This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 29 arm-level results and 6 clinical features across 214 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 29 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 |
RADIATIONEXPOSURE | ||
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 | 6 (3%) | 208 |
1 (1.00) |
0.426 (1.00) |
0.644 (1.00) |
0.285 (1.00) |
0.337 (1.00) |
1 (1.00) |
4p gain | 4 (2%) | 210 |
0.0143 (1.00) |
0.119 (1.00) |
1 (1.00) |
0.783 (1.00) |
0.239 (1.00) |
1 (1.00) |
4q gain | 4 (2%) | 210 |
0.0143 (1.00) |
0.119 (1.00) |
1 (1.00) |
0.783 (1.00) |
0.239 (1.00) |
1 (1.00) |
5p gain | 7 (3%) | 207 |
0.0143 (1.00) |
0.0768 (1.00) |
1 (1.00) |
0.492 (1.00) |
0.382 (1.00) |
1 (1.00) |
5q gain | 7 (3%) | 207 |
0.0143 (1.00) |
0.0768 (1.00) |
1 (1.00) |
0.492 (1.00) |
0.382 (1.00) |
1 (1.00) |
7p gain | 9 (4%) | 205 |
1 (1.00) |
0.0815 (1.00) |
1 (1.00) |
0.324 (1.00) |
1 (1.00) |
1 (1.00) |
7q gain | 11 (5%) | 203 |
1 (1.00) |
0.0464 (1.00) |
0.734 (1.00) |
0.124 (1.00) |
1 (1.00) |
1 (1.00) |
12p gain | 7 (3%) | 207 |
1 (1.00) |
0.36 (1.00) |
0.682 (1.00) |
0.492 (1.00) |
1 (1.00) |
1 (1.00) |
12q gain | 7 (3%) | 207 |
1 (1.00) |
0.36 (1.00) |
0.682 (1.00) |
0.492 (1.00) |
1 (1.00) |
1 (1.00) |
14q gain | 4 (2%) | 210 |
1 (1.00) |
0.549 (1.00) |
0.574 (1.00) |
0.783 (1.00) |
1 (1.00) |
1 (1.00) |
16p gain | 7 (3%) | 207 |
1 (1.00) |
0.508 (1.00) |
0.196 (1.00) |
0.449 (1.00) |
1 (1.00) |
1 (1.00) |
16q gain | 5 (2%) | 209 |
1 (1.00) |
0.344 (1.00) |
0.333 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
17p gain | 6 (3%) | 208 |
1 (1.00) |
0.54 (1.00) |
0.341 (1.00) |
0.564 (1.00) |
1 (1.00) |
1 (1.00) |
17q gain | 7 (3%) | 207 |
1 (1.00) |
0.75 (1.00) |
0.196 (1.00) |
0.794 (1.00) |
1 (1.00) |
1 (1.00) |
19q gain | 3 (1%) | 211 |
0.0143 (1.00) |
0.0178 (1.00) |
1 (1.00) |
0.528 (1.00) |
0.185 (1.00) |
1 (1.00) |
20p gain | 3 (1%) | 211 |
1 (1.00) |
0.59 (1.00) |
0.574 (1.00) |
0.528 (1.00) |
1 (1.00) |
1 (1.00) |
20q gain | 3 (1%) | 211 |
1 (1.00) |
0.59 (1.00) |
0.574 (1.00) |
0.528 (1.00) |
1 (1.00) |
1 (1.00) |
2p loss | 6 (3%) | 208 |
1 (1.00) |
0.196 (1.00) |
1 (1.00) |
0.251 (1.00) |
1 (1.00) |
1 (1.00) |
2q loss | 5 (2%) | 209 |
1 (1.00) |
0.0272 (1.00) |
1 (1.00) |
0.107 (1.00) |
1 (1.00) |
1 (1.00) |
3q loss | 3 (1%) | 211 |
1 (1.00) |
0.204 (1.00) |
1 (1.00) |
0.0837 (1.00) |
1 (1.00) |
1 (1.00) |
9q loss | 4 (2%) | 210 |
1 (1.00) |
0.079 (1.00) |
1 (1.00) |
0.207 (1.00) |
0.239 (1.00) |
0.181 (1.00) |
11p loss | 4 (2%) | 210 |
0.0143 (1.00) |
0.0302 (1.00) |
0.265 (1.00) |
0.259 (1.00) |
0.239 (1.00) |
1 (1.00) |
11q loss | 5 (2%) | 209 |
0.0143 (1.00) |
0.0181 (1.00) |
0.103 (1.00) |
0.107 (1.00) |
0.289 (1.00) |
1 (1.00) |
13q loss | 7 (3%) | 207 |
0.0143 (1.00) |
0.133 (1.00) |
0.372 (1.00) |
0.0225 (1.00) |
0.382 (1.00) |
0.0283 (1.00) |
17p loss | 3 (1%) | 211 |
1 (1.00) |
0.851 (1.00) |
0.574 (1.00) |
0.528 (1.00) |
0.0115 (1.00) |
1 (1.00) |
18p loss | 3 (1%) | 211 |
1 (1.00) |
0.95 (1.00) |
0.574 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
18q loss | 3 (1%) | 211 |
1 (1.00) |
0.95 (1.00) |
0.574 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
21q loss | 4 (2%) | 210 |
1 (1.00) |
0.0044 (0.765) |
0.265 (1.00) |
0.783 (1.00) |
1 (1.00) |
1 (1.00) |
22q loss | 29 (14%) | 185 |
1 (1.00) |
0.634 (1.00) |
0.491 (1.00) |
0.0727 (1.00) |
0.225 (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-TP.clin.merged.picked.txt
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Number of patients = 214
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Number of significantly arm-level cnvs = 29
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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.