This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.
Testing the association between copy number variation 75 focal events and 8 molecular subtypes across 126 patients, 44 significant findings detected with P value < 0.05 and Q value < 0.25.
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amp_3q26.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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amp_11q13.3 cnv correlated to 'CN_CNMF'.
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amp_12p13.33 cnv correlated to 'CN_CNMF'.
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del_2q22.1 cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_MATURE_CNMF'.
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del_3p25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_3p14.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_3p14.2 cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_8p23.2 cnv correlated to 'CN_CNMF'.
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del_9p21.3 cnv correlated to 'CN_CNMF'.
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del_10p11.21 cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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del_11q24.3 cnv correlated to 'CN_CNMF'.
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del_16q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_17p11.2 cnv correlated to 'MIRSEQ_CNMF'.
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del_22q11.1 cnv correlated to 'METHLYATION_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
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 | Fisher's exact test | Fisher's exact test | |
amp 3q26 2 | 90 (71%) | 36 |
1e-05 (0.006) |
1e-05 (0.006) |
0.00422 (1.00) |
0.00024 (0.135) |
1e-05 (0.006) |
1e-05 (0.006) |
1e-05 (0.006) |
1e-05 (0.006) |
del 3p25 3 | 77 (61%) | 49 |
2e-05 (0.0117) |
1e-05 (0.006) |
0.0684 (1.00) |
0.0151 (1.00) |
2e-05 (0.0117) |
0.00012 (0.0682) |
3e-05 (0.0174) |
3e-05 (0.0174) |
del 3p14 3 | 89 (71%) | 37 |
1e-05 (0.006) |
5e-05 (0.0288) |
0.0194 (1.00) |
0.00367 (1.00) |
1e-05 (0.006) |
2e-05 (0.0117) |
2e-05 (0.0117) |
2e-05 (0.0117) |
del 16q23 1 | 53 (42%) | 73 |
1e-05 (0.006) |
1e-05 (0.006) |
0.00125 (0.681) |
0.0062 (1.00) |
1e-05 (0.006) |
1e-05 (0.006) |
1e-05 (0.006) |
1e-05 (0.006) |
del 3p14 2 | 89 (71%) | 37 |
1e-05 (0.006) |
0.0011 (0.601) |
0.308 (1.00) |
0.115 (1.00) |
8e-05 (0.0457) |
6e-05 (0.0344) |
0.00011 (0.0626) |
0.0001 (0.057) |
del 10p11 21 | 32 (25%) | 94 |
0.00039 (0.218) |
0.00062 (0.343) |
0.11 (1.00) |
0.0148 (1.00) |
0.00012 (0.0682) |
0.00179 (0.961) |
6e-05 (0.0344) |
0.00099 (0.543) |
del 22q11 1 | 50 (40%) | 76 |
0.00846 (1.00) |
0.00015 (0.0847) |
0.0149 (1.00) |
0.0884 (1.00) |
0.00084 (0.462) |
0.021 (1.00) |
0.00026 (0.146) |
0.00029 (0.162) |
del 2q22 1 | 46 (37%) | 80 |
0.0104 (1.00) |
0.00021 (0.118) |
0.395 (1.00) |
0.3 (1.00) |
0.00072 (0.397) |
0.0015 (0.81) |
0.00012 (0.0682) |
0.00133 (0.722) |
amp 11q13 3 | 75 (60%) | 51 |
5e-05 (0.0288) |
0.0183 (1.00) |
0.177 (1.00) |
0.124 (1.00) |
0.00334 (1.00) |
0.0134 (1.00) |
0.0317 (1.00) |
0.0105 (1.00) |
amp 12p13 33 | 53 (42%) | 73 |
3e-05 (0.0174) |
0.017 (1.00) |
0.0374 (1.00) |
0.0441 (1.00) |
0.0534 (1.00) |
0.0305 (1.00) |
0.0546 (1.00) |
0.0368 (1.00) |
del 8p23 2 | 57 (45%) | 69 |
0.0002 (0.113) |
0.1 (1.00) |
0.0427 (1.00) |
0.265 (1.00) |
0.00987 (1.00) |
0.235 (1.00) |
0.122 (1.00) |
0.122 (1.00) |
del 9p21 3 | 98 (78%) | 28 |
0.00039 (0.218) |
0.322 (1.00) |
0.0453 (1.00) |
0.0209 (1.00) |
0.0245 (1.00) |
0.0727 (1.00) |
0.0983 (1.00) |
0.0352 (1.00) |
del 11q24 3 | 56 (44%) | 70 |
0.00022 (0.124) |
0.15 (1.00) |
0.673 (1.00) |
0.396 (1.00) |
0.0676 (1.00) |
0.123 (1.00) |
0.163 (1.00) |
0.1 (1.00) |
del 17p11 2 | 57 (45%) | 69 |
0.0871 (1.00) |
0.00471 (1.00) |
0.0152 (1.00) |
0.0384 (1.00) |
7e-05 (0.04) |
0.00287 (1.00) |
0.00131 (0.713) |
0.00063 (0.348) |
amp 1p34 2 | 26 (21%) | 100 |
0.505 (1.00) |
0.325 (1.00) |
0.811 (1.00) |
0.509 (1.00) |
0.384 (1.00) |
0.159 (1.00) |
0.265 (1.00) |
0.205 (1.00) |
amp 1q21 3 | 65 (52%) | 61 |
0.0007 (0.386) |
0.0321 (1.00) |
1 (1.00) |
0.754 (1.00) |
0.102 (1.00) |
0.109 (1.00) |
0.0146 (1.00) |
0.223 (1.00) |
amp 2q14 2 | 41 (33%) | 85 |
0.583 (1.00) |
0.368 (1.00) |
0.613 (1.00) |
0.907 (1.00) |
0.538 (1.00) |
0.507 (1.00) |
0.499 (1.00) |
0.669 (1.00) |
amp 5p15 33 | 73 (58%) | 53 |
0.00055 (0.306) |
0.0748 (1.00) |
0.0517 (1.00) |
0.0705 (1.00) |
0.00714 (1.00) |
0.0145 (1.00) |
0.00343 (1.00) |
0.00593 (1.00) |
amp 6p21 1 | 43 (34%) | 83 |
0.0105 (1.00) |
0.316 (1.00) |
0.288 (1.00) |
0.731 (1.00) |
0.0315 (1.00) |
0.0227 (1.00) |
0.0123 (1.00) |
0.0296 (1.00) |
amp 6q23 3 | 27 (21%) | 99 |
0.0342 (1.00) |
0.178 (1.00) |
0.00796 (1.00) |
0.0316 (1.00) |
0.154 (1.00) |
0.188 (1.00) |
0.111 (1.00) |
0.0957 (1.00) |
amp 7p22 3 | 85 (67%) | 41 |
0.0898 (1.00) |
0.368 (1.00) |
0.00101 (0.552) |
0.0186 (1.00) |
0.00182 (0.976) |
0.685 (1.00) |
0.0157 (1.00) |
0.272 (1.00) |
amp 7p11 2 | 83 (66%) | 43 |
0.148 (1.00) |
0.309 (1.00) |
0.0416 (1.00) |
0.227 (1.00) |
0.0195 (1.00) |
0.58 (1.00) |
0.0247 (1.00) |
0.325 (1.00) |
amp 7q21 2 | 79 (63%) | 47 |
0.0787 (1.00) |
0.0825 (1.00) |
0.982 (1.00) |
1 (1.00) |
0.188 (1.00) |
0.688 (1.00) |
0.0901 (1.00) |
0.386 (1.00) |
amp 8p11 23 | 49 (39%) | 77 |
0.00885 (1.00) |
0.232 (1.00) |
0.287 (1.00) |
0.235 (1.00) |
0.52 (1.00) |
0.175 (1.00) |
0.245 (1.00) |
0.0146 (1.00) |
amp 8p11 21 | 58 (46%) | 68 |
0.00188 (1.00) |
0.507 (1.00) |
0.252 (1.00) |
0.0865 (1.00) |
0.582 (1.00) |
0.767 (1.00) |
0.485 (1.00) |
0.189 (1.00) |
amp 8q24 21 | 99 (79%) | 27 |
0.00093 (0.511) |
0.0244 (1.00) |
0.173 (1.00) |
0.232 (1.00) |
0.00355 (1.00) |
0.0135 (1.00) |
0.0343 (1.00) |
0.0014 (0.757) |
amp 9p13 3 | 27 (21%) | 99 |
0.556 (1.00) |
0.114 (1.00) |
0.328 (1.00) |
0.262 (1.00) |
0.714 (1.00) |
0.169 (1.00) |
0.825 (1.00) |
0.886 (1.00) |
amp 10p11 21 | 34 (27%) | 92 |
0.581 (1.00) |
0.0171 (1.00) |
0.94 (1.00) |
0.849 (1.00) |
0.434 (1.00) |
0.823 (1.00) |
0.516 (1.00) |
0.576 (1.00) |
amp 11p13 | 37 (29%) | 89 |
0.939 (1.00) |
0.935 (1.00) |
0.245 (1.00) |
0.27 (1.00) |
0.538 (1.00) |
0.604 (1.00) |
0.761 (1.00) |
0.786 (1.00) |
amp 12p12 1 | 59 (47%) | 67 |
0.00057 (0.316) |
0.19 (1.00) |
0.358 (1.00) |
0.119 (1.00) |
0.14 (1.00) |
0.0838 (1.00) |
0.137 (1.00) |
0.0746 (1.00) |
amp 13q22 1 | 41 (33%) | 85 |
0.122 (1.00) |
0.173 (1.00) |
0.306 (1.00) |
0.0712 (1.00) |
0.00445 (1.00) |
0.0726 (1.00) |
0.00797 (1.00) |
0.0202 (1.00) |
amp 15q26 3 | 42 (33%) | 84 |
0.127 (1.00) |
0.0129 (1.00) |
0.307 (1.00) |
0.249 (1.00) |
0.00502 (1.00) |
0.0269 (1.00) |
0.006 (1.00) |
0.00222 (1.00) |
amp 17q12 | 46 (37%) | 80 |
0.00413 (1.00) |
0.268 (1.00) |
0.356 (1.00) |
0.278 (1.00) |
0.032 (1.00) |
0.352 (1.00) |
0.117 (1.00) |
0.125 (1.00) |
amp 18p11 32 | 45 (36%) | 81 |
0.00844 (1.00) |
0.311 (1.00) |
0.818 (1.00) |
0.812 (1.00) |
0.117 (1.00) |
0.675 (1.00) |
0.454 (1.00) |
0.52 (1.00) |
amp 18q11 2 | 33 (26%) | 93 |
0.0628 (1.00) |
0.013 (1.00) |
0.362 (1.00) |
0.0333 (1.00) |
0.00583 (1.00) |
0.00334 (1.00) |
0.0413 (1.00) |
0.00205 (1.00) |
amp 19p13 2 | 22 (17%) | 104 |
0.0596 (1.00) |
0.215 (1.00) |
0.221 (1.00) |
0.414 (1.00) |
0.174 (1.00) |
0.462 (1.00) |
0.0589 (1.00) |
0.601 (1.00) |
amp 19q12 | 32 (25%) | 94 |
0.00849 (1.00) |
0.19 (1.00) |
0.432 (1.00) |
0.336 (1.00) |
0.0419 (1.00) |
0.0887 (1.00) |
0.0739 (1.00) |
0.0428 (1.00) |
del 1p36 13 | 43 (34%) | 83 |
0.0598 (1.00) |
0.0356 (1.00) |
0.108 (1.00) |
0.0512 (1.00) |
0.0822 (1.00) |
0.0875 (1.00) |
0.0101 (1.00) |
0.25 (1.00) |
del 1p13 2 | 44 (35%) | 82 |
0.00771 (1.00) |
0.391 (1.00) |
0.259 (1.00) |
0.357 (1.00) |
0.959 (1.00) |
0.115 (1.00) |
0.702 (1.00) |
0.838 (1.00) |
del 1q44 | 15 (12%) | 111 |
0.734 (1.00) |
0.674 (1.00) |
0.262 (1.00) |
0.298 (1.00) |
0.827 (1.00) |
0.662 (1.00) |
0.461 (1.00) |
0.342 (1.00) |
del 2q33 3 | 25 (20%) | 101 |
0.846 (1.00) |
0.109 (1.00) |
0.265 (1.00) |
0.358 (1.00) |
0.0996 (1.00) |
0.056 (1.00) |
0.177 (1.00) |
0.0551 (1.00) |
del 3q11 1 | 18 (14%) | 108 |
0.95 (1.00) |
1 (1.00) |
0.462 (1.00) |
0.138 (1.00) |
0.923 (1.00) |
0.908 (1.00) |
0.595 (1.00) |
0.924 (1.00) |
del 3q26 31 | 11 (9%) | 115 |
0.0683 (1.00) |
0.0189 (1.00) |
0.0676 (1.00) |
0.0966 (1.00) |
0.0148 (1.00) |
0.0122 (1.00) |
0.00692 (1.00) |
0.00165 (0.889) |
del 4p15 2 | 68 (54%) | 58 |
0.0135 (1.00) |
0.226 (1.00) |
0.176 (1.00) |
0.375 (1.00) |
0.00784 (1.00) |
0.594 (1.00) |
0.00435 (1.00) |
0.0906 (1.00) |
del 4q21 23 | 60 (48%) | 66 |
0.00379 (1.00) |
0.18 (1.00) |
0.0519 (1.00) |
0.521 (1.00) |
0.08 (1.00) |
0.509 (1.00) |
0.0173 (1.00) |
0.0627 (1.00) |
del 4q22 1 | 67 (53%) | 59 |
0.00353 (1.00) |
0.519 (1.00) |
0.0325 (1.00) |
0.484 (1.00) |
0.0585 (1.00) |
0.637 (1.00) |
0.0395 (1.00) |
0.174 (1.00) |
del 4q31 3 | 65 (52%) | 61 |
0.0144 (1.00) |
0.0495 (1.00) |
0.188 (1.00) |
0.592 (1.00) |
0.0132 (1.00) |
0.194 (1.00) |
0.0117 (1.00) |
0.0503 (1.00) |
del 5q11 2 | 72 (57%) | 54 |
0.0633 (1.00) |
0.00518 (1.00) |
0.716 (1.00) |
0.655 (1.00) |
0.00905 (1.00) |
0.0422 (1.00) |
0.222 (1.00) |
0.139 (1.00) |
del 5q15 | 72 (57%) | 54 |
0.0764 (1.00) |
0.0513 (1.00) |
0.915 (1.00) |
1 (1.00) |
0.00552 (1.00) |
0.0766 (1.00) |
0.249 (1.00) |
0.21 (1.00) |
del 6p25 3 | 45 (36%) | 81 |
0.0582 (1.00) |
0.172 (1.00) |
0.675 (1.00) |
0.586 (1.00) |
0.198 (1.00) |
0.00886 (1.00) |
0.278 (1.00) |
0.135 (1.00) |
del 6q16 3 | 40 (32%) | 86 |
0.208 (1.00) |
0.635 (1.00) |
0.372 (1.00) |
0.405 (1.00) |
0.227 (1.00) |
0.412 (1.00) |
0.455 (1.00) |
0.698 (1.00) |
del 6q26 | 36 (29%) | 90 |
0.112 (1.00) |
0.482 (1.00) |
0.0708 (1.00) |
0.145 (1.00) |
0.0981 (1.00) |
0.263 (1.00) |
0.203 (1.00) |
0.433 (1.00) |
del 7q31 1 | 34 (27%) | 92 |
0.562 (1.00) |
0.108 (1.00) |
0.319 (1.00) |
0.847 (1.00) |
0.437 (1.00) |
0.562 (1.00) |
0.269 (1.00) |
0.404 (1.00) |
del 7q36 2 | 41 (33%) | 85 |
0.634 (1.00) |
0.332 (1.00) |
0.146 (1.00) |
1 (1.00) |
0.288 (1.00) |
0.473 (1.00) |
0.193 (1.00) |
0.956 (1.00) |
del 10p15 1 | 35 (28%) | 91 |
0.094 (1.00) |
0.396 (1.00) |
0.536 (1.00) |
0.229 (1.00) |
0.312 (1.00) |
0.0555 (1.00) |
0.164 (1.00) |
0.167 (1.00) |
del 10q22 3 | 39 (31%) | 87 |
0.0241 (1.00) |
0.0167 (1.00) |
0.208 (1.00) |
0.124 (1.00) |
0.0603 (1.00) |
0.0253 (1.00) |
0.0731 (1.00) |
0.0734 (1.00) |
del 10q23 31 | 47 (37%) | 79 |
0.174 (1.00) |
0.118 (1.00) |
0.539 (1.00) |
0.509 (1.00) |
0.477 (1.00) |
0.248 (1.00) |
0.362 (1.00) |
0.626 (1.00) |
del 11p15 4 | 54 (43%) | 72 |
0.121 (1.00) |
0.278 (1.00) |
0.0645 (1.00) |
0.0459 (1.00) |
0.887 (1.00) |
0.235 (1.00) |
0.717 (1.00) |
0.437 (1.00) |
del 12q21 2 | 29 (23%) | 97 |
0.743 (1.00) |
0.191 (1.00) |
0.208 (1.00) |
0.164 (1.00) |
0.225 (1.00) |
0.18 (1.00) |
0.33 (1.00) |
0.227 (1.00) |
del 13q12 11 | 56 (44%) | 70 |
0.00509 (1.00) |
0.0229 (1.00) |
0.0227 (1.00) |
0.0617 (1.00) |
0.00507 (1.00) |
0.0129 (1.00) |
0.0178 (1.00) |
0.00955 (1.00) |
del 13q14 2 | 59 (47%) | 67 |
0.0106 (1.00) |
0.00525 (1.00) |
0.0262 (1.00) |
0.0432 (1.00) |
0.00982 (1.00) |
0.0306 (1.00) |
0.0288 (1.00) |
0.0275 (1.00) |
del 13q21 2 | 51 (40%) | 75 |
0.0422 (1.00) |
0.111 (1.00) |
0.34 (1.00) |
0.458 (1.00) |
0.0727 (1.00) |
0.149 (1.00) |
0.201 (1.00) |
0.123 (1.00) |
del 14q31 1 | 44 (35%) | 82 |
0.00363 (1.00) |
0.00325 (1.00) |
0.0208 (1.00) |
0.0147 (1.00) |
0.014 (1.00) |
0.00405 (1.00) |
0.00487 (1.00) |
0.00631 (1.00) |
del 15q11 2 | 41 (33%) | 85 |
0.414 (1.00) |
0.305 (1.00) |
0.801 (1.00) |
0.899 (1.00) |
0.514 (1.00) |
0.324 (1.00) |
0.317 (1.00) |
0.174 (1.00) |
del 17q25 3 | 28 (22%) | 98 |
0.796 (1.00) |
0.612 (1.00) |
0.166 (1.00) |
1 (1.00) |
0.215 (1.00) |
0.775 (1.00) |
0.232 (1.00) |
0.796 (1.00) |
del 18q12 2 | 71 (56%) | 55 |
0.507 (1.00) |
0.0748 (1.00) |
0.114 (1.00) |
0.151 (1.00) |
0.138 (1.00) |
0.105 (1.00) |
0.0746 (1.00) |
0.146 (1.00) |
del 18q21 2 | 77 (61%) | 49 |
0.677 (1.00) |
0.0241 (1.00) |
0.296 (1.00) |
0.36 (1.00) |
0.062 (1.00) |
0.197 (1.00) |
0.0583 (1.00) |
0.152 (1.00) |
del 19p13 3 | 56 (44%) | 70 |
0.0133 (1.00) |
0.598 (1.00) |
0.747 (1.00) |
0.745 (1.00) |
0.0725 (1.00) |
0.0955 (1.00) |
0.0716 (1.00) |
0.253 (1.00) |
del 19q13 31 | 36 (29%) | 90 |
0.0531 (1.00) |
0.0602 (1.00) |
0.333 (1.00) |
0.122 (1.00) |
0.101 (1.00) |
0.074 (1.00) |
0.12 (1.00) |
0.0533 (1.00) |
del 20p12 1 | 23 (18%) | 103 |
0.393 (1.00) |
0.629 (1.00) |
0.58 (1.00) |
0.162 (1.00) |
0.293 (1.00) |
0.0738 (1.00) |
0.471 (1.00) |
0.135 (1.00) |
del 21q11 2 | 75 (60%) | 51 |
0.28 (1.00) |
0.0953 (1.00) |
0.316 (1.00) |
0.247 (1.00) |
0.0475 (1.00) |
0.16 (1.00) |
0.101 (1.00) |
0.0827 (1.00) |
del 21q22 12 | 73 (58%) | 53 |
0.428 (1.00) |
0.0173 (1.00) |
0.0159 (1.00) |
0.00526 (1.00) |
0.0202 (1.00) |
0.151 (1.00) |
0.00933 (1.00) |
0.0233 (1.00) |
del xp21 1 | 50 (40%) | 76 |
0.0132 (1.00) |
0.0557 (1.00) |
0.0481 (1.00) |
0.382 (1.00) |
0.0839 (1.00) |
0.0692 (1.00) |
0.0387 (1.00) |
0.0553 (1.00) |
del xp11 3 | 52 (41%) | 74 |
0.0248 (1.00) |
0.116 (1.00) |
0.0588 (1.00) |
0.0904 (1.00) |
0.00136 (0.737) |
0.00177 (0.952) |
0.0034 (1.00) |
0.00239 (1.00) |
del xq21 33 | 26 (21%) | 100 |
0.671 (1.00) |
0.273 (1.00) |
0.534 (1.00) |
0.125 (1.00) |
0.126 (1.00) |
0.103 (1.00) |
0.264 (1.00) |
0.207 (1.00) |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 52 | 32 |
AMP PEAK 4(3Q26.2) MUTATED | 15 | 52 | 23 |
AMP PEAK 4(3Q26.2) WILD-TYPE | 27 | 0 | 9 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 25 | 60 |
AMP PEAK 4(3Q26.2) MUTATED | 19 | 15 | 56 |
AMP PEAK 4(3Q26.2) WILD-TYPE | 22 | 10 | 4 |
P value = 0.00024 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 20 | 27 | 8 |
AMP PEAK 4(3Q26.2) MUTATED | 15 | 18 | 13 | 7 |
AMP PEAK 4(3Q26.2) WILD-TYPE | 0 | 2 | 14 | 1 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 47 | 68 | 10 |
AMP PEAK 4(3Q26.2) MUTATED | 22 | 62 | 5 |
AMP PEAK 4(3Q26.2) WILD-TYPE | 25 | 6 | 5 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 15 | 43 | 31 |
AMP PEAK 4(3Q26.2) MUTATED | 17 | 5 | 41 | 26 |
AMP PEAK 4(3Q26.2) WILD-TYPE | 19 | 10 | 2 | 5 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 64 | 16 |
AMP PEAK 4(3Q26.2) MUTATED | 21 | 59 | 9 |
AMP PEAK 4(3Q26.2) WILD-TYPE | 24 | 5 | 7 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 10 | 75 |
AMP PEAK 4(3Q26.2) MUTATED | 19 | 3 | 67 |
AMP PEAK 4(3Q26.2) WILD-TYPE | 21 | 7 | 8 |
P value = 5e-05 (Fisher's exact test), Q value = 0.029
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 52 | 32 |
AMP PEAK 17(11Q13.3) MUTATED | 19 | 43 | 13 |
AMP PEAK 17(11Q13.3) WILD-TYPE | 23 | 9 | 19 |
P value = 3e-05 (Fisher's exact test), Q value = 0.017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 52 | 32 |
AMP PEAK 18(12P13.33) MUTATED | 7 | 32 | 14 |
AMP PEAK 18(12P13.33) WILD-TYPE | 35 | 20 | 18 |
P value = 0.00021 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 25 | 60 |
DEL PEAK 4(2Q22.1) MUTATED | 7 | 6 | 33 |
DEL PEAK 4(2Q22.1) WILD-TYPE | 34 | 19 | 27 |
P value = 0.00012 (Fisher's exact test), Q value = 0.068
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 64 | 16 |
DEL PEAK 4(2Q22.1) MUTATED | 9 | 35 | 2 |
DEL PEAK 4(2Q22.1) WILD-TYPE | 36 | 29 | 14 |
P value = 2e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 52 | 32 |
DEL PEAK 6(3P25.3) MUTATED | 19 | 44 | 14 |
DEL PEAK 6(3P25.3) WILD-TYPE | 23 | 8 | 18 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 25 | 60 |
DEL PEAK 6(3P25.3) MUTATED | 15 | 13 | 49 |
DEL PEAK 6(3P25.3) WILD-TYPE | 26 | 12 | 11 |
P value = 2e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 47 | 68 | 10 |
DEL PEAK 6(3P25.3) MUTATED | 19 | 54 | 4 |
DEL PEAK 6(3P25.3) WILD-TYPE | 28 | 14 | 6 |
P value = 0.00012 (Fisher's exact test), Q value = 0.068
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 15 | 43 | 31 |
DEL PEAK 6(3P25.3) MUTATED | 14 | 5 | 34 | 24 |
DEL PEAK 6(3P25.3) WILD-TYPE | 22 | 10 | 9 | 7 |
P value = 3e-05 (Fisher's exact test), Q value = 0.017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 64 | 16 |
DEL PEAK 6(3P25.3) MUTATED | 18 | 52 | 7 |
DEL PEAK 6(3P25.3) WILD-TYPE | 27 | 12 | 9 |
P value = 3e-05 (Fisher's exact test), Q value = 0.017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 10 | 75 |
DEL PEAK 6(3P25.3) MUTATED | 15 | 4 | 58 |
DEL PEAK 6(3P25.3) WILD-TYPE | 25 | 6 | 17 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 52 | 32 |
DEL PEAK 7(3P14.3) MUTATED | 22 | 50 | 17 |
DEL PEAK 7(3P14.3) WILD-TYPE | 20 | 2 | 15 |
P value = 5e-05 (Fisher's exact test), Q value = 0.029
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 25 | 60 |
DEL PEAK 7(3P14.3) MUTATED | 19 | 18 | 52 |
DEL PEAK 7(3P14.3) WILD-TYPE | 22 | 7 | 8 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 47 | 68 | 10 |
DEL PEAK 7(3P14.3) MUTATED | 23 | 60 | 6 |
DEL PEAK 7(3P14.3) WILD-TYPE | 24 | 8 | 4 |
P value = 2e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 15 | 43 | 31 |
DEL PEAK 7(3P14.3) MUTATED | 18 | 6 | 39 | 26 |
DEL PEAK 7(3P14.3) WILD-TYPE | 18 | 9 | 4 | 5 |
P value = 2e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 64 | 16 |
DEL PEAK 7(3P14.3) MUTATED | 22 | 57 | 10 |
DEL PEAK 7(3P14.3) WILD-TYPE | 23 | 7 | 6 |
P value = 2e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 10 | 75 |
DEL PEAK 7(3P14.3) MUTATED | 19 | 5 | 65 |
DEL PEAK 7(3P14.3) WILD-TYPE | 21 | 5 | 10 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 52 | 32 |
DEL PEAK 8(3P14.2) MUTATED | 21 | 49 | 19 |
DEL PEAK 8(3P14.2) WILD-TYPE | 21 | 3 | 13 |
P value = 8e-05 (Fisher's exact test), Q value = 0.046
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 47 | 68 | 10 |
DEL PEAK 8(3P14.2) MUTATED | 25 | 59 | 5 |
DEL PEAK 8(3P14.2) WILD-TYPE | 22 | 9 | 5 |
P value = 6e-05 (Fisher's exact test), Q value = 0.034
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 15 | 43 | 31 |
DEL PEAK 8(3P14.2) MUTATED | 19 | 6 | 38 | 26 |
DEL PEAK 8(3P14.2) WILD-TYPE | 17 | 9 | 5 | 5 |
P value = 0.00011 (Fisher's exact test), Q value = 0.063
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 64 | 16 |
DEL PEAK 8(3P14.2) MUTATED | 24 | 56 | 9 |
DEL PEAK 8(3P14.2) WILD-TYPE | 21 | 8 | 7 |
P value = 1e-04 (Fisher's exact test), Q value = 0.057
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 10 | 75 |
DEL PEAK 8(3P14.2) MUTATED | 21 | 4 | 64 |
DEL PEAK 8(3P14.2) WILD-TYPE | 19 | 6 | 11 |
P value = 2e-04 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 52 | 32 |
DEL PEAK 22(8P23.2) MUTATED | 9 | 32 | 16 |
DEL PEAK 22(8P23.2) WILD-TYPE | 33 | 20 | 16 |
P value = 0.00039 (Fisher's exact test), Q value = 0.22
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 52 | 32 |
DEL PEAK 23(9P21.3) MUTATED | 28 | 49 | 21 |
DEL PEAK 23(9P21.3) WILD-TYPE | 14 | 3 | 11 |
P value = 0.00039 (Fisher's exact test), Q value = 0.22
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 52 | 32 |
DEL PEAK 25(10P11.21) MUTATED | 5 | 23 | 4 |
DEL PEAK 25(10P11.21) WILD-TYPE | 37 | 29 | 28 |
P value = 0.00012 (Fisher's exact test), Q value = 0.068
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 47 | 68 | 10 |
DEL PEAK 25(10P11.21) MUTATED | 3 | 26 | 2 |
DEL PEAK 25(10P11.21) WILD-TYPE | 44 | 42 | 8 |
P value = 6e-05 (Fisher's exact test), Q value = 0.034
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 64 | 16 |
DEL PEAK 25(10P11.21) MUTATED | 3 | 26 | 2 |
DEL PEAK 25(10P11.21) WILD-TYPE | 42 | 38 | 14 |
P value = 0.00022 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 52 | 32 |
DEL PEAK 29(11Q24.3) MUTATED | 10 | 34 | 12 |
DEL PEAK 29(11Q24.3) WILD-TYPE | 32 | 18 | 20 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 52 | 32 |
DEL PEAK 36(16Q23.1) MUTATED | 18 | 10 | 25 |
DEL PEAK 36(16Q23.1) WILD-TYPE | 24 | 42 | 7 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 25 | 60 |
DEL PEAK 36(16Q23.1) MUTATED | 31 | 8 | 14 |
DEL PEAK 36(16Q23.1) WILD-TYPE | 10 | 17 | 46 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 47 | 68 | 10 |
DEL PEAK 36(16Q23.1) MUTATED | 34 | 17 | 1 |
DEL PEAK 36(16Q23.1) WILD-TYPE | 13 | 51 | 9 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 15 | 43 | 31 |
DEL PEAK 36(16Q23.1) MUTATED | 27 | 8 | 8 | 9 |
DEL PEAK 36(16Q23.1) WILD-TYPE | 9 | 7 | 35 | 22 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 64 | 16 |
DEL PEAK 36(16Q23.1) MUTATED | 34 | 16 | 2 |
DEL PEAK 36(16Q23.1) WILD-TYPE | 11 | 48 | 14 |
P value = 1e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 10 | 75 |
DEL PEAK 36(16Q23.1) MUTATED | 31 | 4 | 17 |
DEL PEAK 36(16Q23.1) WILD-TYPE | 9 | 6 | 58 |
P value = 7e-05 (Fisher's exact test), Q value = 0.04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 47 | 68 | 10 |
DEL PEAK 37(17P11.2) MUTATED | 32 | 24 | 1 |
DEL PEAK 37(17P11.2) WILD-TYPE | 15 | 44 | 9 |
P value = 0.00015 (Fisher's exact test), Q value = 0.085
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 25 | 60 |
DEL PEAK 46(22Q11.1) MUTATED | 27 | 8 | 15 |
DEL PEAK 46(22Q11.1) WILD-TYPE | 14 | 17 | 45 |
P value = 0.00026 (Fisher's exact test), Q value = 0.15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 64 | 16 |
DEL PEAK 46(22Q11.1) MUTATED | 28 | 20 | 2 |
DEL PEAK 46(22Q11.1) WILD-TYPE | 17 | 44 | 14 |
P value = 0.00029 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 10 | 75 |
DEL PEAK 46(22Q11.1) MUTATED | 26 | 2 | 22 |
DEL PEAK 46(22Q11.1) WILD-TYPE | 14 | 8 | 53 |
-
Copy number data file = transformed.cor.cli.txt
-
Molecular subtype file = ESCA-TP.transferedmergedcluster.txt
-
Number of patients = 126
-
Number of significantly focal cnvs = 75
-
Number of molecular subtypes = 8
-
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 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.