(WT 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 20 arm-level results and 7 clinical features across 23 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 |
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 | t-test | Chi-square test | |
Amp Peak 1(1p12) | 9 (39%) | 14 |
0.591 (1.00) |
0.681 (1.00) |
0.355 (1.00) |
0.0361 (1.00) |
0.627 (1.00) |
0.638 (1.00) |
|
Amp Peak 2(1q44) | 11 (48%) | 12 |
0.201 (1.00) |
0.298 (1.00) |
0.211 (1.00) |
1 (1.00) |
0.15 (1.00) |
0.625 (1.00) |
|
Amp Peak 3(4q12) | 8 (35%) | 15 |
0.608 (1.00) |
0.246 (1.00) |
0.318 (1.00) |
1 (1.00) |
0.263 (1.00) |
0.233 (1.00) |
|
Amp Peak 4(5p15 33) | 7 (30%) | 16 |
0.248 (1.00) |
0.0206 (1.00) |
0.816 (1.00) |
1 (1.00) |
0.829 (1.00) |
0.103 (1.00) |
|
Amp Peak 5(5q35 3) | 5 (22%) | 18 |
0.361 (1.00) |
0.931 (1.00) |
0.14 (1.00) |
0.317 (1.00) |
0.732 (1.00) |
0.573 (1.00) |
|
Amp Peak 6(8q11 21) | 12 (52%) | 11 |
0.705 (1.00) |
0.322 (1.00) |
1 (1.00) |
0.414 (1.00) |
0.0315 (1.00) |
0.0424 (1.00) |
|
Amp Peak 7(11q13 3) | 5 (22%) | 18 |
0.603 (1.00) |
0.0406 (1.00) |
1 (1.00) |
1 (1.00) |
0.629 (1.00) |
0.525 (1.00) |
|
Amp Peak 8(11q13 3) | 5 (22%) | 18 |
0.603 (1.00) |
0.0406 (1.00) |
1 (1.00) |
1 (1.00) |
0.629 (1.00) |
0.525 (1.00) |
|
Amp Peak 9(12q14 1) | 10 (43%) | 13 |
0.265 (1.00) |
0.0127 (1.00) |
1 (1.00) |
1 (1.00) |
0.404 (1.00) |
0.103 (1.00) |
|
Amp Peak 10(17q25 3) | 10 (43%) | 13 |
0.872 (1.00) |
0.4 (1.00) |
0.126 (1.00) |
0.68 (1.00) |
0.641 (1.00) |
0.342 (1.00) |
|
Amp Peak 11(22q13 1) | 12 (52%) | 11 |
0.324 (1.00) |
0.53 (1.00) |
0.334 (1.00) |
0.684 (1.00) |
0.37 (1.00) |
0.151 (1.00) |
|
Amp Peak 12(Xq28) | 8 (35%) | 15 |
0.632 (1.00) |
0.00453 (0.544) |
0.584 (1.00) |
0.667 (1.00) |
0.843 (1.00) |
0.0986 (1.00) |
|
Del Peak 1(2q37 3) | 7 (30%) | 16 |
0.627 (1.00) |
0.285 (1.00) |
1 (1.00) |
0.371 (1.00) |
0.0615 (1.00) |
0.927 (1.00) |
|
Del Peak 2(4q34 3) | 7 (30%) | 16 |
0.77 (1.00) |
0.515 (1.00) |
0.458 (1.00) |
0.371 (1.00) |
0.843 (1.00) |
0.635 (1.00) |
|
Del Peak 3(5p15 31) | 5 (22%) | 18 |
0.518 (1.00) |
0.887 (1.00) |
0.805 (1.00) |
1 (1.00) |
0.607 (1.00) |
0.194 (1.00) |
|
Del Peak 4(9p21 3) | 14 (61%) | 9 |
0.807 (1.00) |
0.676 (1.00) |
0.502 (1.00) |
0.68 (1.00) |
0.588 (1.00) |
0.841 (1.00) |
|
Del Peak 5(10q26 3) | 13 (57%) | 10 |
0.865 (1.00) |
0.885 (1.00) |
0.843 (1.00) |
0.414 (1.00) |
0.153 (1.00) |
0.61 (1.00) |
|
Del Peak 6(11q23 3) | 14 (61%) | 9 |
0.707 (1.00) |
0.367 (1.00) |
1 (1.00) |
0.214 (1.00) |
0.166 (1.00) |
0.352 (1.00) |
|
Del Peak 7(15q14) | 9 (39%) | 14 |
0.248 (1.00) |
0.44 (1.00) |
0.688 (1.00) |
0.4 (1.00) |
0.691 (1.00) |
0.841 (1.00) |
|
Del Peak 8(16p13 3) | 4 (17%) | 19 |
0.741 (1.00) |
0.0114 (1.00) |
0.753 (1.00) |
0.59 (1.00) |
0.772 (1.00) |
0.0533 (1.00) |
-
Mutation data file = all_lesions.conf_99.cnv.cluster.txt
-
Clinical data file = SKCM-WT.clin.merged.picked.txt
-
Number of patients = 23
-
Number of significantly arm-level cnvs = 20
-
Number of selected clinical features = 7
-
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.