(Regional_Metastatic cohort)
This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 46 arm-level results and 8 clinical features across 147 patients, no significant finding detected with Q value < 0.25.
-
No arm-level cnvs related to clinical features.
Clinical Features |
Time to Death |
AGE |
PRIMARY SITE OF DISEASE |
GENDER |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Fisher's exact test | Chi-square test | Chi-square test | t-test | Chi-square test | |
Amp Peak 1(1p12) | 44 (30%) | 103 |
0.024 (1.00) |
0.581 (1.00) |
0.531 (1.00) |
0.579 (1.00) |
0.382 (1.00) |
0.115 (1.00) |
0.128 (1.00) |
|
Amp Peak 2(1q31 2) | 74 (50%) | 73 |
0.243 (1.00) |
0.91 (1.00) |
0.439 (1.00) |
0.863 (1.00) |
0.41 (1.00) |
0.366 (1.00) |
0.622 (1.00) |
|
Amp Peak 3(1q44) | 76 (52%) | 71 |
0.784 (1.00) |
0.87 (1.00) |
0.175 (1.00) |
0.732 (1.00) |
0.425 (1.00) |
0.279 (1.00) |
0.346 (1.00) |
|
Amp Peak 4(3p13) | 34 (23%) | 113 |
0.673 (1.00) |
0.228 (1.00) |
0.37 (1.00) |
0.688 (1.00) |
0.729 (1.00) |
0.643 (1.00) |
0.798 (1.00) |
|
Amp Peak 5(5p15 33) | 38 (26%) | 109 |
0.176 (1.00) |
0.477 (1.00) |
0.268 (1.00) |
0.559 (1.00) |
0.671 (1.00) |
0.373 (1.00) |
0.149 (1.00) |
|
Amp Peak 6(5q35 3) | 16 (11%) | 131 |
0.729 (1.00) |
0.321 (1.00) |
0.763 (1.00) |
0.581 (1.00) |
0.206 (1.00) |
0.715 (1.00) |
0.747 (1.00) |
|
Amp Peak 7(6p25 3) | 84 (57%) | 63 |
0.00928 (1.00) |
0.0492 (1.00) |
0.558 (1.00) |
0.487 (1.00) |
0.53 (1.00) |
0.0567 (1.00) |
0.587 (1.00) |
|
Amp Peak 8(6q12) | 33 (22%) | 114 |
0.484 (1.00) |
0.269 (1.00) |
0.356 (1.00) |
0.541 (1.00) |
0.784 (1.00) |
0.205 (1.00) |
0.472 (1.00) |
|
Amp Peak 9(7p22 1) | 81 (55%) | 66 |
0.237 (1.00) |
0.786 (1.00) |
0.562 (1.00) |
0.389 (1.00) |
0.485 (1.00) |
0.178 (1.00) |
0.445 (1.00) |
|
Amp Peak 10(7q34) | 85 (58%) | 62 |
0.899 (1.00) |
0.896 (1.00) |
0.33 (1.00) |
0.862 (1.00) |
0.544 (1.00) |
0.119 (1.00) |
0.00837 (1.00) |
|
Amp Peak 11(8q24 21) | 70 (48%) | 77 |
0.75 (1.00) |
0.111 (1.00) |
0.245 (1.00) |
1 (1.00) |
0.425 (1.00) |
0.897 (1.00) |
0.716 (1.00) |
|
Amp Peak 12(9p13 3) | 16 (11%) | 131 |
0.77 (1.00) |
0.331 (1.00) |
0.36 (1.00) |
0.419 (1.00) |
0.947 (1.00) |
0.921 (1.00) |
0.709 (1.00) |
|
Amp Peak 13(11q13 3) | 23 (16%) | 124 |
0.438 (1.00) |
0.274 (1.00) |
0.596 (1.00) |
0.352 (1.00) |
0.894 (1.00) |
0.45 (1.00) |
0.689 (1.00) |
|
Amp Peak 14(12q14 1) | 27 (18%) | 120 |
0.878 (1.00) |
0.514 (1.00) |
0.804 (1.00) |
0.514 (1.00) |
0.697 (1.00) |
0.121 (1.00) |
0.0604 (1.00) |
|
Amp Peak 15(15q24 3) | 48 (33%) | 99 |
0.886 (1.00) |
0.416 (1.00) |
0.681 (1.00) |
0.717 (1.00) |
0.696 (1.00) |
0.353 (1.00) |
0.386 (1.00) |
|
Amp Peak 16(15q26 3) | 53 (36%) | 94 |
0.871 (1.00) |
0.314 (1.00) |
0.32 (1.00) |
1 (1.00) |
0.832 (1.00) |
0.159 (1.00) |
0.362 (1.00) |
|
Amp Peak 17(17q25 3) | 57 (39%) | 90 |
0.837 (1.00) |
0.0155 (1.00) |
0.846 (1.00) |
0.483 (1.00) |
0.827 (1.00) |
0.407 (1.00) |
0.44 (1.00) |
|
Amp Peak 18(19p13 2) | 28 (19%) | 119 |
0.5 (1.00) |
0.611 (1.00) |
0.323 (1.00) |
0.273 (1.00) |
0.0123 (1.00) |
0.463 (1.00) |
0.207 (1.00) |
|
Amp Peak 19(22q13 2) | 64 (44%) | 83 |
0.387 (1.00) |
0.527 (1.00) |
0.846 (1.00) |
0.863 (1.00) |
0.694 (1.00) |
0.163 (1.00) |
0.222 (1.00) |
|
Amp Peak 20(Xq28) | 24 (16%) | 123 |
0.539 (1.00) |
0.536 (1.00) |
0.6 (1.00) |
0.0599 (1.00) |
0.64 (1.00) |
0.809 (1.00) |
0.648 (1.00) |
|
Del Peak 1(1p36 31) | 37 (25%) | 110 |
0.835 (1.00) |
0.426 (1.00) |
0.657 (1.00) |
0.32 (1.00) |
0.114 (1.00) |
0.697 (1.00) |
0.795 (1.00) |
|
Del Peak 2(1p22 1) | 42 (29%) | 105 |
0.744 (1.00) |
0.0475 (1.00) |
0.206 (1.00) |
0.705 (1.00) |
0.16 (1.00) |
0.664 (1.00) |
0.325 (1.00) |
|
Del Peak 3(2q37 3) | 36 (24%) | 111 |
0.206 (1.00) |
0.666 (1.00) |
0.0699 (1.00) |
0.689 (1.00) |
0.0745 (1.00) |
0.66 (1.00) |
0.081 (1.00) |
|
Del Peak 4(3p24 3) | 21 (14%) | 126 |
0.0624 (1.00) |
0.403 (1.00) |
0.783 (1.00) |
0.224 (1.00) |
0.904 (1.00) |
0.264 (1.00) |
0.0902 (1.00) |
|
Del Peak 5(3q23) | 21 (14%) | 126 |
0.953 (1.00) |
0.0647 (1.00) |
1 (1.00) |
0.466 (1.00) |
0.142 (1.00) |
0.622 (1.00) |
0.251 (1.00) |
|
Del Peak 6(4p16 3) | 31 (21%) | 116 |
0.439 (1.00) |
0.752 (1.00) |
0.0158 (1.00) |
0.211 (1.00) |
0.714 (1.00) |
0.71 (1.00) |
0.803 (1.00) |
|
Del Peak 7(4q25) | 33 (22%) | 114 |
0.874 (1.00) |
0.364 (1.00) |
0.166 (1.00) |
0.0978 (1.00) |
0.079 (1.00) |
0.185 (1.00) |
0.549 (1.00) |
|
Del Peak 8(4q34 3) | 35 (24%) | 112 |
0.459 (1.00) |
0.286 (1.00) |
0.113 (1.00) |
0.0271 (1.00) |
0.114 (1.00) |
0.827 (1.00) |
0.362 (1.00) |
|
Del Peak 9(5q11 2) | 44 (30%) | 103 |
0.289 (1.00) |
0.406 (1.00) |
0.835 (1.00) |
0.451 (1.00) |
0.2 (1.00) |
0.62 (1.00) |
0.12 (1.00) |
|
Del Peak 10(5q31 3) | 59 (40%) | 88 |
0.25 (1.00) |
0.89 (1.00) |
1 (1.00) |
0.295 (1.00) |
0.362 (1.00) |
0.595 (1.00) |
0.314 (1.00) |
|
Del Peak 11(6q25 3) | 89 (61%) | 58 |
0.207 (1.00) |
0.218 (1.00) |
0.844 (1.00) |
0.862 (1.00) |
0.83 (1.00) |
0.367 (1.00) |
0.576 (1.00) |
|
Del Peak 12(6q26) | 84 (57%) | 63 |
0.139 (1.00) |
0.202 (1.00) |
0.845 (1.00) |
0.728 (1.00) |
0.812 (1.00) |
0.445 (1.00) |
0.608 (1.00) |
|
Del Peak 13(9p23) | 103 (70%) | 44 |
0.182 (1.00) |
0.629 (1.00) |
0.204 (1.00) |
0.194 (1.00) |
0.483 (1.00) |
0.39 (1.00) |
0.489 (1.00) |
|
Del Peak 14(9p21 3) | 115 (78%) | 32 |
0.439 (1.00) |
0.413 (1.00) |
0.639 (1.00) |
0.0943 (1.00) |
0.732 (1.00) |
0.352 (1.00) |
0.583 (1.00) |
|
Del Peak 15(10p15 3) | 79 (54%) | 68 |
0.0352 (1.00) |
0.54 (1.00) |
0.0529 (1.00) |
0.494 (1.00) |
0.723 (1.00) |
0.442 (1.00) |
0.871 (1.00) |
|
Del Peak 16(10q23 31) | 91 (62%) | 56 |
0.169 (1.00) |
0.132 (1.00) |
0.0454 (1.00) |
0.0506 (1.00) |
0.465 (1.00) |
0.713 (1.00) |
0.608 (1.00) |
|
Del Peak 17(10q26 3) | 92 (63%) | 55 |
0.551 (1.00) |
0.0236 (1.00) |
0.00488 (1.00) |
0.0319 (1.00) |
0.464 (1.00) |
0.843 (1.00) |
0.731 (1.00) |
|
Del Peak 18(11p11 12) | 54 (37%) | 93 |
0.662 (1.00) |
0.0403 (1.00) |
0.046 (1.00) |
0.107 (1.00) |
0.462 (1.00) |
0.182 (1.00) |
0.158 (1.00) |
|
Del Peak 19(11q23 3) | 79 (54%) | 68 |
0.588 (1.00) |
0.54 (1.00) |
1 (1.00) |
0.733 (1.00) |
0.733 (1.00) |
0.0461 (1.00) |
0.473 (1.00) |
|
Del Peak 20(12q24 33) | 33 (22%) | 114 |
0.417 (1.00) |
0.341 (1.00) |
0.0653 (1.00) |
0.409 (1.00) |
0.247 (1.00) |
0.214 (1.00) |
0.881 (1.00) |
|
Del Peak 21(13q34) | 40 (27%) | 107 |
0.431 (1.00) |
0.455 (1.00) |
1 (1.00) |
0.444 (1.00) |
0.0591 (1.00) |
0.375 (1.00) |
0.133 (1.00) |
|
Del Peak 22(14q32 2) | 47 (32%) | 100 |
0.258 (1.00) |
0.942 (1.00) |
0.836 (1.00) |
0.855 (1.00) |
0.443 (1.00) |
0.493 (1.00) |
0.305 (1.00) |
|
Del Peak 23(15q13 3) | 35 (24%) | 112 |
0.698 (1.00) |
0.539 (1.00) |
0.497 (1.00) |
0.315 (1.00) |
0.732 (1.00) |
0.68 (1.00) |
0.412 (1.00) |
|
Del Peak 24(15q15 2) | 37 (25%) | 110 |
0.294 (1.00) |
0.373 (1.00) |
0.657 (1.00) |
0.164 (1.00) |
0.314 (1.00) |
0.831 (1.00) |
0.257 (1.00) |
|
Del Peak 25(16p13 3) | 26 (18%) | 121 |
0.318 (1.00) |
0.0876 (1.00) |
0.32 (1.00) |
0.259 (1.00) |
0.861 (1.00) |
0.193 (1.00) |
0.471 (1.00) |
|
Del Peak 26(16q24 2) | 52 (35%) | 95 |
0.187 (1.00) |
0.358 (1.00) |
0.225 (1.00) |
0.371 (1.00) |
0.83 (1.00) |
0.0942 (1.00) |
0.196 (1.00) |
-
Mutation data file = all_lesions.conf_99.cnv.cluster.txt
-
Clinical data file = SKCM-Regional_Metastatic.clin.merged.picked.txt
-
Number of patients = 147
-
Number of significantly arm-level cnvs = 46
-
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 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.