This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 46 focal events and 8 clinical features across 90 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 |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
GENDER | RACE | ETHNICITY | ||
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 1q22 | 17 (19%) | 73 |
0.00193 (0.71) |
0.595 (1.00) |
0.685 (1.00) |
0.687 (1.00) |
0.679 (1.00) |
0.779 (1.00) |
0.496 (1.00) |
0.618 (1.00) |
amp 4p16 3 | 41 (46%) | 49 |
0.286 (1.00) |
0.789 (1.00) |
0.934 (1.00) |
0.972 (1.00) |
0.75 (1.00) |
0.505 (1.00) |
1 (1.00) |
0.452 (1.00) |
amp 4q35 1 | 29 (32%) | 61 |
0.05 (1.00) |
0.604 (1.00) |
0.213 (1.00) |
0.333 (1.00) |
0.159 (1.00) |
0.164 (1.00) |
1 (1.00) |
1 (1.00) |
amp 5p15 33 | 65 (72%) | 25 |
0.931 (1.00) |
0.675 (1.00) |
0.583 (1.00) |
0.59 (1.00) |
0.721 (1.00) |
0.469 (1.00) |
0.0831 (1.00) |
0.402 (1.00) |
amp 5q35 3 | 63 (70%) | 27 |
0.151 (1.00) |
0.685 (1.00) |
0.77 (1.00) |
0.905 (1.00) |
1 (1.00) |
0.631 (1.00) |
1 (1.00) |
0.691 (1.00) |
amp 6p21 31 | 19 (21%) | 71 |
0.655 (1.00) |
0.00597 (1.00) |
0.863 (1.00) |
0.636 (1.00) |
0.68 (1.00) |
0.188 (1.00) |
0.1 (1.00) |
0.382 (1.00) |
amp 6q24 3 | 19 (21%) | 71 |
0.881 (1.00) |
0.355 (1.00) |
0.724 (1.00) |
0.365 (1.00) |
0.115 (1.00) |
0.792 (1.00) |
0.0906 (1.00) |
0.651 (1.00) |
amp 7p22 1 | 54 (60%) | 36 |
0.756 (1.00) |
0.683 (1.00) |
0.0909 (1.00) |
0.0962 (1.00) |
0.305 (1.00) |
1 (1.00) |
1 (1.00) |
0.699 (1.00) |
amp 9q31 3 | 34 (38%) | 56 |
0.0179 (1.00) |
0.861 (1.00) |
0.0253 (1.00) |
0.0774 (1.00) |
0.0413 (1.00) |
0.498 (1.00) |
1 (1.00) |
0.443 (1.00) |
amp 12q14 1 | 70 (78%) | 20 |
0.571 (1.00) |
0.614 (1.00) |
0.889 (1.00) |
0.874 (1.00) |
0.683 (1.00) |
0.791 (1.00) |
0.543 (1.00) |
0.168 (1.00) |
amp 14q11 2 | 27 (30%) | 63 |
0.428 (1.00) |
0.067 (1.00) |
0.382 (1.00) |
0.395 (1.00) |
0.0585 (1.00) |
0.631 (1.00) |
0.651 (1.00) |
0.41 (1.00) |
amp 16p13 3 | 50 (56%) | 40 |
0.433 (1.00) |
0.968 (1.00) |
0.796 (1.00) |
0.924 (1.00) |
1 (1.00) |
0.119 (1.00) |
0.723 (1.00) |
1 (1.00) |
amp 16q22 1 | 56 (62%) | 34 |
0.689 (1.00) |
0.68 (1.00) |
0.685 (1.00) |
0.66 (1.00) |
0.737 (1.00) |
0.257 (1.00) |
0.0521 (1.00) |
1 (1.00) |
amp 16q24 2 | 49 (54%) | 41 |
0.189 (1.00) |
0.903 (1.00) |
0.739 (1.00) |
0.524 (1.00) |
1 (1.00) |
0.187 (1.00) |
0.732 (1.00) |
0.699 (1.00) |
amp 17q25 3 | 18 (20%) | 72 |
0.557 (1.00) |
0.232 (1.00) |
0.788 (1.00) |
0.491 (1.00) |
0.68 (1.00) |
0.588 (1.00) |
0.476 (1.00) |
1 (1.00) |
amp 19p13 12 | 58 (64%) | 32 |
0.32 (1.00) |
0.129 (1.00) |
0.137 (1.00) |
0.188 (1.00) |
0.484 (1.00) |
1 (1.00) |
1 (1.00) |
0.226 (1.00) |
amp 19q12 | 56 (62%) | 34 |
0.096 (1.00) |
0.0457 (1.00) |
0.0829 (1.00) |
0.12 (1.00) |
0.737 (1.00) |
0.498 (1.00) |
1 (1.00) |
0.226 (1.00) |
amp xp11 22 | 49 (54%) | 41 |
0.901 (1.00) |
0.906 (1.00) |
0.67 (1.00) |
0.859 (1.00) |
0.502 (1.00) |
0.505 (1.00) |
1 (1.00) |
0.0382 (1.00) |
amp xq28 | 46 (51%) | 44 |
0.277 (1.00) |
0.707 (1.00) |
0.883 (1.00) |
0.935 (1.00) |
1 (1.00) |
1 (1.00) |
0.743 (1.00) |
1 (1.00) |
del 1p36 23 | 38 (42%) | 52 |
0.246 (1.00) |
0.49 (1.00) |
0.616 (1.00) |
0.467 (1.00) |
0.736 (1.00) |
0.823 (1.00) |
0.509 (1.00) |
0.41 (1.00) |
del 1q43 | 18 (20%) | 72 |
0.936 (1.00) |
0.948 (1.00) |
0.635 (1.00) |
0.177 (1.00) |
0.399 (1.00) |
0.782 (1.00) |
1 (1.00) |
0.286 (1.00) |
del 2q22 1 | 18 (20%) | 72 |
0.0841 (1.00) |
0.948 (1.00) |
0.432 (1.00) |
0.735 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
del 2q37 3 | 21 (23%) | 69 |
0.5 (1.00) |
0.8 (1.00) |
0.186 (1.00) |
0.978 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.286 (1.00) |
del 3q13 31 | 25 (28%) | 65 |
0.164 (1.00) |
0.474 (1.00) |
0.359 (1.00) |
0.658 (1.00) |
1 (1.00) |
0.0464 (1.00) |
0.32 (1.00) |
0.382 (1.00) |
del 4q34 3 | 25 (28%) | 65 |
0.00774 (1.00) |
0.479 (1.00) |
0.0968 (1.00) |
0.0874 (1.00) |
1 (1.00) |
1 (1.00) |
0.632 (1.00) |
1 (1.00) |
del 4q34 3 | 28 (31%) | 62 |
0.0245 (1.00) |
0.717 (1.00) |
0.205 (1.00) |
0.168 (1.00) |
1 (1.00) |
0.815 (1.00) |
0.65 (1.00) |
0.661 (1.00) |
del 4q35 1 | 30 (33%) | 60 |
0.0249 (1.00) |
0.535 (1.00) |
0.262 (1.00) |
0.205 (1.00) |
1 (1.00) |
0.485 (1.00) |
0.687 (1.00) |
0.672 (1.00) |
del 6p24 3 | 20 (22%) | 70 |
0.376 (1.00) |
0.197 (1.00) |
0.225 (1.00) |
0.759 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
del 6q26 | 21 (23%) | 69 |
0.225 (1.00) |
0.116 (1.00) |
0.0222 (1.00) |
0.0453 (1.00) |
0.697 (1.00) |
0.301 (1.00) |
1 (1.00) |
1 (1.00) |
del 7q36 3 | 11 (12%) | 79 |
0.00945 (1.00) |
0.402 (1.00) |
0.133 (1.00) |
0.0452 (1.00) |
1 (1.00) |
1 (1.00) |
0.34 (1.00) |
1 (1.00) |
del 9p23 | 24 (27%) | 66 |
0.0324 (1.00) |
0.749 (1.00) |
1 (1.00) |
0.744 (1.00) |
0.444 (1.00) |
0.803 (1.00) |
1 (1.00) |
0.661 (1.00) |
del 9p21 3 | 27 (30%) | 63 |
0.0282 (1.00) |
0.35 (1.00) |
0.955 (1.00) |
0.949 (1.00) |
0.27 (1.00) |
1 (1.00) |
0.699 (1.00) |
0.672 (1.00) |
del 10q23 1 | 11 (12%) | 79 |
0.758 (1.00) |
0.242 (1.00) |
0.867 (1.00) |
0.522 (1.00) |
0.607 (1.00) |
0.742 (1.00) |
0.366 (1.00) |
1 (1.00) |
del 11p15 5 | 27 (30%) | 63 |
0.394 (1.00) |
0.609 (1.00) |
0.495 (1.00) |
0.981 (1.00) |
0.139 (1.00) |
0.23 (1.00) |
1 (1.00) |
1 (1.00) |
del 11q14 1 | 25 (28%) | 65 |
0.462 (1.00) |
0.202 (1.00) |
0.117 (1.00) |
0.426 (1.00) |
1 (1.00) |
0.322 (1.00) |
1 (1.00) |
1 (1.00) |
del 12q14 2 | 5 (6%) | 85 |
0.0305 (1.00) |
0.311 (1.00) |
0.393 (1.00) |
0.466 (1.00) |
1 (1.00) |
0.656 (1.00) |
1 (1.00) |
1 (1.00) |
del 13q14 2 | 42 (47%) | 48 |
0.136 (1.00) |
0.269 (1.00) |
0.202 (1.00) |
0.695 (1.00) |
0.75 (1.00) |
0.828 (1.00) |
0.498 (1.00) |
0.691 (1.00) |
del 14q21 2 | 20 (22%) | 70 |
0.639 (1.00) |
0.58 (1.00) |
0.815 (1.00) |
0.893 (1.00) |
0.11 (1.00) |
0.599 (1.00) |
0.234 (1.00) |
0.349 (1.00) |
del 16p13 3 | 7 (8%) | 83 |
0.106 (1.00) |
0.386 (1.00) |
0.614 (1.00) |
0.538 (1.00) |
0.584 (1.00) |
1 (1.00) |
0.0796 (1.00) |
0.14 (1.00) |
del 16q23 1 | 11 (12%) | 79 |
0.00371 (1.00) |
0.108 (1.00) |
0.357 (1.00) |
0.158 (1.00) |
0.35 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
del 17q11 2 | 24 (27%) | 66 |
0.0232 (1.00) |
0.975 (1.00) |
0.192 (1.00) |
0.097 (1.00) |
0.706 (1.00) |
0.0243 (1.00) |
1 (1.00) |
1 (1.00) |
del 17q21 31 | 26 (29%) | 64 |
0.145 (1.00) |
0.742 (1.00) |
0.379 (1.00) |
0.286 (1.00) |
1 (1.00) |
0.055 (1.00) |
1 (1.00) |
0.657 (1.00) |
del 17q24 2 | 24 (27%) | 66 |
0.0223 (1.00) |
0.971 (1.00) |
0.0113 (1.00) |
0.306 (1.00) |
0.26 (1.00) |
0.0802 (1.00) |
1 (1.00) |
1 (1.00) |
del 18q21 2 | 36 (40%) | 54 |
0.944 (1.00) |
0.556 (1.00) |
0.584 (1.00) |
0.919 (1.00) |
0.735 (1.00) |
0.118 (1.00) |
0.281 (1.00) |
1 (1.00) |
del 20p12 1 | 12 (13%) | 78 |
0.112 (1.00) |
0.357 (1.00) |
0.456 (1.00) |
0.426 (1.00) |
0.35 (1.00) |
0.206 (1.00) |
0.366 (1.00) |
0.211 (1.00) |
del 22q12 1 | 50 (56%) | 40 |
0.147 (1.00) |
0.0943 (1.00) |
0.184 (1.00) |
0.147 (1.00) |
0.745 (1.00) |
0.267 (1.00) |
1 (1.00) |
0.243 (1.00) |
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Copy number data file = transformed.cor.cli.txt
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Clinical data file = ACC-TP.merged_data.txt
-
Number of patients = 90
-
Number of significantly focal cnvs = 46
-
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.