This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.
Testing the association between copy number variation of 48 peak regions and 8 molecular subtypes across 83 patients, 34 significant findings detected with Q value < 0.25.
-
Amp Peak 1(1p32.1) cnvs correlated to 'CN_CNMF'.
-
Amp Peak 4(6p21.1) cnvs correlated to 'METHLYATION_CNMF'.
-
Amp Peak 5(6q24.3) cnvs correlated to 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
-
Amp Peak 9(12q15) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
Del Peak 1(1p36.32) cnvs correlated to 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
Del Peak 2(1p32.3) cnvs correlated to 'CN_CNMF'.
-
Del Peak 5(2q37.3) cnvs correlated to 'CN_CNMF'.
-
Del Peak 13(9p24.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 14(9p21.3) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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Del Peak 17(10q23.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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Del Peak 22(13q14.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 30(19q13.33) cnvs correlated to 'METHLYATION_CNMF'.
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Del Peak 32(22q13.32) cnvs correlated to 'METHLYATION_CNMF'.
Molecular subtypes |
CN CNMF |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
Amp Peak 9(12q15) | 0 (0%) | 43 |
3.02e-10 (1.16e-07) |
5.12e-10 (1.95e-07) |
1.58e-08 (5.96e-06) |
3.89e-10 (1.49e-07) |
8.35e-09 (3.16e-06) |
3.35e-08 (1.26e-05) |
6.66e-12 (2.56e-09) |
2.32e-09 (8.81e-07) |
Del Peak 1(1p36 32) | 0 (0%) | 56 |
0.146 (1.00) |
0.00102 (0.358) |
0.00138 (0.475) |
0.000532 (0.19) |
0.000306 (0.11) |
0.000215 (0.0777) |
0.000668 (0.235) |
7.27e-05 (0.027) |
Del Peak 14(9p21 3) | 0 (0%) | 46 |
1.33e-07 (5e-05) |
0.0121 (1.00) |
0.000693 (0.243) |
8.77e-05 (0.0324) |
0.0185 (1.00) |
0.212 (1.00) |
8.97e-05 (0.0331) |
0.22 (1.00) |
Del Peak 17(10q23 31) | 0 (0%) | 42 |
0.000107 (0.0391) |
0.000219 (0.0792) |
0.0039 (1.00) |
0.000587 (0.207) |
0.00433 (1.00) |
0.00293 (0.971) |
0.00133 (0.459) |
0.000573 (0.204) |
Amp Peak 5(6q24 3) | 0 (0%) | 56 |
0.00264 (0.879) |
0.000521 (0.186) |
0.00162 (0.552) |
0.00222 (0.748) |
0.00789 (1.00) |
0.00047 (0.169) |
0.000193 (0.0705) |
0.00112 (0.391) |
Del Peak 13(9p24 3) | 0 (0%) | 50 |
1.96e-06 (0.000735) |
0.0199 (1.00) |
0.011 (1.00) |
0.000499 (0.179) |
0.06 (1.00) |
0.0514 (1.00) |
0.00186 (0.63) |
0.0876 (1.00) |
Del Peak 22(13q14 2) | 0 (0%) | 24 |
0.000194 (0.0706) |
6.44e-05 (0.0239) |
0.0186 (1.00) |
0.00885 (1.00) |
0.00566 (1.00) |
0.0194 (1.00) |
0.00505 (1.00) |
0.00867 (1.00) |
Amp Peak 1(1p32 1) | 0 (0%) | 55 |
0.000208 (0.0754) |
0.00343 (1.00) |
0.506 (1.00) |
0.165 (1.00) |
0.0912 (1.00) |
0.0136 (1.00) |
0.0573 (1.00) |
0.017 (1.00) |
Amp Peak 4(6p21 1) | 0 (0%) | 62 |
0.0105 (1.00) |
9.19e-05 (0.0338) |
0.131 (1.00) |
0.0101 (1.00) |
0.00882 (1.00) |
0.0144 (1.00) |
0.00279 (0.928) |
0.0114 (1.00) |
Del Peak 2(1p32 3) | 0 (0%) | 68 |
1.95e-05 (0.00728) |
0.938 (1.00) |
0.444 (1.00) |
0.805 (1.00) |
0.282 (1.00) |
0.366 (1.00) |
0.551 (1.00) |
0.821 (1.00) |
Del Peak 5(2q37 3) | 0 (0%) | 47 |
0.00011 (0.0403) |
0.028 (1.00) |
0.0813 (1.00) |
0.553 (1.00) |
0.664 (1.00) |
0.204 (1.00) |
0.55 (1.00) |
0.145 (1.00) |
Del Peak 30(19q13 33) | 0 (0%) | 53 |
0.0859 (1.00) |
2.41e-05 (0.00898) |
0.653 (1.00) |
0.132 (1.00) |
0.387 (1.00) |
0.621 (1.00) |
0.17 (1.00) |
0.289 (1.00) |
Del Peak 32(22q13 32) | 0 (0%) | 49 |
0.0431 (1.00) |
0.000586 (0.207) |
0.0402 (1.00) |
0.692 (1.00) |
0.495 (1.00) |
0.218 (1.00) |
0.13 (1.00) |
0.55 (1.00) |
Amp Peak 2(1q24 3) | 0 (0%) | 49 |
0.00514 (1.00) |
0.41 (1.00) |
0.743 (1.00) |
0.692 (1.00) |
0.213 (1.00) |
0.627 (1.00) |
0.687 (1.00) |
0.419 (1.00) |
Amp Peak 3(5p15 33) | 0 (0%) | 51 |
0.00478 (1.00) |
0.225 (1.00) |
0.183 (1.00) |
0.0425 (1.00) |
0.221 (1.00) |
0.324 (1.00) |
0.0463 (1.00) |
0.249 (1.00) |
Amp Peak 6(7p21 3) | 0 (0%) | 55 |
0.162 (1.00) |
0.0307 (1.00) |
0.0301 (1.00) |
0.0558 (1.00) |
0.0314 (1.00) |
0.0544 (1.00) |
0.0192 (1.00) |
0.0712 (1.00) |
Amp Peak 7(11q22 2) | 0 (0%) | 67 |
0.585 (1.00) |
0.25 (1.00) |
0.398 (1.00) |
0.294 (1.00) |
0.245 (1.00) |
0.143 (1.00) |
0.0731 (1.00) |
0.071 (1.00) |
Amp Peak 8(12p12 1) | 0 (0%) | 60 |
0.0491 (1.00) |
0.378 (1.00) |
0.277 (1.00) |
0.595 (1.00) |
0.0182 (1.00) |
0.63 (1.00) |
0.0603 (1.00) |
0.856 (1.00) |
Amp Peak 10(17p11 2) | 0 (0%) | 54 |
0.0357 (1.00) |
0.00522 (1.00) |
0.864 (1.00) |
0.304 (1.00) |
0.0411 (1.00) |
0.544 (1.00) |
0.639 (1.00) |
0.275 (1.00) |
Amp Peak 11(19p13 2) | 0 (0%) | 52 |
0.021 (1.00) |
0.633 (1.00) |
0.0999 (1.00) |
0.422 (1.00) |
0.553 (1.00) |
0.915 (1.00) |
0.713 (1.00) |
0.459 (1.00) |
Amp Peak 12(19q12) | 0 (0%) | 57 |
0.0321 (1.00) |
0.000969 (0.339) |
0.7 (1.00) |
0.182 (1.00) |
0.194 (1.00) |
0.671 (1.00) |
0.196 (1.00) |
0.308 (1.00) |
Amp Peak 13(Xq21 1) | 0 (0%) | 67 |
0.0042 (1.00) |
0.106 (1.00) |
0.142 (1.00) |
0.827 (1.00) |
0.0617 (1.00) |
1 (1.00) |
0.0244 (1.00) |
1 (1.00) |
Del Peak 3(1q44) | 0 (0%) | 54 |
0.00189 (0.639) |
0.0703 (1.00) |
0.0441 (1.00) |
0.0632 (1.00) |
0.293 (1.00) |
0.379 (1.00) |
0.0629 (1.00) |
0.278 (1.00) |
Del Peak 4(2p25 3) | 0 (0%) | 57 |
0.0193 (1.00) |
0.0312 (1.00) |
0.126 (1.00) |
0.0154 (1.00) |
0.0143 (1.00) |
0.00681 (1.00) |
0.00151 (0.516) |
0.00228 (0.764) |
Del Peak 6(3p21 31) | 0 (0%) | 62 |
0.00124 (0.43) |
0.0407 (1.00) |
0.0763 (1.00) |
0.0101 (1.00) |
0.00488 (1.00) |
0.0083 (1.00) |
0.0716 (1.00) |
0.0815 (1.00) |
Del Peak 7(3q25 2) | 0 (0%) | 61 |
0.0153 (1.00) |
0.00126 (0.434) |
0.0237 (1.00) |
0.0126 (1.00) |
0.159 (1.00) |
0.00452 (1.00) |
0.0194 (1.00) |
0.00672 (1.00) |
Del Peak 8(4q34 3) | 0 (0%) | 48 |
0.0436 (1.00) |
0.022 (1.00) |
0.102 (1.00) |
0.408 (1.00) |
0.444 (1.00) |
0.912 (1.00) |
0.524 (1.00) |
0.64 (1.00) |
Del Peak 9(6p24 3) | 0 (0%) | 53 |
0.548 (1.00) |
0.0308 (1.00) |
0.642 (1.00) |
0.176 (1.00) |
0.165 (1.00) |
0.275 (1.00) |
0.0739 (1.00) |
0.596 (1.00) |
Del Peak 10(6q15) | 0 (0%) | 64 |
0.12 (1.00) |
0.148 (1.00) |
0.401 (1.00) |
0.112 (1.00) |
0.279 (1.00) |
0.156 (1.00) |
0.441 (1.00) |
0.0532 (1.00) |
Del Peak 11(7q36 3) | 0 (0%) | 63 |
0.756 (1.00) |
0.475 (1.00) |
0.566 (1.00) |
0.167 (1.00) |
0.977 (1.00) |
0.777 (1.00) |
0.696 (1.00) |
0.2 (1.00) |
Del Peak 12(8p23 3) | 0 (0%) | 61 |
0.00493 (1.00) |
0.00989 (1.00) |
0.234 (1.00) |
0.28 (1.00) |
0.145 (1.00) |
0.0083 (1.00) |
0.19 (1.00) |
0.208 (1.00) |
Del Peak 15(9q34 3) | 0 (0%) | 58 |
0.0048 (1.00) |
0.0416 (1.00) |
0.199 (1.00) |
0.521 (1.00) |
0.248 (1.00) |
0.256 (1.00) |
0.406 (1.00) |
0.135 (1.00) |
Del Peak 16(10p15 3) | 0 (0%) | 44 |
0.0161 (1.00) |
0.0482 (1.00) |
0.124 (1.00) |
0.416 (1.00) |
0.505 (1.00) |
0.245 (1.00) |
0.606 (1.00) |
0.269 (1.00) |
Del Peak 18(11p15 5) | 0 (0%) | 45 |
0.0399 (1.00) |
0.117 (1.00) |
0.561 (1.00) |
0.716 (1.00) |
0.758 (1.00) |
1 (1.00) |
0.761 (1.00) |
0.502 (1.00) |
Del Peak 19(11q22 3) | 0 (0%) | 49 |
0.00179 (0.608) |
0.0172 (1.00) |
0.501 (1.00) |
0.226 (1.00) |
0.0833 (1.00) |
0.172 (1.00) |
0.0966 (1.00) |
0.173 (1.00) |
Del Peak 20(11q24 3) | 0 (0%) | 46 |
0.00477 (1.00) |
0.00941 (1.00) |
0.282 (1.00) |
0.0768 (1.00) |
0.132 (1.00) |
0.0394 (1.00) |
0.039 (1.00) |
0.0572 (1.00) |
Del Peak 21(12p13 1) | 0 (0%) | 58 |
0.0162 (1.00) |
0.0499 (1.00) |
0.402 (1.00) |
0.725 (1.00) |
0.323 (1.00) |
0.215 (1.00) |
0.419 (1.00) |
0.103 (1.00) |
Del Peak 23(14q24 1) | 0 (0%) | 48 |
0.0398 (1.00) |
0.923 (1.00) |
0.00135 (0.464) |
0.542 (1.00) |
0.189 (1.00) |
0.204 (1.00) |
0.275 (1.00) |
0.262 (1.00) |
Del Peak 24(16q12 1) | 0 (0%) | 37 |
0.0709 (1.00) |
0.00198 (0.667) |
0.349 (1.00) |
0.187 (1.00) |
0.0831 (1.00) |
0.0394 (1.00) |
0.107 (1.00) |
0.0139 (1.00) |
Del Peak 25(17p13 1) | 0 (0%) | 56 |
0.0725 (1.00) |
0.023 (1.00) |
0.0888 (1.00) |
0.0369 (1.00) |
0.132 (1.00) |
0.0584 (1.00) |
0.0616 (1.00) |
0.0223 (1.00) |
Del Peak 26(17q25 3) | 0 (0%) | 57 |
0.0327 (1.00) |
0.109 (1.00) |
0.445 (1.00) |
0.0558 (1.00) |
0.639 (1.00) |
0.593 (1.00) |
0.537 (1.00) |
0.259 (1.00) |
Del Peak 27(18p11 32) | 0 (0%) | 58 |
0.188 (1.00) |
0.153 (1.00) |
0.811 (1.00) |
0.865 (1.00) |
0.469 (1.00) |
0.664 (1.00) |
0.855 (1.00) |
0.636 (1.00) |
Del Peak 28(18q23) | 0 (0%) | 52 |
0.226 (1.00) |
0.285 (1.00) |
0.271 (1.00) |
0.377 (1.00) |
1 (1.00) |
0.756 (1.00) |
0.423 (1.00) |
0.603 (1.00) |
Del Peak 29(19p13 3) | 0 (0%) | 60 |
0.00489 (1.00) |
0.00795 (1.00) |
0.0856 (1.00) |
0.0253 (1.00) |
0.112 (1.00) |
0.0348 (1.00) |
0.0262 (1.00) |
0.0694 (1.00) |
Del Peak 31(21q22 3) | 0 (0%) | 56 |
0.468 (1.00) |
0.838 (1.00) |
0.423 (1.00) |
0.647 (1.00) |
0.756 (1.00) |
0.677 (1.00) |
0.462 (1.00) |
1 (1.00) |
Del Peak 33(Xp21 1) | 0 (0%) | 67 |
0.465 (1.00) |
0.0711 (1.00) |
0.636 (1.00) |
0.317 (1.00) |
0.0471 (1.00) |
0.118 (1.00) |
0.151 (1.00) |
0.233 (1.00) |
Del Peak 34(Xq21 1) | 0 (0%) | 48 |
0.52 (1.00) |
0.132 (1.00) |
0.279 (1.00) |
0.0689 (1.00) |
0.321 (1.00) |
0.118 (1.00) |
0.145 (1.00) |
0.0568 (1.00) |
Del Peak 35(Xq27 1) | 0 (0%) | 42 |
0.00258 (0.862) |
0.0509 (1.00) |
0.11 (1.00) |
0.0461 (1.00) |
0.631 (1.00) |
0.456 (1.00) |
0.211 (1.00) |
0.185 (1.00) |
P value = 0.000208 (Fisher's exact test), Q value = 0.075
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 22 | 18 | 19 |
AMP PEAK 1(1P32.1) CNV | 5 | 10 | 12 | 1 |
AMP PEAK 1(1P32.1) WILD-TYPE | 19 | 12 | 6 | 18 |
P value = 9.19e-05 (Fisher's exact test), Q value = 0.034
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 26 | 27 | 30 |
AMP PEAK 4(6P21.1) CNV | 6 | 14 | 1 |
AMP PEAK 4(6P21.1) WILD-TYPE | 20 | 13 | 29 |
P value = 0.000521 (Fisher's exact test), Q value = 0.19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 26 | 27 | 30 |
AMP PEAK 5(6Q24.3) CNV | 15 | 9 | 3 |
AMP PEAK 5(6Q24.3) WILD-TYPE | 11 | 18 | 27 |
P value = 0.00047 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 37 | 43 |
AMP PEAK 5(6Q24.3) CNV | 0 | 5 | 22 |
AMP PEAK 5(6Q24.3) WILD-TYPE | 2 | 32 | 21 |
P value = 0.000193 (Fisher's exact test), Q value = 0.071
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 13 | 36 | 33 |
AMP PEAK 5(6Q24.3) CNV | 8 | 16 | 3 |
AMP PEAK 5(6Q24.3) WILD-TYPE | 5 | 20 | 30 |
P value = 3.02e-10 (Fisher's exact test), Q value = 1.2e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 22 | 18 | 19 |
AMP PEAK 9(12Q15) CNV | 12 | 22 | 4 | 2 |
AMP PEAK 9(12Q15) WILD-TYPE | 12 | 0 | 14 | 17 |
P value = 5.12e-10 (Fisher's exact test), Q value = 1.9e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 26 | 27 | 30 |
AMP PEAK 9(12Q15) CNV | 19 | 20 | 1 |
AMP PEAK 9(12Q15) WILD-TYPE | 7 | 7 | 29 |
P value = 1.58e-08 (Chi-square test), Q value = 6e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 11 | 16 | 2 | 17 | 15 |
AMP PEAK 9(12Q15) CNV | 7 | 9 | 16 | 1 | 1 | 1 |
AMP PEAK 9(12Q15) WILD-TYPE | 7 | 2 | 0 | 1 | 16 | 14 |
P value = 3.89e-10 (Fisher's exact test), Q value = 1.5e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 1 | 31 | 43 |
AMP PEAK 9(12Q15) CNV | 0 | 2 | 33 |
AMP PEAK 9(12Q15) WILD-TYPE | 1 | 29 | 10 |
P value = 8.35e-09 (Fisher's exact test), Q value = 3.2e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 6 | 37 | 12 | 27 |
AMP PEAK 9(12Q15) CNV | 5 | 27 | 6 | 1 |
AMP PEAK 9(12Q15) WILD-TYPE | 1 | 10 | 6 | 26 |
P value = 3.35e-08 (Fisher's exact test), Q value = 1.3e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 37 | 43 |
AMP PEAK 9(12Q15) CNV | 0 | 6 | 33 |
AMP PEAK 9(12Q15) WILD-TYPE | 2 | 31 | 10 |
P value = 6.66e-12 (Fisher's exact test), Q value = 2.6e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 13 | 36 | 33 |
AMP PEAK 9(12Q15) CNV | 10 | 28 | 1 |
AMP PEAK 9(12Q15) WILD-TYPE | 3 | 8 | 32 |
P value = 2.32e-09 (Fisher's exact test), Q value = 8.8e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 1 | 41 | 40 |
AMP PEAK 9(12Q15) CNV | 0 | 33 | 6 |
AMP PEAK 9(12Q15) WILD-TYPE | 1 | 8 | 34 |
P value = 0.000532 (Fisher's exact test), Q value = 0.19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 1 | 31 | 43 |
DEL PEAK 1(1P36.32) CNV | 1 | 17 | 7 |
DEL PEAK 1(1P36.32) WILD-TYPE | 0 | 14 | 36 |
P value = 0.000306 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 6 | 37 | 12 | 27 |
DEL PEAK 1(1P36.32) CNV | 2 | 5 | 3 | 17 |
DEL PEAK 1(1P36.32) WILD-TYPE | 4 | 32 | 9 | 10 |
P value = 0.000215 (Fisher's exact test), Q value = 0.078
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 37 | 43 |
DEL PEAK 1(1P36.32) CNV | 1 | 20 | 6 |
DEL PEAK 1(1P36.32) WILD-TYPE | 1 | 17 | 37 |
P value = 0.000668 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 13 | 36 | 33 |
DEL PEAK 1(1P36.32) CNV | 2 | 6 | 19 |
DEL PEAK 1(1P36.32) WILD-TYPE | 11 | 30 | 14 |
P value = 7.27e-05 (Fisher's exact test), Q value = 0.027
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 1 | 41 | 40 |
DEL PEAK 1(1P36.32) CNV | 1 | 5 | 21 |
DEL PEAK 1(1P36.32) WILD-TYPE | 0 | 36 | 19 |
P value = 1.95e-05 (Fisher's exact test), Q value = 0.0073
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 22 | 18 | 19 |
DEL PEAK 2(1P32.3) CNV | 12 | 0 | 1 | 2 |
DEL PEAK 2(1P32.3) WILD-TYPE | 12 | 22 | 17 | 17 |
P value = 0.00011 (Fisher's exact test), Q value = 0.04
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 22 | 18 | 19 |
DEL PEAK 5(2Q37.3) CNV | 12 | 6 | 15 | 3 |
DEL PEAK 5(2Q37.3) WILD-TYPE | 12 | 16 | 3 | 16 |
P value = 1.96e-06 (Fisher's exact test), Q value = 0.00073
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 22 | 18 | 19 |
DEL PEAK 13(9P24.3) CNV | 19 | 9 | 4 | 1 |
DEL PEAK 13(9P24.3) WILD-TYPE | 5 | 13 | 14 | 18 |
P value = 0.000499 (Fisher's exact test), Q value = 0.18
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 1 | 31 | 43 |
DEL PEAK 13(9P24.3) CNV | 1 | 6 | 26 |
DEL PEAK 13(9P24.3) WILD-TYPE | 0 | 25 | 17 |
P value = 1.33e-07 (Fisher's exact test), Q value = 5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 22 | 18 | 19 |
DEL PEAK 14(9P21.3) CNV | 22 | 8 | 4 | 3 |
DEL PEAK 14(9P21.3) WILD-TYPE | 2 | 14 | 14 | 16 |
P value = 0.000693 (Chi-square test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 11 | 16 | 2 | 17 | 15 |
DEL PEAK 14(9P21.3) CNV | 8 | 10 | 10 | 0 | 5 | 2 |
DEL PEAK 14(9P21.3) WILD-TYPE | 6 | 1 | 6 | 2 | 12 | 13 |
P value = 8.77e-05 (Fisher's exact test), Q value = 0.032
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 1 | 31 | 43 |
DEL PEAK 14(9P21.3) CNV | 1 | 6 | 28 |
DEL PEAK 14(9P21.3) WILD-TYPE | 0 | 25 | 15 |
P value = 8.97e-05 (Fisher's exact test), Q value = 0.033
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 13 | 36 | 33 |
DEL PEAK 14(9P21.3) CNV | 12 | 17 | 8 |
DEL PEAK 14(9P21.3) WILD-TYPE | 1 | 19 | 25 |
P value = 0.000107 (Fisher's exact test), Q value = 0.039
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 22 | 18 | 19 |
DEL PEAK 17(10Q23.31) CNV | 13 | 3 | 15 | 10 |
DEL PEAK 17(10Q23.31) WILD-TYPE | 11 | 19 | 3 | 9 |
P value = 0.000219 (Fisher's exact test), Q value = 0.079
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 26 | 27 | 30 |
DEL PEAK 17(10Q23.31) CNV | 5 | 14 | 22 |
DEL PEAK 17(10Q23.31) WILD-TYPE | 21 | 13 | 8 |
P value = 0.000587 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 1 | 31 | 43 |
DEL PEAK 17(10Q23.31) CNV | 1 | 23 | 14 |
DEL PEAK 17(10Q23.31) WILD-TYPE | 0 | 8 | 29 |
P value = 0.000573 (Fisher's exact test), Q value = 0.2
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 1 | 41 | 40 |
DEL PEAK 17(10Q23.31) CNV | 1 | 12 | 27 |
DEL PEAK 17(10Q23.31) WILD-TYPE | 0 | 29 | 13 |
P value = 0.000194 (Fisher's exact test), Q value = 0.071
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 22 | 18 | 19 |
DEL PEAK 22(13Q14.2) CNV | 19 | 9 | 18 | 13 |
DEL PEAK 22(13Q14.2) WILD-TYPE | 5 | 13 | 0 | 6 |
P value = 6.44e-05 (Fisher's exact test), Q value = 0.024
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 26 | 27 | 30 |
DEL PEAK 22(13Q14.2) CNV | 10 | 22 | 27 |
DEL PEAK 22(13Q14.2) WILD-TYPE | 16 | 5 | 3 |
P value = 2.41e-05 (Fisher's exact test), Q value = 0.009
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 26 | 27 | 30 |
DEL PEAK 30(19Q13.33) CNV | 1 | 16 | 13 |
DEL PEAK 30(19Q13.33) WILD-TYPE | 25 | 11 | 17 |
P value = 0.000586 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 26 | 27 | 30 |
DEL PEAK 32(22Q13.32) CNV | 4 | 18 | 12 |
DEL PEAK 32(22Q13.32) WILD-TYPE | 22 | 9 | 18 |
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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 = SARC-TP.transferedmergedcluster.txt
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Number of patients = 83
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Number of copy number variation regions = 48
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Number of molecular subtypes = 8
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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 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.