(Regional_LN cohort)
This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.
Testing the association between copy number variation of 39 peak regions and 8 molecular subtypes across 112 patients, 10 significant findings detected with Q value < 0.25.
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Amp Peak 1(1p12) cnvs correlated to 'CN_CNMF'.
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Amp Peak 10(8q11.21) cnvs correlated to 'CN_CNMF'.
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Amp Peak 11(8q24.21) cnvs correlated to 'CN_CNMF'.
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Del Peak 2(1p21.3) cnvs correlated to 'MRNASEQ_CNMF'.
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Del Peak 7(6q25.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 8(6q26) cnvs correlated to 'CN_CNMF'.
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Del Peak 10(9p23) cnvs correlated to 'CN_CNMF'.
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Del Peak 11(9p21.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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Del Peak 14(11q23.1) cnvs correlated to 'CN_CNMF'.
Molecular subtypes |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
Del Peak 11(9p21 3) | 86 (77%) | 26 |
0.000155 (0.0475) |
0.0288 (1.00) |
0.0848 (1.00) |
0.811 (1.00) |
2.39e-05 (0.00735) |
0.00169 (0.498) |
0.308 (1.00) |
0.229 (1.00) |
Amp Peak 1(1p12) | 32 (29%) | 80 |
8.51e-05 (0.0261) |
0.225 (1.00) |
0.812 (1.00) |
0.113 (1.00) |
0.0204 (1.00) |
0.185 (1.00) |
0.297 (1.00) |
0.158 (1.00) |
Amp Peak 10(8q11 21) | 41 (37%) | 71 |
1.3e-05 (0.00404) |
0.00223 (0.65) |
0.417 (1.00) |
0.218 (1.00) |
0.191 (1.00) |
0.0317 (1.00) |
0.0715 (1.00) |
0.0711 (1.00) |
Amp Peak 11(8q24 21) | 50 (45%) | 62 |
0.000343 (0.104) |
0.0122 (1.00) |
0.737 (1.00) |
0.399 (1.00) |
0.046 (1.00) |
0.173 (1.00) |
0.317 (1.00) |
0.524 (1.00) |
Del Peak 2(1p21 3) | 30 (27%) | 82 |
0.14 (1.00) |
0.0165 (1.00) |
0.36 (1.00) |
0.164 (1.00) |
0.000327 (0.0993) |
0.00195 (0.574) |
0.646 (1.00) |
0.891 (1.00) |
Del Peak 7(6q25 3) | 67 (60%) | 45 |
2.85e-09 (8.89e-07) |
0.00557 (1.00) |
0.145 (1.00) |
0.335 (1.00) |
0.0261 (1.00) |
0.454 (1.00) |
0.102 (1.00) |
0.718 (1.00) |
Del Peak 8(6q26) | 63 (56%) | 49 |
2.44e-08 (7.59e-06) |
0.0238 (1.00) |
0.269 (1.00) |
0.288 (1.00) |
0.0689 (1.00) |
0.193 (1.00) |
0.356 (1.00) |
0.912 (1.00) |
Del Peak 10(9p23) | 75 (67%) | 37 |
1.32e-05 (0.00408) |
0.277 (1.00) |
0.662 (1.00) |
0.677 (1.00) |
0.00283 (0.82) |
0.0756 (1.00) |
0.782 (1.00) |
0.377 (1.00) |
Del Peak 14(11q23 1) | 61 (54%) | 51 |
0.000236 (0.072) |
0.176 (1.00) |
0.516 (1.00) |
0.787 (1.00) |
0.0402 (1.00) |
0.00127 (0.378) |
0.0102 (1.00) |
0.482 (1.00) |
Amp Peak 2(1q44) | 54 (48%) | 58 |
0.0154 (1.00) |
0.417 (1.00) |
0.643 (1.00) |
0.919 (1.00) |
0.061 (1.00) |
0.278 (1.00) |
0.0568 (1.00) |
0.529 (1.00) |
Amp Peak 3(3p13) | 24 (21%) | 88 |
0.0168 (1.00) |
0.192 (1.00) |
0.101 (1.00) |
0.0377 (1.00) |
0.229 (1.00) |
0.00754 (1.00) |
0.406 (1.00) |
0.325 (1.00) |
Amp Peak 4(5p15 33) | 32 (29%) | 80 |
0.0125 (1.00) |
0.0565 (1.00) |
0.78 (1.00) |
0.742 (1.00) |
0.93 (1.00) |
0.584 (1.00) |
0.0304 (1.00) |
0.717 (1.00) |
Amp Peak 5(5q35 3) | 13 (12%) | 99 |
0.00113 (0.341) |
0.033 (1.00) |
0.215 (1.00) |
0.774 (1.00) |
0.288 (1.00) |
0.422 (1.00) |
0.216 (1.00) |
0.895 (1.00) |
Amp Peak 6(6p25 1) | 61 (54%) | 51 |
0.00618 (1.00) |
0.00163 (0.483) |
0.286 (1.00) |
0.246 (1.00) |
0.97 (1.00) |
0.336 (1.00) |
0.36 (1.00) |
0.032 (1.00) |
Amp Peak 7(6q12) | 23 (21%) | 89 |
0.292 (1.00) |
0.545 (1.00) |
0.495 (1.00) |
0.979 (1.00) |
0.0469 (1.00) |
0.18 (1.00) |
0.0573 (1.00) |
0.536 (1.00) |
Amp Peak 8(7p22 1) | 60 (54%) | 52 |
0.00212 (0.621) |
0.524 (1.00) |
0.971 (1.00) |
0.77 (1.00) |
0.127 (1.00) |
0.703 (1.00) |
0.707 (1.00) |
0.662 (1.00) |
Amp Peak 9(7q34) | 62 (55%) | 50 |
0.00136 (0.403) |
0.438 (1.00) |
0.34 (1.00) |
0.951 (1.00) |
0.761 (1.00) |
0.295 (1.00) |
0.279 (1.00) |
0.524 (1.00) |
Amp Peak 12(9p24 1) | 5 (4%) | 107 |
0.116 (1.00) |
0.511 (1.00) |
0.676 (1.00) |
0.536 (1.00) |
0.365 (1.00) |
0.0675 (1.00) |
1 (1.00) |
0.606 (1.00) |
Amp Peak 13(11q13 3) | 19 (17%) | 93 |
0.146 (1.00) |
0.361 (1.00) |
0.163 (1.00) |
0.971 (1.00) |
0.114 (1.00) |
0.0617 (1.00) |
1 (1.00) |
0.53 (1.00) |
Amp Peak 14(12q14 1) | 20 (18%) | 92 |
0.00275 (0.801) |
0.123 (1.00) |
0.119 (1.00) |
0.238 (1.00) |
0.157 (1.00) |
0.391 (1.00) |
0.773 (1.00) |
0.366 (1.00) |
Amp Peak 15(15q26 2) | 43 (38%) | 69 |
0.176 (1.00) |
0.655 (1.00) |
0.752 (1.00) |
0.511 (1.00) |
0.566 (1.00) |
0.0559 (1.00) |
0.585 (1.00) |
0.647 (1.00) |
Amp Peak 16(17q25 3) | 44 (39%) | 68 |
0.00125 (0.375) |
0.0441 (1.00) |
0.956 (1.00) |
0.554 (1.00) |
0.486 (1.00) |
0.0809 (1.00) |
0.00116 (0.35) |
0.869 (1.00) |
Amp Peak 17(19p13 2) | 19 (17%) | 93 |
0.056 (1.00) |
0.011 (1.00) |
0.701 (1.00) |
0.096 (1.00) |
0.0444 (1.00) |
0.369 (1.00) |
0.52 (1.00) |
0.238 (1.00) |
Amp Peak 18(22q13 2) | 48 (43%) | 64 |
0.234 (1.00) |
0.806 (1.00) |
0.85 (1.00) |
1 (1.00) |
0.543 (1.00) |
0.248 (1.00) |
0.543 (1.00) |
0.956 (1.00) |
Del Peak 1(1p36 31) | 27 (24%) | 85 |
0.0887 (1.00) |
0.102 (1.00) |
0.235 (1.00) |
0.385 (1.00) |
0.00413 (1.00) |
0.0652 (1.00) |
0.378 (1.00) |
0.424 (1.00) |
Del Peak 3(2q37 3) | 21 (19%) | 91 |
0.531 (1.00) |
0.171 (1.00) |
0.562 (1.00) |
0.413 (1.00) |
0.1 (1.00) |
0.192 (1.00) |
0.348 (1.00) |
0.0508 (1.00) |
Del Peak 4(3p24 3) | 17 (15%) | 95 |
0.411 (1.00) |
0.423 (1.00) |
0.183 (1.00) |
0.0654 (1.00) |
0.595 (1.00) |
0.146 (1.00) |
0.388 (1.00) |
0.837 (1.00) |
Del Peak 5(4q34 3) | 23 (21%) | 89 |
0.0542 (1.00) |
0.308 (1.00) |
0.532 (1.00) |
0.797 (1.00) |
0.351 (1.00) |
0.976 (1.00) |
0.47 (1.00) |
0.325 (1.00) |
Del Peak 6(5q31 3) | 45 (40%) | 67 |
0.0636 (1.00) |
0.0943 (1.00) |
0.646 (1.00) |
0.511 (1.00) |
0.208 (1.00) |
0.761 (1.00) |
0.212 (1.00) |
0.25 (1.00) |
Del Peak 9(8p23 3) | 29 (26%) | 83 |
0.108 (1.00) |
0.0808 (1.00) |
0.0735 (1.00) |
0.0634 (1.00) |
0.559 (1.00) |
0.451 (1.00) |
0.463 (1.00) |
0.588 (1.00) |
Del Peak 12(10p15 3) | 55 (49%) | 57 |
0.00118 (0.353) |
0.121 (1.00) |
0.441 (1.00) |
0.233 (1.00) |
0.0614 (1.00) |
0.048 (1.00) |
0.301 (1.00) |
0.695 (1.00) |
Del Peak 13(10q23 31) | 64 (57%) | 48 |
0.107 (1.00) |
0.157 (1.00) |
0.543 (1.00) |
0.122 (1.00) |
0.0131 (1.00) |
0.00446 (1.00) |
0.00536 (1.00) |
0.165 (1.00) |
Del Peak 15(12q24 33) | 21 (19%) | 91 |
0.61 (1.00) |
0.197 (1.00) |
0.417 (1.00) |
0.764 (1.00) |
0.616 (1.00) |
0.252 (1.00) |
0.814 (1.00) |
1 (1.00) |
Del Peak 16(13q34) | 31 (28%) | 81 |
0.306 (1.00) |
0.818 (1.00) |
0.639 (1.00) |
0.965 (1.00) |
0.894 (1.00) |
0.444 (1.00) |
0.0285 (1.00) |
0.265 (1.00) |
Del Peak 17(15q13 3) | 25 (22%) | 87 |
0.028 (1.00) |
0.496 (1.00) |
0.293 (1.00) |
0.599 (1.00) |
0.311 (1.00) |
0.526 (1.00) |
0.803 (1.00) |
1 (1.00) |
Del Peak 18(15q15 3) | 26 (23%) | 86 |
0.0933 (1.00) |
0.731 (1.00) |
0.812 (1.00) |
0.837 (1.00) |
0.812 (1.00) |
0.989 (1.00) |
0.438 (1.00) |
0.442 (1.00) |
Del Peak 19(16p13 3) | 22 (20%) | 90 |
0.21 (1.00) |
0.142 (1.00) |
0.89 (1.00) |
0.63 (1.00) |
0.0375 (1.00) |
0.197 (1.00) |
0.11 (1.00) |
0.81 (1.00) |
Del Peak 20(16q12 1) | 38 (34%) | 74 |
0.106 (1.00) |
0.154 (1.00) |
0.979 (1.00) |
0.662 (1.00) |
0.158 (1.00) |
0.327 (1.00) |
0.255 (1.00) |
0.158 (1.00) |
Del Peak 21(16q24 2) | 43 (38%) | 69 |
0.75 (1.00) |
0.253 (1.00) |
0.382 (1.00) |
0.1 (1.00) |
0.0968 (1.00) |
0.252 (1.00) |
0.0818 (1.00) |
0.422 (1.00) |
P value = 8.51e-05 (Fisher's exact test), Q value = 0.026
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 30 | 18 | 38 | 26 |
AMP PEAK 1(1P12) MUTATED | 15 | 6 | 11 | 0 |
AMP PEAK 1(1P12) WILD-TYPE | 15 | 12 | 27 | 26 |
P value = 1.3e-05 (Fisher's exact test), Q value = 0.004
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 30 | 18 | 38 | 26 |
AMP PEAK 10(8Q11.21) MUTATED | 9 | 16 | 9 | 7 |
AMP PEAK 10(8Q11.21) WILD-TYPE | 21 | 2 | 29 | 19 |
P value = 0.000343 (Fisher's exact test), Q value = 0.1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 30 | 18 | 38 | 26 |
AMP PEAK 11(8Q24.21) MUTATED | 13 | 15 | 9 | 13 |
AMP PEAK 11(8Q24.21) WILD-TYPE | 17 | 3 | 29 | 13 |
P value = 0.000327 (Fisher's exact test), Q value = 0.099
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 27 | 43 |
DEL PEAK 2(1P21.3) MUTATED | 19 | 1 | 10 |
DEL PEAK 2(1P21.3) WILD-TYPE | 23 | 26 | 33 |
P value = 2.85e-09 (Fisher's exact test), Q value = 8.9e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 30 | 18 | 38 | 26 |
DEL PEAK 7(6Q25.3) MUTATED | 23 | 10 | 9 | 25 |
DEL PEAK 7(6Q25.3) WILD-TYPE | 7 | 8 | 29 | 1 |
P value = 2.44e-08 (Fisher's exact test), Q value = 7.6e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 30 | 18 | 38 | 26 |
DEL PEAK 8(6Q26) MUTATED | 21 | 10 | 8 | 24 |
DEL PEAK 8(6Q26) WILD-TYPE | 9 | 8 | 30 | 2 |
P value = 1.32e-05 (Fisher's exact test), Q value = 0.0041
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 30 | 18 | 38 | 26 |
DEL PEAK 10(9P23) MUTATED | 28 | 16 | 18 | 13 |
DEL PEAK 10(9P23) WILD-TYPE | 2 | 2 | 20 | 13 |
P value = 0.000155 (Fisher's exact test), Q value = 0.047
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 30 | 18 | 38 | 26 |
DEL PEAK 11(9P21.3) MUTATED | 28 | 17 | 20 | 21 |
DEL PEAK 11(9P21.3) WILD-TYPE | 2 | 1 | 18 | 5 |
P value = 2.39e-05 (Fisher's exact test), Q value = 0.0073
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 27 | 43 |
DEL PEAK 11(9P21.3) MUTATED | 39 | 12 | 35 |
DEL PEAK 11(9P21.3) WILD-TYPE | 3 | 15 | 8 |
P value = 0.000236 (Fisher's exact test), Q value = 0.072
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 30 | 18 | 38 | 26 |
DEL PEAK 14(11Q23.1) MUTATED | 25 | 12 | 14 | 10 |
DEL PEAK 14(11Q23.1) WILD-TYPE | 5 | 6 | 24 | 16 |
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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 = SKCM-Regional_LN.transferedmergedcluster.txt
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Number of patients = 112
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Number of copy number variation regions = 39
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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 multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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.