This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.
Testing the association between copy number variation of 29 peak regions and 10 molecular subtypes across 494 patients, 70 significant findings detected with Q value < 0.25.
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Amp Peak 1(Xq22.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 2(2p23.1) cnvs 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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Del Peak 3(2q35) cnvs 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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Del Peak 6(6q22.31) cnvs correlated to 'CN_CNMF'.
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Del Peak 9(8p23.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 10(8p22) cnvs correlated to 'CN_CNMF'.
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Del Peak 11(8p12) cnvs correlated to 'CN_CNMF'.
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Del Peak 12(8q24.22) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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Del Peak 13(9q21.13) cnvs correlated to 'CN_CNMF'.
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Del Peak 14(10q21.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 15(10q23.31) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
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Del Peak 16(11p15.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 18(13q21.31) cnvs correlated to 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 19(15q25.3) cnvs correlated to 'MIRSEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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Del Peak 23(18p11.21) cnvs correlated to 'CN_CNMF'.
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Del Peak 25(19p13.2) cnvs correlated to 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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Del Peak 28(21q21.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 29(22q13.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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Del Peak 30(22q13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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Del Peak 31(22q13.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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Del Peak 32(22q13.32) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Molecular subtypes |
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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
Del Peak 2(2p23 1) | 0 (0%) | 482 |
3.58e-10 (9.8e-08) |
1.21e-05 (0.00297) |
0.773 (1.00) |
0.0122 (1.00) |
7.58e-06 (0.00189) |
6.32e-06 (0.00158) |
4.59e-07 (0.000121) |
7.66e-08 (2.05e-05) |
2.4e-06 (0.000616) |
6.31e-08 (1.7e-05) |
Del Peak 3(2q35) | 0 (0%) | 483 |
6.33e-12 (1.74e-09) |
4.68e-06 (0.00119) |
0.562 (1.00) |
0.00257 (0.493) |
2.32e-05 (0.00555) |
4.9e-06 (0.00124) |
1.59e-06 (0.000412) |
3.1e-07 (8.23e-05) |
7.65e-06 (0.0019) |
2.6e-07 (6.91e-05) |
Del Peak 32(22q13 32) | 0 (0%) | 408 |
9.68e-89 (2.68e-86) |
1.11e-05 (0.00274) |
0.124 (1.00) |
0.209 (1.00) |
6.47e-09 (1.77e-06) |
7.15e-07 (0.000188) |
0.000943 (0.2) |
0.000337 (0.0769) |
2.95e-06 (0.000756) |
0.000212 (0.0492) |
Del Peak 12(8q24 22) | 0 (0%) | 487 |
4.62e-05 (0.0109) |
0.000343 (0.0778) |
0.839 (1.00) |
0.0521 (1.00) |
0.00153 (0.315) |
0.000675 (0.146) |
0.000219 (0.0505) |
7.85e-05 (0.0184) |
0.000758 (0.162) |
7.02e-05 (0.0165) |
Del Peak 29(22q13 1) | 0 (0%) | 409 |
1.19e-90 (3.34e-88) |
2.18e-05 (0.00528) |
0.124 (1.00) |
0.209 (1.00) |
1.22e-08 (3.31e-06) |
1.44e-06 (0.000378) |
0.00166 (0.34) |
0.000658 (0.144) |
6.1e-06 (0.00154) |
0.000387 (0.0871) |
Del Peak 30(22q13 2) | 0 (0%) | 409 |
1.19e-90 (3.34e-88) |
2.18e-05 (0.00528) |
0.124 (1.00) |
0.209 (1.00) |
1.22e-08 (3.31e-06) |
1.44e-06 (0.000378) |
0.00166 (0.34) |
0.000658 (0.144) |
6.1e-06 (0.00154) |
0.000387 (0.0871) |
Del Peak 31(22q13 31) | 0 (0%) | 409 |
1.19e-90 (3.34e-88) |
2.18e-05 (0.00528) |
0.124 (1.00) |
0.209 (1.00) |
1.22e-08 (3.31e-06) |
1.44e-06 (0.000378) |
0.00166 (0.34) |
0.000658 (0.144) |
6.1e-06 (0.00154) |
0.000387 (0.0871) |
Del Peak 25(19p13 2) | 0 (0%) | 488 |
0.00452 (0.831) |
0.00139 (0.289) |
0.681 (1.00) |
0.25 (1.00) |
0.00446 (0.826) |
0.00178 (0.355) |
0.000739 (0.159) |
0.000308 (0.0706) |
0.00237 (0.456) |
0.00028 (0.0645) |
Del Peak 15(10q23 31) | 0 (0%) | 483 |
3.37e-05 (0.00802) |
0.0112 (1.00) |
0.0328 (1.00) |
0.0483 (1.00) |
0.00183 (0.362) |
0.00144 (0.297) |
0.0117 (1.00) |
0.00532 (0.942) |
0.00105 (0.221) |
0.00358 (0.68) |
Del Peak 19(15q25 3) | 0 (0%) | 486 |
0.00133 (0.278) |
0.00369 (0.697) |
0.444 (1.00) |
0.079 (1.00) |
0.0113 (1.00) |
0.00614 (1.00) |
0.00168 (0.34) |
0.000573 (0.127) |
0.00454 (0.831) |
0.000587 (0.129) |
Amp Peak 1(Xq22 3) | 0 (0%) | 478 |
1.64e-06 (0.000422) |
0.514 (1.00) |
1 (1.00) |
0.126 (1.00) |
0.623 (1.00) |
0.598 (1.00) |
0.855 (1.00) |
0.651 (1.00) |
0.855 (1.00) |
0.555 (1.00) |
Del Peak 6(6q22 31) | 0 (0%) | 488 |
0.000364 (0.0823) |
0.00505 (0.903) |
0.0381 (1.00) |
0.794 (1.00) |
0.0161 (1.00) |
0.0069 (1.00) |
0.00929 (1.00) |
0.00658 (1.00) |
0.0259 (1.00) |
0.00664 (1.00) |
Del Peak 9(8p23 2) | 0 (0%) | 490 |
1.89e-05 (0.00464) |
0.0149 (1.00) |
0.0444 (1.00) |
0.0219 (1.00) |
0.00833 (1.00) |
0.00467 (0.85) |
0.0227 (1.00) |
0.00439 (0.825) |
||
Del Peak 10(8p22) | 0 (0%) | 490 |
1.89e-05 (0.00464) |
0.0149 (1.00) |
0.0444 (1.00) |
0.0219 (1.00) |
0.00833 (1.00) |
0.00467 (0.85) |
0.0227 (1.00) |
0.00439 (0.825) |
||
Del Peak 11(8p12) | 0 (0%) | 490 |
1.89e-05 (0.00464) |
0.0149 (1.00) |
0.0444 (1.00) |
0.0219 (1.00) |
0.00833 (1.00) |
0.00467 (0.85) |
0.0227 (1.00) |
0.00439 (0.825) |
||
Del Peak 13(9q21 13) | 0 (0%) | 471 |
1.17e-13 (3.23e-11) |
0.0686 (1.00) |
0.211 (1.00) |
0.0102 (1.00) |
0.0961 (1.00) |
0.0978 (1.00) |
0.014 (1.00) |
0.0131 (1.00) |
0.015 (1.00) |
0.00808 (1.00) |
Del Peak 14(10q21 2) | 0 (0%) | 483 |
0.000557 (0.124) |
0.163 (1.00) |
0.133 (1.00) |
1 (1.00) |
0.0336 (1.00) |
0.242 (1.00) |
0.235 (1.00) |
0.0872 (1.00) |
0.0632 (1.00) |
0.126 (1.00) |
Del Peak 16(11p15 1) | 0 (0%) | 487 |
7.98e-08 (2.13e-05) |
0.00956 (1.00) |
0.495 (1.00) |
1 (1.00) |
0.00712 (1.00) |
0.0174 (1.00) |
0.00316 (0.604) |
0.00196 (0.385) |
0.00954 (1.00) |
0.00199 (0.388) |
Del Peak 18(13q21 31) | 0 (0%) | 477 |
0.027 (1.00) |
0.0424 (1.00) |
0.12 (1.00) |
1 (1.00) |
0.0023 (0.447) |
0.000772 (0.164) |
0.00813 (1.00) |
0.00539 (0.948) |
0.00786 (1.00) |
0.00522 (0.929) |
Del Peak 23(18p11 21) | 0 (0%) | 490 |
0.000207 (0.0482) |
0.22 (1.00) |
1 (1.00) |
0.284 (1.00) |
0.242 (1.00) |
0.121 (1.00) |
0.115 (1.00) |
0.037 (1.00) |
0.0227 (1.00) |
0.0402 (1.00) |
Del Peak 28(21q21 1) | 0 (0%) | 485 |
5.66e-05 (0.0134) |
0.486 (1.00) |
0.148 (1.00) |
0.204 (1.00) |
0.406 (1.00) |
0.578 (1.00) |
0.0526 (1.00) |
0.266 (1.00) |
0.0537 (1.00) |
0.0436 (1.00) |
Del Peak 4(5p15 2) | 0 (0%) | 490 |
0.348 (1.00) |
0.394 (1.00) |
0.424 (1.00) |
0.48 (1.00) |
0.555 (1.00) |
0.578 (1.00) |
0.476 (1.00) |
0.684 (1.00) |
||
Del Peak 8(7q34) | 0 (0%) | 490 |
0.64 (1.00) |
0.649 (1.00) |
0.744 (1.00) |
0.395 (1.00) |
0.691 (1.00) |
0.822 (1.00) |
1 (1.00) |
0.828 (1.00) |
||
Del Peak 17(13q12 3) | 0 (0%) | 479 |
0.0228 (1.00) |
0.00192 (0.378) |
0.39 (1.00) |
0.432 (1.00) |
0.00174 (0.35) |
0.0181 (1.00) |
0.0658 (1.00) |
0.0181 (1.00) |
0.0243 (1.00) |
0.0136 (1.00) |
Del Peak 21(16q23 3) | 0 (0%) | 488 |
0.0483 (1.00) |
0.0744 (1.00) |
0.444 (1.00) |
0.102 (1.00) |
0.103 (1.00) |
0.386 (1.00) |
0.197 (1.00) |
0.387 (1.00) |
0.294 (1.00) |
0.293 (1.00) |
Del Peak 22(17p13 1) | 0 (0%) | 486 |
0.00182 (0.362) |
0.335 (1.00) |
1 (1.00) |
0.284 (1.00) |
0.631 (1.00) |
0.626 (1.00) |
0.33 (1.00) |
0.307 (1.00) |
0.672 (1.00) |
0.282 (1.00) |
Del Peak 24(18q22 2) | 0 (0%) | 489 |
0.00134 (0.28) |
0.0757 (1.00) |
1 (1.00) |
0.25 (1.00) |
0.119 (1.00) |
0.0361 (1.00) |
0.0415 (1.00) |
0.0115 (1.00) |
0.00735 (1.00) |
0.0127 (1.00) |
Del Peak 33(Xq22 1) | 0 (0%) | 488 |
0.0736 (1.00) |
0.551 (1.00) |
0.0977 (1.00) |
0.118 (1.00) |
0.593 (1.00) |
0.705 (1.00) |
0.526 (1.00) |
0.294 (1.00) |
0.703 (1.00) |
0.341 (1.00) |
Del Peak 34(Xq22 3) | 0 (0%) | 490 |
0.0538 (1.00) |
0.0594 (1.00) |
0.278 (1.00) |
0.364 (1.00) |
0.0947 (1.00) |
0.258 (1.00) |
0.115 (1.00) |
0.037 (1.00) |
0.226 (1.00) |
0.0402 (1.00) |
P value = 1.64e-06 (Fisher's exact test), Q value = 0.00042
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
AMP PEAK 1(XQ22.3) CNV | 8 | 8 | 0 |
AMP PEAK 1(XQ22.3) WILD-TYPE | 26 | 375 | 77 |
P value = 3.58e-10 (Fisher's exact test), Q value = 9.8e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
DEL PEAK 2(2P23.1) CNV | 9 | 1 | 2 |
DEL PEAK 2(2P23.1) WILD-TYPE | 25 | 382 | 75 |
P value = 1.21e-05 (Fisher's exact test), Q value = 0.003
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
DEL PEAK 2(2P23.1) CNV | 11 | 1 | 0 |
DEL PEAK 2(2P23.1) WILD-TYPE | 140 | 82 | 260 |
P value = 7.58e-06 (Fisher's exact test), Q value = 0.0019
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 150 | 55 | 114 | 161 |
DEL PEAK 2(2P23.1) CNV | 12 | 0 | 0 | 0 |
DEL PEAK 2(2P23.1) WILD-TYPE | 138 | 55 | 114 | 161 |
P value = 6.32e-06 (Fisher's exact test), Q value = 0.0016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 132 | 212 | 94 | 42 |
DEL PEAK 2(2P23.1) CNV | 11 | 0 | 0 | 1 |
DEL PEAK 2(2P23.1) WILD-TYPE | 121 | 212 | 94 | 41 |
P value = 4.59e-07 (Fisher's exact test), Q value = 0.00012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 150 | 173 | 170 |
DEL PEAK 2(2P23.1) CNV | 12 | 0 | 0 |
DEL PEAK 2(2P23.1) WILD-TYPE | 138 | 173 | 170 |
P value = 7.66e-08 (Fisher's exact test), Q value = 2.1e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
DEL PEAK 2(2P23.1) CNV | 0 | 12 | 0 |
DEL PEAK 2(2P23.1) WILD-TYPE | 155 | 118 | 208 |
P value = 2.4e-06 (Fisher's exact test), Q value = 0.00062
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
DEL PEAK 2(2P23.1) CNV | 12 | 0 | 0 |
DEL PEAK 2(2P23.1) WILD-TYPE | 151 | 169 | 161 |
P value = 6.31e-08 (Fisher's exact test), Q value = 1.7e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
DEL PEAK 2(2P23.1) CNV | 0 | 12 | 0 |
DEL PEAK 2(2P23.1) WILD-TYPE | 199 | 116 | 166 |
P value = 6.33e-12 (Fisher's exact test), Q value = 1.7e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
DEL PEAK 3(2Q35) CNV | 10 | 1 | 0 |
DEL PEAK 3(2Q35) WILD-TYPE | 24 | 382 | 77 |
P value = 4.68e-06 (Fisher's exact test), Q value = 0.0012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
DEL PEAK 3(2Q35) CNV | 11 | 0 | 0 |
DEL PEAK 3(2Q35) WILD-TYPE | 140 | 83 | 260 |
P value = 2.32e-05 (Fisher's exact test), Q value = 0.0056
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 150 | 55 | 114 | 161 |
DEL PEAK 3(2Q35) CNV | 11 | 0 | 0 | 0 |
DEL PEAK 3(2Q35) WILD-TYPE | 139 | 55 | 114 | 161 |
P value = 4.9e-06 (Fisher's exact test), Q value = 0.0012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 132 | 212 | 94 | 42 |
DEL PEAK 3(2Q35) CNV | 11 | 0 | 0 | 0 |
DEL PEAK 3(2Q35) WILD-TYPE | 121 | 212 | 94 | 42 |
P value = 1.59e-06 (Fisher's exact test), Q value = 0.00041
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 150 | 173 | 170 |
DEL PEAK 3(2Q35) CNV | 11 | 0 | 0 |
DEL PEAK 3(2Q35) WILD-TYPE | 139 | 173 | 170 |
P value = 3.1e-07 (Fisher's exact test), Q value = 8.2e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
DEL PEAK 3(2Q35) CNV | 0 | 11 | 0 |
DEL PEAK 3(2Q35) WILD-TYPE | 155 | 119 | 208 |
P value = 7.65e-06 (Fisher's exact test), Q value = 0.0019
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
DEL PEAK 3(2Q35) CNV | 11 | 0 | 0 |
DEL PEAK 3(2Q35) WILD-TYPE | 152 | 169 | 161 |
P value = 2.6e-07 (Fisher's exact test), Q value = 6.9e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
DEL PEAK 3(2Q35) CNV | 0 | 11 | 0 |
DEL PEAK 3(2Q35) WILD-TYPE | 199 | 117 | 166 |
P value = 0.000364 (Fisher's exact test), Q value = 0.082
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
DEL PEAK 6(6Q22.31) CNV | 4 | 2 | 0 |
DEL PEAK 6(6Q22.31) WILD-TYPE | 30 | 381 | 77 |
P value = 1.89e-05 (Fisher's exact test), Q value = 0.0046
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
DEL PEAK 9(8P23.2) CNV | 4 | 0 | 0 |
DEL PEAK 9(8P23.2) WILD-TYPE | 30 | 383 | 77 |
P value = 1.89e-05 (Fisher's exact test), Q value = 0.0046
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
DEL PEAK 10(8P22) CNV | 4 | 0 | 0 |
DEL PEAK 10(8P22) WILD-TYPE | 30 | 383 | 77 |
P value = 1.89e-05 (Fisher's exact test), Q value = 0.0046
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
DEL PEAK 11(8P12) CNV | 4 | 0 | 0 |
DEL PEAK 11(8P12) WILD-TYPE | 30 | 383 | 77 |
P value = 4.62e-05 (Fisher's exact test), Q value = 0.011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
DEL PEAK 12(8Q24.22) CNV | 5 | 2 | 0 |
DEL PEAK 12(8Q24.22) WILD-TYPE | 29 | 381 | 77 |
P value = 0.000343 (Fisher's exact test), Q value = 0.078
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
DEL PEAK 12(8Q24.22) CNV | 7 | 0 | 0 |
DEL PEAK 12(8Q24.22) WILD-TYPE | 144 | 83 | 260 |
P value = 0.000675 (Fisher's exact test), Q value = 0.15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 132 | 212 | 94 | 42 |
DEL PEAK 12(8Q24.22) CNV | 7 | 0 | 0 | 0 |
DEL PEAK 12(8Q24.22) WILD-TYPE | 125 | 212 | 94 | 42 |
P value = 0.000219 (Fisher's exact test), Q value = 0.05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 150 | 173 | 170 |
DEL PEAK 12(8Q24.22) CNV | 7 | 0 | 0 |
DEL PEAK 12(8Q24.22) WILD-TYPE | 143 | 173 | 170 |
P value = 7.85e-05 (Fisher's exact test), Q value = 0.018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
DEL PEAK 12(8Q24.22) CNV | 0 | 7 | 0 |
DEL PEAK 12(8Q24.22) WILD-TYPE | 155 | 123 | 208 |
P value = 0.000758 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
DEL PEAK 12(8Q24.22) CNV | 7 | 0 | 0 |
DEL PEAK 12(8Q24.22) WILD-TYPE | 156 | 169 | 161 |
P value = 7.02e-05 (Fisher's exact test), Q value = 0.017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
DEL PEAK 12(8Q24.22) CNV | 0 | 7 | 0 |
DEL PEAK 12(8Q24.22) WILD-TYPE | 199 | 121 | 166 |
P value = 1.17e-13 (Fisher's exact test), Q value = 3.2e-11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
DEL PEAK 13(9Q21.13) CNV | 15 | 7 | 1 |
DEL PEAK 13(9Q21.13) WILD-TYPE | 19 | 376 | 76 |
P value = 0.000557 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
DEL PEAK 14(10Q21.2) CNV | 5 | 6 | 0 |
DEL PEAK 14(10Q21.2) WILD-TYPE | 29 | 377 | 77 |
P value = 3.37e-05 (Fisher's exact test), Q value = 0.008
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
DEL PEAK 15(10Q23.31) CNV | 6 | 5 | 0 |
DEL PEAK 15(10Q23.31) WILD-TYPE | 28 | 378 | 77 |
P value = 0.00105 (Fisher's exact test), Q value = 0.22
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
DEL PEAK 15(10Q23.31) CNV | 9 | 0 | 2 |
DEL PEAK 15(10Q23.31) WILD-TYPE | 154 | 169 | 159 |
P value = 7.98e-08 (Fisher's exact test), Q value = 2.1e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
DEL PEAK 16(11P15.1) CNV | 6 | 0 | 1 |
DEL PEAK 16(11P15.1) WILD-TYPE | 28 | 383 | 76 |
P value = 0.000772 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 132 | 212 | 94 | 42 |
DEL PEAK 18(13Q21.31) CNV | 10 | 1 | 5 | 0 |
DEL PEAK 18(13Q21.31) WILD-TYPE | 122 | 211 | 89 | 42 |
P value = 0.000573 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
DEL PEAK 19(15Q25.3) CNV | 0 | 7 | 1 |
DEL PEAK 19(15Q25.3) WILD-TYPE | 155 | 123 | 207 |
P value = 0.000587 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
DEL PEAK 19(15Q25.3) CNV | 1 | 7 | 0 |
DEL PEAK 19(15Q25.3) WILD-TYPE | 198 | 121 | 166 |
P value = 0.000207 (Fisher's exact test), Q value = 0.048
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
DEL PEAK 23(18P11.21) CNV | 3 | 0 | 1 |
DEL PEAK 23(18P11.21) WILD-TYPE | 31 | 383 | 76 |
P value = 0.000739 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 150 | 173 | 170 |
DEL PEAK 25(19P13.2) CNV | 6 | 0 | 0 |
DEL PEAK 25(19P13.2) WILD-TYPE | 144 | 173 | 170 |
P value = 0.000308 (Fisher's exact test), Q value = 0.071
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
DEL PEAK 25(19P13.2) CNV | 0 | 6 | 0 |
DEL PEAK 25(19P13.2) WILD-TYPE | 155 | 124 | 208 |
P value = 0.00028 (Fisher's exact test), Q value = 0.064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
DEL PEAK 25(19P13.2) CNV | 0 | 6 | 0 |
DEL PEAK 25(19P13.2) WILD-TYPE | 199 | 122 | 166 |
P value = 5.66e-05 (Fisher's exact test), Q value = 0.013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
DEL PEAK 28(21Q21.1) CNV | 5 | 2 | 2 |
DEL PEAK 28(21Q21.1) WILD-TYPE | 29 | 381 | 75 |
P value = 1.19e-90 (Fisher's exact test), Q value = 3.3e-88
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
DEL PEAK 29(22Q13.1) CNV | 8 | 0 | 77 |
DEL PEAK 29(22Q13.1) WILD-TYPE | 26 | 383 | 0 |
P value = 2.18e-05 (Fisher's exact test), Q value = 0.0053
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
DEL PEAK 29(22Q13.1) CNV | 44 | 7 | 34 |
DEL PEAK 29(22Q13.1) WILD-TYPE | 107 | 76 | 226 |
P value = 1.22e-08 (Fisher's exact test), Q value = 3.3e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 150 | 55 | 114 | 161 |
DEL PEAK 29(22Q13.1) CNV | 42 | 6 | 26 | 7 |
DEL PEAK 29(22Q13.1) WILD-TYPE | 108 | 49 | 88 | 154 |
P value = 1.44e-06 (Fisher's exact test), Q value = 0.00038
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 132 | 212 | 94 | 42 |
DEL PEAK 29(22Q13.1) CNV | 38 | 16 | 21 | 6 |
DEL PEAK 29(22Q13.1) WILD-TYPE | 94 | 196 | 73 | 36 |
P value = 0.000658 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
DEL PEAK 29(22Q13.1) CNV | 22 | 37 | 26 |
DEL PEAK 29(22Q13.1) WILD-TYPE | 133 | 93 | 182 |
P value = 6.1e-06 (Fisher's exact test), Q value = 0.0015
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
DEL PEAK 29(22Q13.1) CNV | 48 | 18 | 19 |
DEL PEAK 29(22Q13.1) WILD-TYPE | 115 | 151 | 142 |
P value = 0.000387 (Fisher's exact test), Q value = 0.087
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
DEL PEAK 29(22Q13.1) CNV | 24 | 37 | 24 |
DEL PEAK 29(22Q13.1) WILD-TYPE | 175 | 91 | 142 |
P value = 1.19e-90 (Fisher's exact test), Q value = 3.3e-88
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
DEL PEAK 30(22Q13.2) CNV | 8 | 0 | 77 |
DEL PEAK 30(22Q13.2) WILD-TYPE | 26 | 383 | 0 |
P value = 2.18e-05 (Fisher's exact test), Q value = 0.0053
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
DEL PEAK 30(22Q13.2) CNV | 44 | 7 | 34 |
DEL PEAK 30(22Q13.2) WILD-TYPE | 107 | 76 | 226 |
P value = 1.22e-08 (Fisher's exact test), Q value = 3.3e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 150 | 55 | 114 | 161 |
DEL PEAK 30(22Q13.2) CNV | 42 | 6 | 26 | 7 |
DEL PEAK 30(22Q13.2) WILD-TYPE | 108 | 49 | 88 | 154 |
P value = 1.44e-06 (Fisher's exact test), Q value = 0.00038
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 132 | 212 | 94 | 42 |
DEL PEAK 30(22Q13.2) CNV | 38 | 16 | 21 | 6 |
DEL PEAK 30(22Q13.2) WILD-TYPE | 94 | 196 | 73 | 36 |
P value = 0.000658 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
DEL PEAK 30(22Q13.2) CNV | 22 | 37 | 26 |
DEL PEAK 30(22Q13.2) WILD-TYPE | 133 | 93 | 182 |
P value = 6.1e-06 (Fisher's exact test), Q value = 0.0015
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
DEL PEAK 30(22Q13.2) CNV | 48 | 18 | 19 |
DEL PEAK 30(22Q13.2) WILD-TYPE | 115 | 151 | 142 |
P value = 0.000387 (Fisher's exact test), Q value = 0.087
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
DEL PEAK 30(22Q13.2) CNV | 24 | 37 | 24 |
DEL PEAK 30(22Q13.2) WILD-TYPE | 175 | 91 | 142 |
P value = 1.19e-90 (Fisher's exact test), Q value = 3.3e-88
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
DEL PEAK 31(22Q13.31) CNV | 8 | 0 | 77 |
DEL PEAK 31(22Q13.31) WILD-TYPE | 26 | 383 | 0 |
P value = 2.18e-05 (Fisher's exact test), Q value = 0.0053
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
DEL PEAK 31(22Q13.31) CNV | 44 | 7 | 34 |
DEL PEAK 31(22Q13.31) WILD-TYPE | 107 | 76 | 226 |
P value = 1.22e-08 (Fisher's exact test), Q value = 3.3e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 150 | 55 | 114 | 161 |
DEL PEAK 31(22Q13.31) CNV | 42 | 6 | 26 | 7 |
DEL PEAK 31(22Q13.31) WILD-TYPE | 108 | 49 | 88 | 154 |
P value = 1.44e-06 (Fisher's exact test), Q value = 0.00038
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 132 | 212 | 94 | 42 |
DEL PEAK 31(22Q13.31) CNV | 38 | 16 | 21 | 6 |
DEL PEAK 31(22Q13.31) WILD-TYPE | 94 | 196 | 73 | 36 |
P value = 0.000658 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
DEL PEAK 31(22Q13.31) CNV | 22 | 37 | 26 |
DEL PEAK 31(22Q13.31) WILD-TYPE | 133 | 93 | 182 |
P value = 6.1e-06 (Fisher's exact test), Q value = 0.0015
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
DEL PEAK 31(22Q13.31) CNV | 48 | 18 | 19 |
DEL PEAK 31(22Q13.31) WILD-TYPE | 115 | 151 | 142 |
P value = 0.000387 (Fisher's exact test), Q value = 0.087
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
DEL PEAK 31(22Q13.31) CNV | 24 | 37 | 24 |
DEL PEAK 31(22Q13.31) WILD-TYPE | 175 | 91 | 142 |
P value = 9.68e-89 (Fisher's exact test), Q value = 2.7e-86
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 383 | 77 |
DEL PEAK 32(22Q13.32) CNV | 8 | 1 | 77 |
DEL PEAK 32(22Q13.32) WILD-TYPE | 26 | 382 | 0 |
P value = 1.11e-05 (Fisher's exact test), Q value = 0.0027
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 151 | 83 | 260 |
DEL PEAK 32(22Q13.32) CNV | 45 | 7 | 34 |
DEL PEAK 32(22Q13.32) WILD-TYPE | 106 | 76 | 226 |
P value = 6.47e-09 (Fisher's exact test), Q value = 1.8e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 150 | 55 | 114 | 161 |
DEL PEAK 32(22Q13.32) CNV | 43 | 6 | 26 | 7 |
DEL PEAK 32(22Q13.32) WILD-TYPE | 107 | 49 | 88 | 154 |
P value = 7.15e-07 (Fisher's exact test), Q value = 0.00019
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 132 | 212 | 94 | 42 |
DEL PEAK 32(22Q13.32) CNV | 39 | 16 | 21 | 6 |
DEL PEAK 32(22Q13.32) WILD-TYPE | 93 | 196 | 73 | 36 |
P value = 0.000943 (Fisher's exact test), Q value = 0.2
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 150 | 173 | 170 |
DEL PEAK 32(22Q13.32) CNV | 41 | 24 | 21 |
DEL PEAK 32(22Q13.32) WILD-TYPE | 109 | 149 | 149 |
P value = 0.000337 (Fisher's exact test), Q value = 0.077
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 155 | 130 | 208 |
DEL PEAK 32(22Q13.32) CNV | 22 | 38 | 26 |
DEL PEAK 32(22Q13.32) WILD-TYPE | 133 | 92 | 182 |
P value = 2.95e-06 (Fisher's exact test), Q value = 0.00076
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 163 | 169 | 161 |
DEL PEAK 32(22Q13.32) CNV | 49 | 18 | 19 |
DEL PEAK 32(22Q13.32) WILD-TYPE | 114 | 151 | 142 |
P value = 0.000212 (Fisher's exact test), Q value = 0.049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 199 | 128 | 166 |
DEL PEAK 32(22Q13.32) CNV | 24 | 38 | 24 |
DEL PEAK 32(22Q13.32) WILD-TYPE | 175 | 90 | 142 |
-
Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
-
Molecular subtype file = THCA-TP.transferedmergedcluster.txt
-
Number of patients = 494
-
Number of copy number variation regions = 29
-
Number of molecular subtypes = 10
-
Exclude regions 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.