This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 23 focal events and 8 clinical features across 36 patients, no significant finding detected with Q value < 0.25.
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No focal cnvs related to clinical features.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER | RACE | ||
nCNV (%) | nWild-Type | logrank test | Wilcoxon-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 | |
amp 1p22 3 | 15 (42%) | 21 |
0.547 (0.966) |
0.205 (0.857) |
0.21 (0.857) |
0.372 (0.879) |
0.148 (0.82) |
1 (1.00) |
0.175 (0.82) |
1 (1.00) |
amp 1q22 | 24 (67%) | 12 |
0.182 (0.82) |
0.47 (0.908) |
0.0141 (0.438) |
0.00679 (0.416) |
0.631 (0.966) |
1 (1.00) |
0.481 (0.908) |
1 (1.00) |
amp 11q13 3 | 8 (22%) | 28 |
0.0683 (0.606) |
0.128 (0.82) |
0.373 (0.879) |
0.564 (0.966) |
0.241 (0.857) |
0.282 (0.879) |
0.709 (1.00) |
0.086 (0.633) |
amp 12q13 2 | 10 (28%) | 26 |
0.0115 (0.438) |
0.986 (1.00) |
1 (1.00) |
0.398 (0.904) |
1 (1.00) |
1 (1.00) |
0.285 (0.879) |
0.00624 (0.416) |
del 1p36 21 | 30 (83%) | 6 |
0.926 (1.00) |
0.966 (1.00) |
0.182 (0.82) |
0.0692 (0.606) |
1 (1.00) |
1 (1.00) |
0.672 (0.979) |
0.187 (0.82) |
del 3p25 3 | 28 (78%) | 8 |
0.222 (0.857) |
0.834 (1.00) |
0.0834 (0.633) |
0.00638 (0.416) |
0.0619 (0.6) |
0.282 (0.879) |
0.709 (1.00) |
0.478 (0.908) |
del 3p13 | 28 (78%) | 8 |
0.512 (0.923) |
0.246 (0.857) |
0.084 (0.633) |
0.116 (0.818) |
0.241 (0.857) |
0.0519 (0.6) |
0.422 (0.908) |
0.476 (0.908) |
del 4q34 3 | 23 (64%) | 13 |
0.585 (0.966) |
0.152 (0.82) |
0.444 (0.908) |
0.0498 (0.6) |
0.35 (0.879) |
1 (1.00) |
0.301 (0.879) |
0.477 (0.908) |
del 5q13 3 | 8 (22%) | 28 |
0.472 (0.908) |
0.924 (1.00) |
0.334 (0.879) |
1 (1.00) |
0.173 (0.82) |
0.0519 (0.6) |
0.422 (0.908) |
0.305 (0.879) |
del 6q13 | 21 (58%) | 15 |
0.646 (0.966) |
0.76 (1.00) |
0.452 (0.908) |
0.458 (0.908) |
0.636 (0.966) |
1 (1.00) |
0.741 (1.00) |
0.779 (1.00) |
del 6q25 3 | 25 (69%) | 11 |
0.483 (0.908) |
0.236 (0.857) |
0.676 (0.979) |
0.79 (1.00) |
1 (1.00) |
1 (1.00) |
0.483 (0.908) |
0.187 (0.82) |
del 8p23 1 | 13 (36%) | 23 |
0.277 (0.879) |
0.382 (0.891) |
0.0782 (0.633) |
0.0167 (0.438) |
0.631 (0.966) |
0.63 (0.966) |
0.169 (0.82) |
1 (1.00) |
del 9p21 3 | 23 (64%) | 13 |
0.618 (0.966) |
0.921 (1.00) |
0.458 (0.908) |
0.309 (0.879) |
0.35 (0.879) |
0.36 (0.879) |
0.169 (0.82) |
0.596 (0.966) |
del 9q21 11 | 19 (53%) | 17 |
0.398 (0.904) |
0.0167 (0.438) |
0.567 (0.966) |
0.476 (0.908) |
0.636 (0.966) |
0.152 (0.82) |
1 (1.00) |
0.231 (0.857) |
del 10q26 12 | 12 (33%) | 24 |
0.781 (1.00) |
0.568 (0.966) |
0.47 (0.908) |
1 (1.00) |
0.296 (0.879) |
0.643 (0.966) |
0.729 (1.00) |
0.788 (1.00) |
del 11q25 | 13 (36%) | 23 |
0.0535 (0.6) |
0.339 (0.879) |
0.96 (1.00) |
0.243 (0.857) |
1 (1.00) |
1 (1.00) |
0.493 (0.917) |
1 (1.00) |
del 12q24 13 | 8 (22%) | 28 |
0.517 (0.923) |
0.505 (0.92) |
0.0554 (0.6) |
0.484 (0.908) |
0.0619 (0.6) |
0.0313 (0.6) |
0.257 (0.876) |
1 (1.00) |
del 13q21 32 | 16 (44%) | 20 |
0.226 (0.857) |
0.372 (0.879) |
0.315 (0.879) |
0.247 (0.857) |
0.344 (0.879) |
0.0574 (0.6) |
1 (1.00) |
0.613 (0.966) |
del 14q22 1 | 14 (39%) | 22 |
0.653 (0.969) |
0.673 (0.979) |
0.502 (0.92) |
0.798 (1.00) |
0.147 (0.82) |
0.63 (0.966) |
1 (1.00) |
1 (1.00) |
del 14q32 12 | 20 (56%) | 16 |
0.0432 (0.6) |
0.949 (1.00) |
0.358 (0.879) |
0.329 (0.879) |
0.148 (0.82) |
0.639 (0.966) |
0.737 (1.00) |
0.782 (1.00) |
del 14q32 11 | 20 (56%) | 16 |
0.0432 (0.6) |
0.949 (1.00) |
0.358 (0.879) |
0.329 (0.879) |
0.148 (0.82) |
0.639 (0.966) |
0.737 (1.00) |
0.78 (1.00) |
del 14q32 33 | 20 (56%) | 16 |
0.0432 (0.6) |
0.949 (1.00) |
0.356 (0.879) |
0.329 (0.879) |
0.148 (0.82) |
0.639 (0.966) |
0.737 (1.00) |
0.781 (1.00) |
del 16q23 1 | 7 (19%) | 29 |
0.954 (1.00) |
0.889 (1.00) |
0.824 (1.00) |
1 (1.00) |
1 (1.00) |
0.559 (0.966) |
1 (1.00) |
0.684 (0.984) |
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Copy number data file = all_lesions.txt from GISTIC pipeline
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Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CHOL-TP/15082395/transformed.cor.cli.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/CHOL-TP/15076818/CHOL-TP.merged_data.txt
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Number of patients = 36
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Number of significantly focal cnvs = 23
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Number of selected clinical features = 8
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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 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.