0.37 (1.00) |
0.0794 (1.00) |
0.201 (1.00) |
0.0506 (1.00) |
amp 4q13 3 | 6 (2%) | 325 |
0.0351 (1.00) |
0.22 (1.00) |
0.471 (1.00) |
0.635 (1.00) |
0.03 (1.00) |
0.39 (1.00) |
0.347 (1.00) |
0.212 (1.00) |
0.488 (1.00) |
0.355 (1.00) |
amp 15q11 2 | 9 (3%) | 322 |
0.794 (1.00) |
0.635 (1.00) |
1 (1.00) |
1 (1.00) |
0.837 (1.00) |
0.637 (1.00) |
0.357 (1.00) |
1 (1.00) |
0.752 (1.00) |
0.917 (1.00) |
amp xp22 11 | 12 (4%) | 319 |
0.000759 (0.331) |
0.872 (1.00) |
0.372 (1.00) |
0.618 (1.00) |
0.0468 (1.00) |
0.125 (1.00) |
0.0463 (1.00) |
0.0905 (1.00) |
||
amp xp22 11 | 12 (4%) | 319 |
0.000759 (0.331) |
0.934 (1.00) |
0.0933 (1.00) |
0.275 (1.00) |
0.155 (1.00) |
0.758 (1.00) |
0.286 (1.00) |
0.156 (1.00) |
0.182 (1.00) |
0.439 (1.00) |
amp xp21 1 | 11 (3%) | 320 |
0.00277 (1.00) |
0.232 (1.00) |
0.848 (1.00) |
0.735 (1.00) |
0.268 (1.00) |
0.805 (1.00) |
0.0736 (1.00) |
0.0789 (1.00) |
0.094 (1.00) |
0.384 (1.00) |
amp xq21 1 | 9 (3%) | 322 |
0.0582 (1.00) |
0.362 (1.00) |
0.484 (1.00) |
0.495 (1.00) |
0.104 (1.00) |
0.358 (1.00) |
0.0742 (1.00) |
0.374 (1.00) |
0.248 (1.00) |
0.395 (1.00) |
amp xq21 1 | 7 (2%) | 324 |
0.00379 (1.00) |
0.00166 (0.699) |
0.452 (1.00) |
1 (1.00) |
0.509 (1.00) |
0.159 (1.00) |
0.853 (1.00) |
0.91 (1.00) |
0.754 (1.00) |
0.653 (1.00) |
amp xq21 31 | 7 (2%) | 324 |
0.0134 (1.00) |
0.308 (1.00) |
0.848 (1.00) |
0.735 (1.00) |
0.124 (1.00) |
0.185 (1.00) |
0.756 (1.00) |
0.872 (1.00) |
0.699 (1.00) |
0.949 (1.00) |
amp xq25 | 6 (2%) | 325 |
0.224 (1.00) |
0.0367 (1.00) |
0.624 (1.00) |
1 (1.00) |
0.141 (1.00) |
0.0971 (1.00) |
0.179 (1.00) |
0.575 (1.00) |
0.2 (1.00) |
0.192 (1.00) |
amp xq25 | 9 (3%) | 322 |
0.0902 (1.00) |
0.195 (1.00) |
1 (1.00) |
0.771 (1.00) |
0.202 (1.00) |
0.0224 (1.00) |
0.835 (1.00) |
0.374 (1.00) |
0.63 (1.00) |
0.395 (1.00) |
amp xq27 1 | 11 (3%) | 320 |
0.0143 (1.00) |
0.121 (1.00) |
0.418 (1.00) |
0.308 (1.00) |
0.927 (1.00) |
0.692 (1.00) |
0.00868 (1.00) |
0.0338 (1.00) |
0.0129 (1.00) |
0.00927 (1.00) |
del 1q23 1 | 15 (5%) | 316 |
0.111 (1.00) |
0.00399 (1.00) |
0.297 (1.00) |
0.176 (1.00) |
0.036 (1.00) |
0.0022 (0.916) |
0.169 (1.00) |
0.147 (1.00) |
0.0406 (1.00) |
0.459 (1.00) |
del 2p22 1 | 24 (7%) | 307 |
0.0104 (1.00) |
0.0749 (1.00) |
0.0247 (1.00) |
0.786 (1.00) |
0.00528 (1.00) |
0.0292 (1.00) |
0.23 (1.00) |
0.543 (1.00) |
0.0829 (1.00) |
0.518 (1.00) |
del 3q29 | 19 (6%) | 312 |
0.399 (1.00) |
0.0361 (1.00) |
0.73 (1.00) |
0.415 (1.00) |
0.00763 (1.00) |
0.171 (1.00) |
0.302 (1.00) |
0.914 (1.00) |
0.417 (1.00) |
0.91 (1.00) |
del 11q23 2 | 31 (9%) | 300 |
0.0106 (1.00) |
0.0472 (1.00) |
0.155 (1.00) |
0.109 (1.00) |
0.803 (1.00) |
0.962 (1.00) |
0.18 (1.00) |
0.535 (1.00) |
0.483 (1.00) |
0.45 (1.00) |
del 19q13 2 | 29 (9%) | 302 |
0.0206 (1.00) |
0.113 (1.00) |
0.352 (1.00) |
0.502 (1.00) |
0.0444 (1.00) |
0.367 (1.00) |
0.544 (1.00) |
0.0108 (1.00) |
0.128 (1.00) |
0.167 (1.00) |
del 21q22 2 | 34 (10%) | 297 |
0.0729 (1.00) |
0.0101 (1.00) |
0.394 (1.00) |
0.763 (1.00) |
0.00095 (0.409) |
0.000586 (0.257) |
0.861 (1.00) |
0.574 (1.00) |
0.983 (1.00) |
0.585 (1.00) |
P value = 2.87e-06 (Fisher's exact test), Q value = 0.0014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
AMP PEAK 1(1Q21.3) MUTATED | 1 | 3 | 18 |
AMP PEAK 1(1Q21.3) WILD-TYPE | 43 | 180 | 86 |
P value = 4.34e-11 (Fisher's exact test), Q value = 2.3e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
AMP PEAK 2(3Q22.1) MUTATED | 9 | 3 | 28 |
AMP PEAK 2(3Q22.1) WILD-TYPE | 35 | 180 | 76 |
P value = 3.46e-09 (Fisher's exact test), Q value = 1.8e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
AMP PEAK 3(3Q26.2) MUTATED | 11 | 7 | 29 |
AMP PEAK 3(3Q26.2) WILD-TYPE | 33 | 176 | 75 |
P value = 0.000244 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
AMP PEAK 4(4P16.3) MUTATED | 0 | 2 | 11 |
AMP PEAK 4(4P16.3) WILD-TYPE | 44 | 181 | 93 |
P value = 6.03e-07 (Fisher's exact test), Q value = 3e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
AMP PEAK 6(5Q35.3) MUTATED | 0 | 1 | 15 |
AMP PEAK 6(5Q35.3) WILD-TYPE | 44 | 182 | 89 |
P value = 2.48e-10 (Fisher's exact test), Q value = 1.3e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
AMP PEAK 7(7P15.3) MUTATED | 15 | 11 | 35 |
AMP PEAK 7(7P15.3) WILD-TYPE | 29 | 172 | 69 |
P value = 8.74e-08 (Fisher's exact test), Q value = 4.4e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
AMP PEAK 7(7P15.3) MUTATED | 35 | 6 | 20 |
AMP PEAK 7(7P15.3) WILD-TYPE | 61 | 100 | 109 |
P value = 7.08e-05 (Fisher's exact test), Q value = 0.033
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 121 | 97 | 112 |
AMP PEAK 7(7P15.3) MUTATED | 36 | 7 | 18 |
AMP PEAK 7(7P15.3) WILD-TYPE | 85 | 90 | 94 |
P value = 5e-08 (Fisher's exact test), Q value = 2.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
AMP PEAK 8(8P11.23) MUTATED | 8 | 3 | 21 |
AMP PEAK 8(8P11.23) WILD-TYPE | 36 | 180 | 83 |
P value = 7.44e-05 (Fisher's exact test), Q value = 0.035
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
AMP PEAK 8(8P11.23) MUTATED | 20 | 3 | 9 |
AMP PEAK 8(8P11.23) WILD-TYPE | 76 | 103 | 120 |
P value = 1.48e-16 (Fisher's exact test), Q value = 8e-14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
AMP PEAK 9(8Q24.21) MUTATED | 8 | 18 | 58 |
AMP PEAK 9(8Q24.21) WILD-TYPE | 36 | 165 | 46 |
P value = 1.96e-05 (Fisher's exact test), Q value = 0.0095
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
AMP PEAK 9(8Q24.21) MUTATED | 39 | 13 | 32 |
AMP PEAK 9(8Q24.21) WILD-TYPE | 57 | 93 | 97 |
P value = 0.000311 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 121 | 97 | 112 |
AMP PEAK 9(8Q24.21) MUTATED | 40 | 11 | 33 |
AMP PEAK 9(8Q24.21) WILD-TYPE | 81 | 86 | 79 |
P value = 4.93e-14 (Fisher's exact test), Q value = 2.6e-11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
AMP PEAK 10(9Q34.3) MUTATED | 0 | 3 | 32 |
AMP PEAK 10(9Q34.3) WILD-TYPE | 44 | 180 | 72 |
P value = 1.7e-06 (Fisher's exact test), Q value = 0.00084
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
AMP PEAK 11(11Q13.3) MUTATED | 1 | 2 | 17 |
AMP PEAK 11(11Q13.3) WILD-TYPE | 43 | 181 | 87 |
P value = 9.15e-05 (Fisher's exact test), Q value = 0.042
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
AMP PEAK 12(12Q24.32) MUTATED | 0 | 1 | 11 |
AMP PEAK 12(12Q24.32) WILD-TYPE | 44 | 182 | 93 |
P value = 2.9e-05 (Fisher's exact test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
AMP PEAK 13(14Q21.1) MUTATED | 4 | 1 | 12 |
AMP PEAK 13(14Q21.1) WILD-TYPE | 40 | 182 | 92 |
P value = 0.00023 (Fisher's exact test), Q value = 0.1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
AMP PEAK 15(19Q13.43) MUTATED | 0 | 0 | 8 |
AMP PEAK 15(19Q13.43) WILD-TYPE | 44 | 183 | 96 |
P value = 0.000309 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
AMP PEAK 16(20Q13.31) MUTATED | 2 | 4 | 15 |
AMP PEAK 16(20Q13.31) WILD-TYPE | 42 | 179 | 89 |
P value = 0.000375 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
DEL PEAK 1(1P31.3) MUTATED | 2 | 13 | 23 |
DEL PEAK 1(1P31.3) WILD-TYPE | 42 | 170 | 81 |
P value = 2.32e-05 (Fisher's exact test), Q value = 0.011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
DEL PEAK 1(1P31.3) MUTATED | 10 | 2 | 26 |
DEL PEAK 1(1P31.3) WILD-TYPE | 86 | 104 | 103 |
P value = 3.18e-05 (Fisher's exact test), Q value = 0.015
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 121 | 97 | 112 |
DEL PEAK 1(1P31.3) MUTATED | 12 | 2 | 24 |
DEL PEAK 1(1P31.3) WILD-TYPE | 109 | 95 | 88 |
P value = 2.41e-06 (Fisher's exact test), Q value = 0.0012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 93 | 122 |
DEL PEAK 1(1P31.3) MUTATED | 8 | 2 | 28 |
DEL PEAK 1(1P31.3) WILD-TYPE | 107 | 91 | 94 |
P value = 0.000471 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
DEL PEAK 3(1Q42.2) MUTATED | 17 | 3 | 7 |
DEL PEAK 3(1Q42.2) WILD-TYPE | 79 | 103 | 122 |
P value = 4.56e-15 (Fisher's exact test), Q value = 2.5e-12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
DEL PEAK 5(2Q22.1) MUTATED | 16 | 3 | 31 |
DEL PEAK 5(2Q22.1) WILD-TYPE | 28 | 180 | 73 |
P value = 6.62e-11 (Fisher's exact test), Q value = 3.5e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
DEL PEAK 5(2Q22.1) MUTATED | 34 | 2 | 14 |
DEL PEAK 5(2Q22.1) WILD-TYPE | 62 | 104 | 115 |
P value = 9.14e-05 (Fisher's exact test), Q value = 0.042
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 121 | 97 | 112 |
DEL PEAK 5(2Q22.1) MUTATED | 31 | 5 | 14 |
DEL PEAK 5(2Q22.1) WILD-TYPE | 90 | 92 | 98 |
P value = 2.34e-05 (Fisher's exact test), Q value = 0.011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 93 | 122 |
DEL PEAK 5(2Q22.1) MUTATED | 29 | 3 | 18 |
DEL PEAK 5(2Q22.1) WILD-TYPE | 86 | 90 | 104 |
P value = 0.00013 (Chi-square test), Q value = 0.059
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 80 | 28 | 89 | 95 | 29 |
DEL PEAK 5(2Q22.1) MUTATED | 4 | 1 | 17 | 25 | 1 |
DEL PEAK 5(2Q22.1) WILD-TYPE | 76 | 27 | 72 | 70 | 28 |
P value = 1.18e-15 (Fisher's exact test), Q value = 6.4e-13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
DEL PEAK 6(2Q22.3) MUTATED | 15 | 1 | 28 |
DEL PEAK 6(2Q22.3) WILD-TYPE | 29 | 182 | 76 |
P value = 3.58e-08 (Fisher's exact test), Q value = 1.8e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
DEL PEAK 6(2Q22.3) MUTATED | 28 | 2 | 14 |
DEL PEAK 6(2Q22.3) WILD-TYPE | 68 | 104 | 115 |
P value = 0.000272 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 121 | 97 | 112 |
DEL PEAK 6(2Q22.3) MUTATED | 28 | 5 | 11 |
DEL PEAK 6(2Q22.3) WILD-TYPE | 93 | 92 | 101 |
P value = 2.71e-05 (Fisher's exact test), Q value = 0.013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 93 | 122 |
DEL PEAK 6(2Q22.3) MUTATED | 26 | 2 | 16 |
DEL PEAK 6(2Q22.3) WILD-TYPE | 89 | 91 | 106 |
P value = 1.37e-07 (Fisher's exact test), Q value = 6.9e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
DEL PEAK 7(3P13) MUTATED | 4 | 11 | 39 |
DEL PEAK 7(3P13) WILD-TYPE | 92 | 95 | 90 |
P value = 0.000137 (Fisher's exact test), Q value = 0.063
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 121 | 97 | 112 |
DEL PEAK 7(3P13) MUTATED | 14 | 8 | 32 |
DEL PEAK 7(3P13) WILD-TYPE | 107 | 89 | 80 |
P value = 1.36e-07 (Fisher's exact test), Q value = 6.9e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 93 | 122 |
DEL PEAK 7(3P13) MUTATED | 6 | 10 | 38 |
DEL PEAK 7(3P13) WILD-TYPE | 109 | 83 | 84 |
P value = 8.45e-05 (Fisher's exact test), Q value = 0.039
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
DEL PEAK 9(4Q28.2) MUTATED | 7 | 4 | 14 |
DEL PEAK 9(4Q28.2) WILD-TYPE | 37 | 179 | 90 |
P value = 2.78e-05 (Fisher's exact test), Q value = 0.013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
DEL PEAK 9(4Q28.2) MUTATED | 17 | 1 | 7 |
DEL PEAK 9(4Q28.2) WILD-TYPE | 79 | 105 | 122 |
P value = 1.09e-10 (Fisher's exact test), Q value = 5.7e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
DEL PEAK 10(5Q11.2) MUTATED | 6 | 9 | 37 |
DEL PEAK 10(5Q11.2) WILD-TYPE | 38 | 174 | 67 |
P value = 2.56e-06 (Fisher's exact test), Q value = 0.0013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
DEL PEAK 10(5Q11.2) MUTATED | 25 | 3 | 24 |
DEL PEAK 10(5Q11.2) WILD-TYPE | 71 | 103 | 105 |
P value = 1.45e-15 (Fisher's exact test), Q value = 7.8e-13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
DEL PEAK 11(5Q21.1) MUTATED | 19 | 5 | 33 |
DEL PEAK 11(5Q21.1) WILD-TYPE | 25 | 178 | 71 |
P value = 2.28e-10 (Fisher's exact test), Q value = 1.2e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
DEL PEAK 11(5Q21.1) MUTATED | 38 | 6 | 13 |
DEL PEAK 11(5Q21.1) WILD-TYPE | 58 | 100 | 116 |
P value = 0.000459 (Fisher's exact test), Q value = 0.2
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 121 | 97 | 112 |
DEL PEAK 11(5Q21.1) MUTATED | 34 | 9 | 14 |
DEL PEAK 11(5Q21.1) WILD-TYPE | 87 | 88 | 98 |
P value = 6.6e-05 (Fisher's exact test), Q value = 0.031
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 93 | 122 |
DEL PEAK 11(5Q21.1) MUTATED | 34 | 7 | 16 |
DEL PEAK 11(5Q21.1) WILD-TYPE | 81 | 86 | 106 |
P value = 5.25e-17 (Fisher's exact test), Q value = 2.9e-14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
DEL PEAK 12(6Q14.3) MUTATED | 29 | 23 | 53 |
DEL PEAK 12(6Q14.3) WILD-TYPE | 15 | 160 | 51 |
P value = 5.25e-23 (Fisher's exact test), Q value = 2.9e-20
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
DEL PEAK 12(6Q14.3) MUTATED | 68 | 8 | 29 |
DEL PEAK 12(6Q14.3) WILD-TYPE | 28 | 98 | 100 |
P value = 6.65e-08 (Fisher's exact test), Q value = 3.4e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 121 | 97 | 112 |
DEL PEAK 12(6Q14.3) MUTATED | 61 | 15 | 29 |
DEL PEAK 12(6Q14.3) WILD-TYPE | 60 | 82 | 83 |
P value = 1.19e-09 (Fisher's exact test), Q value = 6.2e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 93 | 122 |
DEL PEAK 12(6Q14.3) MUTATED | 60 | 11 | 34 |
DEL PEAK 12(6Q14.3) WILD-TYPE | 55 | 82 | 88 |
P value = 0.000543 (Chi-square test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 63 | 51 | 86 | 24 | 97 |
DEL PEAK 12(6Q14.3) MUTATED | 22 | 4 | 31 | 5 | 40 |
DEL PEAK 12(6Q14.3) WILD-TYPE | 41 | 47 | 55 | 19 | 57 |
P value = 2.52e-05 (Chi-square test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 80 | 28 | 89 | 95 | 29 |
DEL PEAK 12(6Q14.3) MUTATED | 23 | 3 | 28 | 46 | 2 |
DEL PEAK 12(6Q14.3) WILD-TYPE | 57 | 25 | 61 | 49 | 27 |
P value = 4.19e-09 (Fisher's exact test), Q value = 2.2e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
DEL PEAK 13(8P21.3) MUTATED | 13 | 88 | 81 |
DEL PEAK 13(8P21.3) WILD-TYPE | 31 | 95 | 23 |
P value = 5.51e-09 (Fisher's exact test), Q value = 2.8e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
DEL PEAK 13(8P21.3) MUTATED | 53 | 35 | 94 |
DEL PEAK 13(8P21.3) WILD-TYPE | 43 | 71 | 35 |
P value = 3.08e-07 (Fisher's exact test), Q value = 0.00015
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 121 | 97 | 112 |
DEL PEAK 13(8P21.3) MUTATED | 69 | 33 | 80 |
DEL PEAK 13(8P21.3) WILD-TYPE | 52 | 64 | 32 |
P value = 8.41e-06 (Fisher's exact test), Q value = 0.0041
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 93 | 122 |
DEL PEAK 13(8P21.3) MUTATED | 54 | 40 | 88 |
DEL PEAK 13(8P21.3) WILD-TYPE | 61 | 53 | 34 |
P value = 4.48e-10 (Chi-square test), Q value = 2.3e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 63 | 51 | 86 | 24 | 97 |
DEL PEAK 13(8P21.3) MUTATED | 48 | 12 | 54 | 4 | 59 |
DEL PEAK 13(8P21.3) WILD-TYPE | 15 | 39 | 32 | 20 | 38 |
P value = 3.79e-07 (Chi-square test), Q value = 0.00019
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 80 | 28 | 89 | 95 | 29 |
DEL PEAK 13(8P21.3) MUTATED | 51 | 9 | 56 | 58 | 3 |
DEL PEAK 13(8P21.3) WILD-TYPE | 29 | 19 | 33 | 37 | 26 |
P value = 9.84e-07 (Fisher's exact test), Q value = 0.00049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
DEL PEAK 14(8P11.21) MUTATED | 1 | 62 | 42 |
DEL PEAK 14(8P11.21) WILD-TYPE | 43 | 121 | 62 |
P value = 8.55e-10 (Fisher's exact test), Q value = 4.5e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
DEL PEAK 14(8P11.21) MUTATED | 29 | 12 | 64 |
DEL PEAK 14(8P11.21) WILD-TYPE | 67 | 94 | 65 |
P value = 1.18e-05 (Fisher's exact test), Q value = 0.0057
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 121 | 97 | 112 |
DEL PEAK 14(8P11.21) MUTATED | 42 | 14 | 49 |
DEL PEAK 14(8P11.21) WILD-TYPE | 79 | 83 | 63 |
P value = 0.00026 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 93 | 122 |
DEL PEAK 14(8P11.21) MUTATED | 31 | 19 | 55 |
DEL PEAK 14(8P11.21) WILD-TYPE | 84 | 74 | 67 |
P value = 3.41e-05 (Fisher's exact test), Q value = 0.016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
DEL PEAK 15(9P23) MUTATED | 1 | 6 | 19 |
DEL PEAK 15(9P23) WILD-TYPE | 43 | 177 | 85 |
P value = 2.31e-10 (Fisher's exact test), Q value = 1.2e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
DEL PEAK 16(10Q23.31) MUTATED | 7 | 36 | 58 |
DEL PEAK 16(10Q23.31) WILD-TYPE | 37 | 147 | 46 |
P value = 5.23e-11 (Fisher's exact test), Q value = 2.8e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
DEL PEAK 16(10Q23.31) MUTATED | 23 | 12 | 66 |
DEL PEAK 16(10Q23.31) WILD-TYPE | 73 | 94 | 63 |
P value = 1.32e-14 (Fisher's exact test), Q value = 7.1e-12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 121 | 97 | 112 |
DEL PEAK 16(10Q23.31) MUTATED | 23 | 12 | 66 |
DEL PEAK 16(10Q23.31) WILD-TYPE | 98 | 85 | 46 |
P value = 5.67e-12 (Fisher's exact test), Q value = 3e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 93 | 122 |
DEL PEAK 16(10Q23.31) MUTATED | 15 | 20 | 66 |
DEL PEAK 16(10Q23.31) WILD-TYPE | 100 | 73 | 56 |
P value = 0.000226 (Chi-square test), Q value = 0.1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 63 | 51 | 86 | 24 | 97 |
DEL PEAK 16(10Q23.31) MUTATED | 28 | 7 | 31 | 1 | 31 |
DEL PEAK 16(10Q23.31) WILD-TYPE | 35 | 44 | 55 | 23 | 66 |
P value = 4.05e-05 (Chi-square test), Q value = 0.019
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 80 | 28 | 89 | 95 | 29 |
DEL PEAK 16(10Q23.31) MUTATED | 31 | 1 | 35 | 30 | 1 |
DEL PEAK 16(10Q23.31) WILD-TYPE | 49 | 27 | 54 | 65 | 28 |
P value = 3.68e-05 (Fisher's exact test), Q value = 0.017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
DEL PEAK 18(12P13.1) MUTATED | 4 | 29 | 38 |
DEL PEAK 18(12P13.1) WILD-TYPE | 40 | 154 | 66 |
P value = 0.000159 (Fisher's exact test), Q value = 0.072
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
DEL PEAK 18(12P13.1) MUTATED | 25 | 9 | 37 |
DEL PEAK 18(12P13.1) WILD-TYPE | 71 | 97 | 92 |
P value = 3.8e-06 (Fisher's exact test), Q value = 0.0019
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
DEL PEAK 19(12Q24.31) MUTATED | 2 | 5 | 21 |
DEL PEAK 19(12Q24.31) WILD-TYPE | 42 | 178 | 83 |
P value = 4.88e-12 (Fisher's exact test), Q value = 2.6e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
DEL PEAK 20(13Q14.12) MUTATED | 27 | 45 | 67 |
DEL PEAK 20(13Q14.12) WILD-TYPE | 17 | 138 | 37 |
P value = 4.96e-08 (Fisher's exact test), Q value = 2.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
DEL PEAK 20(13Q14.12) MUTATED | 53 | 21 | 65 |
DEL PEAK 20(13Q14.12) WILD-TYPE | 43 | 85 | 64 |
P value = 8.3e-06 (Fisher's exact test), Q value = 0.004
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 121 | 97 | 112 |
DEL PEAK 20(13Q14.12) MUTATED | 53 | 23 | 63 |
DEL PEAK 20(13Q14.12) WILD-TYPE | 68 | 74 | 49 |
P value = 7.12e-06 (Fisher's exact test), Q value = 0.0035
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 93 | 122 |
DEL PEAK 20(13Q14.12) MUTATED | 51 | 21 | 67 |
DEL PEAK 20(13Q14.12) WILD-TYPE | 64 | 72 | 55 |
P value = 4.69e-14 (Fisher's exact test), Q value = 2.5e-11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
DEL PEAK 21(13Q22.1) MUTATED | 17 | 28 | 62 |
DEL PEAK 21(13Q22.1) WILD-TYPE | 27 | 155 | 42 |
P value = 3.82e-05 (Fisher's exact test), Q value = 0.018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
DEL PEAK 21(13Q22.1) MUTATED | 40 | 17 | 50 |
DEL PEAK 21(13Q22.1) WILD-TYPE | 56 | 89 | 79 |
P value = 1.04e-08 (Fisher's exact test), Q value = 5.3e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
DEL PEAK 22(15Q21.3) MUTATED | 1 | 8 | 29 |
DEL PEAK 22(15Q21.3) WILD-TYPE | 43 | 175 | 75 |
P value = 0.000148 (Fisher's exact test), Q value = 0.068
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
DEL PEAK 22(15Q21.3) MUTATED | 14 | 2 | 22 |
DEL PEAK 22(15Q21.3) WILD-TYPE | 82 | 104 | 107 |
P value = 0.000517 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 121 | 97 | 112 |
DEL PEAK 22(15Q21.3) MUTATED | 17 | 2 | 19 |
DEL PEAK 22(15Q21.3) WILD-TYPE | 104 | 95 | 93 |
P value = 0.000159 (Fisher's exact test), Q value = 0.072
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 93 | 122 |
DEL PEAK 22(15Q21.3) MUTATED | 12 | 2 | 24 |
DEL PEAK 22(15Q21.3) WILD-TYPE | 103 | 91 | 98 |
P value = 8.43e-05 (Fisher's exact test), Q value = 0.039
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 52 | 86 | 104 | 79 |
DEL PEAK 22(15Q21.3) MUTATED | 1 | 18 | 4 | 13 |
DEL PEAK 22(15Q21.3) WILD-TYPE | 51 | 68 | 100 | 66 |
P value = 1.38e-16 (Fisher's exact test), Q value = 7.5e-14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
DEL PEAK 23(16Q22.3) MUTATED | 7 | 40 | 72 |
DEL PEAK 23(16Q22.3) WILD-TYPE | 37 | 143 | 32 |
P value = 1.87e-07 (Fisher's exact test), Q value = 9.4e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
DEL PEAK 23(16Q22.3) MUTATED | 38 | 17 | 64 |
DEL PEAK 23(16Q22.3) WILD-TYPE | 58 | 89 | 65 |
P value = 2.27e-05 (Fisher's exact test), Q value = 0.011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 121 | 97 | 112 |
DEL PEAK 23(16Q22.3) MUTATED | 44 | 19 | 56 |
DEL PEAK 23(16Q22.3) WILD-TYPE | 77 | 78 | 56 |
P value = 1.46e-06 (Fisher's exact test), Q value = 0.00072
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 93 | 122 |
DEL PEAK 23(16Q22.3) MUTATED | 30 | 23 | 66 |
DEL PEAK 23(16Q22.3) WILD-TYPE | 85 | 70 | 56 |
P value = 1.18e-05 (Chi-square test), Q value = 0.0057
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 63 | 51 | 86 | 24 | 97 |
DEL PEAK 23(16Q22.3) MUTATED | 17 | 11 | 33 | 2 | 52 |
DEL PEAK 23(16Q22.3) WILD-TYPE | 46 | 40 | 53 | 22 | 45 |
P value = 4.51e-08 (Fisher's exact test), Q value = 2.3e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 52 | 86 | 104 | 79 |
DEL PEAK 23(16Q22.3) MUTATED | 6 | 51 | 30 | 28 |
DEL PEAK 23(16Q22.3) WILD-TYPE | 46 | 35 | 74 | 51 |
P value = 4.29e-05 (Chi-square test), Q value = 0.02
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 80 | 28 | 89 | 95 | 29 |
DEL PEAK 23(16Q22.3) MUTATED | 21 | 4 | 35 | 50 | 5 |
DEL PEAK 23(16Q22.3) WILD-TYPE | 59 | 24 | 54 | 45 | 24 |
P value = 3.78e-18 (Fisher's exact test), Q value = 2.1e-15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
DEL PEAK 24(16Q23.3) MUTATED | 4 | 50 | 76 |
DEL PEAK 24(16Q23.3) WILD-TYPE | 40 | 133 | 28 |
P value = 5.76e-08 (Fisher's exact test), Q value = 2.9e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
DEL PEAK 24(16Q23.3) MUTATED | 39 | 20 | 71 |
DEL PEAK 24(16Q23.3) WILD-TYPE | 57 | 86 | 58 |
P value = 0.000181 (Fisher's exact test), Q value = 0.082
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 121 | 97 | 112 |
DEL PEAK 24(16Q23.3) MUTATED | 47 | 24 | 59 |
DEL PEAK 24(16Q23.3) WILD-TYPE | 74 | 73 | 53 |
P value = 4.52e-05 (Fisher's exact test), Q value = 0.021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 93 | 122 |
DEL PEAK 24(16Q23.3) MUTATED | 32 | 31 | 67 |
DEL PEAK 24(16Q23.3) WILD-TYPE | 83 | 62 | 55 |
P value = 4.46e-06 (Fisher's exact test), Q value = 0.0022
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 52 | 86 | 104 | 79 |
DEL PEAK 24(16Q23.3) MUTATED | 8 | 50 | 35 | 32 |
DEL PEAK 24(16Q23.3) WILD-TYPE | 44 | 36 | 69 | 47 |
P value = 3.37e-14 (Fisher's exact test), Q value = 1.8e-11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
DEL PEAK 25(17P13.1) MUTATED | 3 | 29 | 58 |
DEL PEAK 25(17P13.1) WILD-TYPE | 41 | 154 | 46 |
P value = 5.85e-08 (Fisher's exact test), Q value = 3e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
DEL PEAK 25(17P13.1) MUTATED | 17 | 15 | 58 |
DEL PEAK 25(17P13.1) WILD-TYPE | 79 | 91 | 71 |
P value = 4.65e-10 (Fisher's exact test), Q value = 2.4e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 121 | 97 | 112 |
DEL PEAK 25(17P13.1) MUTATED | 21 | 13 | 56 |
DEL PEAK 25(17P13.1) WILD-TYPE | 100 | 84 | 56 |
P value = 3.31e-10 (Fisher's exact test), Q value = 1.7e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 93 | 122 |
DEL PEAK 25(17P13.1) MUTATED | 14 | 17 | 59 |
DEL PEAK 25(17P13.1) WILD-TYPE | 101 | 76 | 63 |
P value = 8.68e-07 (Fisher's exact test), Q value = 0.00043
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 52 | 86 | 104 | 79 |
DEL PEAK 25(17P13.1) MUTATED | 4 | 41 | 21 | 21 |
DEL PEAK 25(17P13.1) WILD-TYPE | 48 | 45 | 83 | 58 |
P value = 0.000282 (Chi-square test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 80 | 28 | 89 | 95 | 29 |
DEL PEAK 25(17P13.1) MUTATED | 20 | 2 | 27 | 37 | 1 |
DEL PEAK 25(17P13.1) WILD-TYPE | 60 | 26 | 62 | 58 | 28 |
P value = 9.14e-09 (Fisher's exact test), Q value = 4.7e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
DEL PEAK 26(17Q21.31) MUTATED | 5 | 14 | 46 |
DEL PEAK 26(17Q21.31) WILD-TYPE | 91 | 92 | 83 |
P value = 3.3e-09 (Fisher's exact test), Q value = 1.7e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 121 | 97 | 112 |
DEL PEAK 26(17Q21.31) MUTATED | 13 | 8 | 44 |
DEL PEAK 26(17Q21.31) WILD-TYPE | 108 | 89 | 68 |
P value = 2.87e-05 (Fisher's exact test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 93 | 122 |
DEL PEAK 26(17Q21.31) MUTATED | 10 | 16 | 39 |
DEL PEAK 26(17Q21.31) WILD-TYPE | 105 | 77 | 83 |
P value = 1.71e-07 (Fisher's exact test), Q value = 8.6e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
DEL PEAK 27(18Q22.1) MUTATED | 6 | 30 | 47 |
DEL PEAK 27(18Q22.1) WILD-TYPE | 38 | 153 | 57 |
P value = 5.08e-09 (Fisher's exact test), Q value = 2.6e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 44 | 183 | 104 |
DEL PEAK 30(21Q22.3) MUTATED | 1 | 48 | 50 |
DEL PEAK 30(21Q22.3) WILD-TYPE | 43 | 135 | 54 |
P value = 9.18e-22 (Fisher's exact test), Q value = 5e-19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 96 | 106 | 129 |
DEL PEAK 30(21Q22.3) MUTATED | 7 | 14 | 78 |
DEL PEAK 30(21Q22.3) WILD-TYPE | 89 | 92 | 51 |
P value = 4.08e-20 (Fisher's exact test), Q value = 2.2e-17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 121 | 97 | 112 |
DEL PEAK 30(21Q22.3) MUTATED | 13 | 15 | 71 |
DEL PEAK 30(21Q22.3) WILD-TYPE | 108 | 82 | 41 |
P value = 5.83e-16 (Fisher's exact test), Q value = 3.2e-13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 115 | 93 | 122 |
DEL PEAK 30(21Q22.3) MUTATED | 8 | 24 | 67 |
DEL PEAK 30(21Q22.3) WILD-TYPE | 107 | 69 | 55 |
P value = 0.000124 (Fisher's exact test), Q value = 0.057
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 52 | 86 | 104 | 79 |
DEL PEAK 30(21Q22.3) MUTATED | 5 | 38 | 33 | 20 |
DEL PEAK 30(21Q22.3) WILD-TYPE | 47 | 48 | 71 | 59 |
P value = 0.000554 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 67 | 41 | 88 | 125 |
DEL PEAK 30(21Q22.3) MUTATED | 31 | 4 | 27 | 34 |
DEL PEAK 30(21Q22.3) WILD-TYPE | 36 | 37 | 61 | 91 |
-
Copy number data file = transformed.cor.cli.txt
-
Molecular subtype file = PRAD-TP.transferedmergedcluster.txt
-
Number of patients = 331
-
Number of significantly focal cnvs = 55
-
Number of molecular subtypes = 10
-
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.