This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.
Testing the association between copy number variation of 53 peak regions and 2 molecular subtypes across 50 patients, 3 significant findings detected with Q value < 0.25.
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Amp Peak 4(3q29) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 13(11q13.3) cnvs correlated to 'CN_CNMF'.
Molecular subtypes |
CN CNMF |
METHLYATION CNMF |
||
nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | |
Amp Peak 4(3q29) | 0 (0%) | 12 |
0.000572 (0.0601) |
0.00223 (0.232) |
Amp Peak 13(11q13 3) | 0 (0%) | 17 |
0.000123 (0.013) |
0.0219 (1.00) |
Amp Peak 1(1p13 1) | 0 (0%) | 40 |
0.664 (1.00) |
0.481 (1.00) |
Amp Peak 2(1q25 2) | 0 (0%) | 27 |
0.0403 (1.00) |
0.508 (1.00) |
Amp Peak 3(2q14 2) | 0 (0%) | 33 |
0.645 (1.00) |
0.195 (1.00) |
Amp Peak 5(6p21 1) | 0 (0%) | 37 |
0.101 (1.00) |
1 (1.00) |
Amp Peak 6(6q12) | 0 (0%) | 40 |
0.291 (1.00) |
0.314 (1.00) |
Amp Peak 7(7p11 2) | 0 (0%) | 14 |
0.852 (1.00) |
0.18 (1.00) |
Amp Peak 8(7q21 3) | 0 (0%) | 15 |
0.114 (1.00) |
0.227 (1.00) |
Amp Peak 9(8p11 21) | 0 (0%) | 23 |
0.515 (1.00) |
0.756 (1.00) |
Amp Peak 10(8q24 21) | 0 (0%) | 7 |
0.0991 (1.00) |
0.137 (1.00) |
Amp Peak 11(10p11 21) | 0 (0%) | 35 |
0.628 (1.00) |
0.852 (1.00) |
Amp Peak 12(11p13) | 0 (0%) | 37 |
0.233 (1.00) |
1 (1.00) |
Amp Peak 14(12p13 33) | 0 (0%) | 24 |
0.0358 (1.00) |
0.0313 (1.00) |
Amp Peak 15(12p12 1) | 0 (0%) | 22 |
0.0661 (1.00) |
0.104 (1.00) |
Amp Peak 16(17q24 3) | 0 (0%) | 26 |
0.212 (1.00) |
0.201 (1.00) |
Amp Peak 17(18p11 32) | 0 (0%) | 32 |
0.389 (1.00) |
0.327 (1.00) |
Amp Peak 18(18q11 2) | 0 (0%) | 36 |
0.41 (1.00) |
0.044 (1.00) |
Amp Peak 19(19p13 2) | 0 (0%) | 38 |
0.284 (1.00) |
0.394 (1.00) |
Amp Peak 20(19q12) | 0 (0%) | 31 |
0.0859 (1.00) |
0.135 (1.00) |
Amp Peak 21(Xp11 4) | 0 (0%) | 40 |
0.291 (1.00) |
0.901 (1.00) |
Del Peak 1(1p35 2) | 0 (0%) | 35 |
1 (1.00) |
0.852 (1.00) |
Del Peak 2(1q44) | 0 (0%) | 42 |
0.485 (1.00) |
0.408 (1.00) |
Del Peak 3(2q22 1) | 0 (0%) | 39 |
0.426 (1.00) |
0.612 (1.00) |
Del Peak 4(2q37 2) | 0 (0%) | 37 |
0.461 (1.00) |
0.135 (1.00) |
Del Peak 5(3p14 2) | 0 (0%) | 8 |
0.0854 (1.00) |
0.279 (1.00) |
Del Peak 6(3q11 1) | 0 (0%) | 45 |
1 (1.00) |
0.84 (1.00) |
Del Peak 7(3q26 31) | 0 (0%) | 46 |
0.159 (1.00) |
0.0388 (1.00) |
Del Peak 8(4p15 2) | 0 (0%) | 21 |
0.296 (1.00) |
0.709 (1.00) |
Del Peak 9(4q22 1) | 0 (0%) | 29 |
0.584 (1.00) |
0.239 (1.00) |
Del Peak 10(5q11 2) | 0 (0%) | 20 |
0.44 (1.00) |
0.00275 (0.283) |
Del Peak 11(5q12 3) | 0 (0%) | 18 |
0.608 (1.00) |
0.0079 (0.783) |
Del Peak 12(6p25 3) | 0 (0%) | 30 |
0.875 (1.00) |
0.321 (1.00) |
Del Peak 13(6q26) | 0 (0%) | 36 |
0.568 (1.00) |
0.277 (1.00) |
Del Peak 14(7q31 1) | 0 (0%) | 33 |
0.36 (1.00) |
1 (1.00) |
Del Peak 15(8p23 2) | 0 (0%) | 27 |
0.593 (1.00) |
0.873 (1.00) |
Del Peak 16(9p21 3) | 0 (0%) | 10 |
0.0062 (0.626) |
0.0358 (1.00) |
Del Peak 17(10p11 21) | 0 (0%) | 37 |
0.549 (1.00) |
0.0682 (1.00) |
Del Peak 18(10q23 31) | 0 (0%) | 27 |
0.593 (1.00) |
0.24 (1.00) |
Del Peak 19(11p15 4) | 0 (0%) | 26 |
0.818 (1.00) |
0.36 (1.00) |
Del Peak 20(11q24 3) | 0 (0%) | 25 |
0.0465 (1.00) |
0.823 (1.00) |
Del Peak 21(13q14 2) | 0 (0%) | 22 |
0.00641 (0.641) |
0.0321 (1.00) |
Del Peak 22(15q13 1) | 0 (0%) | 36 |
0.616 (1.00) |
0.555 (1.00) |
Del Peak 23(16q23 1) | 0 (0%) | 33 |
0.00336 (0.343) |
0.114 (1.00) |
Del Peak 24(17q24 3) | 0 (0%) | 45 |
0.00862 (0.845) |
0.228 (1.00) |
Del Peak 25(18q12 2) | 0 (0%) | 24 |
0.245 (1.00) |
0.176 (1.00) |
Del Peak 26(19q13 31) | 0 (0%) | 33 |
0.333 (1.00) |
0.0647 (1.00) |
Del Peak 27(20p12 1) | 0 (0%) | 42 |
0.485 (1.00) |
0.408 (1.00) |
Del Peak 28(21q22 2) | 0 (0%) | 22 |
0.821 (1.00) |
0.812 (1.00) |
Del Peak 29(22q11 1) | 0 (0%) | 30 |
0.0787 (1.00) |
0.0616 (1.00) |
Del Peak 30(Xp21 1) | 0 (0%) | 26 |
0.632 (1.00) |
0.201 (1.00) |
Del Peak 31(Xp11 3) | 0 (0%) | 25 |
0.725 (1.00) |
1 (1.00) |
Del Peak 32(Xq21 33) | 0 (0%) | 38 |
0.839 (1.00) |
0.911 (1.00) |
P value = 0.000572 (Fisher's exact test), Q value = 0.06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 20 | 12 | 18 |
AMP PEAK 4(3Q29) CNV | 20 | 9 | 9 |
AMP PEAK 4(3Q29) WILD-TYPE | 0 | 3 | 9 |
P value = 0.00223 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 24 | 12 | 14 |
AMP PEAK 4(3Q29) CNV | 23 | 8 | 7 |
AMP PEAK 4(3Q29) WILD-TYPE | 1 | 4 | 7 |
P value = 0.000123 (Fisher's exact test), Q value = 0.013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 20 | 12 | 18 |
AMP PEAK 13(11Q13.3) CNV | 19 | 3 | 11 |
AMP PEAK 13(11Q13.3) WILD-TYPE | 1 | 9 | 7 |
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Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
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Molecular subtype file = ESCA-TP.transferedmergedcluster.txt
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Number of patients = 50
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Number of copy number variation regions = 53
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Number of molecular subtypes = 2
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Exclude regions 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 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.