This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 71 focal events and 8 clinical features across 56 patients, no significant finding detected with Q value < 0.25.
-
No focal cnvs related to clinical features.
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER | NUMBERPACKYEARSSMOKED | ||
nCNV (%) | nWild-Type | logrank test | t-test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | t-test | |
amp 1p34 2 | 10 (18%) | 46 |
0.786 (1.00) |
0.435 (1.00) |
0.947 (1.00) |
0.234 (1.00) |
1 (1.00) |
1 (1.00) |
0.623 (1.00) |
0.505 (1.00) |
amp 1q21 3 | 26 (46%) | 30 |
0.663 (1.00) |
0.775 (1.00) |
0.514 (1.00) |
0.92 (1.00) |
0.611 (1.00) |
0.843 (1.00) |
0.712 (1.00) |
0.539 (1.00) |
amp 2q14 2 | 17 (30%) | 39 |
0.94 (1.00) |
0.966 (1.00) |
0.672 (1.00) |
0.751 (1.00) |
0.848 (1.00) |
0.776 (1.00) |
1 (1.00) |
0.902 (1.00) |
amp 3q26 2 | 44 (79%) | 12 |
0.803 (1.00) |
0.296 (1.00) |
0.269 (1.00) |
0.787 (1.00) |
0.578 (1.00) |
0.0781 (1.00) |
0.348 (1.00) |
0.164 (1.00) |
amp 5p15 33 | 30 (54%) | 26 |
0.95 (1.00) |
0.182 (1.00) |
0.0913 (1.00) |
1 (1.00) |
0.117 (1.00) |
1 (1.00) |
1 (1.00) |
0.791 (1.00) |
amp 6p21 1 | 17 (30%) | 39 |
0.892 (1.00) |
0.758 (1.00) |
0.851 (1.00) |
0.503 (1.00) |
0.848 (1.00) |
0.324 (1.00) |
0.0468 (1.00) |
0.0522 (1.00) |
amp 7p22 3 | 38 (68%) | 18 |
0.787 (1.00) |
0.3 (1.00) |
0.296 (1.00) |
0.696 (1.00) |
0.53 (1.00) |
1 (1.00) |
0.703 (1.00) |
0.962 (1.00) |
amp 7p11 2 | 41 (73%) | 15 |
0.699 (1.00) |
0.0822 (1.00) |
0.796 (1.00) |
0.531 (1.00) |
0.911 (1.00) |
1 (1.00) |
1 (1.00) |
0.864 (1.00) |
amp 7q21 2 | 38 (68%) | 18 |
0.233 (1.00) |
0.88 (1.00) |
0.854 (1.00) |
0.764 (1.00) |
1 (1.00) |
0.613 (1.00) |
0.703 (1.00) |
0.0444 (1.00) |
amp 8p11 21 | 29 (52%) | 27 |
0.684 (1.00) |
0.459 (1.00) |
0.553 (1.00) |
0.847 (1.00) |
0.871 (1.00) |
0.848 (1.00) |
0.462 (1.00) |
0.014 (1.00) |
amp 8q24 21 | 46 (82%) | 10 |
0.622 (1.00) |
0.793 (1.00) |
0.515 (1.00) |
0.118 (1.00) |
0.614 (1.00) |
0.69 (1.00) |
0.027 (1.00) |
0.309 (1.00) |
amp 9p13 3 | 10 (18%) | 46 |
0.303 (1.00) |
0.783 (1.00) |
0.683 (1.00) |
0.332 (1.00) |
0.247 (1.00) |
0.295 (1.00) |
0.326 (1.00) |
0.763 (1.00) |
amp 10p11 21 | 13 (23%) | 43 |
0.422 (1.00) |
0.643 (1.00) |
0.222 (1.00) |
0.571 (1.00) |
1 (1.00) |
0.525 (1.00) |
0.177 (1.00) |
0.55 (1.00) |
amp 11p13 | 14 (25%) | 42 |
0.779 (1.00) |
0.58 (1.00) |
0.479 (1.00) |
0.153 (1.00) |
1 (1.00) |
0.0958 (1.00) |
1 (1.00) |
0.942 (1.00) |
amp 11q13 3 | 33 (59%) | 23 |
0.314 (1.00) |
0.693 (1.00) |
0.151 (1.00) |
0.371 (1.00) |
0.417 (1.00) |
0.0327 (1.00) |
0.704 (1.00) |
0.784 (1.00) |
amp 12p13 33 | 24 (43%) | 32 |
0.214 (1.00) |
0.275 (1.00) |
0.52 (1.00) |
0.655 (1.00) |
0.394 (1.00) |
0.827 (1.00) |
0.444 (1.00) |
0.0412 (1.00) |
amp 12p12 1 | 30 (54%) | 26 |
0.114 (1.00) |
0.832 (1.00) |
0.603 (1.00) |
0.266 (1.00) |
0.933 (1.00) |
1 (1.00) |
0.127 (1.00) |
0.019 (1.00) |
amp 13q22 1 | 16 (29%) | 40 |
0.869 (1.00) |
0.954 (1.00) |
0.373 (1.00) |
1 (1.00) |
0.715 (1.00) |
0.794 (1.00) |
0.206 (1.00) |
0.698 (1.00) |
amp 15q26 3 | 17 (30%) | 39 |
0.347 (1.00) |
0.356 (1.00) |
0.222 (1.00) |
0.0784 (1.00) |
1 (1.00) |
0.0717 (1.00) |
0.0468 (1.00) |
0.994 (1.00) |
amp 17q12 | 23 (41%) | 33 |
0.384 (1.00) |
0.886 (1.00) |
0.668 (1.00) |
0.597 (1.00) |
0.2 (1.00) |
0.418 (1.00) |
1 (1.00) |
0.27 (1.00) |
amp 18p11 32 | 23 (41%) | 33 |
0.316 (1.00) |
0.837 (1.00) |
0.16 (1.00) |
0.282 (1.00) |
0.807 (1.00) |
0.176 (1.00) |
0.449 (1.00) |
0.567 (1.00) |
amp 18q11 2 | 17 (30%) | 39 |
0.254 (1.00) |
0.951 (1.00) |
0.0212 (1.00) |
0.0562 (1.00) |
0.0617 (1.00) |
0.231 (1.00) |
0.688 (1.00) |
0.518 (1.00) |
amp 19p13 2 | 12 (21%) | 44 |
0.266 (1.00) |
0.659 (1.00) |
0.632 (1.00) |
1 (1.00) |
0.124 (1.00) |
0.525 (1.00) |
0.18 (1.00) |
0.251 (1.00) |
amp 19q12 | 16 (29%) | 40 |
0.551 (1.00) |
0.239 (1.00) |
0.338 (1.00) |
0.369 (1.00) |
0.107 (1.00) |
0.231 (1.00) |
0.416 (1.00) |
0.0815 (1.00) |
del 1p36 13 | 17 (30%) | 39 |
0.497 (1.00) |
0.111 (1.00) |
0.0613 (1.00) |
0.503 (1.00) |
0.474 (1.00) |
0.176 (1.00) |
0.688 (1.00) |
0.421 (1.00) |
del 1p13 2 | 18 (32%) | 38 |
0.681 (1.00) |
0.509 (1.00) |
0.202 (1.00) |
0.828 (1.00) |
0.57 (1.00) |
0.191 (1.00) |
0.703 (1.00) |
0.925 (1.00) |
del 1q44 | 9 (16%) | 47 |
0.925 (1.00) |
0.417 (1.00) |
0.0483 (1.00) |
0.856 (1.00) |
0.013 (1.00) |
1 (1.00) |
1 (1.00) |
0.19 (1.00) |
del 2q22 1 | 16 (29%) | 40 |
0.686 (1.00) |
0.738 (1.00) |
0.118 (1.00) |
0.226 (1.00) |
0.041 (1.00) |
1 (1.00) |
1 (1.00) |
0.251 (1.00) |
del 2q33 3 | 10 (18%) | 46 |
0.311 (1.00) |
0.935 (1.00) |
0.295 (1.00) |
0.525 (1.00) |
0.162 (1.00) |
1 (1.00) |
1 (1.00) |
0.733 (1.00) |
del 3p14 3 | 43 (77%) | 13 |
0.736 (1.00) |
0.155 (1.00) |
0.331 (1.00) |
0.571 (1.00) |
0.154 (1.00) |
0.0781 (1.00) |
1 (1.00) |
0.948 (1.00) |
del 3p14 2 | 43 (77%) | 13 |
0.833 (1.00) |
0.563 (1.00) |
0.733 (1.00) |
0.571 (1.00) |
0.599 (1.00) |
0.093 (1.00) |
1 (1.00) |
0.787 (1.00) |
del 3q11 1 | 5 (9%) | 51 |
0.6 (1.00) |
0.431 (1.00) |
0.151 (1.00) |
0.8 (1.00) |
0.549 (1.00) |
0.619 (1.00) |
1 (1.00) |
0.383 (1.00) |
del 3q26 31 | 4 (7%) | 52 |
0.246 (1.00) |
0.647 (1.00) |
0.953 (1.00) |
0.0195 (1.00) |
0.466 (1.00) |
0.449 (1.00) |
1 (1.00) |
0.242 (1.00) |
del 4p16 3 | 29 (52%) | 27 |
0.576 (1.00) |
0.606 (1.00) |
0.54 (1.00) |
0.289 (1.00) |
0.193 (1.00) |
0.19 (1.00) |
0.462 (1.00) |
0.777 (1.00) |
del 4p15 2 | 33 (59%) | 23 |
0.751 (1.00) |
0.889 (1.00) |
0.769 (1.00) |
0.715 (1.00) |
0.75 (1.00) |
0.249 (1.00) |
0.704 (1.00) |
0.621 (1.00) |
del 4q21 23 | 28 (50%) | 28 |
0.294 (1.00) |
0.0072 (1.00) |
0.427 (1.00) |
0.435 (1.00) |
1 (1.00) |
0.581 (1.00) |
1 (1.00) |
0.629 (1.00) |
del 4q22 1 | 30 (54%) | 26 |
0.162 (1.00) |
0.000666 (0.378) |
0.317 (1.00) |
0.443 (1.00) |
0.462 (1.00) |
0.341 (1.00) |
1 (1.00) |
0.818 (1.00) |
del 5q11 2 | 31 (55%) | 25 |
0.913 (1.00) |
0.0866 (1.00) |
0.377 (1.00) |
0.182 (1.00) |
0.75 (1.00) |
0.841 (1.00) |
0.277 (1.00) |
0.816 (1.00) |
del 6p25 3 | 21 (38%) | 35 |
0.313 (1.00) |
0.0712 (1.00) |
0.366 (1.00) |
0.342 (1.00) |
0.28 (1.00) |
0.00265 (1.00) |
0.136 (1.00) |
0.174 (1.00) |
del 6q16 1 | 13 (23%) | 43 |
0.396 (1.00) |
0.223 (1.00) |
0.539 (1.00) |
0.799 (1.00) |
0.287 (1.00) |
0.525 (1.00) |
0.177 (1.00) |
0.16 (1.00) |
del 6q26 | 13 (23%) | 43 |
0.97 (1.00) |
0.384 (1.00) |
0.0998 (1.00) |
0.898 (1.00) |
0.142 (1.00) |
0.563 (1.00) |
0.177 (1.00) |
0.967 (1.00) |
del 7q31 1 | 20 (36%) | 36 |
0.722 (1.00) |
0.542 (1.00) |
0.717 (1.00) |
0.836 (1.00) |
0.547 (1.00) |
0.802 (1.00) |
0.236 (1.00) |
0.512 (1.00) |
del 7q36 2 | 24 (43%) | 32 |
0.63 (1.00) |
0.551 (1.00) |
0.476 (1.00) |
0.138 (1.00) |
0.533 (1.00) |
1 (1.00) |
0.444 (1.00) |
0.91 (1.00) |
del 8p23 2 | 29 (52%) | 27 |
0.0999 (1.00) |
0.647 (1.00) |
0.2 (1.00) |
0.21 (1.00) |
0.156 (1.00) |
0.451 (1.00) |
0.0227 (1.00) |
0.0863 (1.00) |
del 9p21 3 | 47 (84%) | 9 |
0.353 (1.00) |
0.31 (1.00) |
0.464 (1.00) |
0.254 (1.00) |
0.0466 (1.00) |
0.14 (1.00) |
0.108 (1.00) |
0.875 (1.00) |
del 10p15 1 | 17 (30%) | 39 |
0.0216 (1.00) |
0.074 (1.00) |
0.697 (1.00) |
0.417 (1.00) |
0.924 (1.00) |
0.449 (1.00) |
0.412 (1.00) |
0.527 (1.00) |
del 10p11 21 | 14 (25%) | 42 |
0.0091 (1.00) |
0.419 (1.00) |
0.295 (1.00) |
0.816 (1.00) |
0.25 (1.00) |
0.303 (1.00) |
0.664 (1.00) |
0.896 (1.00) |
del 10q22 3 | 20 (36%) | 36 |
0.0833 (1.00) |
0.45 (1.00) |
0.41 (1.00) |
0.657 (1.00) |
0.864 (1.00) |
0.404 (1.00) |
1 (1.00) |
0.724 (1.00) |
del 10q23 31 | 23 (41%) | 33 |
0.289 (1.00) |
0.0501 (1.00) |
0.807 (1.00) |
1 (1.00) |
0.929 (1.00) |
0.335 (1.00) |
0.252 (1.00) |
0.679 (1.00) |
del 11p15 4 | 22 (39%) | 34 |
0.551 (1.00) |
0.828 (1.00) |
0.0481 (1.00) |
0.472 (1.00) |
0.484 (1.00) |
0.84 (1.00) |
0.46 (1.00) |
0.0723 (1.00) |
del 11q24 3 | 28 (50%) | 28 |
0.222 (1.00) |
0.372 (1.00) |
0.169 (1.00) |
0.435 (1.00) |
0.611 (1.00) |
0.848 (1.00) |
0.705 (1.00) |
0.365 (1.00) |
del 12q23 1 | 13 (23%) | 43 |
0.238 (1.00) |
0.744 (1.00) |
0.423 (1.00) |
0.638 (1.00) |
1 (1.00) |
0.563 (1.00) |
0.37 (1.00) |
0.828 (1.00) |
del 13q14 2 | 29 (52%) | 27 |
0.375 (1.00) |
0.144 (1.00) |
0.601 (1.00) |
1 (1.00) |
0.569 (1.00) |
0.0895 (1.00) |
0.0227 (1.00) |
0.182 (1.00) |
del 13q21 2 | 26 (46%) | 30 |
0.494 (1.00) |
0.831 (1.00) |
0.842 (1.00) |
0.923 (1.00) |
0.87 (1.00) |
0.44 (1.00) |
0.263 (1.00) |
0.527 (1.00) |
del 15q11 2 | 18 (32%) | 38 |
0.232 (1.00) |
0.838 (1.00) |
0.138 (1.00) |
0.571 (1.00) |
0.453 (1.00) |
0.449 (1.00) |
0.254 (1.00) |
0.978 (1.00) |
del 16p13 3 | 12 (21%) | 44 |
0.682 (1.00) |
0.483 (1.00) |
0.649 (1.00) |
0.562 (1.00) |
0.138 (1.00) |
0.491 (1.00) |
0.348 (1.00) |
0.937 (1.00) |
del 16q23 1 | 21 (38%) | 35 |
0.619 (1.00) |
0.194 (1.00) |
0.775 (1.00) |
0.548 (1.00) |
0.174 (1.00) |
0.492 (1.00) |
1 (1.00) |
0.101 (1.00) |
del 17p11 2 | 22 (39%) | 34 |
0.382 (1.00) |
0.00468 (1.00) |
0.47 (1.00) |
0.843 (1.00) |
0.0805 (1.00) |
0.518 (1.00) |
0.698 (1.00) |
0.365 (1.00) |
del 17q24 3 | 5 (9%) | 51 |
0.141 (1.00) |
0.762 (1.00) |
0.135 (1.00) |
0.13 (1.00) |
0.69 (1.00) |
1 (1.00) |
0.0174 (1.00) |
0.98 (1.00) |
del 17q25 3 | 12 (21%) | 44 |
0.442 (1.00) |
0.278 (1.00) |
0.196 (1.00) |
0.787 (1.00) |
0.328 (1.00) |
0.74 (1.00) |
1 (1.00) |
0.281 (1.00) |
del 18q12 2 | 33 (59%) | 23 |
0.259 (1.00) |
0.108 (1.00) |
0.805 (1.00) |
0.851 (1.00) |
0.484 (1.00) |
0.827 (1.00) |
1 (1.00) |
0.561 (1.00) |
del 18q21 2 | 33 (59%) | 23 |
0.406 (1.00) |
0.0717 (1.00) |
0.805 (1.00) |
0.851 (1.00) |
0.484 (1.00) |
0.827 (1.00) |
0.704 (1.00) |
0.974 (1.00) |
del 19p13 3 | 24 (43%) | 32 |
0.614 (1.00) |
0.426 (1.00) |
0.361 (1.00) |
1 (1.00) |
0.254 (1.00) |
0.547 (1.00) |
1 (1.00) |
0.42 (1.00) |
del 19q13 31 | 17 (30%) | 39 |
0.65 (1.00) |
0.384 (1.00) |
0.391 (1.00) |
0.913 (1.00) |
0.0737 (1.00) |
1 (1.00) |
0.688 (1.00) |
0.4 (1.00) |
del 20p12 1 | 8 (14%) | 48 |
0.483 (1.00) |
0.741 (1.00) |
0.0618 (1.00) |
1 (1.00) |
0.0993 (1.00) |
0.404 (1.00) |
0.585 (1.00) |
|
del 21q11 2 | 34 (61%) | 22 |
0.601 (1.00) |
0.379 (1.00) |
0.598 (1.00) |
0.0977 (1.00) |
0.638 (1.00) |
1 (1.00) |
1 (1.00) |
0.724 (1.00) |
del 21q22 12 | 30 (54%) | 26 |
0.721 (1.00) |
0.16 (1.00) |
0.501 (1.00) |
0.788 (1.00) |
0.933 (1.00) |
1 (1.00) |
0.263 (1.00) |
0.195 (1.00) |
del 22q12 3 | 21 (38%) | 35 |
0.969 (1.00) |
0.157 (1.00) |
0.727 (1.00) |
0.317 (1.00) |
0.174 (1.00) |
0.396 (1.00) |
0.136 (1.00) |
0.456 (1.00) |
del xp21 1 | 25 (45%) | 31 |
0.776 (1.00) |
0.425 (1.00) |
0.326 (1.00) |
0.564 (1.00) |
0.529 (1.00) |
0.827 (1.00) |
0.72 (1.00) |
0.917 (1.00) |
del xp11 3 | 29 (52%) | 27 |
0.895 (1.00) |
0.663 (1.00) |
0.625 (1.00) |
0.521 (1.00) |
0.705 (1.00) |
0.581 (1.00) |
0.462 (1.00) |
0.424 (1.00) |
del xq21 33 | 10 (18%) | 46 |
0.949 (1.00) |
0.493 (1.00) |
0.00311 (1.00) |
0.0264 (1.00) |
0.021 (1.00) |
0.69 (1.00) |
0.623 (1.00) |
0.264 (1.00) |
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = ESCA-TP.merged_data.txt
-
Number of patients = 56
-
Number of significantly focal cnvs = 71
-
Number of selected clinical features = 8
-
Exclude genes that fewer than K tumors have mutations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations 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 mutations using 't.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 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.