This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 62 focal events and 2 clinical features across 56 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 |
AGE | ||
nCNV (%) | nWild-Type | logrank test | t-test | |
amp 1q22 | 42 (75%) | 14 |
0.85 (1.00) |
0.366 (1.00) |
amp 2p14 | 28 (50%) | 28 |
0.253 (1.00) |
0.47 (1.00) |
amp 2q13 | 29 (52%) | 27 |
0.716 (1.00) |
0.221 (1.00) |
amp 3p25 1 | 20 (36%) | 36 |
0.0949 (1.00) |
0.468 (1.00) |
amp 3q26 2 | 37 (66%) | 19 |
0.534 (1.00) |
0.404 (1.00) |
amp 4p16 3 | 25 (45%) | 31 |
0.116 (1.00) |
0.187 (1.00) |
amp 5p13 2 | 26 (46%) | 30 |
0.884 (1.00) |
0.958 (1.00) |
amp 6p24 2 | 37 (66%) | 19 |
0.0753 (1.00) |
0.0983 (1.00) |
amp 8p11 21 | 33 (59%) | 23 |
0.681 (1.00) |
0.0671 (1.00) |
amp 8q11 23 | 38 (68%) | 18 |
0.916 (1.00) |
0.204 (1.00) |
amp 8q24 21 | 42 (75%) | 14 |
0.416 (1.00) |
0.847 (1.00) |
amp 8q24 21 | 40 (71%) | 16 |
0.115 (1.00) |
0.445 (1.00) |
amp 10q22 2 | 26 (46%) | 30 |
0.375 (1.00) |
0.15 (1.00) |
amp 11q13 1 | 19 (34%) | 37 |
0.151 (1.00) |
0.546 (1.00) |
amp 12q12 | 22 (39%) | 34 |
0.415 (1.00) |
0.438 (1.00) |
amp 12q15 | 17 (30%) | 39 |
0.999 (1.00) |
0.122 (1.00) |
amp 13q31 3 | 25 (45%) | 31 |
0.703 (1.00) |
0.381 (1.00) |
amp 16p11 2 | 20 (36%) | 36 |
0.403 (1.00) |
0.108 (1.00) |
amp 17q12 | 27 (48%) | 29 |
0.499 (1.00) |
0.773 (1.00) |
amp 17q25 1 | 32 (57%) | 24 |
0.789 (1.00) |
0.0577 (1.00) |
amp 19p13 2 | 19 (34%) | 37 |
0.987 (1.00) |
0.487 (1.00) |
amp 19q12 | 45 (80%) | 11 |
0.484 (1.00) |
0.543 (1.00) |
amp 20q11 21 | 48 (86%) | 8 |
0.353 (1.00) |
0.495 (1.00) |
amp 20q11 21 | 48 (86%) | 8 |
0.802 (1.00) |
0.985 (1.00) |
amp xp11 21 | 28 (50%) | 28 |
0.598 (1.00) |
0.00929 (1.00) |
del 1p36 21 | 19 (34%) | 37 |
0.843 (1.00) |
0.173 (1.00) |
del 2q22 1 | 11 (20%) | 45 |
0.089 (1.00) |
0.92 (1.00) |
del 3p21 1 | 37 (66%) | 19 |
0.867 (1.00) |
0.744 (1.00) |
del 3p14 1 | 30 (54%) | 26 |
0.99 (1.00) |
0.694 (1.00) |
del 3q13 31 | 19 (34%) | 37 |
0.448 (1.00) |
0.523 (1.00) |
del 4q22 1 | 37 (66%) | 19 |
0.932 (1.00) |
0.766 (1.00) |
del 4q34 3 | 37 (66%) | 19 |
0.454 (1.00) |
0.817 (1.00) |
del 5q11 2 | 26 (46%) | 30 |
0.464 (1.00) |
0.361 (1.00) |
del 6q26 | 10 (18%) | 46 |
0.526 (1.00) |
0.866 (1.00) |
del 7q11 22 | 12 (21%) | 44 |
0.265 (1.00) |
0.817 (1.00) |
del 7q36 2 | 20 (36%) | 36 |
0.0828 (1.00) |
0.671 (1.00) |
del 8p21 3 | 32 (57%) | 24 |
0.323 (1.00) |
0.443 (1.00) |
del 9p23 | 34 (61%) | 22 |
0.661 (1.00) |
0.0357 (1.00) |
del 9q21 13 | 39 (70%) | 17 |
0.511 (1.00) |
0.676 (1.00) |
del 9q33 3 | 38 (68%) | 18 |
0.121 (1.00) |
0.28 (1.00) |
del 10q21 1 | 18 (32%) | 38 |
0.817 (1.00) |
0.965 (1.00) |
del 10q23 31 | 20 (36%) | 36 |
0.602 (1.00) |
0.296 (1.00) |
del 11p15 5 | 25 (45%) | 31 |
0.114 (1.00) |
0.784 (1.00) |
del 11q14 1 | 26 (46%) | 30 |
0.965 (1.00) |
0.0655 (1.00) |
del 11q24 2 | 27 (48%) | 29 |
0.532 (1.00) |
0.332 (1.00) |
del 12q23 1 | 20 (36%) | 36 |
0.134 (1.00) |
0.0621 (1.00) |
del 12q24 31 | 20 (36%) | 36 |
0.225 (1.00) |
0.251 (1.00) |
del 13q12 11 | 30 (54%) | 26 |
0.434 (1.00) |
0.263 (1.00) |
del 13q14 2 | 32 (57%) | 24 |
0.729 (1.00) |
0.834 (1.00) |
del 14q21 1 | 28 (50%) | 28 |
0.432 (1.00) |
0.3 (1.00) |
del 15q15 1 | 43 (77%) | 13 |
0.393 (1.00) |
0.201 (1.00) |
del 16p13 3 | 33 (59%) | 23 |
0.872 (1.00) |
0.787 (1.00) |
del 16q23 1 | 39 (70%) | 17 |
0.0164 (1.00) |
0.24 (1.00) |
del 17p13 1 | 42 (75%) | 14 |
0.59 (1.00) |
0.817 (1.00) |
del 17q21 32 | 19 (34%) | 37 |
0.0271 (1.00) |
0.506 (1.00) |
del 18q22 2 | 26 (46%) | 30 |
0.458 (1.00) |
0.481 (1.00) |
del 19p13 3 | 47 (84%) | 9 |
0.236 (1.00) |
0.331 (1.00) |
del 19q13 33 | 17 (30%) | 39 |
0.306 (1.00) |
0.855 (1.00) |
del 20p12 1 | 9 (16%) | 47 |
0.844 (1.00) |
0.967 (1.00) |
del 22q13 31 | 40 (71%) | 16 |
0.651 (1.00) |
0.421 (1.00) |
del xp21 1 | 18 (32%) | 38 |
0.225 (1.00) |
0.34 (1.00) |
del xq25 | 23 (41%) | 33 |
0.821 (1.00) |
0.323 (1.00) |
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Copy number data file = transformed.cor.cli.txt
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Clinical data file = UCS-TP.merged_data.txt
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Number of patients = 56
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Number of significantly focal cnvs = 62
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Number of selected clinical features = 2
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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 continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.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.