This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.
Testing the association between copy number variation of 44 peak regions and 6 molecular subtypes across 177 patients, 35 significant findings detected with Q value < 0.25.
-
Amp Peak 4(8p11.22) cnvs correlated to 'CN_CNMF'.
-
Amp Peak 5(8q21.13) cnvs correlated to 'CN_CNMF'.
-
Amp Peak 7(12q24.32) cnvs correlated to 'CN_CNMF'.
-
Del Peak 5(2q22.1) cnvs correlated to 'CN_CNMF'.
-
Del Peak 6(2q22.3) cnvs correlated to 'CN_CNMF'.
-
Del Peak 10(5q11.2) cnvs correlated to 'CN_CNMF'.
-
Del Peak 11(5q21.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
Del Peak 12(6q15) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
-
Del Peak 14(8p21.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
Del Peak 15(8p11.21) cnvs correlated to 'METHLYATION_CNMF'.
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Del Peak 16(10q23.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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Del Peak 18(12p13.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 19(13q14.13) cnvs correlated to 'CN_CNMF'.
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Del Peak 20(16q22.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 21(16q24.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 22(17p13.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 23(17q21.31) cnvs correlated to 'METHLYATION_CNMF'.
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Del Peak 24(18q22.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 25(18q23) cnvs correlated to 'CN_CNMF'.
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Del Peak 26(21q22.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 27(21q22.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
Molecular subtypes |
CN CNMF |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ 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 | |
Del Peak 27(21q22 3) | 57 (32%) | 120 |
6.11e-08 (1.53e-05) |
8.77e-11 (2.29e-08) |
1.26e-09 (3.21e-07) |
2.38e-07 (5.9e-05) |
0.0567 (1.00) |
0.00017 (0.0402) |
Del Peak 12(6q15) | 56 (32%) | 121 |
5.01e-16 (1.32e-13) |
7.81e-10 (2e-07) |
0.000903 (0.208) |
0.00209 (0.466) |
0.000276 (0.0647) |
0.824 (1.00) |
Del Peak 26(21q22 2) | 58 (33%) | 119 |
2.8e-08 (7.05e-06) |
2.5e-12 (6.54e-10) |
5.24e-09 (1.33e-06) |
2.68e-07 (6.61e-05) |
0.138 (1.00) |
0.00284 (0.629) |
Del Peak 16(10q23 31) | 63 (36%) | 114 |
1.59e-07 (3.95e-05) |
1.88e-05 (0.00457) |
6.89e-05 (0.0165) |
0.0214 (1.00) |
0.0408 (1.00) |
0.0472 (1.00) |
Del Peak 11(5q21 1) | 31 (18%) | 146 |
1.7e-10 (4.41e-08) |
7.32e-06 (0.00179) |
0.149 (1.00) |
0.47 (1.00) |
0.299 (1.00) |
0.538 (1.00) |
Del Peak 14(8p21 3) | 106 (60%) | 71 |
2.84e-08 (7.12e-06) |
4.63e-05 (0.0112) |
0.0474 (1.00) |
0.0594 (1.00) |
0.00184 (0.415) |
0.0562 (1.00) |
Amp Peak 4(8p11 22) | 16 (9%) | 161 |
0.000449 (0.105) |
0.481 (1.00) |
0.286 (1.00) |
0.491 (1.00) |
0.587 (1.00) |
0.454 (1.00) |
Amp Peak 5(8q21 13) | 44 (25%) | 133 |
3.78e-10 (9.71e-08) |
0.0101 (1.00) |
0.0655 (1.00) |
0.04 (1.00) |
0.372 (1.00) |
0.313 (1.00) |
Amp Peak 7(12q24 32) | 7 (4%) | 170 |
0.000749 (0.173) |
0.264 (1.00) |
0.675 (1.00) |
1 (1.00) |
0.456 (1.00) |
0.864 (1.00) |
Del Peak 5(2q22 1) | 21 (12%) | 156 |
9.66e-05 (0.0231) |
0.00421 (0.914) |
0.586 (1.00) |
0.313 (1.00) |
0.0121 (1.00) |
0.00772 (1.00) |
Del Peak 6(2q22 3) | 23 (13%) | 154 |
4.5e-05 (0.0109) |
0.0319 (1.00) |
0.0398 (1.00) |
0.0112 (1.00) |
0.0038 (0.832) |
0.0855 (1.00) |
Del Peak 10(5q11 2) | 29 (16%) | 148 |
2.4e-06 (0.000587) |
0.0294 (1.00) |
0.798 (1.00) |
0.956 (1.00) |
0.599 (1.00) |
0.68 (1.00) |
Del Peak 15(8p11 21) | 59 (33%) | 118 |
0.0116 (1.00) |
0.000204 (0.048) |
0.0647 (1.00) |
0.0193 (1.00) |
0.281 (1.00) |
0.207 (1.00) |
Del Peak 18(12p13 2) | 38 (21%) | 139 |
0.000529 (0.123) |
0.031 (1.00) |
0.702 (1.00) |
0.651 (1.00) |
0.0527 (1.00) |
0.856 (1.00) |
Del Peak 19(13q14 13) | 81 (46%) | 96 |
0.000113 (0.0269) |
0.00503 (1.00) |
0.0245 (1.00) |
0.0251 (1.00) |
0.306 (1.00) |
0.363 (1.00) |
Del Peak 20(16q22 3) | 57 (32%) | 120 |
6.54e-07 (0.000161) |
0.0146 (1.00) |
0.015 (1.00) |
0.154 (1.00) |
0.0185 (1.00) |
0.0792 (1.00) |
Del Peak 21(16q24 1) | 72 (41%) | 105 |
2.18e-10 (5.61e-08) |
0.00797 (1.00) |
0.0605 (1.00) |
0.373 (1.00) |
0.0395 (1.00) |
0.0325 (1.00) |
Del Peak 22(17p13 1) | 45 (25%) | 132 |
3.97e-09 (1.01e-06) |
0.216 (1.00) |
0.0694 (1.00) |
0.00328 (0.723) |
0.286 (1.00) |
0.0611 (1.00) |
Del Peak 23(17q21 31) | 34 (19%) | 143 |
0.00156 (0.357) |
0.000275 (0.0645) |
0.00426 (0.921) |
0.00464 (0.993) |
0.533 (1.00) |
0.289 (1.00) |
Del Peak 24(18q22 1) | 44 (25%) | 133 |
9.08e-11 (2.36e-08) |
0.625 (1.00) |
0.667 (1.00) |
0.108 (1.00) |
0.0534 (1.00) |
0.152 (1.00) |
Del Peak 25(18q23) | 50 (28%) | 127 |
1.2e-13 (3.16e-11) |
0.525 (1.00) |
0.423 (1.00) |
0.13 (1.00) |
0.104 (1.00) |
0.447 (1.00) |
Amp Peak 1(1q21 3) | 10 (6%) | 167 |
0.0731 (1.00) |
0.361 (1.00) |
0.534 (1.00) |
0.726 (1.00) |
0.0787 (1.00) |
1 (1.00) |
Amp Peak 2(3q26 2) | 25 (14%) | 152 |
0.00195 (0.437) |
0.267 (1.00) |
0.73 (1.00) |
0.631 (1.00) |
0.932 (1.00) |
0.377 (1.00) |
Amp Peak 3(7p15 3) | 33 (19%) | 144 |
0.00185 (0.417) |
0.107 (1.00) |
0.0633 (1.00) |
0.113 (1.00) |
0.87 (1.00) |
0.55 (1.00) |
Amp Peak 6(10q21 2) | 10 (6%) | 167 |
0.00948 (1.00) |
0.434 (1.00) |
0.119 (1.00) |
0.0962 (1.00) |
0.278 (1.00) |
1 (1.00) |
Amp Peak 8(14q21 1) | 8 (5%) | 169 |
0.107 (1.00) |
0.543 (1.00) |
0.132 (1.00) |
0.298 (1.00) |
0.828 (1.00) |
0.265 (1.00) |
Amp Peak 9(Xp22 11) | 5 (3%) | 172 |
0.325 (1.00) |
0.863 (1.00) |
0.858 (1.00) |
0.863 (1.00) |
0.21 (1.00) |
0.396 (1.00) |
Amp Peak 10(Xp22 11) | 5 (3%) | 172 |
0.62 (1.00) |
0.619 (1.00) |
0.551 (1.00) |
0.688 (1.00) |
0.755 (1.00) |
0.325 (1.00) |
Amp Peak 11(Xp21 1) | 4 (2%) | 173 |
0.693 (1.00) |
0.387 (1.00) |
0.839 (1.00) |
1 (1.00) |
0.266 (1.00) |
0.666 (1.00) |
Amp Peak 12(Xq21 1) | 7 (4%) | 170 |
0.351 (1.00) |
0.203 (1.00) |
0.212 (1.00) |
0.438 (1.00) |
0.406 (1.00) |
0.771 (1.00) |
Amp Peak 13(Xq21 1) | 5 (3%) | 172 |
0.0712 (1.00) |
0.00434 (0.934) |
0.51 (1.00) |
0.377 (1.00) |
0.869 (1.00) |
0.845 (1.00) |
Amp Peak 14(Xq21 31) | 5 (3%) | 172 |
0.0904 (1.00) |
0.275 (1.00) |
0.551 (1.00) |
0.234 (1.00) |
0.703 (1.00) |
1 (1.00) |
Amp Peak 15(Xq25) | 4 (2%) | 173 |
0.0327 (1.00) |
0.237 (1.00) |
0.29 (1.00) |
0.631 (1.00) |
0.404 (1.00) |
0.133 (1.00) |
Amp Peak 16(Xq25) | 6 (3%) | 171 |
1 (1.00) |
0.322 (1.00) |
0.193 (1.00) |
0.327 (1.00) |
0.197 (1.00) |
0.405 (1.00) |
Amp Peak 17(Xq27 1) | 9 (5%) | 168 |
0.00408 (0.89) |
0.434 (1.00) |
1 (1.00) |
0.815 (1.00) |
0.0648 (1.00) |
0.0234 (1.00) |
Del Peak 1(1p31 3) | 21 (12%) | 156 |
0.0431 (1.00) |
0.00225 (0.499) |
0.0189 (1.00) |
0.00182 (0.412) |
0.187 (1.00) |
0.152 (1.00) |
Del Peak 2(1p21 3) | 17 (10%) | 160 |
0.00593 (1.00) |
0.745 (1.00) |
0.867 (1.00) |
0.518 (1.00) |
0.0741 (1.00) |
0.89 (1.00) |
Del Peak 3(1q23 1) | 8 (5%) | 169 |
0.0635 (1.00) |
0.127 (1.00) |
0.212 (1.00) |
0.043 (1.00) |
0.0579 (1.00) |
0.707 (1.00) |
Del Peak 4(1q42 13) | 17 (10%) | 160 |
0.114 (1.00) |
0.0123 (1.00) |
0.875 (1.00) |
0.713 (1.00) |
0.27 (1.00) |
0.791 (1.00) |
Del Peak 7(3p13) | 28 (16%) | 149 |
0.387 (1.00) |
0.087 (1.00) |
0.48 (1.00) |
0.885 (1.00) |
0.195 (1.00) |
0.117 (1.00) |
Del Peak 8(3q29) | 12 (7%) | 165 |
0.406 (1.00) |
0.212 (1.00) |
0.0981 (1.00) |
0.15 (1.00) |
0.579 (1.00) |
1 (1.00) |
Del Peak 9(4q28 1) | 12 (7%) | 165 |
0.0172 (1.00) |
0.00141 (0.324) |
0.189 (1.00) |
0.622 (1.00) |
0.263 (1.00) |
0.181 (1.00) |
Del Peak 13(7q36 1) | 8 (5%) | 169 |
0.538 (1.00) |
0.348 (1.00) |
0.534 (1.00) |
0.726 (1.00) |
0.69 (1.00) |
0.564 (1.00) |
Del Peak 17(11q23 2) | 20 (11%) | 157 |
0.121 (1.00) |
0.222 (1.00) |
0.754 (1.00) |
0.753 (1.00) |
0.387 (1.00) |
0.602 (1.00) |
P value = 0.000449 (Fisher's exact test), Q value = 0.1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 83 | 54 | 1 |
AMP PEAK 4(8P11.22) MUTATED | 4 | 1 | 11 | 0 |
AMP PEAK 4(8P11.22) WILD-TYPE | 35 | 82 | 43 | 1 |
P value = 3.78e-10 (Fisher's exact test), Q value = 9.7e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 83 | 54 | 1 |
AMP PEAK 5(8Q21.13) MUTATED | 9 | 5 | 30 | 0 |
AMP PEAK 5(8Q21.13) WILD-TYPE | 30 | 78 | 24 | 1 |
P value = 0.000749 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 83 | 54 | 1 |
AMP PEAK 7(12Q24.32) MUTATED | 0 | 0 | 7 | 0 |
AMP PEAK 7(12Q24.32) WILD-TYPE | 39 | 83 | 47 | 1 |
P value = 9.66e-05 (Fisher's exact test), Q value = 0.023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 83 | 54 | 1 |
DEL PEAK 5(2Q22.1) MUTATED | 9 | 2 | 9 | 1 |
DEL PEAK 5(2Q22.1) WILD-TYPE | 30 | 81 | 45 | 0 |
P value = 4.5e-05 (Fisher's exact test), Q value = 0.011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 83 | 54 | 1 |
DEL PEAK 6(2Q22.3) MUTATED | 8 | 2 | 12 | 1 |
DEL PEAK 6(2Q22.3) WILD-TYPE | 31 | 81 | 42 | 0 |
P value = 2.4e-06 (Fisher's exact test), Q value = 0.00059
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 83 | 54 | 1 |
DEL PEAK 10(5Q11.2) MUTATED | 12 | 2 | 15 | 0 |
DEL PEAK 10(5Q11.2) WILD-TYPE | 27 | 81 | 39 | 1 |
P value = 1.7e-10 (Fisher's exact test), Q value = 4.4e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 83 | 54 | 1 |
DEL PEAK 11(5Q21.1) MUTATED | 16 | 0 | 15 | 0 |
DEL PEAK 11(5Q21.1) WILD-TYPE | 23 | 83 | 39 | 1 |
P value = 7.32e-06 (Fisher's exact test), Q value = 0.0018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 50 | 68 |
DEL PEAK 11(5Q21.1) MUTATED | 20 | 3 | 5 |
DEL PEAK 11(5Q21.1) WILD-TYPE | 33 | 47 | 63 |
P value = 5.01e-16 (Fisher's exact test), Q value = 1.3e-13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 83 | 54 | 1 |
DEL PEAK 12(6Q15) MUTATED | 29 | 4 | 22 | 1 |
DEL PEAK 12(6Q15) WILD-TYPE | 10 | 79 | 32 | 0 |
P value = 7.81e-10 (Fisher's exact test), Q value = 2e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 50 | 68 |
DEL PEAK 12(6Q15) MUTATED | 32 | 2 | 19 |
DEL PEAK 12(6Q15) WILD-TYPE | 21 | 48 | 49 |
P value = 0.000903 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 50 | 41 | 49 |
DEL PEAK 12(6Q15) MUTATED | 24 | 5 | 14 |
DEL PEAK 12(6Q15) WILD-TYPE | 26 | 36 | 35 |
P value = 0.000276 (Fisher's exact test), Q value = 0.065
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 45 | 46 | 25 | 60 |
DEL PEAK 12(6Q15) MUTATED | 23 | 5 | 6 | 21 |
DEL PEAK 12(6Q15) WILD-TYPE | 22 | 41 | 19 | 39 |
P value = 2.84e-08 (Fisher's exact test), Q value = 7.1e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 83 | 54 | 1 |
DEL PEAK 14(8P21.3) MUTATED | 18 | 38 | 49 | 1 |
DEL PEAK 14(8P21.3) WILD-TYPE | 21 | 45 | 5 | 0 |
P value = 4.63e-05 (Fisher's exact test), Q value = 0.011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 50 | 68 |
DEL PEAK 14(8P21.3) MUTATED | 29 | 19 | 53 |
DEL PEAK 14(8P21.3) WILD-TYPE | 24 | 31 | 15 |
P value = 0.000204 (Fisher's exact test), Q value = 0.048
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 50 | 68 |
DEL PEAK 15(8P11.21) MUTATED | 17 | 6 | 32 |
DEL PEAK 15(8P11.21) WILD-TYPE | 36 | 44 | 36 |
P value = 1.59e-07 (Fisher's exact test), Q value = 3.9e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 83 | 54 | 1 |
DEL PEAK 16(10Q23.31) MUTATED | 6 | 21 | 35 | 1 |
DEL PEAK 16(10Q23.31) WILD-TYPE | 33 | 62 | 19 | 0 |
P value = 1.88e-05 (Fisher's exact test), Q value = 0.0046
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 50 | 68 |
DEL PEAK 16(10Q23.31) MUTATED | 13 | 10 | 39 |
DEL PEAK 16(10Q23.31) WILD-TYPE | 40 | 40 | 29 |
P value = 6.89e-05 (Fisher's exact test), Q value = 0.017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 50 | 41 | 49 |
DEL PEAK 16(10Q23.31) MUTATED | 12 | 11 | 31 |
DEL PEAK 16(10Q23.31) WILD-TYPE | 38 | 30 | 18 |
P value = 0.000529 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 83 | 54 | 1 |
DEL PEAK 18(12P13.2) MUTATED | 6 | 10 | 22 | 0 |
DEL PEAK 18(12P13.2) WILD-TYPE | 33 | 73 | 32 | 1 |
P value = 0.000113 (Fisher's exact test), Q value = 0.027
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 83 | 54 | 1 |
DEL PEAK 19(13Q14.13) MUTATED | 25 | 24 | 31 | 1 |
DEL PEAK 19(13Q14.13) WILD-TYPE | 14 | 59 | 23 | 0 |
P value = 6.54e-07 (Fisher's exact test), Q value = 0.00016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 83 | 54 | 1 |
DEL PEAK 20(16Q22.3) MUTATED | 6 | 18 | 33 | 0 |
DEL PEAK 20(16Q22.3) WILD-TYPE | 33 | 65 | 21 | 1 |
P value = 2.18e-10 (Fisher's exact test), Q value = 5.6e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 83 | 54 | 1 |
DEL PEAK 21(16Q24.1) MUTATED | 8 | 22 | 42 | 0 |
DEL PEAK 21(16Q24.1) WILD-TYPE | 31 | 61 | 12 | 1 |
P value = 3.97e-09 (Fisher's exact test), Q value = 1e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 83 | 54 | 1 |
DEL PEAK 22(17P13.1) MUTATED | 3 | 11 | 30 | 1 |
DEL PEAK 22(17P13.1) WILD-TYPE | 36 | 72 | 24 | 0 |
P value = 0.000275 (Fisher's exact test), Q value = 0.065
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 50 | 68 |
DEL PEAK 23(17Q21.31) MUTATED | 4 | 5 | 23 |
DEL PEAK 23(17Q21.31) WILD-TYPE | 49 | 45 | 45 |
P value = 9.08e-11 (Fisher's exact test), Q value = 2.4e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 83 | 54 | 1 |
DEL PEAK 24(18Q22.1) MUTATED | 3 | 9 | 32 | 0 |
DEL PEAK 24(18Q22.1) WILD-TYPE | 36 | 74 | 22 | 1 |
P value = 1.2e-13 (Fisher's exact test), Q value = 3.2e-11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 83 | 54 | 1 |
DEL PEAK 25(18Q23) MUTATED | 4 | 9 | 37 | 0 |
DEL PEAK 25(18Q23) WILD-TYPE | 35 | 74 | 17 | 1 |
P value = 2.8e-08 (Fisher's exact test), Q value = 7e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 83 | 54 | 1 |
DEL PEAK 26(21Q22.2) MUTATED | 0 | 38 | 19 | 1 |
DEL PEAK 26(21Q22.2) WILD-TYPE | 39 | 45 | 35 | 0 |
P value = 2.5e-12 (Fisher's exact test), Q value = 6.5e-10
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 50 | 68 |
DEL PEAK 26(21Q22.2) MUTATED | 4 | 9 | 44 |
DEL PEAK 26(21Q22.2) WILD-TYPE | 49 | 41 | 24 |
P value = 5.24e-09 (Fisher's exact test), Q value = 1.3e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 50 | 41 | 49 |
DEL PEAK 26(21Q22.2) MUTATED | 4 | 14 | 32 |
DEL PEAK 26(21Q22.2) WILD-TYPE | 46 | 27 | 17 |
P value = 2.68e-07 (Fisher's exact test), Q value = 6.6e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 43 | 56 |
DEL PEAK 26(21Q22.2) MUTATED | 3 | 27 | 20 |
DEL PEAK 26(21Q22.2) WILD-TYPE | 38 | 16 | 36 |
P value = 6.11e-08 (Fisher's exact test), Q value = 1.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 39 | 83 | 54 | 1 |
DEL PEAK 27(21Q22.3) MUTATED | 0 | 38 | 19 | 0 |
DEL PEAK 27(21Q22.3) WILD-TYPE | 39 | 45 | 35 | 1 |
P value = 8.77e-11 (Fisher's exact test), Q value = 2.3e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 50 | 68 |
DEL PEAK 27(21Q22.3) MUTATED | 5 | 8 | 42 |
DEL PEAK 27(21Q22.3) WILD-TYPE | 48 | 42 | 26 |
P value = 1.26e-09 (Fisher's exact test), Q value = 3.2e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 50 | 41 | 49 |
DEL PEAK 27(21Q22.3) MUTATED | 4 | 12 | 33 |
DEL PEAK 27(21Q22.3) WILD-TYPE | 46 | 29 | 16 |
P value = 2.38e-07 (Fisher's exact test), Q value = 5.9e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 43 | 56 |
DEL PEAK 27(21Q22.3) MUTATED | 3 | 27 | 19 |
DEL PEAK 27(21Q22.3) WILD-TYPE | 38 | 16 | 37 |
P value = 0.00017 (Fisher's exact test), Q value = 0.04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 30 | 69 | 77 |
DEL PEAK 27(21Q22.3) MUTATED | 3 | 34 | 20 |
DEL PEAK 27(21Q22.3) WILD-TYPE | 27 | 35 | 57 |
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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.
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Molecular subtype file = PRAD-TP.transferedmergedcluster.txt
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Number of patients = 177
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Number of copy number variation regions = 44
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Number of molecular subtypes = 6
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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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.