This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.
Testing the association between copy number variation of 52 peak regions and 6 molecular subtypes across 126 patients, 15 significant findings detected with Q value < 0.25.
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Amp Peak 4(2q32.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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Amp Peak 5(3q26.2) cnvs correlated to 'CN_CNMF'.
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Amp Peak 6(3q28) cnvs correlated to 'CN_CNMF'.
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Amp Peak 14(11q22.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 1(1p36.23) cnvs correlated to 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 5(3p11.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 6(4q22.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 7(4q35.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 14(10q26.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 19(15q15.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 21(16q23.1) cnvs correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 24(19p13.3) cnvs correlated to 'MIRSEQ_CHIERARCHICAL'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 52 regions and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 15 significant findings detected.
|
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 21(16q23 1) | 28 (22%) | 98 |
1 (1.00) |
0.0202 (1.00) |
0.000234 (0.0706) |
3.45e-05 (0.0106) |
0.143 (1.00) |
0.000197 (0.0598) |
| Amp Peak 4(2q32 3) | 20 (16%) | 106 |
0.000238 (0.0715) |
0.0817 (1.00) |
0.000645 (0.193) |
0.00615 (1.00) |
0.795 (1.00) |
0.0185 (1.00) |
| Amp Peak 5(3q26 2) | 95 (75%) | 31 |
1.26e-06 (0.000391) |
0.585 (1.00) |
0.0931 (1.00) |
0.332 (1.00) |
0.85 (1.00) |
0.105 (1.00) |
| Amp Peak 6(3q28) | 94 (75%) | 32 |
6.37e-07 (0.000199) |
0.702 (1.00) |
0.0492 (1.00) |
0.363 (1.00) |
0.818 (1.00) |
0.063 (1.00) |
| Amp Peak 14(11q22 1) | 27 (21%) | 99 |
7.38e-05 (0.0225) |
0.0723 (1.00) |
0.0782 (1.00) |
0.223 (1.00) |
0.0132 (1.00) |
0.123 (1.00) |
| Del Peak 1(1p36 23) | 20 (16%) | 106 |
0.0829 (1.00) |
0.0329 (1.00) |
0.00125 (0.365) |
0.0013 (0.379) |
0.474 (1.00) |
0.000203 (0.0612) |
| Del Peak 5(3p11 1) | 51 (40%) | 75 |
0.000668 (0.199) |
0.0272 (1.00) |
0.39 (1.00) |
0.00232 (0.669) |
0.129 (1.00) |
0.00706 (1.00) |
| Del Peak 6(4q22 1) | 39 (31%) | 87 |
1.5e-06 (0.000464) |
0.0616 (1.00) |
0.0723 (1.00) |
0.534 (1.00) |
0.2 (1.00) |
0.297 (1.00) |
| Del Peak 7(4q35 2) | 47 (37%) | 79 |
1.38e-05 (0.00427) |
0.0323 (1.00) |
0.0499 (1.00) |
0.16 (1.00) |
0.575 (1.00) |
0.323 (1.00) |
| Del Peak 14(10q26 3) | 38 (30%) | 88 |
0.000133 (0.0405) |
0.516 (1.00) |
0.421 (1.00) |
0.398 (1.00) |
0.708 (1.00) |
0.777 (1.00) |
| Del Peak 19(15q15 1) | 29 (23%) | 97 |
2.68e-05 (0.00825) |
0.346 (1.00) |
0.303 (1.00) |
0.292 (1.00) |
0.176 (1.00) |
0.0869 (1.00) |
| Del Peak 24(19p13 3) | 39 (31%) | 87 |
0.00302 (0.862) |
1 (1.00) |
0.00295 (0.844) |
0.0699 (1.00) |
0.0318 (1.00) |
3.54e-05 (0.0108) |
| Amp Peak 1(1q21 3) | 67 (53%) | 59 |
0.0103 (1.00) |
0.098 (1.00) |
0.386 (1.00) |
0.635 (1.00) |
0.58 (1.00) |
0.566 (1.00) |
| Amp Peak 2(1q44) | 68 (54%) | 58 |
0.00905 (1.00) |
0.785 (1.00) |
0.573 (1.00) |
1 (1.00) |
0.21 (1.00) |
0.546 (1.00) |
| Amp Peak 3(2p24 3) | 33 (26%) | 93 |
0.147 (1.00) |
0.505 (1.00) |
0.0605 (1.00) |
0.0689 (1.00) |
0.0869 (1.00) |
0.0056 (1.00) |
| Amp Peak 7(4q12) | 12 (10%) | 114 |
0.507 (1.00) |
0.165 (1.00) |
0.0826 (1.00) |
0.00436 (1.00) |
0.216 (1.00) |
0.0208 (1.00) |
| Amp Peak 8(6p21 33) | 35 (28%) | 91 |
0.00495 (1.00) |
0.00863 (1.00) |
0.00286 (0.82) |
0.0553 (1.00) |
0.182 (1.00) |
0.0319 (1.00) |
| Amp Peak 9(6q12) | 24 (19%) | 102 |
0.342 (1.00) |
0.135 (1.00) |
0.143 (1.00) |
0.00858 (1.00) |
0.239 (1.00) |
0.181 (1.00) |
| Amp Peak 10(8q24 21) | 53 (42%) | 73 |
0.00207 (0.6) |
0.849 (1.00) |
0.647 (1.00) |
0.534 (1.00) |
0.0891 (1.00) |
0.491 (1.00) |
| Amp Peak 11(8q24 21) | 48 (38%) | 78 |
0.00432 (1.00) |
0.287 (1.00) |
0.705 (1.00) |
0.386 (1.00) |
0.34 (1.00) |
0.852 (1.00) |
| Amp Peak 12(9p24 1) | 28 (22%) | 98 |
0.0587 (1.00) |
0.586 (1.00) |
0.806 (1.00) |
0.528 (1.00) |
0.234 (1.00) |
0.685 (1.00) |
| Amp Peak 13(11q13 3) | 18 (14%) | 108 |
0.0384 (1.00) |
0.726 (1.00) |
0.0171 (1.00) |
0.0291 (1.00) |
0.107 (1.00) |
0.885 (1.00) |
| Amp Peak 15(13q22 1) | 27 (21%) | 99 |
0.00534 (1.00) |
0.387 (1.00) |
0.205 (1.00) |
0.224 (1.00) |
0.162 (1.00) |
0.0195 (1.00) |
| Amp Peak 16(14q24 1) | 25 (20%) | 101 |
0.689 (1.00) |
0.78 (1.00) |
0.282 (1.00) |
0.113 (1.00) |
0.705 (1.00) |
0.955 (1.00) |
| Amp Peak 17(15q26 3) | 30 (24%) | 96 |
0.00584 (1.00) |
0.447 (1.00) |
0.316 (1.00) |
0.539 (1.00) |
0.928 (1.00) |
1 (1.00) |
| Amp Peak 18(16p13 2) | 27 (21%) | 99 |
0.0757 (1.00) |
0.201 (1.00) |
0.87 (1.00) |
0.739 (1.00) |
0.779 (1.00) |
0.806 (1.00) |
| Amp Peak 19(16p13 13) | 30 (24%) | 96 |
0.0618 (1.00) |
0.139 (1.00) |
0.647 (1.00) |
0.235 (1.00) |
0.682 (1.00) |
0.465 (1.00) |
| Amp Peak 20(17q12) | 21 (17%) | 105 |
0.0631 (1.00) |
0.0516 (1.00) |
0.0126 (1.00) |
0.0951 (1.00) |
0.112 (1.00) |
0.065 (1.00) |
| Amp Peak 21(17q25 1) | 34 (27%) | 92 |
0.0113 (1.00) |
0.043 (1.00) |
0.0411 (1.00) |
0.429 (1.00) |
0.48 (1.00) |
0.607 (1.00) |
| Amp Peak 22(19q13 31) | 43 (34%) | 83 |
0.0124 (1.00) |
0.642 (1.00) |
0.287 (1.00) |
0.154 (1.00) |
0.0995 (1.00) |
0.874 (1.00) |
| Amp Peak 23(20q11 21) | 61 (48%) | 65 |
0.000998 (0.295) |
0.371 (1.00) |
0.283 (1.00) |
0.256 (1.00) |
0.532 (1.00) |
0.722 (1.00) |
| Amp Peak 24(Xq28) | 36 (29%) | 90 |
0.795 (1.00) |
0.139 (1.00) |
0.673 (1.00) |
0.909 (1.00) |
0.0433 (1.00) |
0.133 (1.00) |
| Del Peak 2(1p13 1) | 12 (10%) | 114 |
0.75 (1.00) |
0.375 (1.00) |
1 (1.00) |
1 (1.00) |
0.316 (1.00) |
0.919 (1.00) |
| Del Peak 3(2q22 1) | 22 (17%) | 104 |
0.0525 (1.00) |
0.633 (1.00) |
0.906 (1.00) |
0.821 (1.00) |
0.911 (1.00) |
0.953 (1.00) |
| Del Peak 4(2q37 1) | 51 (40%) | 75 |
0.00431 (1.00) |
0.0367 (1.00) |
0.201 (1.00) |
0.333 (1.00) |
0.172 (1.00) |
0.0766 (1.00) |
| Del Peak 8(5q14 3) | 36 (29%) | 90 |
0.0245 (1.00) |
0.174 (1.00) |
0.631 (1.00) |
0.144 (1.00) |
0.216 (1.00) |
0.346 (1.00) |
| Del Peak 9(6p24 3) | 18 (14%) | 108 |
0.619 (1.00) |
0.192 (1.00) |
0.258 (1.00) |
0.159 (1.00) |
0.499 (1.00) |
1 (1.00) |
| Del Peak 10(6p12 1) | 20 (16%) | 106 |
0.674 (1.00) |
0.502 (1.00) |
0.466 (1.00) |
0.123 (1.00) |
0.819 (1.00) |
0.135 (1.00) |
| Del Peak 11(6q26) | 48 (38%) | 78 |
0.134 (1.00) |
0.33 (1.00) |
0.363 (1.00) |
0.676 (1.00) |
0.545 (1.00) |
0.495 (1.00) |
| Del Peak 12(7q34) | 28 (22%) | 98 |
0.00527 (1.00) |
0.86 (1.00) |
0.12 (1.00) |
0.668 (1.00) |
0.0683 (1.00) |
0.198 (1.00) |
| Del Peak 13(10q23 31) | 39 (31%) | 87 |
0.0221 (1.00) |
0.668 (1.00) |
0.272 (1.00) |
0.0197 (1.00) |
0.739 (1.00) |
0.87 (1.00) |
| Del Peak 15(11p15 1) | 40 (32%) | 86 |
0.301 (1.00) |
0.0875 (1.00) |
0.162 (1.00) |
0.0665 (1.00) |
0.351 (1.00) |
0.502 (1.00) |
| Del Peak 16(11q25) | 74 (59%) | 52 |
0.00223 (0.645) |
0.149 (1.00) |
0.127 (1.00) |
0.106 (1.00) |
0.0267 (1.00) |
0.447 (1.00) |
| Del Peak 17(13q13 3) | 52 (41%) | 74 |
0.144 (1.00) |
0.0916 (1.00) |
0.398 (1.00) |
0.807 (1.00) |
0.0197 (1.00) |
0.107 (1.00) |
| Del Peak 18(14q32 31) | 25 (20%) | 101 |
0.0774 (1.00) |
0.00839 (1.00) |
0.00118 (0.347) |
0.00122 (0.359) |
0.024 (1.00) |
0.0052 (1.00) |
| Del Peak 20(16q11 2) | 25 (20%) | 101 |
0.75 (1.00) |
0.0362 (1.00) |
0.0103 (1.00) |
0.00812 (1.00) |
0.139 (1.00) |
0.00188 (0.548) |
| Del Peak 22(17p12) | 42 (33%) | 84 |
0.0111 (1.00) |
0.136 (1.00) |
0.233 (1.00) |
0.755 (1.00) |
0.0932 (1.00) |
0.044 (1.00) |
| Del Peak 23(17q25 3) | 22 (17%) | 104 |
0.0451 (1.00) |
0.000907 (0.269) |
0.0359 (1.00) |
0.0345 (1.00) |
0.0484 (1.00) |
0.0426 (1.00) |
| Del Peak 25(20p12 1) | 17 (13%) | 109 |
0.846 (1.00) |
0.342 (1.00) |
0.746 (1.00) |
1 (1.00) |
0.434 (1.00) |
0.451 (1.00) |
| Del Peak 26(21q21 1) | 27 (21%) | 99 |
0.0618 (1.00) |
0.372 (1.00) |
0.569 (1.00) |
0.387 (1.00) |
0.527 (1.00) |
0.8 (1.00) |
| Del Peak 27(Xp11 3) | 37 (29%) | 89 |
0.00441 (1.00) |
0.00424 (1.00) |
0.211 (1.00) |
0.192 (1.00) |
0.0119 (1.00) |
0.00375 (1.00) |
| Del Peak 28(Xq21 33) | 27 (21%) | 99 |
0.0119 (1.00) |
0.00444 (1.00) |
0.164 (1.00) |
0.0901 (1.00) |
0.101 (1.00) |
0.00955 (1.00) |
P value = 0.000238 (Fisher's exact test), Q value = 0.071
Table S1. Gene #4: 'Amp Peak 4(2q32.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 32 | 52 |
| AMP PEAK 4(2Q32.3) MUTATED | 9 | 10 | 1 |
| AMP PEAK 4(2Q32.3) WILD-TYPE | 33 | 22 | 51 |
Figure S1. Get High-res Image Gene #4: 'Amp Peak 4(2q32.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'
P value = 0.000645 (Fisher's exact test), Q value = 0.19
Table S2. Gene #4: 'Amp Peak 4(2q32.3) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 30 | 31 |
| AMP PEAK 4(2Q32.3) MUTATED | 1 | 9 | 6 |
| AMP PEAK 4(2Q32.3) WILD-TYPE | 49 | 21 | 25 |
Figure S2. Get High-res Image Gene #4: 'Amp Peak 4(2q32.3) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'
P value = 1.26e-06 (Fisher's exact test), Q value = 0.00039
Table S3. Gene #5: 'Amp Peak 5(3q26.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 32 | 52 |
| AMP PEAK 5(3Q26.2) MUTATED | 42 | 20 | 33 |
| AMP PEAK 5(3Q26.2) WILD-TYPE | 0 | 12 | 19 |
Figure S3. Get High-res Image Gene #5: 'Amp Peak 5(3q26.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'
P value = 6.37e-07 (Fisher's exact test), Q value = 2e-04
Table S4. Gene #6: 'Amp Peak 6(3q28) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 32 | 52 |
| AMP PEAK 6(3Q28) MUTATED | 42 | 19 | 33 |
| AMP PEAK 6(3Q28) WILD-TYPE | 0 | 13 | 19 |
Figure S4. Get High-res Image Gene #6: 'Amp Peak 6(3q28) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'
P value = 7.38e-05 (Fisher's exact test), Q value = 0.023
Table S5. Gene #14: 'Amp Peak 14(11q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 32 | 52 |
| AMP PEAK 14(11Q22.1) MUTATED | 4 | 16 | 7 |
| AMP PEAK 14(11Q22.1) WILD-TYPE | 38 | 16 | 45 |
Figure S5. Get High-res Image Gene #14: 'Amp Peak 14(11q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'
P value = 0.000203 (Fisher's exact test), Q value = 0.061
Table S6. Gene #25: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 30 | 52 | 32 |
| DEL PEAK 1(1P36.23) MUTATED | 9 | 1 | 8 |
| DEL PEAK 1(1P36.23) WILD-TYPE | 21 | 51 | 24 |
Figure S6. Get High-res Image Gene #25: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'
P value = 0.000668 (Fisher's exact test), Q value = 0.2
Table S7. Gene #29: 'Del Peak 5(3p11.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 32 | 52 |
| DEL PEAK 5(3P11.1) MUTATED | 15 | 22 | 14 |
| DEL PEAK 5(3P11.1) WILD-TYPE | 27 | 10 | 38 |
Figure S7. Get High-res Image Gene #29: 'Del Peak 5(3p11.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'
P value = 1.5e-06 (Fisher's exact test), Q value = 0.00046
Table S8. Gene #30: 'Del Peak 6(4q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 32 | 52 |
| DEL PEAK 6(4Q22.1) MUTATED | 12 | 21 | 6 |
| DEL PEAK 6(4Q22.1) WILD-TYPE | 30 | 11 | 46 |
Figure S8. Get High-res Image Gene #30: 'Del Peak 6(4q22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'
P value = 1.38e-05 (Fisher's exact test), Q value = 0.0043
Table S9. Gene #31: 'Del Peak 7(4q35.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 32 | 52 |
| DEL PEAK 7(4Q35.2) MUTATED | 13 | 23 | 11 |
| DEL PEAK 7(4Q35.2) WILD-TYPE | 29 | 9 | 41 |
Figure S9. Get High-res Image Gene #31: 'Del Peak 7(4q35.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'
P value = 0.000133 (Fisher's exact test), Q value = 0.04
Table S10. Gene #38: 'Del Peak 14(10q26.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 32 | 52 |
| DEL PEAK 14(10Q26.3) MUTATED | 11 | 19 | 8 |
| DEL PEAK 14(10Q26.3) WILD-TYPE | 31 | 13 | 44 |
Figure S10. Get High-res Image Gene #38: 'Del Peak 14(10q26.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'
P value = 2.68e-05 (Fisher's exact test), Q value = 0.0082
Table S11. Gene #43: 'Del Peak 19(15q15.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 42 | 32 | 52 |
| DEL PEAK 19(15Q15.1) MUTATED | 7 | 17 | 5 |
| DEL PEAK 19(15Q15.1) WILD-TYPE | 35 | 15 | 47 |
Figure S11. Get High-res Image Gene #43: 'Del Peak 19(15q15.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'
P value = 0.000234 (Fisher's exact test), Q value = 0.071
Table S12. Gene #45: 'Del Peak 21(16q23.1) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 50 | 30 | 31 |
| DEL PEAK 21(16Q23.1) MUTATED | 3 | 9 | 13 |
| DEL PEAK 21(16Q23.1) WILD-TYPE | 47 | 21 | 18 |
Figure S12. Get High-res Image Gene #45: 'Del Peak 21(16q23.1) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'
P value = 3.45e-05 (Fisher's exact test), Q value = 0.011
Table S13. Gene #45: 'Del Peak 21(16q23.1) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 11 | 64 | 36 |
| DEL PEAK 21(16Q23.1) MUTATED | 6 | 5 | 14 |
| DEL PEAK 21(16Q23.1) WILD-TYPE | 5 | 59 | 22 |
Figure S13. Get High-res Image Gene #45: 'Del Peak 21(16q23.1) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'
P value = 0.000197 (Fisher's exact test), Q value = 0.06
Table S14. Gene #45: 'Del Peak 21(16q23.1) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 30 | 52 | 32 |
| DEL PEAK 21(16Q23.1) MUTATED | 14 | 4 | 6 |
| DEL PEAK 21(16Q23.1) WILD-TYPE | 16 | 48 | 26 |
Figure S14. Get High-res Image Gene #45: 'Del Peak 21(16q23.1) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'
P value = 3.54e-05 (Fisher's exact test), Q value = 0.011
Table S15. Gene #48: 'Del Peak 24(19p13.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 30 | 52 | 32 |
| DEL PEAK 24(19P13.3) MUTATED | 13 | 5 | 16 |
| DEL PEAK 24(19P13.3) WILD-TYPE | 17 | 47 | 16 |
Figure S15. Get High-res Image Gene #48: 'Del Peak 24(19p13.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'
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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 = CESC-TP.transferedmergedcluster.txt
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Number of patients = 126
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Number of copy number variation regions = 52
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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.