This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 59 arm-level results and 2 clinical features across 48 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 59 arm-level results and 2 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.
|
Clinical Features |
VITALSTATUS | GENDER | ||
| nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | |
| 1p gain | 5 (10%) | 43 |
0.348 (1.00) |
1 (1.00) |
| 1q gain | 26 (54%) | 22 |
0.772 (1.00) |
0.557 (1.00) |
| 2p gain | 10 (21%) | 38 |
1 (1.00) |
1 (1.00) |
| 2q gain | 6 (12%) | 42 |
1 (1.00) |
0.197 (1.00) |
| 3q gain | 3 (6%) | 45 |
1 (1.00) |
1 (1.00) |
| 4p gain | 4 (8%) | 44 |
0.609 (1.00) |
0.286 (1.00) |
| 5p gain | 14 (29%) | 34 |
0.111 (1.00) |
1 (1.00) |
| 5q gain | 14 (29%) | 34 |
0.111 (1.00) |
1 (1.00) |
| 6p gain | 13 (27%) | 35 |
1 (1.00) |
1 (1.00) |
| 6q gain | 5 (10%) | 43 |
1 (1.00) |
0.635 (1.00) |
| 7p gain | 13 (27%) | 35 |
1 (1.00) |
0.0188 (1.00) |
| 7q gain | 13 (27%) | 35 |
0.517 (1.00) |
0.0959 (1.00) |
| 8p gain | 8 (17%) | 40 |
0.245 (1.00) |
0.451 (1.00) |
| 8q gain | 23 (48%) | 25 |
0.248 (1.00) |
0.566 (1.00) |
| 9p gain | 3 (6%) | 45 |
0.234 (1.00) |
0.554 (1.00) |
| 9q gain | 3 (6%) | 45 |
0.234 (1.00) |
0.554 (1.00) |
| 10p gain | 6 (12%) | 42 |
0.666 (1.00) |
0.669 (1.00) |
| 12p gain | 3 (6%) | 45 |
0.234 (1.00) |
0.554 (1.00) |
| 12q gain | 3 (6%) | 45 |
1 (1.00) |
1 (1.00) |
| 15q gain | 5 (10%) | 43 |
0.348 (1.00) |
0.372 (1.00) |
| 17q gain | 18 (38%) | 30 |
0.766 (1.00) |
1 (1.00) |
| 19p gain | 4 (8%) | 44 |
0.609 (1.00) |
0.286 (1.00) |
| 19q gain | 5 (10%) | 43 |
1 (1.00) |
0.0724 (1.00) |
| 20p gain | 8 (17%) | 40 |
1 (1.00) |
0.695 (1.00) |
| 20q gain | 10 (21%) | 38 |
1 (1.00) |
1 (1.00) |
| 21q gain | 3 (6%) | 45 |
0.234 (1.00) |
0.056 (1.00) |
| 22q gain | 6 (12%) | 42 |
0.188 (1.00) |
0.197 (1.00) |
| 1p loss | 8 (17%) | 40 |
1 (1.00) |
0.695 (1.00) |
| 3p loss | 7 (15%) | 41 |
1 (1.00) |
0.0967 (1.00) |
| 3q loss | 3 (6%) | 45 |
1 (1.00) |
0.554 (1.00) |
| 4p loss | 8 (17%) | 40 |
0.701 (1.00) |
0.451 (1.00) |
| 4q loss | 14 (29%) | 34 |
1 (1.00) |
0.354 (1.00) |
| 5q loss | 4 (8%) | 44 |
0.609 (1.00) |
1 (1.00) |
| 6q loss | 8 (17%) | 40 |
0.245 (1.00) |
0.236 (1.00) |
| 7p loss | 3 (6%) | 45 |
0.234 (1.00) |
0.554 (1.00) |
| 7q loss | 5 (10%) | 43 |
1 (1.00) |
0.372 (1.00) |
| 8p loss | 24 (50%) | 24 |
1 (1.00) |
1 (1.00) |
| 8q loss | 5 (10%) | 43 |
0.348 (1.00) |
1 (1.00) |
| 9p loss | 13 (27%) | 35 |
1 (1.00) |
0.522 (1.00) |
| 9q loss | 11 (23%) | 37 |
1 (1.00) |
0.488 (1.00) |
| 10p loss | 4 (8%) | 44 |
1 (1.00) |
1 (1.00) |
| 10q loss | 13 (27%) | 35 |
1 (1.00) |
0.321 (1.00) |
| 11p loss | 5 (10%) | 43 |
1 (1.00) |
0.372 (1.00) |
| 11q loss | 9 (19%) | 39 |
0.461 (1.00) |
1 (1.00) |
| 12p loss | 5 (10%) | 43 |
0.348 (1.00) |
1 (1.00) |
| 12q loss | 3 (6%) | 45 |
0.234 (1.00) |
0.554 (1.00) |
| 13q loss | 19 (40%) | 29 |
0.556 (1.00) |
1 (1.00) |
| 14q loss | 16 (33%) | 32 |
0.359 (1.00) |
1 (1.00) |
| 15q loss | 8 (17%) | 40 |
0.701 (1.00) |
0.695 (1.00) |
| 16p loss | 10 (21%) | 38 |
0.724 (1.00) |
0.719 (1.00) |
| 16q loss | 18 (38%) | 30 |
1 (1.00) |
0.762 (1.00) |
| 17p loss | 23 (48%) | 25 |
1 (1.00) |
0.25 (1.00) |
| 17q loss | 4 (8%) | 44 |
0.609 (1.00) |
1 (1.00) |
| 18p loss | 5 (10%) | 43 |
0.348 (1.00) |
1 (1.00) |
| 18q loss | 7 (15%) | 41 |
1 (1.00) |
1 (1.00) |
| 19p loss | 6 (12%) | 42 |
1 (1.00) |
0.381 (1.00) |
| 19q loss | 5 (10%) | 43 |
1 (1.00) |
0.635 (1.00) |
| 21q loss | 8 (17%) | 40 |
0.701 (1.00) |
0.0154 (1.00) |
| 22q loss | 9 (19%) | 39 |
0.137 (1.00) |
0.127 (1.00) |
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Mutation data file = broad_values_by_arm.mutsig.cluster.txt
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Clinical data file = LIHC.clin.merged.picked.txt
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Number of patients = 48
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Number of significantly arm-level cnvs = 59
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Number of selected clinical features = 2
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Exclude genes that fewer than K tumors have mutations, K = 3
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.