This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.
Testing the association between copy number variation 2 focal events and 8 molecular subtypes across 66 patients, 3 significant findings detected with P value < 0.05 and Q value < 0.25.
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amp_8q11.23 cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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amp_15q22.31 cnv correlated to 'MRNASEQ_CNMF'.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
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nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | |
amp 8q11 23 | 19 (29%) | 47 |
0.32 (1.00) |
0.63 (1.00) |
0.00323 (0.0516) |
0.00406 (0.0608) |
1 (1.00) |
1 (1.00) |
0.882 (1.00) |
0.4 (1.00) |
amp 15q22 31 | 23 (35%) | 43 |
0.0522 (0.626) |
0.551 (1.00) |
0.00679 (0.0951) |
0.0248 (0.322) |
0.501 (1.00) |
0.146 (1.00) |
0.93 (1.00) |
0.444 (1.00) |
P value = 0.00323 (Fisher's exact test), Q value = 0.052
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
AMP PEAK 1(8Q11.23) MUTATED | 3 | 13 | 2 | 1 |
AMP PEAK 1(8Q11.23) WILD-TYPE | 16 | 9 | 13 | 9 |
P value = 0.00406 (Chi-square test), Q value = 0.061
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 10 | 10 | 17 | 6 | 23 |
AMP PEAK 1(8Q11.23) MUTATED | 2 | 2 | 11 | 0 | 4 |
AMP PEAK 1(8Q11.23) WILD-TYPE | 8 | 8 | 6 | 6 | 19 |
P value = 0.00679 (Fisher's exact test), Q value = 0.095
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 19 | 22 | 15 | 10 |
AMP PEAK 2(15Q22.31) MUTATED | 5 | 13 | 5 | 0 |
AMP PEAK 2(15Q22.31) WILD-TYPE | 14 | 9 | 10 | 10 |
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Copy number data file = transformed.cor.cli.txt
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Molecular subtype file = KICH-TP.transferedmergedcluster.txt
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Number of patients = 66
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Number of significantly focal cnvs = 2
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Number of molecular subtypes = 8
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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 multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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.