This pipeline computes the correlation between significant copy number variation (cnv) genes and selected clinical features.
Testing the association between copy number variation of 70 peak regions and 5 clinical features across 544 patients, 15 significant findings detected with Q value < 0.25.
-
Amp Peak 8(7p11.2) cnvs correlated to 'Time to Death' and 'AGE'.
-
Amp Peak 9(7q11.21) cnvs correlated to 'Time to Death' and 'AGE'.
-
Amp Peak 10(7q21.2) cnvs correlated to 'AGE'.
-
Del Peak 19(9p21.3) cnvs correlated to 'AGE'.
-
Del Peak 21(10p15.3) cnvs correlated to 'Time to Death' and 'AGE'.
-
Del Peak 22(10p13) cnvs correlated to 'Time to Death' and 'AGE'.
-
Del Peak 23(10p11.23) cnvs correlated to 'Time to Death' and 'AGE'.
-
Del Peak 24(10q23.31) cnvs correlated to 'Time to Death' and 'AGE'.
-
Del Peak 25(10q26.3) cnvs correlated to 'AGE'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 70 regions and 5 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 15 significant findings detected.
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
RADIATIONS RADIATION REGIMENINDICATION |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | t-test | Fisher's exact test | |
Amp Peak 8(7p11 2) | 478 (88%) | 66 |
2.57e-06 (0.000885) |
5.95e-09 (2.08e-06) |
0.502 (1.00) |
0.0351 (1.00) |
0.0239 (1.00) |
Amp Peak 9(7q11 21) | 439 (81%) | 105 |
0.000152 (0.0513) |
8.05e-08 (2.79e-05) |
0.224 (1.00) |
0.658 (1.00) |
0.0268 (1.00) |
Del Peak 21(10p15 3) | 445 (82%) | 99 |
1.06e-05 (0.00361) |
4.22e-08 (1.47e-05) |
0.088 (1.00) |
0.596 (1.00) |
0.0427 (1.00) |
Del Peak 22(10p13) | 447 (82%) | 97 |
6.7e-06 (0.00229) |
2.12e-07 (7.33e-05) |
0.0297 (1.00) |
0.884 (1.00) |
0.151 (1.00) |
Del Peak 23(10p11 23) | 451 (83%) | 93 |
9.14e-07 (0.000315) |
1.16e-08 (4.04e-06) |
0.103 (1.00) |
0.232 (1.00) |
0.18 (1.00) |
Del Peak 24(10q23 31) | 486 (89%) | 58 |
2.27e-05 (0.0077) |
2.71e-06 (0.000931) |
0.572 (1.00) |
0.0751 (1.00) |
0.302 (1.00) |
Amp Peak 10(7q21 2) | 453 (83%) | 91 |
0.000974 (0.326) |
1.06e-05 (0.0036) |
0.483 (1.00) |
0.49 (1.00) |
0.0851 (1.00) |
Del Peak 19(9p21 3) | 399 (73%) | 145 |
0.0223 (1.00) |
0.000156 (0.0524) |
0.552 (1.00) |
0.0926 (1.00) |
0.255 (1.00) |
Del Peak 25(10q26 3) | 487 (90%) | 57 |
0.00151 (0.501) |
2.89e-05 (0.00976) |
0.478 (1.00) |
0.0613 (1.00) |
0.551 (1.00) |
Amp Peak 1(1p36 21) | 87 (16%) | 457 |
0.0861 (1.00) |
0.316 (1.00) |
0.283 (1.00) |
0.653 (1.00) |
0.618 (1.00) |
Amp Peak 2(1q32 1) | 148 (27%) | 396 |
0.436 (1.00) |
0.261 (1.00) |
0.624 (1.00) |
0.279 (1.00) |
0.837 (1.00) |
Amp Peak 3(1q44) | 94 (17%) | 450 |
0.497 (1.00) |
0.903 (1.00) |
0.297 (1.00) |
0.599 (1.00) |
0.903 (1.00) |
Amp Peak 4(2p24 3) | 44 (8%) | 500 |
0.151 (1.00) |
0.268 (1.00) |
0.424 (1.00) |
0.583 (1.00) |
1 (1.00) |
Amp Peak 5(3q26 33) | 105 (19%) | 439 |
0.286 (1.00) |
0.0296 (1.00) |
0.824 (1.00) |
0.688 (1.00) |
0.353 (1.00) |
Amp Peak 6(4p16 3) | 45 (8%) | 499 |
0.554 (1.00) |
0.539 (1.00) |
0.526 (1.00) |
0.429 (1.00) |
0.0943 (1.00) |
Amp Peak 7(4q12) | 103 (19%) | 441 |
0.619 (1.00) |
0.532 (1.00) |
0.219 (1.00) |
0.597 (1.00) |
0.292 (1.00) |
Amp Peak 11(7q31 2) | 446 (82%) | 98 |
0.0246 (1.00) |
0.00146 (0.486) |
0.362 (1.00) |
0.513 (1.00) |
0.0234 (1.00) |
Amp Peak 12(7q36 1) | 451 (83%) | 93 |
0.061 (1.00) |
0.00223 (0.74) |
0.485 (1.00) |
0.732 (1.00) |
0.18 (1.00) |
Amp Peak 13(8q24 21) | 63 (12%) | 481 |
0.381 (1.00) |
0.14 (1.00) |
0.275 (1.00) |
0.804 (1.00) |
0.667 (1.00) |
Amp Peak 14(11p13) | 24 (4%) | 520 |
0.911 (1.00) |
0.237 (1.00) |
0.528 (1.00) |
0.316 (1.00) |
0.269 (1.00) |
Amp Peak 15(12p13 32) | 78 (14%) | 466 |
0.839 (1.00) |
0.145 (1.00) |
0.901 (1.00) |
0.695 (1.00) |
0.795 (1.00) |
Amp Peak 16(12q14 1) | 127 (23%) | 417 |
0.125 (1.00) |
0.87 (1.00) |
0.468 (1.00) |
0.808 (1.00) |
0.665 (1.00) |
Amp Peak 17(12q15) | 87 (16%) | 457 |
0.945 (1.00) |
0.697 (1.00) |
0.339 (1.00) |
0.911 (1.00) |
0.135 (1.00) |
Amp Peak 18(13q34) | 30 (6%) | 514 |
0.828 (1.00) |
0.847 (1.00) |
0.338 (1.00) |
0.838 (1.00) |
1 (1.00) |
Amp Peak 19(14q32 33) | 31 (6%) | 513 |
0.0676 (1.00) |
0.00493 (1.00) |
0.453 (1.00) |
0.254 (1.00) |
1 (1.00) |
Amp Peak 20(17p13 2) | 43 (8%) | 501 |
0.847 (1.00) |
0.749 (1.00) |
0.255 (1.00) |
0.109 (1.00) |
0.497 (1.00) |
Amp Peak 21(17q25 1) | 74 (14%) | 470 |
0.0765 (1.00) |
0.0404 (1.00) |
0.202 (1.00) |
0.837 (1.00) |
0.593 (1.00) |
Amp Peak 22(19p13 2) | 231 (42%) | 313 |
0.143 (1.00) |
0.658 (1.00) |
0.859 (1.00) |
0.441 (1.00) |
0.853 (1.00) |
Amp Peak 23(19q12) | 196 (36%) | 348 |
0.333 (1.00) |
0.397 (1.00) |
0.649 (1.00) |
0.996 (1.00) |
0.849 (1.00) |
Amp Peak 24(21q21 1) | 62 (11%) | 482 |
0.582 (1.00) |
0.0125 (1.00) |
0.681 (1.00) |
0.549 (1.00) |
0.565 (1.00) |
Del Peak 1(1p36 32) | 95 (17%) | 449 |
0.403 (1.00) |
0.817 (1.00) |
0.0503 (1.00) |
0.999 (1.00) |
1 (1.00) |
Del Peak 2(1p36 23) | 131 (24%) | 413 |
0.996 (1.00) |
0.02 (1.00) |
0.0102 (1.00) |
0.193 (1.00) |
0.915 (1.00) |
Del Peak 3(1p32 3) | 59 (11%) | 485 |
0.761 (1.00) |
0.06 (1.00) |
0.159 (1.00) |
0.687 (1.00) |
0.0786 (1.00) |
Del Peak 4(1p22 1) | 46 (8%) | 498 |
0.272 (1.00) |
0.321 (1.00) |
1 (1.00) |
0.585 (1.00) |
1 (1.00) |
Del Peak 5(1q42 11) | 45 (8%) | 499 |
0.0871 (1.00) |
0.0607 (1.00) |
1 (1.00) |
0.0102 (1.00) |
0.137 (1.00) |
Del Peak 6(1q44) | 31 (6%) | 513 |
0.3 (1.00) |
0.286 (1.00) |
0.851 (1.00) |
0.0669 (1.00) |
0.695 (1.00) |
Del Peak 7(2q22 1) | 43 (8%) | 501 |
0.311 (1.00) |
0.0941 (1.00) |
0.198 (1.00) |
0.686 (1.00) |
0.174 (1.00) |
Del Peak 8(2q37 1) | 55 (10%) | 489 |
0.76 (1.00) |
0.345 (1.00) |
0.146 (1.00) |
0.657 (1.00) |
0.361 (1.00) |
Del Peak 9(3p21 1) | 52 (10%) | 492 |
0.0237 (1.00) |
0.0119 (1.00) |
0.883 (1.00) |
0.698 (1.00) |
0.086 (1.00) |
Del Peak 10(3q13 31) | 55 (10%) | 489 |
0.528 (1.00) |
0.063 (1.00) |
0.383 (1.00) |
0.306 (1.00) |
0.29 (1.00) |
Del Peak 11(3q22 1) | 55 (10%) | 489 |
0.656 (1.00) |
0.136 (1.00) |
1 (1.00) |
0.49 (1.00) |
0.29 (1.00) |
Del Peak 12(3q29) | 62 (11%) | 482 |
0.26 (1.00) |
0.194 (1.00) |
0.891 (1.00) |
0.459 (1.00) |
0.193 (1.00) |
Del Peak 13(4p16 3) | 76 (14%) | 468 |
0.313 (1.00) |
0.0312 (1.00) |
0.209 (1.00) |
0.154 (1.00) |
0.427 (1.00) |
Del Peak 14(4q34 3) | 89 (16%) | 455 |
0.165 (1.00) |
0.0944 (1.00) |
0.0581 (1.00) |
0.66 (1.00) |
0.174 (1.00) |
Del Peak 15(5q35 3) | 52 (10%) | 492 |
0.0182 (1.00) |
0.181 (1.00) |
1 (1.00) |
0.564 (1.00) |
0.438 (1.00) |
Del Peak 16(6q22 31) | 152 (28%) | 392 |
0.0438 (1.00) |
0.31 (1.00) |
0.0965 (1.00) |
0.454 (1.00) |
0.683 (1.00) |
Del Peak 17(6q26) | 171 (31%) | 373 |
0.215 (1.00) |
0.665 (1.00) |
0.186 (1.00) |
0.702 (1.00) |
0.767 (1.00) |
Del Peak 18(8p23 2) | 65 (12%) | 479 |
0.181 (1.00) |
0.0441 (1.00) |
0.589 (1.00) |
0.634 (1.00) |
0.48 (1.00) |
Del Peak 20(9q34 2) | 70 (13%) | 474 |
0.441 (1.00) |
0.806 (1.00) |
1 (1.00) |
0.498 (1.00) |
0.784 (1.00) |
Del Peak 26(11p15 5) | 124 (23%) | 420 |
0.0325 (1.00) |
0.00446 (1.00) |
0.145 (1.00) |
0.242 (1.00) |
0.827 (1.00) |
Del Peak 27(11p11 2) | 99 (18%) | 445 |
0.0736 (1.00) |
0.595 (1.00) |
0.139 (1.00) |
0.796 (1.00) |
0.342 (1.00) |
Del Peak 28(11q14 1) | 93 (17%) | 451 |
0.747 (1.00) |
0.865 (1.00) |
0.245 (1.00) |
0.538 (1.00) |
0.0201 (1.00) |
Del Peak 29(12p13 1) | 73 (13%) | 471 |
0.338 (1.00) |
0.795 (1.00) |
0.442 (1.00) |
0.846 (1.00) |
1 (1.00) |
Del Peak 30(12q12) | 74 (14%) | 470 |
0.641 (1.00) |
0.798 (1.00) |
0.898 (1.00) |
0.81 (1.00) |
0.285 (1.00) |
Del Peak 31(12q15) | 74 (14%) | 470 |
0.516 (1.00) |
0.952 (1.00) |
0.371 (1.00) |
0.186 (1.00) |
0.285 (1.00) |
Del Peak 32(13q14 2) | 230 (42%) | 314 |
0.586 (1.00) |
0.538 (1.00) |
0.929 (1.00) |
0.828 (1.00) |
0.355 (1.00) |
Del Peak 33(14q13 1) | 173 (32%) | 371 |
0.756 (1.00) |
0.529 (1.00) |
0.222 (1.00) |
0.262 (1.00) |
0.694 (1.00) |
Del Peak 34(14q24 2) | 168 (31%) | 376 |
0.867 (1.00) |
0.443 (1.00) |
0.394 (1.00) |
0.605 (1.00) |
0.843 (1.00) |
Del Peak 35(14q31 3) | 155 (28%) | 389 |
0.924 (1.00) |
0.721 (1.00) |
0.628 (1.00) |
0.647 (1.00) |
0.685 (1.00) |
Del Peak 36(15q14) | 146 (27%) | 398 |
0.459 (1.00) |
0.0774 (1.00) |
0.622 (1.00) |
0.808 (1.00) |
0.149 (1.00) |
Del Peak 37(16p12 2) | 89 (16%) | 455 |
0.333 (1.00) |
0.31 (1.00) |
0.237 (1.00) |
0.808 (1.00) |
0.804 (1.00) |
Del Peak 38(16q23 3) | 93 (17%) | 451 |
0.219 (1.00) |
0.956 (1.00) |
0.485 (1.00) |
0.266 (1.00) |
0.0288 (1.00) |
Del Peak 39(17p13 2) | 81 (15%) | 463 |
0.601 (1.00) |
0.554 (1.00) |
0.221 (1.00) |
0.189 (1.00) |
0.609 (1.00) |
Del Peak 40(17p13 1) | 91 (17%) | 453 |
0.826 (1.00) |
0.183 (1.00) |
0.0613 (1.00) |
0.797 (1.00) |
0.11 (1.00) |
Del Peak 41(17q11 2) | 67 (12%) | 477 |
0.605 (1.00) |
0.583 (1.00) |
1 (1.00) |
0.245 (1.00) |
0.0498 (1.00) |
Del Peak 42(18q22 3) | 78 (14%) | 466 |
0.918 (1.00) |
0.448 (1.00) |
0.708 (1.00) |
0.128 (1.00) |
0.603 (1.00) |
Del Peak 43(19q13 41) | 98 (18%) | 446 |
0.066 (1.00) |
0.449 (1.00) |
1 (1.00) |
0.264 (1.00) |
0.406 (1.00) |
Del Peak 44(21q22 3) | 58 (11%) | 486 |
0.757 (1.00) |
0.0758 (1.00) |
0.258 (1.00) |
0.198 (1.00) |
0.883 (1.00) |
Del Peak 45(22q13 32) | 204 (38%) | 340 |
0.581 (1.00) |
0.387 (1.00) |
0.856 (1.00) |
0.518 (1.00) |
0.705 (1.00) |
Del Peak 46(Xp22 2) | 122 (22%) | 422 |
0.277 (1.00) |
0.467 (1.00) |
0.675 (1.00) |
0.825 (1.00) |
1 (1.00) |
P value = 2.57e-06 (logrank test), Q value = 0.00088
Table S1. Gene #8: 'Amp Peak 8(7p11.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 544 | 411 | 0.1 - 127.6 (9.6) |
AMP PEAK 8(7P11.2) MUTATED | 478 | 367 | 0.1 - 127.6 (9.2) |
AMP PEAK 8(7P11.2) WILD-TYPE | 66 | 44 | 0.2 - 108.8 (13.5) |
Figure S1. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'
![](D8V1.png)
P value = 5.95e-09 (t-test), Q value = 2.1e-06
Table S2. Gene #8: 'Amp Peak 8(7p11.2) mutation analysis' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 544 | 57.8 (14.3) |
AMP PEAK 8(7P11.2) MUTATED | 478 | 59.7 (12.4) |
AMP PEAK 8(7P11.2) WILD-TYPE | 66 | 43.9 (19.0) |
Figure S2. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2) mutation analysis' versus Clinical Feature #2: 'AGE'
![](D8V2.png)
P value = 0.000152 (logrank test), Q value = 0.051
Table S3. Gene #9: 'Amp Peak 9(7q11.21) mutation analysis' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 544 | 411 | 0.1 - 127.6 (9.6) |
AMP PEAK 9(7Q11.21) MUTATED | 439 | 333 | 0.1 - 127.6 (9.2) |
AMP PEAK 9(7Q11.21) WILD-TYPE | 105 | 78 | 0.2 - 108.8 (12.4) |
Figure S3. Get High-res Image Gene #9: 'Amp Peak 9(7q11.21) mutation analysis' versus Clinical Feature #1: 'Time to Death'
![](D9V1.png)
P value = 8.05e-08 (t-test), Q value = 2.8e-05
Table S4. Gene #9: 'Amp Peak 9(7q11.21) mutation analysis' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 544 | 57.8 (14.3) |
AMP PEAK 9(7Q11.21) MUTATED | 439 | 59.9 (12.3) |
AMP PEAK 9(7Q11.21) WILD-TYPE | 105 | 49.2 (18.3) |
Figure S4. Get High-res Image Gene #9: 'Amp Peak 9(7q11.21) mutation analysis' versus Clinical Feature #2: 'AGE'
![](D9V2.png)
P value = 1.06e-05 (t-test), Q value = 0.0036
Table S5. Gene #10: 'Amp Peak 10(7q21.2) mutation analysis' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 544 | 57.8 (14.3) |
AMP PEAK 10(7Q21.2) MUTATED | 453 | 59.5 (12.2) |
AMP PEAK 10(7Q21.2) WILD-TYPE | 91 | 49.5 (19.9) |
Figure S5. Get High-res Image Gene #10: 'Amp Peak 10(7q21.2) mutation analysis' versus Clinical Feature #2: 'AGE'
![](D10V2.png)
P value = 0.000156 (t-test), Q value = 0.052
Table S6. Gene #43: 'Del Peak 19(9p21.3) mutation analysis' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 544 | 57.8 (14.3) |
DEL PEAK 19(9P21.3) MUTATED | 399 | 59.3 (13.5) |
DEL PEAK 19(9P21.3) WILD-TYPE | 145 | 53.7 (15.7) |
Figure S6. Get High-res Image Gene #43: 'Del Peak 19(9p21.3) mutation analysis' versus Clinical Feature #2: 'AGE'
![](D43V2.png)
P value = 1.06e-05 (logrank test), Q value = 0.0036
Table S7. Gene #45: 'Del Peak 21(10p15.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 544 | 411 | 0.1 - 127.6 (9.6) |
DEL PEAK 21(10P15.3) MUTATED | 445 | 342 | 0.1 - 92.6 (9.4) |
DEL PEAK 21(10P15.3) WILD-TYPE | 99 | 69 | 0.1 - 127.6 (10.6) |
Figure S7. Get High-res Image Gene #45: 'Del Peak 21(10p15.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'
![](D45V1.png)
P value = 4.22e-08 (t-test), Q value = 1.5e-05
Table S8. Gene #45: 'Del Peak 21(10p15.3) mutation analysis' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 544 | 57.8 (14.3) |
DEL PEAK 21(10P15.3) MUTATED | 445 | 59.9 (12.3) |
DEL PEAK 21(10P15.3) WILD-TYPE | 99 | 48.5 (18.4) |
Figure S8. Get High-res Image Gene #45: 'Del Peak 21(10p15.3) mutation analysis' versus Clinical Feature #2: 'AGE'
![](D45V2.png)
P value = 6.7e-06 (logrank test), Q value = 0.0023
Table S9. Gene #46: 'Del Peak 22(10p13) mutation analysis' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 544 | 411 | 0.1 - 127.6 (9.6) |
DEL PEAK 22(10P13) MUTATED | 447 | 343 | 0.1 - 92.6 (9.4) |
DEL PEAK 22(10P13) WILD-TYPE | 97 | 68 | 0.1 - 127.6 (9.8) |
Figure S9. Get High-res Image Gene #46: 'Del Peak 22(10p13) mutation analysis' versus Clinical Feature #1: 'Time to Death'
![](D46V1.png)
P value = 2.12e-07 (t-test), Q value = 7.3e-05
Table S10. Gene #46: 'Del Peak 22(10p13) mutation analysis' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 544 | 57.8 (14.3) |
DEL PEAK 22(10P13) MUTATED | 447 | 59.8 (12.2) |
DEL PEAK 22(10P13) WILD-TYPE | 97 | 48.7 (18.9) |
Figure S10. Get High-res Image Gene #46: 'Del Peak 22(10p13) mutation analysis' versus Clinical Feature #2: 'AGE'
![](D46V2.png)
P value = 9.14e-07 (logrank test), Q value = 0.00032
Table S11. Gene #47: 'Del Peak 23(10p11.23) mutation analysis' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 544 | 411 | 0.1 - 127.6 (9.6) |
DEL PEAK 23(10P11.23) MUTATED | 451 | 345 | 0.1 - 92.6 (9.4) |
DEL PEAK 23(10P11.23) WILD-TYPE | 93 | 66 | 0.1 - 127.6 (12.4) |
Figure S11. Get High-res Image Gene #47: 'Del Peak 23(10p11.23) mutation analysis' versus Clinical Feature #1: 'Time to Death'
![](D47V1.png)
P value = 1.16e-08 (t-test), Q value = 4e-06
Table S12. Gene #47: 'Del Peak 23(10p11.23) mutation analysis' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 544 | 57.8 (14.3) |
DEL PEAK 23(10P11.23) MUTATED | 451 | 60.0 (12.1) |
DEL PEAK 23(10P11.23) WILD-TYPE | 93 | 47.4 (18.8) |
Figure S12. Get High-res Image Gene #47: 'Del Peak 23(10p11.23) mutation analysis' versus Clinical Feature #2: 'AGE'
![](D47V2.png)
P value = 2.27e-05 (logrank test), Q value = 0.0077
Table S13. Gene #48: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 544 | 411 | 0.1 - 127.6 (9.6) |
DEL PEAK 24(10Q23.31) MUTATED | 486 | 372 | 0.1 - 127.6 (9.6) |
DEL PEAK 24(10Q23.31) WILD-TYPE | 58 | 39 | 0.2 - 108.8 (10.9) |
Figure S13. Get High-res Image Gene #48: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #1: 'Time to Death'
![](D48V1.png)
P value = 2.71e-06 (t-test), Q value = 0.00093
Table S14. Gene #48: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 544 | 57.8 (14.3) |
DEL PEAK 24(10Q23.31) MUTATED | 486 | 59.2 (13.0) |
DEL PEAK 24(10Q23.31) WILD-TYPE | 58 | 46.2 (18.7) |
Figure S14. Get High-res Image Gene #48: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #2: 'AGE'
![](D48V2.png)
P value = 2.89e-05 (t-test), Q value = 0.0098
Table S15. Gene #49: 'Del Peak 25(10q26.3) mutation analysis' versus Clinical Feature #2: 'AGE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 544 | 57.8 (14.3) |
DEL PEAK 25(10Q26.3) MUTATED | 487 | 59.0 (13.1) |
DEL PEAK 25(10Q26.3) WILD-TYPE | 57 | 47.4 (19.0) |
Figure S15. Get High-res Image Gene #49: 'Del Peak 25(10q26.3) mutation analysis' versus Clinical Feature #2: 'AGE'
![](D49V2.png)
-
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.
-
Clinical data file = GBM-TP.clin.merged.picked.txt
-
Number of patients = 544
-
Number of copy number variation regions = 70
-
Number of selected clinical features = 5
-
Exclude regions that fewer than K tumors have alterations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene cnvs were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene cnvs using 't.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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.