This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.
Testing the association between copy number variation 29 focal events and 3 molecular subtypes across 28 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.
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No focal cnvs related to molecuar subtypes.
Table 1. Get Full Table Overview of the association between significant copy number variation of 29 focal events and 3 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, no significant finding detected.
|
Clinical Features |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
||
| nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
| 1p | 4 (14%) | 24 |
0.478 (1.00) |
1 (1.00) |
0.601 (1.00) |
| 1q | 5 (18%) | 23 |
0.823 (1.00) |
1 (1.00) |
1 (1.00) |
| 2p | 4 (14%) | 24 |
0.478 (1.00) |
1 (1.00) |
1 (1.00) |
| 2q | 4 (14%) | 24 |
0.478 (1.00) |
1 (1.00) |
1 (1.00) |
| 3p | 5 (18%) | 23 |
0.823 (1.00) |
1 (1.00) |
1 (1.00) |
| 3q | 6 (21%) | 22 |
0.692 (1.00) |
1 (1.00) |
0.634 (1.00) |
| 6p | 4 (14%) | 24 |
0.478 (1.00) |
1 (1.00) |
1 (1.00) |
| 6q | 5 (18%) | 23 |
0.823 (1.00) |
1 (1.00) |
0.626 (1.00) |
| 7p | 8 (29%) | 20 |
0.287 (1.00) |
1 (1.00) |
0.4 (1.00) |
| 7q | 7 (25%) | 21 |
0.616 (1.00) |
0.67 (1.00) |
0.207 (1.00) |
| 8p | 6 (21%) | 22 |
0.692 (1.00) |
0.0691 (1.00) |
0.147 (1.00) |
| 8q | 4 (14%) | 24 |
1 (1.00) |
0.311 (1.00) |
0.601 (1.00) |
| 9p | 3 (11%) | 25 |
1 (1.00) |
1 (1.00) |
0.533 (1.00) |
| 10p | 4 (14%) | 24 |
0.478 (1.00) |
0.311 (1.00) |
0.601 (1.00) |
| 10q | 3 (11%) | 25 |
1 (1.00) |
0.0873 (1.00) |
0.284 (1.00) |
| 11p | 4 (14%) | 24 |
0.478 (1.00) |
0.6 (1.00) |
0.265 (1.00) |
| 11q | 8 (29%) | 20 |
0.547 (1.00) |
0.686 (1.00) |
0.194 (1.00) |
| 12p | 5 (18%) | 23 |
0.823 (1.00) |
0.639 (1.00) |
0.626 (1.00) |
| 12q | 5 (18%) | 23 |
0.823 (1.00) |
0.639 (1.00) |
0.626 (1.00) |
| 13q | 3 (11%) | 25 |
0.179 (1.00) |
0.583 (1.00) |
0.284 (1.00) |
| 15q | 6 (21%) | 22 |
0.11 (1.00) |
0.372 (1.00) |
0.147 (1.00) |
| 16p | 6 (21%) | 22 |
0.563 (1.00) |
0.655 (1.00) |
1 (1.00) |
| 16q | 8 (29%) | 20 |
0.175 (1.00) |
0.686 (1.00) |
1 (1.00) |
| 17p | 4 (14%) | 24 |
1 (1.00) |
1 (1.00) |
1 (1.00) |
| 18p | 7 (25%) | 21 |
0.616 (1.00) |
0.396 (1.00) |
1 (1.00) |
| 18q | 7 (25%) | 21 |
0.616 (1.00) |
0.396 (1.00) |
1 (1.00) |
| 20p | 3 (11%) | 25 |
1 (1.00) |
0.583 (1.00) |
1 (1.00) |
| 21q | 7 (25%) | 21 |
1 (1.00) |
0.67 (1.00) |
0.674 (1.00) |
| xq | 6 (21%) | 22 |
0.0103 (0.897) |
1 (1.00) |
1 (1.00) |
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Copy number data file = transformed.cor.cli.txt
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Molecular subtype file = DLBC-TP.transferedmergedcluster.txt
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Number of patients = 28
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Number of significantly focal cnvs = 29
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Number of molecular subtypes = 3
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Exclude genes that fewer than K tumors have alterations, 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.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.