This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 41 arm-level results and 3 clinical features across 22 patients, one significant finding detected with Q value < 0.25.
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Amp Peak 5(6p21.1) cnv correlated to 'AGE'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 41 arm-level results and 3 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, one significant finding detected.
|
Clinical Features |
Time to Death |
AGE | GENDER | ||
| nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | |
| Amp Peak 5(6p21 1) | 0 (0%) | 13 |
0.536 (1.00) |
0.000112 (0.0137) |
0.192 (1.00) |
| Amp Peak 1(1p32 1) | 0 (0%) | 14 |
0.175 (1.00) |
0.789 (1.00) |
1 (1.00) |
| Amp Peak 2(1q24 3) | 0 (0%) | 13 |
0.724 (1.00) |
0.761 (1.00) |
0.666 (1.00) |
| Amp Peak 3(4p15 2) | 0 (0%) | 13 |
0.393 (1.00) |
0.123 (1.00) |
0.666 (1.00) |
| Amp Peak 4(5p15 33) | 0 (0%) | 9 |
0.346 (1.00) |
0.605 (1.00) |
1 (1.00) |
| Amp Peak 6(6q25 1) | 0 (0%) | 14 |
0.833 (1.00) |
0.236 (1.00) |
1 (1.00) |
| Amp Peak 7(7p15 3) | 0 (0%) | 14 |
0.712 (1.00) |
0.0039 (0.475) |
1 (1.00) |
| Amp Peak 8(11q22 2) | 0 (0%) | 16 |
0.0624 (1.00) |
0.966 (1.00) |
1 (1.00) |
| Amp Peak 9(12p13 32) | 0 (0%) | 16 |
0.165 (1.00) |
0.789 (1.00) |
1 (1.00) |
| Amp Peak 10(12q15) | 0 (0%) | 8 |
0.683 (1.00) |
0.651 (1.00) |
0.00619 (0.749) |
| Amp Peak 11(17p12) | 0 (0%) | 14 |
0.654 (1.00) |
0.259 (1.00) |
0.675 (1.00) |
| Amp Peak 12(19p13 2) | 0 (0%) | 11 |
0.901 (1.00) |
0.63 (1.00) |
0.67 (1.00) |
| Amp Peak 13(Xq21 1) | 0 (0%) | 15 |
0.525 (1.00) |
0.481 (1.00) |
1 (1.00) |
| Del Peak 1(1p36 32) | 0 (0%) | 17 |
0.926 (1.00) |
0.723 (1.00) |
0.00957 (1.00) |
| Del Peak 2(1p32 3) | 0 (0%) | 16 |
0.406 (1.00) |
0.56 (1.00) |
0.348 (1.00) |
| Del Peak 3(1q44) | 0 (0%) | 10 |
0.99 (1.00) |
0.0582 (1.00) |
0.691 (1.00) |
| Del Peak 4(2q37 3) | 0 (0%) | 12 |
0.393 (1.00) |
0.0773 (1.00) |
1 (1.00) |
| Del Peak 5(3p21 31) | 0 (0%) | 15 |
0.0905 (1.00) |
0.0719 (1.00) |
1 (1.00) |
| Del Peak 6(3q25 1) | 0 (0%) | 13 |
0.254 (1.00) |
0.41 (1.00) |
1 (1.00) |
| Del Peak 7(4q35 1) | 0 (0%) | 12 |
0.764 (1.00) |
0.192 (1.00) |
0.0836 (1.00) |
| Del Peak 8(5q23 3) | 0 (0%) | 18 |
0.395 (1.00) |
0.687 (1.00) |
0.0287 (1.00) |
| Del Peak 9(6q15) | 0 (0%) | 18 |
0.828 (1.00) |
0.622 (1.00) |
1 (1.00) |
| Del Peak 10(7q36 3) | 0 (0%) | 16 |
0.254 (1.00) |
0.215 (1.00) |
1 (1.00) |
| Del Peak 11(8p23 2) | 0 (0%) | 14 |
0.452 (1.00) |
0.539 (1.00) |
1 (1.00) |
| Del Peak 12(9p21 3) | 0 (0%) | 10 |
0.586 (1.00) |
0.162 (1.00) |
0.231 (1.00) |
| Del Peak 13(9q34 3) | 0 (0%) | 17 |
0.0456 (1.00) |
0.0857 (1.00) |
0.135 (1.00) |
| Del Peak 14(10p15 3) | 0 (0%) | 11 |
0.603 (1.00) |
0.0164 (1.00) |
0.198 (1.00) |
| Del Peak 15(11p15 5) | 0 (0%) | 11 |
0.655 (1.00) |
0.0504 (1.00) |
0.67 (1.00) |
| Del Peak 16(11q22 3) | 0 (0%) | 11 |
0.182 (1.00) |
0.19 (1.00) |
1 (1.00) |
| Del Peak 17(11q25) | 0 (0%) | 10 |
0.0624 (1.00) |
0.0435 (1.00) |
1 (1.00) |
| Del Peak 18(12p12 3) | 0 (0%) | 15 |
0.92 (1.00) |
0.347 (1.00) |
0.381 (1.00) |
| Del Peak 19(13q14 2) | 0 (0%) | 7 |
0.268 (1.00) |
0.937 (1.00) |
0.381 (1.00) |
| Del Peak 20(13q34) | 0 (0%) | 10 |
0.985 (1.00) |
0.779 (1.00) |
0.691 (1.00) |
| Del Peak 21(14q24 1) | 0 (0%) | 10 |
0.673 (1.00) |
0.806 (1.00) |
0.691 (1.00) |
| Del Peak 22(17p13 1) | 0 (0%) | 17 |
0.774 (1.00) |
0.272 (1.00) |
0.624 (1.00) |
| Del Peak 23(17q25 3) | 0 (0%) | 16 |
0.683 (1.00) |
0.894 (1.00) |
1 (1.00) |
| Del Peak 24(19p13 3) | 0 (0%) | 17 |
0.0741 (1.00) |
0.555 (1.00) |
0.00957 (1.00) |
| Del Peak 25(19q13 33) | 0 (0%) | 12 |
0.00757 (0.908) |
0.897 (1.00) |
0.391 (1.00) |
| Del Peak 26(21q22 3) | 0 (0%) | 14 |
0.696 (1.00) |
0.0797 (1.00) |
0.378 (1.00) |
| Del Peak 27(Xq21 1) | 0 (0%) | 14 |
0.872 (1.00) |
0.227 (1.00) |
0.378 (1.00) |
| Del Peak 28(Xq28) | 0 (0%) | 12 |
0.228 (1.00) |
0.187 (1.00) |
0.231 (1.00) |
P value = 0.000112 (t-test), Q value = 0.014
Table S1. Gene #5: 'Amp Peak 5(6p21.1)' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 22 | 64.6 (7.7) |
| AMP PEAK 5(6P21.1) CNV | 9 | 71.8 (5.8) |
| AMP PEAK 5(6P21.1) WILD-TYPE | 13 | 59.7 (4.0) |
Figure S1. Get High-res Image Gene #5: 'Amp Peak 5(6p21.1)' versus Clinical Feature #2: 'AGE'
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Mutation data file = all_lesions.conf_99.cnv.cluster.txt
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Clinical data file = SARC-TP.clin.merged.picked.txt
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Number of patients = 22
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Number of significantly arm-level cnvs = 41
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Number of selected clinical features = 3
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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.