This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 51 arm-level results and 10 clinical features across 34 patients, no significant finding detected with Q value < 0.25.
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No arm-level cnvs related to clinical features.
Table 1. Get Full Table Overview of the association between significant copy number variation of 51 arm-level results and 10 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 |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBERPACKYEARSSMOKED | TOBACCOSMOKINGHISTORYINDICATOR |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
NUMBER OF LYMPH NODES |
TUMOR STAGECODE |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Fisher's exact test | t-test | t-test | Fisher's exact test | Fisher's exact test | t-test | t-test | |
Amp Peak 1(1q21 3) | 0 (0%) | 10 |
0.298 (1.00) |
0.581 (1.00) |
0.746 (1.00) |
1 (1.00) |
0.287 (1.00) |
0.792 (1.00) |
0.675 (1.00) |
0.687 (1.00) |
0.35 (1.00) |
|
Amp Peak 2(1q44) | 0 (0%) | 12 |
0.35 (1.00) |
0.368 (1.00) |
0.598 (1.00) |
0.705 (1.00) |
0.287 (1.00) |
0.953 (1.00) |
1 (1.00) |
1 (1.00) |
0.503 (1.00) |
|
Amp Peak 3(2p24 3) | 0 (0%) | 24 |
0.0352 (1.00) |
0.238 (1.00) |
0.532 (1.00) |
1 (1.00) |
0.646 (1.00) |
0.544 (1.00) |
1 (1.00) |
1 (1.00) |
0.654 (1.00) |
|
Amp Peak 4(2q32 3) | 0 (0%) | 30 |
0.395 (1.00) |
0.198 (1.00) |
1 (1.00) |
1 (1.00) |
0.693 (1.00) |
1 (1.00) |
1 (1.00) |
0.774 (1.00) |
||
Amp Peak 5(3q26 2) | 0 (0%) | 7 |
0.423 (1.00) |
0.525 (1.00) |
0.28 (1.00) |
1 (1.00) |
0.682 (1.00) |
0.608 (1.00) |
0.287 (1.00) |
0.641 (1.00) |
0.566 (1.00) |
|
Amp Peak 6(3q28) | 0 (0%) | 7 |
0.423 (1.00) |
0.525 (1.00) |
0.28 (1.00) |
1 (1.00) |
0.682 (1.00) |
0.608 (1.00) |
0.287 (1.00) |
0.641 (1.00) |
0.566 (1.00) |
|
Amp Peak 7(4q12) | 0 (0%) | 29 |
0.857 (1.00) |
0.148 (1.00) |
1 (1.00) |
0.3 (1.00) |
0.321 (1.00) |
0.22 (1.00) |
0.537 (1.00) |
0.593 (1.00) |
||
Amp Peak 8(6p21 33) | 0 (0%) | 24 |
0.959 (1.00) |
0.138 (1.00) |
0.193 (1.00) |
1 (1.00) |
0.612 (1.00) |
0.891 (1.00) |
1 (1.00) |
0.417 (1.00) |
0.872 (1.00) |
|
Amp Peak 9(6q12) | 0 (0%) | 30 |
0.285 (1.00) |
0.388 (1.00) |
1 (1.00) |
0.58 (1.00) |
0.671 (1.00) |
1 (1.00) |
0.611 (1.00) |
0.914 (1.00) |
||
Amp Peak 10(8q24 21) | 0 (0%) | 18 |
0.988 (1.00) |
0.748 (1.00) |
1 (1.00) |
0.477 (1.00) |
0.783 (1.00) |
0.186 (1.00) |
0.427 (1.00) |
1 (1.00) |
1 (1.00) |
|
Amp Peak 11(8q24 21) | 0 (0%) | 18 |
0.305 (1.00) |
0.911 (1.00) |
1 (1.00) |
0.477 (1.00) |
0.783 (1.00) |
0.729 (1.00) |
0.427 (1.00) |
0.45 (1.00) |
0.68 (1.00) |
|
Amp Peak 12(9p24 1) | 0 (0%) | 27 |
0.129 (1.00) |
0.122 (1.00) |
0.67 (1.00) |
0.384 (1.00) |
0.805 (1.00) |
1 (1.00) |
0.372 (1.00) |
0.634 (1.00) |
||
Amp Peak 13(11q13 3) | 0 (0%) | 30 |
0.423 (1.00) |
0.28 (1.00) |
1 (1.00) |
0.58 (1.00) |
0.589 (1.00) |
0.532 (1.00) |
0.52 (1.00) |
|||
Amp Peak 14(11q22 1) | 0 (0%) | 27 |
0.9 (1.00) |
0.00543 (1.00) |
1 (1.00) |
1 (1.00) |
0.528 (1.00) |
0.633 (1.00) |
0.372 (1.00) |
0.154 (1.00) |
||
Amp Peak 15(13q22 1) | 0 (0%) | 30 |
0.634 (1.00) |
0.981 (1.00) |
0.243 (1.00) |
1 (1.00) |
0.345 (1.00) |
1 (1.00) |
0.537 (1.00) |
0.593 (1.00) |
||
Amp Peak 16(14q24 1) | 0 (0%) | 27 |
0.285 (1.00) |
0.715 (1.00) |
0.19 (1.00) |
0.384 (1.00) |
0.555 (1.00) |
1 (1.00) |
0.641 (1.00) |
0.527 (1.00) |
||
Amp Peak 17(15q26 3) | 0 (0%) | 24 |
0.829 (1.00) |
0.441 (1.00) |
1 (1.00) |
0.437 (1.00) |
0.676 (1.00) |
0.675 (1.00) |
0.672 (1.00) |
0.271 (1.00) |
||
Amp Peak 18(16p13 2) | 0 (0%) | 26 |
0.317 (1.00) |
0.206 (1.00) |
0.242 (1.00) |
1 (1.00) |
0.645 (1.00) |
0.642 (1.00) |
1 (1.00) |
0.704 (1.00) |
||
Amp Peak 19(16p13 13) | 0 (0%) | 26 |
0.552 (1.00) |
0.112 (1.00) |
0.0374 (1.00) |
1 (1.00) |
0.388 (1.00) |
0.158 (1.00) |
1 (1.00) |
0.704 (1.00) |
||
Amp Peak 20(17q12) | 0 (0%) | 29 |
0.932 (1.00) |
0.89 (1.00) |
0.331 (1.00) |
1 (1.00) |
0.589 (1.00) |
0.153 (1.00) |
0.327 (1.00) |
0.613 (1.00) |
||
Amp Peak 21(17q25 1) | 0 (0%) | 24 |
0.28 (1.00) |
0.914 (1.00) |
0.0477 (1.00) |
1 (1.00) |
0.783 (1.00) |
0.24 (1.00) |
1 (1.00) |
0.225 (1.00) |
0.367 (1.00) |
|
Amp Peak 22(19q13 31) | 0 (0%) | 23 |
0.149 (1.00) |
0.9 (1.00) |
0.577 (1.00) |
0.016 (1.00) |
0.985 (1.00) |
0.524 (1.00) |
0.396 (1.00) |
0.687 (1.00) |
0.692 (1.00) |
|
Amp Peak 23(20q11 21) | 0 (0%) | 15 |
0.0234 (1.00) |
0.373 (1.00) |
0.813 (1.00) |
0.475 (1.00) |
0.113 (1.00) |
0.293 (1.00) |
0.454 (1.00) |
0.142 (1.00) |
0.54 (1.00) |
|
Amp Peak 24(Xq28) | 0 (0%) | 27 |
0.241 (1.00) |
0.691 (1.00) |
0.67 (1.00) |
1 (1.00) |
0.645 (1.00) |
0.158 (1.00) |
1 (1.00) |
0.89 (1.00) |
||
Del Peak 1(1p36 23) | 0 (0%) | 28 |
0.916 (1.00) |
0.242 (1.00) |
0.146 (1.00) |
1 (1.00) |
0.277 (1.00) |
0.728 (1.00) |
0.633 (1.00) |
1 (1.00) |
0.8 (1.00) |
|
Del Peak 2(1p13 1) | 0 (0%) | 27 |
0.719 (1.00) |
0.329 (1.00) |
1 (1.00) |
0.656 (1.00) |
0.235 (1.00) |
0.633 (1.00) |
1 (1.00) |
0.917 (1.00) |
||
Del Peak 3(2q22 1) | 0 (0%) | 30 |
0.747 (1.00) |
0.569 (1.00) |
1 (1.00) |
0.0889 (1.00) |
0.888 (1.00) |
0.532 (1.00) |
1 (1.00) |
0.718 (1.00) |
||
Del Peak 4(2q37 1) | 0 (0%) | 20 |
0.0924 (1.00) |
0.0168 (1.00) |
1 (1.00) |
0.295 (1.00) |
0.0503 (1.00) |
0.206 (1.00) |
1 (1.00) |
0.442 (1.00) |
0.463 (1.00) |
|
Del Peak 5(3p11 1) | 0 (0%) | 17 |
0.68 (1.00) |
0.559 (1.00) |
0.398 (1.00) |
1 (1.00) |
0.534 (1.00) |
0.354 (1.00) |
0.7 (1.00) |
0.257 (1.00) |
0.0769 (1.00) |
|
Del Peak 6(4q22 1) | 0 (0%) | 26 |
0.559 (1.00) |
0.535 (1.00) |
0.707 (1.00) |
1 (1.00) |
0.881 (1.00) |
0.86 (1.00) |
1 (1.00) |
0.372 (1.00) |
0.164 (1.00) |
|
Del Peak 7(4q35 2) | 0 (0%) | 22 |
0.0897 (1.00) |
0.529 (1.00) |
0.769 (1.00) |
1 (1.00) |
0.838 (1.00) |
0.769 (1.00) |
0.675 (1.00) |
0.702 (1.00) |
0.441 (1.00) |
|
Del Peak 8(5q14 3) | 0 (0%) | 18 |
0.327 (1.00) |
0.135 (1.00) |
0.66 (1.00) |
0.477 (1.00) |
0.627 (1.00) |
0.977 (1.00) |
0.688 (1.00) |
0.707 (1.00) |
0.171 (1.00) |
|
Del Peak 9(6p24 3) | 0 (0%) | 28 |
0.986 (1.00) |
0.324 (1.00) |
0.42 (1.00) |
0.638 (1.00) |
0.263 (1.00) |
1 (1.00) |
0.0472 (1.00) |
0.165 (1.00) |
||
Del Peak 11(6q26) | 0 (0%) | 26 |
0.602 (1.00) |
0.114 (1.00) |
0.707 (1.00) |
0.227 (1.00) |
0.696 (1.00) |
0.642 (1.00) |
0.372 (1.00) |
0.634 (1.00) |
||
Del Peak 12(7q34) | 0 (0%) | 27 |
0.00723 (1.00) |
0.811 (1.00) |
1 (1.00) |
0.178 (1.00) |
0.838 (1.00) |
0.608 (1.00) |
1 (1.00) |
1 (1.00) |
0.458 (1.00) |
|
Del Peak 13(10q23 31) | 0 (0%) | 27 |
0.108 (1.00) |
0.903 (1.00) |
1 (1.00) |
0.656 (1.00) |
0.77 (1.00) |
0.0211 (1.00) |
0.633 (1.00) |
0.156 (1.00) |
0.208 (1.00) |
|
Del Peak 14(10q26 3) | 0 (0%) | 28 |
0.285 (1.00) |
0.91 (1.00) |
0.42 (1.00) |
0.363 (1.00) |
0.77 (1.00) |
0.076 (1.00) |
0.076 (1.00) |
0.0472 (1.00) |
0.115 (1.00) |
|
Del Peak 15(11p15 1) | 0 (0%) | 22 |
0.87 (1.00) |
0.938 (1.00) |
0.598 (1.00) |
1 (1.00) |
0.881 (1.00) |
0.953 (1.00) |
0.694 (1.00) |
0.238 (1.00) |
0.0926 (1.00) |
|
Del Peak 16(11q25) | 0 (0%) | 11 |
0.954 (1.00) |
0.644 (1.00) |
0.422 (1.00) |
1 (1.00) |
0.304 (1.00) |
0.744 (1.00) |
1 (1.00) |
0.702 (1.00) |
0.134 (1.00) |
|
Del Peak 17(13q13 3) | 0 (0%) | 21 |
0.63 (1.00) |
0.968 (1.00) |
0.471 (1.00) |
1 (1.00) |
0.881 (1.00) |
0.769 (1.00) |
1 (1.00) |
0.696 (1.00) |
0.182 (1.00) |
|
Del Peak 18(14q32 31) | 0 (0%) | 31 |
0.523 (1.00) |
0.099 (1.00) |
1 (1.00) |
1 (1.00) |
0.861 (1.00) |
0.22 (1.00) |
0.279 (1.00) |
0.00565 (1.00) |
||
Del Peak 19(15q15 1) | 0 (0%) | 29 |
0.986 (1.00) |
0.529 (1.00) |
1 (1.00) |
1 (1.00) |
0.447 (1.00) |
0.568 (1.00) |
1 (1.00) |
0.443 (1.00) |
||
Del Peak 20(16q11 2) | 0 (0%) | 31 |
0.734 (1.00) |
1 (1.00) |
0.535 (1.00) |
1 (1.00) |
0.52 (1.00) |
|||||
Del Peak 21(16q23 1) | 0 (0%) | 31 |
0.893 (1.00) |
0.0329 (1.00) |
1 (1.00) |
0.532 (1.00) |
1 (1.00) |
|||||
Del Peak 22(17p12) | 0 (0%) | 22 |
0.644 (1.00) |
0.194 (1.00) |
0.235 (1.00) |
0.459 (1.00) |
0.533 (1.00) |
0.276 (1.00) |
1 (1.00) |
0.702 (1.00) |
0.441 (1.00) |
|
Del Peak 23(17q25 3) | 0 (0%) | 26 |
0.0882 (1.00) |
0.307 (1.00) |
0.707 (1.00) |
1 (1.00) |
0.373 (1.00) |
0.86 (1.00) |
1 (1.00) |
0.641 (1.00) |
0.527 (1.00) |
|
Del Peak 24(19p13 3) | 0 (0%) | 25 |
0.447 (1.00) |
0.612 (1.00) |
0.278 (1.00) |
0.111 (1.00) |
0.764 (1.00) |
0.837 (1.00) |
1 (1.00) |
1 (1.00) |
0.566 (1.00) |
|
Del Peak 25(20p12 1) | 0 (0%) | 28 |
0.296 (1.00) |
0.804 (1.00) |
0.224 (1.00) |
0.145 (1.00) |
0.733 (1.00) |
0.728 (1.00) |
0.287 (1.00) |
1 (1.00) |
0.8 (1.00) |
|
Del Peak 26(21q21 1) | 0 (0%) | 25 |
0.337 (1.00) |
0.605 (1.00) |
0.492 (1.00) |
0.0172 (1.00) |
0.03 (1.00) |
1 (1.00) |
0.419 (1.00) |
0.547 (1.00) |
||
Del Peak 27(Xp11 3) | 0 (0%) | 21 |
0.844 (1.00) |
0.187 (1.00) |
0.789 (1.00) |
0.262 (1.00) |
0.0867 (1.00) |
0.268 (1.00) |
0.205 (1.00) |
1 (1.00) |
0.323 (1.00) |
|
Del Peak 28(Xq21 33) | 0 (0%) | 24 |
0.00867 (1.00) |
0.897 (1.00) |
0.746 (1.00) |
0.232 (1.00) |
0.166 (1.00) |
0.549 (1.00) |
1 (1.00) |
1 (1.00) |
0.4 (1.00) |
-
Mutation data file = all_lesions.conf_99.cnv.cluster.txt
-
Clinical data file = CESC-TP.clin.merged.picked.txt
-
Number of patients = 34
-
Number of significantly arm-level cnvs = 51
-
Number of selected clinical features = 10
-
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 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.