This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Testing the association between copy number variation 24 arm-level events and 7 molecular subtypes across 28 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.
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No arm-level cnvs related to molecular subtypes.
Clinical Features |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
1q gain | 4 (14%) | 24 |
1 (1.00) |
1 (1.00) |
0.638 (1.00) |
0.326 (1.00) |
0.804 (1.00) |
0.279 (1.00) |
0.69 (1.00) |
3p gain | 5 (18%) | 23 |
1 (1.00) |
1 (1.00) |
0.673 (1.00) |
1 (1.00) |
0.439 (1.00) |
1 (1.00) |
0.0887 (1.00) |
3q gain | 6 (21%) | 22 |
1 (1.00) |
1 (1.00) |
0.515 (1.00) |
1 (1.00) |
0.541 (1.00) |
1 (1.00) |
0.196 (1.00) |
6p gain | 3 (11%) | 25 |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.596 (1.00) |
0.522 (1.00) |
0.751 (1.00) |
0.181 (1.00) |
7p gain | 8 (29%) | 20 |
0.686 (1.00) |
1 (1.00) |
0.459 (1.00) |
1 (1.00) |
0.56 (1.00) |
1 (1.00) |
0.0167 (1.00) |
7q gain | 7 (25%) | 21 |
1 (1.00) |
0.67 (1.00) |
0.123 (1.00) |
0.678 (1.00) |
0.507 (1.00) |
1 (1.00) |
0.0165 (1.00) |
10p gain | 3 (11%) | 25 |
1 (1.00) |
0.583 (1.00) |
0.763 (1.00) |
0.596 (1.00) |
0.889 (1.00) |
1 (1.00) |
0.181 (1.00) |
11p gain | 4 (14%) | 24 |
0.311 (1.00) |
0.6 (1.00) |
0.146 (1.00) |
0.0978 (1.00) |
0.547 (1.00) |
1 (1.00) |
1 (1.00) |
11q gain | 8 (29%) | 20 |
0.41 (1.00) |
0.686 (1.00) |
0.0873 (1.00) |
0.385 (1.00) |
0.12 (1.00) |
0.631 (1.00) |
0.876 (1.00) |
12p gain | 3 (11%) | 25 |
0.583 (1.00) |
0.583 (1.00) |
0.108 (1.00) |
1 (1.00) |
0.767 (1.00) |
1 (1.00) |
0.831 (1.00) |
12q gain | 4 (14%) | 24 |
0.311 (1.00) |
1 (1.00) |
0.145 (1.00) |
0.596 (1.00) |
0.549 (1.00) |
1 (1.00) |
0.967 (1.00) |
16p gain | 4 (14%) | 24 |
0.311 (1.00) |
0.6 (1.00) |
0.21 (1.00) |
0.596 (1.00) |
0.804 (1.00) |
0.276 (1.00) |
0.892 (1.00) |
16q gain | 4 (14%) | 24 |
0.0349 (1.00) |
0.6 (1.00) |
1 (1.00) |
1 (1.00) |
0.802 (1.00) |
1 (1.00) |
1 (1.00) |
18p gain | 5 (18%) | 23 |
1 (1.00) |
1 (1.00) |
0.676 (1.00) |
1 (1.00) |
0.857 (1.00) |
1 (1.00) |
0.0892 (1.00) |
18q gain | 5 (18%) | 23 |
1 (1.00) |
1 (1.00) |
0.676 (1.00) |
1 (1.00) |
0.857 (1.00) |
1 (1.00) |
0.0892 (1.00) |
21q gain | 6 (21%) | 22 |
1 (1.00) |
1 (1.00) |
0.425 (1.00) |
0.165 (1.00) |
0.122 (1.00) |
0.315 (1.00) |
0.193 (1.00) |
xq gain | 3 (11%) | 25 |
0.0873 (1.00) |
1 (1.00) |
0.385 (1.00) |
1 (1.00) |
0.764 (1.00) |
0.75 (1.00) |
0.978 (1.00) |
1p loss | 3 (11%) | 25 |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.596 (1.00) |
0.889 (1.00) |
1 (1.00) |
0.612 (1.00) |
6q loss | 3 (11%) | 25 |
0.583 (1.00) |
1 (1.00) |
0.387 (1.00) |
0.222 (1.00) |
0.488 (1.00) |
1 (1.00) |
0.828 (1.00) |
8p loss | 4 (14%) | 24 |
1 (1.00) |
0.311 (1.00) |
0.355 (1.00) |
0.326 (1.00) |
0.513 (1.00) |
1 (1.00) |
0.0661 (1.00) |
15q loss | 5 (18%) | 23 |
0.333 (1.00) |
0.639 (1.00) |
0.449 (1.00) |
0.648 (1.00) |
0.438 (1.00) |
1 (1.00) |
0.024 (1.00) |
16q loss | 4 (14%) | 24 |
1 (1.00) |
1 (1.00) |
0.641 (1.00) |
1 (1.00) |
0.863 (1.00) |
1 (1.00) |
0.435 (1.00) |
17p loss | 3 (11%) | 25 |
1 (1.00) |
1 (1.00) |
0.766 (1.00) |
1 (1.00) |
0.887 (1.00) |
0.75 (1.00) |
0.231 (1.00) |
xq loss | 3 (11%) | 25 |
0.0873 (1.00) |
0.583 (1.00) |
0.564 (1.00) |
0.596 (1.00) |
0.487 (1.00) |
0.0871 (1.00) |
0.341 (1.00) |
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Copy number data file = transformed.cor.cli.txt
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Molecular subtypes file = DLBC-TP.transferedmergedcluster.txt
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Number of patients = 28
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Number of significantly arm-level cnvs = 24
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Number of molecular subtypes = 7
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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.
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.