This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.
Testing the association between copy number variation 58 focal events and 8 molecular subtypes across 150 patients, 76 significant findings detected with P value < 0.05 and Q value < 0.25.
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amp_1p32.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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amp_1q24.3 cnv correlated to 'CN_CNMF'.
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amp_5p15.33 cnv correlated to 'CN_CNMF'.
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amp_6p21.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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amp_6q24.3 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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amp_12q15 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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amp_17p11.2 cnv correlated to 'CN_CNMF'.
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amp_17q24.3 cnv correlated to 'METHLYATION_CNMF'.
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amp_19p13.2 cnv correlated to 'CN_CNMF'.
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amp_19q12 cnv correlated to 'CN_CNMF'.
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amp_21q21.1 cnv correlated to 'CN_CNMF'.
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amp_xp21.1 cnv correlated to 'CN_CNMF'.
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del_1p36.32 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_1q44 cnv correlated to 'CN_CNMF'.
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del_2p25.3 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_2q37.3 cnv correlated to 'CN_CNMF'.
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del_2q37.3 cnv correlated to 'CN_CNMF'.
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del_3p21.31 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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del_4q35.1 cnv correlated to 'CN_CNMF'.
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del_6q14.1 cnv correlated to 'CN_CNMF'.
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del_9p24.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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del_9p21.3 cnv correlated to 'CN_CNMF'.
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del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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del_11p15.5 cnv correlated to 'CN_CNMF'.
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del_11q24.3 cnv correlated to 'CN_CNMF'.
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del_12p13.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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del_13q14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_16q12.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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del_17p13.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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del_17q11.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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del_19p13.3 cnv correlated to 'METHLYATION_CNMF'.
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del_22q13.31 cnv correlated to 'CN_CNMF'.
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del_xq21.1 cnv correlated to 'METHLYATION_CNMF'.
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del_xq27.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_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 | 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 | |
amp 12q15 | 58 (39%) | 92 |
3.94e-17 (1.83e-14) |
8.67e-10 (3.94e-07) |
5.17e-10 (2.36e-07) |
3.47e-13 (1.6e-10) |
2.88e-10 (1.32e-07) |
1.03e-11 (4.77e-09) |
5.53e-11 (2.55e-08) |
1.03e-11 (4.77e-09) |
amp 6q24 3 | 47 (31%) | 103 |
0.00291 (1.00) |
2.06e-05 (0.00883) |
0.000218 (0.0882) |
9.54e-06 (0.00413) |
2.36e-05 (0.01) |
2.74e-05 (0.0117) |
1.11e-05 (0.00481) |
0.000142 (0.058) |
del 1p36 32 | 46 (31%) | 104 |
0.0281 (1.00) |
1.35e-06 (0.000597) |
2.77e-05 (0.0117) |
4.56e-06 (0.00199) |
2e-06 (0.000878) |
3.48e-09 (1.58e-06) |
6.19e-07 (0.000277) |
3.48e-09 (1.58e-06) |
del 10q23 31 | 84 (56%) | 66 |
6.14e-10 (2.8e-07) |
3.5e-10 (1.6e-07) |
3.76e-09 (1.7e-06) |
3.3e-07 (0.000148) |
0.00176 (0.642) |
0.000606 (0.237) |
0.00148 (0.549) |
0.000606 (0.237) |
del 2p25 3 | 52 (35%) | 98 |
0.00207 (0.738) |
2.29e-05 (0.00978) |
0.000317 (0.127) |
4.79e-06 (0.00208) |
0.00176 (0.642) |
8.81e-05 (0.0363) |
0.00283 (0.983) |
8.81e-05 (0.0363) |
del 13q14 2 | 106 (71%) | 44 |
6.33e-07 (0.000282) |
7.15e-07 (0.000318) |
2.08e-05 (0.00892) |
4.37e-06 (0.0019) |
0.0138 (1.00) |
0.0141 (1.00) |
0.00805 (1.00) |
0.0141 (1.00) |
del 17p13 1 | 71 (47%) | 79 |
0.00044 (0.174) |
0.000961 (0.369) |
3.34e-05 (0.0141) |
0.000263 (0.106) |
0.0684 (1.00) |
0.0518 (1.00) |
0.0303 (1.00) |
0.0518 (1.00) |
del xq27 1 | 74 (49%) | 76 |
0.000611 (0.238) |
0.000303 (0.122) |
0.0403 (1.00) |
0.00051 (0.201) |
0.00607 (1.00) |
0.00115 (0.438) |
0.00553 (1.00) |
0.00115 (0.438) |
amp 1p32 1 | 55 (37%) | 95 |
1.32e-06 (0.000584) |
9.87e-07 (0.000438) |
0.887 (1.00) |
0.219 (1.00) |
0.017 (1.00) |
0.00269 (0.941) |
0.0596 (1.00) |
0.00834 (1.00) |
amp 6p21 1 | 36 (24%) | 114 |
4.82e-05 (0.0202) |
7.31e-05 (0.0304) |
0.0015 (0.554) |
0.00129 (0.482) |
0.0177 (1.00) |
0.0015 (0.554) |
0.00825 (1.00) |
0.00643 (1.00) |
del 3p21 31 | 33 (22%) | 117 |
0.012 (1.00) |
0.00019 (0.0773) |
0.00194 (0.695) |
0.000343 (0.136) |
0.0089 (1.00) |
0.0152 (1.00) |
0.00505 (1.00) |
0.00409 (1.00) |
del 9p24 3 | 58 (39%) | 92 |
0.000266 (0.107) |
0.0283 (1.00) |
0.172 (1.00) |
0.00114 (0.435) |
0.00289 (1.00) |
0.000341 (0.136) |
0.0021 (0.746) |
0.00113 (0.433) |
del 12p13 1 | 52 (35%) | 98 |
5.89e-05 (0.0245) |
7.32e-05 (0.0304) |
0.281 (1.00) |
0.269 (1.00) |
0.0468 (1.00) |
0.0315 (1.00) |
0.0819 (1.00) |
0.0315 (1.00) |
del 16q12 1 | 83 (55%) | 67 |
4.93e-05 (0.0206) |
0.000406 (0.161) |
0.0457 (1.00) |
0.00556 (1.00) |
0.0472 (1.00) |
0.00586 (1.00) |
0.0399 (1.00) |
0.00586 (1.00) |
del 17q11 2 | 45 (30%) | 105 |
3.5e-06 (0.00153) |
0.00012 (0.0494) |
0.139 (1.00) |
0.179 (1.00) |
0.00234 (0.828) |
0.000696 (0.269) |
0.00127 (0.475) |
0.0027 (0.943) |
amp 1q24 3 | 65 (43%) | 85 |
5.84e-05 (0.0243) |
0.00482 (1.00) |
0.747 (1.00) |
0.28 (1.00) |
0.268 (1.00) |
0.154 (1.00) |
0.142 (1.00) |
0.305 (1.00) |
amp 5p15 33 | 67 (45%) | 83 |
0.000629 (0.245) |
0.0258 (1.00) |
0.237 (1.00) |
0.386 (1.00) |
0.273 (1.00) |
0.113 (1.00) |
0.178 (1.00) |
0.212 (1.00) |
amp 17p11 2 | 60 (40%) | 90 |
1.73e-07 (7.77e-05) |
0.0174 (1.00) |
0.456 (1.00) |
0.319 (1.00) |
1 (1.00) |
1 (1.00) |
0.841 (1.00) |
1 (1.00) |
amp 17q24 3 | 45 (30%) | 105 |
0.085 (1.00) |
0.000162 (0.0658) |
0.00505 (1.00) |
0.5 (1.00) |
0.0353 (1.00) |
0.00121 (0.456) |
0.0671 (1.00) |
0.00358 (1.00) |
amp 19p13 2 | 60 (40%) | 90 |
4.12e-05 (0.0174) |
0.527 (1.00) |
1 (1.00) |
0.428 (1.00) |
0.659 (1.00) |
0.562 (1.00) |
0.892 (1.00) |
0.562 (1.00) |
amp 19q12 | 53 (35%) | 97 |
1.09e-06 (0.000482) |
0.00143 (0.532) |
0.777 (1.00) |
0.0638 (1.00) |
0.391 (1.00) |
0.228 (1.00) |
0.539 (1.00) |
0.228 (1.00) |
amp 21q21 1 | 48 (32%) | 102 |
4.36e-05 (0.0184) |
0.000889 (0.342) |
0.763 (1.00) |
0.271 (1.00) |
0.191 (1.00) |
0.268 (1.00) |
0.164 (1.00) |
0.268 (1.00) |
amp xp21 1 | 52 (35%) | 98 |
2.3e-06 (0.00101) |
0.0273 (1.00) |
1 (1.00) |
0.451 (1.00) |
0.913 (1.00) |
0.788 (1.00) |
0.882 (1.00) |
1 (1.00) |
del 1q44 | 47 (31%) | 103 |
1.19e-05 (0.00513) |
0.00786 (1.00) |
0.42 (1.00) |
0.0625 (1.00) |
0.077 (1.00) |
0.0658 (1.00) |
0.129 (1.00) |
0.183 (1.00) |
del 2q37 3 | 63 (42%) | 87 |
2.62e-08 (1.18e-05) |
0.0278 (1.00) |
0.0664 (1.00) |
0.467 (1.00) |
0.705 (1.00) |
0.751 (1.00) |
0.639 (1.00) |
0.751 (1.00) |
del 2q37 3 | 65 (43%) | 85 |
1.21e-08 (5.44e-06) |
0.0083 (1.00) |
0.0134 (1.00) |
0.216 (1.00) |
0.872 (1.00) |
1 (1.00) |
0.859 (1.00) |
1 (1.00) |
del 4q35 1 | 56 (37%) | 94 |
1.3e-05 (0.00561) |
0.207 (1.00) |
0.057 (1.00) |
0.766 (1.00) |
0.729 (1.00) |
0.675 (1.00) |
0.611 (1.00) |
0.675 (1.00) |
del 6q14 1 | 43 (29%) | 107 |
0.000574 (0.226) |
0.0389 (1.00) |
0.42 (1.00) |
0.749 (1.00) |
0.23 (1.00) |
0.237 (1.00) |
0.282 (1.00) |
0.159 (1.00) |
del 9p21 3 | 63 (42%) | 87 |
0.0004 (0.159) |
0.00866 (1.00) |
0.328 (1.00) |
0.00398 (1.00) |
0.0102 (1.00) |
0.00363 (1.00) |
0.00164 (0.598) |
0.00943 (1.00) |
del 11p15 5 | 67 (45%) | 83 |
4.79e-05 (0.0201) |
0.00121 (0.455) |
0.298 (1.00) |
0.222 (1.00) |
0.852 (1.00) |
0.896 (1.00) |
0.771 (1.00) |
1 (1.00) |
del 11q24 3 | 65 (43%) | 85 |
2.43e-06 (0.00106) |
0.00305 (1.00) |
0.359 (1.00) |
0.0129 (1.00) |
0.00346 (1.00) |
0.00532 (1.00) |
0.00719 (1.00) |
0.0144 (1.00) |
del 19p13 3 | 45 (30%) | 105 |
0.00141 (0.525) |
7.93e-05 (0.0328) |
0.00736 (1.00) |
0.0216 (1.00) |
0.0213 (1.00) |
0.031 (1.00) |
0.0149 (1.00) |
0.031 (1.00) |
del 22q13 31 | 53 (35%) | 97 |
0.00033 (0.132) |
0.0221 (1.00) |
0.00225 (0.795) |
0.388 (1.00) |
0.491 (1.00) |
0.324 (1.00) |
0.545 (1.00) |
0.324 (1.00) |
del xq21 1 | 72 (48%) | 78 |
0.106 (1.00) |
0.00013 (0.0534) |
0.0137 (1.00) |
0.00316 (1.00) |
0.00921 (1.00) |
0.00181 (0.653) |
0.0109 (1.00) |
0.00181 (0.653) |
amp 3p11 2 | 36 (24%) | 114 |
0.0104 (1.00) |
0.0983 (1.00) |
0.627 (1.00) |
1 (1.00) |
0.608 (1.00) |
0.407 (1.00) |
0.268 (1.00) |
0.692 (1.00) |
amp 7q31 1 | 44 (29%) | 106 |
0.000825 (0.318) |
0.0379 (1.00) |
0.494 (1.00) |
0.0578 (1.00) |
0.0707 (1.00) |
0.0405 (1.00) |
0.0154 (1.00) |
0.115 (1.00) |
amp 8q21 12 | 54 (36%) | 96 |
0.0199 (1.00) |
0.0323 (1.00) |
0.852 (1.00) |
0.577 (1.00) |
0.807 (1.00) |
0.873 (1.00) |
0.843 (1.00) |
0.873 (1.00) |
amp 11q22 2 | 25 (17%) | 125 |
0.226 (1.00) |
0.098 (1.00) |
0.0485 (1.00) |
0.0499 (1.00) |
0.0578 (1.00) |
0.0649 (1.00) |
0.0762 (1.00) |
0.0649 (1.00) |
amp 12p13 32 | 28 (19%) | 122 |
0.291 (1.00) |
0.594 (1.00) |
0.302 (1.00) |
0.0785 (1.00) |
0.086 (1.00) |
0.284 (1.00) |
0.122 (1.00) |
0.129 (1.00) |
amp 13q34 | 28 (19%) | 122 |
0.00158 (0.581) |
0.00162 (0.593) |
0.212 (1.00) |
0.391 (1.00) |
0.736 (1.00) |
1 (1.00) |
0.843 (1.00) |
0.789 (1.00) |
amp 20q13 33 | 62 (41%) | 88 |
0.00136 (0.506) |
0.0086 (1.00) |
0.253 (1.00) |
0.00877 (1.00) |
0.0103 (1.00) |
0.0736 (1.00) |
0.0112 (1.00) |
0.0302 (1.00) |
amp xq21 2 | 24 (16%) | 126 |
0.00394 (1.00) |
0.0179 (1.00) |
0.191 (1.00) |
0.616 (1.00) |
0.349 (1.00) |
0.334 (1.00) |
0.382 (1.00) |
0.334 (1.00) |
del 1p32 3 | 26 (17%) | 124 |
0.315 (1.00) |
0.145 (1.00) |
0.048 (1.00) |
1 (1.00) |
0.752 (1.00) |
0.04 (1.00) |
0.757 (1.00) |
0.04 (1.00) |
del 3q29 | 35 (23%) | 115 |
0.00592 (1.00) |
0.00237 (0.835) |
0.0551 (1.00) |
0.161 (1.00) |
0.28 (1.00) |
0.214 (1.00) |
0.326 (1.00) |
0.214 (1.00) |
del 6p25 1 | 52 (35%) | 98 |
0.376 (1.00) |
0.0448 (1.00) |
0.0421 (1.00) |
0.0106 (1.00) |
0.107 (1.00) |
0.233 (1.00) |
0.117 (1.00) |
0.233 (1.00) |
del 7q36 3 | 38 (25%) | 112 |
0.00119 (0.451) |
0.209 (1.00) |
0.821 (1.00) |
0.611 (1.00) |
0.397 (1.00) |
0.43 (1.00) |
0.782 (1.00) |
0.43 (1.00) |
del 8p23 3 | 44 (29%) | 106 |
0.0822 (1.00) |
0.00212 (0.751) |
0.188 (1.00) |
0.0988 (1.00) |
0.00487 (1.00) |
0.00503 (1.00) |
0.00268 (0.939) |
0.00179 (0.647) |
del 9q34 3 | 42 (28%) | 108 |
0.00436 (1.00) |
0.0976 (1.00) |
0.00509 (1.00) |
0.156 (1.00) |
0.176 (1.00) |
0.101 (1.00) |
0.134 (1.00) |
0.101 (1.00) |
del 10p15 3 | 76 (51%) | 74 |
0.00809 (1.00) |
0.00069 (0.268) |
0.0463 (1.00) |
0.138 (1.00) |
0.959 (1.00) |
0.62 (1.00) |
0.863 (1.00) |
0.62 (1.00) |
del 12q12 | 29 (19%) | 121 |
0.0999 (1.00) |
0.0642 (1.00) |
0.203 (1.00) |
0.585 (1.00) |
0.478 (1.00) |
1 (1.00) |
0.514 (1.00) |
1 (1.00) |
del 14q24 1 | 51 (34%) | 99 |
0.68 (1.00) |
0.0105 (1.00) |
0.00104 (0.398) |
0.268 (1.00) |
0.566 (1.00) |
0.156 (1.00) |
0.534 (1.00) |
0.275 (1.00) |
del 15q11 2 | 30 (20%) | 120 |
0.453 (1.00) |
0.206 (1.00) |
0.0752 (1.00) |
0.135 (1.00) |
0.112 (1.00) |
0.108 (1.00) |
0.0611 (1.00) |
0.108 (1.00) |
del 17q25 3 | 40 (27%) | 110 |
0.00515 (1.00) |
0.0573 (1.00) |
0.335 (1.00) |
0.078 (1.00) |
0.357 (1.00) |
0.192 (1.00) |
0.273 (1.00) |
0.317 (1.00) |
del 18q23 | 50 (33%) | 100 |
0.0593 (1.00) |
0.0312 (1.00) |
0.632 (1.00) |
0.137 (1.00) |
0.0409 (1.00) |
0.291 (1.00) |
0.0514 (1.00) |
0.429 (1.00) |
del 19q13 43 | 63 (42%) | 87 |
0.00601 (1.00) |
0.00443 (1.00) |
0.166 (1.00) |
0.0769 (1.00) |
0.0533 (1.00) |
0.0815 (1.00) |
0.104 (1.00) |
0.0815 (1.00) |
del 21q11 2 | 28 (19%) | 122 |
0.383 (1.00) |
0.257 (1.00) |
0.565 (1.00) |
0.297 (1.00) |
0.055 (1.00) |
0.153 (1.00) |
0.137 (1.00) |
0.153 (1.00) |
del 21q22 3 | 39 (26%) | 111 |
0.052 (1.00) |
0.05 (1.00) |
0.875 (1.00) |
0.269 (1.00) |
0.552 (1.00) |
0.804 (1.00) |
0.442 (1.00) |
0.804 (1.00) |
del xp22 32 | 47 (31%) | 103 |
0.0979 (1.00) |
0.00196 (0.702) |
0.0171 (1.00) |
0.0219 (1.00) |
0.0594 (1.00) |
0.0254 (1.00) |
0.0312 (1.00) |
0.0254 (1.00) |
P value = 1.32e-06 (Fisher's exact test), Q value = 0.00058
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
AMP PEAK 1(1P32.1) MUTATED | 15 | 33 | 7 |
AMP PEAK 1(1P32.1) WILD-TYPE | 26 | 22 | 47 |
P value = 9.87e-07 (Chi-square test), Q value = 0.00044
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3 |
AMP PEAK 1(1P32.1) MUTATED | 9 | 11 | 3 | 19 | 1 | 10 | 2 |
AMP PEAK 1(1P32.1) WILD-TYPE | 21 | 17 | 12 | 2 | 17 | 25 | 1 |
P value = 5.84e-05 (Fisher's exact test), Q value = 0.024
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
AMP PEAK 2(1Q24.3) MUTATED | 21 | 33 | 11 |
AMP PEAK 2(1Q24.3) WILD-TYPE | 20 | 22 | 43 |
P value = 0.000629 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
AMP PEAK 4(5P15.33) MUTATED | 23 | 31 | 13 |
AMP PEAK 4(5P15.33) WILD-TYPE | 18 | 24 | 41 |
P value = 4.82e-05 (Fisher's exact test), Q value = 0.02
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
AMP PEAK 5(6P21.1) MUTATED | 11 | 22 | 3 |
AMP PEAK 5(6P21.1) WILD-TYPE | 30 | 33 | 51 |
P value = 7.31e-05 (Chi-square test), Q value = 0.03
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3 |
AMP PEAK 5(6P21.1) MUTATED | 5 | 12 | 5 | 10 | 0 | 2 | 2 |
AMP PEAK 5(6P21.1) WILD-TYPE | 25 | 16 | 10 | 11 | 18 | 33 | 1 |
P value = 2.06e-05 (Chi-square test), Q value = 0.0088
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3 |
AMP PEAK 6(6Q24.3) MUTATED | 13 | 18 | 3 | 8 | 1 | 3 | 1 |
AMP PEAK 6(6Q24.3) WILD-TYPE | 17 | 10 | 12 | 13 | 17 | 32 | 2 |
P value = 0.000218 (Fisher's exact test), Q value = 0.088
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 30 | 32 |
AMP PEAK 6(6Q24.3) MUTATED | 21 | 6 | 3 |
AMP PEAK 6(6Q24.3) WILD-TYPE | 20 | 24 | 29 |
P value = 9.54e-06 (Fisher's exact test), Q value = 0.0041
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 53 | 4 |
AMP PEAK 6(6Q24.3) MUTATED | 4 | 26 | 0 |
AMP PEAK 6(6Q24.3) WILD-TYPE | 42 | 27 | 4 |
P value = 2.36e-05 (Fisher's exact test), Q value = 0.01
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 64 | 63 | 22 |
AMP PEAK 6(6Q24.3) MUTATED | 8 | 27 | 12 |
AMP PEAK 6(6Q24.3) WILD-TYPE | 56 | 36 | 10 |
P value = 2.74e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 82 | 2 | 65 |
AMP PEAK 6(6Q24.3) MUTATED | 38 | 0 | 9 |
AMP PEAK 6(6Q24.3) WILD-TYPE | 44 | 2 | 56 |
P value = 1.11e-05 (Fisher's exact test), Q value = 0.0048
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 62 | 65 | 22 |
AMP PEAK 6(6Q24.3) MUTATED | 7 | 28 | 12 |
AMP PEAK 6(6Q24.3) WILD-TYPE | 55 | 37 | 10 |
P value = 0.000142 (Fisher's exact test), Q value = 0.058
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 65 | 82 |
AMP PEAK 6(6Q24.3) MUTATED | 0 | 10 | 37 |
AMP PEAK 6(6Q24.3) WILD-TYPE | 2 | 55 | 45 |
P value = 3.94e-17 (Fisher's exact test), Q value = 1.8e-14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
AMP PEAK 11(12Q15) MUTATED | 38 | 13 | 7 |
AMP PEAK 11(12Q15) WILD-TYPE | 3 | 42 | 47 |
P value = 8.67e-10 (Chi-square test), Q value = 3.9e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3 |
AMP PEAK 11(12Q15) MUTATED | 20 | 20 | 9 | 6 | 1 | 1 | 1 |
AMP PEAK 11(12Q15) WILD-TYPE | 10 | 8 | 6 | 15 | 17 | 34 | 2 |
P value = 5.17e-10 (Fisher's exact test), Q value = 2.4e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 30 | 32 |
AMP PEAK 11(12Q15) MUTATED | 30 | 9 | 1 |
AMP PEAK 11(12Q15) WILD-TYPE | 11 | 21 | 31 |
P value = 3.47e-13 (Fisher's exact test), Q value = 1.6e-10
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 53 | 4 |
AMP PEAK 11(12Q15) MUTATED | 2 | 38 | 0 |
AMP PEAK 11(12Q15) WILD-TYPE | 44 | 15 | 4 |
P value = 2.88e-10 (Fisher's exact test), Q value = 1.3e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 64 | 63 | 22 |
AMP PEAK 11(12Q15) MUTATED | 6 | 38 | 13 |
AMP PEAK 11(12Q15) WILD-TYPE | 58 | 25 | 9 |
P value = 1.03e-11 (Fisher's exact test), Q value = 4.8e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 82 | 2 | 65 |
AMP PEAK 11(12Q15) MUTATED | 51 | 0 | 6 |
AMP PEAK 11(12Q15) WILD-TYPE | 31 | 2 | 59 |
P value = 5.53e-11 (Fisher's exact test), Q value = 2.5e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 62 | 65 | 22 |
AMP PEAK 11(12Q15) MUTATED | 5 | 41 | 11 |
AMP PEAK 11(12Q15) WILD-TYPE | 57 | 24 | 11 |
P value = 1.03e-11 (Fisher's exact test), Q value = 4.8e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 65 | 82 |
AMP PEAK 11(12Q15) MUTATED | 0 | 6 | 51 |
AMP PEAK 11(12Q15) WILD-TYPE | 2 | 59 | 31 |
P value = 1.73e-07 (Fisher's exact test), Q value = 7.8e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
AMP PEAK 13(17P11.2) MUTATED | 8 | 38 | 14 |
AMP PEAK 13(17P11.2) WILD-TYPE | 33 | 17 | 40 |
P value = 0.000162 (Chi-square test), Q value = 0.066
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3 |
AMP PEAK 14(17Q24.3) MUTATED | 6 | 13 | 8 | 9 | 3 | 3 | 3 |
AMP PEAK 14(17Q24.3) WILD-TYPE | 24 | 15 | 7 | 12 | 15 | 32 | 0 |
P value = 4.12e-05 (Fisher's exact test), Q value = 0.017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
AMP PEAK 15(19P13.2) MUTATED | 17 | 33 | 10 |
AMP PEAK 15(19P13.2) WILD-TYPE | 24 | 22 | 44 |
P value = 1.09e-06 (Fisher's exact test), Q value = 0.00048
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
AMP PEAK 16(19Q12) MUTATED | 13 | 33 | 7 |
AMP PEAK 16(19Q12) WILD-TYPE | 28 | 22 | 47 |
P value = 4.36e-05 (Fisher's exact test), Q value = 0.018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
AMP PEAK 18(21Q21.1) MUTATED | 9 | 30 | 9 |
AMP PEAK 18(21Q21.1) WILD-TYPE | 32 | 25 | 45 |
P value = 2.3e-06 (Fisher's exact test), Q value = 0.001
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
AMP PEAK 19(XP21.1) MUTATED | 11 | 33 | 8 |
AMP PEAK 19(XP21.1) WILD-TYPE | 30 | 22 | 46 |
P value = 1.35e-06 (Chi-square test), Q value = 6e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3 |
DEL PEAK 1(1P36.32) MUTATED | 0 | 6 | 5 | 3 | 8 | 22 | 2 |
DEL PEAK 1(1P36.32) WILD-TYPE | 30 | 22 | 10 | 18 | 10 | 13 | 1 |
P value = 2.77e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 30 | 32 |
DEL PEAK 1(1P36.32) MUTATED | 5 | 15 | 19 |
DEL PEAK 1(1P36.32) WILD-TYPE | 36 | 15 | 13 |
P value = 4.56e-06 (Fisher's exact test), Q value = 0.002
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 53 | 4 |
DEL PEAK 1(1P36.32) MUTATED | 29 | 10 | 0 |
DEL PEAK 1(1P36.32) WILD-TYPE | 17 | 43 | 4 |
P value = 2e-06 (Fisher's exact test), Q value = 0.00088
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 64 | 63 | 22 |
DEL PEAK 1(1P36.32) MUTATED | 34 | 9 | 3 |
DEL PEAK 1(1P36.32) WILD-TYPE | 30 | 54 | 19 |
P value = 3.48e-09 (Fisher's exact test), Q value = 1.6e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 82 | 2 | 65 |
DEL PEAK 1(1P36.32) MUTATED | 9 | 2 | 35 |
DEL PEAK 1(1P36.32) WILD-TYPE | 73 | 0 | 30 |
P value = 6.19e-07 (Fisher's exact test), Q value = 0.00028
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 62 | 65 | 22 |
DEL PEAK 1(1P36.32) MUTATED | 34 | 9 | 3 |
DEL PEAK 1(1P36.32) WILD-TYPE | 28 | 56 | 19 |
P value = 3.48e-09 (Fisher's exact test), Q value = 1.6e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 65 | 82 |
DEL PEAK 1(1P36.32) MUTATED | 2 | 35 | 9 |
DEL PEAK 1(1P36.32) WILD-TYPE | 0 | 30 | 73 |
P value = 1.19e-05 (Fisher's exact test), Q value = 0.0051
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
DEL PEAK 3(1Q44) MUTATED | 15 | 27 | 5 |
DEL PEAK 3(1Q44) WILD-TYPE | 26 | 28 | 49 |
P value = 2.29e-05 (Chi-square test), Q value = 0.0098
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3 |
DEL PEAK 4(2P25.3) MUTATED | 3 | 10 | 1 | 7 | 6 | 22 | 3 |
DEL PEAK 4(2P25.3) WILD-TYPE | 27 | 18 | 14 | 14 | 12 | 13 | 0 |
P value = 0.000317 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 30 | 32 |
DEL PEAK 4(2P25.3) MUTATED | 6 | 10 | 19 |
DEL PEAK 4(2P25.3) WILD-TYPE | 35 | 20 | 13 |
P value = 4.79e-06 (Fisher's exact test), Q value = 0.0021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 53 | 4 |
DEL PEAK 4(2P25.3) MUTATED | 27 | 8 | 0 |
DEL PEAK 4(2P25.3) WILD-TYPE | 19 | 45 | 4 |
P value = 8.81e-05 (Fisher's exact test), Q value = 0.036
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 82 | 2 | 65 |
DEL PEAK 4(2P25.3) MUTATED | 17 | 0 | 34 |
DEL PEAK 4(2P25.3) WILD-TYPE | 65 | 2 | 31 |
P value = 8.81e-05 (Fisher's exact test), Q value = 0.036
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 65 | 82 |
DEL PEAK 4(2P25.3) MUTATED | 0 | 34 | 17 |
DEL PEAK 4(2P25.3) WILD-TYPE | 2 | 31 | 65 |
P value = 2.62e-08 (Fisher's exact test), Q value = 1.2e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
DEL PEAK 5(2Q37.3) MUTATED | 12 | 40 | 11 |
DEL PEAK 5(2Q37.3) WILD-TYPE | 29 | 15 | 43 |
P value = 1.21e-08 (Fisher's exact test), Q value = 5.4e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
DEL PEAK 6(2Q37.3) MUTATED | 13 | 41 | 11 |
DEL PEAK 6(2Q37.3) WILD-TYPE | 28 | 14 | 43 |
P value = 0.00019 (Chi-square test), Q value = 0.077
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3 |
DEL PEAK 7(3P21.31) MUTATED | 4 | 14 | 5 | 7 | 2 | 1 | 0 |
DEL PEAK 7(3P21.31) WILD-TYPE | 26 | 14 | 10 | 14 | 16 | 34 | 3 |
P value = 0.000343 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 53 | 4 |
DEL PEAK 7(3P21.31) MUTATED | 3 | 20 | 0 |
DEL PEAK 7(3P21.31) WILD-TYPE | 43 | 33 | 4 |
P value = 1.3e-05 (Fisher's exact test), Q value = 0.0056
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
DEL PEAK 9(4Q35.1) MUTATED | 14 | 33 | 9 |
DEL PEAK 9(4Q35.1) WILD-TYPE | 27 | 22 | 45 |
P value = 0.000574 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
DEL PEAK 11(6Q14.1) MUTATED | 9 | 26 | 8 |
DEL PEAK 11(6Q14.1) WILD-TYPE | 32 | 29 | 46 |
P value = 0.000266 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
DEL PEAK 14(9P24.3) MUTATED | 25 | 22 | 11 |
DEL PEAK 14(9P24.3) WILD-TYPE | 16 | 33 | 43 |
P value = 0.000341 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 82 | 2 | 65 |
DEL PEAK 14(9P24.3) MUTATED | 41 | 2 | 15 |
DEL PEAK 14(9P24.3) WILD-TYPE | 41 | 0 | 50 |
P value = 4e-04 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
DEL PEAK 15(9P21.3) MUTATED | 25 | 26 | 12 |
DEL PEAK 15(9P21.3) WILD-TYPE | 16 | 29 | 42 |
P value = 6.14e-10 (Fisher's exact test), Q value = 2.8e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
DEL PEAK 18(10Q23.31) MUTATED | 7 | 45 | 32 |
DEL PEAK 18(10Q23.31) WILD-TYPE | 34 | 10 | 22 |
P value = 3.5e-10 (Chi-square test), Q value = 1.6e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3 |
DEL PEAK 18(10Q23.31) MUTATED | 5 | 12 | 5 | 18 | 8 | 33 | 3 |
DEL PEAK 18(10Q23.31) WILD-TYPE | 25 | 16 | 10 | 3 | 10 | 2 | 0 |
P value = 3.76e-09 (Fisher's exact test), Q value = 1.7e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 30 | 32 |
DEL PEAK 18(10Q23.31) MUTATED | 10 | 17 | 30 |
DEL PEAK 18(10Q23.31) WILD-TYPE | 31 | 13 | 2 |
P value = 3.3e-07 (Fisher's exact test), Q value = 0.00015
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 53 | 4 |
DEL PEAK 18(10Q23.31) MUTATED | 38 | 19 | 0 |
DEL PEAK 18(10Q23.31) WILD-TYPE | 8 | 34 | 4 |
P value = 0.000606 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 82 | 2 | 65 |
DEL PEAK 18(10Q23.31) MUTATED | 35 | 2 | 46 |
DEL PEAK 18(10Q23.31) WILD-TYPE | 47 | 0 | 19 |
P value = 0.000606 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 65 | 82 |
DEL PEAK 18(10Q23.31) MUTATED | 2 | 46 | 35 |
DEL PEAK 18(10Q23.31) WILD-TYPE | 0 | 19 | 47 |
P value = 4.79e-05 (Fisher's exact test), Q value = 0.02
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
DEL PEAK 19(11P15.5) MUTATED | 20 | 35 | 12 |
DEL PEAK 19(11P15.5) WILD-TYPE | 21 | 20 | 42 |
P value = 2.43e-06 (Fisher's exact test), Q value = 0.0011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
DEL PEAK 20(11Q24.3) MUTATED | 24 | 32 | 9 |
DEL PEAK 20(11Q24.3) WILD-TYPE | 17 | 23 | 45 |
P value = 5.89e-05 (Fisher's exact test), Q value = 0.025
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
DEL PEAK 21(12P13.1) MUTATED | 14 | 30 | 8 |
DEL PEAK 21(12P13.1) WILD-TYPE | 27 | 25 | 46 |
P value = 7.32e-05 (Chi-square test), Q value = 0.03
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3 |
DEL PEAK 21(12P13.1) MUTATED | 4 | 18 | 2 | 13 | 4 | 10 | 1 |
DEL PEAK 21(12P13.1) WILD-TYPE | 26 | 10 | 13 | 8 | 14 | 25 | 2 |
P value = 6.33e-07 (Fisher's exact test), Q value = 0.00028
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
DEL PEAK 23(13Q14.2) MUTATED | 21 | 52 | 33 |
DEL PEAK 23(13Q14.2) WILD-TYPE | 20 | 3 | 21 |
P value = 7.15e-07 (Chi-square test), Q value = 0.00032
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3 |
DEL PEAK 23(13Q14.2) MUTATED | 11 | 21 | 7 | 19 | 11 | 34 | 3 |
DEL PEAK 23(13Q14.2) WILD-TYPE | 19 | 7 | 8 | 2 | 7 | 1 | 0 |
P value = 2.08e-05 (Fisher's exact test), Q value = 0.0089
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 30 | 32 |
DEL PEAK 23(13Q14.2) MUTATED | 19 | 24 | 30 |
DEL PEAK 23(13Q14.2) WILD-TYPE | 22 | 6 | 2 |
P value = 4.37e-06 (Fisher's exact test), Q value = 0.0019
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 53 | 4 |
DEL PEAK 23(13Q14.2) MUTATED | 42 | 31 | 0 |
DEL PEAK 23(13Q14.2) WILD-TYPE | 4 | 22 | 4 |
P value = 4.93e-05 (Fisher's exact test), Q value = 0.021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
DEL PEAK 26(16Q12.1) MUTATED | 13 | 42 | 28 |
DEL PEAK 26(16Q12.1) WILD-TYPE | 28 | 13 | 26 |
P value = 0.000406 (Chi-square test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3 |
DEL PEAK 26(16Q12.1) MUTATED | 6 | 17 | 6 | 15 | 11 | 26 | 2 |
DEL PEAK 26(16Q12.1) WILD-TYPE | 24 | 11 | 9 | 6 | 7 | 9 | 1 |
P value = 0.00044 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
DEL PEAK 27(17P13.1) MUTATED | 9 | 33 | 29 |
DEL PEAK 27(17P13.1) WILD-TYPE | 32 | 22 | 25 |
P value = 3.34e-05 (Fisher's exact test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 30 | 32 |
DEL PEAK 27(17P13.1) MUTATED | 8 | 13 | 23 |
DEL PEAK 27(17P13.1) WILD-TYPE | 33 | 17 | 9 |
P value = 0.000263 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 53 | 4 |
DEL PEAK 27(17P13.1) MUTATED | 29 | 15 | 0 |
DEL PEAK 27(17P13.1) WILD-TYPE | 17 | 38 | 4 |
P value = 3.5e-06 (Fisher's exact test), Q value = 0.0015
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
DEL PEAK 28(17Q11.2) MUTATED | 14 | 27 | 4 |
DEL PEAK 28(17Q11.2) WILD-TYPE | 27 | 28 | 50 |
P value = 0.00012 (Chi-square test), Q value = 0.049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3 |
DEL PEAK 28(17Q11.2) MUTATED | 5 | 15 | 7 | 11 | 0 | 6 | 1 |
DEL PEAK 28(17Q11.2) WILD-TYPE | 25 | 13 | 8 | 10 | 18 | 29 | 2 |
P value = 7.93e-05 (Chi-square test), Q value = 0.033
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3 |
DEL PEAK 31(19P13.3) MUTATED | 1 | 4 | 5 | 11 | 6 | 15 | 3 |
DEL PEAK 31(19P13.3) WILD-TYPE | 29 | 24 | 10 | 10 | 12 | 20 | 0 |
P value = 0.00033 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
DEL PEAK 35(22Q13.31) MUTATED | 15 | 29 | 9 |
DEL PEAK 35(22Q13.31) WILD-TYPE | 26 | 26 | 45 |
P value = 0.00013 (Chi-square test), Q value = 0.053
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3 |
DEL PEAK 37(XQ21.1) MUTATED | 5 | 15 | 6 | 10 | 9 | 27 | 0 |
DEL PEAK 37(XQ21.1) WILD-TYPE | 25 | 13 | 9 | 11 | 9 | 8 | 3 |
P value = 0.000611 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 55 | 54 |
DEL PEAK 38(XQ27.1) MUTATED | 13 | 38 | 23 |
DEL PEAK 38(XQ27.1) WILD-TYPE | 28 | 17 | 31 |
P value = 0.000303 (Chi-square test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 |
---|---|---|---|---|---|---|---|
ALL | 30 | 28 | 15 | 21 | 18 | 35 | 3 |
DEL PEAK 38(XQ27.1) MUTATED | 7 | 13 | 4 | 11 | 9 | 27 | 3 |
DEL PEAK 38(XQ27.1) WILD-TYPE | 23 | 15 | 11 | 10 | 9 | 8 | 0 |
P value = 0.00051 (Fisher's exact test), Q value = 0.2
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 53 | 4 |
DEL PEAK 38(XQ27.1) MUTATED | 33 | 22 | 0 |
DEL PEAK 38(XQ27.1) WILD-TYPE | 13 | 31 | 4 |
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Copy number data file = transformed.cor.cli.txt
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Molecular subtype file = SARC-TP.transferedmergedcluster.txt
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Number of patients = 150
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Number of significantly focal cnvs = 58
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Number of molecular subtypes = 8
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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.