Skin Cutaneous Melanoma: Correlation between copy number variation genes and selected clinical features
Maintained by TCGA GDAC Team
(Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction
Summary
Testing the association between copy number variation of 51 peak regions and 3 clinical features across 144 patients, no significant finding detected with Q value < 0.25.
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No gene cnvs related to clinical features.
Results
Overview of the results
Table 1. Get Full Table Overview of the association between significant copy number variation of 51 regions and 3 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.
|
Clinical Features |
Time to Death |
AGE | GENDER | ||
| nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | |
| Amp Peak 1(1p12) | 45 (31%) | 99 |
0.0252 (1.00) |
0.894 (1.00) |
0.851 (1.00) |
| Amp Peak 2(1q21 3) | 78 (54%) | 66 |
0.756 (1.00) |
0.503 (1.00) |
1 (1.00) |
| Amp Peak 3(1q44) | 79 (55%) | 65 |
0.141 (1.00) |
0.716 (1.00) |
0.49 (1.00) |
| Amp Peak 4(3p13) | 32 (22%) | 112 |
0.157 (1.00) |
0.0359 (1.00) |
0.298 (1.00) |
| Amp Peak 5(4q12) | 29 (20%) | 115 |
0.344 (1.00) |
0.199 (1.00) |
0.516 (1.00) |
| Amp Peak 6(5p15 33) | 40 (28%) | 104 |
0.088 (1.00) |
0.409 (1.00) |
1 (1.00) |
| Amp Peak 7(5q35 3) | 19 (13%) | 125 |
0.638 (1.00) |
0.341 (1.00) |
0.304 (1.00) |
| Amp Peak 8(6p25 1) | 87 (60%) | 57 |
0.0186 (1.00) |
0.0714 (1.00) |
1 (1.00) |
| Amp Peak 9(6q12) | 31 (22%) | 113 |
0.739 (1.00) |
0.953 (1.00) |
0.833 (1.00) |
| Amp Peak 10(7p22 3) | 84 (58%) | 60 |
0.791 (1.00) |
0.841 (1.00) |
0.597 (1.00) |
| Amp Peak 11(7q34) | 85 (59%) | 59 |
0.93 (1.00) |
0.367 (1.00) |
0.376 (1.00) |
| Amp Peak 12(8q11 21) | 59 (41%) | 85 |
0.591 (1.00) |
0.101 (1.00) |
0.376 (1.00) |
| Amp Peak 13(8q24 21) | 69 (48%) | 75 |
0.432 (1.00) |
0.187 (1.00) |
0.486 (1.00) |
| Amp Peak 14(9p24 1) | 12 (8%) | 132 |
0.585 (1.00) |
0.663 (1.00) |
0.346 (1.00) |
| Amp Peak 15(11q13 3) | 22 (15%) | 122 |
0.633 (1.00) |
0.562 (1.00) |
0.0897 (1.00) |
| Amp Peak 16(11q13 4) | 22 (15%) | 122 |
0.811 (1.00) |
0.996 (1.00) |
0.0897 (1.00) |
| Amp Peak 17(12q14 1) | 22 (15%) | 122 |
0.913 (1.00) |
0.748 (1.00) |
0.811 (1.00) |
| Amp Peak 18(12q15) | 17 (12%) | 127 |
0.564 (1.00) |
0.37 (1.00) |
1 (1.00) |
| Amp Peak 19(15q24 3) | 47 (33%) | 97 |
0.652 (1.00) |
0.517 (1.00) |
1 (1.00) |
| Amp Peak 20(17q25 3) | 58 (40%) | 86 |
0.363 (1.00) |
0.011 (1.00) |
0.22 (1.00) |
| Amp Peak 21(19p13 2) | 29 (20%) | 115 |
0.752 (1.00) |
0.943 (1.00) |
0.667 (1.00) |
| Amp Peak 22(20q13 2) | 78 (54%) | 66 |
0.474 (1.00) |
0.171 (1.00) |
0.225 (1.00) |
| Amp Peak 23(22q13 2) | 69 (48%) | 75 |
0.6 (1.00) |
0.877 (1.00) |
0.728 (1.00) |
| Del Peak 1(1p36 31) | 35 (24%) | 109 |
0.654 (1.00) |
0.356 (1.00) |
0.841 (1.00) |
| Del Peak 2(1p22 1) | 37 (26%) | 107 |
0.0261 (1.00) |
0.00906 (1.00) |
0.842 (1.00) |
| Del Peak 3(2q37 3) | 37 (26%) | 107 |
0.301 (1.00) |
0.686 (1.00) |
0.55 (1.00) |
| Del Peak 4(3q23) | 21 (15%) | 123 |
0.93 (1.00) |
0.129 (1.00) |
0.224 (1.00) |
| Del Peak 5(4q34 3) | 38 (26%) | 106 |
0.505 (1.00) |
0.11 (1.00) |
0.0169 (1.00) |
| Del Peak 6(5q11 2) | 44 (31%) | 100 |
0.134 (1.00) |
0.98 (1.00) |
1 (1.00) |
| Del Peak 7(5q31 3) | 58 (40%) | 86 |
0.115 (1.00) |
0.471 (1.00) |
1 (1.00) |
| Del Peak 8(6q26) | 91 (63%) | 53 |
0.91 (1.00) |
0.386 (1.00) |
0.369 (1.00) |
| Del Peak 9(7q31 1) | 13 (9%) | 131 |
0.45 (1.00) |
0.8 (1.00) |
1 (1.00) |
| Del Peak 10(8p23 3) | 35 (24%) | 109 |
0.778 (1.00) |
0.0272 (1.00) |
0.418 (1.00) |
| Del Peak 11(9p23) | 100 (69%) | 44 |
0.945 (1.00) |
0.996 (1.00) |
0.351 (1.00) |
| Del Peak 12(9p21 3) | 115 (80%) | 29 |
0.417 (1.00) |
0.39 (1.00) |
0.195 (1.00) |
| Del Peak 13(10p15 3) | 79 (55%) | 65 |
0.343 (1.00) |
0.505 (1.00) |
0.0838 (1.00) |
| Del Peak 14(10q23 31) | 89 (62%) | 55 |
0.566 (1.00) |
0.151 (1.00) |
0.00764 (1.00) |
| Del Peak 15(10q26 3) | 89 (62%) | 55 |
0.306 (1.00) |
0.0264 (1.00) |
0.00764 (1.00) |
| Del Peak 16(11q23 3) | 86 (60%) | 58 |
0.302 (1.00) |
0.345 (1.00) |
0.381 (1.00) |
| Del Peak 17(12p13 31) | 20 (14%) | 124 |
0.371 (1.00) |
0.391 (1.00) |
0.207 (1.00) |
| Del Peak 18(12q23 3) | 30 (21%) | 114 |
0.433 (1.00) |
0.612 (1.00) |
1 (1.00) |
| Del Peak 19(12q24 33) | 31 (22%) | 113 |
0.657 (1.00) |
0.873 (1.00) |
0.404 (1.00) |
| Del Peak 20(13q34) | 38 (26%) | 106 |
0.255 (1.00) |
0.814 (1.00) |
0.845 (1.00) |
| Del Peak 21(14q32 2) | 46 (32%) | 98 |
0.638 (1.00) |
0.419 (1.00) |
0.264 (1.00) |
| Del Peak 22(15q13 3) | 35 (24%) | 109 |
0.293 (1.00) |
0.929 (1.00) |
0.841 (1.00) |
| Del Peak 23(15q15 3) | 34 (24%) | 110 |
0.145 (1.00) |
0.711 (1.00) |
0.421 (1.00) |
| Del Peak 24(16p13 3) | 26 (18%) | 118 |
0.839 (1.00) |
0.487 (1.00) |
0.041 (1.00) |
| Del Peak 25(16q12 1) | 49 (34%) | 95 |
0.0826 (1.00) |
0.943 (1.00) |
0.201 (1.00) |
| Del Peak 26(16q24 3) | 51 (35%) | 93 |
0.0247 (1.00) |
0.743 (1.00) |
0.202 (1.00) |
| Del Peak 27(19p13 3) | 45 (31%) | 99 |
0.766 (1.00) |
0.833 (1.00) |
0.265 (1.00) |
| Del Peak 28(22q13 31) | 19 (13%) | 125 |
0.104 (1.00) |
0.63 (1.00) |
0.608 (1.00) |
Methods & Data
Copyright © 2013
Broad Institute TCGA GDAC as part of the TCGA Research Network.
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