This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.
Testing the association between copy number variation of 38 peak regions and 8 molecular subtypes across 77 patients, 27 significant findings detected with Q value < 0.25.
-
Amp Peak 1(1q22) cnvs correlated to 'MRNASEQ_CHIERARCHICAL'.
-
Amp Peak 3(4q35.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
-
Amp Peak 4(5p15.33) cnvs correlated to 'CN_CNMF'.
-
Amp Peak 5(5q35.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
Amp Peak 7(9q34.3) cnvs correlated to 'CN_CNMF'.
-
Amp Peak 8(12q14.1) cnvs correlated to 'CN_CNMF'.
-
Amp Peak 9(14q11.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
Amp Peak 10(16q22.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
-
Amp Peak 12(19p13.12) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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Amp Peak 13(19q12) cnvs correlated to 'CN_CNMF'.
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Amp Peak 14(19q13.33) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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Amp Peak 15(Xq28) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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Del Peak 11(9p23) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 12(9p21.3) cnvs correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Molecular subtypes |
CN CNMF |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nCNV (%) | nWild-Type | 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 | Fisher's exact test | |
Amp Peak 5(5q35 3) | 0 (0%) | 23 |
3.98e-07 (0.000119) |
0.000585 (0.163) |
2.02e-07 (6.04e-05) |
2.36e-06 (0.000693) |
0.33 (1.00) |
0.754 (1.00) |
0.746 (1.00) |
0.615 (1.00) |
Amp Peak 9(14q11 2) | 0 (0%) | 55 |
1.46e-05 (0.00425) |
0.0283 (1.00) |
2.89e-06 (0.000848) |
5.93e-07 (0.000176) |
0.0204 (1.00) |
0.0116 (1.00) |
0.0204 (1.00) |
0.0217 (1.00) |
Del Peak 11(9p23) | 0 (0%) | 57 |
0.000178 (0.0499) |
0.00298 (0.794) |
1.55e-05 (0.00449) |
0.000785 (0.217) |
0.505 (1.00) |
0.513 (1.00) |
1 (1.00) |
0.172 (1.00) |
Amp Peak 3(4q35 1) | 0 (0%) | 52 |
4.74e-05 (0.0135) |
0.209 (1.00) |
0.000777 (0.215) |
0.00911 (1.00) |
0.13 (1.00) |
0.179 (1.00) |
0.366 (1.00) |
0.366 (1.00) |
Amp Peak 10(16q22 1) | 0 (0%) | 31 |
8.76e-09 (2.63e-06) |
0.173 (1.00) |
0.00446 (1.00) |
0.000815 (0.224) |
0.767 (1.00) |
0.735 (1.00) |
1 (1.00) |
0.57 (1.00) |
Amp Peak 12(19p13 12) | 0 (0%) | 28 |
0.000101 (0.0286) |
0.12 (1.00) |
0.00084 (0.23) |
0.00443 (1.00) |
0.768 (1.00) |
0.854 (1.00) |
0.768 (1.00) |
1 (1.00) |
Amp Peak 14(19q13 33) | 0 (0%) | 29 |
1.23e-05 (0.00358) |
0.207 (1.00) |
0.000408 (0.114) |
0.00396 (1.00) |
1 (1.00) |
0.623 (1.00) |
1 (1.00) |
0.845 (1.00) |
Amp Peak 15(Xq28) | 0 (0%) | 32 |
3.92e-05 (0.0113) |
0.366 (1.00) |
9.64e-05 (0.0273) |
0.00684 (1.00) |
1 (1.00) |
0.858 (1.00) |
0.566 (1.00) |
0.923 (1.00) |
Del Peak 12(9p21 3) | 0 (0%) | 55 |
0.00198 (0.535) |
0.00111 (0.301) |
1.43e-06 (0.000423) |
4.45e-05 (0.0127) |
0.205 (1.00) |
0.839 (1.00) |
0.528 (1.00) |
0.142 (1.00) |
Amp Peak 1(1q22) | 0 (0%) | 63 |
0.00193 (0.524) |
0.00429 (1.00) |
0.00971 (1.00) |
0.000415 (0.116) |
0.486 (1.00) |
0.141 (1.00) |
0.486 (1.00) |
0.128 (1.00) |
Amp Peak 4(5p15 33) | 0 (0%) | 19 |
1.95e-06 (0.000574) |
0.657 (1.00) |
0.00482 (1.00) |
0.0534 (1.00) |
1 (1.00) |
0.817 (1.00) |
1 (1.00) |
0.811 (1.00) |
Amp Peak 7(9q34 3) | 0 (0%) | 52 |
4.43e-05 (0.0127) |
0.00439 (1.00) |
0.00453 (1.00) |
0.00253 (0.681) |
0.3 (1.00) |
0.32 (1.00) |
0.731 (1.00) |
0.729 (1.00) |
Amp Peak 8(12q14 1) | 0 (0%) | 18 |
2.21e-05 (0.0064) |
0.275 (1.00) |
0.0111 (1.00) |
0.0416 (1.00) |
1 (1.00) |
0.826 (1.00) |
1 (1.00) |
0.811 (1.00) |
Amp Peak 13(19q12) | 0 (0%) | 30 |
8.46e-05 (0.024) |
0.0767 (1.00) |
0.00102 (0.278) |
0.00808 (1.00) |
1 (1.00) |
0.623 (1.00) |
1 (1.00) |
0.845 (1.00) |
Amp Peak 2(4p16 3) | 0 (0%) | 44 |
0.00666 (1.00) |
0.463 (1.00) |
0.00523 (1.00) |
0.00951 (1.00) |
0.561 (1.00) |
0.8 (1.00) |
1 (1.00) |
0.855 (1.00) |
Amp Peak 6(6q24 3) | 0 (0%) | 61 |
0.123 (1.00) |
0.852 (1.00) |
0.0609 (1.00) |
0.88 (1.00) |
0.269 (1.00) |
0.457 (1.00) |
0.715 (1.00) |
1 (1.00) |
Amp Peak 11(17q25 3) | 0 (0%) | 64 |
0.193 (1.00) |
0.0638 (1.00) |
0.00681 (1.00) |
0.0413 (1.00) |
0.715 (1.00) |
1 (1.00) |
1 (1.00) |
0.877 (1.00) |
Del Peak 1(1p36 23) | 0 (0%) | 47 |
0.0572 (1.00) |
0.0423 (1.00) |
0.239 (1.00) |
0.0335 (1.00) |
0.566 (1.00) |
0.154 (1.00) |
0.566 (1.00) |
0.526 (1.00) |
Del Peak 2(1q24 1) | 0 (0%) | 67 |
0.0874 (1.00) |
0.0334 (1.00) |
0.711 (1.00) |
0.631 (1.00) |
0.158 (1.00) |
0.0824 (1.00) |
0.158 (1.00) |
0.042 (1.00) |
Del Peak 3(2q37 3) | 0 (0%) | 61 |
0.017 (1.00) |
0.0282 (1.00) |
0.734 (1.00) |
0.469 (1.00) |
0.734 (1.00) |
0.325 (1.00) |
0.734 (1.00) |
0.49 (1.00) |
Del Peak 4(3q13 31) | 0 (0%) | 56 |
0.213 (1.00) |
0.292 (1.00) |
0.00665 (1.00) |
0.123 (1.00) |
0.15 (1.00) |
0.457 (1.00) |
0.475 (1.00) |
0.279 (1.00) |
Del Peak 5(3q13 31) | 0 (0%) | 56 |
0.53 (1.00) |
0.291 (1.00) |
0.0361 (1.00) |
0.286 (1.00) |
0.505 (1.00) |
0.912 (1.00) |
1 (1.00) |
0.811 (1.00) |
Del Peak 6(4q34 3) | 0 (0%) | 58 |
0.00293 (0.783) |
0.0704 (1.00) |
0.0138 (1.00) |
0.0284 (1.00) |
0.475 (1.00) |
1 (1.00) |
0.475 (1.00) |
0.279 (1.00) |
Del Peak 7(4q35 1) | 0 (0%) | 57 |
0.0311 (1.00) |
0.0447 (1.00) |
0.0754 (1.00) |
0.0324 (1.00) |
1 (1.00) |
0.624 (1.00) |
1 (1.00) |
0.886 (1.00) |
Del Peak 8(6p25 2) | 0 (0%) | 66 |
0.415 (1.00) |
0.625 (1.00) |
0.434 (1.00) |
0.5 (1.00) |
1 (1.00) |
0.688 (1.00) |
1 (1.00) |
1 (1.00) |
Del Peak 9(6q26) | 0 (0%) | 61 |
0.0909 (1.00) |
0.248 (1.00) |
0.0638 (1.00) |
0.167 (1.00) |
1 (1.00) |
0.679 (1.00) |
1 (1.00) |
0.877 (1.00) |
Del Peak 10(7q32 3) | 0 (0%) | 71 |
0.158 (1.00) |
0.00702 (1.00) |
0.00938 (1.00) |
0.00292 (0.783) |
1 (1.00) |
0.779 (1.00) |
1 (1.00) |
1 (1.00) |
Del Peak 13(10q26 3) | 0 (0%) | 68 |
0.749 (1.00) |
0.163 (1.00) |
0.371 (1.00) |
0.227 (1.00) |
0.242 (1.00) |
0.416 (1.00) |
0.242 (1.00) |
0.42 (1.00) |
Del Peak 14(11p15 5) | 0 (0%) | 58 |
0.145 (1.00) |
0.0144 (1.00) |
0.169 (1.00) |
0.28 (1.00) |
1 (1.00) |
0.017 (1.00) |
1 (1.00) |
0.0803 (1.00) |
Del Peak 15(11q24 3) | 0 (0%) | 56 |
0.133 (1.00) |
0.0594 (1.00) |
0.289 (1.00) |
0.442 (1.00) |
0.746 (1.00) |
0.433 (1.00) |
1 (1.00) |
0.685 (1.00) |
Del Peak 16(12q14 2) | 0 (0%) | 73 |
0.561 (1.00) |
0.514 (1.00) |
0.434 (1.00) |
0.56 (1.00) |
1 (1.00) |
0.651 (1.00) |
1 (1.00) |
0.631 (1.00) |
Del Peak 17(13q14 2) | 0 (0%) | 47 |
0.00645 (1.00) |
0.0771 (1.00) |
0.061 (1.00) |
0.262 (1.00) |
0.543 (1.00) |
0.617 (1.00) |
0.543 (1.00) |
0.783 (1.00) |
Del Peak 18(16p13 3) | 0 (0%) | 71 |
0.158 (1.00) |
0.37 (1.00) |
0.38 (1.00) |
1 (1.00) |
0.194 (1.00) |
0.194 (1.00) |
||
Del Peak 19(16q23 1) | 0 (0%) | 71 |
0.158 (1.00) |
0.521 (1.00) |
0.017 (1.00) |
0.166 (1.00) |
1 (1.00) |
1 (1.00) |
||
Del Peak 20(17q11 2) | 0 (0%) | 58 |
0.0366 (1.00) |
0.00716 (1.00) |
0.0919 (1.00) |
0.0997 (1.00) |
0.269 (1.00) |
0.881 (1.00) |
0.269 (1.00) |
0.333 (1.00) |
Del Peak 21(17q21 31) | 0 (0%) | 56 |
0.0149 (1.00) |
0.00939 (1.00) |
0.117 (1.00) |
0.0351 (1.00) |
0.0152 (1.00) |
0.125 (1.00) |
0.0152 (1.00) |
0.038 (1.00) |
Del Peak 22(17q24 2) | 0 (0%) | 57 |
0.0138 (1.00) |
0.00944 (1.00) |
0.259 (1.00) |
0.0223 (1.00) |
0.0809 (1.00) |
0.666 (1.00) |
0.0809 (1.00) |
0.0783 (1.00) |
Del Peak 23(22q12 1) | 0 (0%) | 36 |
0.0132 (1.00) |
0.231 (1.00) |
0.779 (1.00) |
0.588 (1.00) |
0.248 (1.00) |
0.438 (1.00) |
0.0823 (1.00) |
0.303 (1.00) |
P value = 0.000415 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 23 | 32 | 21 |
AMP PEAK 1(1Q22) CNV | 10 | 4 | 0 |
AMP PEAK 1(1Q22) WILD-TYPE | 13 | 28 | 21 |
P value = 4.74e-05 (Fisher's exact test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 29 | 19 | 19 | 10 |
AMP PEAK 3(4Q35.1) CNV | 2 | 6 | 9 | 8 |
AMP PEAK 3(4Q35.1) WILD-TYPE | 27 | 13 | 10 | 2 |
P value = 0.000777 (Fisher's exact test), Q value = 0.22
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 12 | 17 | 23 |
AMP PEAK 3(4Q35.1) CNV | 1 | 4 | 9 | 11 |
AMP PEAK 3(4Q35.1) WILD-TYPE | 23 | 8 | 8 | 12 |
P value = 1.95e-06 (Fisher's exact test), Q value = 0.00057
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 29 | 19 | 19 | 10 |
AMP PEAK 4(5P15.33) CNV | 12 | 18 | 18 | 10 |
AMP PEAK 4(5P15.33) WILD-TYPE | 17 | 1 | 1 | 0 |
P value = 3.98e-07 (Fisher's exact test), Q value = 0.00012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 29 | 19 | 19 | 10 |
AMP PEAK 5(5Q35.3) CNV | 10 | 19 | 17 | 8 |
AMP PEAK 5(5Q35.3) WILD-TYPE | 19 | 0 | 2 | 2 |
P value = 0.000585 (Chi-square test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 11 | 19 | 18 | 11 |
AMP PEAK 5(5Q35.3) CNV | 6 | 7 | 18 | 13 | 10 |
AMP PEAK 5(5Q35.3) WILD-TYPE | 12 | 4 | 1 | 5 | 1 |
P value = 2.02e-07 (Fisher's exact test), Q value = 6e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 12 | 17 | 23 |
AMP PEAK 5(5Q35.3) CNV | 6 | 11 | 16 | 20 |
AMP PEAK 5(5Q35.3) WILD-TYPE | 18 | 1 | 1 | 3 |
P value = 2.36e-06 (Fisher's exact test), Q value = 0.00069
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 23 | 32 | 21 |
AMP PEAK 5(5Q35.3) CNV | 7 | 26 | 20 |
AMP PEAK 5(5Q35.3) WILD-TYPE | 16 | 6 | 1 |
P value = 4.43e-05 (Fisher's exact test), Q value = 0.013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 29 | 19 | 19 | 10 |
AMP PEAK 7(9Q34.3) CNV | 8 | 1 | 14 | 2 |
AMP PEAK 7(9Q34.3) WILD-TYPE | 21 | 18 | 5 | 8 |
P value = 2.21e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 29 | 19 | 19 | 10 |
AMP PEAK 8(12Q14.1) CNV | 14 | 19 | 18 | 8 |
AMP PEAK 8(12Q14.1) WILD-TYPE | 15 | 0 | 1 | 2 |
P value = 1.46e-05 (Fisher's exact test), Q value = 0.0043
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 29 | 19 | 19 | 10 |
AMP PEAK 9(14Q11.2) CNV | 3 | 4 | 14 | 1 |
AMP PEAK 9(14Q11.2) WILD-TYPE | 26 | 15 | 5 | 9 |
P value = 2.89e-06 (Fisher's exact test), Q value = 0.00085
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 12 | 17 | 23 |
AMP PEAK 9(14Q11.2) CNV | 4 | 6 | 11 | 0 |
AMP PEAK 9(14Q11.2) WILD-TYPE | 20 | 6 | 6 | 23 |
P value = 5.93e-07 (Fisher's exact test), Q value = 0.00018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 23 | 32 | 21 |
AMP PEAK 9(14Q11.2) CNV | 4 | 2 | 15 |
AMP PEAK 9(14Q11.2) WILD-TYPE | 19 | 30 | 6 |
P value = 8.76e-09 (Fisher's exact test), Q value = 2.6e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 29 | 19 | 19 | 10 |
AMP PEAK 10(16Q22.1) CNV | 7 | 19 | 16 | 4 |
AMP PEAK 10(16Q22.1) WILD-TYPE | 22 | 0 | 3 | 6 |
P value = 0.000815 (Fisher's exact test), Q value = 0.22
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 23 | 32 | 21 |
AMP PEAK 10(16Q22.1) CNV | 7 | 20 | 18 |
AMP PEAK 10(16Q22.1) WILD-TYPE | 16 | 12 | 3 |
P value = 0.000101 (Fisher's exact test), Q value = 0.029
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 29 | 19 | 19 | 10 |
AMP PEAK 12(19P13.12) CNV | 12 | 11 | 19 | 7 |
AMP PEAK 12(19P13.12) WILD-TYPE | 17 | 8 | 0 | 3 |
P value = 0.00084 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 12 | 17 | 23 |
AMP PEAK 12(19P13.12) CNV | 11 | 12 | 14 | 11 |
AMP PEAK 12(19P13.12) WILD-TYPE | 13 | 0 | 3 | 12 |
P value = 8.46e-05 (Fisher's exact test), Q value = 0.024
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 29 | 19 | 19 | 10 |
AMP PEAK 13(19Q12) CNV | 12 | 10 | 19 | 6 |
AMP PEAK 13(19Q12) WILD-TYPE | 17 | 9 | 0 | 4 |
P value = 1.23e-05 (Fisher's exact test), Q value = 0.0036
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 29 | 19 | 19 | 10 |
AMP PEAK 14(19Q13.33) CNV | 10 | 13 | 19 | 6 |
AMP PEAK 14(19Q13.33) WILD-TYPE | 19 | 6 | 0 | 4 |
P value = 0.000408 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 12 | 17 | 23 |
AMP PEAK 14(19Q13.33) CNV | 10 | 12 | 14 | 11 |
AMP PEAK 14(19Q13.33) WILD-TYPE | 14 | 0 | 3 | 12 |
P value = 3.92e-05 (Fisher's exact test), Q value = 0.011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 29 | 19 | 19 | 10 |
AMP PEAK 15(XQ28) CNV | 8 | 16 | 16 | 5 |
AMP PEAK 15(XQ28) WILD-TYPE | 21 | 3 | 3 | 5 |
P value = 9.64e-05 (Fisher's exact test), Q value = 0.027
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 12 | 17 | 23 |
AMP PEAK 15(XQ28) CNV | 6 | 11 | 14 | 14 |
AMP PEAK 15(XQ28) WILD-TYPE | 18 | 1 | 3 | 9 |
P value = 0.000178 (Fisher's exact test), Q value = 0.05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 29 | 19 | 19 | 10 |
DEL PEAK 11(9P23) CNV | 15 | 0 | 4 | 1 |
DEL PEAK 11(9P23) WILD-TYPE | 14 | 19 | 15 | 9 |
P value = 1.55e-05 (Fisher's exact test), Q value = 0.0045
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 12 | 17 | 23 |
DEL PEAK 11(9P23) CNV | 15 | 1 | 3 | 1 |
DEL PEAK 11(9P23) WILD-TYPE | 9 | 11 | 14 | 22 |
P value = 0.000785 (Fisher's exact test), Q value = 0.22
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 23 | 32 | 21 |
DEL PEAK 11(9P23) CNV | 13 | 4 | 3 |
DEL PEAK 11(9P23) WILD-TYPE | 10 | 28 | 18 |
P value = 1.43e-06 (Fisher's exact test), Q value = 0.00042
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 24 | 12 | 17 | 23 |
DEL PEAK 12(9P21.3) CNV | 17 | 1 | 2 | 2 |
DEL PEAK 12(9P21.3) WILD-TYPE | 7 | 11 | 15 | 21 |
P value = 4.45e-05 (Fisher's exact test), Q value = 0.013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 23 | 32 | 21 |
DEL PEAK 12(9P21.3) CNV | 15 | 4 | 3 |
DEL PEAK 12(9P21.3) WILD-TYPE | 8 | 28 | 18 |
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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.
-
Molecular subtype file = ACC-TP.transferedmergedcluster.txt
-
Number of patients = 77
-
Number of copy number variation regions = 38
-
Number of molecular subtypes = 8
-
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.
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.