This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.
Testing the association between copy number variation of 22 peak regions and 8 molecular subtypes across 117 patients, 21 significant findings detected with Q value < 0.25.
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Amp Peak 2(3p14.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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Amp Peak 5(7q22.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Amp Peak 6(17q25.2) cnvs correlated to 'CN_CNMF'.
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Amp Peak 7(19p13.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 1(1p36.31) cnvs correlated to 'CN_CNMF'.
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Del Peak 4(3p22.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 5(4q31.22) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 6(5q35.2) cnvs correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 8(9p21.3) cnvs correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
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Del Peak 9(14q11.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 10(14q23.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 11(14q32.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 13(Xq21.31) cnvs correlated to 'CN_CNMF'.
Molecular subtypes |
MRNA CNMF |
MRNA CHIERARCHICAL |
CN CNMF |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Fisher's exact 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 | Fisher's exact test | |
Amp Peak 2(3p14 1) | 31 (26%) | 86 |
1 (1.00) |
0.537 (1.00) |
2.36e-17 (3.76e-15) |
0.0858 (1.00) |
0.00279 (0.373) |
1.79e-06 (0.000274) |
0.00534 (0.688) |
0.000228 (0.0335) |
Amp Peak 5(7q22 1) | 68 (58%) | 49 |
1 (1.00) |
0.808 (1.00) |
3.56e-09 (5.52e-07) |
0.00792 (1.00) |
0.00172 (0.239) |
0.000515 (0.0746) |
0.0134 (1.00) |
0.0157 (1.00) |
Del Peak 4(3p22 1) | 8 (7%) | 109 |
0.438 (1.00) |
0.000862 (0.122) |
0.000694 (0.0985) |
0.0206 (1.00) |
0.00417 (0.547) |
0.0159 (1.00) |
0.111 (1.00) |
|
Del Peak 5(4q31 22) | 13 (11%) | 104 |
1 (1.00) |
0.000304 (0.0444) |
0.000543 (0.0782) |
0.00681 (0.872) |
0.024 (1.00) |
0.582 (1.00) |
0.61 (1.00) |
|
Del Peak 6(5q35 2) | 8 (7%) | 109 |
1 (1.00) |
0.319 (1.00) |
0.00185 (0.253) |
0.000616 (0.088) |
0.00116 (0.162) |
0.394 (1.00) |
0.12 (1.00) |
|
Del Peak 8(9p21 3) | 18 (15%) | 99 |
1 (1.00) |
0.75 (1.00) |
0.00471 (0.612) |
4.27e-05 (0.00636) |
3.4e-05 (0.0051) |
0.00182 (0.251) |
0.0341 (1.00) |
0.0922 (1.00) |
Amp Peak 6(17q25 2) | 80 (68%) | 37 |
0.585 (1.00) |
1 (1.00) |
2.9e-06 (0.000438) |
0.233 (1.00) |
0.28 (1.00) |
0.0388 (1.00) |
0.826 (1.00) |
0.477 (1.00) |
Amp Peak 7(19p13 2) | 14 (12%) | 103 |
0.0885 (1.00) |
0.615 (1.00) |
4.94e-09 (7.61e-07) |
0.161 (1.00) |
0.0683 (1.00) |
0.765 (1.00) |
0.722 (1.00) |
0.682 (1.00) |
Del Peak 1(1p36 31) | 25 (21%) | 92 |
0.585 (1.00) |
1 (1.00) |
2.27e-06 (0.000346) |
0.172 (1.00) |
0.0316 (1.00) |
0.0382 (1.00) |
0.255 (1.00) |
0.124 (1.00) |
Del Peak 9(14q11 2) | 26 (22%) | 91 |
0.596 (1.00) |
0.167 (1.00) |
2.56e-10 (3.99e-08) |
0.3 (1.00) |
0.0934 (1.00) |
0.177 (1.00) |
0.835 (1.00) |
0.953 (1.00) |
Del Peak 10(14q23 3) | 25 (21%) | 92 |
1 (1.00) |
0.385 (1.00) |
2.2e-12 (3.48e-10) |
0.139 (1.00) |
0.0351 (1.00) |
0.0295 (1.00) |
0.719 (1.00) |
0.886 (1.00) |
Del Peak 11(14q32 2) | 25 (21%) | 92 |
1 (1.00) |
0.385 (1.00) |
1.29e-11 (2.02e-09) |
0.3 (1.00) |
0.0775 (1.00) |
0.0648 (1.00) |
0.719 (1.00) |
0.886 (1.00) |
Del Peak 13(Xq21 31) | 17 (15%) | 100 |
1 (1.00) |
0.000118 (0.0175) |
0.00263 (0.355) |
0.00278 (0.373) |
0.0354 (1.00) |
0.768 (1.00) |
0.806 (1.00) |
|
Amp Peak 1(2q32 1) | 20 (17%) | 97 |
0.55 (1.00) |
0.75 (1.00) |
0.00237 (0.322) |
0.397 (1.00) |
0.942 (1.00) |
1 (1.00) |
0.832 (1.00) |
0.439 (1.00) |
Amp Peak 3(5q35 2) | 15 (13%) | 102 |
0.0625 (1.00) |
0.141 (1.00) |
0.2 (1.00) |
0.0369 (1.00) |
0.678 (1.00) |
0.0565 (1.00) |
0.566 (1.00) |
0.0452 (1.00) |
Amp Peak 4(6p12 3) | 4 (3%) | 113 |
0.438 (1.00) |
0.199 (1.00) |
0.114 (1.00) |
0.35 (1.00) |
0.165 (1.00) |
0.186 (1.00) |
||
Amp Peak 8(19q13 11) | 4 (3%) | 113 |
0.69 (1.00) |
0.199 (1.00) |
0.201 (1.00) |
0.13 (1.00) |
0.331 (1.00) |
0.473 (1.00) |
||
Del Peak 2(2p11 2) | 3 (3%) | 114 |
0.884 (1.00) |
0.791 (1.00) |
0.028 (1.00) |
0.0273 (1.00) |
||||
Del Peak 3(2q37 3) | 5 (4%) | 112 |
1 (1.00) |
0.331 (1.00) |
0.163 (1.00) |
0.684 (1.00) |
0.35 (1.00) |
0.704 (1.00) |
0.84 (1.00) |
|
Del Peak 7(6q22 31) | 13 (11%) | 104 |
1 (1.00) |
0.0489 (1.00) |
0.114 (1.00) |
0.0976 (1.00) |
0.175 (1.00) |
0.787 (1.00) |
0.337 (1.00) |
|
Del Peak 12(19q13 42) | 10 (9%) | 107 |
0.163 (1.00) |
0.885 (1.00) |
0.732 (1.00) |
0.232 (1.00) |
0.471 (1.00) |
0.438 (1.00) |
||
Del Peak 14(Xq28) | 16 (14%) | 101 |
1 (1.00) |
0.00368 (0.486) |
0.045 (1.00) |
0.0436 (1.00) |
0.253 (1.00) |
0.713 (1.00) |
0.941 (1.00) |
P value = 2.36e-17 (Fisher's exact test), Q value = 3.8e-15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 20 | 28 | 45 |
AMP PEAK 2(3P14.1) MUTATED | 23 | 4 | 0 | 4 |
AMP PEAK 2(3P14.1) WILD-TYPE | 1 | 16 | 28 | 41 |
P value = 1.79e-06 (Fisher's exact test), Q value = 0.00027
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 37 | 21 |
AMP PEAK 2(3P14.1) MUTATED | 1 | 19 | 0 |
AMP PEAK 2(3P14.1) WILD-TYPE | 17 | 18 | 21 |
P value = 0.000228 (Fisher's exact test), Q value = 0.033
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 27 | 45 | 12 | 33 |
AMP PEAK 2(3P14.1) MUTATED | 2 | 8 | 8 | 13 |
AMP PEAK 2(3P14.1) WILD-TYPE | 25 | 37 | 4 | 20 |
P value = 3.56e-09 (Fisher's exact test), Q value = 5.5e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 20 | 28 | 45 |
AMP PEAK 5(7Q22.1) MUTATED | 21 | 20 | 9 | 18 |
AMP PEAK 5(7Q22.1) WILD-TYPE | 3 | 0 | 19 | 27 |
P value = 0.00172 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 24 | 25 |
AMP PEAK 5(7Q22.1) MUTATED | 22 | 8 | 13 |
AMP PEAK 5(7Q22.1) WILD-TYPE | 5 | 16 | 12 |
P value = 0.000515 (Fisher's exact test), Q value = 0.075
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 37 | 21 |
AMP PEAK 5(7Q22.1) MUTATED | 8 | 29 | 6 |
AMP PEAK 5(7Q22.1) WILD-TYPE | 10 | 8 | 15 |
P value = 2.9e-06 (Fisher's exact test), Q value = 0.00044
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 20 | 28 | 45 |
AMP PEAK 6(17Q25.2) MUTATED | 22 | 20 | 14 | 24 |
AMP PEAK 6(17Q25.2) WILD-TYPE | 2 | 0 | 14 | 21 |
P value = 4.94e-09 (Fisher's exact test), Q value = 7.6e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 20 | 28 | 45 |
AMP PEAK 7(19P13.2) MUTATED | 0 | 11 | 3 | 0 |
AMP PEAK 7(19P13.2) WILD-TYPE | 24 | 9 | 25 | 45 |
P value = 2.27e-06 (Fisher's exact test), Q value = 0.00035
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 20 | 28 | 45 |
DEL PEAK 1(1P36.31) MUTATED | 2 | 0 | 16 | 7 |
DEL PEAK 1(1P36.31) WILD-TYPE | 22 | 20 | 12 | 38 |
P value = 0.000862 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 20 | 28 | 45 |
DEL PEAK 4(3P22.1) MUTATED | 0 | 0 | 7 | 1 |
DEL PEAK 4(3P22.1) WILD-TYPE | 24 | 20 | 21 | 44 |
P value = 0.000694 (Fisher's exact test), Q value = 0.098
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 21 | 27 | 39 |
DEL PEAK 4(3P22.1) MUTATED | 0 | 6 | 0 |
DEL PEAK 4(3P22.1) WILD-TYPE | 21 | 21 | 39 |
P value = 0.000304 (Fisher's exact test), Q value = 0.044
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 20 | 28 | 45 |
DEL PEAK 5(4Q31.22) MUTATED | 3 | 0 | 9 | 1 |
DEL PEAK 5(4Q31.22) WILD-TYPE | 21 | 20 | 19 | 44 |
P value = 0.000543 (Fisher's exact test), Q value = 0.078
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 21 | 27 | 39 |
DEL PEAK 5(4Q31.22) MUTATED | 0 | 8 | 1 |
DEL PEAK 5(4Q31.22) WILD-TYPE | 21 | 19 | 38 |
P value = 0.000616 (Fisher's exact test), Q value = 0.088
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 24 | 25 |
DEL PEAK 6(5Q35.2) MUTATED | 0 | 6 | 0 |
DEL PEAK 6(5Q35.2) WILD-TYPE | 27 | 18 | 25 |
P value = 0.00116 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 18 | 37 | 21 |
DEL PEAK 6(5Q35.2) MUTATED | 5 | 0 | 1 |
DEL PEAK 6(5Q35.2) WILD-TYPE | 13 | 37 | 20 |
P value = 4.27e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 21 | 27 | 39 |
DEL PEAK 8(9P21.3) MUTATED | 4 | 10 | 0 |
DEL PEAK 8(9P21.3) WILD-TYPE | 17 | 17 | 39 |
P value = 3.4e-05 (Fisher's exact test), Q value = 0.0051
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 27 | 24 | 25 |
DEL PEAK 8(9P21.3) MUTATED | 1 | 12 | 2 |
DEL PEAK 8(9P21.3) WILD-TYPE | 26 | 12 | 23 |
P value = 2.56e-10 (Fisher's exact test), Q value = 4e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 20 | 28 | 45 |
DEL PEAK 9(14Q11.2) MUTATED | 5 | 0 | 19 | 2 |
DEL PEAK 9(14Q11.2) WILD-TYPE | 19 | 20 | 9 | 43 |
P value = 2.2e-12 (Fisher's exact test), Q value = 3.5e-10
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 20 | 28 | 45 |
DEL PEAK 10(14Q23.3) MUTATED | 4 | 0 | 20 | 1 |
DEL PEAK 10(14Q23.3) WILD-TYPE | 20 | 20 | 8 | 44 |
P value = 1.29e-11 (Fisher's exact test), Q value = 2e-09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 20 | 28 | 45 |
DEL PEAK 11(14Q32.2) MUTATED | 3 | 0 | 20 | 2 |
DEL PEAK 11(14Q32.2) WILD-TYPE | 21 | 20 | 8 | 43 |
P value = 0.000118 (Fisher's exact test), Q value = 0.018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 20 | 28 | 45 |
DEL PEAK 13(XQ21.31) MUTATED | 4 | 0 | 11 | 2 |
DEL PEAK 13(XQ21.31) WILD-TYPE | 20 | 20 | 17 | 43 |
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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 = KIRP-TP.transferedmergedcluster.txt
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Number of patients = 117
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Number of copy number variation regions = 22
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Number of molecular subtypes = 8
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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.