This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.
Testing the association between copy number variation 65 arm-level results and 2 molecular subtypes across 50 patients, 2 significant findings detected with Q value < 0.25.
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3q gain cnv correlated to 'CN_CNMF'.
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12p gain cnv correlated to 'CN_CNMF'.
Molecular subtypes |
CN CNMF |
METHLYATION CNMF |
||
nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | |
3q gain | 0 (0%) | 31 |
2.78e-05 (0.00361) |
0.00322 (0.406) |
12p gain | 0 (0%) | 33 |
0.00137 (0.177) |
0.0095 (1.00) |
1p gain | 0 (0%) | 47 |
0.449 (1.00) |
0.597 (1.00) |
1q gain | 0 (0%) | 38 |
0.0666 (1.00) |
1 (1.00) |
2p gain | 0 (0%) | 39 |
0.00591 (0.727) |
0.201 (1.00) |
2q gain | 0 (0%) | 43 |
0.0217 (1.00) |
0.0989 (1.00) |
3p gain | 0 (0%) | 44 |
0.0677 (1.00) |
0.29 (1.00) |
4p gain | 0 (0%) | 47 |
0.449 (1.00) |
0.794 (1.00) |
5p gain | 0 (0%) | 37 |
0.461 (1.00) |
0.317 (1.00) |
6p gain | 0 (0%) | 47 |
0.239 (1.00) |
1 (1.00) |
7p gain | 0 (0%) | 26 |
0.0835 (1.00) |
0.188 (1.00) |
7q gain | 0 (0%) | 35 |
0.241 (1.00) |
0.528 (1.00) |
8p gain | 0 (0%) | 35 |
0.241 (1.00) |
0.178 (1.00) |
8q gain | 0 (0%) | 26 |
0.552 (1.00) |
0.36 (1.00) |
9p gain | 0 (0%) | 47 |
0.239 (1.00) |
0.317 (1.00) |
9q gain | 0 (0%) | 44 |
0.213 (1.00) |
0.743 (1.00) |
10p gain | 0 (0%) | 44 |
0.868 (1.00) |
0.527 (1.00) |
10q gain | 0 (0%) | 47 |
0.0112 (1.00) |
1 (1.00) |
12q gain | 0 (0%) | 45 |
0.191 (1.00) |
0.289 (1.00) |
13q gain | 0 (0%) | 44 |
0.00312 (0.396) |
0.00365 (0.457) |
14q gain | 0 (0%) | 42 |
0.628 (1.00) |
0.167 (1.00) |
16p gain | 0 (0%) | 47 |
1 (1.00) |
0.317 (1.00) |
17p gain | 0 (0%) | 43 |
0.39 (1.00) |
0.08 (1.00) |
17q gain | 0 (0%) | 43 |
1 (1.00) |
0.575 (1.00) |
18p gain | 0 (0%) | 39 |
0.152 (1.00) |
0.333 (1.00) |
18q gain | 0 (0%) | 47 |
0.78 (1.00) |
1 (1.00) |
19q gain | 0 (0%) | 43 |
0.017 (1.00) |
0.242 (1.00) |
20p gain | 0 (0%) | 31 |
0.935 (1.00) |
0.526 (1.00) |
20q gain | 0 (0%) | 27 |
0.419 (1.00) |
0.439 (1.00) |
21q gain | 0 (0%) | 47 |
0.239 (1.00) |
0.597 (1.00) |
22q gain | 0 (0%) | 43 |
0.885 (1.00) |
0.575 (1.00) |
Xq gain | 0 (0%) | 42 |
0.886 (1.00) |
0.107 (1.00) |
3p loss | 0 (0%) | 30 |
0.661 (1.00) |
0.394 (1.00) |
3q loss | 0 (0%) | 47 |
0.449 (1.00) |
0.794 (1.00) |
4p loss | 0 (0%) | 32 |
0.0961 (1.00) |
0.0505 (1.00) |
4q loss | 0 (0%) | 36 |
0.115 (1.00) |
0.0211 (1.00) |
5p loss | 0 (0%) | 42 |
0.628 (1.00) |
0.246 (1.00) |
5q loss | 0 (0%) | 36 |
0.149 (1.00) |
0.0257 (1.00) |
6p loss | 0 (0%) | 42 |
0.886 (1.00) |
0.363 (1.00) |
6q loss | 0 (0%) | 47 |
0.78 (1.00) |
0.597 (1.00) |
7p loss | 0 (0%) | 47 |
0.449 (1.00) |
0.597 (1.00) |
8p loss | 0 (0%) | 40 |
0.739 (1.00) |
0.656 (1.00) |
8q loss | 0 (0%) | 46 |
0.159 (1.00) |
0.0388 (1.00) |
9p loss | 0 (0%) | 31 |
0.213 (1.00) |
0.236 (1.00) |
9q loss | 0 (0%) | 42 |
0.101 (1.00) |
0.167 (1.00) |
10p loss | 0 (0%) | 41 |
1 (1.00) |
0.573 (1.00) |
10q loss | 0 (0%) | 39 |
0.0614 (1.00) |
0.0237 (1.00) |
11p loss | 0 (0%) | 39 |
0.192 (1.00) |
0.0681 (1.00) |
11q loss | 0 (0%) | 36 |
0.00297 (0.38) |
0.0338 (1.00) |
12p loss | 0 (0%) | 43 |
0.773 (1.00) |
0.504 (1.00) |
12q loss | 0 (0%) | 45 |
0.613 (1.00) |
0.228 (1.00) |
13q loss | 0 (0%) | 36 |
0.0193 (1.00) |
0.0281 (1.00) |
14q loss | 0 (0%) | 44 |
1 (1.00) |
0.861 (1.00) |
15q loss | 0 (0%) | 41 |
0.804 (1.00) |
0.514 (1.00) |
16p loss | 0 (0%) | 42 |
0.0854 (1.00) |
0.0908 (1.00) |
16q loss | 0 (0%) | 41 |
0.00604 (0.737) |
0.408 (1.00) |
17p loss | 0 (0%) | 40 |
0.664 (1.00) |
0.00558 (0.692) |
18p loss | 0 (0%) | 40 |
0.228 (1.00) |
0.192 (1.00) |
18q loss | 0 (0%) | 34 |
0.861 (1.00) |
0.123 (1.00) |
19p loss | 0 (0%) | 46 |
1 (1.00) |
0.562 (1.00) |
19q loss | 0 (0%) | 47 |
0.78 (1.00) |
0.794 (1.00) |
20p loss | 0 (0%) | 45 |
0.719 (1.00) |
1 (1.00) |
21q loss | 0 (0%) | 27 |
1 (1.00) |
0.128 (1.00) |
22q loss | 0 (0%) | 44 |
0.545 (1.00) |
0.0636 (1.00) |
Xq loss | 0 (0%) | 47 |
1 (1.00) |
0.428 (1.00) |
P value = 2.78e-05 (Fisher's exact test), Q value = 0.0036
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 20 | 12 | 18 |
3Q GAIN CNV | 12 | 7 | 0 |
3Q GAIN WILD-TYPE | 8 | 5 | 18 |
P value = 0.00137 (Fisher's exact test), Q value = 0.18
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 20 | 12 | 18 |
12P GAIN CNV | 12 | 4 | 1 |
12P GAIN WILD-TYPE | 8 | 8 | 17 |
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Mutation data file = broad_values_by_arm.mutsig.cluster.txt
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Molecular subtypes file = ESCA-TP.transferedmergedcluster.txt
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Number of patients = 50
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Number of significantly arm-level cnvs = 65
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Number of molecular subtypes = 2
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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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.