(primary solid tumor 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 53 arm-level results and 8 clinical features across 68 patients, no significant finding detected with Q value < 0.25.
-
No arm-level cnvs related to clinical features.
Clinical Features |
Time to Death |
AGE | GENDER |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
COMPLETENESS OF RESECTION |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | t-test | Chi-square test | |
Amp Peak 1(1p22 3) | 19 (28%) | 49 |
0.77 (1.00) |
0.278 (1.00) |
1 (1.00) |
0.274 (1.00) |
0.118 (1.00) |
0.158 (1.00) |
0.106 (1.00) |
|
Amp Peak 2(1q22) | 52 (76%) | 16 |
0.503 (1.00) |
0.889 (1.00) |
0.551 (1.00) |
1 (1.00) |
0.816 (1.00) |
0.917 (1.00) |
0.581 (1.00) |
|
Amp Peak 3(1q42 3) | 44 (65%) | 24 |
0.308 (1.00) |
0.56 (1.00) |
0.438 (1.00) |
0.764 (1.00) |
0.33 (1.00) |
1 (1.00) |
0.388 (1.00) |
|
Amp Peak 4(2p24 1) | 17 (25%) | 51 |
0.632 (1.00) |
0.971 (1.00) |
0.257 (1.00) |
1 (1.00) |
0.358 (1.00) |
0.921 (1.00) |
0.262 (1.00) |
|
Amp Peak 5(2q33 1) | 16 (24%) | 52 |
0.499 (1.00) |
0.382 (1.00) |
0.0713 (1.00) |
1 (1.00) |
0.135 (1.00) |
0.678 (1.00) |
0.374 (1.00) |
|
Amp Peak 6(3q26 31) | 14 (21%) | 54 |
0.35 (1.00) |
0.626 (1.00) |
0.542 (1.00) |
0.621 (1.00) |
0.0435 (1.00) |
0.755 (1.00) |
0.0523 (1.00) |
|
Amp Peak 7(4q31 3) | 8 (12%) | 60 |
0.68 (1.00) |
0.981 (1.00) |
1 (1.00) |
0.491 (1.00) |
0.727 (1.00) |
0.466 (1.00) |
0.642 (1.00) |
|
Amp Peak 8(5p15 33) | 32 (47%) | 36 |
0.955 (1.00) |
0.815 (1.00) |
1 (1.00) |
0.212 (1.00) |
0.838 (1.00) |
1 (1.00) |
0.475 (1.00) |
|
Amp Peak 9(5q35 3) | 24 (35%) | 44 |
0.801 (1.00) |
0.528 (1.00) |
0.596 (1.00) |
0.518 (1.00) |
0.569 (1.00) |
0.0913 (1.00) |
0.558 (1.00) |
|
Amp Peak 10(6p25 2) | 27 (40%) | 41 |
0.31 (1.00) |
0.9 (1.00) |
1 (1.00) |
0.601 (1.00) |
0.293 (1.00) |
0.788 (1.00) |
0.642 (1.00) |
|
Amp Peak 11(6p21 1) | 29 (43%) | 39 |
0.833 (1.00) |
0.94 (1.00) |
0.799 (1.00) |
0.411 (1.00) |
0.583 (1.00) |
0.838 (1.00) |
0.663 (1.00) |
|
Amp Peak 12(6q12) | 21 (31%) | 47 |
0.883 (1.00) |
0.85 (1.00) |
0.42 (1.00) |
0.0864 (1.00) |
0.429 (1.00) |
0.524 (1.00) |
0.357 (1.00) |
|
Amp Peak 13(7q21 2) | 25 (37%) | 43 |
0.726 (1.00) |
0.093 (1.00) |
0.298 (1.00) |
0.772 (1.00) |
0.562 (1.00) |
0.848 (1.00) |
0.666 (1.00) |
|
Amp Peak 14(8q13 1) | 35 (51%) | 33 |
0.888 (1.00) |
0.783 (1.00) |
0.128 (1.00) |
0.819 (1.00) |
0.421 (1.00) |
0.843 (1.00) |
0.569 (1.00) |
|
Amp Peak 15(8q24 13) | 40 (59%) | 28 |
0.709 (1.00) |
0.744 (1.00) |
0.128 (1.00) |
1 (1.00) |
0.442 (1.00) |
1 (1.00) |
0.766 (1.00) |
|
Amp Peak 16(10p15 1) | 12 (18%) | 56 |
0.435 (1.00) |
0.901 (1.00) |
0.321 (1.00) |
0.331 (1.00) |
0.0206 (1.00) |
0.902 (1.00) |
0.11 (1.00) |
|
Amp Peak 17(11q13 3) | 11 (16%) | 57 |
0.503 (1.00) |
0.216 (1.00) |
0.734 (1.00) |
0.188 (1.00) |
0.567 (1.00) |
0.0145 (1.00) |
0.086 (1.00) |
|
Amp Peak 18(12q23 1) | 13 (19%) | 55 |
0.384 (1.00) |
0.362 (1.00) |
1 (1.00) |
0.179 (1.00) |
0.166 (1.00) |
0.252 (1.00) |
0.0632 (1.00) |
|
Amp Peak 19(13q32 3) | 14 (21%) | 54 |
0.58 (1.00) |
0.114 (1.00) |
0.542 (1.00) |
1 (1.00) |
0.145 (1.00) |
0.207 (1.00) |
0.293 (1.00) |
|
Amp Peak 20(15q21 3) | 12 (18%) | 56 |
0.729 (1.00) |
0.227 (1.00) |
0.0961 (1.00) |
0.596 (1.00) |
0.0552 (1.00) |
1 (1.00) |
0.696 (1.00) |
|
Amp Peak 21(15q26 3) | 12 (18%) | 56 |
0.142 (1.00) |
0.958 (1.00) |
0.321 (1.00) |
1 (1.00) |
0.312 (1.00) |
1 (1.00) |
0.956 (1.00) |
|
Amp Peak 22(17p11 2) | 11 (16%) | 57 |
0.0963 (1.00) |
0.674 (1.00) |
0.177 (1.00) |
0.567 (1.00) |
0.18 (1.00) |
0.316 (1.00) |
0.885 (1.00) |
|
Amp Peak 23(17q23 1) | 33 (49%) | 35 |
0.382 (1.00) |
0.945 (1.00) |
1 (1.00) |
0.819 (1.00) |
0.643 (1.00) |
0.675 (1.00) |
0.63 (1.00) |
|
Amp Peak 24(17q25 3) | 34 (50%) | 34 |
0.23 (1.00) |
0.386 (1.00) |
0.447 (1.00) |
0.649 (1.00) |
0.866 (1.00) |
0.171 (1.00) |
0.748 (1.00) |
|
Amp Peak 25(19q13 11) | 23 (34%) | 45 |
0.387 (1.00) |
0.634 (1.00) |
0.18 (1.00) |
0.0254 (1.00) |
0.0358 (1.00) |
0.225 (1.00) |
0.0337 (1.00) |
|
Amp Peak 26(20q13 13) | 22 (32%) | 46 |
0.158 (1.00) |
0.146 (1.00) |
0.591 (1.00) |
0.474 (1.00) |
0.0799 (1.00) |
0.0941 (1.00) |
0.241 (1.00) |
|
Del Peak 1(1p36 32) | 32 (47%) | 36 |
0.558 (1.00) |
0.232 (1.00) |
1 (1.00) |
0.481 (1.00) |
0.643 (1.00) |
0.195 (1.00) |
0.0564 (1.00) |
|
Del Peak 2(2q22 1) | 7 (10%) | 61 |
0.328 (1.00) |
0.765 (1.00) |
0.691 (1.00) |
0.709 (1.00) |
0.485 (1.00) |
0.841 (1.00) |
0.66 (1.00) |
|
Del Peak 3(2q37 3) | 12 (18%) | 56 |
0.193 (1.00) |
0.813 (1.00) |
0.741 (1.00) |
0.783 (1.00) |
0.789 (1.00) |
0.902 (1.00) |
0.653 (1.00) |
|
Del Peak 4(3p13) | 12 (18%) | 56 |
0.464 (1.00) |
0.758 (1.00) |
0.0961 (1.00) |
1 (1.00) |
0.58 (1.00) |
0.902 (1.00) |
0.402 (1.00) |
|
Del Peak 5(4q24) | 31 (46%) | 37 |
0.0679 (1.00) |
0.279 (1.00) |
0.799 (1.00) |
0.295 (1.00) |
0.537 (1.00) |
0.269 (1.00) |
0.265 (1.00) |
|
Del Peak 6(4q35 1) | 30 (44%) | 38 |
0.00769 (1.00) |
0.0804 (1.00) |
0.803 (1.00) |
0.354 (1.00) |
0.677 (1.00) |
0.584 (1.00) |
0.0654 (1.00) |
|
Del Peak 7(5q23 1) | 9 (13%) | 59 |
0.392 (1.00) |
0.873 (1.00) |
0.476 (1.00) |
1 (1.00) |
0.134 (1.00) |
0.502 (1.00) |
0.0348 (1.00) |
|
Del Peak 8(6q16 3) | 24 (35%) | 44 |
0.129 (1.00) |
0.445 (1.00) |
0.796 (1.00) |
0.111 (1.00) |
0.395 (1.00) |
0.624 (1.00) |
0.429 (1.00) |
|
Del Peak 9(6q26) | 25 (37%) | 43 |
0.293 (1.00) |
0.326 (1.00) |
0.794 (1.00) |
0.0253 (1.00) |
0.183 (1.00) |
0.473 (1.00) |
0.642 (1.00) |
|
Del Peak 10(8p23 2) | 43 (63%) | 25 |
0.462 (1.00) |
0.155 (1.00) |
0.298 (1.00) |
1 (1.00) |
0.33 (1.00) |
1 (1.00) |
0.726 (1.00) |
|
Del Peak 11(9p21 3) | 29 (43%) | 39 |
0.15 (1.00) |
0.405 (1.00) |
1 (1.00) |
0.27 (1.00) |
0.326 (1.00) |
0.327 (1.00) |
0.0715 (1.00) |
|
Del Peak 12(10p15 3) | 4 (6%) | 64 |
0.0147 (1.00) |
0.91 (1.00) |
0.289 (1.00) |
0.617 (1.00) |
1 (1.00) |
1 (1.00) |
0.91 (1.00) |
|
Del Peak 13(10q23 31) | 22 (32%) | 46 |
0.654 (1.00) |
0.721 (1.00) |
0.591 (1.00) |
0.478 (1.00) |
1 (1.00) |
0.214 (1.00) |
0.244 (1.00) |
|
Del Peak 14(10q24 33) | 19 (28%) | 49 |
0.326 (1.00) |
0.686 (1.00) |
1 (1.00) |
0.634 (1.00) |
1 (1.00) |
0.338 (1.00) |
0.64 (1.00) |
|
Del Peak 15(11q14 1) | 14 (21%) | 54 |
0.816 (1.00) |
0.0561 (1.00) |
1 (1.00) |
1 (1.00) |
0.0777 (1.00) |
0.59 (1.00) |
0.334 (1.00) |
|
Del Peak 16(12p12 1) | 13 (19%) | 55 |
0.249 (1.00) |
0.333 (1.00) |
1 (1.00) |
0.273 (1.00) |
0.265 (1.00) |
0.153 (1.00) |
0.114 (1.00) |
|
Del Peak 17(12q24 33) | 9 (13%) | 59 |
0.19 (1.00) |
0.0991 (1.00) |
0.261 (1.00) |
0.745 (1.00) |
0.75 (1.00) |
0.845 (1.00) |
0.306 (1.00) |
|
Del Peak 18(13q14 2) | 32 (47%) | 36 |
0.295 (1.00) |
0.978 (1.00) |
0.802 (1.00) |
0.481 (1.00) |
1 (1.00) |
0.232 (1.00) |
0.0899 (1.00) |
|
Del Peak 19(14q23 3) | 27 (40%) | 41 |
0.0927 (1.00) |
0.99 (1.00) |
1 (1.00) |
0.486 (1.00) |
0.442 (1.00) |
0.492 (1.00) |
0.537 (1.00) |
|
Del Peak 20(15q15 1) | 15 (22%) | 53 |
0.37 (1.00) |
0.203 (1.00) |
0.547 (1.00) |
0.494 (1.00) |
0.289 (1.00) |
0.914 (1.00) |
0.142 (1.00) |
|
Del Peak 21(16q23 1) | 30 (44%) | 38 |
0.223 (1.00) |
0.306 (1.00) |
0.61 (1.00) |
0.409 (1.00) |
0.677 (1.00) |
0.16 (1.00) |
0.561 (1.00) |
|
Del Peak 22(17p12) | 41 (60%) | 27 |
0.14 (1.00) |
0.647 (1.00) |
1 (1.00) |
0.351 (1.00) |
0.446 (1.00) |
0.856 (1.00) |
0.849 (1.00) |
|
Del Peak 23(18q21 2) | 13 (19%) | 55 |
0.0656 (1.00) |
0.13 (1.00) |
0.52 (1.00) |
1 (1.00) |
0.0118 (1.00) |
1 (1.00) |
0.212 (1.00) |
|
Del Peak 24(19p13 3) | 17 (25%) | 51 |
0.922 (1.00) |
0.179 (1.00) |
0.77 (1.00) |
0.279 (1.00) |
0.14 (1.00) |
1 (1.00) |
0.196 (1.00) |
|
Del Peak 25(22q12 1) | 14 (21%) | 54 |
0.322 (1.00) |
0.973 (1.00) |
0.0671 (1.00) |
0.491 (1.00) |
0.606 (1.00) |
0.567 (1.00) |
0.833 (1.00) |
|
Del Peak 26(22q13 32) | 18 (26%) | 50 |
0.476 (1.00) |
0.983 (1.00) |
0.156 (1.00) |
0.47 (1.00) |
0.669 (1.00) |
0.605 (1.00) |
0.37 (1.00) |
|
Del Peak 27(Xq27 3) | 11 (16%) | 57 |
0.0649 (1.00) |
0.903 (1.00) |
0.5 (1.00) |
1 (1.00) |
0.769 (1.00) |
0.522 (1.00) |
0.472 (1.00) |
-
Mutation data file = all_lesions.conf_99.cnv.cluster.txt
-
Clinical data file = LIHC-TP.clin.merged.picked.txt
-
Number of patients = 68
-
Number of significantly arm-level cnvs = 53
-
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.