This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.
Testing the association between copy number variation 38 arm-level results and molecular subtype 'METHLYATION_CNMF' across 20 patients, no significant finding detected with Q value < 0.25.
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No arm-level cnvs related to molecular subtypes.
Table 1. Get Full Table Overview of the association between significant copy number variation of 38 arm-level results and 1 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.
|
Molecular subtypes |
METHLYATION CNMF |
||
| nCNV (%) | nWild-Type | Fisher's exact test | |
| 1q gain | 0 (0%) | 16 |
0.569 (1.00) |
| 2p gain | 0 (0%) | 17 |
0.711 (1.00) |
| 3p gain | 0 (0%) | 16 |
1 (1.00) |
| 3q gain | 0 (0%) | 13 |
0.223 (1.00) |
| 5p gain | 0 (0%) | 14 |
1 (1.00) |
| 7p gain | 0 (0%) | 13 |
0.164 (1.00) |
| 7q gain | 0 (0%) | 14 |
1 (1.00) |
| 8p gain | 0 (0%) | 13 |
0.553 (1.00) |
| 8q gain | 0 (0%) | 9 |
0.835 (1.00) |
| 9q gain | 0 (0%) | 16 |
1 (1.00) |
| 10p gain | 0 (0%) | 16 |
0.0788 (1.00) |
| 12p gain | 0 (0%) | 11 |
0.0677 (1.00) |
| 14q gain | 0 (0%) | 16 |
0.569 (1.00) |
| 17p gain | 0 (0%) | 15 |
0.198 (1.00) |
| 17q gain | 0 (0%) | 15 |
0.147 (1.00) |
| 18p gain | 0 (0%) | 16 |
1 (1.00) |
| 20p gain | 0 (0%) | 10 |
1 (1.00) |
| 20q gain | 0 (0%) | 10 |
1 (1.00) |
| 21q gain | 0 (0%) | 17 |
1 (1.00) |
| 22q gain | 0 (0%) | 15 |
1 (1.00) |
| Xq gain | 0 (0%) | 16 |
1 (1.00) |
| 3p loss | 0 (0%) | 13 |
0.655 (1.00) |
| 4p loss | 0 (0%) | 14 |
0.51 (1.00) |
| 4q loss | 0 (0%) | 15 |
0.198 (1.00) |
| 5p loss | 0 (0%) | 16 |
0.569 (1.00) |
| 5q loss | 0 (0%) | 16 |
0.569 (1.00) |
| 6p loss | 0 (0%) | 14 |
0.51 (1.00) |
| 6q loss | 0 (0%) | 17 |
1 (1.00) |
| 9p loss | 0 (0%) | 17 |
0.344 (1.00) |
| 10p loss | 0 (0%) | 16 |
1 (1.00) |
| 10q loss | 0 (0%) | 17 |
0.711 (1.00) |
| 11p loss | 0 (0%) | 17 |
0.711 (1.00) |
| 13q loss | 0 (0%) | 13 |
0.223 (1.00) |
| 16q loss | 0 (0%) | 16 |
1 (1.00) |
| 18p loss | 0 (0%) | 14 |
0.408 (1.00) |
| 18q loss | 0 (0%) | 13 |
1 (1.00) |
| 21q loss | 0 (0%) | 10 |
0.443 (1.00) |
| 22q loss | 0 (0%) | 17 |
0.518 (1.00) |
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Mutation data file = broad_values_by_arm.mutsig.cluster.txt
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Molecular subtypes file = ESCA-TP.transferedmergedcluster.txt
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Number of patients = 20
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Number of significantly arm-level cnvs = 38
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Number of molecular subtypes = 1: 'METHLYATION_CNMF'
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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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.