This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 52 arm-level results and 8 clinical features across 72 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) | 0 (0%) | 52 |
0.77 (1.00) |
0.235 (1.00) |
1 (1.00) |
0.241 (1.00) |
0.149 (1.00) |
0.142 (1.00) |
0.111 (1.00) |
|
Amp Peak 2(1q22) | 0 (0%) | 16 |
0.503 (1.00) |
0.92 (1.00) |
0.392 (1.00) |
1 (1.00) |
0.815 (1.00) |
0.915 (1.00) |
0.739 (1.00) |
|
Amp Peak 3(1q42 3) | 0 (0%) | 25 |
0.308 (1.00) |
0.52 (1.00) |
0.605 (1.00) |
0.718 (1.00) |
0.275 (1.00) |
1 (1.00) |
0.451 (1.00) |
|
Amp Peak 4(2p24 1) | 0 (0%) | 55 |
0.632 (1.00) |
0.779 (1.00) |
0.253 (1.00) |
1 (1.00) |
0.335 (1.00) |
0.793 (1.00) |
0.326 (1.00) |
|
Amp Peak 5(2q31 2) | 0 (0%) | 54 |
0.756 (1.00) |
0.645 (1.00) |
0.0458 (1.00) |
1 (1.00) |
0.359 (1.00) |
0.501 (1.00) |
0.257 (1.00) |
|
Amp Peak 6(3q26 31) | 0 (0%) | 57 |
0.35 (1.00) |
0.481 (1.00) |
0.762 (1.00) |
0.636 (1.00) |
0.0545 (1.00) |
0.758 (1.00) |
0.0548 (1.00) |
|
Amp Peak 7(4q13 3) | 0 (0%) | 60 |
0.406 (1.00) |
0.344 (1.00) |
0.741 (1.00) |
1 (1.00) |
0.576 (1.00) |
0.33 (1.00) |
0.471 (1.00) |
|
Amp Peak 8(5p15 33) | 0 (0%) | 38 |
0.955 (1.00) |
0.745 (1.00) |
0.805 (1.00) |
0.139 (1.00) |
0.575 (1.00) |
1 (1.00) |
0.431 (1.00) |
|
Amp Peak 9(5q35 3) | 0 (0%) | 46 |
0.801 (1.00) |
0.694 (1.00) |
0.44 (1.00) |
0.542 (1.00) |
0.681 (1.00) |
0.109 (1.00) |
0.43 (1.00) |
|
Amp Peak 10(6p22 3) | 0 (0%) | 44 |
0.136 (1.00) |
0.488 (1.00) |
0.614 (1.00) |
0.262 (1.00) |
0.576 (1.00) |
0.823 (1.00) |
0.345 (1.00) |
|
Amp Peak 11(6p21 1) | 0 (0%) | 41 |
0.833 (1.00) |
0.956 (1.00) |
1 (1.00) |
0.309 (1.00) |
0.757 (1.00) |
0.839 (1.00) |
0.719 (1.00) |
|
Amp Peak 12(6q12) | 0 (0%) | 49 |
0.883 (1.00) |
0.677 (1.00) |
0.606 (1.00) |
0.0538 (1.00) |
0.45 (1.00) |
0.557 (1.00) |
0.463 (1.00) |
|
Amp Peak 13(7q21 2) | 0 (0%) | 45 |
0.726 (1.00) |
0.14 (1.00) |
0.45 (1.00) |
1 (1.00) |
0.429 (1.00) |
0.855 (1.00) |
0.734 (1.00) |
|
Amp Peak 14(8q11 21) | 0 (0%) | 40 |
0.348 (1.00) |
0.795 (1.00) |
0.0493 (1.00) |
0.492 (1.00) |
0.241 (1.00) |
0.827 (1.00) |
0.314 (1.00) |
|
Amp Peak 15(8q24 13) | 0 (0%) | 29 |
0.709 (1.00) |
0.764 (1.00) |
0.0763 (1.00) |
0.832 (1.00) |
0.606 (1.00) |
0.953 (1.00) |
0.693 (1.00) |
|
Amp Peak 16(10p15 1) | 0 (0%) | 58 |
0.435 (1.00) |
0.708 (1.00) |
0.539 (1.00) |
0.483 (1.00) |
0.0702 (1.00) |
1 (1.00) |
0.108 (1.00) |
|
Amp Peak 17(11q13 3) | 0 (0%) | 60 |
0.503 (1.00) |
0.464 (1.00) |
0.524 (1.00) |
0.24 (1.00) |
0.439 (1.00) |
0.0179 (1.00) |
0.0748 (1.00) |
|
Amp Peak 18(12q23 1) | 0 (0%) | 59 |
0.384 (1.00) |
0.247 (1.00) |
0.757 (1.00) |
0.173 (1.00) |
0.13 (1.00) |
0.211 (1.00) |
0.0654 (1.00) |
|
Amp Peak 19(13q32 3) | 0 (0%) | 57 |
0.58 (1.00) |
0.177 (1.00) |
0.762 (1.00) |
0.81 (1.00) |
0.199 (1.00) |
0.214 (1.00) |
0.281 (1.00) |
|
Amp Peak 20(15q26 3) | 0 (0%) | 60 |
0.142 (1.00) |
0.789 (1.00) |
0.32 (1.00) |
1 (1.00) |
0.304 (1.00) |
1 (1.00) |
0.975 (1.00) |
|
Amp Peak 21(17p11 2) | 0 (0%) | 61 |
0.64 (1.00) |
0.732 (1.00) |
0.497 (1.00) |
0.0685 (1.00) |
0.396 (1.00) |
0.0896 (1.00) |
0.105 (1.00) |
|
Amp Peak 22(17q23 1) | 0 (0%) | 38 |
0.382 (1.00) |
0.799 (1.00) |
1 (1.00) |
0.624 (1.00) |
0.761 (1.00) |
0.515 (1.00) |
0.575 (1.00) |
|
Amp Peak 23(17q25 3) | 0 (0%) | 36 |
0.23 (1.00) |
0.45 (1.00) |
0.322 (1.00) |
0.494 (1.00) |
1 (1.00) |
0.173 (1.00) |
0.788 (1.00) |
|
Amp Peak 24(19p13 12) | 0 (0%) | 54 |
0.856 (1.00) |
0.745 (1.00) |
0.155 (1.00) |
0.0194 (1.00) |
0.245 (1.00) |
0.312 (1.00) |
0.156 (1.00) |
|
Amp Peak 25(19q13 11) | 0 (0%) | 49 |
0.387 (1.00) |
0.863 (1.00) |
0.121 (1.00) |
0.0222 (1.00) |
0.0364 (1.00) |
0.297 (1.00) |
0.0176 (1.00) |
|
Amp Peak 26(20q13 13) | 0 (0%) | 48 |
0.158 (1.00) |
0.252 (1.00) |
0.795 (1.00) |
0.487 (1.00) |
0.147 (1.00) |
0.137 (1.00) |
0.289 (1.00) |
|
Del Peak 1(1p36 32) | 0 (0%) | 37 |
0.558 (1.00) |
0.434 (1.00) |
1 (1.00) |
0.565 (1.00) |
0.636 (1.00) |
0.274 (1.00) |
0.0908 (1.00) |
|
Del Peak 2(1p35 2) | 0 (0%) | 45 |
0.289 (1.00) |
0.881 (1.00) |
1 (1.00) |
0.266 (1.00) |
0.164 (1.00) |
0.404 (1.00) |
0.169 (1.00) |
|
Del Peak 3(2q22 1) | 0 (0%) | 65 |
0.328 (1.00) |
0.847 (1.00) |
0.688 (1.00) |
0.706 (1.00) |
0.478 (1.00) |
0.844 (1.00) |
0.696 (1.00) |
|
Del Peak 4(2q37 3) | 0 (0%) | 60 |
0.193 (1.00) |
0.669 (1.00) |
0.741 (1.00) |
0.783 (1.00) |
1 (1.00) |
0.89 (1.00) |
0.755 (1.00) |
|
Del Peak 5(3p13) | 0 (0%) | 57 |
0.439 (1.00) |
0.956 (1.00) |
0.362 (1.00) |
1 (1.00) |
0.809 (1.00) |
1 (1.00) |
0.558 (1.00) |
|
Del Peak 6(4q24) | 0 (0%) | 39 |
0.0679 (1.00) |
0.249 (1.00) |
0.62 (1.00) |
0.207 (1.00) |
0.419 (1.00) |
0.274 (1.00) |
0.323 (1.00) |
|
Del Peak 7(4q35 1) | 0 (0%) | 39 |
0.00769 (1.00) |
0.0682 (1.00) |
0.62 (1.00) |
0.207 (1.00) |
0.419 (1.00) |
0.541 (1.00) |
0.138 (1.00) |
|
Del Peak 8(5q23 1) | 0 (0%) | 63 |
0.392 (1.00) |
0.772 (1.00) |
0.482 (1.00) |
1 (1.00) |
0.13 (1.00) |
0.483 (1.00) |
0.0366 (1.00) |
|
Del Peak 9(6q26) | 0 (0%) | 45 |
0.293 (1.00) |
0.463 (1.00) |
0.611 (1.00) |
0.0142 (1.00) |
0.124 (1.00) |
0.48 (1.00) |
0.63 (1.00) |
|
Del Peak 10(8p23 3) | 0 (0%) | 29 |
0.43 (1.00) |
0.0176 (1.00) |
0.45 (1.00) |
0.688 (1.00) |
0.076 (1.00) |
0.588 (1.00) |
0.729 (1.00) |
|
Del Peak 11(8p23 2) | 0 (0%) | 28 |
0.462 (1.00) |
0.073 (1.00) |
0.312 (1.00) |
1 (1.00) |
0.401 (1.00) |
1 (1.00) |
0.715 (1.00) |
|
Del Peak 12(8p21 1) | 0 (0%) | 26 |
0.361 (1.00) |
0.0473 (1.00) |
0.318 (1.00) |
1 (1.00) |
0.275 (1.00) |
0.857 (1.00) |
0.668 (1.00) |
|
Del Peak 13(9p21 3) | 0 (0%) | 41 |
0.15 (1.00) |
0.348 (1.00) |
0.805 (1.00) |
0.394 (1.00) |
0.46 (1.00) |
0.333 (1.00) |
0.0466 (1.00) |
|
Del Peak 14(10q23 31) | 0 (0%) | 47 |
0.654 (1.00) |
0.564 (1.00) |
1 (1.00) |
0.15 (1.00) |
0.684 (1.00) |
0.357 (1.00) |
0.0815 (1.00) |
|
Del Peak 15(10q24 33) | 0 (0%) | 51 |
0.326 (1.00) |
0.807 (1.00) |
1 (1.00) |
0.527 (1.00) |
0.7 (1.00) |
0.464 (1.00) |
0.499 (1.00) |
|
Del Peak 16(11q14 1) | 0 (0%) | 57 |
0.816 (1.00) |
0.0525 (1.00) |
1 (1.00) |
1 (1.00) |
0.111 (1.00) |
0.596 (1.00) |
0.316 (1.00) |
|
Del Peak 17(12p12 1) | 0 (0%) | 57 |
0.249 (1.00) |
0.356 (1.00) |
0.553 (1.00) |
0.303 (1.00) |
0.253 (1.00) |
0.141 (1.00) |
0.139 (1.00) |
|
Del Peak 18(12q24 33) | 0 (0%) | 61 |
0.15 (1.00) |
0.236 (1.00) |
0.497 (1.00) |
0.563 (1.00) |
0.565 (1.00) |
0.681 (1.00) |
0.0303 (1.00) |
|
Del Peak 19(13q14 2) | 0 (0%) | 39 |
0.295 (1.00) |
0.612 (1.00) |
0.809 (1.00) |
0.454 (1.00) |
0.853 (1.00) |
0.641 (1.00) |
0.141 (1.00) |
|
Del Peak 20(14q23 3) | 0 (0%) | 42 |
0.0927 (1.00) |
0.869 (1.00) |
1 (1.00) |
0.209 (1.00) |
0.295 (1.00) |
0.582 (1.00) |
0.298 (1.00) |
|
Del Peak 21(14q32 33) | 0 (0%) | 42 |
0.46 (1.00) |
0.936 (1.00) |
1 (1.00) |
0.539 (1.00) |
0.66 (1.00) |
0.582 (1.00) |
0.33 (1.00) |
|
Del Peak 22(16q23 1) | 0 (0%) | 39 |
0.223 (1.00) |
0.276 (1.00) |
0.809 (1.00) |
0.196 (1.00) |
0.419 (1.00) |
0.148 (1.00) |
0.415 (1.00) |
|
Del Peak 23(17p12) | 0 (0%) | 28 |
0.14 (1.00) |
0.653 (1.00) |
1 (1.00) |
0.172 (1.00) |
0.221 (1.00) |
0.943 (1.00) |
0.842 (1.00) |
|
Del Peak 24(19p13 3) | 0 (0%) | 54 |
0.922 (1.00) |
0.224 (1.00) |
0.575 (1.00) |
0.201 (1.00) |
0.0978 (1.00) |
1 (1.00) |
0.178 (1.00) |
|
Del Peak 25(22q12 1) | 0 (0%) | 58 |
0.322 (1.00) |
0.763 (1.00) |
0.0645 (1.00) |
0.617 (1.00) |
0.6 (1.00) |
0.399 (1.00) |
0.753 (1.00) |
|
Del Peak 26(22q13 32) | 0 (0%) | 54 |
0.476 (1.00) |
0.78 (1.00) |
0.155 (1.00) |
0.479 (1.00) |
0.648 (1.00) |
0.543 (1.00) |
0.298 (1.00) |
-
Mutation data file = all_lesions.conf_99.cnv.cluster.txt
-
Clinical data file = LIHC-TP.clin.merged.picked.txt
-
Number of patients = 72
-
Number of significantly arm-level cnvs = 52
-
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.