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 8 molecular subtypes across 65 patients, 61 significant findings detected with Q value < 0.25.
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Amp Peak 3(7q22.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 4(8q24.21) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
-
Amp Peak 7(12p13.33) cnvs correlated to 'CN_CNMF'.
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Amp Peak 8(12p11.21) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
Amp Peak 12(18q11.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
Amp Peak 14(20q13.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 2(1p36.11) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 3(1p21.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 4(5q14.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 5(5q15) cnvs correlated to 'CN_CNMF'.
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Del Peak 6(6p25.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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Del Peak 7(6p22.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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Del Peak 8(6q22.33) 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 10(8p21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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Del Peak 12(9p21.3) 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 13(10q23.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 15(12p12.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 16(12q12) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 17(12q24.31) cnvs correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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Del Peak 18(15q15.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 19(17p11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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Del Peak 20(17q22) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 28(Xq21.1) cnvs correlated to 'CN_CNMF'.
Molecular subtypes |
CN CNMF |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nCNV (%) | nWild-Type | 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 | Fisher's exact test | |
Del Peak 12(9p21 3) | 0 (0%) | 24 |
1.43e-06 (0.000496) |
9.11e-08 (3.2e-05) |
2.16e-05 (0.00726) |
4.09e-06 (0.00141) |
2.95e-05 (0.00987) |
4.02e-05 (0.0133) |
2.78e-07 (9.69e-05) |
4.88e-06 (0.00167) |
Del Peak 8(6q22 33) | 0 (0%) | 34 |
0.000728 (0.216) |
3.79e-05 (0.0126) |
0.00218 (0.607) |
4.39e-06 (0.00151) |
0.000693 (0.207) |
0.000148 (0.0477) |
0.000163 (0.052) |
0.000466 (0.143) |
Del Peak 10(8p21 3) | 0 (0%) | 46 |
2.52e-05 (0.00847) |
0.000211 (0.0666) |
8.93e-05 (0.0292) |
0.000538 (0.165) |
0.000789 (0.233) |
0.00201 (0.561) |
0.000163 (0.052) |
0.00115 (0.328) |
Del Peak 19(17p11 2) | 0 (0%) | 39 |
5.43e-05 (0.0179) |
1.13e-08 (3.99e-06) |
0.000809 (0.238) |
0.000824 (0.241) |
0.00233 (0.643) |
0.000332 (0.104) |
0.000246 (0.0774) |
0.00165 (0.467) |
Amp Peak 12(18q11 2) | 0 (0%) | 46 |
0.000293 (0.0919) |
0.00369 (0.983) |
0.000369 (0.115) |
0.00807 (1.00) |
0.00589 (1.00) |
0.00109 (0.313) |
0.000478 (0.147) |
0.000556 (0.17) |
Del Peak 6(6p25 2) | 0 (0%) | 39 |
4.12e-05 (0.0136) |
1.76e-05 (0.00596) |
0.000193 (0.0611) |
0.00724 (1.00) |
0.0226 (1.00) |
0.00597 (1.00) |
0.00737 (1.00) |
0.018 (1.00) |
Del Peak 7(6p22 3) | 0 (0%) | 40 |
0.000854 (0.249) |
6.32e-05 (0.0207) |
0.000119 (0.0386) |
0.00228 (0.63) |
0.00633 (1.00) |
0.00252 (0.694) |
0.00497 (1.00) |
0.0134 (1.00) |
Del Peak 17(12q24 31) | 0 (0%) | 49 |
0.000948 (0.275) |
9.01e-05 (0.0294) |
0.0138 (1.00) |
0.000169 (0.0538) |
0.00107 (0.31) |
0.00541 (1.00) |
0.000454 (0.14) |
0.00402 (1.00) |
Amp Peak 3(7q22 1) | 0 (0%) | 47 |
0.000766 (0.227) |
0.000101 (0.0328) |
0.27 (1.00) |
0.191 (1.00) |
0.125 (1.00) |
0.218 (1.00) |
0.109 (1.00) |
0.162 (1.00) |
Amp Peak 4(8q24 21) | 0 (0%) | 40 |
7.91e-06 (0.0027) |
0.00287 (0.778) |
0.000579 (0.176) |
0.00333 (0.895) |
0.0284 (1.00) |
0.0744 (1.00) |
0.00983 (1.00) |
0.0358 (1.00) |
Amp Peak 8(12p11 21) | 0 (0%) | 51 |
1.52e-05 (0.00514) |
0.000696 (0.208) |
0.00328 (0.885) |
0.0824 (1.00) |
0.00428 (1.00) |
0.017 (1.00) |
0.00584 (1.00) |
0.0135 (1.00) |
Del Peak 2(1p36 11) | 0 (0%) | 47 |
0.00068 (0.205) |
0.000619 (0.187) |
0.00953 (1.00) |
0.26 (1.00) |
0.0801 (1.00) |
0.0769 (1.00) |
0.00911 (1.00) |
0.0518 (1.00) |
Del Peak 16(12q12) | 0 (0%) | 55 |
0.00014 (0.0453) |
3.91e-05 (0.013) |
0.0244 (1.00) |
0.0185 (1.00) |
0.108 (1.00) |
0.0614 (1.00) |
0.0138 (1.00) |
0.0413 (1.00) |
Del Peak 20(17q22) | 0 (0%) | 47 |
9.68e-06 (0.00329) |
3.54e-05 (0.0118) |
0.0403 (1.00) |
0.00272 (0.74) |
0.0142 (1.00) |
0.0299 (1.00) |
0.00822 (1.00) |
0.0183 (1.00) |
Amp Peak 7(12p13 33) | 0 (0%) | 55 |
2.52e-07 (8.8e-05) |
0.00565 (1.00) |
0.0587 (1.00) |
0.0562 (1.00) |
0.0436 (1.00) |
0.113 (1.00) |
0.0158 (1.00) |
0.0791 (1.00) |
Amp Peak 14(20q13 2) | 0 (0%) | 48 |
2.88e-06 (0.000992) |
0.121 (1.00) |
0.053 (1.00) |
0.191 (1.00) |
0.146 (1.00) |
0.218 (1.00) |
0.0368 (1.00) |
0.162 (1.00) |
Del Peak 3(1p21 2) | 0 (0%) | 54 |
0.000152 (0.0489) |
0.0382 (1.00) |
0.153 (1.00) |
0.252 (1.00) |
0.0668 (1.00) |
0.316 (1.00) |
0.0137 (1.00) |
0.209 (1.00) |
Del Peak 4(5q14 2) | 0 (0%) | 53 |
0.000601 (0.182) |
0.329 (1.00) |
0.234 (1.00) |
0.245 (1.00) |
0.184 (1.00) |
0.5 (1.00) |
0.0517 (1.00) |
0.467 (1.00) |
Del Peak 5(5q15) | 0 (0%) | 51 |
0.000688 (0.206) |
0.0877 (1.00) |
0.546 (1.00) |
0.113 (1.00) |
0.124 (1.00) |
0.331 (1.00) |
0.029 (1.00) |
0.256 (1.00) |
Del Peak 13(10q23 2) | 0 (0%) | 51 |
1.2e-07 (4.2e-05) |
0.0371 (1.00) |
0.0892 (1.00) |
0.0209 (1.00) |
0.0421 (1.00) |
0.0149 (1.00) |
0.00118 (0.336) |
0.0107 (1.00) |
Del Peak 15(12p12 3) | 0 (0%) | 54 |
0.000408 (0.127) |
0.00266 (0.729) |
0.125 (1.00) |
0.134 (1.00) |
0.0436 (1.00) |
0.00989 (1.00) |
0.0181 (1.00) |
0.00739 (1.00) |
Del Peak 18(15q15 1) | 0 (0%) | 51 |
1.29e-06 (0.000446) |
0.00359 (0.962) |
0.0414 (1.00) |
0.00942 (1.00) |
0.0194 (1.00) |
0.0346 (1.00) |
0.000994 (0.287) |
0.0159 (1.00) |
Del Peak 28(Xq21 1) | 0 (0%) | 58 |
0.00041 (0.127) |
0.0299 (1.00) |
0.365 (1.00) |
0.782 (1.00) |
0.252 (1.00) |
0.554 (1.00) |
0.0704 (1.00) |
0.396 (1.00) |
Amp Peak 1(1p34 2) | 0 (0%) | 60 |
0.173 (1.00) |
0.729 (1.00) |
1 (1.00) |
1 (1.00) |
0.656 (1.00) |
1 (1.00) |
0.821 (1.00) |
1 (1.00) |
Amp Peak 2(1p12) | 0 (0%) | 54 |
0.0445 (1.00) |
0.251 (1.00) |
0.952 (1.00) |
0.746 (1.00) |
0.889 (1.00) |
0.885 (1.00) |
0.474 (1.00) |
0.791 (1.00) |
Amp Peak 5(9p13 3) | 0 (0%) | 58 |
0.077 (1.00) |
0.404 (1.00) |
0.133 (1.00) |
0.119 (1.00) |
0.305 (1.00) |
0.226 (1.00) |
0.161 (1.00) |
0.166 (1.00) |
Amp Peak 6(11p11 2) | 0 (0%) | 59 |
0.0888 (1.00) |
0.059 (1.00) |
0.314 (1.00) |
0.195 (1.00) |
0.571 (1.00) |
0.195 (1.00) |
0.312 (1.00) |
0.206 (1.00) |
Amp Peak 9(12q15) | 0 (0%) | 57 |
0.00549 (1.00) |
0.0311 (1.00) |
0.237 (1.00) |
0.0355 (1.00) |
0.0225 (1.00) |
0.0131 (1.00) |
0.00463 (1.00) |
0.00874 (1.00) |
Amp Peak 10(17p11 2) | 0 (0%) | 62 |
0.635 (1.00) |
0.338 (1.00) |
0.885 (1.00) |
0.683 (1.00) |
0.577 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
Amp Peak 11(17q21 33) | 0 (0%) | 58 |
0.0162 (1.00) |
0.239 (1.00) |
0.609 (1.00) |
0.72 (1.00) |
1 (1.00) |
0.756 (1.00) |
0.67 (1.00) |
0.768 (1.00) |
Amp Peak 13(19q13 13) | 0 (0%) | 51 |
0.0229 (1.00) |
0.0745 (1.00) |
0.309 (1.00) |
0.0443 (1.00) |
0.286 (1.00) |
0.22 (1.00) |
0.286 (1.00) |
0.434 (1.00) |
Amp Peak 15(Xp22 11) | 0 (0%) | 61 |
0.248 (1.00) |
0.667 (1.00) |
0.885 (1.00) |
0.312 (1.00) |
1 (1.00) |
0.818 (1.00) |
0.821 (1.00) |
0.816 (1.00) |
Amp Peak 16(Xq27 1) | 0 (0%) | 59 |
0.0165 (1.00) |
0.873 (1.00) |
0.391 (1.00) |
0.615 (1.00) |
0.463 (1.00) |
1 (1.00) |
0.624 (1.00) |
0.744 (1.00) |
Del Peak 1(1p36 22) | 0 (0%) | 51 |
0.0207 (1.00) |
0.00361 (0.964) |
0.0753 (1.00) |
0.134 (1.00) |
0.0339 (1.00) |
0.186 (1.00) |
0.0686 (1.00) |
0.107 (1.00) |
Del Peak 9(7q36 1) | 0 (0%) | 58 |
0.00189 (0.533) |
0.0439 (1.00) |
0.133 (1.00) |
0.119 (1.00) |
0.305 (1.00) |
0.74 (1.00) |
0.461 (1.00) |
0.643 (1.00) |
Del Peak 11(8q12 1) | 0 (0%) | 60 |
0.0349 (1.00) |
0.077 (1.00) |
0.314 (1.00) |
0.257 (1.00) |
0.571 (1.00) |
0.195 (1.00) |
0.312 (1.00) |
0.206 (1.00) |
Del Peak 14(11p15 4) | 0 (0%) | 53 |
0.0304 (1.00) |
0.467 (1.00) |
0.761 (1.00) |
0.592 (1.00) |
0.525 (1.00) |
1 (1.00) |
0.732 (1.00) |
1 (1.00) |
Del Peak 21(18p11 32) | 0 (0%) | 44 |
0.124 (1.00) |
1 (1.00) |
0.542 (1.00) |
1 (1.00) |
0.218 (1.00) |
0.935 (1.00) |
0.664 (1.00) |
1 (1.00) |
Del Peak 22(18q12 1) | 0 (0%) | 28 |
0.02 (1.00) |
0.0844 (1.00) |
0.113 (1.00) |
0.338 (1.00) |
0.0835 (1.00) |
0.0889 (1.00) |
0.0632 (1.00) |
0.141 (1.00) |
Del Peak 23(18q21 2) | 0 (0%) | 20 |
0.00267 (0.729) |
0.000946 (0.275) |
0.00907 (1.00) |
0.0226 (1.00) |
0.00861 (1.00) |
0.00197 (0.551) |
0.00115 (0.328) |
0.00436 (1.00) |
Del Peak 24(19q13 33) | 0 (0%) | 58 |
0.00189 (0.533) |
0.0851 (1.00) |
0.819 (1.00) |
1 (1.00) |
0.848 (1.00) |
0.74 (1.00) |
0.461 (1.00) |
0.643 (1.00) |
Del Peak 25(21q22 11) | 0 (0%) | 43 |
0.0192 (1.00) |
0.158 (1.00) |
0.154 (1.00) |
0.00376 (0.996) |
0.0379 (1.00) |
0.265 (1.00) |
0.0685 (1.00) |
0.181 (1.00) |
Del Peak 26(21q22 11) | 0 (0%) | 43 |
0.0192 (1.00) |
0.158 (1.00) |
0.154 (1.00) |
0.00376 (0.996) |
0.0379 (1.00) |
0.265 (1.00) |
0.0685 (1.00) |
0.181 (1.00) |
Del Peak 27(22q13 31) | 0 (0%) | 49 |
0.006 (1.00) |
0.15 (1.00) |
0.358 (1.00) |
0.26 (1.00) |
0.38 (1.00) |
0.424 (1.00) |
0.286 (1.00) |
0.326 (1.00) |
P value = 0.000766 (Chi-square test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 35 | 9 | 9 | 1 |
AMP PEAK 3(7Q22.1) CNV | 4 | 4 | 7 | 2 | 1 |
AMP PEAK 3(7Q22.1) WILD-TYPE | 7 | 31 | 2 | 7 | 0 |
P value = 0.000101 (Fisher's exact test), Q value = 0.033
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 25 | 15 |
AMP PEAK 3(7Q22.1) CNV | 10 | 0 | 7 |
AMP PEAK 3(7Q22.1) WILD-TYPE | 14 | 25 | 8 |
P value = 7.91e-06 (Chi-square test), Q value = 0.0027
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 35 | 9 | 9 | 1 |
AMP PEAK 4(8Q24.21) CNV | 11 | 6 | 6 | 2 | 0 |
AMP PEAK 4(8Q24.21) WILD-TYPE | 0 | 29 | 3 | 7 | 1 |
P value = 0.000579 (Fisher's exact test), Q value = 0.18
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 12 | 12 | 10 |
AMP PEAK 4(8Q24.21) CNV | 14 | 5 | 2 | 0 |
AMP PEAK 4(8Q24.21) WILD-TYPE | 7 | 7 | 10 | 10 |
P value = 2.52e-07 (Chi-square test), Q value = 8.8e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 35 | 9 | 9 | 1 |
AMP PEAK 7(12P13.33) CNV | 8 | 0 | 2 | 0 | 0 |
AMP PEAK 7(12P13.33) WILD-TYPE | 3 | 35 | 7 | 9 | 1 |
P value = 1.52e-05 (Chi-square test), Q value = 0.0051
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 35 | 9 | 9 | 1 |
AMP PEAK 8(12P11.21) CNV | 7 | 0 | 2 | 4 | 1 |
AMP PEAK 8(12P11.21) WILD-TYPE | 4 | 35 | 7 | 5 | 0 |
P value = 0.000696 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 25 | 15 |
AMP PEAK 8(12P11.21) CNV | 8 | 0 | 6 |
AMP PEAK 8(12P11.21) WILD-TYPE | 16 | 25 | 9 |
P value = 0.000293 (Chi-square test), Q value = 0.092
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 35 | 9 | 9 | 1 |
AMP PEAK 12(18Q11.2) CNV | 4 | 3 | 5 | 7 | 0 |
AMP PEAK 12(18Q11.2) WILD-TYPE | 7 | 32 | 4 | 2 | 1 |
P value = 0.000369 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 12 | 12 | 10 |
AMP PEAK 12(18Q11.2) CNV | 13 | 3 | 0 | 1 |
AMP PEAK 12(18Q11.2) WILD-TYPE | 8 | 9 | 12 | 9 |
P value = 0.000478 (Fisher's exact test), Q value = 0.15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 25 | 10 | 23 |
AMP PEAK 12(18Q11.2) CNV | 14 | 1 | 2 |
AMP PEAK 12(18Q11.2) WILD-TYPE | 11 | 9 | 21 |
P value = 0.000556 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 12 | 26 | 20 |
AMP PEAK 12(18Q11.2) CNV | 0 | 14 | 3 |
AMP PEAK 12(18Q11.2) WILD-TYPE | 12 | 12 | 17 |
P value = 2.88e-06 (Chi-square test), Q value = 0.00099
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 35 | 9 | 9 | 1 |
AMP PEAK 14(20Q13.2) CNV | 10 | 3 | 3 | 1 | 0 |
AMP PEAK 14(20Q13.2) WILD-TYPE | 1 | 32 | 6 | 8 | 1 |
P value = 0.00068 (Chi-square test), Q value = 0.2
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 35 | 9 | 9 | 1 |
DEL PEAK 2(1P36.11) CNV | 8 | 3 | 3 | 4 | 0 |
DEL PEAK 2(1P36.11) WILD-TYPE | 3 | 32 | 6 | 5 | 1 |
P value = 0.000619 (Fisher's exact test), Q value = 0.19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 25 | 15 |
DEL PEAK 2(1P36.11) CNV | 9 | 1 | 8 |
DEL PEAK 2(1P36.11) WILD-TYPE | 15 | 24 | 7 |
P value = 0.000152 (Chi-square test), Q value = 0.049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 35 | 9 | 9 | 1 |
DEL PEAK 3(1P21.2) CNV | 7 | 1 | 2 | 1 | 0 |
DEL PEAK 3(1P21.2) WILD-TYPE | 4 | 34 | 7 | 8 | 1 |
P value = 0.000601 (Chi-square test), Q value = 0.18
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 35 | 9 | 9 | 1 |
DEL PEAK 4(5Q14.2) CNV | 6 | 2 | 4 | 0 | 0 |
DEL PEAK 4(5Q14.2) WILD-TYPE | 5 | 33 | 5 | 9 | 1 |
P value = 0.000688 (Chi-square test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 35 | 9 | 9 | 1 |
DEL PEAK 5(5Q15) CNV | 6 | 2 | 5 | 1 | 0 |
DEL PEAK 5(5Q15) WILD-TYPE | 5 | 33 | 4 | 8 | 1 |
P value = 4.12e-05 (Chi-square test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 35 | 9 | 9 | 1 |
DEL PEAK 6(6P25.2) CNV | 9 | 6 | 8 | 3 | 0 |
DEL PEAK 6(6P25.2) WILD-TYPE | 2 | 29 | 1 | 6 | 1 |
P value = 1.76e-05 (Fisher's exact test), Q value = 0.006
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 25 | 15 |
DEL PEAK 6(6P25.2) CNV | 17 | 2 | 6 |
DEL PEAK 6(6P25.2) WILD-TYPE | 7 | 23 | 9 |
P value = 0.000193 (Fisher's exact test), Q value = 0.061
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 12 | 12 | 10 |
DEL PEAK 6(6P25.2) CNV | 15 | 4 | 2 | 0 |
DEL PEAK 6(6P25.2) WILD-TYPE | 6 | 8 | 10 | 10 |
P value = 0.000854 (Chi-square test), Q value = 0.25
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 35 | 9 | 9 | 1 |
DEL PEAK 7(6P22.3) CNV | 8 | 6 | 7 | 4 | 0 |
DEL PEAK 7(6P22.3) WILD-TYPE | 3 | 29 | 2 | 5 | 1 |
P value = 6.32e-05 (Fisher's exact test), Q value = 0.021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 25 | 15 |
DEL PEAK 7(6P22.3) CNV | 16 | 2 | 6 |
DEL PEAK 7(6P22.3) WILD-TYPE | 8 | 23 | 9 |
P value = 0.000119 (Fisher's exact test), Q value = 0.039
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 12 | 12 | 10 |
DEL PEAK 7(6P22.3) CNV | 15 | 3 | 2 | 0 |
DEL PEAK 7(6P22.3) WILD-TYPE | 6 | 9 | 10 | 10 |
P value = 0.000728 (Chi-square test), Q value = 0.22
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 35 | 9 | 9 | 1 |
DEL PEAK 8(6Q22.33) CNV | 9 | 9 | 8 | 5 | 0 |
DEL PEAK 8(6Q22.33) WILD-TYPE | 2 | 26 | 1 | 4 | 1 |
P value = 3.79e-05 (Fisher's exact test), Q value = 0.013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 25 | 15 |
DEL PEAK 8(6Q22.33) CNV | 19 | 4 | 7 |
DEL PEAK 8(6Q22.33) WILD-TYPE | 5 | 21 | 8 |
P value = 4.39e-06 (Fisher's exact test), Q value = 0.0015
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 5 | 22 | 28 |
DEL PEAK 8(6Q22.33) CNV | 0 | 18 | 6 |
DEL PEAK 8(6Q22.33) WILD-TYPE | 5 | 4 | 22 |
P value = 0.000693 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 29 | 11 | 18 |
DEL PEAK 8(6Q22.33) CNV | 20 | 3 | 3 |
DEL PEAK 8(6Q22.33) WILD-TYPE | 9 | 8 | 15 |
P value = 0.000148 (Fisher's exact test), Q value = 0.048
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 11 | 20 | 27 |
DEL PEAK 8(6Q22.33) CNV | 2 | 4 | 20 |
DEL PEAK 8(6Q22.33) WILD-TYPE | 9 | 16 | 7 |
P value = 0.000163 (Fisher's exact test), Q value = 0.052
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 25 | 10 | 23 |
DEL PEAK 8(6Q22.33) CNV | 19 | 2 | 5 |
DEL PEAK 8(6Q22.33) WILD-TYPE | 6 | 8 | 18 |
P value = 0.000466 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 12 | 26 | 20 |
DEL PEAK 8(6Q22.33) CNV | 3 | 19 | 4 |
DEL PEAK 8(6Q22.33) WILD-TYPE | 9 | 7 | 16 |
P value = 2.52e-05 (Chi-square test), Q value = 0.0085
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 35 | 9 | 9 | 1 |
DEL PEAK 10(8P21.3) CNV | 9 | 2 | 4 | 4 | 0 |
DEL PEAK 10(8P21.3) WILD-TYPE | 2 | 33 | 5 | 5 | 1 |
P value = 0.000211 (Fisher's exact test), Q value = 0.067
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 25 | 15 |
DEL PEAK 10(8P21.3) CNV | 13 | 1 | 4 |
DEL PEAK 10(8P21.3) WILD-TYPE | 11 | 24 | 11 |
P value = 8.93e-05 (Fisher's exact test), Q value = 0.029
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 12 | 12 | 10 |
DEL PEAK 10(8P21.3) CNV | 13 | 1 | 1 | 0 |
DEL PEAK 10(8P21.3) WILD-TYPE | 8 | 11 | 11 | 10 |
P value = 0.000538 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 5 | 22 | 28 |
DEL PEAK 10(8P21.3) CNV | 1 | 12 | 2 |
DEL PEAK 10(8P21.3) WILD-TYPE | 4 | 10 | 26 |
P value = 0.000789 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 29 | 11 | 18 |
DEL PEAK 10(8P21.3) CNV | 15 | 1 | 1 |
DEL PEAK 10(8P21.3) WILD-TYPE | 14 | 10 | 17 |
P value = 0.000163 (Fisher's exact test), Q value = 0.052
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 25 | 10 | 23 |
DEL PEAK 10(8P21.3) CNV | 14 | 2 | 1 |
DEL PEAK 10(8P21.3) WILD-TYPE | 11 | 8 | 22 |
P value = 1.43e-06 (Chi-square test), Q value = 5e-04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 35 | 9 | 9 | 1 |
DEL PEAK 12(9P21.3) CNV | 11 | 11 | 9 | 9 | 1 |
DEL PEAK 12(9P21.3) WILD-TYPE | 0 | 24 | 0 | 0 | 0 |
P value = 9.11e-08 (Fisher's exact test), Q value = 3.2e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 25 | 15 |
DEL PEAK 12(9P21.3) CNV | 24 | 7 | 9 |
DEL PEAK 12(9P21.3) WILD-TYPE | 0 | 18 | 6 |
P value = 2.16e-05 (Fisher's exact test), Q value = 0.0073
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 12 | 12 | 10 |
DEL PEAK 12(9P21.3) CNV | 20 | 6 | 3 | 3 |
DEL PEAK 12(9P21.3) WILD-TYPE | 1 | 6 | 9 | 7 |
P value = 4.09e-06 (Fisher's exact test), Q value = 0.0014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 5 | 22 | 28 |
DEL PEAK 12(9P21.3) CNV | 1 | 21 | 10 |
DEL PEAK 12(9P21.3) WILD-TYPE | 4 | 1 | 18 |
P value = 2.95e-05 (Fisher's exact test), Q value = 0.0099
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 29 | 11 | 18 |
DEL PEAK 12(9P21.3) CNV | 25 | 5 | 4 |
DEL PEAK 12(9P21.3) WILD-TYPE | 4 | 6 | 14 |
P value = 4.02e-05 (Fisher's exact test), Q value = 0.013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 11 | 20 | 27 |
DEL PEAK 12(9P21.3) CNV | 3 | 7 | 24 |
DEL PEAK 12(9P21.3) WILD-TYPE | 8 | 13 | 3 |
P value = 2.78e-07 (Fisher's exact test), Q value = 9.7e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 25 | 10 | 23 |
DEL PEAK 12(9P21.3) CNV | 24 | 4 | 6 |
DEL PEAK 12(9P21.3) WILD-TYPE | 1 | 6 | 17 |
P value = 4.88e-06 (Fisher's exact test), Q value = 0.0017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 12 | 26 | 20 |
DEL PEAK 12(9P21.3) CNV | 3 | 24 | 7 |
DEL PEAK 12(9P21.3) WILD-TYPE | 9 | 2 | 13 |
P value = 1.2e-07 (Chi-square test), Q value = 4.2e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 35 | 9 | 9 | 1 |
DEL PEAK 13(10Q23.2) CNV | 5 | 1 | 8 | 0 | 0 |
DEL PEAK 13(10Q23.2) WILD-TYPE | 6 | 34 | 1 | 9 | 1 |
P value = 0.000408 (Chi-square test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 35 | 9 | 9 | 1 |
DEL PEAK 15(12P12.3) CNV | 3 | 1 | 1 | 5 | 1 |
DEL PEAK 15(12P12.3) WILD-TYPE | 8 | 34 | 8 | 4 | 0 |
P value = 0.00014 (Chi-square test), Q value = 0.045
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 35 | 9 | 9 | 1 |
DEL PEAK 16(12Q12) CNV | 2 | 1 | 6 | 1 | 0 |
DEL PEAK 16(12Q12) WILD-TYPE | 9 | 34 | 3 | 8 | 1 |
P value = 3.91e-05 (Fisher's exact test), Q value = 0.013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 25 | 15 |
DEL PEAK 16(12Q12) CNV | 10 | 0 | 0 |
DEL PEAK 16(12Q12) WILD-TYPE | 14 | 25 | 15 |
P value = 9.01e-05 (Fisher's exact test), Q value = 0.029
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 25 | 15 |
DEL PEAK 17(12Q24.31) CNV | 13 | 1 | 2 |
DEL PEAK 17(12Q24.31) WILD-TYPE | 11 | 24 | 13 |
P value = 0.000169 (Fisher's exact test), Q value = 0.054
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 5 | 22 | 28 |
DEL PEAK 17(12Q24.31) CNV | 0 | 11 | 1 |
DEL PEAK 17(12Q24.31) WILD-TYPE | 5 | 11 | 27 |
P value = 0.000454 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 25 | 10 | 23 |
DEL PEAK 17(12Q24.31) CNV | 11 | 2 | 0 |
DEL PEAK 17(12Q24.31) WILD-TYPE | 14 | 8 | 23 |
P value = 1.29e-06 (Chi-square test), Q value = 0.00045
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 35 | 9 | 9 | 1 |
DEL PEAK 18(15Q15.1) CNV | 7 | 0 | 6 | 1 | 0 |
DEL PEAK 18(15Q15.1) WILD-TYPE | 4 | 35 | 3 | 8 | 1 |
P value = 5.43e-05 (Chi-square test), Q value = 0.018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 35 | 9 | 9 | 1 |
DEL PEAK 19(17P11.2) CNV | 10 | 5 | 5 | 5 | 1 |
DEL PEAK 19(17P11.2) WILD-TYPE | 1 | 30 | 4 | 4 | 0 |
P value = 1.13e-08 (Fisher's exact test), Q value = 4e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 25 | 15 |
DEL PEAK 19(17P11.2) CNV | 18 | 0 | 8 |
DEL PEAK 19(17P11.2) WILD-TYPE | 6 | 25 | 7 |
P value = 0.000809 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 12 | 12 | 10 |
DEL PEAK 19(17P11.2) CNV | 15 | 3 | 2 | 1 |
DEL PEAK 19(17P11.2) WILD-TYPE | 6 | 9 | 10 | 9 |
P value = 0.000824 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 5 | 22 | 28 |
DEL PEAK 19(17P11.2) CNV | 1 | 15 | 5 |
DEL PEAK 19(17P11.2) WILD-TYPE | 4 | 7 | 23 |
P value = 0.000332 (Fisher's exact test), Q value = 0.1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 11 | 20 | 27 |
DEL PEAK 19(17P11.2) CNV | 1 | 4 | 18 |
DEL PEAK 19(17P11.2) WILD-TYPE | 10 | 16 | 9 |
P value = 0.000246 (Fisher's exact test), Q value = 0.077
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 25 | 10 | 23 |
DEL PEAK 19(17P11.2) CNV | 17 | 3 | 3 |
DEL PEAK 19(17P11.2) WILD-TYPE | 8 | 7 | 20 |
P value = 9.68e-06 (Chi-square test), Q value = 0.0033
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 35 | 9 | 9 | 1 |
DEL PEAK 20(17Q22) CNV | 9 | 2 | 2 | 4 | 1 |
DEL PEAK 20(17Q22) WILD-TYPE | 2 | 33 | 7 | 5 | 0 |
P value = 3.54e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 25 | 15 |
DEL PEAK 20(17Q22) CNV | 12 | 0 | 6 |
DEL PEAK 20(17Q22) WILD-TYPE | 12 | 25 | 9 |
P value = 0.00041 (Chi-square test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 35 | 9 | 9 | 1 |
DEL PEAK 28(XQ21.1) CNV | 5 | 0 | 2 | 0 | 0 |
DEL PEAK 28(XQ21.1) WILD-TYPE | 6 | 35 | 7 | 9 | 1 |
-
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 = PAAD-TP.transferedmergedcluster.txt
-
Number of patients = 65
-
Number of copy number variation regions = 44
-
Number of molecular subtypes = 8
-
Exclude regions that fewer than K tumors have alterations, K = 3
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 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.