This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 28 arm-level results and 6 clinical features across 182 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 28 arm-level results and 6 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 | GENDER |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
NEOADJUVANT THERAPY |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
1q gain | 5 (3%) | 177 |
1 (1.00) |
0.244 (1.00) |
0.62 (1.00) |
0.431 (1.00) |
0.333 (1.00) |
1 (1.00) |
4p gain | 4 (2%) | 178 |
0.0143 (1.00) |
0.119 (1.00) |
1 (1.00) |
0.801 (1.00) |
0.276 (1.00) |
1 (1.00) |
4q gain | 4 (2%) | 178 |
0.0143 (1.00) |
0.119 (1.00) |
1 (1.00) |
0.801 (1.00) |
0.276 (1.00) |
1 (1.00) |
5p gain | 7 (4%) | 175 |
0.0143 (1.00) |
0.077 (1.00) |
1 (1.00) |
0.532 (1.00) |
0.435 (1.00) |
1 (1.00) |
5q gain | 7 (4%) | 175 |
0.0143 (1.00) |
0.077 (1.00) |
1 (1.00) |
0.532 (1.00) |
0.435 (1.00) |
1 (1.00) |
7p gain | 8 (4%) | 174 |
1 (1.00) |
0.167 (1.00) |
1 (1.00) |
0.695 (1.00) |
1 (1.00) |
1 (1.00) |
7q gain | 10 (5%) | 172 |
1 (1.00) |
0.0995 (1.00) |
0.728 (1.00) |
0.261 (1.00) |
1 (1.00) |
1 (1.00) |
12p gain | 7 (4%) | 175 |
1 (1.00) |
0.365 (1.00) |
0.675 (1.00) |
0.532 (1.00) |
1 (1.00) |
1 (1.00) |
12q gain | 7 (4%) | 175 |
1 (1.00) |
0.365 (1.00) |
0.675 (1.00) |
0.532 (1.00) |
1 (1.00) |
1 (1.00) |
14q gain | 4 (2%) | 178 |
1 (1.00) |
0.555 (1.00) |
0.578 (1.00) |
0.801 (1.00) |
1 (1.00) |
1 (1.00) |
16p gain | 7 (4%) | 175 |
1 (1.00) |
0.516 (1.00) |
0.193 (1.00) |
0.483 (1.00) |
1 (1.00) |
1 (1.00) |
16q gain | 5 (3%) | 177 |
1 (1.00) |
0.348 (1.00) |
0.324 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
17p gain | 6 (3%) | 176 |
1 (1.00) |
0.545 (1.00) |
0.187 (1.00) |
0.776 (1.00) |
1 (1.00) |
1 (1.00) |
17q gain | 7 (4%) | 175 |
1 (1.00) |
0.758 (1.00) |
0.193 (1.00) |
0.811 (1.00) |
1 (1.00) |
1 (1.00) |
19q gain | 3 (2%) | 179 |
0.0143 (1.00) |
0.0172 (1.00) |
1 (1.00) |
0.566 (1.00) |
0.215 (1.00) |
1 (1.00) |
20p gain | 3 (2%) | 179 |
1 (1.00) |
0.593 (1.00) |
0.561 (1.00) |
0.566 (1.00) |
1 (1.00) |
1 (1.00) |
20q gain | 3 (2%) | 179 |
1 (1.00) |
0.593 (1.00) |
0.561 (1.00) |
0.566 (1.00) |
1 (1.00) |
1 (1.00) |
2p loss | 5 (3%) | 177 |
1 (1.00) |
0.394 (1.00) |
1 (1.00) |
0.517 (1.00) |
1 (1.00) |
1 (1.00) |
2q loss | 4 (2%) | 178 |
1 (1.00) |
0.0908 (1.00) |
1 (1.00) |
0.298 (1.00) |
1 (1.00) |
1 (1.00) |
9q loss | 4 (2%) | 178 |
1 (1.00) |
0.079 (1.00) |
1 (1.00) |
0.236 (1.00) |
0.276 (1.00) |
1 (1.00) |
11p loss | 3 (2%) | 179 |
0.0143 (1.00) |
0.102 (1.00) |
0.19 (1.00) |
0.566 (1.00) |
0.215 (1.00) |
1 (1.00) |
11q loss | 4 (2%) | 178 |
0.0143 (1.00) |
0.0587 (1.00) |
0.0673 (1.00) |
0.298 (1.00) |
0.276 (1.00) |
1 (1.00) |
13q loss | 6 (3%) | 176 |
0.0143 (1.00) |
0.243 (1.00) |
0.352 (1.00) |
0.039 (1.00) |
0.386 (1.00) |
1 (1.00) |
17p loss | 3 (2%) | 179 |
1 (1.00) |
0.858 (1.00) |
0.561 (1.00) |
0.566 (1.00) |
0.0158 (1.00) |
1 (1.00) |
18p loss | 3 (2%) | 179 |
1 (1.00) |
0.942 (1.00) |
0.561 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
18q loss | 3 (2%) | 179 |
1 (1.00) |
0.942 (1.00) |
0.561 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
21q loss | 3 (2%) | 179 |
1 (1.00) |
0.0289 (1.00) |
0.19 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
22q loss | 28 (15%) | 154 |
1 (1.00) |
0.772 (1.00) |
0.649 (1.00) |
0.121 (1.00) |
0.132 (1.00) |
1 (1.00) |
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Mutation data file = broad_values_by_arm.mutsig.cluster.txt
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Clinical data file = THCA.clin.merged.picked.txt
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Number of patients = 182
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Number of significantly arm-level cnvs = 28
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Number of selected clinical features = 6
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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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.